Citrus Sinensis ID: 031208

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160----
Protein Sequence
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA
Secondary Structure (PSIPRED)
ccHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHcccccccEEEHHHHHHHHHcccccHHHHHHHHHHHHcccccccEEHHHHHHHHHccccHHHHHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHcccccccccHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMIcngfrpdkftfPFVIKACIASLAIEkgkevhglavkagfsrdmFVQSTLMDLYLKcgdvdggrkmfdKMRVRSVVSWTTMISGLAASGDLDAA
Flexible Loop (DISEMBL)
mqkiiryglsndqLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMisglaasgdldaa
Low Complexity Region (SEG)
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA
Disordered region (IsUnstruct)
***IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGL*********
Disordered Region (DISOPRED)
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL***
Disordered Region (DISEMBL)
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA
Disordered Region (DISPRO)
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	164	2.2.26 [Sep-21-2011]
Q38959	455	Pentatricopeptide repeat-	yes	no	0.987	0.356	0.582	1e-50
Q9LN01	741	Pentatricopeptide repeat-	no	no	0.987	0.218	0.345	2e-26
Q9MA95	565	Putative pentatricopeptid	no	no	0.981	0.284	0.347	6e-26
Q9LUJ2	842	Pentatricopeptide repeat-	no	no	0.945	0.184	0.389	7e-26
Q0WQW5	638	Pentatricopeptide repeat-	no	no	0.920	0.236	0.424	7e-26
O80647	836	Pentatricopeptide repeat-	no	no	0.902	0.177	0.369	3e-24
Q9SIL5	534	Pentatricopeptide repeat-	no	no	0.981	0.301	0.351	3e-24
Q9STF3	657	Pentatricopeptide repeat-	no	no	0.963	0.240	0.370	7e-24
O49619	804	Pentatricopeptide repeat-	no	no	0.908	0.185	0.373	2e-23
Q9LUS3	654	Pentatricopeptide repeat-	no	no	0.841	0.211	0.391	6e-23

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

 Score =  198 bits (504), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 95/163 (58%), Positives = 127/163 (77%), Gaps = 1/163 (0%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KII++ L+NDQLLVR+L+ + S +G+T +A LVF+Q++ P  FTWNLMIR+L+++    +
Sbjct: 42  KIIKHNLTNDQLLVRQLISVSSSFGETQYASLVFNQLQSPSTFTWNLMIRSLSVNHKPRE 101

Query: 63  ALLLYNLM-ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM 121
           ALLL+ LM I +  + DKFTFPFVIKAC+AS +I  G +VHGLA+KAGF  D+F Q+TLM
Sbjct: 102 ALLLFILMMISHQSQFDKFTFPFVIKACLASSSIRLGTQVHGLAIKAGFFNDVFFQNTLM 161

Query: 122 DLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           DLY KCG  D GRK+FDKM  RS+VSWTTM+ GL ++  LD+A
Sbjct: 162 DLYFKCGKPDSGRKVFDKMPGRSIVSWTTMLYGLVSNSQLDSA 204

Arabidopsis thaliana (taxid: 3702)

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

 Score =  118 bits (295), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/165 (34%), Positives = 97/165 (58%), Gaps = 3/165 (1%)

Query: 3   KIIRYGLSNDQLLVRKLLDLC---SFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGS 59
           ++I+ GL N    + KL++ C     +    +A+ VF  I+ P++  WN M R   +   
Sbjct: 55  QMIKIGLHNTNYALSKLIEFCILSPHFEGLPYAISVFKTIQEPNLLIWNTMFRGHALSSD 114

Query: 60  SLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQST 119
            + AL LY  MI  G  P+ +TFPFV+K+C  S A ++G+++HG  +K G   D++V ++
Sbjct: 115 PVSALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHTS 174

Query: 120 LMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           L+ +Y++ G ++   K+FDK   R VVS+T +I G A+ G ++ A
Sbjct: 175 LISMYVQNGRLEDAHKVFDKSPHRDVVSYTALIKGYASRGYIENA 219

Arabidopsis thaliana (taxid: 3702)

>sp|Q9MA95|PP214_ARATH Putative pentatricopeptide repeat-containing protein At3g05240 OS=Arabidopsis thaliana GN=PCMP-E82 PE=3 SV=2

 Score =  116 bits (291), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 95/164 (57%), Gaps = 3/164 (1%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKT---DHALLVFSQIRCPHVFTWNLMIRALTIDGSS 60
           +I+  +  + + + +L+D C+   +T    +A  VF  I CP V+ WN MIR  +   + 
Sbjct: 29  MIKSSVIRNVIPLSRLIDFCTTCPETMNLSYARSVFESIDCPSVYIWNSMIRGYSNSPNP 88

Query: 61  LQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTL 120
            +AL+ Y  M+  G+ PD FTFP+V+KAC     I+ G  VHG  VK GF  +M+V + L
Sbjct: 89  DKALIFYQEMLRKGYSPDYFTFPYVLKACSGLRDIQFGSCVHGFVVKTGFEVNMYVSTCL 148

Query: 121 MDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           + +Y+ CG+V+ G ++F+ +   +VV+W ++ISG   +     A
Sbjct: 149 LHMYMCCGEVNYGLRVFEDIPQWNVVAWGSLISGFVNNNRFSDA 192

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUJ2|PP249_ARATH Pentatricopeptide repeat-containing protein At3g22690 OS=Arabidopsis thaliana GN=PCMP-H56 PE=2 SV=1

 Score =  116 bits (290), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 62/159 (38%), Positives = 93/159 (58%), Gaps = 4/159 (2%)

Query: 2   QKIIRYGLSNDQLLVRKLLDLCSFYGKTDH---ALLVFSQIRC-PHVFTWNLMIRALTID 57
           + + + GL ND   + KL+      G  +    A  VF         F +N +IR     
Sbjct: 53  RSLTKQGLDNDVSTITKLVARSCELGTRESLSFAKEVFENSESYGTCFMYNSLIRGYASS 112

Query: 58  GSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQ 117
           G   +A+LL+  M+ +G  PDK+TFPF + AC  S A   G ++HGL VK G+++D+FVQ
Sbjct: 113 GLCNEAILLFLRMMNSGISPDKYTFPFGLSACAKSRAKGNGIQIHGLIVKMGYAKDLFVQ 172

Query: 118 STLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLA 156
           ++L+  Y +CG++D  RK+FD+M  R+VVSWT+MI G A
Sbjct: 173 NSLVHFYAECGELDSARKVFDEMSERNVVSWTSMICGYA 211

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WQW5|PPR85_ARATH Pentatricopeptide repeat-containing protein At1g59720, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H51 PE=2 SV=2

 Score =  116 bits (290), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 65/153 (42%), Positives = 87/153 (56%), Gaps = 2/153 (1%)

Query: 14  LLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGS-SLQALLLYNLMIC 72
            L  K+L L S +   ++A  VF  I     F WN +IRA   D S   +A +LY  M+ 
Sbjct: 84  FLYGKILQLSSSFSDVNYAFRVFDSIENHSSFMWNTLIRACAHDVSRKEEAFMLYRKMLE 143

Query: 73  NG-FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD 131
            G   PDK TFPFV+KAC       +GK+VH   VK GF  D++V + L+ LY  CG +D
Sbjct: 144 RGESSPDKHTFPFVLKACAYIFGFSEGKQVHCQIVKHGFGGDVYVNNGLIHLYGSCGCLD 203

Query: 132 GGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
             RK+FD+M  RS+VSW +MI  L   G+ D+A
Sbjct: 204 LARKVFDEMPERSLVSWNSMIDALVRFGEYDSA 236

Arabidopsis thaliana (taxid: 3702)

>sp|O80647|PP195_ARATH Pentatricopeptide repeat-containing protein At2g39620 OS=Arabidopsis thaliana GN=PCMP-E33 PE=3 SV=1

 Score =  110 bits (276), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 55/149 (36%), Positives = 87/149 (58%), Gaps = 1/149 (0%)

Query: 17  RKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GF 75
            +L++  S + + D + ++F  +R P V  WN MIR  T  G   +AL  +  M    G 
Sbjct: 37  NQLINAYSLFQRQDLSRVIFDSVRDPGVVLWNSMIRGYTRAGLHREALGFFGYMSEEKGI 96

Query: 76  RPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRK 135
            PDK++F F +KAC  S+  +KG  +H L  + G   D+++ + L+++Y K  D+   R+
Sbjct: 97  DPDKYSFTFALKACAGSMDFKKGLRIHDLIAEMGLESDVYIGTALVEMYCKARDLVSARQ 156

Query: 136 MFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           +FDKM V+ VV+W TM+SGLA +G   AA
Sbjct: 157 VFDKMHVKDVVTWNTMVSGLAQNGCSSAA 185

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (276), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 57/162 (35%), Positives = 93/162 (57%), Gaps = 1/162 (0%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           II +GLS    +V K++D C      D+A  +F+Q+  P+VF +N +IRA T +      
Sbjct: 33  IIIHGLSQSSFMVTKMVDFCDKIEDMDYATRLFNQVSNPNVFLYNSIIRAYTHNSLYCDV 92

Query: 64  LLLYNLMICNGFR-PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           + +Y  ++   F  PD+FTFPF+ K+C +  +   GK+VHG   K G    +  ++ L+D
Sbjct: 93  IRIYKQLLRKSFELPDRFTFPFMFKSCASLGSCYLGKQVHGHLCKFGPRFHVVTENALID 152

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           +Y+K  D+    K+FD+M  R V+SW +++SG A  G +  A
Sbjct: 153 MYMKFDDLVDAHKVFDEMYERDVISWNSLLSGYARLGQMKKA 194

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (273), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 60/162 (37%), Positives = 92/162 (56%), Gaps = 4/162 (2%)

Query: 2   QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSL 61
           + I+  G   D  L  KL+ + S  G  D+A  VF + R   ++ WN + RALT+ G   
Sbjct: 101 RHILDNGSDQDPFLATKLIGMYSDLGSVDYARKVFDKTRKRTIYVWNALFRALTLAGHGE 160

Query: 62  QALLLYNLMICNGFRPDKFTFPFVIKACIASLA----IEKGKEVHGLAVKAGFSRDMFVQ 117
           + L LY  M   G   D+FT+ +V+KAC+AS      + KGKE+H    + G+S  +++ 
Sbjct: 161 EVLGLYWKMNRIGVESDRFTYTYVLKACVASECTVNHLMKGKEIHAHLTRRGYSSHVYIM 220

Query: 118 STLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
           +TL+D+Y + G VD    +F  M VR+VVSW+ MI+  A +G
Sbjct: 221 TTLVDMYARFGCVDYASYVFGGMPVRNVVSWSAMIACYAKNG 262

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

Arabidopsis thaliana (taxid: 3702)

>sp|O49619|PP350_ARATH Pentatricopeptide repeat-containing protein At4g35130, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H27 PE=3 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/150 (37%), Positives = 87/150 (58%), Gaps = 1/150 (0%)

Query: 11  NDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLM 70
           ND  L R L          D AL +F ++     F WN+MI+  T  G  ++A+  Y+ M
Sbjct: 63  NDPALTRALRGFADSRLMED-ALQLFDEMNKADAFLWNVMIKGFTSCGLYIEAVQFYSRM 121

Query: 71  ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV 130
           +  G + D FT+PFVIK+     ++E+GK++H + +K GF  D++V ++L+ LY+K G  
Sbjct: 122 VFAGVKADTFTYPFVIKSVAGISSLEEGKKIHAMVIKLGFVSDVYVCNSLISLYMKLGCA 181

Query: 131 DGGRKMFDKMRVRSVVSWTTMISGLAASGD 160
               K+F++M  R +VSW +MISG  A GD
Sbjct: 182 WDAEKVFEEMPERDIVSWNSMISGYLALGD 211

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUS3|PP237_ARATH Pentatricopeptide repeat-containing protein At3g16610 OS=Arabidopsis thaliana GN=PCMP-E91 PE=2 SV=1

 Score =  106 bits (265), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 56/143 (39%), Positives = 85/143 (59%), Gaps = 5/143 (3%)

Query: 19  LLDLCSFYGKTDHALL---VFSQIRCPHV--FTWNLMIRALTIDGSSLQALLLYNLMICN 73
           L++L   Y   +   L   VF +I  P +    W+LMIRA   +  + +AL LY  M+ +
Sbjct: 38  LVNLTRLYASCNEVELARHVFDEIPHPRINPIAWDLMIRAYASNDFAEKALDLYYKMLNS 97

Query: 74  GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGG 133
           G RP K+T+PFV+KAC    AI+ GK +H     + F+ DM+V + L+D Y KCG+++  
Sbjct: 98  GVRPTKYTYPFVLKACAGLRAIDDGKLIHSHVNCSDFATDMYVCTALVDFYAKCGELEMA 157

Query: 134 RKMFDKMRVRSVVSWTTMISGLA 156
            K+FD+M  R +V+W  MISG +
Sbjct: 158 IKVFDEMPKRDMVAWNAMISGFS 180

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	164
255543449	480	pentatricopeptide repeat-containing prot	0.951	0.325	0.679	2e-60
356560406	483	PREDICTED: pentatricopeptide repeat-cont	0.981	0.333	0.617	1e-52
297818204	451	pentatricopeptide repeat-containing prot	0.981	0.356	0.574	6e-49
15231592	455	pentatricopeptide repeat-containing prot	0.987	0.356	0.582	6e-49
449455978	2598	PREDICTED: uncharacterized protein LOC10	0.969	0.061	0.604	3e-48
449492963	1725	PREDICTED: uncharacterized protein LOC10	0.981	0.093	0.604	3e-48
357508535	476	Pentatricopeptide repeat-containing prot	0.987	0.340	0.576	2e-47
356570285	474	PREDICTED: pentatricopeptide repeat-cont	0.987	0.341	0.567	1e-46
224064796	222	predicted protein [Populus trichocarpa]	0.810	0.599	0.669	4e-46
359488803	1291	PREDICTED: putative pentatricopeptide re	0.945	0.120	0.439	6e-32

>gi|255543449|ref|XP_002512787.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223547798|gb|EEF49290.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 110/162 (67%), Positives = 128/162 (79%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KIIR  LS+DQLLVRKLL LC  Y K D+A L+F QI+ PH FTWN MIRA   +G+S Q
Sbjct: 54  KIIRNNLSDDQLLVRKLLRLCFSYQKVDYATLIFDQIQNPHTFTWNFMIRAYNYNGNSQQ 113

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           ALLLYNLMIC GF PDKFTFPFVIKAC+   A++KGKEVHG A+K GF +D F+ +TLMD
Sbjct: 114 ALLLYNLMICEGFSPDKFTFPFVIKACLDHSALDKGKEVHGFAIKTGFWKDTFLSNTLMD 173

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           LY KCGD+D  RK+FDKM VRSVVSWTT ++GL A G+LD A
Sbjct: 174 LYFKCGDLDYARKLFDKMAVRSVVSWTTFVAGLVACGELDTA 215

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560406|ref|XP_003548483.1| PREDICTED: pentatricopeptide repeat-containing protein At3g26630, chloroplastic-like [Glycine max]

 Score =  210 bits (535), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 100/162 (61%), Positives = 124/162 (76%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KIIR+GL+ DQLL+RKL+ L S YGK  +A LVF Q+  P VFTWN+MIRA TI GS   
Sbjct: 47  KIIRFGLTYDQLLMRKLIQLSSSYGKMKYATLVFDQLNAPDVFTWNVMIRAFTIGGSPKM 106

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           ALLL+  M+C GF PDKFT+PFVI AC+AS A++ G   H LA+K GF  D++VQ+T+M+
Sbjct: 107 ALLLFKAMLCQGFAPDKFTYPFVINACMASSALDLGIVAHALAIKMGFWGDLYVQNTMMN 166

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           LY KC +VD GRK+FDKMRVR+V +WTT+ISGL A G LD A
Sbjct: 167 LYFKCENVDDGRKVFDKMRVRNVFAWTTVISGLVACGKLDTA 208

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297818204|ref|XP_002876985.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297322823|gb|EFH53244.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  198 bits (504), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 93/162 (57%), Positives = 127/162 (78%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KII++ L+NDQLLVR+L+ + S +G+T +A LVF+Q++ P  FTWNLMIR+L+++    +
Sbjct: 42  KIIKHNLTNDQLLVRQLISVSSSFGETQYASLVFNQLQSPSTFTWNLMIRSLSLNHKPRE 101

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           ALLL+ LM+ +  + DKFTFPFVIKAC+AS ++  G +VHGLA+KAGF  D+F Q+TLMD
Sbjct: 102 ALLLFILMLSHQPQFDKFTFPFVIKACLASSSLRLGTQVHGLAIKAGFFNDVFFQNTLMD 161

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           LY KCG  D GRK+FDKM  RS+VSWTTM+ GL ++  LD+A
Sbjct: 162 LYFKCGKPDCGRKVFDKMPGRSIVSWTTMLYGLVSNSQLDSA 203

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231592|ref|NP_189297.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75275188|sp|Q38959.1|PP257_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At3g26630, chloroplastic; Flags: Precursor gi|1402883|emb|CAA66814.1| hypothetical protein [Arabidopsis thaliana] gi|1495263|emb|CAA66119.1| orf09 [Arabidopsis thaliana] gi|11994298|dbj|BAB01728.1| unnamed protein product [Arabidopsis thaliana] gi|20466384|gb|AAM20509.1| unknown protein [Arabidopsis thaliana] gi|23198064|gb|AAN15559.1| unknown protein [Arabidopsis thaliana] gi|332643668|gb|AEE77189.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  198 bits (504), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 95/163 (58%), Positives = 127/163 (77%), Gaps = 1/163 (0%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KII++ L+NDQLLVR+L+ + S +G+T +A LVF+Q++ P  FTWNLMIR+L+++    +
Sbjct: 42  KIIKHNLTNDQLLVRQLISVSSSFGETQYASLVFNQLQSPSTFTWNLMIRSLSVNHKPRE 101

Query: 63  ALLLYNLM-ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM 121
           ALLL+ LM I +  + DKFTFPFVIKAC+AS +I  G +VHGLA+KAGF  D+F Q+TLM
Sbjct: 102 ALLLFILMMISHQSQFDKFTFPFVIKACLASSSIRLGTQVHGLAIKAGFFNDVFFQNTLM 161

Query: 122 DLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           DLY KCG  D GRK+FDKM  RS+VSWTTM+ GL ++  LD+A
Sbjct: 162 DLYFKCGKPDSGRKVFDKMPGRSIVSWTTMLYGLVSNSQLDSA 204

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455978|ref|XP_004145727.1| PREDICTED: uncharacterized protein LOC101212001 [Cucumis sativus]

 Score =  196 bits (498), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 98/162 (60%), Positives = 120/162 (74%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KIIR GLSNDQLL RKL+ L S +G+  +A+L+F QI+ P  FTWNL+IRA TI+G S Q
Sbjct: 49  KIIRSGLSNDQLLTRKLIHLYSTHGRIAYAILLFYQIQNPCTFTWNLIIRANTINGLSEQ 108

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           AL+LY  M+C G   DKFTFPFVIKAC   L+I+ GK VHG  +K GFS D+FVQ+ L+D
Sbjct: 109 ALMLYKNMVCQGIAADKFTFPFVIKACTNFLSIDLGKVVHGSLIKYGFSGDVFVQNNLID 168

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
            Y KCG      K+F+KMRVR+VVSWTT+ISGL + GDL  A
Sbjct: 169 FYFKCGHTRFALKVFEKMRVRNVVSWTTVISGLISCGDLQEA 210

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  196 bits (497), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 98/162 (60%), Positives = 120/162 (74%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KIIR GLSNDQLL RKL+ L S +G+  +A+L+F QI+ P  FTWNL+IRA TI+G S Q
Sbjct: 49  KIIRSGLSNDQLLTRKLIHLYSTHGRIAYAILLFYQIQNPCTFTWNLIIRANTINGLSEQ 108

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           AL+LY  M+C G   DKFTFPFVIKAC   L+I+ GK VHG  +K GFS D+FVQ+ L+D
Sbjct: 109 ALMLYKNMVCQGIAADKFTFPFVIKACTNFLSIDLGKVVHGSLIKYGFSGDVFVQNNLID 168

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
            Y KCG      K+F+KMRVR+VVSWTT+ISGL + GDL  A
Sbjct: 169 FYFKCGHTRFALKVFEKMRVRNVVSWTTVISGLISCGDLQEA 210

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357508535|ref|XP_003624556.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355499571|gb|AES80774.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  193 bits (490), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 94/163 (57%), Positives = 121/163 (74%), Gaps = 1/163 (0%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           +IIR+ L++DQLL+RKL  + S YGK D+A LVF Q+  P +FTWN+MIRA    G   +
Sbjct: 42  RIIRFRLTHDQLLIRKLCQISSSYGKIDYASLVFDQLNDPDIFTWNVMIRAYNTSGLPQK 101

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           ++ L+  MIC GF PDKFT+PFVI ACIAS  I+ G+  HGLA+K GF  D++VQ+ +M+
Sbjct: 102 SIFLFKDMICCGFLPDKFTYPFVINACIASGVIDFGRLTHGLAIKMGFWSDVYVQNNMMN 161

Query: 123 LYLKC-GDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           LY K  GDVD G K+FDKMRVR+VVSWTT+I+GL A G LD A
Sbjct: 162 LYFKIGGDVDDGWKVFDKMRVRNVVSWTTVIAGLVACGKLDTA 204

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356570285|ref|XP_003553320.1| PREDICTED: pentatricopeptide repeat-containing protein At3g26630, chloroplastic-like [Glycine max]

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/162 (56%), Positives = 116/162 (71%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KIIRYGL+ DQLLVRKL+ L   YGK  +A LVF Q+  P VFTWN+MIRA TI GS   
Sbjct: 46  KIIRYGLTYDQLLVRKLIQLSPSYGKMKYATLVFDQLNAPDVFTWNVMIRAYTIGGSPKM 105

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           A LL+  M+  GF PDKFT+P VI AC+A  A++ G+  H LA+K GF  D++VQ+T+M+
Sbjct: 106 AFLLFKAMLYQGFAPDKFTYPCVINACMAYNALDVGRVAHALAIKMGFWGDLYVQNTMMN 165

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           LY KC +VD G  +FDKM VR+V +WTT+I+G  A G LD A
Sbjct: 166 LYFKCENVDDGWNVFDKMCVRNVFAWTTVIAGFVACGKLDTA 207

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224064796|ref|XP_002301563.1| predicted protein [Populus trichocarpa] gi|222843289|gb|EEE80836.1| predicted protein [Populus trichocarpa]

 Score =  189 bits (479), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 89/133 (66%), Positives = 106/133 (79%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KIIR  LS +QLLVRKL+ LCS YG+ D+A L+F Q++ PH FTWN +IR  TI G S++
Sbjct: 62  KIIRNALSANQLLVRKLIHLCSSYGRLDYAALLFHQVQEPHTFTWNFLIRTYTIHGYSMK 121

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           ALLLYNLMI  GF PDKFTFPFV+KAC+AS +I KGKEVHGLA+K GFS+DMF+ +TLMD
Sbjct: 122 ALLLYNLMIRRGFPPDKFTFPFVVKACLASGSIRKGKEVHGLAIKTGFSKDMFLYNTLMD 181

Query: 123 LYLKCGDVDGGRK 135
           LY  CGD   GRK
Sbjct: 182 LYFSCGDEGYGRK 194

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 69/157 (43%), Positives = 96/157 (61%)

Query: 3   KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
           KI  YGL  D  ++ K   +   + + D A +VF  I  P  F WN+MIR    DG  L 
Sbjct: 742 KIFAYGLQYDSRILTKFAIMYVSFNRIDAASIVFEDIPNPCSFLWNVMIRGFATDGRFLS 801

Query: 63  ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
           +L LY+ M+  G +PDKF FPF +K+C     +++GK +H   V  G S D+FV + L+D
Sbjct: 802 SLELYSKMMEKGLKPDKFAFPFALKSCAGLSDLQRGKVIHQHLVCCGCSNDLFVDAALVD 861

Query: 123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
           +Y KCGD++  R +FDKM VR +VSWT+MISG A +G
Sbjct: 862 MYAKCGDIEAARLVFDKMAVRDLVSWTSMISGYAHNG 898

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	164
TAIR|locus:2090857	455	AT3G26630 "AT3G26630" [Arabido	0.987	0.356	0.582	8.8e-47
TAIR|locus:2025946	638	CRR28 "CHLORORESPIRATORY REDUC	0.914	0.235	0.427	1e-24
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.981	0.217	0.355	2.3e-24
TAIR|locus:2054789	534	MEF21 "mitochondrial editing f	0.981	0.301	0.351	7.3e-24
TAIR|locus:2039817	836	AT2G39620 "AT2G39620" [Arabido	0.896	0.175	0.371	2.8e-23
TAIR|locus:2102852	657	CRR2 "AT3G46790" [Arabidopsis	0.951	0.237	0.375	5.8e-23
TAIR|locus:2131631	804	AT4G35130 "AT4G35130" [Arabido	0.908	0.185	0.373	8.8e-23
TAIR|locus:2063771	689	AT2G03380 [Arabidopsis thalian	0.890	0.211	0.374	1.4e-22
TAIR|locus:2161018	530	AT5G56310 "AT5G56310" [Arabido	0.957	0.296	0.35	4e-22
TAIR|locus:2086964	601	MEF25 "mitochondrial RNA editi	0.951	0.259	0.369	5.7e-22

TAIR|locus:2090857 AT3G26630 "AT3G26630" [Arabidopsis thaliana (taxid:3702)]

 Score = 490 (177.5 bits), Expect = 8.8e-47, P = 8.8e-47
 Identities = 95/163 (58%), Positives = 127/163 (77%)

Query:     3 KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
             KII++ L+NDQLLVR+L+ + S +G+T +A LVF+Q++ P  FTWNLMIR+L+++    +
Sbjct:    42 KIIKHNLTNDQLLVRQLISVSSSFGETQYASLVFNQLQSPSTFTWNLMIRSLSVNHKPRE 101

Query:    63 ALLLYNLM-ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM 121
             ALLL+ LM I +  + DKFTFPFVIKAC+AS +I  G +VHGLA+KAGF  D+F Q+TLM
Sbjct:   102 ALLLFILMMISHQSQFDKFTFPFVIKACLASSSIRLGTQVHGLAIKAGFFNDVFFQNTLM 161

Query:   122 DLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
             DLY KCG  D GRK+FDKM  RS+VSWTTM+ GL ++  LD+A
Sbjct:   162 DLYFKCGKPDSGRKVFDKMPGRSIVSWTTMLYGLVSNSQLDSA 204

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2025946 CRR28 "CHLORORESPIRATORY REDUCTION28" [Arabidopsis thaliana (taxid:3702)]

 Score = 290 (107.1 bits), Expect = 1.0e-24, P = 1.0e-24
 Identities = 65/152 (42%), Positives = 87/152 (57%)

Query:    15 LVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ-ALLLYNLMICN 73
             L  K+L L S +   ++A  VF  I     F WN +IRA   D S  + A +LY  M+  
Sbjct:    85 LYGKILQLSSSFSDVNYAFRVFDSIENHSSFMWNTLIRACAHDVSRKEEAFMLYRKMLER 144

Query:    74 G-FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDG 132
             G   PDK TFPFV+KAC       +GK+VH   VK GF  D++V + L+ LY  CG +D 
Sbjct:   145 GESSPDKHTFPFVLKACAYIFGFSEGKQVHCQIVKHGFGGDVYVNNGLIHLYGSCGCLDL 204

Query:   133 GRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
              RK+FD+M  RS+VSW +MI  L   G+ D+A
Sbjct:   205 ARKVFDEMPERSLVSWNSMIDALVRFGEYDSA 236

GO:0005739 "mitochondrion" evidence=ISM

GO:0004519 "endonuclease activity" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA;IMP

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

 Score = 288 (106.4 bits), Expect = 2.3e-24, P = 2.3e-24
 Identities = 59/166 (35%), Positives = 98/166 (59%)

Query:     3 KIIRYGLSNDQLLVRKLLDLC----SFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDG 58
             ++I+ GL N    + KL++ C     F G   +A+ VF  I+ P++  WN M R   +  
Sbjct:    55 QMIKIGLHNTNYALSKLIEFCILSPHFEG-LPYAISVFKTIQEPNLLIWNTMFRGHALSS 113

Query:    59 SSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS 118
               + AL LY  MI  G  P+ +TFPFV+K+C  S A ++G+++HG  +K G   D++V +
Sbjct:   114 DPVSALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHT 173

Query:   119 TLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
             +L+ +Y++ G ++   K+FDK   R VVS+T +I G A+ G ++ A
Sbjct:   174 SLISMYVQNGRLEDAHKVFDKSPHRDVVSYTALIKGYASRGYIENA 219

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

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

 Score = 280 (103.6 bits), Expect = 7.3e-24, P = 7.3e-24
 Identities = 57/162 (35%), Positives = 93/162 (57%)

Query:     4 IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
             II +GLS    +V K++D C      D+A  +F+Q+  P+VF +N +IRA T +      
Sbjct:    33 IIIHGLSQSSFMVTKMVDFCDKIEDMDYATRLFNQVSNPNVFLYNSIIRAYTHNSLYCDV 92

Query:    64 LLLYNLMICNGFR-PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
             + +Y  ++   F  PD+FTFPF+ K+C +  +   GK+VHG   K G    +  ++ L+D
Sbjct:    93 IRIYKQLLRKSFELPDRFTFPFMFKSCASLGSCYLGKQVHGHLCKFGPRFHVVTENALID 152

Query:   123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
             +Y+K  D+    K+FD+M  R V+SW +++SG A  G +  A
Sbjct:   153 MYMKFDDLVDAHKVFDEMYERDVISWNSLLSGYARLGQMKKA 194

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2039817 AT2G39620 "AT2G39620" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.8e-23, P = 2.8e-23
 Identities = 55/148 (37%), Positives = 87/148 (58%)

Query:    18 KLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GFR 76
             +L++  S + + D + ++F  +R P V  WN MIR  T  G   +AL  +  M    G  
Sbjct:    38 QLINAYSLFQRQDLSRVIFDSVRDPGVVLWNSMIRGYTRAGLHREALGFFGYMSEEKGID 97

Query:    77 PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKM 136
             PDK++F F +KAC  S+  +KG  +H L  + G   D+++ + L+++Y K  D+   R++
Sbjct:    98 PDKYSFTFALKACAGSMDFKKGLRIHDLIAEMGLESDVYIGTALVEMYCKARDLVSARQV 157

Query:   137 FDKMRVRSVVSWTTMISGLAASGDLDAA 164
             FDKM V+ VV+W TM+SGLA +G   AA
Sbjct:   158 FDKMHVKDVVTWNTMVSGLAQNGCSSAA 185

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 274 (101.5 bits), Expect = 5.8e-23, P = 5.8e-23
 Identities = 60/160 (37%), Positives = 91/160 (56%)

Query:     4 IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
             I+  G   D  L  KL+ + S  G  D+A  VF + R   ++ WN + RALT+ G   + 
Sbjct:   103 ILDNGSDQDPFLATKLIGMYSDLGSVDYARKVFDKTRKRTIYVWNALFRALTLAGHGEEV 162

Query:    64 LLLYNLMICNGFRPDKFTFPFVIKACIASLA----IEKGKEVHGLAVKAGFSRDMFVQST 119
             L LY  M   G   D+FT+ +V+KAC+AS      + KGKE+H    + G+S  +++ +T
Sbjct:   163 LGLYWKMNRIGVESDRFTYTYVLKACVASECTVNHLMKGKEIHAHLTRRGYSSHVYIMTT 222

Query:   120 LMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
             L+D+Y + G VD    +F  M VR+VVSW+ MI+  A +G
Sbjct:   223 LVDMYARFGCVDYASYVFGGMPVRNVVSWSAMIACYAKNG 262

GO:0009507 "chloroplast" evidence=ISS

GO:0031425 "chloroplast RNA processing" evidence=IMP

GO:0031426 "polycistronic mRNA processing" evidence=IMP

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

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

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

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

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

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

TAIR|locus:2131631 AT4G35130 "AT4G35130" [Arabidopsis thaliana (taxid:3702)]

 Score = 274 (101.5 bits), Expect = 8.8e-23, P = 8.8e-23
 Identities = 56/150 (37%), Positives = 87/150 (58%)

Query:    11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLM 70
             ND  L R L          D AL +F ++     F WN+MI+  T  G  ++A+  Y+ M
Sbjct:    63 NDPALTRALRGFADSRLMED-ALQLFDEMNKADAFLWNVMIKGFTSCGLYIEAVQFYSRM 121

Query:    71 ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV 130
             +  G + D FT+PFVIK+     ++E+GK++H + +K GF  D++V ++L+ LY+K G  
Sbjct:   122 VFAGVKADTFTYPFVIKSVAGISSLEEGKKIHAMVIKLGFVSDVYVCNSLISLYMKLGCA 181

Query:   131 DGGRKMFDKMRVRSVVSWTTMISGLAASGD 160
                 K+F++M  R +VSW +MISG  A GD
Sbjct:   182 WDAEKVFEEMPERDIVSWNSMISGYLALGD 211

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2063771 AT2G03380 [Arabidopsis thaliana (taxid:3702)]

 Score = 271 (100.5 bits), Expect = 1.4e-22, P = 1.4e-22
 Identities = 55/147 (37%), Positives = 87/147 (59%)

Query:     8 GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLY 67
             GL  D  +  KL+ L  F+G T  A LVF QI  P  + W +M+R   ++  S++ + LY
Sbjct:    71 GLMGDISIATKLVSLYGFFGYTKDARLVFDQIPEPDFYLWKVMLRCYCLNKESVEVVKLY 130

Query:    68 NLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC 127
             +L++ +GFR D   F   +KAC     ++ GK++H   VK   S D  V + L+D+Y KC
Sbjct:   131 DLLMKHGFRYDDIVFSKALKACTELQDLDNGKKIHCQLVKVP-SFDNVVLTGLLDMYAKC 189

Query:   128 GDVDGGRKMFDKMRVRSVVSWTTMISG 154
             G++    K+F+ + +R+VV WT+MI+G
Sbjct:   190 GEIKSAHKVFNDITLRNVVCWTSMIAG 216

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2161018 AT5G56310 "AT5G56310" [Arabidopsis thaliana (taxid:3702)]

 Score = 264 (98.0 bits), Expect = 4.0e-22, P = 4.0e-22
 Identities = 56/160 (35%), Positives = 88/160 (55%)

Query:     8 GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTI-DGSSLQ--AL 64
             GL+ D L V K ++ CS  G   +A  VF+   CP+ +  N MIRAL++ D  +    A+
Sbjct:    42 GLNRDNLNVAKFIEACSNAGHLRYAYSVFTHQPCPNTYLHNTMIRALSLLDEPNAHSIAI 101

Query:    65 LLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY 124
              +Y  +     +PD FTFPFV+K  +    +  G+++HG  V  GF   + V + L+ +Y
Sbjct:   102 TVYRKLWALCAKPDTFTFPFVLKIAVRVSDVWFGRQIHGQVVVFGFDSSVHVVTGLIQMY 161

Query:   125 LKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
               CG +   RKMFD+M V+ V  W  +++G    G++D A
Sbjct:   162 FSCGGLGDARKMFDEMLVKDVNVWNALLAGYGKVGEMDEA 201

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2086964 MEF25 "mitochondrial RNA editing factor 25" [Arabidopsis thaliana (taxid:3702)]

 Score = 264 (98.0 bits), Expect = 5.7e-22, P = 5.7e-22
 Identities = 58/157 (36%), Positives = 88/157 (56%)

Query:     4 IIRYG-LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQ 62
             +I  G L N   + R L+  C   G+  +A  VF ++    V  +N MI   +   +  +
Sbjct:    40 VISTGNLLNGSSISRDLIASCGRIGEISYARKVFDELPQRGVSVYNSMIVVYSRGKNPDE 99

Query:    63 ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD 122
              L LY+ MI    +PD  TF   IKAC++ L +EKG+ V   AV  G+  D+FV S++++
Sbjct:   100 VLRLYDQMIAEKIQPDSSTFTMTIKACLSGLVLEKGEAVWCKAVDFGYKNDVFVCSSVLN 159

Query:   123 LYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
             LY+KCG +D    +F KM  R V+ WTTM++G A +G
Sbjct:   160 LYMKCGKMDEAEVLFGKMAKRDVICWTTMVTGFAQAG 196

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: AT3G26630 pentatricopeptide (PPR) repeat-containing protein; pentatricopeptide (PPR) repeat-containing protein; INVOLVED IN- biological_process unknown; EXPRESSED IN- 22 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Pentatricopeptide repeat (InterPro-IPR002885); BEST Arabidopsis thaliana protein match is- pentatricopeptide (PPR) repeat-containing protein (TAIR-AT5G66520.1); Has 11770 Blast hits to 4443 proteins in 83 species- Archae - 0; Bacteria - 0; Metazoa - 5; Fungi - 21; Plants - 11596; Viruses - 0; Other Eukaryotes - 148 (source- NCBI BLink). (455 aa) (Arabidopsis thaliana)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	164
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-29
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	7e-23
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-22
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-20
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	5e-20
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-19
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-12
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	7e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-05
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-04

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

 Score =  111 bits (280), Expect = 3e-29
 Identities = 50/129 (38%), Positives = 77/129 (59%)

Query: 26  YGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV 85
           +G+  HA  VF ++    +F+WN+++      G   +AL LY+ M+  G RPD +TFP V
Sbjct: 134 FGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCV 193

Query: 86  IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSV 145
           ++ C     + +G+EVH   V+ GF  D+ V + L+ +Y+KCGDV   R +FD+M  R  
Sbjct: 194 LRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDC 253

Query: 146 VSWTTMISG 154
           +SW  MISG
Sbjct: 254 ISWNAMISG 262

Length = 857

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

 Score = 93.8 bits (233), Expect = 7e-23
 Identities = 46/156 (29%), Positives = 79/156 (50%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           +++ G+  D  +   L+D+ S  G  + A  VF  +       WN M+    + G S +A
Sbjct: 250 VLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEA 309

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL 123
           L LY  M  +G   D+FTF  +I+       +E  K+ H   ++ GF  D+   + L+DL
Sbjct: 310 LCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDL 369

Query: 124 YLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
           Y K G ++  R +FD+M  ++++SW  +I+G    G
Sbjct: 370 YSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHG 405

Length = 697

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

 Score = 91.4 bits (227), Expect = 4e-22
 Identities = 54/161 (33%), Positives = 78/161 (48%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           ++R+G   D  +V  L+ +    G    A LVF ++      +WN MI     +G  L+ 
Sbjct: 213 VVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEG 272

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL 123
           L L+  M      PD  T   VI AC        G+E+HG  VK GF+ D+ V ++L+ +
Sbjct: 273 LELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQM 332

Query: 124 YLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           YL  G      K+F +M  +  VSWT MISG   +G  D A
Sbjct: 333 YLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKA 373

Length = 857

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

 Score = 87.2 bits (216), Expect = 1e-20
 Identities = 42/152 (27%), Positives = 76/152 (50%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           +++ G + D  +   L+ +    G    A  VFS++      +W  MI     +G   +A
Sbjct: 314 VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKA 373

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL 123
           L  Y LM  +   PD+ T   V+ AC     ++ G ++H LA + G    + V + L+++
Sbjct: 374 LETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEM 433

Query: 124 YLKCGDVDGGRKMFDKMRVRSVVSWTTMISGL 155
           Y KC  +D   ++F  +  + V+SWT++I+GL
Sbjct: 434 YSKCKCIDKALEVFHNIPEKDVISWTSIIAGL 465

Length = 857

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

 Score = 85.3 bits (211), Expect = 5e-20
 Identities = 42/156 (26%), Positives = 79/156 (50%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           +   G   DQ ++ ++L +    G    A  +F ++   ++ +W  +I  L   G+  +A
Sbjct: 149 VESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREA 208

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL 123
             L+  M  +G   +  TF  +++A     +   G+++H   +K G   D FV   L+D+
Sbjct: 209 FALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDM 268

Query: 124 YLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
           Y KCGD++  R +FD M  ++ V+W +M++G A  G
Sbjct: 269 YSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHG 304

Length = 697

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

 Score = 82.6 bits (204), Expect = 5e-19
 Identities = 44/155 (28%), Positives = 77/155 (49%), Gaps = 2/155 (1%)

Query: 5   IRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQAL 64
            R GL +  ++   L+++ S     D AL VF  I    V +W  +I  L ++    +AL
Sbjct: 416 ERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEAL 475

Query: 65  LLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY 124
           + +  M+    +P+  T    + AC    A+  GKE+H   ++ G   D F+ + L+DLY
Sbjct: 476 IFFRQMLLT-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLY 534

Query: 125 LKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASG 159
           ++CG ++     F+    + VVSW  +++G  A G
Sbjct: 535 VRCGRMNYAWNQFNSHE-KDVVSWNILLTGYVAHG 568

Length = 857

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

 Score = 61.8 bits (150), Expect = 8e-12
 Identities = 34/115 (29%), Positives = 62/115 (53%), Gaps = 1/115 (0%)

Query: 51  IRALTIDGSSLQALLLYNLMICNG-FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAG 109
           I  L   G   +AL L+ ++     F     T+  +++ACIA  +I   K V+     +G
Sbjct: 94  IEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSG 153

Query: 110 FSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           F  D ++ + ++ +++KCG +   R++FD+M  R++ SW T+I GL  +G+   A
Sbjct: 154 FEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREA 208

Length = 697

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

 Score = 51.0 bits (122), Expect = 4e-08
 Identities = 30/98 (30%), Positives = 50/98 (51%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           +IR G   D +    L+DL S +G+ + A  VF ++   ++ +WN +I      G   +A
Sbjct: 351 LIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKA 410

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEV 101
           + ++  MI  G  P+  TF  V+ AC  S   E+G E+
Sbjct: 411 VEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEI 448

Length = 697

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

 Score = 44.7 bits (107), Expect = 3e-07
 Identities = 15/48 (31%), Positives = 24/48 (50%)

Query: 42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC 89
          P V T+N +I      G   +AL L+N M   G +P+ +T+  +I   
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 47.5 bits (113), Expect = 7e-07
 Identities = 30/117 (25%), Positives = 55/117 (47%)

Query: 48  NLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVK 107
           N  +RAL   G   QAL L   M       D+  +  + + C    A+E+G  V   A+ 
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALS 114

Query: 108 AGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA 164
           +  S  + + + ++ ++++ G++     +F KM  R + SW  ++ G A +G  D A
Sbjct: 115 SHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEA 171

Length = 857

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

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 36/140 (25%), Positives = 67/140 (47%), Gaps = 2/140 (1%)

Query: 4   IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQA 63
           ++R G+  D  L   LLDL    G+ ++A   F+      V +WN+++      G    A
Sbjct: 515 VLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFN-SHEKDVVSWNILLTGYVAHGKGSMA 573

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEV-HGLAVKAGFSRDMFVQSTLMD 122
           + L+N M+ +G  PD+ TF  ++ AC  S  + +G E  H +  K   + ++   + ++D
Sbjct: 574 VELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVD 633

Query: 123 LYLKCGDVDGGRKMFDKMRV 142
           L  + G +       +KM +
Sbjct: 634 LLGRAGKLTEAYNFINKMPI 653

Length = 857

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

 Score = 38.9 bits (92), Expect = 4e-05
 Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 4/42 (9%)

Query: 119 TLMDLYLKCGDVDGGRKMFDKMRVR----SVVSWTTMISGLA 156
           TL+D Y K G V+   K+F++M+ R    +V +++ +I GL 
Sbjct: 8   TLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 41/176 (23%), Positives = 70/176 (39%), Gaps = 28/176 (15%)

Query: 8   GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC----PHVFTWNLMIRALTIDGSSLQA 63
           GL  D  L   L+  C+  GK D    VF ++       +V T+  +I      G   +A
Sbjct: 467 GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKA 526

Query: 64  LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQST---- 119
              Y +M     +PD+  F  +I AC  S A+++  +V  LA       +M  ++     
Sbjct: 527 FGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDV--LA-------EMKAETHPIDP 577

Query: 120 -------LMDLYLKCGDVDGGR---KMFDKMRVR-SVVSWTTMISGLAASGDLDAA 164
                  LM      G VD  +   +M  +  ++ +   +T  ++  +  GD D A
Sbjct: 578 DHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFA 633

Length = 1060

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	164
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PF13041	50	PPR_2: PPR repeat family	99.73
PF13041	50	PPR_2: PPR repeat family	99.69
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.47
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.4
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.35
PF12854	34	PPR_1: PPR repeat	99.29
PF12854	34	PPR_1: PPR repeat	99.29
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.22
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.2
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.16
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.05
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.03
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.97
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.94
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.92
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.9
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.88
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.83
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.8
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.8
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.77
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.76
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.74
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.71
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.68
PRK12370	553	invasion protein regulator; Provisional	98.65
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.65
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.59
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.57
PRK14574	822	hmsH outer membrane protein; Provisional	98.55
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.54
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.53
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.53
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.52
PRK12370	553	invasion protein regulator; Provisional	98.49
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.47
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.33
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.33
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.32
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.27
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.26
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.23
PRK15359	144	type III secretion system chaperone protein SscB;	98.23
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.23
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.22
PRK15359	144	type III secretion system chaperone protein SscB;	98.19
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.17
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.16
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.14
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.11
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.09
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.08
PRK14574	822	hmsH outer membrane protein; Provisional	98.07
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.06
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.06
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.06
PRK11189	296	lipoprotein NlpI; Provisional	98.05
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.04
KOG1129	478	consensus TPR repeat-containing protein [General f	98.03
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.02
KOG1126	638	consensus DNA-binding cell division cycle control	97.99
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.97
KOG2003	840	consensus TPR repeat-containing protein [General f	97.96
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.96
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.94
PRK11189	296	lipoprotein NlpI; Provisional	97.92
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.9
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.87
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.86
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.85
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.84
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.83
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.83
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.81
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.81
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.8
KOG1126	638	consensus DNA-binding cell division cycle control	97.77
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.76
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.75
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.75
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.72
KOG2003	840	consensus TPR repeat-containing protein [General f	97.71
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.7
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.7
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.69
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.68
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.67
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.66
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.66
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.66
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.63
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.63
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.59
KOG1129	478	consensus TPR repeat-containing protein [General f	97.58
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.56
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.46
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.46
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.45
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.43
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.43
PF12688	120	TPR_5: Tetratrico peptide repeat	97.42
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.41
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.4
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.36
KOG2076	895	consensus RNA polymerase III transcription factor	97.34
KOG3941	406	consensus Intermediate in Toll signal transduction	97.33
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.32
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.29
KOG4570	418	consensus Uncharacterized conserved protein [Funct	97.27
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.24
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.23
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.22
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.22
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.2
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.2
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.14
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.11
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.1
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.09
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.97
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	96.97
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.96
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	96.91
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.78
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.76
KOG0553	304	consensus TPR repeat-containing protein [General f	96.75
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.74
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.73
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.71
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.7
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.64
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.62
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.59
KOG2076	895	consensus RNA polymerase III transcription factor	96.57
KOG0495	913	consensus HAT repeat protein [RNA processing and m	96.57
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.52
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.48
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	96.46
KOG2047	835	consensus mRNA splicing factor [RNA processing and	96.4
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.33
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.32
PLN02789	320	farnesyltranstransferase	96.29
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	96.26
PRK10803	263	tol-pal system protein YbgF; Provisional	96.25
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.24
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.23
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.23
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.21
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.19
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.19
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.13
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	96.04
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.04
PF13371	73	TPR_9: Tetratricopeptide repeat	96.03
PF13371	73	TPR_9: Tetratricopeptide repeat	95.99
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.96
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.89
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	95.88
KOG0547	606	consensus Translocase of outer mitochondrial membr	95.87
KOG2796	366	consensus Uncharacterized conserved protein [Funct	95.87
KOG1125	579	consensus TPR repeat-containing protein [General f	95.85
PRK14720	906	transcript cleavage factor/unknown domain fusion p	95.72
KOG3785	557	consensus Uncharacterized conserved protein [Funct	95.72
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.69
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.69
PRK14720	906	transcript cleavage factor/unknown domain fusion p	95.68
KOG0495	913	consensus HAT repeat protein [RNA processing and m	95.64
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	95.63
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	95.6
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	95.57
PRK10803	263	tol-pal system protein YbgF; Provisional	95.57
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.53
KOG1125	579	consensus TPR repeat-containing protein [General f	95.51
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.47
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.42
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	95.26
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.14
PF12688	120	TPR_5: Tetratrico peptide repeat	95.09
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.08
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.0
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	94.93
KOG3941	406	consensus Intermediate in Toll signal transduction	94.93
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	94.91
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	94.72
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	94.63
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	94.55
KOG3060	289	consensus Uncharacterized conserved protein [Funct	94.47
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	94.46
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	94.42
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	94.36
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	94.24
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.21
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.19
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	94.1
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.97
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	93.91
smart00299	140	CLH Clathrin heavy chain repeat homology.	93.89
COG4700	251	Uncharacterized protein conserved in bacteria cont	93.82
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	93.78
PF13762	145	MNE1: Mitochondrial splicing apparatus component	93.68
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	93.65
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	93.52
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	93.43
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.36
KOG2376	652	consensus Signal recognition particle, subunit Srp	93.34
PRK15331	165	chaperone protein SicA; Provisional	93.26
KOG4340	459	consensus Uncharacterized conserved protein [Funct	93.2
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	93.18
PLN02789	320	farnesyltranstransferase	93.12
PRK15331	165	chaperone protein SicA; Provisional	93.11
PF13762	145	MNE1: Mitochondrial splicing apparatus component	93.1
PF13512	142	TPR_18: Tetratricopeptide repeat	92.84
PRK04841	903	transcriptional regulator MalT; Provisional	92.81
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	92.71
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.67
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.49
KOG0553	304	consensus TPR repeat-containing protein [General f	92.31
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	92.29
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.28
PRK04841	903	transcriptional regulator MalT; Provisional	92.1
KOG2796	366	consensus Uncharacterized conserved protein [Funct	91.93
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	91.51
PF13929	292	mRNA_stabil: mRNA stabilisation	91.5
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	91.25
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	91.13
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	90.81
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	90.54
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	90.49
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	90.46
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	90.37
PF13428	44	TPR_14: Tetratricopeptide repeat	90.34
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	90.18
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	90.05
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	90.0
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	89.86
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.69
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	89.24
PF13428	44	TPR_14: Tetratricopeptide repeat	89.22
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	89.16
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.77
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	88.74
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	88.74
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.72
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	88.6
PF13929	292	mRNA_stabil: mRNA stabilisation	88.24
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	88.19
COG4700	251	Uncharacterized protein conserved in bacteria cont	87.78
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	87.34
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	87.3
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	87.25
KOG2376	652	consensus Signal recognition particle, subunit Srp	87.12
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	86.91
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	86.68
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	86.63
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	86.61
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	86.44
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	86.25
COG4455	273	ImpE Protein of avirulence locus involved in tempe	85.98
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	85.72
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	85.64
KOG4555	175	consensus TPR repeat-containing protein [Function	85.41
cd08819	88	CARD_MDA5_2 Caspase activation and recruitment dom	85.27
PF13431	34	TPR_17: Tetratricopeptide repeat	85.16
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	84.56
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	84.11
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	84.09
KOG4648	536	consensus Uncharacterized conserved protein, conta	84.08
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	83.58
COG4105	254	ComL DNA uptake lipoprotein [General function pred	83.54
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	83.1
COG3947	361	Response regulator containing CheY-like receiver a	82.91
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	82.83
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	82.46
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	82.23
COG3118	304	Thioredoxin domain-containing protein [Posttransla	81.87
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	81.81
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	81.76
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	81.27
cd08326	84	CARD_CASP9 Caspase activation and recruitment doma	81.07
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	80.56
PRK10564	303	maltose regulon periplasmic protein; Provisional	80.41
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	80.39
PRK10564	303	maltose regulon periplasmic protein; Provisional	80.39
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	80.19
COG1747	711	Uncharacterized N-terminal domain of the transcrip	80.14

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

Probab=100.00  E-value=7.5e-37  Score=236.02  Aligned_cols=162  Identities=29%  Similarity=0.536  Sum_probs=157.1

Q ss_pred             hHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccH
Q 031208            3 KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTF   82 (164)
Q Consensus         3 ~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~   82 (164)
                      .+.+.|+.||..++++||++|++.|++++|.++|+.|.++|.++||.+|.+|++.|++++|.++|++|.+.|+.||..||
T Consensus       249 ~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~  328 (697)
T PLN03081        249 CVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTF  328 (697)
T ss_pred             HHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            45677888888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCCC
Q 031208           83 PFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        83 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~~  162 (164)
                      ++++.+|++.|++++|.+++++|.+.|+.||..+|+.|+++|+++|++++|.++|++|.+||+.+||+||.+|++.|+.+
T Consensus       329 ~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~  408 (697)
T PLN03081        329 SIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGT  408 (697)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CC
Q 031208          163 AA  164 (164)
Q Consensus       163 ~A  164 (164)
                      +|
T Consensus       409 ~A  410 (697)
T PLN03081        409 KA  410 (697)
T ss_pred             HH
Confidence            75

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.5e-35  Score=231.92  Aligned_cols=163  Identities=33%  Similarity=0.531  Sum_probs=157.3

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCccc
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      .+|.+.|+.||..+++++|.+|++.|+++.|.++|+.|+.||.++||++|.+|++.|++++|+++|.+|...|+.||..|
T Consensus       211 ~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~t  290 (857)
T PLN03077        211 AHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMT  290 (857)
T ss_pred             HHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhH
Confidence            35667788888888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCC
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~  161 (164)
                      |+++|.+|++.|+.+.|.+++.+|.+.|+.||..+|+.||++|++.|++++|.++|++|..||.++||+||.+|++.|++
T Consensus       291 y~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~  370 (857)
T PLN03077        291 ITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLP  370 (857)
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 031208          162 DAA  164 (164)
Q Consensus       162 ~~A  164 (164)
                      ++|
T Consensus       371 ~~A  373 (857)
T PLN03077        371 DKA  373 (857)
T ss_pred             HHH
Confidence            865

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=6e-35  Score=229.79  Aligned_cols=163  Identities=26%  Similarity=0.470  Sum_probs=158.4

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCccc
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      ..|.+.|+.||..+|+++|.+|++.|++++|.++|+.|..||.++||.+|.+|++.|++++|.++|++|.+.|+.||..|
T Consensus       312 ~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t  391 (857)
T PLN03077        312 GYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEIT  391 (857)
T ss_pred             HHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCcee
Confidence            46778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCC
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~  161 (164)
                      |++++.+|++.|+++.|.++++.|.+.|+.|+..+|+.||++|+++|++++|.++|++|.++|.++||++|.+|++.|+.
T Consensus       392 ~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~  471 (857)
T PLN03077        392 IASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRC  471 (857)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 031208          162 DAA  164 (164)
Q Consensus       162 ~~A  164 (164)
                      ++|
T Consensus       472 ~eA  474 (857)
T PLN03077        472 FEA  474 (857)
T ss_pred             HHH
Confidence            764

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

Probab=100.00  E-value=9.9e-35  Score=224.30  Aligned_cols=163  Identities=26%  Similarity=0.474  Sum_probs=159.5

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCccc
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      ..|.+.|+.||..+|+.++++|++.|+++.|.++|++|.+||.++||++|.+|++.|++++|+++|++|.+.|+.|+..|
T Consensus       147 ~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t  226 (697)
T PLN03081        147 WHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRT  226 (697)
T ss_pred             HHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhh
Confidence            46888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCC
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~  161 (164)
                      |+.++.+|++.|+.+.+.+++..+.+.|+.||..+|+.||++|+++|++++|.++|++|.++|+++||+||.+|++.|++
T Consensus       227 ~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~  306 (697)
T PLN03081        227 FVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYS  306 (697)
T ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q 031208          162 DAA  164 (164)
Q Consensus       162 ~~A  164 (164)
                      ++|
T Consensus       307 ~eA  309 (697)
T PLN03081        307 EEA  309 (697)
T ss_pred             HHH
Confidence            875

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.4e-34  Score=228.18  Aligned_cols=164  Identities=23%  Similarity=0.369  Sum_probs=135.2

Q ss_pred             ChhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC
Q 031208            1 MQKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFR   76 (164)
Q Consensus         1 ~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   76 (164)
                      |++|.+.|+.||..+|+++|.+|++.|+++.|.++|++|.    .||..+|+.+|.+|++.|++++|.++|++|.+.|+.
T Consensus       460 f~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~  539 (1060)
T PLN03218        460 LRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVK  539 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCC
Confidence            3567788888888888888888888888888888888887    478888888888888888888888888888888888


Q ss_pred             CCcccHHHHHHHHHhccchhhHHHHHHHHHH--hCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC----CCCcchHHH
Q 031208           77 PDKFTFPFVIKACIASLAIEKGKEVHGLAVK--AGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR----VRSVVSWTT  150 (164)
Q Consensus        77 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~--~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~----~~~~~~~~~  150 (164)
                      ||..||+.+|.+|++.|++++|.+++++|..  .|+.||..+|+.+|.+|++.|++++|.++|++|.    .|+..+|++
T Consensus       540 PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tyns  619 (1060)
T PLN03218        540 PDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTI  619 (1060)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHH
Confidence            8888888888888888888888888888875  5678888888888888888888888888888886    345678888


Q ss_pred             HHHHHHhcCCCCCC
Q 031208          151 MISGLAASGDLDAA  164 (164)
Q Consensus       151 li~~~~~~g~~~~A  164 (164)
                      +|.+|++.|++++|
T Consensus       620 LI~ay~k~G~~deA  633 (1060)
T PLN03218        620 AVNSCSQKGDWDFA  633 (1060)
T ss_pred             HHHHHHhcCCHHHH
Confidence            88888888877654

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.7e-34  Score=226.57  Aligned_cols=158  Identities=20%  Similarity=0.287  Sum_probs=104.0

Q ss_pred             hcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccH
Q 031208            7 YGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTF   82 (164)
Q Consensus         7 ~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~   82 (164)
                      .|+.||..+|+++|.+|++.|++++|.++|+.|.    .|+..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||
T Consensus       573 ~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~Ty  652 (1060)
T PLN03218        573 HPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFF  652 (1060)
T ss_pred             CCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            3455666666666666666666666666666554    245566666666666666666666666666666666666666


Q ss_pred             HHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC----CCCcchHHHHHHHHHhc
Q 031208           83 PFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR----VRSVVSWTTMISGLAAS  158 (164)
Q Consensus        83 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~  158 (164)
                      +++|++|++.|++++|.+++++|.+.|+.|+..+|+.||++|++.|++++|.++|++|.    .||..+||+||.+|++.
T Consensus       653 nsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~  732 (1060)
T PLN03218        653 SALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEG  732 (1060)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC
Confidence            66666666666666666666666666666777777777777777777777777777664    56777777777777777


Q ss_pred             CCCCCC
Q 031208          159 GDLDAA  164 (164)
Q Consensus       159 g~~~~A  164 (164)
                      |++++|
T Consensus       733 G~~eeA  738 (1060)
T PLN03218        733 NQLPKA  738 (1060)
T ss_pred             CCHHHH
Confidence            766654

>PF13041 PPR_2: PPR repeat family

Probab=99.73  E-value=1.2e-17  Score=86.77  Aligned_cols=50  Identities=30%  Similarity=0.523  Sum_probs=37.4

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      ||+++||++|.+|++.|++++|.++|++|.+.|+.||..||+++|++|++
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            67777777777777777777777777777777777777777777777764

>PF13041 PPR_2: PPR repeat family

Probab=99.69  E-value=8.7e-17  Score=83.52  Aligned_cols=50  Identities=20%  Similarity=0.262  Sum_probs=48.8

Q ss_pred             CCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Q 031208           77 PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        77 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                      ||..+||++|++|++.|++++|.++|++|++.|+.||..||+.+|++|+|
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            89999999999999999999999999999999999999999999999985

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.47  E-value=8.8e-13  Score=94.31  Aligned_cols=130  Identities=14%  Similarity=0.153  Sum_probs=110.3

Q ss_pred             cCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208            8 GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus         8 g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      -.+-+..++.+||.+.||....+.|.+++++-.    +-+..+||.+|.+-+-...    .++..+|.+..++||..|||
T Consensus       202 ~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfN  277 (625)
T KOG4422|consen  202 TLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFN  277 (625)
T ss_pred             hcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHH
Confidence            345578899999999999999999999999876    4677889988877654433    78999999999999999999


Q ss_pred             HHHHHHHhccchhh----HHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchh-HHHHhcccC
Q 031208           84 FVIKACIASLAIEK----GKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDG-GRKMFDKMR  141 (164)
Q Consensus        84 ~ll~~~~~~~~~~~----a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~-a~~~~~~m~  141 (164)
                      +++++..+.|+++.    |.+++.+|++-|++|...+|..+|..+.+.++..+ +..+..++.
T Consensus       278 alL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~  340 (625)
T KOG4422|consen  278 ALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQ  340 (625)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHH
Confidence            99999999998876    56788999999999999999999999999887643 555555543

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.40  E-value=8.6e-12  Score=91.04  Aligned_cols=147  Identities=14%  Similarity=0.053  Sum_probs=68.8

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc----ccHHHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK----FTFPFVIK   87 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~   87 (164)
                      .+..+...+.+.|+++.|..+|+.+.+   ++..+++.+...+.+.|++++|.+.++++.+.+-.+..    ..+..+..
T Consensus       109 ~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~  188 (389)
T PRK11788        109 ALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQ  188 (389)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHH
Confidence            344555555555555555555555542   33445555555555555555555555555443211111    12233444


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCC--cchHHHHHHHHHhcCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRS--VVSWTTMISGLAASGDLD  162 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~--~~~~~~li~~~~~~g~~~  162 (164)
                      .+.+.|+.++|...++++.+.. +.+...+..+...|.+.|++++|.++|+++.  .|+  ..+++.+..+|.+.|+++
T Consensus       189 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~  266 (389)
T PRK11788        189 QALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEA  266 (389)
T ss_pred             HHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHH
Confidence            4445555555555555554432 1223344444445555555555555555444  121  123444445555554444

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.35  E-value=5.4e-11  Score=86.87  Aligned_cols=135  Identities=12%  Similarity=0.011  Sum_probs=61.7

Q ss_pred             HHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      ...+.+.|++++|..+|+++.+  | +...+..+...+.+.|++++|.+.|+++...+......+++.+..+|...|+.+
T Consensus       187 a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~  266 (389)
T PRK11788        187 AQQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEA  266 (389)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHH
Confidence            3334444444444444444331  2 223344444445555555555555555543321111233444455555555555


Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHH
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLA  156 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~  156 (164)
                      +|.+.++.+.+.  .|+...+..+...+.+.|++++|.++|+++.  .|+..+++.++..+.
T Consensus       267 ~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~  326 (389)
T PRK11788        267 EGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHL  326 (389)
T ss_pred             HHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhh
Confidence            555555554443  2333344445555555555555555555443  344445554444443

>PF12854 PPR_1: PPR repeat

Probab=99.29  E-value=3.6e-12  Score=60.25  Aligned_cols=33  Identities=39%  Similarity=0.655  Sum_probs=21.7

Q ss_pred             CCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          109 GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       109 g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |+.||..+|++||++|++.|++++|.++|++|+
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            566666666666666666666666666666663

>PF12854 PPR_1: PPR repeat

Probab=99.29  E-value=4.5e-12  Score=59.91  Aligned_cols=34  Identities=24%  Similarity=0.384  Sum_probs=28.0

Q ss_pred             hcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC
Q 031208            7 YGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR   40 (164)
Q Consensus         7 ~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~   40 (164)
                      +|++||..+|++||++||+.|++++|.++|++|+
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            4788888888888888888888888888888774

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.22  E-value=5.4e-10  Score=80.37  Aligned_cols=156  Identities=18%  Similarity=0.199  Sum_probs=120.5

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHh--ccCCcHH-------------------------HHHHHhccCCCcHhHHHHHHHHH
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCS--FYGKTDH-------------------------ALLVFSQIRCPHVFTWNLMIRAL   54 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~--~~~~~~~-------------------------a~~~~~~~~~~~~~~~~~li~~~   54 (164)
                      +.|+..|.+.+..+--.|+..-+  ....+-.                         |.-+|+..+ ....+|.++|.+.
T Consensus       139 ~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~~P-KT~et~s~mI~Gl  217 (625)
T KOG4422|consen  139 ERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFETLP-KTDETVSIMIAGL  217 (625)
T ss_pred             HHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhhcC-CCchhHHHHHHHH
Confidence            45777788888777777766433  2222221                         222222222 2346899999999


Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHH
Q 031208           55 TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGR  134 (164)
Q Consensus        55 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~  134 (164)
                      |+-...+.|.+++++-.....+.+..+||.+|.+..-..+    .+++.+|....+.||..|+|+++.+.++.|+++.|.
T Consensus       218 ~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar  293 (625)
T KOG4422|consen  218 CKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDAR  293 (625)
T ss_pred             HHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHH
Confidence            9999999999999999888889999999999987655433    789999999999999999999999999999998765


Q ss_pred             ----HHhcccC----CCCcchHHHHHHHHHhcCCCC
Q 031208          135 ----KMFDKMR----VRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus       135 ----~~~~~m~----~~~~~~~~~li~~~~~~g~~~  162 (164)
                          +++.+|+    +|...+|..+|..+.+.++..
T Consensus       294 ~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~  329 (625)
T KOG4422|consen  294 KAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQ  329 (625)
T ss_pred             HHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCch
Confidence                4555665    789999999999999887653

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

Probab=99.20  E-value=8.8e-10  Score=87.47  Aligned_cols=149  Identities=15%  Similarity=0.057  Sum_probs=69.8

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...|..+...+.+.|++++|...|+.+.+   .+...+..+...+.+.|++++|...|+++.+.. +.+..++..+...
T Consensus       600 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~  678 (899)
T TIGR02917       600 SPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQL  678 (899)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            444555555555555555555555554431   233344445555555555555555555554321 1223344444444


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHhcCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~~g~~~  162 (164)
                      +...|++++|.++++.+...+ +++...+..+...+.+.|++++|.+.|+.+.  .|+..++..+...+.+.|+++
T Consensus       679 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  753 (899)
T TIGR02917       679 LLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTA  753 (899)
T ss_pred             HHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHH
Confidence            555555555555555444433 2333444444445555555555555555443  223334444444444444443

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

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

Probab=99.16  E-value=1.5e-09  Score=86.18  Aligned_cols=146  Identities=13%  Similarity=0.114  Sum_probs=64.4

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      +..+...+.+.|+++.|..+++.+.   ..+...|..+...+...|++++|...|+++.+.. +.+...+..+...+.+.
T Consensus       570 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~  648 (899)
T TIGR02917       570 ALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVM  648 (899)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHc
Confidence            3333444444444444444444432   1233444444444444444444444444443321 12233344444444444


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHHHHHhcCCCCC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~  163 (164)
                      |++++|..+++.+.+.. +.+...+..+...+...|++++|.++++.+.+   ++...+..+...|.+.|++++
T Consensus       649 ~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  721 (899)
T TIGR02917       649 KNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPA  721 (899)
T ss_pred             CCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHH
Confidence            55555555444444332 22344444445555555555555555554431   133344445555555555443

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.

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

Probab=99.05  E-value=3.1e-09  Score=82.17  Aligned_cols=60  Identities=17%  Similarity=0.241  Sum_probs=52.6

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC----------------------------CCcHhHHHHHHHH
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR----------------------------CPHVFTWNLMIRA   53 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----------------------------~~~~~~~~~li~~   53 (164)
                      ..+...|+.|+.++|.++|.-||..|+++.|- +|..|.                            .|...+|+.|+.+
T Consensus        14 a~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll~a   92 (1088)
T KOG4318|consen   14 ALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLLKA   92 (1088)
T ss_pred             HHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHHHHH
Confidence            35678899999999999999999999999998 888775                            1567899999999


Q ss_pred             HHhcCChhH
Q 031208           54 LTIDGSSLQ   62 (164)
Q Consensus        54 ~~~~~~~~~   62 (164)
                      |...|+...
T Consensus        93 yr~hGDli~  101 (1088)
T KOG4318|consen   93 YRIHGDLIL  101 (1088)
T ss_pred             HHhccchHH
Confidence            999998755

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

Probab=99.03  E-value=1.5e-09  Score=76.06  Aligned_cols=151  Identities=18%  Similarity=0.137  Sum_probs=107.4

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC-----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR-----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPF   84 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~   84 (164)
                      +++..+...+..+.+.++.+.+.++++...     .++...|..+-..+.+.|++++|.+.+++..+.  .| |......
T Consensus       108 ~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~  185 (280)
T PF13429_consen  108 GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNA  185 (280)
T ss_dssp             ----------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHH
T ss_pred             cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHH
Confidence            566778888889999999999999988854     356677888888899999999999999999775  46 4667888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDL  161 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~  161 (164)
                      ++..+...|+.+++.+++....+.. +.+...+..+..+|...|+.++|..+|++..  .| |......+..++...|+.
T Consensus       186 l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~  264 (280)
T PF13429_consen  186 LAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGRK  264 (280)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT-----
T ss_pred             HHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccccccccccccccccccccccc
Confidence            9999999999999999999888765 5667788899999999999999999999876  34 778888899999999999


Q ss_pred             CCC
Q 031208          162 DAA  164 (164)
Q Consensus       162 ~~A  164 (164)
                      ++|
T Consensus       265 ~~A  267 (280)
T PF13429_consen  265 DEA  267 (280)
T ss_dssp             ---
T ss_pred             ccc
Confidence            886

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.97  E-value=1.5e-09  Score=51.53  Aligned_cols=34  Identities=35%  Similarity=0.542  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK   79 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   79 (164)
                      +||++|.+|++.|++++|.++|++|.+.|++||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            6777888888888888888888888777777763

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.94  E-value=8.4e-08  Score=64.55  Aligned_cols=149  Identities=16%  Similarity=0.074  Sum_probs=73.2

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKA   88 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~   88 (164)
                      ...+..+...+...|+++.|.+.++...   ..+...+..+...+...|++++|...+.+.......| ....+..+...
T Consensus        65 ~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~  144 (234)
T TIGR02521        65 YLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLC  144 (234)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHH
Confidence            3444444555555555555555555443   1233344444555555555666655555554432111 22234444455


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~  162 (164)
                      +...|++++|...+.+..+.. +.+...+..+...+.+.|++++|.+.+++..   ..+...+..+...+...|+.+
T Consensus       145 ~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (234)
T TIGR02521       145 ALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVA  220 (234)
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHH
Confidence            555566666666665555432 1233445555555566666666666555443   123334444445554544443

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=98.92  E-value=9.1e-08  Score=64.39  Aligned_cols=152  Identities=11%  Similarity=-0.052  Sum_probs=121.8

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      ....+..+...+...|++++|...+++..  .| +...+..+...+...|++++|.+.+++..+.. +.+...+..+...
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~  108 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH
Confidence            35667778889999999999999999865  23 46678888889999999999999999987753 3344567778889


Q ss_pred             HHhccchhhHHHHHHHHHHhCCC-CchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFS-RDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +...|++++|.+.+++....... .....+..+...+.+.|++++|...|++..  .| +...+..+...+...|++++|
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  188 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDA  188 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999998865322 234567777888999999999999998775  23 456788888889888887754

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.90  E-value=3e-09  Score=50.18  Aligned_cols=33  Identities=33%  Similarity=0.526  Sum_probs=23.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRP   77 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   77 (164)
                      .+|+.+|.+|++.|+++.|.++|++|++.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            467777777777777777777777777666665

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

Probab=98.88  E-value=3.5e-08  Score=72.23  Aligned_cols=121  Identities=15%  Similarity=0.104  Sum_probs=106.5

Q ss_pred             hcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC-CcH-----hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc
Q 031208            7 YGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC-PHV-----FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF   80 (164)
Q Consensus         7 ~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-~~~-----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~   80 (164)
                      ++.+.+.....++++.+....+++.+.+++-+++. |+.     .|.+++|..|.+.|..+.++++++.=.+.|+-||..
T Consensus        60 ~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~  139 (429)
T PF10037_consen   60 RKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNF  139 (429)
T ss_pred             cCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChh
Confidence            45677888899999999999999999998888763 322     356799999999999999999999999999999999


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC  127 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  127 (164)
                      |||.||+.+.+.|++..|.++..+|...+.-.+..|+..-+.+|.+.
T Consensus       140 s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  140 SFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             hHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            99999999999999999999999999888777788888777777766

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 [].

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

Probab=98.83  E-value=1.8e-07  Score=72.50  Aligned_cols=150  Identities=11%  Similarity=0.006  Sum_probs=116.6

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CCc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...+..+-..+...|++++|...|++..  .|+ ...|..+-..+...|++++|...|++..+.. +-+...|..+...+
T Consensus       331 a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~  409 (615)
T TIGR00990       331 AIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLH  409 (615)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            4456666667778999999999998875  344 4577777788888999999999999886642 33456788888888


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...|++++|...+++..+.. +.+...+..+...+.+.|++++|...|++..  .| +...|+.+-..+...|++++|
T Consensus       410 ~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A  486 (615)
T TIGR00990       410 FIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEA  486 (615)
T ss_pred             HHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHH
Confidence            99999999999999887654 3346667777888888999999999998765  33 566888888888888887754

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.80  E-value=2.9e-07  Score=71.85  Aligned_cols=116  Identities=9%  Similarity=-0.046  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--CCc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--CPH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      ..+..+...+...|++++|...+..+.  .|+ ...+..+ ..+...|++++|...++.+....-.++...+..+...+.
T Consensus       145 ~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~  223 (656)
T PRK15174        145 QIFALHLRTLVLMDKELQAISLARTQAQEVPPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLC  223 (656)
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHH
Confidence            334444444455555555554444332  111 1111111 223444444555444444433221122222222334444


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      ..|+.++|...++...... +.+...+..+-..|.+.|+++
T Consensus       224 ~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~  263 (656)
T PRK15174        224 AVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSR  263 (656)
T ss_pred             HCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCch
Confidence            4445555544444444332 122333344444444444444

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.80  E-value=1.1e-08  Score=48.41  Aligned_cols=35  Identities=17%  Similarity=0.260  Sum_probs=32.6

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCch
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDM  114 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~  114 (164)
                      .+|+++|++|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            48999999999999999999999999999999973

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

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.77  E-value=1.7e-08  Score=47.50  Aligned_cols=33  Identities=12%  Similarity=0.244  Sum_probs=31.2

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCC
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSR  112 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~  112 (164)
                      .||+++|++|++.|+++.|.+++++|++.|+.|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            589999999999999999999999999999887

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

Probab=98.76  E-value=2.7e-07  Score=54.89  Aligned_cols=82  Identities=15%  Similarity=0.000  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCCcccHHHHHHHHHhcc--------chhhHHHHHHHHHHhCCCCchHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGF-RPDKFTFPFVIKACIASL--------AIEKGKEVHGLAVKAGFSRDMFV  116 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~m~~~g~~~~~~~  116 (164)
                      +-...|..+...+++.....+|+.++++|+ .|+..+|+.++++.++..        +.-....+++.|...++.|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            445567777778999999999999999999 999999999999998774        34457789999999999999999


Q ss_pred             HHHHHHHHHhc
Q 031208          117 QSTLMDLYLKC  127 (164)
Q Consensus       117 ~~~ll~~~~~~  127 (164)
                      |+.++....+.
T Consensus       107 Ynivl~~Llkg  117 (120)
T PF08579_consen  107 YNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHh
Confidence            99999988764

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 [, , ].

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.74  E-value=1.1e-06  Score=68.69  Aligned_cols=149  Identities=9%  Similarity=-0.049  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...+..+-..+.+.|+++.|...+++...  | +...+..+...+...|++++|...++.+....  |+.......+..+
T Consensus       110 ~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~--P~~~~a~~~~~~l  187 (656)
T PRK15174        110 PEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEV--PPRGDMIATCLSF  187 (656)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC--CCCHHHHHHHHHH
Confidence            44555566677777777777777777652  3 45567777777777888888888777775543  2222222222346


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      ...|++++|...++.+.+..-.++...+..+...+.+.|++++|...|++..  .| +...+..+-..|...|++++
T Consensus       188 ~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~e  264 (656)
T PRK15174        188 LNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSRE  264 (656)
T ss_pred             HHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchh
Confidence            6778888888877777655322334444555667778888888888887765  22 45567777777788887764

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

Probab=98.71  E-value=1.7e-07  Score=65.73  Aligned_cols=131  Identities=15%  Similarity=0.068  Sum_probs=95.2

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      .+++...|..+-..+.+.|+.++|.+.+++..  .| |....+.++..+...|+.+++.+++....... +.|...+..+
T Consensus       142 ~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~l  220 (280)
T PF13429_consen  142 APDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDAL  220 (280)
T ss_dssp             --T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHH
Confidence            45678889999999999999999999999876  46 46788899999999999999999999987664 5666778899


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..++...|+.++|..++++..+.. +.|......+.+++.+.|+.++|.++.++..
T Consensus       221 a~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  221 AAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT----------------
T ss_pred             HHHhcccccccccccccccccccc-ccccccccccccccccccccccccccccccc
Confidence            999999999999999999988765 4578888899999999999999999887653

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

Probab=98.68  E-value=3.1e-08  Score=45.58  Aligned_cols=29  Identities=28%  Similarity=0.328  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      +|+++|++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            56666666666666666666666666655

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.

>PRK12370 invasion protein regulator; Provisional

Probab=98.65  E-value=2.9e-06  Score=65.16  Aligned_cols=147  Identities=11%  Similarity=0.015  Sum_probs=108.0

Q ss_pred             CC-CHHHHHHHHHHHhccCCcHHHHHHHhccC--CCc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHH
Q 031208           10 SN-DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPF   84 (164)
Q Consensus        10 ~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~   84 (164)
                      .| +...+..+-..+...|++++|...|++..  .|+ ...+..+-..+...|++++|...+++..+..  |+. ..+..
T Consensus       334 dP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~--P~~~~~~~~  411 (553)
T PRK12370        334 DHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLKLD--PTRAAAGIT  411 (553)
T ss_pred             CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCChhhHHH
Confidence            44 45666666677888999999999999876  354 5567778888999999999999999997753  543 23334


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCC-chHHHHHHHHHHHhcCCchhHHHHhcccCC--C-CcchHHHHHHHHHhcC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMISGLAASG  159 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~g  159 (164)
                      +...+...|++++|...+++..+.. .| +...+..+-..|...|+.++|...+.++..  | +...++.+...|.+.|
T Consensus       412 ~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  489 (553)
T PRK12370        412 KLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS  489 (553)
T ss_pred             HHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH
Confidence            4556777899999999999887654 34 344566777888899999999999988763  2 3334555555666555

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.65  E-value=7.4e-07  Score=72.07  Aligned_cols=103  Identities=13%  Similarity=0.057  Sum_probs=52.0

Q ss_pred             CChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHh
Q 031208           58 GSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMF  137 (164)
Q Consensus        58 ~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~  137 (164)
                      |++++|...+++..+.  .|+...+..+-..+.+.|+.++|...+++..... +.+...++.+-..+...|+.++|...|
T Consensus       590 Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l  666 (987)
T PRK09782        590 GQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREML  666 (987)
T ss_pred             CCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            5555555555555432  2344445555555555555555555555554442 223334444444555555555555555


Q ss_pred             cccC--CC-CcchHHHHHHHHHhcCCCCC
Q 031208          138 DKMR--VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       138 ~~m~--~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      ++..  .| +...+..+-.++...|++++
T Consensus       667 ~~AL~l~P~~~~a~~nLA~al~~lGd~~e  695 (987)
T PRK09782        667 ERAHKGLPDDPALIRQLAYVNQRLDDMAA  695 (987)
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHCCCHHH
Confidence            5443  22 34455555555555555544

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

Probab=98.59  E-value=2.5e-06  Score=66.32  Aligned_cols=151  Identities=13%  Similarity=0.061  Sum_probs=73.3

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ..+|..+-..+...|++++|...|++..  .| +...+..+-..+.+.|++++|...|++..+.. +-+...++.+-..+
T Consensus       399 ~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~  477 (615)
T TIGR00990       399 PDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELL  477 (615)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHH
Confidence            3444444445555555555555555443  12 23344444455555555555555555554421 22334555555555


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCch------HHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDM------FVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGD  160 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~------~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~  160 (164)
                      ...|++++|...+++.....-..+.      ..++.....|...|++++|.+++++..  .| +...+..+...+.+.|+
T Consensus       478 ~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~  557 (615)
T TIGR00990       478 LDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGD  557 (615)
T ss_pred             HHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccC
Confidence            6666666666666555443211000      011112222333466666666665532  22 33456666667777766


Q ss_pred             CCCC
Q 031208          161 LDAA  164 (164)
Q Consensus       161 ~~~A  164 (164)
                      +++|
T Consensus       558 ~~eA  561 (615)
T TIGR00990       558 VDEA  561 (615)
T ss_pred             HHHH
Confidence            6554

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

Probab=98.57  E-value=3.8e-06  Score=61.41  Aligned_cols=126  Identities=18%  Similarity=0.186  Sum_probs=99.8

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      ......++..+...++++.|.++|+++.+.+......+...+...++-.+|.+++++..+.. +-+......-.+.+.+.
T Consensus       169 NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~k  247 (395)
T PF09295_consen  169 NYLVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLSK  247 (395)
T ss_pred             hHHHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhc
Confidence            44555667777778999999999999986555566668888888888899999999987542 22444444455678888


Q ss_pred             cchhhHHHHHHHHHHhCCCCch-HHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDM-FVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ++.+.|..+.++....  .|+. .+|..|..+|.+.|+++.|+-.++.++
T Consensus       248 ~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  248 KKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            9999999999998876  4654 599999999999999999999999887

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

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.55  E-value=5.4e-06  Score=66.01  Aligned_cols=162  Identities=8%  Similarity=-0.003  Sum_probs=123.2

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCC---------cHhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCP---------HVFTWNLMIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      +.|...|.+....+-..+-++|...+++++|..++.....+         +......|..++...+++++|..+++++..
T Consensus       316 ~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~  395 (822)
T PRK14574        316 EAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSE  395 (822)
T ss_pred             HHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHh
Confidence            34556676656668888999999999999999999987421         233357789999999999999999999987


Q ss_pred             cCC-----------CCCc---ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhc
Q 031208           73 NGF-----------RPDK---FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFD  138 (164)
Q Consensus        73 ~~~-----------~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  138 (164)
                      ..-           .||.   .-+..+...+.-.|+..+|++.++++.... +-|..+...+-+.+...|+..+|.+.++
T Consensus       396 ~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~v~~~Rg~p~~A~~~~k  474 (822)
T PRK14574        396 QTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTA-PANQNLRIALASIYLARDLPRKAEQELK  474 (822)
T ss_pred             cCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            311           1222   123345677888999999999999997665 5678899999999999999999999997


Q ss_pred             ccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          139 KMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       139 ~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...  .| +..+......++...|++++|
T Consensus       475 ~a~~l~P~~~~~~~~~~~~al~l~e~~~A  503 (822)
T PRK14574        475 AVESLAPRSLILERAQAETAMALQEWHQM  503 (822)
T ss_pred             HHhhhCCccHHHHHHHHHHHHhhhhHHHH
Confidence            654  44 555666677777777776543

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

Probab=98.54  E-value=1.3e-07  Score=43.35  Aligned_cols=31  Identities=19%  Similarity=0.177  Sum_probs=24.2

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCC
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGF  110 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~  110 (164)
                      +||+++|++|++.|++++|.+++++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4778888888888888888888888877664

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.

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.53  E-value=5.5e-06  Score=65.95  Aligned_cols=144  Identities=7%  Similarity=-0.064  Sum_probs=91.8

Q ss_pred             HHHHHhccCCcHHHHHHHhccCC--Cc-----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-----------CCCCc-
Q 031208           19 LLDLCSFYGKTDHALLVFSQIRC--PH-----VFTWNLMIRALTIDGSSLQALLLYNLMICNG-----------FRPDK-   79 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~~--~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----------~~p~~-   79 (164)
                      +-..+...|++++|...|+....  |.     ......+..++...|++++|...++++....           -.|+. 
T Consensus       278 la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~  357 (765)
T PRK10049        278 VASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDD  357 (765)
T ss_pred             HHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCch
Confidence            35567777788888777776542  21     2345555666777788888888877776542           01221 


Q ss_pred             --ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHH
Q 031208           80 --FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISG  154 (164)
Q Consensus        80 --~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~  154 (164)
                        ..+..+...+...|+.++|.+.++++.... +.+...+..+...+...|+.++|.+.+++..  .| +...+-.....
T Consensus       358 ~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~  436 (765)
T PRK10049        358 WLQGQSLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWT  436 (765)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHH
Confidence              123445566777778888888877776553 4456677777777777888888888877665  34 34455555556


Q ss_pred             HHhcCCCCC
Q 031208          155 LAASGDLDA  163 (164)
Q Consensus       155 ~~~~g~~~~  163 (164)
                      +.+.|++++
T Consensus       437 al~~~~~~~  445 (765)
T PRK10049        437 ALDLQEWRQ  445 (765)
T ss_pred             HHHhCCHHH
Confidence            666666654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.53  E-value=4.8e-06  Score=67.52  Aligned_cols=151  Identities=9%  Similarity=-0.056  Sum_probs=104.2

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPFVI   86 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll   86 (164)
                      .|+......+...+...|++++|...|+++..  |+...+..+...+.+.|++++|...+++..+..  |+. ..+..+.
T Consensus       506 ~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~--P~~~~l~~~La  583 (987)
T PRK09782        506 QPDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG--LGDNALYWWLH  583 (987)
T ss_pred             CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CccHHHHHHHH
Confidence            35543322233344578888888888886552  444445556667788888888888888887654  433 2222233


Q ss_pred             HHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCC
Q 031208           87 KACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      ....+.|++++|...+++..+.  .|+...+..+-..+.+.|+.++|...|++..  .| +...++.+-..+...|++++
T Consensus       584 ~~l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~ee  661 (987)
T PRK09782        584 AQRYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQ  661 (987)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHH
Confidence            3344558999999998888765  4677788888888999999999999998776  34 55677777778888888765


Q ss_pred             C
Q 031208          164 A  164 (164)
Q Consensus       164 A  164 (164)
                      |
T Consensus       662 A  662 (987)
T PRK09782        662 S  662 (987)
T ss_pred             H
Confidence            4

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

Probab=98.52  E-value=1.3e-06  Score=58.09  Aligned_cols=98  Identities=10%  Similarity=0.047  Sum_probs=82.9

Q ss_pred             HHHHHhcc--CCCcHhHHHHHHHHHHhc-----CChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc------------
Q 031208           32 ALLVFSQI--RCPHVFTWNLMIRALTID-----GSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS------------   92 (164)
Q Consensus        32 a~~~~~~~--~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~------------   92 (164)
                      -.+.|+..  ...|..+|..++..|.+.     |..+-....++.|.+.|+.-|..+|+.||+.+-+.            
T Consensus        33 ~~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F  112 (228)
T PF06239_consen   33 HEELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEF  112 (228)
T ss_pred             hHHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHh
Confidence            44566665  468889999999998764     77888999999999999999999999999998653            


Q ss_pred             ----cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 031208           93 ----LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus        93 ----~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                          ..-+-|.+++++|..+|+.||..++..|++.+.+.+.
T Consensus       113 ~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  113 MHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             ccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence                2345688999999999999999999999999987765

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

>PRK12370 invasion protein regulator; Provisional

Probab=98.49  E-value=8.1e-06  Score=62.71  Aligned_cols=135  Identities=12%  Similarity=-0.011  Sum_probs=103.6

Q ss_pred             cCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhHHHH
Q 031208           26 YGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKGKEV  101 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~  101 (164)
                      .+++++|...+++..+  | +...+..+-..+...|++++|...|++..+.+  |+ ...+..+-..+...|++++|...
T Consensus       317 ~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~G~~~eAi~~  394 (553)
T PRK12370        317 QNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS--PISADIKYYYGWNLFMAGQLEEALQT  394 (553)
T ss_pred             chHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            3457889999988763  4 56677777778889999999999999998754  54 55677888899999999999999


Q ss_pred             HHHHHHhCCCCch-HHHHHHHHHHHhcCCchhHHHHhcccC---CCC-cchHHHHHHHHHhcCCCCCC
Q 031208          102 HGLAVKAGFSRDM-FVQSTLMDLYLKCGDVDGGRKMFDKMR---VRS-VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       102 ~~~m~~~g~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~-~~~~~~li~~~~~~g~~~~A  164 (164)
                      +++..+..  |+. ..+..+...+...|++++|...+++..   .|+ ...+..+-..|...|+.++|
T Consensus       395 ~~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA  460 (553)
T PRK12370        395 INECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELA  460 (553)
T ss_pred             HHHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHH
Confidence            99988764  442 233344555677899999999998874   243 34567777888899998765

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

Probab=98.47  E-value=2.3e-07  Score=72.23  Aligned_cols=88  Identities=16%  Similarity=0.203  Sum_probs=56.0

Q ss_pred             HHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCc
Q 031208           66 LYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSV  145 (164)
Q Consensus        66 ~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  145 (164)
                      ++..++..|+.||.+||.++|.-||..|+++.|- +|.-|+......+...++.++.+-.+.++.+.+.       +|..
T Consensus        12 fla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-------ep~a   83 (1088)
T KOG4318|consen   12 FLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-------EPLA   83 (1088)
T ss_pred             HHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-------CCch
Confidence            4555666666666666666666666666666666 6666666665566666666666666666655443       5555


Q ss_pred             chHHHHHHHHHhcCCC
Q 031208          146 VSWTTMISGLAASGDL  161 (164)
Q Consensus       146 ~~~~~li~~~~~~g~~  161 (164)
                      -||+.|..+|..+|++
T Consensus        84 Dtyt~Ll~ayr~hGDl   99 (1088)
T KOG4318|consen   84 DTYTNLLKAYRIHGDL   99 (1088)
T ss_pred             hHHHHHHHHHHhccch
Confidence            5666666666666654

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.33  E-value=5.2e-05  Score=56.02  Aligned_cols=143  Identities=13%  Similarity=0.013  Sum_probs=107.3

Q ss_pred             HHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc
Q 031208           17 RKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL   93 (164)
Q Consensus        17 ~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~   93 (164)
                      ..++.......+.+...++++..+.   .+......+..++...|+.++|.+++.+..+.  .|+..  -.++.+....+
T Consensus       233 ~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~--l~~l~~~l~~~  308 (398)
T PRK10747        233 IGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER--LVLLIPRLKTN  308 (398)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH--HHHHHhhccCC
Confidence            3344444445566777777777762   46677888888999999999999999888763  44442  23455555668


Q ss_pred             chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHhcCCCCCC
Q 031208           94 AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        94 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +.+++.+..+...+.. +-|......+-..+.+.+++++|.+.|+...  .|+...+..+-..+.+.|+.++|
T Consensus       309 ~~~~al~~~e~~lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A  380 (398)
T PRK10747        309 NPEQLEKVLRQQIKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEA  380 (398)
T ss_pred             ChHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHH
Confidence            8889999998887664 3456667788888999999999999999876  67888888899999998887654

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.33  E-value=3.7e-05  Score=61.37  Aligned_cols=150  Identities=9%  Similarity=0.006  Sum_probs=100.9

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      +.+.......+....-.|+.++|.+++.....   .+...+..+...+...|++++|..++++..+.. +.+...+..+.
T Consensus        12 ~~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la   90 (765)
T PRK10049         12 ALSNNQIADWLQIALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLI   90 (765)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            34555666777777788888888888877652   344457777777888888888888888876542 22344556666


Q ss_pred             HHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCC
Q 031208           87 KACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~  162 (164)
                      ..+...|+.++|...+++..+.. +.+.. +..+-..+...|+.++|...+++..  .| +...+..+...+...|+.+
T Consensus        91 ~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e  167 (765)
T PRK10049         91 LTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSA  167 (765)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChH
Confidence            77778888888888888777652 23344 6667777777888888888887765  33 3444555566665555544

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

Probab=98.32  E-value=8.3e-06  Score=60.09  Aligned_cols=117  Identities=13%  Similarity=0.084  Sum_probs=96.4

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc--CCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICN--GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQST  119 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  119 (164)
                      -+.....++++.+....+.+++..++.+.+..  ....-..|..++++.|.+.|..+.+..++..=...|+=||..++|.
T Consensus        64 vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~  143 (429)
T PF10037_consen   64 VSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNL  143 (429)
T ss_pred             CcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHH
Confidence            45567777888888888899999999998765  3334455678999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCchhHHHHhcccCCC----CcchHHHHHHHHHhc
Q 031208          120 LMDLYLKCGDVDGGRKMFDKMRVR----SVVSWTTMISGLAAS  158 (164)
Q Consensus       120 ll~~~~~~~~~~~a~~~~~~m~~~----~~~~~~~li~~~~~~  158 (164)
                      ||+.+.+.|++..|.++.-+|...    +..|+.-.+.+|.+.
T Consensus       144 Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  144 LMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999999999999999999988632    445555555555554

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 [].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.27  E-value=8.4e-05  Score=50.76  Aligned_cols=149  Identities=13%  Similarity=0.065  Sum_probs=107.8

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcH----hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc----c
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHV----FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF----T   81 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----t   81 (164)
                      +...+-.+...+.+.|+++.|...|+....  |+.    ..+-.+-.++...|++++|...++++.+..  |+..    .
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a  109 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLH--PNHPDADYA  109 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCchHHH
Confidence            355566667788899999999999997752  432    356777788999999999999999997643  4322    3


Q ss_pred             HHHHHHHHHhc--------cchhhHHHHHHHHHHhCCCCch-HHH-----------------HHHHHHHHhcCCchhHHH
Q 031208           82 FPFVIKACIAS--------LAIEKGKEVHGLAVKAGFSRDM-FVQ-----------------STLMDLYLKCGDVDGGRK  135 (164)
Q Consensus        82 ~~~ll~~~~~~--------~~~~~a~~~~~~m~~~g~~~~~-~~~-----------------~~ll~~~~~~~~~~~a~~  135 (164)
                      +..+-.++...        |+.+.|.+.++...+..  |+. ..+                 ..+-..|.+.|++++|..
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~  187 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY--PNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAIN  187 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC--CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            33444444443        67888999999887663  332 121                 134456788999999999


Q ss_pred             HhcccC--CCC----cchHHHHHHHHHhcCCCCCC
Q 031208          136 MFDKMR--VRS----VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       136 ~~~~m~--~~~----~~~~~~li~~~~~~g~~~~A  164 (164)
                      .++...  .|+    ...+..+..++...|++++|
T Consensus       188 ~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A  222 (235)
T TIGR03302       188 RFETVVENYPDTPATEEALARLVEAYLKLGLKDLA  222 (235)
T ss_pred             HHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHH
Confidence            998875  222    35888999999999998865

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

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.26  E-value=4.3e-05  Score=63.54  Aligned_cols=83  Identities=13%  Similarity=0.070  Sum_probs=46.4

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-CcchHHHHHHHHH
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMISGLA  156 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~  156 (164)
                      ..+..+-..+.+.|+.++|...+++..+.. +.+...+..+...|...|+.++|.+.++....  | +...+..+..++.
T Consensus       604 ~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~  682 (1157)
T PRK11447        604 RIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWA  682 (1157)
T ss_pred             hHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHH
Confidence            344445555666666666666666665543 23455566666666666666666666665542  2 3334444555555


Q ss_pred             hcCCCCC
Q 031208          157 ASGDLDA  163 (164)
Q Consensus       157 ~~g~~~~  163 (164)
                      ..|++++
T Consensus       683 ~~g~~~e  689 (1157)
T PRK11447        683 ALGDTAA  689 (1157)
T ss_pred             hCCCHHH
Confidence            5555544

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

Probab=98.23  E-value=3e-05  Score=56.85  Aligned_cols=115  Identities=11%  Similarity=0.145  Sum_probs=93.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      .....|+..+...++++.|..+|+++.+..  |+.  ...+.+.+...++-.+|.+++.+..+.. +.+........+.+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            345667777888899999999999998765  553  4568888888888889999998887543 34566666667888


Q ss_pred             HhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          125 LKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       125 ~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+.++.+.|..+.++..  .| +..+|..|..+|.+.|++++|
T Consensus       245 l~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~A  287 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENA  287 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHH
Confidence            89999999999999987  45 456999999999999999876

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

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.23  E-value=6.7e-05  Score=47.49  Aligned_cols=90  Identities=9%  Similarity=-0.071  Sum_probs=48.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                      +-..+...|++++|...|+...... +.+...|..+-.++.+.|++++|...++...+.. +.+...+..+-.++.+.|+
T Consensus        30 ~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~  107 (144)
T PRK15359         30 SGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGE  107 (144)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCC
Confidence            3444555566666666666654432 2244455555555566666666666666555432 2344555555555566666


Q ss_pred             chhHHHHhcccC
Q 031208          130 VDGGRKMFDKMR  141 (164)
Q Consensus       130 ~~~a~~~~~~m~  141 (164)
                      .++|...|+...
T Consensus       108 ~~eAi~~~~~Al  119 (144)
T PRK15359        108 PGLAREAFQTAI  119 (144)
T ss_pred             HHHHHHHHHHHH
Confidence            666666665543

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.23  E-value=4.1e-05  Score=63.71  Aligned_cols=144  Identities=13%  Similarity=0.059  Sum_probs=104.5

Q ss_pred             HHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhh
Q 031208           18 KLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEK   97 (164)
Q Consensus        18 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~   97 (164)
                      .....+...|+.++|..+++.-+ .+...+..+-..+.+.|++++|...|++..+.. +.+...+..+...+...|+.++
T Consensus       578 ~~a~~l~~~G~~~eA~~~l~~~p-~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~e  655 (1157)
T PRK11447        578 ETANRLRDSGKEAEAEALLRQQP-PSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAA  655 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCC-CCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHH
Confidence            34556778899999999988432 344556667778889999999999999987753 3356678888889999999999


Q ss_pred             HHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--CC-------cchHHHHHHHHHhcCCCCCC
Q 031208           98 GKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--RS-------VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        98 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~~-------~~~~~~li~~~~~~g~~~~A  164 (164)
                      |.+.++...+.. +.+...+..+...+.+.|++++|.++++.+..  |+       ...+..+...+...|+.++|
T Consensus       656 A~~~l~~ll~~~-p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A  730 (1157)
T PRK11447        656 ARAQLAKLPATA-NDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQA  730 (1157)
T ss_pred             HHHHHHHHhccC-CCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHH
Confidence            999999776542 23345566677788889999999999988752  21       12444455666777776554

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

Probab=98.22  E-value=2.5e-05  Score=55.21  Aligned_cols=135  Identities=11%  Similarity=0.028  Sum_probs=93.0

Q ss_pred             HHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh----ccchh
Q 031208           21 DLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA----SLAIE   96 (164)
Q Consensus        21 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~~~~~   96 (164)
                      ..+...|++++|.++++..  .+.......+..+.+.++++.|.+.++.|.+..  .|. +...+..++..    ...+.
T Consensus       110 ~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~-~l~qLa~awv~l~~g~e~~~  184 (290)
T PF04733_consen  110 TILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQID--EDS-ILTQLAEAWVNLATGGEKYQ  184 (290)
T ss_dssp             HHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCH-HHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcH-HHHHHHHHHHHHHhCchhHH
Confidence            3556688888888888765  556667778888889999999999999997642  333 34444444433    23588


Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC---CcchHHHHHHHHHhcCCC
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR---SVVSWTTMISGLAASGDL  161 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~g~~  161 (164)
                      +|.-+|+++.. ...+++.+.+.+.-+....|++++|.+++.+..+.   +..+.-.++......|+.
T Consensus       185 ~A~y~f~El~~-~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~  251 (290)
T PF04733_consen  185 DAFYIFEELSD-KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKP  251 (290)
T ss_dssp             HHHHHHHHHHC-CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-T
T ss_pred             HHHHHHHHHHh-ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCC
Confidence            89999999754 35678888888888888999999999988876533   444555566666666654

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.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.19  E-value=0.00013  Score=46.15  Aligned_cols=102  Identities=13%  Similarity=-0.109  Sum_probs=83.6

Q ss_pred             hcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208            7 YGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus         7 ~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      ..++.++..+...-..+...|++++|...|+...  . .+...|..+-.++...|++++|...|++..... +.+...+.
T Consensus        18 ~al~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~   96 (144)
T PRK15359         18 QLLSVDPETVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVY   96 (144)
T ss_pred             HHHHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHH
Confidence            3334444445566778889999999999999876  2 467788889999999999999999999998753 44677888


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      .+-.++.+.|+.++|...++...+..
T Consensus        97 ~lg~~l~~~g~~~eAi~~~~~Al~~~  122 (144)
T PRK15359         97 QTGVCLKMMGEPGLAREAFQTAIKMS  122 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            88899999999999999999988764

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.17  E-value=0.00017  Score=53.30  Aligned_cols=140  Identities=13%  Similarity=0.001  Sum_probs=82.7

Q ss_pred             HhccCCcHHHHHHHhccCC--CcHhHHH--HHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhH
Q 031208           23 CSFYGKTDHALLVFSQIRC--PHVFTWN--LMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKG   98 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~~--~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a   98 (164)
                      ..+.|+++.|...+.++.+  |+.....  .....+...|+++.|...+++..+.. +-+......+...|.+.|+++.+
T Consensus       128 A~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a  206 (398)
T PRK10747        128 AQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSL  206 (398)
T ss_pred             HHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHH
Confidence            3677788888888877653  4433222  22445677788888888888876654 22455667777778888888888


Q ss_pred             HHHHHHHHHhCCCCch-------HHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHHHHHhcCCCCC
Q 031208           99 KEVHGLAVKAGFSRDM-------FVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        99 ~~~~~~m~~~g~~~~~-------~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~  163 (164)
                      .+++..+.+.+..++.       ..|..++....+..+.+...++++.++.   .+......+..++...|+.++
T Consensus       207 ~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~  281 (398)
T PRK10747        207 LDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDT  281 (398)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHH
Confidence            8888777776543222       1222333333333444445555555541   244455556666666665544

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.16  E-value=6.9e-05  Score=56.57  Aligned_cols=152  Identities=14%  Similarity=0.099  Sum_probs=114.1

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC----------CCcHh-HHHHHHHHHHhcCChhHHHHHHHHHHH---cCCCCC
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR----------CPHVF-TWNLMIRALTIDGSSLQALLLYNLMIC---NGFRPD   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~----------~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p~   78 (164)
                      ..+++.|-.+|.+.|++++|...++...          .|.+. ..+.+...+...+++++|..+++.-.+   .-+.++
T Consensus       283 a~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~  362 (508)
T KOG1840|consen  283 AATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGED  362 (508)
T ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhcccc
Confidence            4456666678999999998888777654          13333 367777788999999999999987632   223333


Q ss_pred             c----ccHHHHHHHHHhccchhhHHHHHHHHHHh-----C-CCC-chHHHHHHHHHHHhcCCchhHHHHhcccC------
Q 031208           79 K----FTFPFVIKACIASLAIEKGKEVHGLAVKA-----G-FSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR------  141 (164)
Q Consensus        79 ~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----g-~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~------  141 (164)
                      .    -+++-+-..|.+.|++++|.+++++....     | ..+ ....++.|-..|.+.+....|.++|.+-.      
T Consensus       363 ~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~  442 (508)
T KOG1840|consen  363 NVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLC  442 (508)
T ss_pred             chHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHh
Confidence            3    47889999999999999999999977643     1 122 24567788888999999999999988654      


Q ss_pred             ---CCC-cchHHHHHHHHHhcCCCCCC
Q 031208          142 ---VRS-VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       142 ---~~~-~~~~~~li~~~~~~g~~~~A  164 (164)
                         .|+ ..+|..|...|.+.|++|+|
T Consensus       443 g~~~~~~~~~~~nL~~~Y~~~g~~e~a  469 (508)
T KOG1840|consen  443 GPDHPDVTYTYLNLAALYRAQGNYEAA  469 (508)
T ss_pred             CCCCCchHHHHHHHHHHHHHcccHHHH
Confidence               223 35889999999999999875

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

Probab=98.14  E-value=0.00021  Score=51.54  Aligned_cols=145  Identities=12%  Similarity=-0.034  Sum_probs=111.3

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      .+|..+++-....+..+.-...|+..+   +.+...-.+++.-+...|+.++|.++..+-...+..|+    -..+-.+.
T Consensus       230 ~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~----L~~~~~~l  305 (400)
T COG3071         230 QAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR----LCRLIPRL  305 (400)
T ss_pred             HHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh----HHHHHhhc
Confidence            456667776666666666666777766   34566677788889999999999999999988877777    23344556


Q ss_pred             hccchhhHHHHHHHHH-HhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHhcCCCCCC
Q 031208           91 ASLAIEKGKEVHGLAV-KAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~-~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +.++...-.+..++-. ..+..  +..+..|-..|.+.+.|.+|.+.|+...  .|+..+|+.+-.+|.+.|+.++|
T Consensus       306 ~~~d~~~l~k~~e~~l~~h~~~--p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A  380 (400)
T COG3071         306 RPGDPEPLIKAAEKWLKQHPED--PLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEA  380 (400)
T ss_pred             CCCCchHHHHHHHHHHHhCCCC--hhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHH
Confidence            6677777776666554 34444  4788888999999999999999999654  67999999999999999987654

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

Probab=98.11  E-value=0.00055  Score=46.81  Aligned_cols=118  Identities=10%  Similarity=0.001  Sum_probs=70.1

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      ..-+.......+.|++..|...+++...- -++|...|+.+--+|.+.|++++|..-+.+..+.. .-+....|.|.-.|
T Consensus       101 ~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~  178 (257)
T COG5010         101 ELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSL  178 (257)
T ss_pred             HHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHH
Confidence            34444566666667777777777766543 24566666666677777777777776666665543 22334455555555


Q ss_pred             HhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208          125 LKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       125 ~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .-.|+.+.|..++..-.   ..|..+-..+.-.....|++++|
T Consensus       179 ~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A  221 (257)
T COG5010         179 LLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREA  221 (257)
T ss_pred             HHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHH
Confidence            66667777766665543   22555555555555666665543

>TIGR00540 hemY_coli hemY protein

Probab=98.09  E-value=0.00033  Score=51.98  Aligned_cols=134  Identities=12%  Similarity=-0.014  Sum_probs=90.0

Q ss_pred             CcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccH-HHHHHHH--HhccchhhHHHH
Q 031208           28 KTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTF-PFVIKAC--IASLAIEKGKEV  101 (164)
Q Consensus        28 ~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~-~~ll~~~--~~~~~~~~a~~~  101 (164)
                      ..+...+.++..+.   .+...+..+...+...|+.++|.+++++..+..  |+.... ..++..+  ...++.+.+.+.
T Consensus       244 ~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~  321 (409)
T TIGR00540       244 GIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKL  321 (409)
T ss_pred             CHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHH
Confidence            34455566666553   377778888888899999999999998887753  443321 0123322  334566777777


Q ss_pred             HHHHHHhCCCCch--HHHHHHHHHHHhcCCchhHHHHhc--cc--CCCCcchHHHHHHHHHhcCCCCCC
Q 031208          102 HGLAVKAGFSRDM--FVQSTLMDLYLKCGDVDGGRKMFD--KM--RVRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       102 ~~~m~~~g~~~~~--~~~~~ll~~~~~~~~~~~a~~~~~--~m--~~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ++...+.. +-|.  ....++-..+.+.|++++|.+.|+  ..  ..|+...+..+...+.+.|+.++|
T Consensus       322 ~e~~lk~~-p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A  389 (409)
T TIGR00540       322 IEKQAKNV-DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEA  389 (409)
T ss_pred             HHHHHHhC-CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHH
Confidence            77666542 2233  455677788888899999999998  34  267777788888888888886654

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.

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

Probab=98.08  E-value=6.3e-05  Score=53.17  Aligned_cols=129  Identities=10%  Similarity=0.070  Sum_probs=93.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhH---HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFT---WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      .+.......+..+.+.++++.|.+.++.|.+  .|...   ...++....-...+.+|..+|+++.+. ..++..+.+.+
T Consensus       129 ~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~  207 (290)
T PF04733_consen  129 GSLELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGL  207 (290)
T ss_dssp             TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHH
T ss_pred             CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHH
Confidence            3455666788999999999999999999985  33322   333444443345799999999998654 56788889999


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCc-hhHHHHhcccC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV-DGGRKMFDKMR  141 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~-~~a~~~~~~m~  141 (164)
                      ..++...|++++|.+++.+..... +-+..+...++-+..-.|+. +.+.+++.++.
T Consensus       208 A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~  263 (290)
T PF04733_consen  208 AVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLK  263 (290)
T ss_dssp             HHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHH
Confidence            999999999999999999876443 33455666677777777776 66778888887

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

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.07  E-value=0.0002  Score=57.42  Aligned_cols=139  Identities=12%  Similarity=0.003  Sum_probs=66.5

Q ss_pred             HHHHHHhccCCcHHHHHHHhccCCC-cHhHHHHH--HHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc
Q 031208           18 KLLDLCSFYGKTDHALLVFSQIRCP-HVFTWNLM--IRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLA   94 (164)
Q Consensus        18 ~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l--i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~   94 (164)
                      .++..+...|+.++|..++++...| +...+..+  ...+...|++++|.++|+++.+.. +-+...+..++..+...++
T Consensus        73 dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q  151 (822)
T PRK14574         73 DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGR  151 (822)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCC
Confidence            5555555556666666666655543 22222222  234455566666666666665432 1123334444555555566


Q ss_pred             hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcC
Q 031208           95 IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASG  159 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g  159 (164)
                      .++|.+.++.+...  .|+...+-.++..+...++..+|.+.++++.  .| +...+..++.+..+.|
T Consensus       152 ~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~  217 (822)
T PRK14574        152 GGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVRLAPTSEEVLKNHLEILQRNR  217 (822)
T ss_pred             HHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC
Confidence            66666666555443  2333333223223323344434555555554  23 3334444444444444

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

Probab=98.06  E-value=5.1e-05  Score=45.34  Aligned_cols=77  Identities=6%  Similarity=0.031  Sum_probs=63.9

Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCC-CCchHHHHHHHHHHHhcCC--------chhHHHHhcccC----CCCcchH
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGF-SRDMFVQSTLMDLYLKCGD--------VDGGRKMFDKMR----VRSVVSW  148 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~ll~~~~~~~~--------~~~a~~~~~~m~----~~~~~~~  148 (164)
                      -..-|..|...+++.....+++.++++|+ .|+..+|+.++.+.+++.-        +...+.++++|.    .|+..+|
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etY  107 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETY  107 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHH
Confidence            34557777888999999999999999999 9999999999999987643        334566777775    7899999


Q ss_pred             HHHHHHHHhc
Q 031208          149 TTMISGLAAS  158 (164)
Q Consensus       149 ~~li~~~~~~  158 (164)
                      +.++..+.+.
T Consensus       108 nivl~~Llkg  117 (120)
T PF08579_consen  108 NIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHh
Confidence            9999988763

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

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

Probab=98.06  E-value=6.4e-05  Score=50.17  Aligned_cols=101  Identities=15%  Similarity=0.134  Sum_probs=78.9

Q ss_pred             cCCCCHHHHHHHHHHHhcc-----CCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcC----------------ChhH
Q 031208            8 GLSNDQLLVRKLLDLCSFY-----GKTDHALLVFSQIR----CPHVFTWNLMIRALTIDG----------------SSLQ   62 (164)
Q Consensus         8 g~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~----------------~~~~   62 (164)
                      +-..+..+|..+++.|.+.     |..+-...-+..|.    +.|..+|+.||+.+-+..                +-+-
T Consensus        42 ~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c  121 (228)
T PF06239_consen   42 GQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQEC  121 (228)
T ss_pred             hccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHH
Confidence            3556788899999988864     45555555555554    589999999999998732                3478


Q ss_pred             HHHHHHHHHHcCCCCCcccHHHHHHHHHhccch-hhHHHHHHHHHHh
Q 031208           63 ALLLYNLMICNGFRPDKFTFPFVIKACIASLAI-EKGKEVHGLAVKA  108 (164)
Q Consensus        63 a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~m~~~  108 (164)
                      |++++++|+..|+.||..|+..|+..+.+.+.. .+..++.-.|.+.
T Consensus       122 ~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rmmYWmpkf  168 (228)
T PF06239_consen  122 AIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRMMYWMPKF  168 (228)
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999988864 4566666666653

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

>TIGR00540 hemY_coli hemY protein

Probab=98.06  E-value=0.00044  Score=51.33  Aligned_cols=155  Identities=15%  Similarity=0.054  Sum_probs=96.2

Q ss_pred             CCCCHHHHHHH-HHHHhccCCcHHHHHHHhccC--CCcH--hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208            9 LSNDQLLVRKL-LDLCSFYGKTDHALLVFSQIR--CPHV--FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus         9 ~~~~~~~~~~l-i~~~~~~~~~~~a~~~~~~~~--~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      ..|+...+-.+ -....+.|+.+.|...+.+..  .|+.  ..--.....+...|+++.|...++++.+.. +-+.....
T Consensus       113 ~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~-P~~~~~l~  191 (409)
T TIGR00540       113 HAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHGVDKLLEMA-PRHKEVLK  191 (409)
T ss_pred             cCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHH
Confidence            34554333333 345667788888888888753  2333  233334666777888999999988887764 22455677


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH-------HHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHH
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS-------TLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMIS  153 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~-------~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~  153 (164)
                      .+...+.+.|+++.+.+.+..+.+.+..+......       .+++.-......+...++++..+.   .+...+..+..
T Consensus       192 ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~  271 (409)
T TIGR00540       192 LAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAE  271 (409)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHH
Confidence            88888888899998888888888876543322211       112111222223344445555542   36677777777


Q ss_pred             HHHhcCCCCCC
Q 031208          154 GLAASGDLDAA  164 (164)
Q Consensus       154 ~~~~~g~~~~A  164 (164)
                      .+...|+.++|
T Consensus       272 ~l~~~g~~~~A  282 (409)
T TIGR00540       272 HLIDCDDHDSA  282 (409)
T ss_pred             HHHHCCChHHH
Confidence            88888877654

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.05  E-value=0.0004  Score=49.31  Aligned_cols=122  Identities=15%  Similarity=-0.021  Sum_probs=78.3

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKAC   89 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~   89 (164)
                      ..|..+-..+.+.|+.+.|...|++..  .| +...|+.+-..+...|++++|...|++..+.  .|+ ...|..+-.++
T Consensus        65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l  142 (296)
T PRK11189         65 QLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIAL  142 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHH
Confidence            345555556677788888888777664  23 4567777777788888888888888887653  353 45666666677


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      ...|++++|.+.++...+..  |+..........+...++.++|...|.+
T Consensus       143 ~~~g~~~eA~~~~~~al~~~--P~~~~~~~~~~l~~~~~~~~~A~~~l~~  190 (296)
T PRK11189        143 YYGGRYELAQDDLLAFYQDD--PNDPYRALWLYLAESKLDPKQAKENLKQ  190 (296)
T ss_pred             HHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHccCCHHHHHHHHHH
Confidence            77788888888887776543  4322112222223345667777777744

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

Probab=98.04  E-value=0.00034  Score=43.47  Aligned_cols=88  Identities=17%  Similarity=0.126  Sum_probs=40.0

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCc
Q 031208           51 IRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV  130 (164)
Q Consensus        51 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  130 (164)
                      ...+...|++++|.+.|+.....+ +.+...+..+-..+.+.|++++|...+++..+.+ +.+...+..+-..|...|++
T Consensus        24 a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~~  101 (135)
T TIGR02552        24 AYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGEP  101 (135)
T ss_pred             HHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCCH
Confidence            334444455555555555544322 2233344444444445555555555555444332 22334444444445555555


Q ss_pred             hhHHHHhccc
Q 031208          131 DGGRKMFDKM  140 (164)
Q Consensus       131 ~~a~~~~~~m  140 (164)
                      +.|...|+..
T Consensus       102 ~~A~~~~~~a  111 (135)
T TIGR02552       102 ESALKALDLA  111 (135)
T ss_pred             HHHHHHHHHH
Confidence            5555555444

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

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

Probab=98.03  E-value=4.7e-05  Score=53.88  Aligned_cols=120  Identities=13%  Similarity=0.035  Sum_probs=52.3

Q ss_pred             HHHHHhccCCcHHHHHHHhccC--CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR--CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      +-.+|.+.|.+.+|.+.|+...  .|-..||-.|-.+|.+...+..|+.+|.+-... ++.+.....-..+.+-..+..+
T Consensus       229 ~gkCylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~eam~~~~  307 (478)
T KOG1129|consen  229 MGKCYLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEAMEQQE  307 (478)
T ss_pred             HHHHHHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHHHHhHH
Confidence            3334445555555555554433  244444544555555555555555555444332 1222222222334444444444


Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      +|.++++...+.. +.++....++-..|.-.++.+.|+++++.+
T Consensus       308 ~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRi  350 (478)
T KOG1129|consen  308 DALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRI  350 (478)
T ss_pred             HHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHH
Confidence            4444444444332 223333333334444444444444444433

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

Probab=98.02  E-value=4.2e-05  Score=56.21  Aligned_cols=149  Identities=13%  Similarity=0.052  Sum_probs=117.2

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      .|++++-+-|+-.++-++|..+|++..+  | ....|+.+=.-|...++...|.+-|+....-. +.|-..|=.|=.+|.
T Consensus       331 ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYe  409 (559)
T KOG1155|consen  331 ETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYE  409 (559)
T ss_pred             cceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHHHH
Confidence            3566666777778889999999998764  3 34678888888999999999999999987632 335667778888888


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      -.+...=|.-.|++..+.. +.|...|.+|-++|.+.++.++|.+.|+...   +.+...+..|-..|-+.++.++|
T Consensus       410 im~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eA  485 (559)
T KOG1155|consen  410 IMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEA  485 (559)
T ss_pred             HhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHH
Confidence            8888888888888877654 5578899999999999999999999998765   33456788888888777766543

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

Probab=97.99  E-value=8.2e-05  Score=56.62  Aligned_cols=151  Identities=11%  Similarity=0.091  Sum_probs=90.0

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHH----------------------------------H
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIR----------------------------------A   53 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~----------------------------------~   53 (164)
                      -++.+|..+=+.|+-.++.+.|.+.|++..+  | ...+|+.+=.                                  .
T Consensus       419 ~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~v  498 (638)
T KOG1126|consen  419 NSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTV  498 (638)
T ss_pred             CCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhh
Confidence            3577888888888888888888888887653  2 2233333322                                  3


Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchh
Q 031208           54 LTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDG  132 (164)
Q Consensus        54 ~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~  132 (164)
                      |.+.++++.|.-.|++..+  +.| +.+....+...+.+.|+.++|.+++++.....- .|+-.--.-...+...++.++
T Consensus       499 y~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~-kn~l~~~~~~~il~~~~~~~e  575 (638)
T KOG1126|consen  499 YLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDP-KNPLCKYHRASILFSLGRYVE  575 (638)
T ss_pred             eeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCC-CCchhHHHHHHHHHhhcchHH
Confidence            4445555555555555544  223 444555555666666777777777766654431 222222223334445566677


Q ss_pred             HHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208          133 GRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       133 a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      |...+++++   ..+..++-.+...|.+.|+.+.|
T Consensus       576 al~~LEeLk~~vP~es~v~~llgki~k~~~~~~~A  610 (638)
T KOG1126|consen  576 ALQELEELKELVPQESSVFALLGKIYKRLGNTDLA  610 (638)
T ss_pred             HHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHH
Confidence            777766665   23566777777788777776543

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

Probab=97.97  E-value=0.00046  Score=42.85  Aligned_cols=105  Identities=16%  Similarity=0.050  Sum_probs=82.9

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      .....+...+.+.|+.++|.+.|+...   ..+...|..+-..+.+.|++++|...+++....+ +.+...+..+-..+.
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~   96 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLL   96 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHH
Confidence            344555677888999999999999875   2466788888889999999999999999987654 445667777888999


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      ..|+.+.|...++...+.  .|+...+..+.
T Consensus        97 ~~g~~~~A~~~~~~al~~--~p~~~~~~~~~  125 (135)
T TIGR02552        97 ALGEPESALKALDLAIEI--CGENPEYSELK  125 (135)
T ss_pred             HcCCHHHHHHHHHHHHHh--ccccchHHHHH
Confidence            999999999999988876  36655544443

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

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

Probab=97.96  E-value=8.9e-05  Score=54.72  Aligned_cols=135  Identities=10%  Similarity=0.045  Sum_probs=73.4

Q ss_pred             hccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHH
Q 031208           24 SFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKE  100 (164)
Q Consensus        24 ~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~  100 (164)
                      -+.|++++|.+.|-+++   ..+..+.-.+.+.|--..++.+|.+++.+.... ++-|+...+.|-..|-+.|+..+|++
T Consensus       535 e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq  613 (840)
T KOG2003|consen  535 EALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQ  613 (840)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhh
Confidence            34566666666666554   234444444555566666666666666544321 33356667777777777777777776


Q ss_pred             HHHHHHH--------------------------------hCCCCchHHHHHHHHHHH-hcCCchhHHHHhcccCCC---C
Q 031208          101 VHGLAVK--------------------------------AGFSRDMFVQSTLMDLYL-KCGDVDGGRKMFDKMRVR---S  144 (164)
Q Consensus       101 ~~~~m~~--------------------------------~g~~~~~~~~~~ll~~~~-~~~~~~~a~~~~~~m~~~---~  144 (164)
                      ++-+--+                                .-+.|+.+-|-.++..|. +.|++.+|.++++++.++   |
T Consensus       614 ~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfped  693 (840)
T KOG2003|consen  614 CHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPED  693 (840)
T ss_pred             hhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccc
Confidence            5433211                                123455555555544333 345555555555555422   4


Q ss_pred             cchHHHHHHHHHhcC
Q 031208          145 VVSWTTMISGLAASG  159 (164)
Q Consensus       145 ~~~~~~li~~~~~~g  159 (164)
                      +.....|++.+...|
T Consensus       694 ldclkflvri~~dlg  708 (840)
T KOG2003|consen  694 LDCLKFLVRIAGDLG  708 (840)
T ss_pred             hHHHHHHHHHhcccc
Confidence            455555555554444

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

Probab=97.96  E-value=0.00068  Score=45.29  Aligned_cols=97  Identities=11%  Similarity=0.072  Sum_probs=79.0

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHH-Hhccc--hhhHHHHHHHHHHhCCCCchHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKAC-IASLA--IEKGKEVHGLAVKAGFSRDMFVQ  117 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~-~~~~~--~~~a~~~~~~m~~~g~~~~~~~~  117 (164)
                      .|...|..+-..|...|++++|...|++..+..  | +...+..+-.++ ...|+  .++|.+++++..+.. +-+...+
T Consensus        71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~--P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-P~~~~al  147 (198)
T PRK10370         71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQLR--GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-ANEVTAL  147 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CCChhHH
Confidence            467789999999999999999999999987753  5 455666666654 66676  489999999998876 3466788


Q ss_pred             HHHHHHHHhcCCchhHHHHhcccC
Q 031208          118 STLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       118 ~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..+-..+.+.|++++|...|+++.
T Consensus       148 ~~LA~~~~~~g~~~~Ai~~~~~aL  171 (198)
T PRK10370        148 MLLASDAFMQADYAQAIELWQKVL  171 (198)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH
Confidence            888888999999999999999875

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

Probab=97.94  E-value=0.00031  Score=50.31  Aligned_cols=111  Identities=16%  Similarity=0.201  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL   93 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~   93 (164)
                      .+.+..|.-+...|+...|.++-.+++-|+..-|-..+.+++..++|++-..+-..      +-++.-|..++.+|.+.|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~~~  251 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLKYG  251 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHHCC
Confidence            34556677788899999999999999999999999999999999999988776432      345689999999999999


Q ss_pred             chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           94 AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        94 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      +..+|..++..+          .+..-+..|.++|++.+|.+.--+.
T Consensus       252 ~~~eA~~yI~k~----------~~~~rv~~y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  252 NKKEASKYIPKI----------PDEERVEMYLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             CHHHHHHHHHhC----------ChHHHHHHHHHCCCHHHHHHHHHHc
Confidence            999999888772          2255677788888888886654433

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.92  E-value=0.00059  Score=48.48  Aligned_cols=93  Identities=15%  Similarity=-0.042  Sum_probs=68.4

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...|+.+-..+...|+++.|...|+...  .| +..+|..+-..+...|++++|.+.|++..+.  .|+..........
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l  174 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYL  174 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            57788888889999999999999999875  34 4567777777888899999999999998764  3543322222223


Q ss_pred             HHhccchhhHHHHHHHHH
Q 031208           89 CIASLAIEKGKEVHGLAV  106 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~  106 (164)
                      +...++.++|...+++..
T Consensus       175 ~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        175 AESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHccCCHHHHHHHHHHHH
Confidence            345567888888886544

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

Probab=97.90  E-value=0.00027  Score=40.00  Aligned_cols=90  Identities=14%  Similarity=0.021  Sum_probs=49.7

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 031208           49 LMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCG  128 (164)
Q Consensus        49 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~  128 (164)
                      .+...+...|++++|...+++..+.. +.+...+..+...+...+++++|.+.++...+.. +.+...+..+...+...|
T Consensus         5 ~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   82 (100)
T cd00189           5 NLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLG   82 (100)
T ss_pred             HHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHH
Confidence            34444555666666666666665432 1122445555555666666666666666655443 223345555566666666


Q ss_pred             CchhHHHHhccc
Q 031208          129 DVDGGRKMFDKM  140 (164)
Q Consensus       129 ~~~~a~~~~~~m  140 (164)
                      +.+.|...+...
T Consensus        83 ~~~~a~~~~~~~   94 (100)
T cd00189          83 KYEEALEAYEKA   94 (100)
T ss_pred             hHHHHHHHHHHH
Confidence            666666665543

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

Probab=97.87  E-value=0.00087  Score=42.39  Aligned_cols=123  Identities=16%  Similarity=0.150  Sum_probs=80.4

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--CcH--hHHHH--HHHHHHhcCChhHHHHHHHHHHHcCCCCCc--ccHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--PHV--FTWNL--MIRALTIDGSSLQALLLYNLMICNGFRPDK--FTFPFV   85 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~--~~~~~--li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~~l   85 (164)
                      ..|..++..+. .++...+...++.+..  |+.  .....  +-..+...|++++|...|+........|+.  ...-.+
T Consensus        13 ~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            45666666664 7777777777777653  322  12222  335567788888888888888776522322  233345


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      ...+...|++++|...++......  .....+...-+.|.+.|+.++|...|+.
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~--~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEA--FKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcc--hHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            677788888888888886643322  3344566677888888888888888764

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

Probab=97.86  E-value=8.5e-05  Score=52.32  Aligned_cols=126  Identities=13%  Similarity=0.172  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHH---H-HHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIR---A-LTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~---~-~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      .+|..+|...-+.+..+.|+.+|.+..+.+..+|...+.   . +...++.+.|..+|+...+. ++.+..-|..-++.+
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Confidence            578889999999999999999999987543333333322   2 33356777799999998764 566777788888999


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCc---hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRD---MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+.++.+.+..+|+..... +.++   ...|...++.=.+.|+++.+.++.+.+.
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~  134 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAE  134 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999999988755 3232   3599999999999999999888887665

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.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.85  E-value=0.0016  Score=51.46  Aligned_cols=130  Identities=11%  Similarity=0.023  Sum_probs=106.8

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC--CCc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPF   84 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~   84 (164)
                      ...++..+--|-......|+.++|..+++...  .|| ......+...+.+.+++++|+..+++....  .|+. .....
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~  159 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILL  159 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHH
Confidence            44557777778888889999999999999887  364 456778888999999999999999999875  4654 45566


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +-.++.+.|+.++|..+|++....+ .-+...+..+-..+-+.|+.++|...|+...
T Consensus       160 ~a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~  215 (694)
T PRK15179        160 EAKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGL  215 (694)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            6778888999999999999999843 3447788888888999999999999998775

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.84  E-value=0.0014  Score=42.44  Aligned_cols=118  Identities=12%  Similarity=0.037  Sum_probs=79.6

Q ss_pred             HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC--CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           44 VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP--DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        44 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      ...|..+...+...|++++|...|++.......|  ...++..+-..+...|+.++|...++...... +.....+..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            3456667777788899999999999986543222  12467788888899999999999998887653 22344555666


Q ss_pred             HHHH-------hcCCchh-------HHHHhcccCCCCcchHHHHHHHHHhcCCCC
Q 031208          122 DLYL-------KCGDVDG-------GRKMFDKMRVRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus       122 ~~~~-------~~~~~~~-------a~~~~~~m~~~~~~~~~~li~~~~~~g~~~  162 (164)
                      ..|.       +.|+++.       |..+|++....+...+......+...|+|+
T Consensus       114 ~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~a~~~~p~~~~~~~~~~~~~~~~~  168 (168)
T CHL00033        114 VICHYRGEQAIEQGDSEIAEAWFDQAAEYWKQAIALAPGNYIEAQNWLKITGRFE  168 (168)
T ss_pred             HHHHHhhHHHHHcccHHHHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHhcCCC
Confidence            6666       6777664       445555555555555566666666666664

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

Probab=97.83  E-value=0.0023  Score=43.90  Aligned_cols=129  Identities=16%  Similarity=0.038  Sum_probs=106.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~   87 (164)
                      |....+.......+.|++..|...|.+..   .+|...|+.+=.+|-+.|+.++|..-|.+..+-  .| +...++-+.-
T Consensus        99 d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlgm  176 (257)
T COG5010          99 DRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALEL--APNEPSIANNLGM  176 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHHH
Confidence            44456667788888999999999999876   468899999999999999999999999998763  44 3456677888


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR  143 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  143 (164)
                      .+.-.|+.+.|..++......+ .-|..+-..|.-.-...|+++.|..+-..-..+
T Consensus       177 s~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~i~~~e~~~  231 (257)
T COG5010         177 SLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDIAVQELLS  231 (257)
T ss_pred             HHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhhccccccc
Confidence            8888999999999999988776 346667777888889999999999988765543

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

Probab=97.83  E-value=0.00063  Score=43.03  Aligned_cols=117  Identities=15%  Similarity=0.140  Sum_probs=86.5

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc----ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc--hHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK----FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD--MFVQS  118 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~  118 (164)
                      ..|..++..+ ..++...+...+..+....  |+.    ...-.+-..+...|++++|...++......-.|+  ....-
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~--~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l   89 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDY--PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARL   89 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence            4566677776 4888999999999997753  433    2223345788899999999999999998763333  23444


Q ss_pred             HHHHHHHhcCCchhHHHHhcccCCC--CcchHHHHHHHHHhcCCCCCC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMRVR--SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~~~--~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .|...+...|++++|...++....+  ....+...=+.|.+.|++++|
T Consensus        90 ~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A  137 (145)
T PF09976_consen   90 RLARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEA  137 (145)
T ss_pred             HHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHH
Confidence            5678888999999999999886643  344666677788899988765

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

Probab=97.81  E-value=0.0013  Score=43.91  Aligned_cols=111  Identities=10%  Similarity=0.060  Sum_probs=86.6

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHH-HhcCC--hhHHHHHHHHHHHcCCCCCcccHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRAL-TIDGS--SLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~-~~~~~--~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      +.|...|..+-..|...|+++.|...|++..  .| |...+..+-.++ ...|+  .++|..++++..+.. +-+...+.
T Consensus        70 P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-P~~~~al~  148 (198)
T PRK10370         70 PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-ANEVTALM  148 (198)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CCChhHHH
Confidence            3467888888889999999999999999876  34 566777776654 67777  599999999998764 22556788


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      .+-..+.+.|++++|...|+.+.+.. +|+..-+..+ ..
T Consensus       149 ~LA~~~~~~g~~~~Ai~~~~~aL~l~-~~~~~r~~~i-~~  186 (198)
T PRK10370        149 LLASDAFMQADYAQAIELWQKVLDLN-SPRVNRTQLV-ES  186 (198)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-CCCccHHHHH-HH
Confidence            88899999999999999999998775 4555444333 54

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

Probab=97.81  E-value=0.00037  Score=49.28  Aligned_cols=142  Identities=13%  Similarity=0.076  Sum_probs=88.9

Q ss_pred             HHHHhccCCcHHHHHHHhccCC-Cc--HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc----ccHHHHHHHHHhc
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC-PH--VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK----FTFPFVIKACIAS   92 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~-~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~   92 (164)
                      -.=|...|-++.|..+|..+.+ |.  ...-..|+..|-...+|++|++.-+++...+-.+..    .-|+-+...+...
T Consensus       114 ~~Dym~aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~  193 (389)
T COG2956         114 GRDYMAAGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALAS  193 (389)
T ss_pred             HHHHHHhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhh
Confidence            3445667777777777777664 32  234566777888888888888887777654422221    2234444444555


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHH-HHHHHHHhcCCchhHHHHhcccCCCC----cchHHHHHHHHHhcCCCCC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQS-TLMDLYLKCGDVDGGRKMFDKMRVRS----VVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~-~ll~~~~~~~~~~~a~~~~~~m~~~~----~~~~~~li~~~~~~g~~~~  163 (164)
                      .+.+.|..+++...+..  |+-+--+ .+-+.+...|+++.|.+.++.+.+.|    ..+...|..+|...|+.++
T Consensus       194 ~~~d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~  267 (389)
T COG2956         194 SDVDRARELLKKALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAE  267 (389)
T ss_pred             hhHHHHHHHHHHHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHH
Confidence            66777777777665543  3333333 33456677788888888887776443    2466777788888877654

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

Probab=97.80  E-value=0.0006  Score=52.33  Aligned_cols=123  Identities=17%  Similarity=0.155  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--CCcH-hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--CPHV-FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKAC   89 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~   89 (164)
                      .++.-+--.|...|+++.|...+++..  +|+. ..|+.|-.++-..|++.+|.+.|++....  .|+ ....+-|-..+
T Consensus       287 ~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l--~p~hadam~NLgni~  364 (966)
T KOG4626|consen  287 VAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRL--CPNHADAMNNLGNIY  364 (966)
T ss_pred             hhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHh--CCccHHHHHHHHHHH
Confidence            344444445555666666666665543  2332 45555666666666666666665555442  222 23344455555


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      ...|.++.|..++......  -|. ...++.|-..|-+.|++++|...+++.
T Consensus       365 ~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykea  414 (966)
T KOG4626|consen  365 REQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEA  414 (966)
T ss_pred             HHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHH
Confidence            5555555555555544332  122 234444555555555555555555443

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

Probab=97.77  E-value=0.00012  Score=55.80  Aligned_cols=144  Identities=16%  Similarity=0.117  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC------------------------------------C-cHhHHHHHHHHHHh
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC------------------------------------P-HVFTWNLMIRALTI   56 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~------------------------------------~-~~~~~~~li~~~~~   56 (164)
                      .+...+=.+|...+++++|.++|+..++                                    | ...+|.++=++|+-
T Consensus       354 wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~~sPesWca~GNcfSL  433 (638)
T KOG1126|consen  354 WVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDPNSPESWCALGNCFSL  433 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCCCCcHHHHHhcchhhh
Confidence            3444455578888899999999987751                                    1 22567777777777


Q ss_pred             cCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHH---HHHHHhcCCchh
Q 031208           57 DGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTL---MDLYLKCGDVDG  132 (164)
Q Consensus        57 ~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l---l~~~~~~~~~~~  132 (164)
                      .++.+.|++.|++-.+-  .| ..++|+.+=+-+.....++.|...|+...    ..++..|++.   --.|.|.++++.
T Consensus       434 Qkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al----~~~~rhYnAwYGlG~vy~Kqek~e~  507 (638)
T KOG1126|consen  434 QKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKAL----GVDPRHYNAWYGLGTVYLKQEKLEF  507 (638)
T ss_pred             hhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhh----cCCchhhHHHHhhhhheeccchhhH
Confidence            88888888888887763  35 45666666555666666666666665543    2344444443   335566666666


Q ss_pred             HHHHhcccC--CC-CcchHHHHHHHHHhcCCCCC
Q 031208          133 GRKMFDKMR--VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       133 a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      |.--|+...  +| |.+....+-..+-+.|+.|+
T Consensus       508 Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~  541 (638)
T KOG1126|consen  508 AEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDK  541 (638)
T ss_pred             HHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhH
Confidence            666666554  22 44444444444555555444

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.76  E-value=0.002  Score=41.92  Aligned_cols=116  Identities=14%  Similarity=0.110  Sum_probs=76.0

Q ss_pred             HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           44 VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD--KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        44 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      ...+..+-..+...|++++|...|++.......++  ...+..+...+.+.|++++|...+.+..... +-+...+..+.
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg  113 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNIA  113 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence            34566666677788888888888888866443332  2467777788888888888888888877653 22345555566


Q ss_pred             HHHHhcCC--------------chhHHHHhcccCCCCcchHHHHHHHHHhcCC
Q 031208          122 DLYLKCGD--------------VDGGRKMFDKMRVRSVVSWTTMISGLAASGD  160 (164)
Q Consensus       122 ~~~~~~~~--------------~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~  160 (164)
                      ..|...|+              ++.|.+++++....+...|..++.-+...|+
T Consensus       114 ~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~  166 (172)
T PRK02603        114 VIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRLAPNNYIEAQNWLKTTGR  166 (172)
T ss_pred             HHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhhCchhHHHHHHHHHhcCc
Confidence            66666665              4556666666654444446666666655554

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

Probab=97.75  E-value=4.7e-05  Score=43.47  Aligned_cols=81  Identities=16%  Similarity=0.137  Sum_probs=53.7

Q ss_pred             cCChhHHHHHHHHHHHcCCC-CCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHH
Q 031208           57 DGSSLQALLLYNLMICNGFR-PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRK  135 (164)
Q Consensus        57 ~~~~~~a~~~~~~m~~~~~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~  135 (164)
                      .|+++.|..+++++.+..-. |+...+-.+..++.+.|+++.|..+++. .+.+. .+....-.+-.+|.+.|++++|.+
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHH
Confidence            57888888888888765421 2333444478888888999999888888 32221 223344455778888899999988


Q ss_pred             Hhcc
Q 031208          136 MFDK  139 (164)
Q Consensus       136 ~~~~  139 (164)
                      .|++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            8764

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

Probab=97.75  E-value=0.0004  Score=51.28  Aligned_cols=156  Identities=13%  Similarity=0.060  Sum_probs=87.6

Q ss_pred             HhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 031208            4 IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP   77 (164)
Q Consensus         4 m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   77 (164)
                      +...|++-+...-+..-.+.....+++.|.++|+++.+      .|..+|+.++..-....+.    ..+.+-...=-+-
T Consensus       253 l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skL----s~LA~~v~~idKy  328 (559)
T KOG1155|consen  253 LSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKL----SYLAQNVSNIDKY  328 (559)
T ss_pred             HHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHH----HHHHHHHHHhccC
Confidence            44567777777666666677788999999999999873      3456666655443332211    1111111111122


Q ss_pred             CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchh-------------------------
Q 031208           78 DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDG-------------------------  132 (164)
Q Consensus        78 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~-------------------------  132 (164)
                      ...|++++-+.|+-.++.++|...|+...+.+ +.....|+.+-+-|..-++...                         
T Consensus       329 R~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQa  407 (559)
T KOG1155|consen  329 RPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQA  407 (559)
T ss_pred             CccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHH
Confidence            23344555555555555555555555554433 1223344444444444444444                         


Q ss_pred             ---------HHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          133 ---------GRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       133 ---------a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                               |+-.|++..  .| |...|.+|=++|.+.++.++|
T Consensus       408 Yeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eA  451 (559)
T KOG1155|consen  408 YEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEA  451 (559)
T ss_pred             HHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHH
Confidence                     444444332  23 788999999999999988765

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

Probab=97.72  E-value=0.003  Score=43.62  Aligned_cols=118  Identities=11%  Similarity=-0.025  Sum_probs=79.4

Q ss_pred             HHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc----cch
Q 031208           20 LDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS----LAI   95 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~----~~~   95 (164)
                      ...|+..|++++|.+......  +......=...+.+..+.+.|...+++|.+.   -+..|.+-|..++.+.    +.+
T Consensus       115 a~i~~~~~~~deAl~~~~~~~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~  189 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHLGE--NLEAAALNVQILLKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKI  189 (299)
T ss_pred             hHHhhcCCChHHHHHHHhccc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhh
Confidence            457888899999998888733  3333333445566777778888888888653   3444555555555443    356


Q ss_pred             hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC
Q 031208           96 EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR  143 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  143 (164)
                      .+|.-+|++|-. ...|+..+-+-..-+....|++++|..++++...+
T Consensus       190 qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  190 QDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             hhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            777778877753 24677777777777777788888888888777644

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

Probab=97.71  E-value=0.0018  Score=48.09  Aligned_cols=128  Identities=17%  Similarity=0.195  Sum_probs=95.8

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      ++.|+.+.+.|-+.|-+.|+-..|...+-..-   .-|..+...|-.-|....=++.+...|++..-  +.|+..-|-.+
T Consensus       588 ip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlm  665 (840)
T KOG2003|consen  588 IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLM  665 (840)
T ss_pred             CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHH
Confidence            44578889999999999999888887654433   24666766677777888888999999887633  67999999888


Q ss_pred             HHHHH-hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           86 IKACI-ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        86 l~~~~-~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      +..|. +.|++..|+.++.+..+ .++-|..+...|+..+...|. .++.+.-+++
T Consensus       666 iasc~rrsgnyqka~d~yk~~hr-kfpedldclkflvri~~dlgl-~d~key~~kl  719 (840)
T KOG2003|consen  666 IASCFRRSGNYQKAFDLYKDIHR-KFPEDLDCLKFLVRIAGDLGL-KDAKEYADKL  719 (840)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHH-hCccchHHHHHHHHHhccccc-hhHHHHHHHH
Confidence            87765 56899999999999764 457788888888887776664 3355544443

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

Probab=97.70  E-value=0.00021  Score=54.74  Aligned_cols=152  Identities=15%  Similarity=0.132  Sum_probs=109.7

Q ss_pred             CCCC-HHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHH
Q 031208            9 LSND-QLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFP   83 (164)
Q Consensus         9 ~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~   83 (164)
                      +.|+ ...|+-|-.++-..|++.+|...+++..  .| ...+.+.|-..+...|.+++|..+|..-.+  +.|. ...++
T Consensus       315 ~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~--v~p~~aaa~n  392 (966)
T KOG4626|consen  315 LQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALE--VFPEFAAAHN  392 (966)
T ss_pred             cCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHh--hChhhhhhhh
Confidence            3444 5668888888888888888888888765  33 345677777888888888888888887765  3443 34677


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcC
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASG  159 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g  159 (164)
                      -|-..|-+.|+.++|...+++..+-  .|+ ...|+.+-..|-.-|+++.|...+....  +| =....+.|-+.|-.+|
T Consensus       393 NLa~i~kqqgnl~~Ai~~YkealrI--~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsG  470 (966)
T KOG4626|consen  393 NLASIYKQQGNLDDAIMCYKEALRI--KPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSG  470 (966)
T ss_pred             hHHHHHHhcccHHHHHHHHHHHHhc--CchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccC
Confidence            7888888888888888888877653  454 5577777777888888888888877655  33 2346677888888888


Q ss_pred             CCCCC
Q 031208          160 DLDAA  164 (164)
Q Consensus       160 ~~~~A  164 (164)
                      ++.+|
T Consensus       471 ni~~A  475 (966)
T KOG4626|consen  471 NIPEA  475 (966)
T ss_pred             CcHHH
Confidence            77654

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

Probab=97.70  E-value=0.00081  Score=48.69  Aligned_cols=89  Identities=15%  Similarity=0.010  Sum_probs=45.1

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCC-CCch--HHHHHHHHHHHhcC
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGF-SRDM--FVQSTLMDLYLKCG  128 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~--~~~~~ll~~~~~~~  128 (164)
                      ..+...|++++|...+++..+.. +.+...+..+-..+...|++++|..++++.....- .|+.  ..|..+...+...|
T Consensus       122 ~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G  200 (355)
T cd05804         122 FGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERG  200 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCC
Confidence            34455566666666666655432 22333445555555556666666666555543321 1121  12334555555666


Q ss_pred             CchhHHHHhcccC
Q 031208          129 DVDGGRKMFDKMR  141 (164)
Q Consensus       129 ~~~~a~~~~~~m~  141 (164)
                      +.++|..++++..
T Consensus       201 ~~~~A~~~~~~~~  213 (355)
T cd05804         201 DYEAALAIYDTHI  213 (355)
T ss_pred             CHHHHHHHHHHHh
Confidence            6666666666554

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

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

Probab=97.69  E-value=0.0008  Score=37.98  Aligned_cols=92  Identities=17%  Similarity=0.044  Sum_probs=73.2

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      +..+...+...|+++.|..+++...+  | +...+..+-..+...+++++|.+.+.+..... +.+..++..+...+...
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   81 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHH
Confidence            45566777889999999999998752  3 44677778888889999999999999987754 33445778888899999


Q ss_pred             cchhhHHHHHHHHHHh
Q 031208           93 LAIEKGKEVHGLAVKA  108 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~  108 (164)
                      |+.+.|...+....+.
T Consensus        82 ~~~~~a~~~~~~~~~~   97 (100)
T cd00189          82 GKYEEALEAYEKALEL   97 (100)
T ss_pred             HhHHHHHHHHHHHHcc
Confidence            9999999998877643

>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=97.68  E-value=0.0011  Score=40.88  Aligned_cols=83  Identities=10%  Similarity=-0.084  Sum_probs=58.2

Q ss_pred             HhHHHHHHHHHHhcCChhHHHHHHHHHH---------------HcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHH-H
Q 031208           44 VFTWNLMIRALTIDGSSLQALLLYNLMI---------------CNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAV-K  107 (164)
Q Consensus        44 ~~~~~~li~~~~~~~~~~~a~~~~~~m~---------------~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~-~  107 (164)
                      ..++..+|.++++.|+.+....+++..-               .....|+..+..+++.+|+..+++..|.++++... .
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~   81 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRK   81 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            4455666666666666666666665541               12355777888888888888888888888888776 4


Q ss_pred             hCCCCchHHHHHHHHHHHh
Q 031208          108 AGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus       108 ~g~~~~~~~~~~ll~~~~~  126 (164)
                      .+++.+...|..|+.-...
T Consensus        82 Y~I~i~~~~W~~Ll~W~~v  100 (126)
T PF12921_consen   82 YPIPIPKEFWRRLLEWAYV  100 (126)
T ss_pred             cCCCCCHHHHHHHHHHHHH
Confidence            5677778888888874443

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

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.67  E-value=0.0035  Score=37.66  Aligned_cols=89  Identities=13%  Similarity=-0.028  Sum_probs=37.0

Q ss_pred             HHHHhccCCcHHHHHHHhccCC--Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC--CCcccHHHHHHHHHh
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC--PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFR--PDKFTFPFVIKACIA   91 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--p~~~t~~~ll~~~~~   91 (164)
                      ...+.+.|+++.|.+.|+.+.+  |+    ...+-.+...+.+.|+++.|...|++.....-.  .....+..+..++.+
T Consensus         9 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~   88 (119)
T TIGR02795         9 ALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQE   88 (119)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHH
Confidence            3344444555555555544431  21    122333444444455555555555544332100  012223333444444


Q ss_pred             ccchhhHHHHHHHHHHh
Q 031208           92 SLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~  108 (164)
                      .|+.++|...++++.+.
T Consensus        89 ~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        89 LGDKEKAKATLQQVIKR  105 (119)
T ss_pred             hCChHHHHHHHHHHHHH
Confidence            45555555555444443

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.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.66  E-value=0.0018  Score=51.14  Aligned_cols=119  Identities=18%  Similarity=0.161  Sum_probs=96.8

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      +...+-.|-......|+.++|..+++...+  +.|+. .....+...+.+.+++++|....++..... +-+......+-
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~a  161 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLEA  161 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHHH
Confidence            456677778888889999999999999987  46755 567778899999999999999999998775 33455666667


Q ss_pred             HHHHhcCCchhHHHHhcccCCC---CcchHHHHHHHHHhcCCCCCC
Q 031208          122 DLYLKCGDVDGGRKMFDKMRVR---SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .++.+.|++++|..+|++...+   +..+|...-.++-..|+.++|
T Consensus       162 ~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A  207 (694)
T PRK15179        162 KSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRA  207 (694)
T ss_pred             HHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHH
Confidence            7888899999999999998743   356888888888888887765

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

Probab=97.66  E-value=0.0056  Score=45.60  Aligned_cols=115  Identities=13%  Similarity=0.164  Sum_probs=82.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDL  123 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~  123 (164)
                      .-|..-+ .+-..|..++|...++.+... .+-|..-.......+.+.++..+|.+.++.+...  .|+ ....-.+-.+
T Consensus       308 a~YG~A~-~~~~~~~~d~A~~~l~~L~~~-~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~a  383 (484)
T COG4783         308 AQYGRAL-QTYLAGQYDEALKLLQPLIAA-QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQA  383 (484)
T ss_pred             HHHHHHH-HHHHhcccchHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHH
Confidence            3455444 345677888888888887664 2334444555567788888888888888888765  355 5566667788


Q ss_pred             HHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCC
Q 031208          124 YLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      |.+.|+..+|..+++...  .| |...|..|-++|...|+..+
T Consensus       384 ll~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~  426 (484)
T COG4783         384 LLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAE  426 (484)
T ss_pred             HHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHH
Confidence            888888888888888765  33 67788888888888887654

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

Probab=97.66  E-value=0.0028  Score=42.89  Aligned_cols=140  Identities=12%  Similarity=-0.052  Sum_probs=86.7

Q ss_pred             HHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccch
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAI   95 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~   95 (164)
                      --+|...|+...|..-+++..+  | +..+|..+-..|-+.|+.+.|.+-|++-.+.  .|+ -...|--=.-+|..|.+
T Consensus        42 al~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~FLC~qg~~  119 (250)
T COG3063          42 ALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSL--APNNGDVLNNYGAFLCAQGRP  119 (250)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHHHHhCCCh
Confidence            3366677777777777776653  3 3356777777777778888887777777653  343 23444444555777777


Q ss_pred             hhHHHHHHHHHHhC-CCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-CcchHHHHHHHHHhcCCC
Q 031208           96 EKGKEVHGLAVKAG-FSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMISGLAASGDL  161 (164)
Q Consensus        96 ~~a~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~g~~  161 (164)
                      ++|.+.|++....- +.--..+|..+.-+..+.|+.+.|...|++-.+  | ...+.-.+.....+.|++
T Consensus       120 ~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y  189 (250)
T COG3063         120 EEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDY  189 (250)
T ss_pred             HHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccc
Confidence            77777777766532 222345677777777777777777777776542  2 223444444444444443

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

Probab=97.63  E-value=0.00036  Score=37.91  Aligned_cols=50  Identities=16%  Similarity=0.238  Sum_probs=30.8

Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +.|++++|.++++++.... +-+...+-.+..+|.+.|++++|.++++.+.
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~   52 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLL   52 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4566666666666666553 2245555566666777777777777776665

...

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

Probab=97.63  E-value=0.0049  Score=41.72  Aligned_cols=134  Identities=14%  Similarity=0.046  Sum_probs=104.2

Q ss_pred             CCC-CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHH
Q 031208            9 LSN-DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFP   83 (164)
Q Consensus         9 ~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~   83 (164)
                      +.| +..+|..+-..|.+.|+.+.|.+-|++..  .| +..+.|--=.-+|..|++++|...|++-...---| ...||.
T Consensus        64 ~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~e  143 (250)
T COG3063          64 HDPSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLE  143 (250)
T ss_pred             hCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhh
Confidence            345 46788889999999999999999999865  23 44454444445688899999999999987654333 345788


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR  143 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  143 (164)
                      -+--+..+.|+++.|...++.-.+.. .-.....-.+.....+.|++-.|..+++.....
T Consensus       144 N~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~  202 (250)
T COG3063         144 NLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPARLYLERYQQR  202 (250)
T ss_pred             hhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHHHHHHHHHhc
Confidence            88888899999999999999988764 223456677888888999999999998877643

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

Probab=97.59  E-value=0.0043  Score=47.45  Aligned_cols=136  Identities=15%  Similarity=0.156  Sum_probs=102.6

Q ss_pred             hHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC------------------CCcHhHH--HHHHHHHHhcCChhH
Q 031208            3 KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR------------------CPHVFTW--NLMIRALTIDGSSLQ   62 (164)
Q Consensus         3 ~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~------------------~~~~~~~--~~li~~~~~~~~~~~   62 (164)
                      .+.+.|+++   +|+.+-..|......+-..+++....                  .|....|  .-+-..|-..|++++
T Consensus       136 ~~l~KgvPs---lF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~  212 (517)
T PF12569_consen  136 PQLRKGVPS---LFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEK  212 (517)
T ss_pred             HHHhcCCch---HHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHH
Confidence            345566543   46666667776655555555555432                  1344445  455667889999999


Q ss_pred             HHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           63 ALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        63 a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |++.+++-...  +|+ +.-|..-.+.+-+.|++.+|.+.+++..... .-|.++-+.....+.|+|++++|.+++....
T Consensus       213 Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ft  289 (517)
T PF12569_consen  213 ALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFT  289 (517)
T ss_pred             HHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhc
Confidence            99999998775  465 4577788899999999999999999988776 3688899999999999999999999998877


Q ss_pred             CCC
Q 031208          142 VRS  144 (164)
Q Consensus       142 ~~~  144 (164)
                      .++
T Consensus       290 r~~  292 (517)
T PF12569_consen  290 RED  292 (517)
T ss_pred             CCC
Confidence            554

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

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

Probab=97.58  E-value=0.00091  Score=47.62  Aligned_cols=129  Identities=14%  Similarity=0.003  Sum_probs=99.5

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHH-HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTW-NLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~-~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      ..|-+.+|--|-.+|.+..++..|..+|.+-.+  |-.+|| .-+...+-..++.++|.++|++..+.. +.+.....++
T Consensus       252 q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~-~~nvEaiAci  330 (478)
T KOG1129|consen  252 QFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLH-PINVEAIACI  330 (478)
T ss_pred             cCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcC-Cccceeeeee
Confidence            457888999999999999999999999998763  655555 344556677788999999999986643 3456677778


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      -..|.-.++.+-|..+++.+.+.|+ -++..|+.+--+|.-.+.+|.++.-|..
T Consensus       331 a~~yfY~~~PE~AlryYRRiLqmG~-~speLf~NigLCC~yaqQ~D~~L~sf~R  383 (478)
T KOG1129|consen  331 AVGYFYDNNPEMALRYYRRILQMGA-QSPELFCNIGLCCLYAQQIDLVLPSFQR  383 (478)
T ss_pred             eeccccCCChHHHHHHHHHHHHhcC-CChHHHhhHHHHHHhhcchhhhHHHHHH
Confidence            8888888999999999999999986 4556777776677666777766655544

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.56  E-value=0.0036  Score=37.62  Aligned_cols=94  Identities=11%  Similarity=0.012  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----cccHHHHHHHHHhccchhhHHHHHHHHHHhCC--CCchHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPD----KFTFPFVIKACIASLAIEKGKEVHGLAVKAGF--SRDMFVQST  119 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~~~~~~~  119 (164)
                      ++-.+...+.+.|++++|.+.|.++.+..  |+    ...+..+...+.+.|+++.|...++......-  ......+..
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~   81 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKY--PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLK   81 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHH
Confidence            34456667888999999999999997643  32    24556688999999999999999999886531  122456777


Q ss_pred             HHHHHHhcCCchhHHHHhcccC
Q 031208          120 LMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       120 ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +...+.+.|+.+.|.+.++++.
T Consensus        82 ~~~~~~~~~~~~~A~~~~~~~~  103 (119)
T TIGR02795        82 LGMSLQELGDKEKAKATLQQVI  103 (119)
T ss_pred             HHHHHHHhCChHHHHHHHHHHH
Confidence            8888999999999999999876

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.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.46  E-value=0.0034  Score=47.70  Aligned_cols=127  Identities=13%  Similarity=0.057  Sum_probs=97.9

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC-------CC-c---HhHHHHHHHHHHhcCChhHHHHHHHHHHHc------CCCC
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR-------CP-H---VFTWNLMIRALTIDGSSLQALLLYNLMICN------GFRP   77 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~-------~~-~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~p   77 (164)
                      .++.+...|+..++++.|..++....       .+ +   .-+++.|-..|-+.|++++|.+++++..+.      +..+
T Consensus       327 ~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~  406 (508)
T KOG1840|consen  327 QLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDY  406 (508)
T ss_pred             HHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcCh
Confidence            35566778888999999998888654       12 2   246899999999999999999999998542      1122


Q ss_pred             C-cccHHHHHHHHHhccchhhHHHHHHHH----HHhCC-CC-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           78 D-KFTFPFVIKACIASLAIEKGKEVHGLA----VKAGF-SR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        78 ~-~~t~~~ll~~~~~~~~~~~a~~~~~~m----~~~g~-~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      . -..++-+-..|.+.+++..|.++|.+-    +..|. .| ...+|..|...|.+-|++++|.++.+...
T Consensus       407 ~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  407 GVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             hhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            2 356788889999999999999988754    33442 22 36789999999999999999999988765

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

Probab=97.46  E-value=0.0017  Score=41.02  Aligned_cols=72  Identities=15%  Similarity=0.094  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHH-----hCCCCchHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVK-----AGFSRDMFVQS  118 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~-----~g~~~~~~~~~  118 (164)
                      ....++..+...|+++.|..+.+...... +.+...|..+|.++...|+...|.+.++.+.+     .|+.|+..+-.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            34556666777899999999999997753 45788999999999999999999999987753     48888876543

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

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

Probab=97.45  E-value=0.0043  Score=45.34  Aligned_cols=98  Identities=11%  Similarity=-0.081  Sum_probs=67.9

Q ss_pred             HHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhh
Q 031208           21 DLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEK   97 (164)
Q Consensus        21 ~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~   97 (164)
                      ......|+++.|...|++...   .+...|..+-.+|.+.|++++|+..+++..+.. +.+...|..+-.+|...|++++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~e   88 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQT   88 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHH
Confidence            345567888888888887652   355667777777888888888888888886643 2244567777778888888888


Q ss_pred             HHHHHHHHHHhCCCCchHHHHHHH
Q 031208           98 GKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        98 a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      |...+++..+..  |+.......+
T Consensus        89 A~~~~~~al~l~--P~~~~~~~~l  110 (356)
T PLN03088         89 AKAALEKGASLA--PGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHhC--CCCHHHHHHH
Confidence            888888877653  4433333333

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

Probab=97.43  E-value=0.0073  Score=50.45  Aligned_cols=122  Identities=11%  Similarity=0.069  Sum_probs=73.7

Q ss_pred             cCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC--------CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc
Q 031208            8 GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--------CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK   79 (164)
Q Consensus         8 g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   79 (164)
                      +-+.+...|-..|......++++.|++++++..        +--.-.|.++++.-...|.-+...++|++..+..  -.-
T Consensus      1453 ssPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~ 1530 (1710)
T KOG1070|consen 1453 SSPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAY 1530 (1710)
T ss_pred             cCCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chH
Confidence            334467778888888888888888888888764        1223456666666666666666666666666542  122


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHh-CCCCchHHHHHHHHHHHhcCCchhH
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKA-GFSRDMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      ..|..|...|.+...+++|.+++++|.+. |  -...+|...++.+.+..+-+.|
T Consensus      1531 ~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa 1583 (1710)
T KOG1070|consen 1531 TVHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAA 1583 (1710)
T ss_pred             HHHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHH
Confidence            34566666666666666666666666542 3  3334455555544444443333

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

Probab=97.43  E-value=0.0045  Score=47.33  Aligned_cols=131  Identities=18%  Similarity=0.147  Sum_probs=103.2

Q ss_pred             CCCHHHHHH--HHHHHhccCCcHHHHHHHhccC--CCc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208           10 SNDQLLVRK--LLDLCSFYGKTDHALLVFSQIR--CPH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        10 ~~~~~~~~~--li~~~~~~~~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      +|+...|..  +-..|-..|+.++|.++++...  .|. +..|-.--..+-+.|++++|.+.+++.+.-. .-|.+.-+.
T Consensus       189 ~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD-~~DRyiNsK  267 (517)
T PF12569_consen  189 PPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELD-LADRYINSK  267 (517)
T ss_pred             CchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCC-hhhHHHHHH
Confidence            466655644  4567778999999999999765  455 5678888888999999999999999998754 457788888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHH--------HHHHHHHHhcCCchhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQ--------STLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~--------~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..+.+.+.|++++|.+++....+.+..|-...+        ...-.+|.+.|++..|++-|+.+.
T Consensus       268 ~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~  332 (517)
T PF12569_consen  268 CAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVL  332 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            999999999999999999999887765533222        233468889999999988777664

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

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.42  E-value=0.0058  Score=37.41  Aligned_cols=104  Identities=12%  Similarity=0.029  Sum_probs=72.6

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCC--cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc----hHHHHHHHHHHH
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPD--KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD----MFVQSTLMDLYL  125 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~ll~~~~  125 (164)
                      .++-..|+.++|..+|++-...|....  ...+..+-..+...|+.++|..++++.....  |+    ......+--++.
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHH
Confidence            355667888999999999888886654  2355566777888889999999988877542  32    222233334666


Q ss_pred             hcCCchhHHHHhcccCCCCcchHHHHHHHHHh
Q 031208          126 KCGDVDGGRKMFDKMRVRSVVSWTTMISGLAA  157 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~  157 (164)
                      ..|+.++|.+++-...-++...|..-|..|..
T Consensus        87 ~~gr~~eAl~~~l~~la~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   87 NLGRPKEALEWLLEALAETLPRYRRAIRFYAD  118 (120)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            77888888888866555566677777777654

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.41  E-value=0.0081  Score=40.99  Aligned_cols=126  Identities=13%  Similarity=0.019  Sum_probs=91.0

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--CcHh----HHHHHHHHHHhc--------CChhHHHHHHHHHHHcCCCCCc
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVF----TWNLMIRALTID--------GSSLQALLLYNLMICNGFRPDK   79 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~----~~~~li~~~~~~--------~~~~~a~~~~~~m~~~~~~p~~   79 (164)
                      ..+..+-..+.+.|+++.|...++.+.+  |+..    .+..+-.++...        |++++|.+.|++.....  |+.
T Consensus        71 ~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--p~~  148 (235)
T TIGR03302        71 QAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY--PNS  148 (235)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC--CCC
Confidence            4566677888999999999999998852  3221    233333333333        67899999999997653  443


Q ss_pred             c-cHH-----------------HHHHHHHhccchhhHHHHHHHHHHhC--CCCchHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           80 F-TFP-----------------FVIKACIASLAIEKGKEVHGLAVKAG--FSRDMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        80 ~-t~~-----------------~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      . .+.                 .+...+.+.|++.+|...++......  -+.....+..+...|.+.|+.++|..+++.
T Consensus       149 ~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~  228 (235)
T TIGR03302       149 EYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAV  228 (235)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            2 211                 33456788899999999999988663  122457888999999999999999999887


Q ss_pred             cC
Q 031208          140 MR  141 (164)
Q Consensus       140 m~  141 (164)
                      +.
T Consensus       229 l~  230 (235)
T TIGR03302       229 LG  230 (235)
T ss_pred             HH
Confidence            65

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

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

Probab=97.40  E-value=0.016  Score=41.99  Aligned_cols=139  Identities=15%  Similarity=0.177  Sum_probs=84.7

Q ss_pred             HHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCc-ccHHHHHHHHHhcc
Q 031208           22 LCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFRPDK-FTFPFVIKACIASL   93 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~~   93 (164)
                      .+...|+++.|.+++++..  .| |...+.. ...+..    .+..+.+.+.+..  .....|+. .....+...+...|
T Consensus        52 ~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G  128 (355)
T cd05804          52 SAWIAGDLPKALALLEQLLDDYPRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAG  128 (355)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCCCcHHHHHH-hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcC
Confidence            4556788888888887754  24 3333332 222222    3344444444433  11222332 23334455777888


Q ss_pred             chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC-----CCc--chHHHHHHHHHhcCCCCCC
Q 031208           94 AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-----RSV--VSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        94 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~~~--~~~~~li~~~~~~g~~~~A  164 (164)
                      ++++|.+.+++..+.. +.+...+..+-..|...|++++|..++++...     ++.  ..|..+...+...|++++|
T Consensus       129 ~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A  205 (355)
T cd05804         129 QYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAA  205 (355)
T ss_pred             CHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHH
Confidence            8888888888887764 34456677777888888888888888887652     121  3455677778888877654

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

>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=97.36  E-value=0.0053  Score=37.94  Aligned_cols=84  Identities=12%  Similarity=0.083  Sum_probs=71.4

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC-------------------CCcHhHHHHHHHHHHhcCChhHHHHHHHHH-H
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR-------------------CPHVFTWNLMIRALTIDGSSLQALLLYNLM-I   71 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~-------------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m-~   71 (164)
                      |..++..+|-++++.|+++....+.+..=                   .|+..+-.+++.+|+.++++..|+++.+.. .
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            45688999999999999999998886531                   278899999999999999999999999998 6


Q ss_pred             HcCCCCCcccHHHHHHHHHhccch
Q 031208           72 CNGFRPDKFTFPFVIKACIASLAI   95 (164)
Q Consensus        72 ~~~~~p~~~t~~~ll~~~~~~~~~   95 (164)
                      ..+++.+...|..|+.=+....+.
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v~s~~  104 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYVLSSK  104 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHHhcCC
Confidence            778888889999999877665543

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

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

Probab=97.34  E-value=0.0088  Score=47.64  Aligned_cols=134  Identities=15%  Similarity=0.107  Sum_probs=99.4

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTF   82 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~   82 (164)
                      ++++..++ .++-++......+....+.....+      -+...|--+..++...|++++|+.+|..+.....--+...|
T Consensus       374 ~s~~l~v~-rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw  452 (895)
T KOG2076|consen  374 LSYDLRVI-RLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVW  452 (895)
T ss_pred             CCccchhH-hHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhh
Confidence            44555442 333444444444444444444432      34567888999999999999999999999887666667789


Q ss_pred             HHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCC
Q 031208           83 PFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRS  144 (164)
Q Consensus        83 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~  144 (164)
                      --+-.+|-..|..++|.+.++..+... +-+...--.|-..|-+.|+.++|.+.++.|..||
T Consensus       453 ~~~a~c~~~l~e~e~A~e~y~kvl~~~-p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D  513 (895)
T KOG2076|consen  453 YKLARCYMELGEYEEAIEFYEKVLILA-PDNLDARITLASLYQQLGNHEKALETLEQIINPD  513 (895)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHhcC-CCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCC
Confidence            999999999999999999999988653 2234455566677889999999999999988665

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

Probab=97.33  E-value=0.0029  Score=44.25  Aligned_cols=99  Identities=9%  Similarity=-0.036  Sum_probs=80.1

Q ss_pred             HHHHHhccC--CCcHhHHHHHHHHHHhc-----CChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccch---------
Q 031208           32 ALLVFSQIR--CPHVFTWNLMIRALTID-----GSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAI---------   95 (164)
Q Consensus        32 a~~~~~~~~--~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~---------   95 (164)
                      ..+.|....  ++|..+|-..+..|...     +.++-....++.|.+.|+.-|..+|+.||..+-+..-+         
T Consensus        53 ~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F  132 (406)
T KOG3941|consen   53 VEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVF  132 (406)
T ss_pred             hhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHH
Confidence            345565555  57888888888887654     56788888899999999999999999999888665321         


Q ss_pred             -------hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCc
Q 031208           96 -------EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV  130 (164)
Q Consensus        96 -------~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  130 (164)
                             +=+..++++|...|+.||-.+-..|+.++.+-+..
T Consensus       133 ~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  133 LHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence                   23678999999999999999999999999887653

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

Probab=97.32  E-value=0.006  Score=50.89  Aligned_cols=145  Identities=19%  Similarity=0.223  Sum_probs=117.7

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      -+|-++++.-...|.-+...++|++..+  ..-..|..|...|.+.+.+++|-++++.|.+. +.-....|...+..+.+
T Consensus      1498 NiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~ 1576 (1710)
T KOG1070|consen 1498 NIWIAYLNLENAYGTEESLKKVFERACQYCDAYTVHLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLR 1576 (1710)
T ss_pred             HHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhc
Confidence            4688888888889999999999999885  33467899999999999999999999999654 33555678888999999


Q ss_pred             ccchhhHHHHHHHHHHhCCCCc---hHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHHHHHhcCCC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRD---MFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~g~~  161 (164)
                      ..+-+.|..++.+..+.  -|.   .....-..+.-.+.|+.+++..+|+....   +-.-.|+..|+.=.++|+.
T Consensus      1577 ~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~ 1650 (1710)
T KOG1070|consen 1577 QNEAEAARELLKRALKS--LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDI 1650 (1710)
T ss_pred             ccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCH
Confidence            99999999999887765  343   55566667777899999999999998872   2456899998887777654

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

Probab=97.29  E-value=0.0048  Score=43.54  Aligned_cols=115  Identities=16%  Similarity=0.230  Sum_probs=82.2

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH-HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA-CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~-~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      .+|..+|...-+.+..+.|..+|.+.++.+ ..+...|...... +...++.+.|..+|+...+. +..+...|...++.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            578999999999999999999999998542 2233344444444 33356777799999998865 45677889999999


Q ss_pred             HHhcCCchhHHHHhcccCCC------CcchHHHHHHHHHhcCCC
Q 031208          124 YLKCGDVDGGRKMFDKMRVR------SVVSWTTMISGLAASGDL  161 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~~~------~~~~~~~li~~~~~~g~~  161 (164)
                      +.+.++.+.|..+|+.....      -...|...++-=.+.|+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl  123 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDL  123 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-H
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCH
Confidence            99999999999999987632      234777776655555543

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.

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.27  E-value=0.0035  Score=44.42  Aligned_cols=103  Identities=22%  Similarity=0.290  Sum_probs=80.3

Q ss_pred             hhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC-CCcHh-----HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc
Q 031208            6 RYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR-CPHVF-----TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK   79 (164)
Q Consensus         6 ~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~-~~~~~-----~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   79 (164)
                      ..|.+.+..+...++..-....+++.+..++-+++ +|+..     +-.+++.. +-.-++++++.++..-.+.|+-||.
T Consensus        57 ~~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irl-llky~pq~~i~~l~npIqYGiF~dq  135 (418)
T KOG4570|consen   57 ERGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRL-LLKYDPQKAIYTLVNPIQYGIFPDQ  135 (418)
T ss_pred             hcCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHH-HHccChHHHHHHHhCcchhccccch
Confidence            45677777788888888888889999988877776 33321     11222333 3344688999999999999999999


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      .+++.+|+.+.+.+++.+|.++.-+|....
T Consensus       136 f~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  136 FTFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             hhHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            999999999999999999999998887665

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

Probab=97.24  E-value=0.011  Score=44.02  Aligned_cols=115  Identities=12%  Similarity=0.054  Sum_probs=85.5

Q ss_pred             HhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhH
Q 031208           23 CSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKG   98 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a   98 (164)
                      ....|+++.|...++.+.  .| |..-+......+.+.++.++|.+.++++...  .|+ ....-.+-.++.+.|++.+|
T Consensus       316 ~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~ea  393 (484)
T COG4783         316 TYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEA  393 (484)
T ss_pred             HHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHH
Confidence            345677788888877765  35 4555666677788999999999999998774  466 44555667888999999999


Q ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           99 KEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        99 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      ..++....... +.|...|..|-.+|...|+..++..-..+.
T Consensus       394 i~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         394 IRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             HHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence            98888877654 567888999999998887777665544443

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

Probab=97.23  E-value=0.0062  Score=46.22  Aligned_cols=134  Identities=12%  Similarity=0.002  Sum_probs=93.8

Q ss_pred             HhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHH--cCCC----CCcccHHHHHHHHHhcc
Q 031208           23 CSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMIC--NGFR----PDKFTFPFVIKACIASL   93 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~----p~~~t~~~ll~~~~~~~   93 (164)
                      |.+.+.++.|.++|.+..  .| |....+-+=-..-..+.+.+|...|+.-.+  ..+.    ....+++-|-++|.+.+
T Consensus       390 y~~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~  469 (611)
T KOG1173|consen  390 YMRTNNLKLAEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLN  469 (611)
T ss_pred             HHHhccHHHHHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHh
Confidence            445666777777777655  23 445555555455567788888888887652  1111    23345777778888999


Q ss_pred             chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHh
Q 031208           94 AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAA  157 (164)
Q Consensus        94 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~  157 (164)
                      .+++|...+++..... +.+..++.++--.|...|+++.|.+.|++-.  .||-.+-+.++..+..
T Consensus       470 ~~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  470 KYEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLAIE  534 (611)
T ss_pred             hHHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHHHH
Confidence            9999999998887654 5678888888888999999999999998765  6666555555554443

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

Probab=97.22  E-value=0.0044  Score=46.99  Aligned_cols=153  Identities=13%  Similarity=0.057  Sum_probs=103.0

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCc---HhHHHHHHHHHHhcC----------------------------
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPH---VFTWNLMIRALTIDG----------------------------   58 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~~----------------------------   58 (164)
                      +-.+.+|-++=--|...|...+|++.|.+...-|   ...|-..-..|+-.+                            
T Consensus       309 P~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlgm  388 (611)
T KOG1173|consen  309 PSKALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLGM  388 (611)
T ss_pred             CCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHHH
Confidence            3457778777667777799999999999765311   223333333334444                            


Q ss_pred             ------ChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHh--CCC----CchHHHHHHHHHHH
Q 031208           59 ------SSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKA--GFS----RDMFVQSTLMDLYL  125 (164)
Q Consensus        59 ------~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~----~~~~~~~~ll~~~~  125 (164)
                            ..+.|-++|.+..  ++.| |+...+-+--...+.+.+.+|..+|+..+..  .+.    .-..+++.|-+.|.
T Consensus       389 ey~~t~n~kLAe~Ff~~A~--ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~R  466 (611)
T KOG1173|consen  389 EYMRTNNLKLAEKFFKQAL--AIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYR  466 (611)
T ss_pred             HHHHhccHHHHHHHHHHHH--hcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHH
Confidence                  4444444444433  2444 4555555555556677888888888766521  111    13456788889999


Q ss_pred             hcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208          126 KCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +.+++++|+..|++..   ..|..++.++--.|...|+++.|
T Consensus       467 kl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~A  508 (611)
T KOG1173|consen  467 KLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKA  508 (611)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHH
Confidence            9999999999999754   55888999999999999998875

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

Probab=97.22  E-value=0.0067  Score=41.98  Aligned_cols=121  Identities=8%  Similarity=0.005  Sum_probs=86.7

Q ss_pred             HHHHhccCCcHHHHHHHhccCCC-cHhHHHHHHHHH----HhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc
Q 031208           20 LDLCSFYGKTDHALLVFSQIRCP-HVFTWNLMIRAL----TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLA   94 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~----~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~   94 (164)
                      +..+.+..+++.|..-+++|.+- +..+.+-|-.++    .-.+...+|+-+|++|-+. .+|+..+.+-...++...|+
T Consensus       144 VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~  222 (299)
T KOG3081|consen  144 VQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGR  222 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcC
Confidence            45566778899999999999864 445555555444    3446799999999999764 57888888999999999999


Q ss_pred             hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           95 IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +++|..++++.....-.......|.+..+.....+.+...+...+..
T Consensus       223 ~eeAe~lL~eaL~kd~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk  269 (299)
T KOG3081|consen  223 YEEAESLLEEALDKDAKDPETLANLIVLALHLGKDAEVTERNLSQLK  269 (299)
T ss_pred             HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCChHHHHHHHHHHH
Confidence            99999999999876533333444444444444444444556666554

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

Probab=97.20  E-value=0.00052  Score=39.10  Aligned_cols=76  Identities=11%  Similarity=0.099  Sum_probs=54.6

Q ss_pred             cCCcHHHHHHHhccCC--C---cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhHH
Q 031208           26 YGKTDHALLVFSQIRC--P---HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~--~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      .|+++.|..+++++.+  |   +...+-.+-.++.+.|++++|..++++ ..  ..|+ ....-.+-.++.+.|++++|.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~--~~~~~~~~~~l~a~~~~~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LK--LDPSNPDIHYLLARCLLKLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HT--HHHCHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hC--CCCCCHHHHHHHHHHHHHhCCHHHHH
Confidence            5788899999998862  4   344455578889999999999999988 22  2232 233345578889999999999


Q ss_pred             HHHHH
Q 031208          100 EVHGL  104 (164)
Q Consensus       100 ~~~~~  104 (164)
                      +.+++
T Consensus        79 ~~l~~   83 (84)
T PF12895_consen   79 KALEK   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            98875

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

Probab=97.20  E-value=0.0014  Score=35.48  Aligned_cols=63  Identities=11%  Similarity=0.040  Sum_probs=41.2

Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHH
Q 031208           55 TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTL  120 (164)
Q Consensus        55 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  120 (164)
                      .+.|++++|.+.|++..+.. +-+....-.+..+|.+.|++++|.++++.+....  |+...|..+
T Consensus         2 l~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~--~~~~~~~~l   64 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQD--PDNPEYQQL   64 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG--TTHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCHHHHHHH
Confidence            45677888888888876643 2255556667788888888888888888777653  553444333

...

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

Probab=97.14  E-value=0.015  Score=42.56  Aligned_cols=88  Identities=11%  Similarity=-0.016  Sum_probs=68.9

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      ..+...|++++|++.|++..+.. +-+...|..+..++.+.|++++|...+++..... +.+...|..+-.+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHH
Confidence            34567789999999999987643 2245567777788889999999999998887764 335667778888888999999


Q ss_pred             hHHHHhcccC
Q 031208          132 GGRKMFDKMR  141 (164)
Q Consensus       132 ~a~~~~~~m~  141 (164)
                      +|...|++..
T Consensus        88 eA~~~~~~al   97 (356)
T PLN03088         88 TAKAALEKGA   97 (356)
T ss_pred             HHHHHHHHHH
Confidence            9999998765

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

Probab=97.11  E-value=0.0023  Score=40.46  Aligned_cols=67  Identities=24%  Similarity=0.315  Sum_probs=50.4

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHH-----HcCCCCCccc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMI-----CNGFRPDKFT   81 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~-----~~~~~p~~~t   81 (164)
                      ....++..+...|+++.|..+.....  .| |...|..+|.++...|+...|.+.|+++.     +.|+.|+..+
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            45556777778999999999999886  34 77899999999999999999999999984     3599998765

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.10  E-value=0.023  Score=36.81  Aligned_cols=92  Identities=12%  Similarity=-0.052  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CCc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      ...|..+...+...|++++|...|+...  .|+    ..+|..+-..+...|++++|...+++..... +....++..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            4456666777778999999999999874  232    2467788888999999999999999987642 22334566666


Q ss_pred             HHHH-------hccchhhHHHHHHHH
Q 031208           87 KACI-------ASLAIEKGKEVHGLA  105 (164)
Q Consensus        87 ~~~~-------~~~~~~~a~~~~~~m  105 (164)
                      ..+.       +.|+++.|...+++-
T Consensus       114 ~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        114 VICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            6666       778888776666544

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

Probab=97.09  E-value=0.015  Score=45.16  Aligned_cols=140  Identities=11%  Similarity=0.097  Sum_probs=71.4

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc------CCCCCcccHHHHHHHH
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICN------GFRPDKFTFPFVIKAC   89 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~p~~~t~~~ll~~~   89 (164)
                      |.-.+...-..+-++.+..++.+..+-+...-+--|.-+++.+++++|-+.+......      .-+.+..-|.-+.+..
T Consensus       141 W~lyl~Fv~~~~lPets~rvyrRYLk~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdli  220 (835)
T KOG2047|consen  141 WDLYLKFVESHGLPETSIRVYRRYLKVAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLI  220 (835)
T ss_pred             hHHHHHHHHhCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHH
Confidence            3333444444444445555554444333333344455555555666665555555321      1233444555555555


Q ss_pred             HhccchhhHH---HHHHHHHHhCCCCc--hHHHHHHHHHHHhcCCchhHHHHhcccCCC--CcchHHHHHHHHHh
Q 031208           90 IASLAIEKGK---EVHGLAVKAGFSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKMRVR--SVVSWTTMISGLAA  157 (164)
Q Consensus        90 ~~~~~~~~a~---~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--~~~~~~~li~~~~~  157 (164)
                      ++..+.-...   .++..+..  .-+|  ...|+.|.+.|.+.|++++|..+|++-.+.  .+.-++.+.++|+.
T Consensus       221 s~~p~~~~slnvdaiiR~gi~--rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v~tvrDFt~ifd~Ya~  293 (835)
T KOG2047|consen  221 SQNPDKVQSLNVDAIIRGGIR--RFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTVMTVRDFTQIFDAYAQ  293 (835)
T ss_pred             HhCcchhcccCHHHHHHhhcc--cCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhheehhhHHHHHHHHHH
Confidence            5544433222   22222211  1233  357888888888888888888888865533  34445555555553

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.97  E-value=0.014  Score=42.26  Aligned_cols=22  Identities=9%  Similarity=0.084  Sum_probs=17.6

Q ss_pred             HHHHHhccCCcHHHHHHHhccC
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR   40 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~   40 (164)
                      ++--|.+.+++++|..+.+++.
T Consensus       291 L~iYyL~q~dVqeA~~L~Kdl~  312 (557)
T KOG3785|consen  291 LIIYYLNQNDVQEAISLCKDLD  312 (557)
T ss_pred             heeeecccccHHHHHHHHhhcC
Confidence            4556778889999999988876

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

Probab=96.97  E-value=0.022  Score=40.70  Aligned_cols=125  Identities=11%  Similarity=0.021  Sum_probs=91.6

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCCcH--------hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCPHV--------FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFV   85 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~l   85 (164)
                      ...-|+..|.+..++++|.++-+++.+.+.        .-|.-+-..+....+.+.|..++.+-.+.+  |+-+ .-..+
T Consensus       143 AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~--~~cvRAsi~l  220 (389)
T COG2956         143 ALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQAD--KKCVRASIIL  220 (389)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhC--ccceehhhhh
Confidence            355678888899999999888776653222        234555556666778888999888887654  3332 22344


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -+.....|++..|.+.++...+.+-.--..+...|..+|...|+.++...++..+.
T Consensus       221 G~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~  276 (389)
T COG2956         221 GRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAM  276 (389)
T ss_pred             hHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            56778889999999999998888755567788888999999999998888877664

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

Probab=96.96  E-value=0.052  Score=39.12  Aligned_cols=82  Identities=11%  Similarity=0.023  Sum_probs=63.7

Q ss_pred             CCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHH
Q 031208           77 PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLA  156 (164)
Q Consensus        77 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~  156 (164)
                      ....+.+..|.-+...|....|.++..+.   + .|+..-|..-+.+++..++|++..++...  .++.+.|...+.+|.
T Consensus       175 f~~~Sl~~Ti~~li~~~~~k~A~kl~k~F---k-v~dkrfw~lki~aLa~~~~w~eL~~fa~s--kKsPIGyepFv~~~~  248 (319)
T PF04840_consen  175 FVGLSLNDTIRKLIEMGQEKQAEKLKKEF---K-VPDKRFWWLKIKALAENKDWDELEKFAKS--KKSPIGYEPFVEACL  248 (319)
T ss_pred             hhcCCHHHHHHHHHHCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHHHhcCCHHHHHHHHhC--CCCCCChHHHHHHHH
Confidence            33457777788888889888887776554   3 48888899999999999999988887665  456688888888888


Q ss_pred             hcCCCCCC
Q 031208          157 ASGDLDAA  164 (164)
Q Consensus       157 ~~g~~~~A  164 (164)
                      +.|+..+|
T Consensus       249 ~~~~~~eA  256 (319)
T PF04840_consen  249 KYGNKKEA  256 (319)
T ss_pred             HCCCHHHH
Confidence            88876554

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

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

Probab=96.91  E-value=0.042  Score=40.10  Aligned_cols=127  Identities=13%  Similarity=0.009  Sum_probs=95.9

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHHHHHHHHHHhcCChhHHHHHHHHH-HHcCCCCCcccHHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTWNLMIRALTIDGSSLQALLLYNLM-ICNGFRPDKFTFPFV   85 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m-~~~~~~p~~~t~~~l   85 (164)
                      .+.++..-.+++.-+.++|+.++|.++..+..+  -|..  =.....+.+-++++.-.+..++- .+.+..|  ..+.+|
T Consensus       259 lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~--L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tL  334 (400)
T COG3071         259 LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR--LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTL  334 (400)
T ss_pred             hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh--HHHHHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHH
Confidence            344566677788889999999999999887653  2333  22233456667777777766665 4444445  566778


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      =.-|.+.+.+.+|...++...+.  .|+..+|+.+-+++.+.|+.++|..++++-.
T Consensus       335 G~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L  388 (400)
T COG3071         335 GRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREAL  388 (400)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            88999999999999999965544  6999999999999999999999999887643

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

Probab=96.78  E-value=0.029  Score=44.04  Aligned_cols=141  Identities=16%  Similarity=0.158  Sum_probs=81.2

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLA   94 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~   94 (164)
                      .-..+-..+.+.|-...|..+|++..     .|.-.|.+|...|+-+.|..+..+-.+  -+|+..-|..+.+......-
T Consensus       400 ~q~~laell~slGitksAl~I~Erle-----mw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~s~  472 (777)
T KOG1128|consen  400 LQRLLAELLLSLGITKSALVIFERLE-----MWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDPSL  472 (777)
T ss_pred             HHHHHHHHHHHcchHHHHHHHHHhHH-----HHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccChHH
Confidence            33344556666666777777766554     556666666666666666666665554  24566666666555444333


Q ss_pred             hhhHHHHHHHH----------------------------HHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-
Q 031208           95 IEKGKEVHGLA----------------------------VKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-  143 (164)
Q Consensus        95 ~~~a~~~~~~m----------------------------~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-  143 (164)
                      +++|+++.+..                            .+.+ +.-..+|-.+--+..+.+++..|.+.|..-.  +| 
T Consensus       473 yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd  551 (777)
T KOG1128|consen  473 YEKAWELSNYISARAQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPD  551 (777)
T ss_pred             HHHHHHHhhhhhHHHHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCC
Confidence            44444444322                            2211 1223344444444456777777777777554  45 


Q ss_pred             CcchHHHHHHHHHhcCCCCC
Q 031208          144 SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       144 ~~~~~~~li~~~~~~g~~~~  163 (164)
                      +...||.+-.+|.+.|+-.+
T Consensus       552 ~~eaWnNls~ayi~~~~k~r  571 (777)
T KOG1128|consen  552 NAEAWNNLSTAYIRLKKKKR  571 (777)
T ss_pred             chhhhhhhhHHHHHHhhhHH
Confidence            56788888888888776544

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.76  E-value=0.018  Score=45.61  Aligned_cols=113  Identities=9%  Similarity=-0.000  Sum_probs=75.6

Q ss_pred             HHHhccCCcHHHHHHHhccCCCcHhH--HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhH
Q 031208           21 DLCSFYGKTDHALLVFSQIRCPHVFT--WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKG   98 (164)
Q Consensus        21 ~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a   98 (164)
                      .+-....++.+|..+++.+...++.+  |..+...|+..|+++-|.++|.+--         -++-.|..|.+.|++.+|
T Consensus       740 eaai~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw~da  810 (1636)
T KOG3616|consen  740 EAAIGAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKWEDA  810 (1636)
T ss_pred             HHHhhhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccHHHH
Confidence            33444566777777777666555544  6777777888888888877776532         345677788888888888


Q ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCC
Q 031208           99 KEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRS  144 (164)
Q Consensus        99 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~  144 (164)
                      .++-++.  .|-+.+.+.|-+-..-.-+.|++.+|.+++-.+.+|+
T Consensus       811 ~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~  854 (1636)
T KOG3616|consen  811 FKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPD  854 (1636)
T ss_pred             HHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCch
Confidence            7776554  3434455555555566667777777777777777664

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

Probab=96.75  E-value=0.035  Score=39.08  Aligned_cols=98  Identities=13%  Similarity=0.006  Sum_probs=77.2

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhH
Q 031208           54 LTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        54 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      +.+.+++++|+..|.+-.+.. +-|.+-|+--..+|++.|..+.|.+-.+....-. +-....|..|-.+|...|++++|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-p~yskay~RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID-PHYSKAYGRLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHccCcHHHH
Confidence            456789999999999998742 3477888889999999999999888776665543 23467999999999999999999


Q ss_pred             HHHhcccC--CCCcchHHHHHH
Q 031208          134 RKMFDKMR--VRSVVSWTTMIS  153 (164)
Q Consensus       134 ~~~~~~m~--~~~~~~~~~li~  153 (164)
                      .+.|++..  .|+-.+|..=+.
T Consensus       169 ~~aykKaLeldP~Ne~~K~nL~  190 (304)
T KOG0553|consen  169 IEAYKKALELDPDNESYKSNLK  190 (304)
T ss_pred             HHHHHhhhccCCCcHHHHHHHH
Confidence            99998876  566556655443

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

Probab=96.74  E-value=0.0056  Score=32.83  Aligned_cols=55  Identities=9%  Similarity=0.029  Sum_probs=30.9

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      .+...|++++|...|++..+.. +-+...+..+-.++...|++++|...+++..+.
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4555666666666666665543 123445555556666666666666666665543

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

Probab=96.73  E-value=0.011  Score=31.68  Aligned_cols=53  Identities=11%  Similarity=0.088  Sum_probs=27.3

Q ss_pred             HHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           87 KACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      ..+.+.|++++|...+++..+.. +-+...+..+-.++.+.|++++|..+|++.
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a   57 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERA   57 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34455555555555555555443 224445555555555555555555555544

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.71  E-value=0.097  Score=36.25  Aligned_cols=128  Identities=16%  Similarity=0.162  Sum_probs=90.2

Q ss_pred             CCCCHH-HHHHHHHHHhccCCcHHHHHHHhccCC--CcHh----HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCccc
Q 031208            9 LSNDQL-LVRKLLDLCSFYGKTDHALLVFSQIRC--PHVF----TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus         9 ~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~----~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      ..|+.. +|..++-+....|+.+.|...++.+..  |+..    ....+   +-..|++++|.+.++...+.. +.|..+
T Consensus        47 ~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~---lEa~~~~~~A~e~y~~lL~dd-pt~~v~  122 (289)
T KOG3060|consen   47 LGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAML---LEATGNYKEAIEYYESLLEDD-PTDTVI  122 (289)
T ss_pred             cCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHH---HHHhhchhhHHHHHHHHhccC-cchhHH
Confidence            344432 345566677778899999988888652  3221    22222   344688999999999998776 556677


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +--=+...-..|+--+|.+-+.+..+. +..|...|.-+-..|...|++++|.-.++++.
T Consensus       123 ~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~l  181 (289)
T KOG3060|consen  123 RKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELL  181 (289)
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            776666666677666666666555543 36788899999999999999999999998876

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.70  E-value=0.08  Score=34.43  Aligned_cols=80  Identities=11%  Similarity=-0.009  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFV   85 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~l   85 (164)
                      ...+..+-..+...|++++|...|++...  |+    ...+..+-..+.+.|++++|...+.+..+.  .| +...+..+
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l  112 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNI  112 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHH
Confidence            34566666778889999999999998752  22    357888888999999999999999998774  34 34455556


Q ss_pred             HHHHHhccc
Q 031208           86 IKACIASLA   94 (164)
Q Consensus        86 l~~~~~~~~   94 (164)
                      ...+...|+
T Consensus       113 g~~~~~~g~  121 (172)
T PRK02603        113 AVIYHKRGE  121 (172)
T ss_pred             HHHHHHcCC
Confidence            666666665

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.64  E-value=0.11  Score=40.08  Aligned_cols=139  Identities=9%  Similarity=0.021  Sum_probs=92.9

Q ss_pred             hcCCCCHHHHHHHHHHHhccC-----CcHHHHHHHhccC--CCcH-hHHHHHHHHHHhcCC--------hhHHHHHHHHH
Q 031208            7 YGLSNDQLLVRKLLDLCSFYG-----KTDHALLVFSQIR--CPHV-FTWNLMIRALTIDGS--------SLQALLLYNLM   70 (164)
Q Consensus         7 ~g~~~~~~~~~~li~~~~~~~-----~~~~a~~~~~~~~--~~~~-~~~~~li~~~~~~~~--------~~~a~~~~~~m   70 (164)
                      .+.+.|...|...+.+.....     ..+.|..+|++..  .|+- ..|..+..++.....        ...+.+...+.
T Consensus       331 ~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a  410 (517)
T PRK10153        331 QGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNI  410 (517)
T ss_pred             ccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHh
Confidence            455678889999999866533     3678999999876  4653 445544333322211        22233333332


Q ss_pred             HHc-CCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcch
Q 031208           71 ICN-GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVS  147 (164)
Q Consensus        71 ~~~-~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~  147 (164)
                      ... ....+...|..+--.....|++++|...+++.....  |+...|..+-..+...|+.++|.+.+++..  .|...+
T Consensus       411 ~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt  488 (517)
T PRK10153        411 VALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENT  488 (517)
T ss_pred             hhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCch
Confidence            221 123344567777666667799999999999988775  688889999999999999999999998764  444333

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.62  E-value=0.011  Score=32.07  Aligned_cols=61  Identities=13%  Similarity=0.016  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc-chhhHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL-AIEKGKEVHGLAV  106 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~  106 (164)
                      ..|..+-..+...|++++|...|.+..+.. +-+...|..+-.++...| ++++|.+.+++..
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            344445555555555555555555554432 113334444445555555 4555555555443

...

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

Probab=96.59  E-value=0.051  Score=40.95  Aligned_cols=78  Identities=17%  Similarity=0.198  Sum_probs=37.0

Q ss_pred             CChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHh
Q 031208           58 GSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMF  137 (164)
Q Consensus        58 ~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~  137 (164)
                      |++..|.++|.+-..  ..|+...|.+.|+-=.+-+.++.|..+++..+-.  .|++..|-.....=-+.|.+..|..+|
T Consensus       155 gNi~gaRqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~Vy  230 (677)
T KOG1915|consen  155 GNIAGARQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVY  230 (677)
T ss_pred             cccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            444444444444433  2355555555555555555555555555444332  255544444444444455555555444


Q ss_pred             cc
Q 031208          138 DK  139 (164)
Q Consensus       138 ~~  139 (164)
                      +.
T Consensus       231 er  232 (677)
T KOG1915|consen  231 ER  232 (677)
T ss_pred             HH
Confidence            43

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

Probab=96.57  E-value=0.14  Score=41.19  Aligned_cols=116  Identities=16%  Similarity=0.150  Sum_probs=66.6

Q ss_pred             HHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhh
Q 031208           22 LCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEK   97 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~   97 (164)
                      .+++ |+.++|.+++.+..+   .+...|-+|-..|-..|+.+++...+-..-  .+.| |..-|..+-....+.|++++
T Consensus       149 lfar-g~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAA--HL~p~d~e~W~~ladls~~~~~i~q  225 (895)
T KOG2076|consen  149 LFAR-GDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAA--HLNPKDYELWKRLADLSEQLGNINQ  225 (895)
T ss_pred             HHHh-CCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHH--hcCCCChHHHHHHHHHHHhcccHHH
Confidence            3444 777777777776642   345567777777777776666665543332  2333 33455555555566666666


Q ss_pred             HHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           98 GKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        98 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |.-++.+..+.. +++...+.-=...|-+.|+...|.+-|.++-
T Consensus       226 A~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~  268 (895)
T KOG2076|consen  226 ARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLL  268 (895)
T ss_pred             HHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHH
Confidence            666666665554 3344444444555556666666655555543

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

Probab=96.57  E-value=0.13  Score=40.37  Aligned_cols=124  Identities=10%  Similarity=0.051  Sum_probs=69.9

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      |..--+.|.+.+.++-|+.+|....+   .+...|......=-..|..+....+|++.... ++-.+.-|-...+-+-..
T Consensus       519 w~~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqkav~~-~pkae~lwlM~ake~w~a  597 (913)
T KOG0495|consen  519 WLDDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQ-CPKAEILWLMYAKEKWKA  597 (913)
T ss_pred             HhhhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCcchhHHHHHHHHHHhc
Confidence            33334444444444444444444332   23344544444444455566666666666543 222333444444555566


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |+...|..++.+..+.. +.+..+|-+-+..-.....++.|..+|.+..
T Consensus       598 gdv~~ar~il~~af~~~-pnseeiwlaavKle~en~e~eraR~llakar  645 (913)
T KOG0495|consen  598 GDVPAARVILDQAFEAN-PNSEEIWLAAVKLEFENDELERARDLLAKAR  645 (913)
T ss_pred             CCcHHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccccHHHHHHHHHHHh
Confidence            77777777777776554 3366777777777777777777777777655

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.52  E-value=0.053  Score=34.75  Aligned_cols=86  Identities=16%  Similarity=0.089  Sum_probs=51.6

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCccc-HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRPDKFT-FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      -+...|++++|..+|+-....  .|.... |-.|--++-..|++++|...+....... +.+...+-.+-.++.+.|+.+
T Consensus        44 ~ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~L~lG~~~  120 (157)
T PRK15363         44 QLMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECYLACDNVC  120 (157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHH
Confidence            445667777777777776553  343333 3334444445567777777777666555 345556666666677777777


Q ss_pred             hHHHHhcccC
Q 031208          132 GGRKMFDKMR  141 (164)
Q Consensus       132 ~a~~~~~~m~  141 (164)
                      .|.+.|+...
T Consensus       121 ~A~~aF~~Ai  130 (157)
T PRK15363        121 YAIKALKAVV  130 (157)
T ss_pred             HHHHHHHHHH
Confidence            7777666543

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.48  E-value=0.055  Score=34.68  Aligned_cols=89  Identities=8%  Similarity=-0.127  Sum_probs=70.5

Q ss_pred             HHHHHhccCCcHHHHHHHhccC--CCcH-hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccch
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR--CPHV-FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAI   95 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~--~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~   95 (164)
                      +-..+...|++++|.++|+...  .|.. .-|-.|=.++-..|++++|+..|....... +-|...+-.+-.++...|+.
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~L~lG~~  119 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECYLACDNV  119 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCH
Confidence            3445667999999999999876  4544 445555566777899999999999998765 34566777788899999999


Q ss_pred             hhHHHHHHHHHHh
Q 031208           96 EKGKEVHGLAVKA  108 (164)
Q Consensus        96 ~~a~~~~~~m~~~  108 (164)
                      +.|.+.|+.....
T Consensus       120 ~~A~~aF~~Ai~~  132 (157)
T PRK15363        120 CYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999977654

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

Probab=96.46  E-value=0.014  Score=47.01  Aligned_cols=113  Identities=11%  Similarity=0.049  Sum_probs=89.7

Q ss_pred             CcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHH
Q 031208           28 KTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGL  104 (164)
Q Consensus        28 ~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  104 (164)
                      ..+.|..+|.+...   .|...-|=+-..++..|++.+|.++|.+..+... -+..+|--+-++|...|.+..|.++|+.
T Consensus       627 ~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~  705 (1018)
T KOG2002|consen  627 HQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYEN  705 (1018)
T ss_pred             HHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHH
Confidence            45778888876553   3555556666678999999999999999988753 3445677899999999999999999997


Q ss_pred             HH-HhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          105 AV-KAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       105 m~-~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .. +..-..++.+-+.|-.++.++|.+.+|.+..-...
T Consensus       706 ~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~  743 (1018)
T KOG2002|consen  706 CLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKAR  743 (1018)
T ss_pred             HHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            65 55556678889999999999999999988775443

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

Probab=96.40  E-value=0.078  Score=41.41  Aligned_cols=147  Identities=14%  Similarity=0.109  Sum_probs=108.3

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC-----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR-----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      ..|-.-+....+.|++-..+..|+...     ......|...+.-....+-++.+..+|++..+.  .|..  -+--|..
T Consensus       103 RIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~--~P~~--~eeyie~  178 (835)
T KOG2047|consen  103 RIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV--APEA--REEYIEY  178 (835)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc--CHHH--HHHHHHH
Confidence            345555666667777777777777653     234467888888888889999999999998763  3443  6778899


Q ss_pred             HHhccchhhHHHHHHHHHHh------CCCCchHHHHHHHHHHHhcCCc---hhHHHHhcccCCC--C--cchHHHHHHHH
Q 031208           89 CIASLAIEKGKEVHGLAVKA------GFSRDMFVQSTLMDLYLKCGDV---DGGRKMFDKMRVR--S--VVSWTTMISGL  155 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~------g~~~~~~~~~~ll~~~~~~~~~---~~a~~~~~~m~~~--~--~~~~~~li~~~  155 (164)
                      +++.++.++|.+.+...+..      ..+-+...|.-+.+..++.-+.   -....+++.+..+  |  ...|++|.+-|
T Consensus       179 L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYY  258 (835)
T KOG2047|consen  179 LAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYY  258 (835)
T ss_pred             HHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHH
Confidence            99999999999888876532      2245677888888888765432   2345666666633  3  46999999999


Q ss_pred             HhcCCCCCC
Q 031208          156 AASGDLDAA  164 (164)
Q Consensus       156 ~~~g~~~~A  164 (164)
                      .+.|++|+|
T Consensus       259 Ir~g~~eka  267 (835)
T KOG2047|consen  259 IRSGLFEKA  267 (835)
T ss_pred             HHhhhhHHH
Confidence            999999976

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

Probab=96.33  E-value=0.15  Score=38.57  Aligned_cols=120  Identities=11%  Similarity=0.113  Sum_probs=64.4

Q ss_pred             ccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHHHHHHHhccchhhHHH
Q 031208           25 FYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFVIKACIASLAIEKGKE  100 (164)
Q Consensus        25 ~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~  100 (164)
                      ..++++.|.++|++...   .+...|---+..=.++..+..|..++++....  -|... -|---+..=-..|++..|.+
T Consensus        85 sq~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~--lPRVdqlWyKY~ymEE~LgNi~gaRq  162 (677)
T KOG1915|consen   85 SQKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI--LPRVDQLWYKYIYMEEMLGNIAGARQ  162 (677)
T ss_pred             hHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh--cchHHHHHHHHHHHHHHhcccHHHHH
Confidence            35556666666665542   34444544555555566666666666665442  23221 22222333344466666666


Q ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchH
Q 031208          101 VHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSW  148 (164)
Q Consensus       101 ~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~  148 (164)
                      +|+.-..  .+|+...|.+.|+.=.+.+.++.|..+++...  .|++..|
T Consensus       163 iferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~w  210 (677)
T KOG1915|consen  163 IFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNW  210 (677)
T ss_pred             HHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHH
Confidence            6665432  35666666666666666666666666666543  4444433

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.32  E-value=0.034  Score=30.02  Aligned_cols=59  Identities=17%  Similarity=0.113  Sum_probs=36.2

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcC-CchhHHHHhcc
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCG-DVDGGRKMFDK  139 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~-~~~~a~~~~~~  139 (164)
                      ..|..+-..+...|++++|...|++..+.. +.+...|..+-.+|.+.| ++++|.+.|++
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~   63 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEK   63 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHH
Confidence            345555566666666777777666666654 334556666666666666 56666666654

...

>PLN02789 farnesyltranstransferase

Probab=96.29  E-value=0.26  Score=35.64  Aligned_cols=143  Identities=9%  Similarity=-0.004  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--Cc-HhHHHHHHHHHHhcC-ChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--PH-VFTWNLMIRALTIDG-SSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      .+++.+-..+.+.++.+.|..+.++..+  |+ ..+|+..=..+...| .+++++..++++.+.. +-+...|+..-..+
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~l  116 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWLA  116 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHHH
Confidence            4566667777888999999999998763  43 345555444555556 5799999999998764 23444566554455


Q ss_pred             Hhccch--hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHHHHHhc
Q 031208           90 IASLAI--EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMISGLAAS  158 (164)
Q Consensus        90 ~~~~~~--~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~  158 (164)
                      .+.++.  +.+..+.+.+.+.. +-+...|+..--.+.+.|+++++.+.++++.+   .|...|+.....+.+.
T Consensus       117 ~~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~~  189 (320)
T PLN02789        117 EKLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRS  189 (320)
T ss_pred             HHcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHhc
Confidence            555653  56778888887665 45678888888888889999999999998863   3667777766555443

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

Probab=96.26  E-value=0.18  Score=41.63  Aligned_cols=140  Identities=9%  Similarity=0.037  Sum_probs=89.6

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      .+.+|+.+-.+=.+.|.+.+|.+-|-+  ..|...|.-++....+.|.+++-.+.+...++..-.|.+.  +.||-+|++
T Consensus      1103 ~p~vWsqlakAQL~~~~v~dAieSyik--adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAk 1178 (1666)
T KOG0985|consen 1103 EPAVWSQLAKAQLQGGLVKDAIESYIK--ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAK 1178 (1666)
T ss_pred             ChHHHHHHHHHHHhcCchHHHHHHHHh--cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHH
Confidence            345677777777777777777766543  3455567788888888888888888877777776677666  468888888


Q ss_pred             ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC------------------------CCCcch
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR------------------------VRSVVS  147 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~------------------------~~~~~~  147 (164)
                      .++..+.++++.       .|+......+-+-|...|.++.|.-+|..+.                        -.+..|
T Consensus      1179 t~rl~elE~fi~-------gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAns~kt 1251 (1666)
T KOG0985|consen 1179 TNRLTELEEFIA-------GPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKANSTKT 1251 (1666)
T ss_pred             hchHHHHHHHhc-------CCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhccchhH
Confidence            888766554432       3444444444444444444444444443322                        115567


Q ss_pred             HHHHHHHHHhcCCCC
Q 031208          148 WTTMISGLAASGDLD  162 (164)
Q Consensus       148 ~~~li~~~~~~g~~~  162 (164)
                      |.-+--+|...++|.
T Consensus      1252 WK~VcfaCvd~~EFr 1266 (1666)
T KOG0985|consen 1252 WKEVCFACVDKEEFR 1266 (1666)
T ss_pred             HHHHHHHHhchhhhh
Confidence            777777777766654

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.25  E-value=0.15  Score=35.79  Aligned_cols=95  Identities=9%  Similarity=0.041  Sum_probs=68.3

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc----ccHHHHHHHHHhccchhhHHHHHHHHHHhC--CCCchHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK----FTFPFVIKACIASLAIEKGKEVHGLAVKAG--FSRDMFVQS  118 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~~~~~~  118 (164)
                      ..|...+....+.|++++|...|+.+...-  |+.    ..+-.+-..|...|++++|...|+.+.+.-  -......+-
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~  221 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMF  221 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHH
Confidence            456666666667789999999999987643  443    355567788888999999999999887642  111233444


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+...|...|+.+.|.++|+.+.
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi  244 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVI  244 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHH
Confidence            45566778899999999998776

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.24  E-value=0.098  Score=37.27  Aligned_cols=115  Identities=12%  Similarity=0.136  Sum_probs=79.1

Q ss_pred             cCCcHHHHHHHhccC-CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHH-cCCCCCcccHHHHHHHHHhccchhhHHHHHH
Q 031208           26 YGKTDHALLVFSQIR-CPHVFTWNLMIRALTIDGSSLQALLLYNLMIC-NGFRPDKFTFPFVIKACIASLAIEKGKEVHG  103 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  103 (164)
                      .+++.-++.+.++.+ +.+..+-+..-...-+.|+.+.|++-|+...+ .|..|- ..|+..+.. .+.++.+.|.+...
T Consensus       125 e~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpl-lAYniALaH-y~~~qyasALk~iS  202 (459)
T KOG4340|consen  125 EGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPL-LAYNLALAH-YSSRQYASALKHIS  202 (459)
T ss_pred             cccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCch-hHHHHHHHH-HhhhhHHHHHHHHH
Confidence            556666667777666 34444544444455778999999999999855 565554 467766654 46678999999999


Q ss_pred             HHHHhCCC-------------Cch--------HHHHHHHHH-------HHhcCCchhHHHHhcccCC
Q 031208          104 LAVKAGFS-------------RDM--------FVQSTLMDL-------YLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus       104 ~m~~~g~~-------------~~~--------~~~~~ll~~-------~~~~~~~~~a~~~~~~m~~  142 (164)
                      ++..+|+.             ||+        ..-+.++.+       +.+.|+++.|.+-+-+|+.
T Consensus       203 EIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPP  269 (459)
T KOG4340|consen  203 EIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPP  269 (459)
T ss_pred             HHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCC
Confidence            99988762             221        223344443       3578999999999999983

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

Probab=96.23  E-value=0.2  Score=38.45  Aligned_cols=115  Identities=12%  Similarity=0.127  Sum_probs=74.3

Q ss_pred             HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           44 VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        44 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      ..+|...|+.-.+..-++.|..+|.+..+.+..+ ....++++|..+|. ++...|.++|+--.+.- ..++.--...++
T Consensus       366 tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf-~d~p~yv~~Yld  443 (656)
T KOG1914|consen  366 TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKF-GDSPEYVLKYLD  443 (656)
T ss_pred             ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhc-CCChHHHHHHHH
Confidence            3457777777777777788888888887777777 66677777766664 46677777777544321 223333455667


Q ss_pred             HHHhcCCchhHHHHhcccCCC------CcchHHHHHHHHHhcCC
Q 031208          123 LYLKCGDVDGGRKMFDKMRVR------SVVSWTTMISGLAASGD  160 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~~~------~~~~~~~li~~~~~~g~  160 (164)
                      .+...++-+.+.-+|+.....      ....|..+|+-=...|+
T Consensus       444 fL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGd  487 (656)
T KOG1914|consen  444 FLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGD  487 (656)
T ss_pred             HHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhccc
Confidence            777777777777777766532      33567777665555554

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.23  E-value=0.14  Score=31.97  Aligned_cols=125  Identities=10%  Similarity=0.106  Sum_probs=90.7

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      ...++..+.+.+.+.....+++.+..   .+....|.++..|++.. .....+.+..      .++.+....+++.|.+.
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~   82 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKA   82 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHc
Confidence            45678888888899999998887653   45668899999998774 4445555553      35567777899999999


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc-CCchhHHHHhcccCCCCcchHHHHHHHHHhc
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC-GDVDGGRKMFDKMRVRSVVSWTTMISGLAAS  158 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~  158 (164)
                      +-.+++..++..+..         +...+..+... ++.+.|.+++.+-.  +...|..++..+...
T Consensus        83 ~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~~~--~~~lw~~~~~~~l~~  138 (140)
T smart00299       83 KLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVKQN--NPELWAEVLKALLDK  138 (140)
T ss_pred             CcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHhCC--CHHHHHHHHHHHHcc
Confidence            988888888877532         23344555555 88999999988744  555888888877653

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

Probab=96.21  E-value=0.053  Score=40.90  Aligned_cols=22  Identities=27%  Similarity=0.511  Sum_probs=8.8

Q ss_pred             HHHHHHHHHhcCCchhHHHHhc
Q 031208          117 QSTLMDLYLKCGDVDGGRKMFD  138 (164)
Q Consensus       117 ~~~ll~~~~~~~~~~~a~~~~~  138 (164)
                      |-.|-..-.+.|+.++|+++|+
T Consensus       540 ~~tlaq~~lQ~~~i~eAielFE  561 (606)
T KOG0547|consen  540 YETLAQFELQRGKIDEAIELFE  561 (606)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHH
Confidence            3333333334444444444443

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

Probab=96.19  E-value=0.024  Score=44.42  Aligned_cols=98  Identities=10%  Similarity=0.105  Sum_probs=71.8

Q ss_pred             hcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHH
Q 031208           56 IDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGR  134 (164)
Q Consensus        56 ~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~  134 (164)
                      +.++++.|..-|..-..  ..|+ ...||.+-.+|.+.++..+|...+.+..+.+ .-+...|...+....+.|.+++|.
T Consensus       531 qlek~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~  607 (777)
T KOG1128|consen  531 QLEKEQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAI  607 (777)
T ss_pred             HHhhhHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHH
Confidence            34455566655555544  3464 4689999999999999999999999998887 456678888888889999999999


Q ss_pred             HHhcccC-----CCCcchHHHHHHHHH
Q 031208          135 KMFDKMR-----VRSVVSWTTMISGLA  156 (164)
Q Consensus       135 ~~~~~m~-----~~~~~~~~~li~~~~  156 (164)
                      +.++++.     ..|..+...++.+-.
T Consensus       608 ~A~~rll~~~~~~~d~~vl~~iv~~~~  634 (777)
T KOG1128|consen  608 KAYHRLLDLRKKYKDDEVLLIIVRTVL  634 (777)
T ss_pred             HHHHHHHHhhhhcccchhhHHHHHHHH
Confidence            9998775     125555555555444

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.19  E-value=0.03  Score=44.46  Aligned_cols=100  Identities=12%  Similarity=0.081  Sum_probs=77.3

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhH
Q 031208           54 LTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        54 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      ......|..|+.+++.++...  ...--|.-+.+.|+..|+++.|+++|-+.         ..++-.|+.|.+.|+|++|
T Consensus       742 ai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw~da  810 (1636)
T KOG3616|consen  742 AIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWEDA  810 (1636)
T ss_pred             HhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHHHH
Confidence            344567888888888886653  33345788899999999999999998653         2456778999999999999


Q ss_pred             HHHhcccCCC--CcchHHHHHHHHHhcCCCCCC
Q 031208          134 RKMFDKMRVR--SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       134 ~~~~~~m~~~--~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .++-.+...|  .++.|-+-.+-+-+.|++.+|
T Consensus       811 ~kla~e~~~~e~t~~~yiakaedldehgkf~ea  843 (1636)
T KOG3616|consen  811 FKLAEECHGPEATISLYIAKAEDLDEHGKFAEA  843 (1636)
T ss_pred             HHHHHHhcCchhHHHHHHHhHHhHHhhcchhhh
Confidence            9999887766  456777777777788887665

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

Probab=96.13  E-value=0.029  Score=31.16  Aligned_cols=61  Identities=20%  Similarity=0.091  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc--CCC---CC-cccHHHHHHHHHhccchhhHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICN--GFR---PD-KFTFPFVIKACIASLAIEKGKEVHGLAV  106 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~---p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~  106 (164)
                      +++.+-..|...|++++|++.|++..+.  ...   |+ ..++..+-..+...|++++|.+.+++..
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4555666666666666666666665321  111   11 2345555556666666666666665543

...

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

Probab=96.04  E-value=0.26  Score=40.22  Aligned_cols=95  Identities=13%  Similarity=0.086  Sum_probs=47.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCCC------cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc--cHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRCP------HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF--TFP   83 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--t~~   83 (164)
                      ++++.+.|-.-|.-.|+++.+..+...+..-      -..+|=.+-.+|...|++++|...|.+-.+.  .|+..  .+-
T Consensus       269 nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~--~~d~~~l~~~  346 (1018)
T KOG2002|consen  269 NPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKA--DNDNFVLPLV  346 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHcc--CCCCcccccc
Confidence            3444555555555555555555555544311      1123444555555566666666655555432  23222  222


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHh
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      -|-..+.+.|+.+.+...|+.+.+.
T Consensus       347 GlgQm~i~~~dle~s~~~fEkv~k~  371 (1018)
T KOG2002|consen  347 GLGQMYIKRGDLEESKFCFEKVLKQ  371 (1018)
T ss_pred             chhHHHHHhchHHHHHHHHHHHHHh
Confidence            3445555556666666666655544

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

Probab=96.04  E-value=0.21  Score=37.21  Aligned_cols=32  Identities=22%  Similarity=0.144  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR   40 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~   40 (164)
                      ++-|.+....+-+.+...|+.+.|...|++..
T Consensus       228 lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~  259 (564)
T KOG1174|consen  228 LRCNEHLMMALGKCLYYNGDYFQAEDIFSSTL  259 (564)
T ss_pred             CCccHHHHHHHhhhhhhhcCchHHHHHHHHHh
Confidence            44566677777777777777777777777655

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.03  E-value=0.1  Score=28.44  Aligned_cols=56  Identities=11%  Similarity=-0.078  Sum_probs=34.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      ..|.+.++++.|.+.++++...+ +.+...+...-..+.+.|++.+|.+.++...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34566677777777777766542 224445555566666777777777777766654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.99  E-value=0.027  Score=30.79  Aligned_cols=55  Identities=11%  Similarity=0.048  Sum_probs=47.8

Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -..+.+.++++.|.++++.+...+ +.+...+...-..+.+.|+++.|.+.|+...
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l   56 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERAL   56 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHH
Confidence            357889999999999999999875 4567788888899999999999999999876

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

Probab=95.96  E-value=0.023  Score=31.55  Aligned_cols=59  Identities=20%  Similarity=0.140  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC---------Cc-HhHHHHHHHHHHhcCChhHHHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC---------PH-VFTWNLMIRALTIDGSSLQALLLYNLMI   71 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~---------~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~   71 (164)
                      ..+++.+-..|...|++++|...|++..+         |+ ..++..+-..+...|++++|.+.+++..
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45677788899999999999999987651         33 4578888889999999999999998864

...

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.89  E-value=0.38  Score=36.21  Aligned_cols=62  Identities=11%  Similarity=-0.066  Sum_probs=49.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CCcH----hHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPHV----FTWNLMIRALTIDGSSLQALLLYNLMICN   73 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~   73 (164)
                      +...++.+-.+|.+.|++++|...|++..  .|+.    .+|..+-.+|...|+.++|+..+++..+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            56677788888888999999999988754  4553    35888888889999999999888888664

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

Probab=95.88  E-value=0.28  Score=37.65  Aligned_cols=129  Identities=11%  Similarity=0.075  Sum_probs=101.0

Q ss_pred             cCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC----C-cHhHHHHHHHHHHhcCChhHHHHHHHH-HHHcCCCCCccc
Q 031208            8 GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC----P-HVFTWNLMIRALTIDGSSLQALLLYNL-MICNGFRPDKFT   81 (164)
Q Consensus         8 g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~-~~~~~~~li~~~~~~~~~~~a~~~~~~-m~~~~~~p~~~t   81 (164)
                      ...|+. +|...|..--+...++.|+.+|.+..+    + ++...+++|.-+| .++..-|.++|+- |+..|-  +..-
T Consensus       362 ~~~~tL-v~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d--~p~y  437 (656)
T KOG1914|consen  362 DIDLTL-VYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGD--SPEY  437 (656)
T ss_pred             ccCCce-ehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCC--ChHH
Confidence            344554 588888988899999999999999873    3 6677788886655 5778999999987 444432  2223


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCc--hHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      -..-++-+...++-..+..+|+.....++.|+  ..+|..+|+.=+..|+++.+.++-+++
T Consensus       438 v~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~  498 (656)
T KOG1914|consen  438 VLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRR  498 (656)
T ss_pred             HHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            35668888999999999999999998877765  579999999999999999888776654

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

Probab=95.87  E-value=0.22  Score=37.84  Aligned_cols=123  Identities=12%  Similarity=0.047  Sum_probs=97.1

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHh
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIA   91 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~   91 (164)
                      |-.+-..|....+.++....|+....   .|..+|..--..+.-.+++++|..=|++-++  +.| +.+.|.-+--+..+
T Consensus       363 yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~--L~pe~~~~~iQl~~a~Yr  440 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAIS--LDPENAYAYIQLCCALYR  440 (606)
T ss_pred             HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhh--cChhhhHHHHHHHHHHHH
Confidence            66677788889999999999987652   4566777777777777889999988888876  345 56677777777788


Q ss_pred             ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+.+.++...|++.++. ++.-+.+|+..-..+...+++++|.+-|+...
T Consensus       441 ~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai  489 (606)
T KOG0547|consen  441 QHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAI  489 (606)
T ss_pred             HHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHH
Confidence            88999999999998754 45557788888899999999999999887543

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.87  E-value=0.081  Score=36.96  Aligned_cols=96  Identities=10%  Similarity=-0.006  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH---
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD---  122 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~---  122 (164)
                      .-++++..+.-.|++.-.+.++++..+..-+.++.-...|.+..-+.||.+.|...|+...+..-..+..+.+.++.   
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            34566666777788888899999998876666777788888888899999999999998876544566666666554   


Q ss_pred             --HHHhcCCchhHHHHhcccC
Q 031208          123 --LYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       123 --~~~~~~~~~~a~~~~~~m~  141 (164)
                        .|.-.+++..|.+.|.++.
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~  279 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEIL  279 (366)
T ss_pred             hhheecccchHHHHHHHhhcc
Confidence              3444566677777776665

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

Probab=95.85  E-value=0.38  Score=37.02  Aligned_cols=130  Identities=17%  Similarity=0.078  Sum_probs=90.3

Q ss_pred             hhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-c
Q 031208            6 RYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-T   81 (164)
Q Consensus         6 ~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t   81 (164)
                      ..+.++|+.+...|=-.|.-.|.++.|...|+...  +| |..+||.|=..++...+.++|+.-|++.++  +.|+-+ .
T Consensus       423 ~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~yVR~  500 (579)
T KOG1125|consen  423 QLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPGYVRV  500 (579)
T ss_pred             hCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCCeeee
Confidence            34555778888887778888999999999999765  45 667899998888988999999999999877  456532 2


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHH---HhCC------CCchHHHHHHHHHHHhcCCchhHHHHh
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAV---KAGF------SRDMFVQSTLMDLYLKCGDVDGGRKMF  137 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~---~~g~------~~~~~~~~~ll~~~~~~~~~~~a~~~~  137 (164)
                      .--|--+|...|.+++|...+=...   +.+.      .++..+|..|=.++.-.++.|.+.+..
T Consensus       501 RyNlgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a~  565 (579)
T KOG1125|consen  501 RYNLGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEAA  565 (579)
T ss_pred             ehhhhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHhc
Confidence            2334446777888888877664332   2211      224457777666666666666555443

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

Probab=95.72  E-value=0.36  Score=39.66  Aligned_cols=139  Identities=10%  Similarity=0.027  Sum_probs=71.0

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH---H
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK---A   88 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~---~   88 (164)
                      .+-.+-.+|-+.|+.++|..++++..+   .|...-|-+-..|+.. +.++|..++.+....-+.  ..-|+.+..   -
T Consensus       118 Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~~i~--~kq~~~~~e~W~k  194 (906)
T PRK14720        118 ALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAIYRFIK--KKQYVGIEEIWSK  194 (906)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHh--hhcchHHHHHHHH
Confidence            344445555556666666666666542   3445555555566666 666666666655433110  001111111   0


Q ss_pred             HHhc--cchhhHHHHHHHHHHh-CCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHH
Q 031208           89 CIAS--LAIEKGKEVHGLAVKA-GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLA  156 (164)
Q Consensus        89 ~~~~--~~~~~a~~~~~~m~~~-g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~  156 (164)
                      ++..  -+++.-.++.+.+... |...-..++-.+-..|-..++++++..+|+.+.   ..|.....-++..|.
T Consensus       195 ~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        195 LVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             HHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH
Confidence            0100  1122222222222221 333334555566677888889999999999876   335555566666665

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.72  E-value=0.11  Score=37.96  Aligned_cols=91  Identities=12%  Similarity=0.041  Sum_probs=44.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH-HHHHHHHhcCC
Q 031208           51 IRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS-TLMDLYLKCGD  129 (164)
Q Consensus        51 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~-~ll~~~~~~~~  129 (164)
                      ...+.-...+++++-.++.++..=..-|...|| +..+.+..|+..+|+++|-.+....+. |..+|- .|..+|.++++
T Consensus       366 As~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkk  443 (557)
T KOG3785|consen  366 ASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKK  443 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCC
Confidence            333444445555555555555443333333332 345555556666666655554433332 223333 33455555666


Q ss_pred             chhHHHHhcccCCC
Q 031208          130 VDGGRKMFDKMRVR  143 (164)
Q Consensus       130 ~~~a~~~~~~m~~~  143 (164)
                      .+.|++++-.+..|
T Consensus       444 P~lAW~~~lk~~t~  457 (557)
T KOG3785|consen  444 PQLAWDMMLKTNTP  457 (557)
T ss_pred             chHHHHHHHhcCCc
Confidence            66666655555544

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

Probab=95.69  E-value=0.15  Score=41.14  Aligned_cols=103  Identities=14%  Similarity=0.062  Sum_probs=55.7

Q ss_pred             cCCcHHHHHHHhccC-CCcHhHHHHHHHHH--HhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHH
Q 031208           26 YGKTDHALLVFSQIR-CPHVFTWNLMIRAL--TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVH  102 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~-~~~~~~~~~li~~~--~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~  102 (164)
                      .+++..|..-.+++. +..-..|..++.++  .+.|+.++|..+++.....+.. |..|...+-..|...+..+++..++
T Consensus        22 ~~qfkkal~~~~kllkk~Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Y  100 (932)
T KOG2053|consen   22 SSQFKKALAKLGKLLKKHPNALYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLY  100 (932)
T ss_pred             hHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHH
Confidence            344555555444433 22223344444444  4556666666666655443322 5556666666666666666666666


Q ss_pred             HHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208          103 GLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus       103 ~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      +.....  .|+...-..+..+|+|.+.+.
T Consensus       101 e~~~~~--~P~eell~~lFmayvR~~~yk  127 (932)
T KOG2053|consen  101 ERANQK--YPSEELLYHLFMAYVREKSYK  127 (932)
T ss_pred             HHHHhh--CCcHHHHHHHHHHHHHHHHHH
Confidence            665433  355555555666666665544

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.69  E-value=0.37  Score=36.25  Aligned_cols=99  Identities=12%  Similarity=0.008  Sum_probs=71.4

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc----ccHHHHHHHHHhccchhhHHHHHHHHHHhC--------C
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK----FTFPFVIKACIASLAIEKGKEVHGLAVKAG--------F  110 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--------~  110 (164)
                      +...|+.+-.+|.+.|++++|+..|++-.+.  .|+.    .+|..+-.+|.+.|+.++|.+.+++..+.+        .
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALelsn~~f~~i~~  151 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDYNLKFSTILN  151 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcchhHHHHHh
Confidence            4567889999999999999999999998774  4764    358999999999999999999999887752        1


Q ss_pred             CCch------HHHHHHHHHHHhcCC-----chhHHHHhcccCCC
Q 031208          111 SRDM------FVQSTLMDLYLKCGD-----VDGGRKMFDKMRVR  143 (164)
Q Consensus       111 ~~~~------~~~~~ll~~~~~~~~-----~~~a~~~~~~m~~~  143 (164)
                      .|+.      .-+..++....+.|.     ...-.++..+...|
T Consensus       152 DpdL~plR~~pef~eLlee~rk~G~~~g~~~~~~~kL~~E~~aP  195 (453)
T PLN03098        152 DPDLAPFRASPEFKELQEEARKGGEDIGSSFRRDLKLISEVQAP  195 (453)
T ss_pred             CcchhhhcccHHHHHHHHHHHHhCCccCCchhhHHHHHHHHhch
Confidence            1211      245566666666664     22234555555544

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

Probab=95.68  E-value=0.33  Score=39.88  Aligned_cols=126  Identities=15%  Similarity=0.015  Sum_probs=83.9

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CCcHhHH-HHHHHHHHhcCChhHHHHH------------------HHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPHVFTW-NLMIRALTIDGSSLQALLL------------------YNLM   70 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~-~~li~~~~~~~~~~~a~~~------------------~~~m   70 (164)
                      +...|..|+..+...+++++|..+.+...  .|+...+ -.+-..+...++.+++..+                  ...|
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~~~~i  109 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHICDKI  109 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHHHHHHHH
Confidence            46778889999999999999999988544  2443221 1111134444444444444                  2222


Q ss_pred             HHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           71 ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        71 ~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ...  .-+...+-.+..+|-+.|+.+++..+++++.+.. +-|...-|.+-..|+.. ++++|.+++.+..
T Consensus       110 ~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV  176 (906)
T PRK14720        110 LLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAI  176 (906)
T ss_pred             Hhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHH
Confidence            221  1222455667777788899999999999998877 55677888888888888 8888888776653

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

Probab=95.64  E-value=0.62  Score=36.88  Aligned_cols=160  Identities=14%  Similarity=0.052  Sum_probs=118.1

Q ss_pred             hHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC------CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC
Q 031208            3 KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR------CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFR   76 (164)
Q Consensus         3 ~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   76 (164)
                      .+...|+..+..-|-.=-..|-+.|..-.++.+.....      +.-..||..--..|.+.+.++-|..+|....+. ++
T Consensus       469 ~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqv-fp  547 (913)
T KOG0495|consen  469 ELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQV-FP  547 (913)
T ss_pred             HHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhh-cc
Confidence            45667777788888777778888888888887776554      133467888888899999999999999988774 33


Q ss_pred             CCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHH
Q 031208           77 PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMIS  153 (164)
Q Consensus        77 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~  153 (164)
                      .+...|......--..|..+....++++....- +-.+..|-.....+-..|++..|..++...-  .| +...|-+-+.
T Consensus       548 ~k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavK  626 (913)
T KOG0495|consen  548 CKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVK  626 (913)
T ss_pred             chhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHH
Confidence            345555555555566688888888988887653 4566777777888888999999998888664  33 5567877777


Q ss_pred             HHHhcCCCCCC
Q 031208          154 GLAASGDLDAA  164 (164)
Q Consensus       154 ~~~~~g~~~~A  164 (164)
                      .-.++.++|+|
T Consensus       627 le~en~e~era  637 (913)
T KOG0495|consen  627 LEFENDELERA  637 (913)
T ss_pred             HhhccccHHHH
Confidence            77777766643

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.63  E-value=0.028  Score=35.27  Aligned_cols=80  Identities=18%  Similarity=0.104  Sum_probs=45.5

Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC----------CcchHHHHHHH
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR----------SVVSWTTMISG  154 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----------~~~~~~~li~~  154 (164)
                      +++.+.+.+.+....++++.+...+...+....+.++..|++.+..+...++++....-          ....|...+-.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~yd~~~~~~~c~~~~l~~~a~~L   92 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNNYDLDKALRLCEKHGLYEEAVYL   92 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSSS-CTHHHHHHHTTTSHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccccCHHHHHHHHHhcchHHHHHHH
Confidence            45555556666666666666665554555666666666666666666666666643321          22245555556


Q ss_pred             HHhcCCCCCC
Q 031208          155 LAASGDLDAA  164 (164)
Q Consensus       155 ~~~~g~~~~A  164 (164)
                      |.+.|++++|
T Consensus        93 y~~~~~~~~a  102 (143)
T PF00637_consen   93 YSKLGNHDEA  102 (143)
T ss_dssp             HHCCTTHTTC
T ss_pred             HHHcccHHHH
Confidence            6666665554

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

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

Probab=95.60  E-value=0.37  Score=37.71  Aligned_cols=131  Identities=18%  Similarity=0.113  Sum_probs=94.6

Q ss_pred             CCCHHHHHH--HHHHHhccCCcHHHHHHHhccCC--CcH-hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208           10 SNDQLLVRK--LLDLCSFYGKTDHALLVFSQIRC--PHV-FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        10 ~~~~~~~~~--li~~~~~~~~~~~a~~~~~~~~~--~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      +|++..|+.  +...+-+.|+++.|..+++..-.  |+. ..|-.=-..+..+|++++|..++.+..+-. .||...-+-
T Consensus       366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INsK  444 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINSK  444 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHHH
Confidence            577777776  46677789999999999997653  443 234444567788899999999999987754 566665556


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCC------CchHHHHHH--HHHHHhcCCchhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFS------RDMFVQSTL--MDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~------~~~~~~~~l--l~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -.+...+++.+++|.++.....+.|..      .-..+|-.+  -.+|.+.|++-.|++=|+.+.
T Consensus       445 cAKYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkfh~i~  509 (700)
T KOG1156|consen  445 CAKYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKFHEIE  509 (700)
T ss_pred             HHHHHHHccccHHHHHHHHHhhhcccchhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHHhhHH
Confidence            778888999999999999988887741      011223222  246778888888887777665

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.57  E-value=0.015  Score=36.54  Aligned_cols=125  Identities=7%  Similarity=0.071  Sum_probs=72.0

Q ss_pred             HHHHHhccCCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLA   94 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~   94 (164)
                      +++.+.+.+.++....+++.+.    ..+....+.++..|++.++.+...++++       ..+.+....+++.|.+.|-
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~-------~~~~yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK-------TSNNYDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT-------SSSSS-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc-------cccccCHHHHHHHHHhcch
Confidence            4666666677766666666554    2456677888888888877677777666       1222333456666666666


Q ss_pred             hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCC
Q 031208           95 IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~  161 (164)
                      ++.+.-++..+....         ..+..+...++++.|.+++.+..  +...|..++..|...+++
T Consensus        86 ~~~a~~Ly~~~~~~~---------~al~i~~~~~~~~~a~e~~~~~~--~~~l~~~l~~~~l~~~~~  141 (143)
T PF00637_consen   86 YEEAVYLYSKLGNHD---------EALEILHKLKDYEEAIEYAKKVD--DPELWEQLLKYCLDSKPF  141 (143)
T ss_dssp             HHHHHHHHHCCTTHT---------TCSSTSSSTHCSCCCTTTGGGCS--SSHHHHHHHHHHCTSTCT
T ss_pred             HHHHHHHHHHcccHH---------HHHHHHHHHccHHHHHHHHHhcC--cHHHHHHHHHHHHhcCcc
Confidence            655555544432211         11111233344455554444443  567999999999887765

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.57  E-value=0.32  Score=34.12  Aligned_cols=95  Identities=15%  Similarity=0.023  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--CcH----hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----cccH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHV----FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD----KFTF   82 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~   82 (164)
                      ...|..-+....+.|+++.|...|+.+.+  |+.    ..+-.+-..|...|++++|...|+.+...-  |+    ...+
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~y--P~s~~~~dAl  220 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNY--PKSPKAADAM  220 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCCcchhHHH
Confidence            44566666666778999999999998862  543    355567778899999999999999997642  32    2233


Q ss_pred             HHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           83 PFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        83 ~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      -.+...+...|+.+.|..+++.+.+..
T Consensus       221 ~klg~~~~~~g~~~~A~~~~~~vi~~y  247 (263)
T PRK10803        221 FKVGVIMQDKGDTAKAKAVYQQVIKKY  247 (263)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            334566778999999999999988763

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

Probab=95.53  E-value=0.34  Score=34.23  Aligned_cols=80  Identities=10%  Similarity=0.006  Sum_probs=67.8

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHH-----hCCCCchHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVK-----AGFSRDMFVQST  119 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~-----~g~~~~~~~~~~  119 (164)
                      .+++.++..+...|+.+.+.+.++++.... +-++..|..+|.+|.+.|+...|...++++.+     .|+.|...+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            456778888889999999999999998753 45888999999999999999999999998876     489999888887


Q ss_pred             HHHHHH
Q 031208          120 LMDLYL  125 (164)
Q Consensus       120 ll~~~~  125 (164)
                      ......
T Consensus       233 y~~~~~  238 (280)
T COG3629         233 YEEILR  238 (280)
T ss_pred             HHHHhc
Confidence            777643

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

Probab=95.51  E-value=0.049  Score=41.60  Aligned_cols=105  Identities=8%  Similarity=-0.067  Sum_probs=76.2

Q ss_pred             CChhHHHHHHHHH-HHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHH
Q 031208           58 GSSLQALLLYNLM-ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKM  136 (164)
Q Consensus        58 ~~~~~a~~~~~~m-~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  136 (164)
                      ....+..++|-++ .+.+.++|......|=-.|--.|+++.|...|+..+... +-|..+||.|-...+...+.++|.+.
T Consensus       408 ~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsA  486 (579)
T KOG1125|consen  408 SHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISA  486 (579)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHH
Confidence            3456677777777 556645666666777777888899999999999988764 55788999999999999999999999


Q ss_pred             hcccC--CCC-cchHHHHHHHHHhcCCCCC
Q 031208          137 FDKMR--VRS-VVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       137 ~~~m~--~~~-~~~~~~li~~~~~~g~~~~  163 (164)
                      |++..  +|+ +.++..|--+|...|-++|
T Consensus       487 Y~rALqLqP~yVR~RyNlgIS~mNlG~ykE  516 (579)
T KOG1125|consen  487 YNRALQLQPGYVRVRYNLGISCMNLGAYKE  516 (579)
T ss_pred             HHHHHhcCCCeeeeehhhhhhhhhhhhHHH
Confidence            99876  453 2233334444444444433

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.47  E-value=0.28  Score=39.02  Aligned_cols=115  Identities=17%  Similarity=0.185  Sum_probs=89.6

Q ss_pred             cCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208            8 GLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus         8 g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      |..-.-.+.+.-+.-+..-|+...|.++-.+++-||...|-.=+.+++..++|++-.++=+.++      ++.-|.-...
T Consensus       679 ~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe  752 (829)
T KOG2280|consen  679 GGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVE  752 (829)
T ss_pred             ccccccCcHHHHHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHH
Confidence            3334444566677888889999999999999999999999999999999999998876655542      2667888999


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHh
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMF  137 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~  137 (164)
                      +|.+.|+.++|.+++-..-  |    .   .-...+|.+.|++.+|.++-
T Consensus       753 ~c~~~~n~~EA~KYiprv~--~----l---~ekv~ay~~~~~~~eAad~A  793 (829)
T KOG2280|consen  753 ACLKQGNKDEAKKYIPRVG--G----L---QEKVKAYLRVGDVKEAADLA  793 (829)
T ss_pred             HHHhcccHHHHhhhhhccC--C----h---HHHHHHHHHhccHHHHHHHH
Confidence            9999999999998886642  1    1   15667778888777776543

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

Probab=95.42  E-value=0.17  Score=35.85  Aligned_cols=132  Identities=11%  Similarity=0.020  Sum_probs=77.7

Q ss_pred             cCCcHHHHHHHhccC-------CCcH--hHHHHHHHHHHhc-CChhHHHHHHHHHHH----cCCCCC-cccHHHHHHHHH
Q 031208           26 YGKTDHALLVFSQIR-------CPHV--FTWNLMIRALTID-GSSLQALLLYNLMIC----NGFRPD-KFTFPFVIKACI   90 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~-------~~~~--~~~~~li~~~~~~-~~~~~a~~~~~~m~~----~~~~p~-~~t~~~ll~~~~   90 (164)
                      ..+++.|...+++..       .++.  ..+..+-..|-.. |+++.|++.|.+-..    .|-+-. ...+..+...+.
T Consensus        87 ~~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~  166 (282)
T PF14938_consen   87 KGDPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYA  166 (282)
T ss_dssp             HTTHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred             hhCHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence            336666666655543       2322  2455556666666 788888888888643    331111 235667778889


Q ss_pred             hccchhhHHHHHHHHHHhCCCC-----chH-HHHHHHHHHHhcCCchhHHHHhcccCC--C------CcchHHHHHHHHH
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSR-----DMF-VQSTLMDLYLKCGDVDGGRKMFDKMRV--R------SVVSWTTMISGLA  156 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~-----~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~--~------~~~~~~~li~~~~  156 (164)
                      +.|++++|.+++++....-...     +.. .+-..+-++...|+...|.+.|++...  |      .......||.+|-
T Consensus       167 ~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~  246 (282)
T PF14938_consen  167 RLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYE  246 (282)
T ss_dssp             HTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHH
Confidence            9999999999999887653321     222 233344467778999999999987652  2      1234555566654


Q ss_pred             h
Q 031208          157 A  157 (164)
Q Consensus       157 ~  157 (164)
                      .
T Consensus       247 ~  247 (282)
T PF14938_consen  247 E  247 (282)
T ss_dssp             T
T ss_pred             h
Confidence            3

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=95.26  E-value=0.63  Score=32.27  Aligned_cols=143  Identities=10%  Similarity=-0.032  Sum_probs=86.7

Q ss_pred             HHHHhccCCcHHHHHHHhccCC--CcHhH----HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh--
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC--PHVFT----WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA--   91 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~--~~~~~----~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~--   91 (164)
                      -..+.+.|+++.|.+.|+.+..  |+...    .=.+..++-+.+++++|...+++..+..-.-...-|...+.+.+.  
T Consensus        39 A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~  118 (243)
T PRK10866         39 AQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNMA  118 (243)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhhh
Confidence            3344557888999999888763  43321    123456778899999999999998765322223345555555442  


Q ss_pred             c---------------cc---hhhHHHHHHHHHHhCCCCch------H-----HHH-------HHHHHHHhcCCchhHHH
Q 031208           92 S---------------LA---IEKGKEVHGLAVKAGFSRDM------F-----VQS-------TLMDLYLKCGDVDGGRK  135 (164)
Q Consensus        92 ~---------------~~---~~~a~~~~~~m~~~g~~~~~------~-----~~~-------~ll~~~~~~~~~~~a~~  135 (164)
                      .               .|   ...|...++.+++.  -|+.      .     +.+       .+...|.+.|.+.-|..
T Consensus       119 ~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~--yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~AA~~  196 (243)
T PRK10866        119 LDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRG--YPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVN  196 (243)
T ss_pred             cchhhhhhccCCCccccCHHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHH
Confidence            0               12   23455666666554  1221      1     111       22345778888888888


Q ss_pred             HhcccCC--C----CcchHHHHHHHHHhcCCCCCC
Q 031208          136 MFDKMRV--R----SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       136 ~~~~m~~--~----~~~~~~~li~~~~~~g~~~~A  164 (164)
                      -|+.+.+  |    .....-.++.+|...|..++|
T Consensus       197 r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a  231 (243)
T PRK10866        197 RVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQA  231 (243)
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHH
Confidence            7777763  2    334667788899888887654

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.14  E-value=0.16  Score=36.25  Aligned_cols=122  Identities=12%  Similarity=0.160  Sum_probs=78.6

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhc--c----CCcHHHHHHHhccCC-------CcHhHHHHHHHHHHhcCC----hhHHH
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSF--Y----GKTDHALLVFSQIRC-------PHVFTWNLMIRALTIDGS----SLQAL   64 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~--~----~~~~~a~~~~~~~~~-------~~~~~~~~li~~~~~~~~----~~~a~   64 (164)
                      +.|.+.|++-+..++-+-......  .    .....|.++|+.|++       ++-.++..++..  ...+    .+.+.
T Consensus        86 ~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e~l~~~~E  163 (297)
T PF13170_consen   86 EKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVEELAERME  163 (297)
T ss_pred             HHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHHHHHHHHH
Confidence            567888999888666653333322  1    246778899999983       566777777655  3333    35667


Q ss_pred             HHHHHHHHcCCCCCc--ccHHHHHHHHHhccc--hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Q 031208           65 LLYNLMICNGFRPDK--FTFPFVIKACIASLA--IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        65 ~~~~~m~~~~~~p~~--~t~~~ll~~~~~~~~--~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                      ..|+.+...|+..+-  +..+.++..+-....  ...+.++++.+.+.|+.+....|..+ +..+-
T Consensus       164 ~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l-GlLal  228 (297)
T PF13170_consen  164 QCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL-GLLAL  228 (297)
T ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH-HHHHh
Confidence            778888888888744  333444433322222  45788899999999998887775544 44443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.09  E-value=0.12  Score=31.70  Aligned_cols=80  Identities=15%  Similarity=0.027  Sum_probs=55.6

Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCc--hHHHHHHHHHHHhcCCchhHHHHhcccC--CCC----cchHHHHHHHHH
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRS----VVSWTTMISGLA  156 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~----~~~~~~li~~~~  156 (164)
                      +-.++-..|+.++|..++++....|....  ...+-.+-..|...|++++|..+|++..  .|+    ......+..++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            34567788999999999999999887654  3344556677888999999999998765  243    122222334556


Q ss_pred             hcCCCCCC
Q 031208          157 ASGDLDAA  164 (164)
Q Consensus       157 ~~g~~~~A  164 (164)
                      ..|+.++|
T Consensus        87 ~~gr~~eA   94 (120)
T PF12688_consen   87 NLGRPKEA   94 (120)
T ss_pred             HCCCHHHH
Confidence            66666553

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

Probab=95.08  E-value=0.45  Score=35.98  Aligned_cols=115  Identities=13%  Similarity=0.183  Sum_probs=80.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNG-FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      ..|.+.|+.-.+..-.+.|..+|-+..+.| +.++.+.+++.|..++. |+...|..+|+.-... ++.+..--+..+..
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~-f~d~~~y~~kyl~f  475 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK-FPDSTLYKEKYLLF  475 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh-CCCchHHHHHHHHH
Confidence            467888888888888999999999998888 77888899998887765 5777888888765433 12333344566677


Q ss_pred             HHhcCCchhHHHHhcccCCC---C--cchHHHHHHHHHhcCCC
Q 031208          124 YLKCGDVDGGRKMFDKMRVR---S--VVSWTTMISGLAASGDL  161 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~~~---~--~~~~~~li~~~~~~g~~  161 (164)
                      +.+-++-+.|..+|+.-.++   +  ...|..+|+-=...|+.
T Consensus       476 Li~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~l  518 (660)
T COG5107         476 LIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSL  518 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcch
Confidence            77788888888888844322   2  34666666554444443

>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=95.00  E-value=0.61  Score=30.67  Aligned_cols=97  Identities=13%  Similarity=-0.036  Sum_probs=69.2

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc--ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCC-chHHHH--H
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK--FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSR-DMFVQS--T  119 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~--~  119 (164)
                      ..+..+...|.+.|+.+.|++.|.++......|..  ..+-.+|+.....+++..+...+.+....--.+ |...-+  .
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk  116 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK  116 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence            56788899999999999999999999887655543  466778889999999999998888766432221 121111  1


Q ss_pred             HHH--HHHhcCCchhHHHHhcccC
Q 031208          120 LMD--LYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       120 ll~--~~~~~~~~~~a~~~~~~m~  141 (164)
                      ...  .+...+++..|.+.|-+..
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHccC
Confidence            122  2235689999998887765

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.

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=94.93  E-value=0.47  Score=36.73  Aligned_cols=122  Identities=16%  Similarity=0.001  Sum_probs=79.8

Q ss_pred             CCcHhHHHHHHHHHHhcC-----ChhHHHHHHHHHHHcCCCCCc-ccHHHHHHHHHhccc--------hhhHHHHHHHHH
Q 031208           41 CPHVFTWNLMIRALTIDG-----SSLQALLLYNLMICNGFRPDK-FTFPFVIKACIASLA--------IEKGKEVHGLAV  106 (164)
Q Consensus        41 ~~~~~~~~~li~~~~~~~-----~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~~~--------~~~a~~~~~~m~  106 (164)
                      ..|...|...+.+.....     ..+.|..+|++..+.  .|+- ..|..+..++.....        ...+.+..+...
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            367788999999865533     367899999998774  4654 344444333322211        122222232222


Q ss_pred             Hh-CCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHhcCCCCCC
Q 031208          107 KA-GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       107 ~~-g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .. ....+...|.++--.....|++++|...+++..  +|+...|..+-..|...|+.++|
T Consensus       412 al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA  472 (517)
T PRK10153        412 ALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLA  472 (517)
T ss_pred             hcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHH
Confidence            21 233455677777666667899999999999876  66777888888899999998765

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

Probab=94.93  E-value=0.18  Score=35.69  Aligned_cols=98  Identities=11%  Similarity=0.003  Sum_probs=67.2

Q ss_pred             CCCHHHHHHHHHHHhcc-----CCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcC----------------ChhHHH
Q 031208           10 SNDQLLVRKLLDLCSFY-----GKTDHALLVFSQIR----CPHVFTWNLMIRALTIDG----------------SSLQAL   64 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~----------------~~~~a~   64 (164)
                      +.|..+|-..+..+...     +.++--..-++.|+    ++|..+|+.||+.+-+-.                .-+-+.
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            44666676666666543     23333333333333    578888888888776643                236688


Q ss_pred             HHHHHHHHcCCCCCcccHHHHHHHHHhccch-hhHHHHHHHHHH
Q 031208           65 LLYNLMICNGFRPDKFTFPFVIKACIASLAI-EKGKEVHGLAVK  107 (164)
Q Consensus        65 ~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~m~~  107 (164)
                      +++++|+..|+.||..+--.|+.++.+.+-. .+..++.-.|-+
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmPk  187 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWMPK  187 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhhhh
Confidence            9999999999999999999999999988754 345555555544

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=94.91  E-value=0.36  Score=28.29  Aligned_cols=62  Identities=10%  Similarity=0.088  Sum_probs=45.7

Q ss_pred             ChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHH-HhCCCCchHHHHHHHH
Q 031208           59 SSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAV-KAGFSRDMFVQSTLMD  122 (164)
Q Consensus        59 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~-~~g~~~~~~~~~~ll~  122 (164)
                      +.=++.+-++.+....+.|++....+.+++|-+-+++..|.++++-.+ +.|  .+...|..+++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~--~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCG--AHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--CchhhHHHHHH
Confidence            334566667777777888888888888999998899999998888776 333  24446666665

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.

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

Probab=94.72  E-value=1.1  Score=36.44  Aligned_cols=113  Identities=19%  Similarity=0.196  Sum_probs=87.7

Q ss_pred             CCHHHHHHHHHHHh--ccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           11 NDQLLVRKLLDLCS--FYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        11 ~~~~~~~~li~~~~--~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      |+. .|..++.++.  +.|+.++|..+++...   ..|..|...+-..|.+.+..++|..+|++..+.  -|+..-...+
T Consensus        40 Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~l  116 (932)
T KOG2053|consen   40 PNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHL  116 (932)
T ss_pred             CCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHH
Confidence            443 3556666555  6899999999998775   358889999999999999999999999999764  4888888889


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC  127 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  127 (164)
                      +.+|.+.+++.+-.+.--++-+ ..+-+.+.+..++..+...
T Consensus       117 FmayvR~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~Slilqs  157 (932)
T KOG2053|consen  117 FMAYVREKSYKKQQKAALQLYK-NFPKRAYYFWSVISLILQS  157 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-hCCcccchHHHHHHHHHHh
Confidence            9999999998876665555544 3355677777887777654

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=94.63  E-value=0.74  Score=29.96  Aligned_cols=123  Identities=10%  Similarity=0.019  Sum_probs=78.1

Q ss_pred             HhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcC--ChhHHHHHHHHHHHcCCCCCccc
Q 031208            4 IIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDG--SSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus         4 m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      +.+.|++|+...+..+++.+.+.|++..-..++..-.-+|.......+-.+....  -.+-|++++.++..        .
T Consensus        20 l~~~~i~~~~~L~~lli~lLi~~~~~~~L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~--------~   91 (167)
T PF07035_consen   20 LNQHNIPVQHELYELLIDLLIRNGQFSQLHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGT--------A   91 (167)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhh--------h
Confidence            4567889999999999999999999888888877666566655555554443322  24455555555542        3


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhc
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFD  138 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  138 (164)
                      +..++..+...|++-+|.++........    ......++.+-.+.++...=..+|+
T Consensus        92 ~~~iievLL~~g~vl~ALr~ar~~~~~~----~~~~~~fLeAA~~~~D~~lf~~V~~  144 (167)
T PF07035_consen   92 YEEIIEVLLSKGQVLEALRYARQYHKVD----SVPARKFLEAAANSNDDQLFYAVFR  144 (167)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcCCcc----cCCHHHHHHHHHHcCCHHHHHHHHH
Confidence            4667788888888888888887653221    1222445566555555444333333

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

Probab=94.55  E-value=0.21  Score=41.00  Aligned_cols=128  Identities=10%  Similarity=-0.041  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCCcccHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG-FRPDKFTFPFVIKA   88 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~ll~~   88 (164)
                      ...|..|=+.|+..-+...|...|+..-+   .+...+..+..-|+...+++.|..+.-.--+.. .......|..+=-.
T Consensus       492 apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~y  571 (1238)
T KOG1127|consen  492 APAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPY  571 (1238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhcccc
Confidence            34567776777776678888888887653   466788889999999999999999833332211 11111222222233


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |.+.++...+..-|+...+.. +.|...|..+..+|.++|++..|.++|.+..
T Consensus       572 yLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs  623 (1238)
T KOG1127|consen  572 YLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKAS  623 (1238)
T ss_pred             ccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhH
Confidence            456667777777777766554 4578899999999999999999999997765

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.47  E-value=1.1  Score=31.27  Aligned_cols=116  Identities=13%  Similarity=0.145  Sum_probs=88.2

Q ss_pred             hccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHH
Q 031208           24 SFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKE  100 (164)
Q Consensus        24 ~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~  100 (164)
                      -..|..++|.++++...+   .|.+++-.=+...-..|+.-+|++-+.+.... +..|...|.-+-..|...|+++.|.-
T Consensus        97 Ea~~~~~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~f  175 (289)
T KOG3060|consen   97 EATGNYKEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAF  175 (289)
T ss_pred             HHhhchhhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHH
Confidence            347889999999999874   36777877777777788888999888888765 77899999999999999999999999


Q ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHhcC---CchhHHHHhcccC
Q 031208          101 VHGLAVKAGFSRDMFVQSTLMDLYLKCG---DVDGGRKMFDKMR  141 (164)
Q Consensus       101 ~~~~m~~~g~~~~~~~~~~ll~~~~~~~---~~~~a~~~~~~m~  141 (164)
                      +++++.-.. +.+...+..+-+.+.-.|   +.+.+.+.|.+..
T Consensus       176 ClEE~ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~al  218 (289)
T KOG3060|consen  176 CLEELLLIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERAL  218 (289)
T ss_pred             HHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            999998763 234444555555544333   4555667776654

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

Probab=94.46  E-value=1  Score=31.95  Aligned_cols=111  Identities=15%  Similarity=0.113  Sum_probs=77.9

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc---cchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS---LAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~---~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      .|...|-.|=..|...|+.+.|..-|++-.+-. ++|...+..+-.++...   ....++..+++++.+.. +-++..-.
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral~  231 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHHH
Confidence            367789999999999999999999999986531 23444444444444333   24567889999988764 33455555


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHH
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISG  154 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~  154 (164)
                      -|--.+...|++.+|...|+.|.  .|....+..+|+.
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie~  269 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIER  269 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHHH
Confidence            66678889999999999999987  3344455555543

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=94.42  E-value=1.1  Score=35.94  Aligned_cols=70  Identities=19%  Similarity=0.114  Sum_probs=55.9

Q ss_pred             hHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 031208            3 KIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus         3 ~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      ++....+..+..+|..+.-+...+|+++.+.+.|++...   .-...|+.+-..+...|.-..|+.+.++-..
T Consensus       313 k~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~  385 (799)
T KOG4162|consen  313 KLRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLK  385 (799)
T ss_pred             HHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcc
Confidence            344455678999999999999999999999999998763   3446788888888888888888888887643

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

Probab=94.36  E-value=0.39  Score=28.44  Aligned_cols=61  Identities=7%  Similarity=-0.006  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           62 QALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        62 ~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      +..+-++.+-...+.|++....+.+++|.+.+++..|.++++-++..- .+....|..+++-
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lqE   88 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQE   88 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHHH
Confidence            566667777777888888888888888888888888888888776332 2333377766653

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 ....

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=94.24  E-value=0.96  Score=34.21  Aligned_cols=130  Identities=12%  Similarity=0.077  Sum_probs=87.4

Q ss_pred             hccCCcHHHHHHHhccCC---Cc------HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH--Hhc
Q 031208           24 SFYGKTDHALLVFSQIRC---PH------VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC--IAS   92 (164)
Q Consensus        24 ~~~~~~~~a~~~~~~~~~---~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~--~~~   92 (164)
                      .+.+++++|.++|.+..+   .+      .+.-+.++++|.... .+.....+.+..+.  .| ...|-.++.+.  .+.
T Consensus        17 qkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~n-ld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~Y~~   92 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNN-LDLMEKQLMELRQQ--FG-KSAYLPLFKALVAYKQ   92 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhh-HHHHHHHHHHHHHh--cC-CchHHHHHHHHHHHHh
Confidence            368899999999998762   12      244577888876654 56665666666443  24 34566666655  456


Q ss_pred             cchhhHHHHHHHHHHh--CCC------------CchHHHHHHHHHHHhcCCchhHHHHhcccCC--------CCcchHHH
Q 031208           93 LAIEKGKEVHGLAVKA--GFS------------RDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--------RSVVSWTT  150 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~--g~~------------~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--------~~~~~~~~  150 (164)
                      +.+++|.+.+..-..+  +..            +|-..-++..++....|++.++..++++|.+        -|+.+|+.
T Consensus        93 k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~  172 (549)
T PF07079_consen   93 KEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDR  172 (549)
T ss_pred             hhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHH
Confidence            7788888777765544  322            2334445677888899999999999988862        27788888


Q ss_pred             HHHHHHh
Q 031208          151 MISGLAA  157 (164)
Q Consensus       151 li~~~~~  157 (164)
                      ++-.+++
T Consensus       173 ~vlmlsr  179 (549)
T PF07079_consen  173 AVLMLSR  179 (549)
T ss_pred             HHHHHhH
Confidence            6666554

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.21  E-value=1.4  Score=33.43  Aligned_cols=112  Identities=14%  Similarity=0.067  Sum_probs=65.5

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC---------------------CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR---------------------CPHVFTWNLMIRALTIDGSSLQALLLYNLMICN   73 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~---------------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   73 (164)
                      -.++++..+-+.|.++.|..+..+-.                     ..+...|..|-....+.|+++-|.+.|.+..  
T Consensus       297 ~~~~i~~fL~~~G~~e~AL~~~~D~~~rFeLAl~lg~L~~A~~~a~~~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~--  374 (443)
T PF04053_consen  297 QGQSIARFLEKKGYPELALQFVTDPDHRFELALQLGNLDIALEIAKELDDPEKWKQLGDEALRQGNIELAEECYQKAK--  374 (443)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHSS-HHHHHHHHHHCT-HHHHHHHCCCCSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT--
T ss_pred             HHHHHHHHHHHCCCHHHHHhhcCChHHHhHHHHhcCCHHHHHHHHHhcCcHHHHHHHHHHHHHcCCHHHHHHHHHhhc--
Confidence            36666777777777777776654322                     1345567777777777777777766666543  


Q ss_pred             CCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           74 GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        74 ~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                             -|..|+--|.-.|+.+...++.+.....|      -++....++.-.|+.++..+++.+-.
T Consensus       375 -------d~~~L~lLy~~~g~~~~L~kl~~~a~~~~------~~n~af~~~~~lgd~~~cv~lL~~~~  429 (443)
T PF04053_consen  375 -------DFSGLLLLYSSTGDREKLSKLAKIAEERG------DINIAFQAALLLGDVEECVDLLIETG  429 (443)
T ss_dssp             --------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHHHHT-HHHHHHHHHHTT
T ss_pred             -------CccccHHHHHHhCCHHHHHHHHHHHHHcc------CHHHHHHHHHHcCCHHHHHHHHHHcC
Confidence                   34556666666666666666665555554      24555555666666666666665544

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

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

Probab=94.19  E-value=0.56  Score=33.19  Aligned_cols=75  Identities=13%  Similarity=0.126  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHH-----cCCCCCcccHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMIC-----NGFRPDKFTFPFV   85 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~t~~~l   85 (164)
                      .++..++..+...|+.+.+.+.++.+..   -|...|..+|.+|.+.|+...|...|+.+.+     .|+.|...+....
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            4566678888889999999999998763   3778999999999999999999999999865     5888888776666


Q ss_pred             HHH
Q 031208           86 IKA   88 (164)
Q Consensus        86 l~~   88 (164)
                      ...
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            655

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=94.10  E-value=1.8  Score=32.12  Aligned_cols=78  Identities=15%  Similarity=0.020  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCCC-cH------hHHHHHHHHHHh---cCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRCP-HV------FTWNLMIRALTI---DGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~------~~~~~li~~~~~---~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      .+...++-.|-...+++...++++.+..+ +.      ..--...-++.+   .|+.+.|.+++..+....-.++..||.
T Consensus       142 div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~g  221 (374)
T PF13281_consen  142 DIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLG  221 (374)
T ss_pred             hHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHH
Confidence            33445555688889999999999999853 11      111122334455   889999999999976666778888888


Q ss_pred             HHHHHHHh
Q 031208           84 FVIKACIA   91 (164)
Q Consensus        84 ~ll~~~~~   91 (164)
                      .+-+.|-.
T Consensus       222 L~GRIyKD  229 (374)
T PF13281_consen  222 LLGRIYKD  229 (374)
T ss_pred             HHHHHHHH
Confidence            88777733

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=93.97  E-value=0.93  Score=28.45  Aligned_cols=115  Identities=6%  Similarity=0.020  Sum_probs=67.3

Q ss_pred             cCCcHHHHHHHhccCC-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CC----------------CCCcccHHHHHH
Q 031208           26 YGKTDHALLVFSQIRC-PHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GF----------------RPDKFTFPFVIK   87 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~----------------~p~~~t~~~ll~   87 (164)
                      .|.+++..++..+... .+..-+|-+|.-....-+=+-.+++++.+-.. .+                ..+..-+...++
T Consensus        15 dG~V~qGveii~k~v~Ssni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n~~se~vD~ALd   94 (161)
T PF09205_consen   15 DGDVKQGVEIIEKTVNSSNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRNKLSEYVDLALD   94 (161)
T ss_dssp             TT-HHHHHHHHHHHHHHS-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT---HHHHHHHH
T ss_pred             hchHHHHHHHHHHHcCcCCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhcchHHHHHHHHH
Confidence            6777777787776653 44455555555555555555555555554221 11                112223455677


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +..+.|+-++..++..++.+++ ++++...-.+-.+|.+.|+..++.+++++.-
T Consensus        95 ~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~AC  147 (161)
T PF09205_consen   95 ILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEAC  147 (161)
T ss_dssp             HHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Confidence            7788888888888888887755 6777777888889999999999988887654

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

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

Probab=93.91  E-value=0.77  Score=34.38  Aligned_cols=43  Identities=14%  Similarity=0.095  Sum_probs=21.7

Q ss_pred             HHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHhcCC
Q 031208          118 STLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAASGD  160 (164)
Q Consensus       118 ~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~~g~  160 (164)
                      +.+...+.+.|...++..+++.-.  .+|...-+.|-+.+...+.
T Consensus       442 ~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne  486 (564)
T KOG1174|consen  442 NLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNE  486 (564)
T ss_pred             HHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhh
Confidence            344445555666666666665433  3455544544444444433

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=93.89  E-value=0.94  Score=28.23  Aligned_cols=89  Identities=7%  Similarity=-0.062  Sum_probs=62.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      .....++..+...+.+.....+++.+...+ ..+...++.++..|++.... .....+..      ..+.+-...++..|
T Consensus         8 ~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~~-~ll~~l~~------~~~~yd~~~~~~~c   79 (140)
T smart00299        8 IDVSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDPQ-KEIERLDN------KSNHYDIEKVGKLC   79 (140)
T ss_pred             CCHHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCHH-HHHHHHHh------ccccCCHHHHHHHH
Confidence            345567888888899999999999998776 36777889999999887433 33333331      12334445567777


Q ss_pred             HhcCCchhHHHHhcccC
Q 031208          125 LKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       125 ~~~~~~~~a~~~~~~m~  141 (164)
                      .+.+.++.+..++..+.
T Consensus        80 ~~~~l~~~~~~l~~k~~   96 (140)
T smart00299       80 EKAKLYEEAVELYKKDG   96 (140)
T ss_pred             HHcCcHHHHHHHHHhhc
Confidence            77777777777777665

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=93.82  E-value=1.3  Score=29.63  Aligned_cols=95  Identities=11%  Similarity=-0.014  Sum_probs=41.1

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC----CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC---CCCCcccHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC----PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG---FRPDKFTFP   83 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~t~~   83 (164)
                      |+...--.|-.+....|+..+|...|++...    .|....-.+-++....+++..|...++++-+..   ..||.  --
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~--~L  164 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDG--HL  164 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCc--hH
Confidence            3333333444444445555555555444331    333333334444444445555555554443322   12222  22


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHH
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~  107 (164)
                      .+-+.+...|+..+|+.-|+....
T Consensus       165 l~aR~laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         165 LFARTLAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHH
Confidence            334444445555555555554443

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=93.78  E-value=0.64  Score=27.28  Aligned_cols=60  Identities=3%  Similarity=-0.031  Sum_probs=47.3

Q ss_pred             chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC---CcchHHHHHH
Q 031208           94 AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR---SVVSWTTMIS  153 (164)
Q Consensus        94 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~  153 (164)
                      +.-++.+-+..+....+.|++.+..+.+++|.|.+++..|.++|+.++.+   +...|..+++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHHH
Confidence            34456666667777788999999999999999999999999999977622   3446777665

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.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=93.68  E-value=1.1  Score=28.41  Aligned_cols=115  Identities=10%  Similarity=-0.011  Sum_probs=81.1

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcH--hHHHHHHHHHHhcCChhHHHHHHHHHHHcC---C--CCCccc
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHV--FTWNLMIRALTIDGSSLQALLLYNLMICNG---F--RPDKFT   81 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~--~p~~~t   81 (164)
                      +.++..+|...+.-...        .+-+.--.++.  ...|+++...+..+.....+.+++.+..-.   +  ..+..+
T Consensus        10 ~~~nL~~w~~fi~~~~~--------y~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ss   81 (145)
T PF13762_consen   10 VLANLEVWKTFINSHLP--------YMQEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSS   81 (145)
T ss_pred             hhhhHHHHHHHHHHHHH--------HhhhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccch
Confidence            44677778777763311        11111112222  346888888888889998888888873311   1  245679


Q ss_pred             HHHHHHHHHhccc-hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           82 FPFVIKACIASLA-IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        82 ~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      |.+++++...... .-.+..+|..+++.+.++++.-|..+|.++.+....+
T Consensus        82 f~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g~~~~  132 (145)
T PF13762_consen   82 FHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRGYFHD  132 (145)
T ss_pred             HHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCCc
Confidence            9999999988877 5678899999999889999999999999887764433

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

Probab=93.65  E-value=1.8  Score=30.67  Aligned_cols=132  Identities=10%  Similarity=0.053  Sum_probs=75.7

Q ss_pred             HHHHHHHHHhcc-CCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-----c
Q 031208           15 LVRKLLDLCSFY-GKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-----K   79 (164)
Q Consensus        15 ~~~~li~~~~~~-~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-----~   79 (164)
                      .+..+-..|-.. |+++.|.+.|++...     .+    ...+..+...+.+.|++++|.++|++........+     .
T Consensus       116 ~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~  195 (282)
T PF14938_consen  116 CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSA  195 (282)
T ss_dssp             HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhH
Confidence            334444455555 666666666665441     11    23456677788999999999999999976533222     2


Q ss_pred             c-cHHHHHHHHHhccchhhHHHHHHHHHHh--CCCCc--hHHHHHHHHHHHh--cCCchhHHHHhcccCCCCcc
Q 031208           80 F-TFPFVIKACIASLAIEKGKEVHGLAVKA--GFSRD--MFVQSTLMDLYLK--CGDVDGGRKMFDKMRVRSVV  146 (164)
Q Consensus        80 ~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~~~--~~~~~~ll~~~~~--~~~~~~a~~~~~~m~~~~~~  146 (164)
                      . .|-..+-++...||...|...++.....  ++..+  -.....||.+|-.  ...++.+..-|+.+.+-|..
T Consensus       196 ~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~ld~w  269 (282)
T PF14938_consen  196 KEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRLDNW  269 (282)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS---HH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCccHHH
Confidence            1 2223334566778999999999987643  33333  3455566666643  23456666777777765543

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

Probab=93.52  E-value=1.3  Score=37.04  Aligned_cols=85  Identities=16%  Similarity=0.094  Sum_probs=64.0

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      |+..|.-+++...+.|.+++-.+++.-.+    +|.+  =+.||-+|++.++..+..+++       ..||....-.+=+
T Consensus      1132 Dps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~i--d~eLi~AyAkt~rl~elE~fi-------~gpN~A~i~~vGd 1202 (1666)
T KOG0985|consen 1132 DPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYI--DSELIFAYAKTNRLTELEEFI-------AGPNVANIQQVGD 1202 (1666)
T ss_pred             CcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccc--hHHHHHHHHHhchHHHHHHHh-------cCCCchhHHHHhH
Confidence            56778999999999999999888876433    4444  356899999999987765554       3477777777777


Q ss_pred             HHHhccchhhHHHHHHHH
Q 031208           88 ACIASLAIEKGKEVHGLA  105 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m  105 (164)
                      -|...+.++.|.-++...
T Consensus      1203 rcf~~~~y~aAkl~y~~v 1220 (1666)
T KOG0985|consen 1203 RCFEEKMYEAAKLLYSNV 1220 (1666)
T ss_pred             HHhhhhhhHHHHHHHHHh
Confidence            888888887777666543

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

Probab=93.43  E-value=0.24  Score=29.34  Aligned_cols=58  Identities=2%  Similarity=0.011  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC---CcchHHHHHHH
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR---SVVSWTTMISG  154 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~  154 (164)
                      +..+-+..+....+.|++.+..+.+.+|.|.+++..|.++|+.++.+   ....|..+++-
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~lqE   88 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYILQE   88 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHHHH
Confidence            44555555556678899999999999999999999999999988722   22277777653

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 ....

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.36  E-value=1.6  Score=33.46  Aligned_cols=126  Identities=10%  Similarity=0.038  Sum_probs=81.9

Q ss_pred             HHHHHHHHHhc----cCCcHHHHHHHhccCC--CcHhHHHHHHHH-HHhcCChhHHHHHHHHHHH--cCCCC-CcccHHH
Q 031208           15 LVRKLLDLCSF----YGKTDHALLVFSQIRC--PHVFTWNLMIRA-LTIDGSSLQALLLYNLMIC--NGFRP-DKFTFPF   84 (164)
Q Consensus        15 ~~~~li~~~~~----~~~~~~a~~~~~~~~~--~~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~--~~~~p-~~~t~~~   84 (164)
                      +|+.++..++.    ....+.|.++++.+.+  |+...|...-.- +...|++++|.+.|++...  ...+. ....+--
T Consensus       231 ~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~E  310 (468)
T PF10300_consen  231 WYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRYPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFE  310 (468)
T ss_pred             HHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHH
Confidence            44555554443    3467788899988875  888877555443 3667899999999997643  11111 2233444


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH-HHHhcCCc-------hhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD-LYLKCGDV-------DGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~-~~~~~~~~-------~~a~~~~~~m~  141 (164)
                      +...+.-..++++|...+..+.+..- =+..+|.-+.. ++...++.       ++|.++|.+++
T Consensus       311 l~w~~~~~~~w~~A~~~f~~L~~~s~-WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  311 LAWCHMFQHDWEEAAEYFLRLLKESK-WSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHHHHchHHHHHHHHHHHHhccc-cHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            55667778899999999999987542 23344444433 34456777       88888888776

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

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

Probab=93.34  E-value=3.1  Score=32.56  Aligned_cols=142  Identities=13%  Similarity=0.122  Sum_probs=89.4

Q ss_pred             HHHHHHHHHhccC--CcHHHHHHHhccCC--C--cHhHHHHHHHHHHhcCChhHHHHHHH--------HHHHcCCCCCcc
Q 031208           15 LVRKLLDLCSFYG--KTDHALLVFSQIRC--P--HVFTWNLMIRALTIDGSSLQALLLYN--------LMICNGFRPDKF   80 (164)
Q Consensus        15 ~~~~li~~~~~~~--~~~~a~~~~~~~~~--~--~~~~~~~li~~~~~~~~~~~a~~~~~--------~m~~~~~~p~~~   80 (164)
                      .+.+++..+.+..  ....|.+++...-+  |  ..++-=.++......|+++.|.+++.        .+...+..|-.+
T Consensus       341 ~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V  420 (652)
T KOG2376|consen  341 LFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTV  420 (652)
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHH
Confidence            4555555544422  35556666665542  3  23444556667788899999999988        555555555554


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHh------CCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHH
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKA------GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTM  151 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~l  151 (164)
                        ..+...+.+.++.+.|.+++.+...-      +-.--..++.-+...=.+.|.-++|.++++++.+   +|..+...+
T Consensus       421 --~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d~~~l~~l  498 (652)
T KOG2376|consen  421 --GAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFNPNDTDLLVQL  498 (652)
T ss_pred             --HHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCchHHHHHHH
Confidence              55666777777776677776655431      1111223444444555677999999999998873   467778888


Q ss_pred             HHHHHhc
Q 031208          152 ISGLAAS  158 (164)
Q Consensus       152 i~~~~~~  158 (164)
                      +.+|++.
T Consensus       499 V~a~~~~  505 (652)
T KOG2376|consen  499 VTAYARL  505 (652)
T ss_pred             HHHHHhc
Confidence            8888764

>PRK15331 chaperone protein SicA; Provisional

Probab=93.26  E-value=1  Score=29.23  Aligned_cols=84  Identities=11%  Similarity=0.013  Sum_probs=43.9

Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCcccH-HHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhH
Q 031208           55 TIDGSSLQALLLYNLMICNGFRPDKFTF-PFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        55 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      -..|++++|..+|+-+...+  |...-| ..|-.++-..+.+++|...+...-..+. -|+...-..-.+|...|+.+.|
T Consensus        48 y~~Gk~~eA~~~F~~L~~~d--~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCIYD--FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHCCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHH
Confidence            44566666666666665432  222222 2333333444566666666665544332 2333344445566666666666


Q ss_pred             HHHhcccC
Q 031208          134 RKMFDKMR  141 (164)
Q Consensus       134 ~~~~~~m~  141 (164)
                      ...|+...
T Consensus       125 ~~~f~~a~  132 (165)
T PRK15331        125 RQCFELVN  132 (165)
T ss_pred             HHHHHHHH
Confidence            66666544

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.20  E-value=0.79  Score=32.90  Aligned_cols=53  Identities=19%  Similarity=0.177  Sum_probs=41.0

Q ss_pred             HhccCCcHHHHHHHhccCC----CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC
Q 031208           23 CSFYGKTDHALLVFSQIRC----PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFR   76 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   76 (164)
                      ..+.|+.+.|..-|+...+    .....||..+..| +.++.+.|++...++.+.|++
T Consensus       154 lykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r  210 (459)
T KOG4340|consen  154 LYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIR  210 (459)
T ss_pred             eeccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhh
Confidence            3468899999988887653    4567888888554 567899999999999887653

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=93.18  E-value=1.4  Score=31.13  Aligned_cols=90  Identities=14%  Similarity=0.055  Sum_probs=64.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH--cCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMIC--NGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      +..=|.+++..++|.+++...-+--+  ..++|.+.  ..-|--|.+.+.+..+.++-+.-...--.-+...|..+...|
T Consensus        86 cvvGIQALAEmnrWreVLsWvlqyYq~pEklPpkIl--eLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELy  163 (309)
T PF07163_consen   86 CVVGIQALAEMNRWREVLSWVLQYYQVPEKLPPKIL--ELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELY  163 (309)
T ss_pred             hhhhHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHH--HHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHH
Confidence            45569999999999999997666533  34555554  444556889999999998888776643233344578777777


Q ss_pred             Hh-----cCCchhHHHHhc
Q 031208          125 LK-----CGDVDGGRKMFD  138 (164)
Q Consensus       125 ~~-----~~~~~~a~~~~~  138 (164)
                      ..     .|.+++|.++..
T Consensus       164 Ll~VLlPLG~~~eAeelv~  182 (309)
T PF07163_consen  164 LLHVLLPLGHFSEAEELVV  182 (309)
T ss_pred             HHHHHhccccHHHHHHHHh
Confidence            65     499999988874

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>PLN02789 farnesyltranstransferase

Probab=93.12  E-value=2.5  Score=30.71  Aligned_cols=141  Identities=9%  Similarity=-0.026  Sum_probs=80.9

Q ss_pred             HHHHHHHHHhccC-CcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCCh--hHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           15 LVRKLLDLCSFYG-KTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSS--LQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        15 ~~~~li~~~~~~~-~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~--~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +|+.--..+.+.| +++++...++.+.+  | +..+|+..-..+.+.|+.  ++++++++++.+.. +-|-..|+..-..
T Consensus        73 aW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~  151 (320)
T PLN02789         73 VWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWV  151 (320)
T ss_pred             HHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            4444334444555 56777777776542  2 344566544444455542  56777777776543 2355677777777


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc---CCc----hhHHHHhcccC--CC-CcchHHHHHHHHHh
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC---GDV----DGGRKMFDKMR--VR-SVVSWTTMISGLAA  157 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~---~~~----~~a~~~~~~m~--~~-~~~~~~~li~~~~~  157 (164)
                      +.+.|+++++.+.++++.+.+. -+...|+.....+.+.   |..    +...+...+..  .| |...|+.+-..+..
T Consensus       152 l~~l~~~~eeL~~~~~~I~~d~-~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~  229 (320)
T PLN02789        152 LRTLGGWEDELEYCHQLLEEDV-RNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKD  229 (320)
T ss_pred             HHHhhhHHHHHHHHHHHHHHCC-CchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhc
Confidence            7777888888888888877663 3445555554444433   222    23444443322  33 66677766666655

>PRK15331 chaperone protein SicA; Provisional

Probab=93.11  E-value=1.3  Score=28.77  Aligned_cols=85  Identities=13%  Similarity=-0.048  Sum_probs=61.5

Q ss_pred             HhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHH
Q 031208           23 CSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      +...|++++|..+|..+.  .| |..-|--|-.++-..+++++|...|...-..+. -|...+=..-.++...|+.+.|.
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A~  125 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKAR  125 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHHH
Confidence            446899999999999876  33 434444555556667899999999998754331 22222334667888999999999


Q ss_pred             HHHHHHHHh
Q 031208          100 EVHGLAVKA  108 (164)
Q Consensus       100 ~~~~~m~~~  108 (164)
                      ..|+.....
T Consensus       126 ~~f~~a~~~  134 (165)
T PRK15331        126 QCFELVNER  134 (165)
T ss_pred             HHHHHHHhC
Confidence            999988773

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=93.10  E-value=1.4  Score=27.94  Aligned_cols=93  Identities=14%  Similarity=0.270  Sum_probs=69.5

Q ss_pred             HhhhcCCCCH--HHHHHHHHHHhccCCcHHHHHHHhccC---------CCcHhHHHHHHHHHHhcCC-hhHHHHHHHHHH
Q 031208            4 IIRYGLSNDQ--LLVRKLLDLCSFYGKTDHALLVFSQIR---------CPHVFTWNLMIRALTIDGS-SLQALLLYNLMI   71 (164)
Q Consensus         4 m~~~g~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~~~---------~~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~   71 (164)
                      |.+.+..++.  ...|.++.-.+..+.+.-...+++.+.         ..+..+|++++.+.+...- --.+..+|+-|+
T Consensus        28 ~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk  107 (145)
T PF13762_consen   28 MQEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLK  107 (145)
T ss_pred             hhhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHH
Confidence            4555666664  345677777777788888887777765         2455679999999977776 456778888898


Q ss_pred             HcCCCCCcccHHHHHHHHHhccchh
Q 031208           72 CNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        72 ~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      +.+.+++...|..+|+++.+-...+
T Consensus       108 ~~~~~~t~~dy~~li~~~l~g~~~~  132 (145)
T PF13762_consen  108 KNDIEFTPSDYSCLIKAALRGYFHD  132 (145)
T ss_pred             HcCCCCCHHHHHHHHHHHHcCCCCc
Confidence            8888999999999999988764333

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=92.84  E-value=1.6  Score=27.67  Aligned_cols=76  Identities=11%  Similarity=0.034  Sum_probs=53.3

Q ss_pred             HHHHhccCCcHHHHHHHhccCC--C----cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC--P----HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL   93 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~--~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~   93 (164)
                      -....+.|+++.|.+.|+.+..  |    ....-=.|+.+|.+.+++++|...+++..+..-.....-|...+.+++...
T Consensus        17 a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~~   96 (142)
T PF13512_consen   17 AQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYYE   96 (142)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHH
Confidence            3445567888999988888763  1    223444578888899999999999999877654444467777777776655


Q ss_pred             ch
Q 031208           94 AI   95 (164)
Q Consensus        94 ~~   95 (164)
                      ..
T Consensus        97 ~~   98 (142)
T PF13512_consen   97 QD   98 (142)
T ss_pred             Hh
Confidence            43

>PRK04841 transcriptional regulator MalT; Provisional

Probab=92.81  E-value=4.3  Score=33.64  Aligned_cols=149  Identities=10%  Similarity=0.018  Sum_probs=87.7

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC-------C----cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc--CCCCC--c
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC-------P----HVFTWNLMIRALTIDGSSLQALLLYNLMICN--GFRPD--K   79 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~--~   79 (164)
                      +...+-..+...|+++.|...+++...       +    ....+..+-..+...|++++|...+.+....  ...+.  .
T Consensus       533 ~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~  612 (903)
T PRK04841        533 SLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQL  612 (903)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHH
Confidence            334445567788999999888776431       1    1223334444566679999999998887442  11122  2


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCCC-CchHHH-----HHHHHHHHhcCCchhHHHHhcccCCCCc---c----
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGFS-RDMFVQ-----STLMDLYLKCGDVDGGRKMFDKMRVRSV---V----  146 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~-----~~ll~~~~~~~~~~~a~~~~~~m~~~~~---~----  146 (164)
                      ..+..+.......|+.+.|...+++.....-. .....+     ...+..+...|+.+.|.+++.....+..   .    
T Consensus       613 ~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~  692 (903)
T PRK04841        613 QCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQG  692 (903)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHH
Confidence            33444556777889999999988887543111 111111     1123445567888999888866553321   1    


Q ss_pred             hHHHHHHHHHhcCCCCC
Q 031208          147 SWTTMISGLAASGDLDA  163 (164)
Q Consensus       147 ~~~~li~~~~~~g~~~~  163 (164)
                      .+..+..++...|+.++
T Consensus       693 ~~~~~a~~~~~~g~~~~  709 (903)
T PRK04841        693 QWRNIARAQILLGQFDE  709 (903)
T ss_pred             HHHHHHHHHHHcCCHHH
Confidence            13345556667776554

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=92.71  E-value=2.1  Score=31.74  Aligned_cols=117  Identities=13%  Similarity=-0.013  Sum_probs=77.7

Q ss_pred             HHhccCCcHHHHHHHhccC------------------CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208           22 LCSFYGKTDHALLVFSQIR------------------CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~------------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      .+.+.|++..|..-|++..                  ..-...+..+..++.+.+++..|+..-++....+ ++|.-..=
T Consensus       217 ~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALy  295 (397)
T KOG0543|consen  217 VLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALY  295 (397)
T ss_pred             HHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHH
Confidence            5677888888887776632                  0223456777778899999999999999987643 33433222


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHH-HHHHHHhcCCchhH-HHHhcccC
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQST-LMDLYLKCGDVDGG-RKMFDKMR  141 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~-ll~~~~~~~~~~~a-~~~~~~m~  141 (164)
                      ---.++...|+++.|...|+.+++.  .|+...... |+.+--+..+.... .++|..|-
T Consensus       296 RrG~A~l~~~e~~~A~~df~ka~k~--~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF  353 (397)
T KOG0543|consen  296 RRGQALLALGEYDLARDDFQKALKL--EPSNKAARAELIKLKQKIREYEEKEKKMYANMF  353 (397)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3347888889999999999999876  565544444 44444444444333 56666653

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

Probab=92.67  E-value=0.16  Score=23.68  Aligned_cols=24  Identities=17%  Similarity=0.387  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHhcc
Q 031208          116 VQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus       116 ~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      +|+.|-..|.+.|++++|.++|++
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHH
Confidence            356677788888888888888776

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

Probab=92.49  E-value=0.51  Score=21.90  Aligned_cols=22  Identities=23%  Similarity=0.232  Sum_probs=10.0

Q ss_pred             HHHHHHHHhcCChhHHHHHHHH
Q 031208           48 NLMIRALTIDGSSLQALLLYNL   69 (164)
Q Consensus        48 ~~li~~~~~~~~~~~a~~~~~~   69 (164)
                      +.|-..|.+.|++++|.++|++
T Consensus         3 ~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    3 NNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHH
Confidence            3444444445555555554444

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

Probab=92.31  E-value=1.4  Score=31.46  Aligned_cols=97  Identities=11%  Similarity=-0.020  Sum_probs=68.4

Q ss_pred             HhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhH
Q 031208           23 CSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKG   98 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a   98 (164)
                      .++.+++++|...|.+..+   .|.+-|.---.+|++.|.++.|++=...-.+.  .|. ..+|..|=.+|...|++++|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHHHH
Confidence            4456778888888887652   46667777788888888888888776666553  343 34788888888888888888


Q ss_pred             HHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           99 KEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        99 ~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      .+.|+..+.  +.|+-.+|-.=|+.
T Consensus       169 ~~aykKaLe--ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  169 IEAYKKALE--LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHhhhc--cCCCcHHHHHHHHH
Confidence            888776553  45666566555443

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

Probab=92.29  E-value=2.8  Score=31.96  Aligned_cols=125  Identities=14%  Similarity=0.157  Sum_probs=92.1

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFVI   86 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll   86 (164)
                      ..+|+..|+..-+...++.|+.+|.+..+     +++..++++|.-++ .|+...|..+|.-=...  -||.. --+-.+
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHH
Confidence            45788889999999999999999998873     77888999887655 57788888888763322  24443 335567


Q ss_pred             HHHHhccchhhHHHHHHHHHHhCCCCc--hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           87 KACIASLAIEKGKEVHGLAVKAGFSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .-+...++-+.|..+|+.-..+- ..+  ..+|..+|+.=+..|++..+..+=+.|.
T Consensus       474 ~fLi~inde~naraLFetsv~r~-~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~  529 (660)
T COG5107         474 LFLIRINDEENARALFETSVERL-EKTQLKRIYDKMIEYESMVGSLNNVYSLEERFR  529 (660)
T ss_pred             HHHHHhCcHHHHHHHHHHhHHHH-HHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHH
Confidence            78888999999999998443221 122  4689999999999999987765555443

>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=92.28  E-value=1.6  Score=28.66  Aligned_cols=94  Identities=14%  Similarity=0.054  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      ...+..+.+.|++.|+.+.|.+.|.++.+      .-...+=.+|......+++..+...+.+....--.+.......-+
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrl  115 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRL  115 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHH
Confidence            35677889999999999999999999874      223456778888889999999999988875432222212222222


Q ss_pred             HHH-----HhccchhhHHHHHHHHH
Q 031208           87 KAC-----IASLAIEKGKEVHGLAV  106 (164)
Q Consensus        87 ~~~-----~~~~~~~~a~~~~~~m~  106 (164)
                      +++     ...+++..|.+.|-+..
T Consensus       116 k~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  116 KVYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHHhchHHHHHHHHHccC
Confidence            222     34567887777776553

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=92.10  E-value=3.1  Score=34.39  Aligned_cols=126  Identities=13%  Similarity=0.191  Sum_probs=81.7

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC-------CcH--hHHHHHHHHHHhcCChhHHHHHHHHHHH----cCCC--C-Cc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC-------PHV--FTWNLMIRALTIDGSSLQALLLYNLMIC----NGFR--P-DK   79 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~-------~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~--p-~~   79 (164)
                      .+.+-..+...|+++.|...+.+...       +..  .+...+-..+...|++++|...+++...    .+..  | ..
T Consensus       494 ~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~  573 (903)
T PRK04841        494 TSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHE  573 (903)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHH
Confidence            34444566779999999988877641       222  2344455567889999999999888643    2221  1 12


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHh--CCCCc--hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKA--GFSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..+..+-..+...|++++|...+++....  ...+.  ...+..+...+...|+.+.|.+.+.+..
T Consensus       574 ~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~  639 (903)
T PRK04841        574 FLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLE  639 (903)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            23444555677789999999998877543  11122  3334445567778999999988887663

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.93  E-value=3.3  Score=29.34  Aligned_cols=121  Identities=9%  Similarity=0.015  Sum_probs=72.1

Q ss_pred             HHHHHhccCCcHHHHHHHhcc----CCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH-----HH
Q 031208           19 LLDLCSFYGKTDHALLVFSQI----RCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK-----AC   89 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~-----~~   89 (164)
                      ++..+.-.|.+.-....+++.    .+.+...-..|...-...|+.+.|-..|++.++..-+.|..+++.+..     .+
T Consensus       183 ~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~  262 (366)
T KOG2796|consen  183 MANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLH  262 (366)
T ss_pred             HHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhhe
Confidence            333333344443333333333    234566667777777788999999999998876666677777666653     22


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHH--HHHHHHHhcCCchhHHHHhcccCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQS--TLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~--~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      .-.+++..|...+.+..... .-|....|  +|+..|  .|+..+|.+..+.|.+
T Consensus       263 lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllY--lg~l~DAiK~~e~~~~  314 (366)
T KOG2796|consen  263 LGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLY--LGKLKDALKQLEAMVQ  314 (366)
T ss_pred             ecccchHHHHHHHhhccccC-CCchhhhchHHHHHHH--HHHHHHHHHHHHHHhc
Confidence            33456666666666666543 12222223  344444  4778888888888874

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.51  E-value=3.1  Score=29.23  Aligned_cols=93  Identities=14%  Similarity=0.093  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh-CCCCc-hHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNG----FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA-GFSRD-MFVQST  119 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~-~~~~~~  119 (164)
                      .|+.-+.. .+.|++.+|...|....+..    ..||..  =.|-.++...|++++|..+|..+.+. +-.|. +...--
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~--yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallK  220 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAY--YWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLK  220 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhH--HHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHH
Confidence            44444432 34455555555555554431    222222  22455555555555555555555432 11111 233333


Q ss_pred             HHHHHHhcCCchhHHHHhcccC
Q 031208          120 LMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       120 ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |-....+.|+.++|...|+++.
T Consensus       221 lg~~~~~l~~~d~A~atl~qv~  242 (262)
T COG1729         221 LGVSLGRLGNTDEACATLQQVI  242 (262)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHH
Confidence            4444455555555555555544

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=91.50  E-value=3.8  Score=29.20  Aligned_cols=132  Identities=13%  Similarity=0.093  Sum_probs=84.8

Q ss_pred             cCCCCHHHHHHHHHHHhc----------------cCCcHHHHHHHhccC-----CCcHhHHHHHHHHHHhcC--ChhHHH
Q 031208            8 GLSNDQLLVRKLLDLCSF----------------YGKTDHALLVFSQIR-----CPHVFTWNLMIRALTIDG--SSLQAL   64 (164)
Q Consensus         8 g~~~~~~~~~~li~~~~~----------------~~~~~~a~~~~~~~~-----~~~~~~~~~li~~~~~~~--~~~~a~   64 (164)
                      |.+++..-+-.+++.+..                ...+.+|.++|+...     -.|..+-..++.......  ....-.
T Consensus       107 g~~Lt~~Dli~FL~~~i~~~~~~k~~~Y~~LVk~N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alY  186 (292)
T PF13929_consen  107 GCELTKEDLISFLKLVIINLSSNKSFNYWDLVKRNKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALY  186 (292)
T ss_pred             CCCCcHHHHHHHHHHHHhccccccchHHHHHHHhhHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHH
Confidence            666665555555555332                112445566666322     135556666666665522  233333


Q ss_pred             HHHHHHH-HcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh-CCCCchHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           65 LLYNLMI-CNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA-GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        65 ~~~~~m~-~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      ++.+-+. ..|-.++..+...+|..++..++...-.++++..... +..-|...|..+|+.....|+..-...+.++
T Consensus       187 EvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  187 EVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            3444443 2345677778888999999999999988888877655 5566888899999999999998877777764

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.25  E-value=1.1  Score=35.79  Aligned_cols=104  Identities=16%  Similarity=0.130  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL  125 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  125 (164)
                      +.+--+.-+...|+...|.++-.+.+    .||..-|..-+.+++..+++++.+++-+.++      ++.-|...+..|.
T Consensus       686 Sl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c~  755 (829)
T KOG2280|consen  686 SLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEACL  755 (829)
T ss_pred             cHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHHH
Confidence            44555666777888888877666653    5888899999999999999887776665532      2567788899999


Q ss_pred             hcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCCCCC
Q 031208          126 KCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +.|+.++|.+++.....-.     -.+.+|.+.|++.+|
T Consensus       756 ~~~n~~EA~KYiprv~~l~-----ekv~ay~~~~~~~eA  789 (829)
T KOG2280|consen  756 KQGNKDEAKKYIPRVGGLQ-----EKVKAYLRVGDVKEA  789 (829)
T ss_pred             hcccHHHHhhhhhccCChH-----HHHHHHHHhccHHHH
Confidence            9999999999998876321     456667776666543

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=91.13  E-value=7.1  Score=31.64  Aligned_cols=123  Identities=15%  Similarity=0.108  Sum_probs=89.3

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCC---cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHHHHHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCP---HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPFVIKACI   90 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~   90 (164)
                      .|...-+.+.+.+..+.|...+.+..+-   ....|...=..+-..|...+|.+.|..-..  +.|+. .+-+++-..+.
T Consensus       652 lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~--ldP~hv~s~~Ala~~ll  729 (799)
T KOG4162|consen  652 LWLLAADLFLLSGNDDEARSCLLEASKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALA--LDPDHVPSMTALAELLL  729 (799)
T ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHh--cCCCCcHHHHHHHHHHH
Confidence            4555566777788888887666655532   223344333445566788888888877765  45654 47788889999


Q ss_pred             hccchhhHHH--HHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           91 ASLAIEKGKE--VHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        91 ~~~~~~~a~~--~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      +.|+...+..  +...+.+.+ +.+...|-.+-..+-+.|+.+.|.+.|...
T Consensus       730 e~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa  780 (799)
T KOG4162|consen  730 ELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLGEVFKKLGDSKQAAECFQAA  780 (799)
T ss_pred             HhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHccchHHHHHHHHHH
Confidence            9998887777  888888877 466788888889999999999999998754

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

Probab=90.81  E-value=5.6  Score=31.61  Aligned_cols=97  Identities=13%  Similarity=0.222  Sum_probs=77.2

Q ss_pred             CcHhHHH--HHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           42 PHVFTWN--LMIRALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        42 ~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      |....|+  .+...+=+.|+++.|...++.....  +|+.+ -|..=.+.+...|++++|..++++.++.. .+|..+-+
T Consensus       367 PttllWt~y~laqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INs  443 (700)
T KOG1156|consen  367 PTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINS  443 (700)
T ss_pred             chHHHHHHHHHHHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHH
Confidence            4455554  4677788899999999999988764  46543 44445589999999999999999998777 58888877


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .-.....+.++.++|.++.....
T Consensus       444 KcAKYmLrAn~i~eA~~~~skFT  466 (700)
T KOG1156|consen  444 KCAKYMLRANEIEEAEEVLSKFT  466 (700)
T ss_pred             HHHHHHHHccccHHHHHHHHHhh
Confidence            88888899999999998887665

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=90.54  E-value=3.3  Score=26.78  Aligned_cols=114  Identities=16%  Similarity=0.162  Sum_probs=68.3

Q ss_pred             HHHHHHHHHH---hccCCcHHHHHHHhccC--CCcH---hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           14 LLVRKLLDLC---SFYGKTDHALLVFSQIR--CPHV---FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        14 ~~~~~li~~~---~~~~~~~~a~~~~~~~~--~~~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      .+.+.||...   .+.++.+.+..++.-+.  .|..   .++..+  .+...|+|.+|..+|+++....  |.......|
T Consensus         8 ~iv~gLie~~~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~--l~i~r~~w~dA~rlLr~l~~~~--~~~p~~kAL   83 (160)
T PF09613_consen    8 EIVGGLIEVLSVALRLGDPDDAEALLDALRVLRPEFPELDLFDGW--LHIVRGDWDDALRLLRELEERA--PGFPYAKAL   83 (160)
T ss_pred             HHHHHHHHHHHHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHH--HHHHhCCHHHHHHHHHHHhccC--CCChHHHHH
Confidence            3445555543   45789999999999876  4544   334333  3578899999999999987653  444333444


Q ss_pred             HHHHHhccchhhHHHHH-HHHHHhCCCCchHHHHHHHHHHHhcCCchhHHH
Q 031208           86 IKACIASLAIEKGKEVH-GLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRK  135 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~-~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~  135 (164)
                      +..|. ...-+..++.+ +++...+-.|+.   ..|++.+....+...|..
T Consensus        84 lA~CL-~~~~D~~Wr~~A~evle~~~d~~a---~~Lv~~Ll~~~~~~~a~~  130 (160)
T PF09613_consen   84 LALCL-YALGDPSWRRYADEVLESGADPDA---RALVRALLARADLEPAHE  130 (160)
T ss_pred             HHHHH-HHcCChHHHHHHHHHHhcCCChHH---HHHHHHHHHhccccchhh
Confidence            44444 43444444444 445555544443   455666666655555544

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

Probab=90.49  E-value=4.9  Score=28.67  Aligned_cols=110  Identities=11%  Similarity=-0.001  Sum_probs=79.8

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHH---HhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRAL---TIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~---~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      +-|...|--|=..|...|+.+.|..-|..-.   -+|...+..+-.++   +......++..+|++..... +-|+.+..
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral~  231 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRALS  231 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHHH
Confidence            3478889999999999999999999998765   24555544444443   33345779999999998753 23455666


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      .|-..+...|++.+|...|+.|.+..  |....+..+|.
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~l--p~~~~rr~~ie  268 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDLL--PADDPRRSLIE  268 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcC--CCCCchHHHHH
Confidence            67788999999999999999999875  33334444443

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.46  E-value=3.7  Score=27.20  Aligned_cols=120  Identities=13%  Similarity=0.103  Sum_probs=80.2

Q ss_pred             HhccCCcHHHHHHHhccCCCcHhHHHHH-----HHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHHHH--HHHhccc
Q 031208           23 CSFYGKTDHALLVFSQIRCPHVFTWNLM-----IRALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFVIK--ACIASLA   94 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~~~~~~~~~~l-----i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll~--~~~~~~~   94 (164)
                      .++.+..++|..-|..+.+.+--.|-.|     -......|+...|+.-|++.-...-.|-.. ...-|=.  .+...|.
T Consensus        68 lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gs  147 (221)
T COG4649          68 LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGS  147 (221)
T ss_pred             HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhcccc
Confidence            3456778888888888875443333332     233567899999999999997655445443 2222222  2355677


Q ss_pred             hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC
Q 031208           95 IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      +++...-++.+-..|-+.....-..|--+-.+.|++.+|.++|..+.+
T Consensus       148 y~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         148 YDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            887777777766555444555556676677789999999999998874

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.37  E-value=4.7  Score=28.33  Aligned_cols=91  Identities=15%  Similarity=0.135  Sum_probs=68.5

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC--------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCc-ccHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC--------PHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GFRPDK-FTFPF   84 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~--------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~-~t~~~   84 (164)
                      .|+.-++. .+.|++..|..-|....+        ||..-|  |-.++...|++++|-..|..+.+. +-.|.. .+.--
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW--LGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallK  220 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW--LGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLK  220 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHH--HHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHH
Confidence            57766654 456779999998887762        444444  888999999999999999999653 333332 45566


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHh
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      |-....+.|+.++|..+++++.+.
T Consensus       221 lg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         221 LGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHH
Confidence            677788889999999999999876

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=90.34  E-value=1.2  Score=21.56  Aligned_cols=23  Identities=22%  Similarity=0.140  Sum_probs=9.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHH
Q 031208           50 MIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      +-..|...|++++|.++|++..+
T Consensus         7 la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    7 LARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            33344444444444444444433

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=90.18  E-value=2  Score=34.20  Aligned_cols=36  Identities=22%  Similarity=0.384  Sum_probs=22.3

Q ss_pred             hhHhhhcCCCCHHHHHHHHHHHhccCCcHHHHHHHhccC
Q 031208            2 QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR   40 (164)
Q Consensus         2 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~   40 (164)
                      +++.++|-.|+.....   ..|+-.|.+.+|.++|.+.-
T Consensus       624 ~~~k~rge~P~~iLlA---~~~Ay~gKF~EAAklFk~~G  659 (1081)
T KOG1538|consen  624 EERKKRGETPNDLLLA---DVFAYQGKFHEAAKLFKRSG  659 (1081)
T ss_pred             HHHHhcCCCchHHHHH---HHHHhhhhHHHHHHHHHHcC
Confidence            4677788888876443   34555666666666666543

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=90.05  E-value=7.1  Score=29.83  Aligned_cols=84  Identities=12%  Similarity=0.075  Sum_probs=67.0

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      .++...|..|-+...+.|+++.|.+.|.+..     -|..|+-.|.-.|+.+...++-+.-...|      -++..+.++
T Consensus       344 ~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~-----d~~~L~lLy~~~g~~~~L~kl~~~a~~~~------~~n~af~~~  412 (443)
T PF04053_consen  344 LDDPEKWKQLGDEALRQGNIELAEECYQKAK-----DFSGLLLLYSSTGDREKLSKLAKIAEERG------DINIAFQAA  412 (443)
T ss_dssp             CSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHH
T ss_pred             cCcHHHHHHHHHHHHHcCCHHHHHHHHHhhc-----CccccHHHHHHhCCHHHHHHHHHHHHHcc------CHHHHHHHH
Confidence            3578899999999999999999999999988     46677778889999888877777777666      578888888


Q ss_pred             HhccchhhHHHHHHH
Q 031208           90 IASLAIEKGKEVHGL  104 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~  104 (164)
                      .-.|++++..+++.+
T Consensus       413 ~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  413 LLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHT-HHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHH
Confidence            888998877776654

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

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

Probab=90.00  E-value=4.1  Score=31.39  Aligned_cols=78  Identities=6%  Similarity=-0.068  Sum_probs=54.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcC-CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCC-chHHHHHHHHHHHhc
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNG-FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSR-DMFVQSTLMDLYLKC  127 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~  127 (164)
                      +-.++-+.|+.++|.+.|++|.+.. ..-+......|+.++...+.+.++..++..-.+...+. -..+|+..+-.+-..
T Consensus       265 LAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaRav  344 (539)
T PF04184_consen  265 LAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKARAV  344 (539)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHHhh
Confidence            4455567799999999999997543 11234467789999999999999999998875433322 245777666444333

The molecular function of this protein is uncertain.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=89.86  E-value=1.1  Score=22.09  Aligned_cols=24  Identities=17%  Similarity=0.228  Sum_probs=13.4

Q ss_pred             HHHHHHhccchhhHHHHHHHHHHh
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +.++|...|+.+.|..+++++...
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~   28 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEE   28 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHc
Confidence            345555555665565555555543

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.

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.69  E-value=8.7  Score=31.61  Aligned_cols=117  Identities=19%  Similarity=0.086  Sum_probs=79.3

Q ss_pred             HHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHH----HhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           17 RKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRAL----TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        17 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~----~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      ..-++...+...+..|..+-+.-. .|...-..++..|    -+.|++++|..-|-+-... +.|     ..+|+-|...
T Consensus       338 e~kL~iL~kK~ly~~Ai~LAk~~~-~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLda  410 (933)
T KOG2114|consen  338 ETKLDILFKKNLYKVAINLAKSQH-LDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDA  410 (933)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHhcC-CCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCH
Confidence            344556666666677776665443 3333333444444    4568899988877665432 223     3467777888


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .++...-.+++.+.+.|+ -+...-+.|+.+|.+.++.++..++.+.-.
T Consensus       411 q~IknLt~YLe~L~~~gl-a~~dhttlLLncYiKlkd~~kL~efI~~~~  458 (933)
T KOG2114|consen  411 QRIKNLTSYLEALHKKGL-ANSDHTTLLLNCYIKLKDVEKLTEFISKCD  458 (933)
T ss_pred             HHHHHHHHHHHHHHHccc-ccchhHHHHHHHHHHhcchHHHHHHHhcCC
Confidence            888888888888888886 455667888999999998888888777665

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

Probab=89.24  E-value=1.4  Score=20.60  Aligned_cols=25  Identities=24%  Similarity=0.185  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLM   70 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m   70 (164)
                      +++.|-..|...|++++|..++++.
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~a   28 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEA   28 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHH
Confidence            4455555556666666666665554

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=89.22  E-value=1.4  Score=21.34  Aligned_cols=28  Identities=7%  Similarity=-0.025  Sum_probs=23.9

Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +..+-..|...|++++|.++++...+..
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~   31 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALALD   31 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            4567788999999999999999998874

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

Probab=89.16  E-value=5.8  Score=30.69  Aligned_cols=100  Identities=14%  Similarity=0.026  Sum_probs=78.1

Q ss_pred             HHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHHHHHHHHhccchhh
Q 031208           22 LCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPFVIKACIASLAIEK   97 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~~~~~~   97 (164)
                      +.+..|+++.|...|..-.   .+|.+.|+--..+|+..|++++|++==.+-++  +.|+. --|+-.-.++.-.|++++
T Consensus        11 aa~s~~d~~~ai~~~t~ai~l~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~--l~p~w~kgy~r~Gaa~~~lg~~~e   88 (539)
T KOG0548|consen   11 AAFSSGDFETAIRLFTEAIMLSPTNHVLYSNRSAAYASLGSYEKALKDATKTRR--LNPDWAKGYSRKGAALFGLGDYEE   88 (539)
T ss_pred             hhcccccHHHHHHHHHHHHccCCCccchhcchHHHHHHHhhHHHHHHHHHHHHh--cCCchhhHHHHhHHHHHhcccHHH
Confidence            4567899999999998754   46888899999999999999999775444443  56754 467777888888899999


Q ss_pred             HHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           98 GKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        98 a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      |..-+.+-++.. +.+...++-+.+++
T Consensus        89 A~~ay~~GL~~d-~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   89 AILAYSEGLEKD-PSNKQLKTGLAQAY  114 (539)
T ss_pred             HHHHHHHHhhcC-CchHHHHHhHHHhh
Confidence            999999877664 34567778887777

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.77  E-value=2  Score=31.08  Aligned_cols=98  Identities=12%  Similarity=0.060  Sum_probs=73.8

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc---CCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICN---GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      ....+...++..-....+++++...+-+++..   -..|+... ..+++-|.+- +..++..+...-...|+=||..+++
T Consensus        62 ~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~-~~~irlllky-~pq~~i~~l~npIqYGiF~dqf~~c  139 (418)
T KOG4570|consen   62 VSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTI-HTWIRLLLKY-DPQKAIYTLVNPIQYGIFPDQFTFC  139 (418)
T ss_pred             cceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccH-HHHHHHHHcc-ChHHHHHHHhCcchhccccchhhHH
Confidence            35566777777777788899999988888643   23444432 3444444443 5667888888778899999999999


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+|+.+.+.+++.+|.++.-.|.
T Consensus       140 ~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  140 LLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHH
Confidence            99999999999999998877665

>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=88.74  E-value=4.3  Score=25.59  Aligned_cols=67  Identities=16%  Similarity=0.032  Sum_probs=49.1

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCC
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGF  110 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~  110 (164)
                      +..-+...+....+.|+-|+-.++++++... -.|++...-.+-.+|.+.|+..++.+++.+.-+.|+
T Consensus        85 ~se~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   85 LSEYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             --HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            3345677788889999999999999998653 356666677889999999999999999999998886

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

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

Probab=88.74  E-value=1.9  Score=21.60  Aligned_cols=33  Identities=15%  Similarity=0.067  Sum_probs=19.3

Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      .+.|-++++..++++|.+.|+-.+...+..++.
T Consensus        13 k~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen   13 KRRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HHcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            344555566666666666666666655555543

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

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

Probab=88.72  E-value=1.1  Score=20.93  Aligned_cols=28  Identities=18%  Similarity=0.032  Sum_probs=21.3

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHH
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~  107 (164)
                      .+++.+-..|...|++++|..++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            3667788888888888888888887754

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=88.60  E-value=13  Score=30.95  Aligned_cols=118  Identities=10%  Similarity=0.035  Sum_probs=63.3

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC-------------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC-------------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP   77 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   77 (164)
                      -+..+|.-|-..|.+.++++-|.-.+..|..             ++ .+=.-..-.....|..++|..+|++-++.    
T Consensus       755 kS~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~----  829 (1416)
T KOG3617|consen  755 KSDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRY----  829 (1416)
T ss_pred             hhhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHH----
Confidence            4566788888888888888877777777752             21 11111111224556677777777766543    


Q ss_pred             CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           78 DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        78 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                           ..+=+-|-..|.+++|.++-+.=-+-   .=..||....+.+-.+++.+.|++.|++-.
T Consensus       830 -----DLlNKlyQs~g~w~eA~eiAE~~DRi---HLr~Tyy~yA~~Lear~Di~~AleyyEK~~  885 (1416)
T KOG3617|consen  830 -----DLLNKLYQSQGMWSEAFEIAETKDRI---HLRNTYYNYAKYLEARRDIEAALEYYEKAG  885 (1416)
T ss_pred             -----HHHHHHHHhcccHHHHHHHHhhccce---ehhhhHHHHHHHHHhhccHHHHHHHHHhcC
Confidence                 22333444455666666554431111   112344444444445566666666665544

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=88.24  E-value=7.5  Score=27.77  Aligned_cols=116  Identities=15%  Similarity=0.046  Sum_probs=82.8

Q ss_pred             CCHHHHHHHHHHHhc-cC-CcHHHHHHHhccC-----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCcccH
Q 031208           11 NDQLLVRKLLDLCSF-YG-KTDHALLVFSQIR-----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GFRPDKFTF   82 (164)
Q Consensus        11 ~~~~~~~~li~~~~~-~~-~~~~a~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~t~   82 (164)
                      -|..+...+++.... .+ ....-.++.+.+.     .++..+-..+|..+++.++|...++++..-... +..-|..-|
T Consensus       162 ~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW  241 (292)
T PF13929_consen  162 FDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPW  241 (292)
T ss_pred             eChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchH
Confidence            356666666665554 22 2222233333332     467778888999999999999999999988655 666788899


Q ss_pred             HHHHHHHHhccchhhHHHHHH-----HHHHhCCCCchHHHHHHHHHHHh
Q 031208           83 PFVIKACIASLAIEKGKEVHG-----LAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        83 ~~ll~~~~~~~~~~~a~~~~~-----~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                      ..+|+.....|+......+..     .+++.|+..+...-..+-..+-+
T Consensus       242 ~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~L~~~L~~LF~~  290 (292)
T PF13929_consen  242 AEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDELRSQLSELFKK  290 (292)
T ss_pred             HHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHHHHHHHHHHHHh
Confidence            999999999999998888877     34566777777776666555443

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=88.19  E-value=1.4  Score=21.76  Aligned_cols=25  Identities=28%  Similarity=0.183  Sum_probs=21.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      +-.+|...|+.+.|.+++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5678999999999999999998654

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.

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=87.78  E-value=6.5  Score=26.47  Aligned_cols=99  Identities=15%  Similarity=0.073  Sum_probs=80.1

Q ss_pred             CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhC---CCCchHHH
Q 031208           41 CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAG---FSRDMFVQ  117 (164)
Q Consensus        41 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g---~~~~~~~~  117 (164)
                      .|.+..--.|-.+..+.|+..+|...|.+-...-+--|....-.+.++....+++..|...++.+.+..   -.||  .-
T Consensus        86 ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd--~~  163 (251)
T COG4700          86 APTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPD--GH  163 (251)
T ss_pred             chhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCC--ch
Confidence            355555566788899999999999999999877677788888889999999999999999999887653   3344  33


Q ss_pred             HHHHHHHHhcCCchhHHHHhcccC
Q 031208          118 STLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       118 ~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -.+-..|...|+.++|..-|+...
T Consensus       164 Ll~aR~laa~g~~a~Aesafe~a~  187 (251)
T COG4700         164 LLFARTLAAQGKYADAESAFEVAI  187 (251)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHH
Confidence            455678888999999999888765

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

Probab=87.34  E-value=5.2  Score=24.91  Aligned_cols=60  Identities=8%  Similarity=0.020  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           62 QALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        62 ~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      +..+.++......+.|+.-....-+++|-+-+|+..|.++++-++.. +.+-..+|-.+++
T Consensus        67 EvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K-~g~~k~~Y~y~v~  126 (149)
T KOG4077|consen   67 EVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDK-CGAQKQVYPYYVK  126 (149)
T ss_pred             HHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHh-cccHHHHHHHHHH
Confidence            45556666777788888888888888888888888888888877632 2333334555543

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

Probab=87.30  E-value=5.5  Score=30.80  Aligned_cols=100  Identities=13%  Similarity=-0.002  Sum_probs=76.3

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCch
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~  131 (164)
                      +....|+++.|+..|.+-..-. ++|.+-|+--..+|...|++.+|.+=-.+-.+  +.|+ ..-|+..-.+..-.|+++
T Consensus        11 aa~s~~d~~~ai~~~t~ai~l~-p~nhvlySnrsaa~a~~~~~~~al~da~k~~~--l~p~w~kgy~r~Gaa~~~lg~~~   87 (539)
T KOG0548|consen   11 AAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRR--LNPDWAKGYSRKGAALFGLGDYE   87 (539)
T ss_pred             hhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHh--cCCchhhHHHHhHHHHHhcccHH
Confidence            4567899999999999987764 44888999999999999999988876555443  4576 457888888888889999


Q ss_pred             hHHHHhcccCC--C-CcchHHHHHHHH
Q 031208          132 GGRKMFDKMRV--R-SVVSWTTMISGL  155 (164)
Q Consensus       132 ~a~~~~~~m~~--~-~~~~~~~li~~~  155 (164)
                      +|..-|.+=.+  | |...++-+.+++
T Consensus        88 eA~~ay~~GL~~d~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   88 EAILAYSEGLEKDPSNKQLKTGLAQAY  114 (539)
T ss_pred             HHHHHHHHHhhcCCchHHHHHhHHHhh
Confidence            99999987552  3 444555555544

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=87.25  E-value=5.8  Score=25.39  Aligned_cols=96  Identities=14%  Similarity=0.131  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHh---ccCCcHHHHHHHhccC--CCc---HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           14 LLVRKLLDLCS---FYGKTDHALLVFSQIR--CPH---VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        14 ~~~~~li~~~~---~~~~~~~a~~~~~~~~--~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      .+.+.||+...   ..++++++..+++-+.  .|+   ..++.-.+  +...|+|++|..+|++..+.+..+   .|..-
T Consensus         8 ~iv~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~~~~---p~~kA   82 (153)
T TIGR02561         8 RLLGGLIEVLMYALRSADPYDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSAGAP---PYGKA   82 (153)
T ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccCCCc---hHHHH
Confidence            34445554433   4888999999999876  343   34554443  578899999999999998765222   45555


Q ss_pred             HHHHHhccchhhHHHHH-HHHHHhCCCCch
Q 031208           86 IKACIASLAIEKGKEVH-GLAVKAGFSRDM  114 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~-~~m~~~g~~~~~  114 (164)
                      +.++|-...-+-.++.+ .++...|-.|+.
T Consensus        83 L~A~CL~al~Dp~Wr~~A~~~le~~~~~~a  112 (153)
T TIGR02561        83 LLALCLNAKGDAEWHVHADEVLARDADADA  112 (153)
T ss_pred             HHHHHHHhcCChHHHHHHHHHHHhCCCHhH
Confidence            66666555555555544 344555544444

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

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

Probab=87.12  E-value=13  Score=29.35  Aligned_cols=127  Identities=13%  Similarity=0.045  Sum_probs=91.2

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHh--------ccC--CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc--CCCCCcc
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFS--------QIR--CPHVFTWNLMIRALTIDGSSLQALLLYNLMICN--GFRPDKF   80 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~--------~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~   80 (164)
                      ..+--.++......|+++.|.+++.        .+.  .....+...+...+.+.++.+.|-.++.+-...  .-.+...
T Consensus       376 ~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~  455 (652)
T KOG2376|consen  376 KVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSI  455 (652)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccch
Confidence            4556667788889999999999999        333  233345666778888888888888888887442  1122223


Q ss_pred             cHHHHHHH----HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           81 TFPFVIKA----CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        81 t~~~ll~~----~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ...+++.-    -.+.|+.++|..+++++.+.. ++|..+-..++.+|++. +.+.|..+-+.+.
T Consensus       456 ~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~-d~eka~~l~k~L~  518 (652)
T KOG2376|consen  456 ALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL-DPEKAESLSKKLP  518 (652)
T ss_pred             HHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc-CHHHHHHHhhcCC
Confidence            33344333    356699999999999999865 68888999999999865 4577777777665

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=86.91  E-value=4.2  Score=29.23  Aligned_cols=82  Identities=15%  Similarity=0.188  Sum_probs=52.3

Q ss_pred             CcHhHHHHHHHHHHh--cCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh--c----cchhhHHHHHHHHHHhCC---
Q 031208           42 PHVFTWNLMIRALTI--DGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA--S----LAIEKGKEVHGLAVKAGF---  110 (164)
Q Consensus        42 ~~~~~~~~li~~~~~--~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~--~----~~~~~a~~~~~~m~~~g~---  110 (164)
                      ....++..++.....  ...+++...+++.|.+.|++-+.++|-+..-....  .    ..+..+..+++.|++...   
T Consensus        58 ~~~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLT  137 (297)
T PF13170_consen   58 NHRFILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLT  137 (297)
T ss_pred             cHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCcccc
Confidence            334555555544433  12356777889999999999999877664433333  2    235678899999987642   


Q ss_pred             CCchHHHHHHHHH
Q 031208          111 SRDMFVQSTLMDL  123 (164)
Q Consensus       111 ~~~~~~~~~ll~~  123 (164)
                      .++-..+..++..
T Consensus       138 s~~D~~~a~lLA~  150 (297)
T PF13170_consen  138 SPEDYPFAALLAM  150 (297)
T ss_pred             CccchhHHHHHhc
Confidence            3455666666554

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=86.68  E-value=2.4  Score=28.53  Aligned_cols=68  Identities=9%  Similarity=-0.074  Sum_probs=46.1

Q ss_pred             hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC-------CCCcchHHHHHHHHHhcCCCCCC
Q 031208           96 EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR-------VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~-------~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +.|.+.|-++...+.--+....-.|...|. ..+.+++..++....       +.|...+.+|...|-+.|+++.|
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            456777777776665556666666666565 556677776665543       44677888888888888887765

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=86.63  E-value=11  Score=31.30  Aligned_cols=80  Identities=19%  Similarity=0.153  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                      |.-.-.-+-..|+.+.|+.+|...+.         |=++.+..|-.|+.++|.++-++      .-|...+-.|-..|-.
T Consensus       915 ~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~e------sgd~AAcYhlaR~YEn  979 (1416)
T KOG3617|consen  915 YSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEE------SGDKAACYHLARMYEN  979 (1416)
T ss_pred             HHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHh------cccHHHHHHHHHHhhh
Confidence            33333333445666666666665543         33455555666777777766655      2344455566667777


Q ss_pred             cCCchhHHHHhcccC
Q 031208          127 CGDVDGGRKMFDKMR  141 (164)
Q Consensus       127 ~~~~~~a~~~~~~m~  141 (164)
                      .|++-+|..+|-+.+
T Consensus       980 ~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  980 DGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             hHHHHHHHHHHHHHH
Confidence            777777776665543

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

Probab=86.61  E-value=2.8  Score=21.03  Aligned_cols=35  Identities=14%  Similarity=0.111  Sum_probs=29.0

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      ..-+.|-.+++..++++|.+.|+..+...|..+++
T Consensus        11 ~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen   11 LAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            34677888899999999999999988888777765

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

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=86.44  E-value=8.1  Score=28.87  Aligned_cols=88  Identities=14%  Similarity=0.052  Sum_probs=66.4

Q ss_pred             HHHhcCChhHHHHHHHHHHHc-----CCC---------CCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           53 ALTIDGSSLQALLLYNLMICN-----GFR---------PDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~-----~~~---------p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      .+.+.|++..|..-|++....     +..         .-...+.-|.-++.+.+++..|.+.-...+..+ ++|+-..-
T Consensus       217 ~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALy  295 (397)
T KOG0543|consen  217 VLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALY  295 (397)
T ss_pred             HHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHH
Confidence            567788888888888875331     111         223456778888899999999999999888776 45665555


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .=-.++...|+++.|+..|+.+.
T Consensus       296 RrG~A~l~~~e~~~A~~df~ka~  318 (397)
T KOG0543|consen  296 RRGQALLALGEYDLARDDFQKAL  318 (397)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHH
Confidence            55678888999999999999887

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=86.25  E-value=12  Score=27.94  Aligned_cols=92  Identities=10%  Similarity=-0.095  Sum_probs=60.0

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCC--CCc-ccHHHHHHHHHh---ccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           48 NLMIRALTIDGSSLQALLLYNLMICNGFR--PDK-FTFPFVIKACIA---SLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        48 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~--p~~-~t~~~ll~~~~~---~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      ..++-+|....+++..+++.+.+..---.  ++. ..--...-++.+   .|+.++|.+++..+....-.++..+|..+-
T Consensus       145 ~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~G  224 (374)
T PF13281_consen  145 INLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLG  224 (374)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHH
Confidence            34555799999999999999999764211  111 111122334455   789999999999976666678888888777


Q ss_pred             HHHH----hc-----CCchhHHHHhcc
Q 031208          122 DLYL----KC-----GDVDGGRKMFDK  139 (164)
Q Consensus       122 ~~~~----~~-----~~~~~a~~~~~~  139 (164)
                      ..|-    .+     ..+++|...|.+
T Consensus       225 RIyKD~~~~s~~~d~~~ldkAi~~Y~k  251 (374)
T PF13281_consen  225 RIYKDLFLESNFTDRESLDKAIEWYRK  251 (374)
T ss_pred             HHHHHHHHHcCccchHHHHHHHHHHHH
Confidence            6553    21     225566666654

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=85.98  E-value=4.4  Score=27.90  Aligned_cols=77  Identities=17%  Similarity=-0.024  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh--CCCCchHHHHHHHHHH
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA--GFSRDMFVQSTLMDLY  124 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~~~~~~~~~ll~~~  124 (164)
                      -+..++.+.+.+..++++...++=.+.. +.|..+-..+++-+|-.|++++|..=++-.-..  ...+-..+|..+|.+-
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~e   82 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRCE   82 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHHH
Confidence            4455677888889999998887766553 447778888999999999999887655544332  2345567888888753

>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=85.72  E-value=1.5  Score=27.47  Aligned_cols=31  Identities=26%  Similarity=0.425  Sum_probs=17.6

Q ss_pred             hcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           56 IDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        56 ~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +.|.-.+|..+|++|..+|-+||.  |+.|+..
T Consensus       107 ~ygsk~DaY~VF~kML~~G~pPdd--W~~Ll~~  137 (140)
T PF11663_consen  107 AYGSKTDAYAVFRKMLERGNPPDD--WDALLKE  137 (140)
T ss_pred             hhccCCcHHHHHHHHHhCCCCCcc--HHHHHHH
Confidence            334455666666666666666653  4555544

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 [].

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=85.64  E-value=7.1  Score=24.79  Aligned_cols=66  Identities=12%  Similarity=-0.002  Sum_probs=50.4

Q ss_pred             HHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           65 LLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        65 ~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      ++...+.+.|++++.. -..+++.+.+.++.-.|.++++++.+.+...+..|--..++.+...|-+.
T Consensus         7 ~~~~~lk~~glr~T~q-R~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~   72 (145)
T COG0735           7 DAIERLKEAGLRLTPQ-RLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVH   72 (145)
T ss_pred             HHHHHHHHcCCCcCHH-HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEE
Confidence            3455667888877764 35788888888888999999999999887777666666777777777544

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=85.41  E-value=7.1  Score=24.64  Aligned_cols=87  Identities=18%  Similarity=0.121  Sum_probs=56.7

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH---HHHHhcCC
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM---DLYLKCGD  129 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll---~~~~~~~~  129 (164)
                      +.+..|+.+.|++.|.+-..- .+-+...||.-..++.-.|+.++|..=+.+..+..-.-+...+.+.+   ..|...|+
T Consensus        52 alaE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~  130 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGN  130 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCc
Confidence            457778888888888887653 23356678888888888888888887777666542222332222322   34556677


Q ss_pred             chhHHHHhccc
Q 031208          130 VDGGRKMFDKM  140 (164)
Q Consensus       130 ~~~a~~~~~~m  140 (164)
                      -+.|..=|+..
T Consensus       131 dd~AR~DFe~A  141 (175)
T KOG4555|consen  131 DDAARADFEAA  141 (175)
T ss_pred             hHHHHHhHHHH
Confidence            77777766643

>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat

Probab=85.27  E-value=5.3  Score=23.00  Aligned_cols=61  Identities=10%  Similarity=0.207  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCC
Q 031208           99 KEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        99 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~  161 (164)
                      .++++.+...|+ .+....+.+-.+--..|+.+.|.++++.++ +..-.|...++++..+|+-
T Consensus        22 ~~v~d~ll~~~i-lT~~d~e~I~aa~~~~g~~~~ar~LL~~L~-rg~~aF~~Fl~aLreT~~~   82 (88)
T cd08819          22 RDVCDKCLEQGL-LTEEDRNRIEAATENHGNESGARELLKRIV-QKEGWFSKFLQALRETEHH   82 (88)
T ss_pred             HHHHHHHHhcCC-CCHHHHHHHHHhccccCcHHHHHHHHHHhc-cCCcHHHHHHHHHHHcCch
Confidence            344444444442 222223333222224456666666666666 5555666666666666553

Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=85.16  E-value=1.7  Score=19.93  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=12.4

Q ss_pred             chHHHHHHHHHHHhcCCchhHH
Q 031208          113 DMFVQSTLMDLYLKCGDVDGGR  134 (164)
Q Consensus       113 ~~~~~~~ll~~~~~~~~~~~a~  134 (164)
                      +...|+.+-..|...|++++|.
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            4555555555666666655553

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=84.56  E-value=11  Score=26.15  Aligned_cols=62  Identities=11%  Similarity=-0.040  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cH---HHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-TF---PFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~---~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ..|..-. .+...|++++|.+.|+++...  -|+.. .-   -.+..++.+.++++.|...+++..+..
T Consensus        34 ~~Y~~A~-~~~~~g~y~~Ai~~f~~l~~~--yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~   99 (243)
T PRK10866         34 EIYATAQ-QKLQDGNWKQAITQLEALDNR--YPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN   99 (243)
T ss_pred             HHHHHHH-HHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            3444444 456789999999999999874  34332 22   345678899999999999999998763

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=84.11  E-value=11  Score=25.54  Aligned_cols=73  Identities=11%  Similarity=-0.066  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh---CCCCchHHHHHHHHHHHhcCCchhHH
Q 031208           61 LQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA---GFSRDMFVQSTLMDLYLKCGDVDGGR  134 (164)
Q Consensus        61 ~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~---g~~~~~~~~~~ll~~~~~~~~~~~a~  134 (164)
                      +.|...|-++...+..-++..--.|.. |....+.+++.+++-.....   +-.+|+..+..|...|.+.|+++.|.
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAt-yY~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALAT-YYTKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHH-HHHccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            678888888887776655544444444 44467888899988877653   33678999999999999999999875

>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=84.09  E-value=2.2  Score=18.09  Aligned_cols=20  Identities=25%  Similarity=0.419  Sum_probs=10.1

Q ss_pred             HHHHHHHhcCCchhHHHHhc
Q 031208          119 TLMDLYLKCGDVDGGRKMFD  138 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~  138 (164)
                      .+-..+...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34444555555555555543

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

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=84.08  E-value=4.9  Score=29.64  Aligned_cols=70  Identities=13%  Similarity=0.093  Sum_probs=44.2

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      -|.+.|.+++|.+.|..-..  +.| |.+++..-..+|.+..++..|+.=-......        -...+.+|+|.+.-.
T Consensus       106 ~yFKQgKy~EAIDCYs~~ia--~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaL--------d~~Y~KAYSRR~~AR  175 (536)
T KOG4648|consen  106 TYFKQGKYEEAIDCYSTAIA--VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIAL--------DKLYVKAYSRRMQAR  175 (536)
T ss_pred             hhhhccchhHHHHHhhhhhc--cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHh--------hHHHHHHHHHHHHHH
Confidence            35667788888888877544  345 7788888888888888777666544443322        134456666654433


Q ss_pred             h
Q 031208          132 G  132 (164)
Q Consensus       132 ~  132 (164)
                      .
T Consensus       176 ~  176 (536)
T KOG4648|consen  176 E  176 (536)
T ss_pred             H
Confidence            3

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

Probab=83.58  E-value=2.9  Score=18.63  Aligned_cols=27  Identities=19%  Similarity=0.080  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      +|..+-..+...|++++|+..|++..+
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            344444555555555555555555443

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 ....

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=83.54  E-value=13  Score=26.09  Aligned_cols=149  Identities=15%  Similarity=0.119  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--C----cHhHHHHHHHHHHhcCChhHHHHHHHHHHH-cCCCCCcccHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--P----HVFTWNLMIRALTIDGSSLQALLLYNLMIC-NGFRPDKFTFPFVI   86 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~p~~~t~~~ll   86 (164)
                      ..|+. ...-.+.|++++|.+.|+.+..  |    ...+--.++.++-+.+++++|+..+++..+ .+-.||. -|..-|
T Consensus        36 ~LY~~-g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~-dY~~Yl  113 (254)
T COG4105          36 ELYNE-GLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNA-DYAYYL  113 (254)
T ss_pred             HHHHH-HHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCCh-hHHHHH
Confidence            34444 3344568999999999998873  2    223445567777889999999999999855 4444444 555556


Q ss_pred             HHHHhcc-------chhhHHHHHH---HHHHh----CCCCchHH-----------H-HHHHHHHHhcCCchhHHHHhccc
Q 031208           87 KACIASL-------AIEKGKEVHG---LAVKA----GFSRDMFV-----------Q-STLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        87 ~~~~~~~-------~~~~a~~~~~---~m~~~----g~~~~~~~-----------~-~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      .+++...       |...+.+-+.   +++..    ...||...           + -.+-..|.+.|.+..|..-+++|
T Consensus       114 kgLs~~~~i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v  193 (254)
T COG4105         114 KGLSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEV  193 (254)
T ss_pred             HHHHHhccCCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            5554432       3333444444   43332    12222211           1 13345778999999999888888


Q ss_pred             CCC------CcchHHHHHHHHHhcCCCCCC
Q 031208          141 RVR------SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       141 ~~~------~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+.      ....+-.|..+|-..|-.++|
T Consensus       194 ~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a  223 (254)
T COG4105         194 LENYPDTSAVREALARLEEAYYALGLTDEA  223 (254)
T ss_pred             HhccccccchHHHHHHHHHHHHHhCChHHH
Confidence            732      234666677888887776654

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=83.10  E-value=9.8  Score=24.40  Aligned_cols=51  Identities=12%  Similarity=0.085  Sum_probs=35.9

Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCc---ccHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           55 TIDGSSLQALLLYNLMICNGFRPDK---FTFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        55 ~~~~~~~~a~~~~~~m~~~~~~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ...++++++..++..|.-  +.|+.   .+|.  -..+...|++.+|.++++++...+
T Consensus        21 L~~~d~~D~e~lLdALrv--LrP~~~e~d~~d--g~l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRV--LRPNLKELDMFD--GWLLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HhcCCHHHHHHHHHHHHH--hCCCccccchhH--HHHHHHcCCHHHHHHHHHhhhccC
Confidence            447888888888888865  34543   3333  334567788999999999887664

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=82.91  E-value=15  Score=26.50  Aligned_cols=58  Identities=9%  Similarity=-0.123  Sum_probs=35.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHH
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLA  105 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  105 (164)
                      .+..-..|..+|.+.+|.++.++..... +.+...+-.++..+...|+--.+.+-++.+
T Consensus       282 lgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyery  339 (361)
T COG3947         282 LGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERY  339 (361)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHH
Confidence            3444455666777777777766665543 346666667777777777655555444443

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=82.83  E-value=7.9  Score=23.10  Aligned_cols=57  Identities=14%  Similarity=0.214  Sum_probs=29.3

Q ss_pred             hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHH
Q 031208           96 EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMIS  153 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~  153 (164)
                      ++|..+-+.+...+-. .+.+--+-+..+...|+++.|..+.+...-||...|-++-.
T Consensus        22 qEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce   78 (115)
T TIGR02508        22 QEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE   78 (115)
T ss_pred             HHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH
Confidence            3444444444433311 22333333444555666666666666666666666655543

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=82.46  E-value=12  Score=25.02  Aligned_cols=141  Identities=13%  Similarity=0.077  Sum_probs=84.0

Q ss_pred             HHHHhccCCcHHHHHHHhccCC--Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc-
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC--PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS-   92 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~-   92 (164)
                      -..+...|++..|.+.|+.+..  |+    ....=.+..++-+.|+++.|...+++..+.--.-...-+...+.+.+.. 
T Consensus        12 a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~~   91 (203)
T PF13525_consen   12 ALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYYK   91 (203)
T ss_dssp             HHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHH
Confidence            3456678999999999998862  22    1334456778899999999999999987643111222333333333321 


Q ss_pred             ------------cchhhHHHHHHHHHHhCCCCch-H----------HH-------HHHHHHHHhcCCchhHHHHhcccCC
Q 031208           93 ------------LAIEKGKEVHGLAVKAGFSRDM-F----------VQ-------STLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        93 ------------~~~~~a~~~~~~m~~~g~~~~~-~----------~~-------~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                                  +...+|...++.+.+.-  |+. .          +.       -.+.+.|.+.|.+..|..-++.+.+
T Consensus        92 ~~~~~~~~~~D~~~~~~A~~~~~~li~~y--P~S~y~~~A~~~l~~l~~~la~~e~~ia~~Y~~~~~y~aA~~r~~~v~~  169 (203)
T PF13525_consen   92 QIPGILRSDRDQTSTRKAIEEFEELIKRY--PNSEYAEEAKKRLAELRNRLAEHELYIARFYYKRGKYKAAIIRFQYVIE  169 (203)
T ss_dssp             HHHHHH-TT---HHHHHHHHHHHHHHHH---TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHH
T ss_pred             hCccchhcccChHHHHHHHHHHHHHHHHC--cCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence                        12345677777766542  221 1          11       1234567788888888888887762


Q ss_pred             --CCc----chHHHHHHHHHhcCCCC
Q 031208          143 --RSV----VSWTTMISGLAASGDLD  162 (164)
Q Consensus       143 --~~~----~~~~~li~~~~~~g~~~  162 (164)
                        |++    ...-.++.+|.+.|..+
T Consensus       170 ~yp~t~~~~~al~~l~~~y~~l~~~~  195 (203)
T PF13525_consen  170 NYPDTPAAEEALARLAEAYYKLGLKQ  195 (203)
T ss_dssp             HSTTSHHHHHHHHHHHHHHHHTT-HH
T ss_pred             HCCCCchHHHHHHHHHHHHHHhCChH
Confidence              333    36677888888887643

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=82.23  E-value=11  Score=28.55  Aligned_cols=130  Identities=12%  Similarity=0.048  Sum_probs=68.4

Q ss_pred             CCHHHHHHH-HHHHhccCCcHHHHHHHhccCCCcH-hHHHHHHHHHHh--cCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           11 NDQLLVRKL-LDLCSFYGKTDHALLVFSQIRCPHV-FTWNLMIRALTI--DGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        11 ~~~~~~~~l-i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~li~~~~~--~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      |....|..+ ..++.-.|+.+.|..+-....+.|. ..+...+++.+-  ..+.+.+...|++-...  .|+...-.+.-
T Consensus       166 pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~l--dpdh~~sk~~~  243 (486)
T KOG0550|consen  166 PACFKAKLLKAECLAFLGDYDEAQSEAIDILKLDATNAEALYVRGLCLYYNDNADKAINHFQQALRL--DPDHQKSKSAS  243 (486)
T ss_pred             chhhHHHHhhhhhhhhcccchhHHHHHHHHHhcccchhHHHHhcccccccccchHHHHHHHhhhhcc--ChhhhhHHhHh
Confidence            333444444 2244557777777766555443322 234444444332  34556666666655443  34443332222


Q ss_pred             H-------------HHHhccchhhHHHHHHHHHHh---CCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC
Q 031208           87 K-------------ACIASLAIEKGKEVHGLAVKA---GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        87 ~-------------~~~~~~~~~~a~~~~~~m~~~---g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      .             -..+.|++..|.+.+.+....   ...|+...|...-.+..+.|+.++|+.--++...
T Consensus       244 ~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~  315 (486)
T KOG0550|consen  244 MMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALK  315 (486)
T ss_pred             hhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhh
Confidence            1             225556777777777666532   3445555666666666677777777666655543

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=81.87  E-value=17  Score=26.20  Aligned_cols=116  Identities=10%  Similarity=-0.026  Sum_probs=64.4

Q ss_pred             HhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHH
Q 031208           23 CSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      ....|++..|..+|+....   .+...--.+..+|...|+.+.|..++..+...--.........-|..+.+.....+..
T Consensus       144 ~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~~~  223 (304)
T COG3118         144 LIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPEIQ  223 (304)
T ss_pred             hhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCCHH
Confidence            3446677777777666542   2334455566777788888888888877644322222222223344444444444444


Q ss_pred             HHHHHHHHhCCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          100 EVHGLAVKAGFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       100 ~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+.+..-.   .| |...--.+-..|...|+.+.|.+.+=.+.
T Consensus       224 ~l~~~~aa---dPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l  263 (304)
T COG3118         224 DLQRRLAA---DPDDVEAALALADQLHLVGRNEAALEHLLALL  263 (304)
T ss_pred             HHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44444333   24 45555566666777777777766554443

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.81  E-value=25  Score=28.21  Aligned_cols=85  Identities=15%  Similarity=0.072  Sum_probs=61.0

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      .+..-|..|=.+....+++..|.+-|..-.         .|..|+-.+...|+.+....+-+..++.|.      .|...
T Consensus       664 ~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~---------d~~~LlLl~t~~g~~~~l~~la~~~~~~g~------~N~AF  728 (794)
T KOG0276|consen  664 NSEVKWRQLGDAALSAGELPLASECFLRAR---------DLGSLLLLYTSSGNAEGLAVLASLAKKQGK------NNLAF  728 (794)
T ss_pred             cchHHHHHHHHHHhhcccchhHHHHHHhhc---------chhhhhhhhhhcCChhHHHHHHHHHHhhcc------cchHH
Confidence            345567778888888888888877776654         456777777788887766666666666663      35556


Q ss_pred             HHHHhcCCchhHHHHhcccC
Q 031208          122 DLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -+|...|+++++.+++-+-.
T Consensus       729 ~~~~l~g~~~~C~~lLi~t~  748 (794)
T KOG0276|consen  729 LAYFLSGDYEECLELLISTQ  748 (794)
T ss_pred             HHHHHcCCHHHHHHHHHhcC
Confidence            67788899999988887653

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

Probab=81.76  E-value=18  Score=28.14  Aligned_cols=76  Identities=11%  Similarity=0.099  Sum_probs=55.3

Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhC-CCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CC--cchHHHHHHHHHhc
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAG-FSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RS--VVSWTTMISGLAAS  158 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~--~~~~~~li~~~~~~  158 (164)
                      +-.++-+.|+.++|.+.+.+|.+.. ..-...+...|+.++...+.+.++..++.+-.+   |.  ..+|++.+--+-..
T Consensus       265 LAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaRav  344 (539)
T PF04184_consen  265 LAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKARAV  344 (539)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHHhh
Confidence            3455567799999999999997653 223456888999999999999999999987652   32  35777766554444


Q ss_pred             CC
Q 031208          159 GD  160 (164)
Q Consensus       159 g~  160 (164)
                      |+
T Consensus       345 ~d  346 (539)
T PF04184_consen  345 GD  346 (539)
T ss_pred             cc
Confidence            43

The molecular function of this protein is uncertain.

>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=81.27  E-value=2.5  Score=26.46  Aligned_cols=35  Identities=14%  Similarity=-0.016  Sum_probs=27.8

Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      ..-+.|.-.+|-.+|+.|+++|-+||  .|+.|+...
T Consensus       104 tlR~ygsk~DaY~VF~kML~~G~pPd--dW~~Ll~~a  138 (140)
T PF11663_consen  104 TLRAYGSKTDAYAVFRKMLERGNPPD--DWDALLKEA  138 (140)
T ss_pred             chhhhccCCcHHHHHHHHHhCCCCCc--cHHHHHHHh
Confidence            44556788899999999999998887  577777643

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 [].

>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9

Probab=81.07  E-value=2.9  Score=23.84  Aligned_cols=36  Identities=17%  Similarity=0.338  Sum_probs=23.0

Q ss_pred             hcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCC
Q 031208          126 KCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDL  161 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~  161 (164)
                      ...+.+++.++++.++.++...|....+++-..|+.
T Consensus        42 ~~tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~~~~   77 (84)
T cd08326          42 AGSRRDQARQLLIDLETRGKQAFPAFLSALRETGQT   77 (84)
T ss_pred             CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCch
Confidence            344566666666666666666677776666666553

Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt

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

Probab=80.56  E-value=3.9  Score=25.46  Aligned_cols=45  Identities=4%  Similarity=0.044  Sum_probs=38.9

Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +..+-+..+....+.|++.+....+.++.+.+++..|.++|+.++
T Consensus        67 EvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK  111 (149)
T KOG4077|consen   67 EVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIK  111 (149)
T ss_pred             HHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            445555666677889999999999999999999999999999887

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=80.41  E-value=5.4  Score=28.62  Aligned_cols=35  Identities=17%  Similarity=0.167  Sum_probs=20.6

Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHH
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFV  116 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~  116 (164)
                      |+.-|+.-.+.||+++|.++++|.++.|+.--..+
T Consensus       260 y~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~t  294 (303)
T PRK10564        260 FNQAIKQAVKKGDVDKALKLLDEAERLGSTSARST  294 (303)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHH
Confidence            45666666666666666666666666665433333

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

Probab=80.39  E-value=14  Score=24.44  Aligned_cols=53  Identities=11%  Similarity=-0.091  Sum_probs=30.9

Q ss_pred             hcCChhHHHHHHHHHHH-cCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           56 IDGSSLQALLLYNLMIC-NGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        56 ~~~~~~~a~~~~~~m~~-~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      ...+.+......+..++ ....|+...|..++.++...|+.++|.++.+++...
T Consensus       120 ~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~l  173 (193)
T PF11846_consen  120 LPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARARRL  173 (193)
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            44444444433333322 234577777777777777777777777777766543

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

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=80.39  E-value=3.6  Score=29.46  Aligned_cols=44  Identities=20%  Similarity=0.118  Sum_probs=36.2

Q ss_pred             CcHhH-HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           42 PHVFT-WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        42 ~~~~~-~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      ||..+ |+..|....+.|++++|+.+++|-++.|+.--..+|-.-
T Consensus       254 ~dTe~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~  298 (303)
T PRK10564        254 NDTESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISS  298 (303)
T ss_pred             chHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHH
Confidence            45544 789999999999999999999999999987766665443

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=80.19  E-value=10  Score=22.64  Aligned_cols=53  Identities=17%  Similarity=0.098  Sum_probs=29.8

Q ss_pred             HHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           20 LDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      +..+...|+++.|..+.+.+..||...|-.|-  -.+.|..+....-+.+|..+|
T Consensus        46 lsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALc--e~rlGl~s~l~~rl~rla~sg   98 (115)
T TIGR02508        46 LSSLMNRGDYQSALQLGNKLCYPDLEPWLALC--EWRLGLGSALESRLNRLAASG   98 (115)
T ss_pred             HHHHHccchHHHHHHhcCCCCCchHHHHHHHH--HHhhccHHHHHHHHHHHHhCC
Confidence            33455566666666666666666666664432  234555555555555555554

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=80.14  E-value=18  Score=28.41  Aligned_cols=94  Identities=10%  Similarity=0.001  Sum_probs=68.2

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      |-...-+++..++.+-.+.-+..+..+|...|  -+...|-.++..|... ..++-..+|+.+.+..+  +......-+.
T Consensus        65 ~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~df--nDvv~~ReLa  139 (711)
T COG1747          65 DDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDF--NDVVIGRELA  139 (711)
T ss_pred             cchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcc--hhHHHHHHHH
Confidence            33344567888888888999999999998865  6677888899999888 66778888888887754  3334444444


Q ss_pred             HHHhcCCchhHHHHhcccC
Q 031208          123 LYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+...++...+..+|.+..
T Consensus       140 ~~yEkik~sk~a~~f~Ka~  158 (711)
T COG1747         140 DKYEKIKKSKAAEFFGKAL  158 (711)
T ss_pred             HHHHHhchhhHHHHHHHHH
Confidence            4444477788888777654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	164
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-06

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 45.2 bits (105), Expect = 3e-06
 Identities = 13/150 (8%), Positives = 40/150 (26%), Gaps = 8/150 (5%)

Query: 2   QKIIRYGLSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR-------CPHVFTWNLMIRAL 54
            +  +  LS  Q  +      C    +   A  +               +  +N ++   
Sbjct: 116 GQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGW 175

Query: 55  TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI-ASLAIEKGKEVHGLAVKAGFSRD 113
              G+  + + +  ++   G  PD  ++   ++            +       + G    
Sbjct: 176 ARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQ 235

Query: 114 MFVQSTLMDLYLKCGDVDGGRKMFDKMRVR 143
               + L+    +   +    K+     + 
Sbjct: 236 ALFTAVLLSEEDRATVLKAVHKVKPTFSLP 265

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	164
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.94
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.91
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.72
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.7
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.39
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.39
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.35
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.34
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.34
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.34
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.32
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.32
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.31
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.29
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.28
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.27
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.27
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.25
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.25
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.23
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.21
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.21
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.2
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.19
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.18
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.18
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.17
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.15
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.15
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.12
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.1
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.09
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.07
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.05
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.05
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.04
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.03
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.02
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.02
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.0
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.99
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.99
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.98
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.96
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.94
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.92
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.87
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.87
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.86
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.85
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.84
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.84
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.84
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.84
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.81
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.8
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.78
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.77
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.77
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.76
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.75
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.74
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.74
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.74
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.73
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.73
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.66
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.66
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.66
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.63
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.62
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.62
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.61
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.61
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.58
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.56
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.55
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.55
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.54
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.5
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.49
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.48
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.48
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.48
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.47
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.46
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.44
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.44
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.42
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.42
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.42
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.42
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.42
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.39
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.39
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.39
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.37
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.37
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.33
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.31
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.3
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.3
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.3
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.3
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.28
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.28
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.28
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.28
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.28
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.27
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.27
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.27
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.26
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.26
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.25
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.25
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.24
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.23
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.22
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.21
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.2
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.2
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.19
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.17
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.15
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.15
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.14
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.14
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.14
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.13
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.13
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.13
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.13
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.12
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.12
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.1
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.08
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.08
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.07
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.06
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.06
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.05
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.04
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.04
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.02
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.98
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.97
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.97
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.95
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.94
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.94
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.93
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.93
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.92
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.92
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.9
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.86
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.85
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.84
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.82
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.81
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.8
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.78
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.77
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.77
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.77
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.76
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.76
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.73
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.7
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.68
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.65
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.64
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.61
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.53
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.52
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.44
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.42
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.38
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.36
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.35
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.31
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.28
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.26
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.17
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.1
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.1
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.09
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.98
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.95
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.87
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.84
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.83
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.81
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.8
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.78
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.7
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.69
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.66
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.32
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.3
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	95.95
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.95
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	95.89
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	95.81
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	95.74
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	95.66
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.59
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.57
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.54
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	95.49
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	95.43
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.28
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.99
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.85
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	94.47
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	94.46
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.3
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	94.14
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	93.96
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	93.84
1klx_A	138	Cysteine rich protein B; structural genomics, heli	93.8
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	93.5
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.2
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.16
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	93.02
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.76
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.51
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	92.48
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	92.43
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	92.35
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	92.3
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	92.18
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	91.48
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	91.23
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	89.4
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	87.22
2ion_A	152	PDCD4, programmed cell death 4, PDCD4; alpha-helic	86.72
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	86.59
2p58_C	116	Putative type III secretion protein YSCG; type III	86.31
1pc2_A	152	Mitochondria fission protein; unknown function; NM	86.13
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	86.0
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	85.81
2p58_C	116	Putative type III secretion protein YSCG; type III	85.23
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	84.25
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	83.88
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	83.45
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	82.8
2d2s_A	235	Exocyst complex component EXO84; tethering complex	82.45
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	82.19
3ltj_A	201	Alpharep-4; protein engineering, heat-like repeat,	81.38
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	80.9
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	80.41
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	80.12

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

Probab=100.00  E-value=3.3e-36  Score=223.62  Aligned_cols=158  Identities=16%  Similarity=0.167  Sum_probs=150.9

Q ss_pred             ChhHhhhcCCCCHHHHHHHHHHHhccCC---------cHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHH
Q 031208            1 MQKIIRYGLSNDQLLVRKLLDLCSFYGK---------TDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLY   67 (164)
Q Consensus         1 ~~~m~~~g~~~~~~~~~~li~~~~~~~~---------~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~   67 (164)
                      |++|.+.|++||..+||+||.+|++.+.         ++.|.++|++|.    .||..|||++|.+|++.|++++|.++|
T Consensus        49 f~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~  128 (501)
T 4g26_A           49 YDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMV  128 (501)
T ss_dssp             HHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            4689999999999999999999998765         678999999997    599999999999999999999999999


Q ss_pred             HHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC----CC
Q 031208           68 NLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR----VR  143 (164)
Q Consensus        68 ~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~----~~  143 (164)
                      ++|.+.|+.||..||+++|.+|++.|+.++|.++|++|.+.|+.||..+|++||++|++.|++++|.++|++|.    .|
T Consensus       129 ~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~p  208 (501)
T 4g26_A          129 KQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQV  208 (501)
T ss_dssp             HHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSB
T ss_pred             HHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997    78


Q ss_pred             CcchHHHHHHHHHhc
Q 031208          144 SVVSWTTMISGLAAS  158 (164)
Q Consensus       144 ~~~~~~~li~~~~~~  158 (164)
                      +..||+.++..|...
T Consensus       209 s~~T~~~l~~~F~s~  223 (501)
T 4g26_A          209 SKSTFDMIEEWFKSE  223 (501)
T ss_dssp             CHHHHHHHHHHHHSH
T ss_pred             CHHHHHHHHHHHhcC
Confidence            999999999998764

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

Probab=100.00  E-value=6.4e-36  Score=222.11  Aligned_cols=162  Identities=15%  Similarity=0.214  Sum_probs=145.1

Q ss_pred             hHhhhcCCCCH-HHHHHHHHHHhccCCcHHHHHHHhccC----CCcHhHHHHHHHHHHhcCC---------hhHHHHHHH
Q 031208            3 KIIRYGLSNDQ-LLVRKLLDLCSFYGKTDHALLVFSQIR----CPHVFTWNLMIRALTIDGS---------SLQALLLYN   68 (164)
Q Consensus         3 ~m~~~g~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~---------~~~a~~~~~   68 (164)
                      ++.+.+..+++ .+++.+|++|++.|++++|.++|++|.    .||..+||+||.+|++.+.         .+.|.++|+
T Consensus        15 ~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~   94 (501)
T 4g26_A           15 KAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFK   94 (501)
T ss_dssp             ---------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHH
T ss_pred             HHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHH
Confidence            45666766554 468999999999999999999999997    6999999999999998765         688999999


Q ss_pred             HHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC----CCC
Q 031208           69 LMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR----VRS  144 (164)
Q Consensus        69 ~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~----~~~  144 (164)
                      +|...|+.||..||+++|++|++.|++++|.+++++|.+.|+.||..+|++||.+|++.|++++|.++|++|.    .||
T Consensus        95 ~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd  174 (501)
T 4g26_A           95 QMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPE  174 (501)
T ss_dssp             HHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCC
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999997    689


Q ss_pred             cchHHHHHHHHHhcCCCCCC
Q 031208          145 VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       145 ~~~~~~li~~~~~~g~~~~A  164 (164)
                      ..||++||.+|++.|++++|
T Consensus       175 ~~ty~~Li~~~~~~g~~d~A  194 (501)
T 4g26_A          175 EPELAALLKVSMDTKNADKV  194 (501)
T ss_dssp             HHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhhCCCHHHH
Confidence            99999999999999998764

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

Probab=99.94  E-value=2.7e-27  Score=183.58  Aligned_cols=149  Identities=9%  Similarity=0.079  Sum_probs=129.4

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC-------CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR-------CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      --..+||++|++||+.|++++|.++|+.|.       .||++|||+||.+|++.|++++|.++|++|.+.|+.||.+|||
T Consensus       125 ~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYn  204 (1134)
T 3spa_A          125 GQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYA  204 (1134)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence            346789999999999999999999997764       5999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhccch-hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC-----CcchHHHHHHHHHh
Q 031208           84 FVIKACIASLAI-EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR-----SVVSWTTMISGLAA  157 (164)
Q Consensus        84 ~ll~~~~~~~~~-~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~  157 (164)
                      ++|+++++.|+. ++|.+++++|.+.|+.||..+|++++.++.+.+-++.+.+++.++..+     .+.+...|.+-|.+
T Consensus       205 tLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p~~~~~~~~~t~~LL~dl~s~  284 (1134)
T 3spa_A          205 AALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAK  284 (1134)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCCCCCCCCCCCTTTHHHHCC
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCcccCCCCCCcccccchHHHHHHHcc
Confidence            999999999985 789999999999999999999999999999888777777777666522     23344445555555


Q ss_pred             cC
Q 031208          158 SG  159 (164)
Q Consensus       158 ~g  159 (164)
                      .+
T Consensus       285 d~  286 (1134)
T 3spa_A          285 DG  286 (1134)
T ss_dssp             CS
T ss_pred             CC
Confidence            44

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

Probab=99.91  E-value=8.2e-25  Score=169.88  Aligned_cols=115  Identities=9%  Similarity=-0.040  Sum_probs=106.5

Q ss_pred             HhHHHHHHHHHHhcCChhHHHHHHHHHH---HcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHH
Q 031208           44 VFTWNLMIRALTIDGSSLQALLLYNLMI---CNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTL  120 (164)
Q Consensus        44 ~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  120 (164)
                      ..|||++|++|++.|++++|.++|.+|.   ..|+.||.+|||+||++||+.|++++|.++|++|.+.|+.||.+|||+|
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            3689999999999999999999998875   4689999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCc-hhHHHHhcccC----CCCcchHHHHHHHHHhc
Q 031208          121 MDLYLKCGDV-DGGRKMFDKMR----VRSVVSWTTMISGLAAS  158 (164)
Q Consensus       121 l~~~~~~~~~-~~a~~~~~~m~----~~~~~~~~~li~~~~~~  158 (164)
                      |+++++.|+. ++|.++|++|.    .||.++|++++.++.+.
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~  249 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA  249 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH
Confidence            9999999985 78999999997    78999999877766554

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

Probab=99.72  E-value=2.2e-17  Score=124.38  Aligned_cols=151  Identities=10%  Similarity=0.010  Sum_probs=80.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      ++..+|+.+..+|.+.|++++|.++|+++.   ..+..+|+.++.++.+.|++++|..+++++.+.. +.+..++..+..
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  381 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGI  381 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHH
Confidence            445555555555555555555555555443   1234445555555555555555555555554321 234445555556


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~  163 (164)
                      .|.+.|++++|.++|+++.+.. +.+..+|+.++..|.+.|++++|.++|+++.   ..+..+|+.+..+|.+.|++++
T Consensus       382 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  459 (597)
T 2xpi_A          382 YYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILL  459 (597)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHH
Confidence            6666666666666666555432 2334556666666666666666666665543   2245566666666666665544

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

Probab=99.70  E-value=2.3e-16  Score=118.81  Aligned_cols=152  Identities=13%  Similarity=0.056  Sum_probs=97.4

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      +.+..+|+.+..+|.+.|++++|.++|+++.   ..+..+|+.+..+|.+.|++++|.++|+++.+.+ +.+..+|..+.
T Consensus       370 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~  448 (597)
T 2xpi_A          370 PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLG  448 (597)
T ss_dssp             TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHH
Confidence            3456677777777777777777777777654   2345677777777777777777777777776542 33556666666


Q ss_pred             HHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--------CCC--cchHHHHHHHHH
Q 031208           87 KACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--------VRS--VVSWTTMISGLA  156 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--------~~~--~~~~~~li~~~~  156 (164)
                      .+|.+.|++++|.++++++.+.. +.+..+|+.+...|.+.|++++|.++|+++.        .|+  ..+|..+..+|.
T Consensus       449 ~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~  527 (597)
T 2xpi_A          449 MQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYR  527 (597)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHH
Confidence            66666666666666666666543 3355666666666666666666666666653        233  456666666666


Q ss_pred             hcCCCCC
Q 031208          157 ASGDLDA  163 (164)
Q Consensus       157 ~~g~~~~  163 (164)
                      +.|++++
T Consensus       528 ~~g~~~~  534 (597)
T 2xpi_A          528 KLKMYDA  534 (597)
T ss_dssp             HTTCHHH
T ss_pred             HhcCHHH
Confidence            6666554

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

Probab=99.39  E-value=2.1e-11  Score=84.86  Aligned_cols=156  Identities=7%  Similarity=-0.026  Sum_probs=123.3

Q ss_pred             hHhhhcCCCC-HHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCccc
Q 031208            3 KIIRYGLSND-QLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus         3 ~m~~~g~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      ++...+..|+ ...+..+-..+...|++++|.+.+++  ..+...+..+...+.+.|++++|...|+++.+..  |+...
T Consensus        90 ~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~  165 (291)
T 3mkr_A           90 REMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD--EDATL  165 (291)
T ss_dssp             HHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHH
T ss_pred             HHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--cCcHH
Confidence            3444455564 44555555788999999999999998  5677889999999999999999999999998764  66431


Q ss_pred             H---HHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHH
Q 031208           82 F---PFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGL  155 (164)
Q Consensus        82 ~---~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~  155 (164)
                      .   ...+..+...|++++|..+++++.+.. +.+...++.+..++.+.|++++|.+.|++..  .| +..+|..+...+
T Consensus       166 ~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~  244 (291)
T 3mkr_A          166 TQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLS  244 (291)
T ss_dssp             HHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            1   122344445589999999999998873 5678899999999999999999999999865  34 677899999999


Q ss_pred             HhcCCCCC
Q 031208          156 AASGDLDA  163 (164)
Q Consensus       156 ~~~g~~~~  163 (164)
                      ...|+.++
T Consensus       245 ~~~g~~~e  252 (291)
T 3mkr_A          245 QHLGKPPE  252 (291)
T ss_dssp             HHTTCCHH
T ss_pred             HHcCCCHH
Confidence            99998753

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.39  E-value=2.2e-11  Score=87.34  Aligned_cols=148  Identities=13%  Similarity=0.077  Sum_probs=108.3

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      .+..+-..+...|++++|...|++..  .| +..++..+...+.+.|++++|...|+++.+.. +.+..+|..+...+.+
T Consensus       205 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~  283 (388)
T 1w3b_A          205 AYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKE  283 (388)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHH
Confidence            34444444444555555555544432  23 45677788888888888888888888887643 2245678888888888


Q ss_pred             ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-CcchHHHHHHHHHhcCCCCCC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .|++++|...++++.+.. +.+..++..+...|.+.|++++|.+.|+++.+  | +..+|..+...|.+.|++++|
T Consensus       284 ~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A  358 (388)
T 1w3b_A          284 KGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEA  358 (388)
T ss_dssp             HSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHH
T ss_pred             cCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHH
Confidence            899999999998888764 55677888888888899999999998888763  3 456888888888888888764

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.35  E-value=2.3e-11  Score=88.51  Aligned_cols=148  Identities=11%  Similarity=0.027  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-c---ccHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-K---FTFPFV   85 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~---~t~~~l   85 (164)
                      ..+|..+...+.+.|++++|...|+.+.+   .+...+..+...+.+.|++++|...|+++.+.  .|+ .   ..+..+
T Consensus        60 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l  137 (450)
T 2y4t_A           60 YIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQL  137 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHH
Confidence            44444444444444444444444444331   23344444444455555555555555554432  122 1   233333


Q ss_pred             HHH------------HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHH
Q 031208           86 IKA------------CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTT  150 (164)
Q Consensus        86 l~~------------~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~  150 (164)
                      ...            +...|++++|...++++.+.. +.+...+..+...|.+.|++++|.++|+++.   ..+..+|..
T Consensus       138 ~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  216 (450)
T 2y4t_A          138 IKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYK  216 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            222            444455555555555544432 2344455555555555555555555555543   224455555


Q ss_pred             HHHHHHhcCCCCC
Q 031208          151 MISGLAASGDLDA  163 (164)
Q Consensus       151 li~~~~~~g~~~~  163 (164)
                      +...|...|++++
T Consensus       217 l~~~~~~~g~~~~  229 (450)
T 2y4t_A          217 ISTLYYQLGDHEL  229 (450)
T ss_dssp             HHHHHHHTTCHHH
T ss_pred             HHHHHHHcCCHHH
Confidence            5555555555543

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.34  E-value=2.5e-11  Score=88.35  Aligned_cols=152  Identities=14%  Similarity=0.013  Sum_probs=126.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      .+...+..+...+.+.|++++|..+|+.+.   ..+...|..+..++...|++++|...|+++.+.+ +.+...+..+..
T Consensus        24 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  102 (450)
T 2y4t_A           24 ADVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGH  102 (450)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHH
Confidence            457778888999999999999999999875   3467889999999999999999999999998764 335678889999


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCch---HHHHHHHH------------HHHhcCCchhHHHHhcccC---CCCcchHH
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDM---FVQSTLMD------------LYLKCGDVDGGRKMFDKMR---VRSVVSWT  149 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~---~~~~~ll~------------~~~~~~~~~~a~~~~~~m~---~~~~~~~~  149 (164)
                      .+.+.|++++|.+.++++.+.. +.+.   ..+..+..            .|.+.|++++|..+|+++.   ..+..++.
T Consensus       103 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  181 (450)
T 2y4t_A          103 LLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRE  181 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHH
Confidence            9999999999999999988654 2233   55555543            4889999999999999876   33677899


Q ss_pred             HHHHHHHhcCCCCCC
Q 031208          150 TMISGLAASGDLDAA  164 (164)
Q Consensus       150 ~li~~~~~~g~~~~A  164 (164)
                      .+...|.+.|++++|
T Consensus       182 ~l~~~~~~~g~~~~A  196 (450)
T 2y4t_A          182 LRAECFIKEGEPRKA  196 (450)
T ss_dssp             HHHHHHHHTTCGGGG
T ss_pred             HHHHHHHHCCCHHHH
Confidence            999999999998875

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.34  E-value=1.8e-13  Score=99.41  Aligned_cols=138  Identities=11%  Similarity=0.083  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-------------------
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNG-------------------   74 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-------------------   74 (164)
                      .+|..+..++.+.|++++|.+.|.+.  +|...|..++.++...|++++|...++..++..                   
T Consensus        33 ~vWs~La~A~l~~g~~~eAIdsfika--~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~~~~~~i~~~Li~~Y~Klg~l  110 (449)
T 1b89_A           33 AVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRL  110 (449)
T ss_dssp             ------------------------------------------------------------------------------CH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHcC--CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHhCCH
Confidence            35555555555555555555555432  333344444444444444444444333332210                   


Q ss_pred             -------CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcch
Q 031208           75 -------FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVS  147 (164)
Q Consensus        75 -------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~  147 (164)
                             -.|+..+|..+...|...|.+++|..+|..+         ..|..+..++.+.|+++.|.+.++++.  ++.+
T Consensus       111 ~e~e~f~~~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA~--~~~~  179 (449)
T 1b89_A          111 AELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN--STRT  179 (449)
T ss_dssp             HHHTTTTTCC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHHT--CHHH
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHcC--Cchh
Confidence                   0244445555555555555555555555543         245555555555555555555555552  6677


Q ss_pred             HHHHHHHHHhcCCCCCC
Q 031208          148 WTTMISGLAASGDLDAA  164 (164)
Q Consensus       148 ~~~li~~~~~~g~~~~A  164 (164)
                      |..++.+|...|+|++|
T Consensus       180 Wk~v~~aCv~~~ef~lA  196 (449)
T 1b89_A          180 WKEVCFACVDGKEFRLA  196 (449)
T ss_dssp             HHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHcCcHHHH
Confidence            88888888887776654

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

Probab=99.34  E-value=9.2e-11  Score=78.46  Aligned_cols=152  Identities=11%  Similarity=0.015  Sum_probs=127.3

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      .+...+..+...+.+.|++++|...+++..   ..+...+..+...+...|++++|...+++..+.. +.+...+..+..
T Consensus        55 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~  133 (243)
T 2q7f_A           55 EDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGT  133 (243)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            357778888889999999999999999875   3467788888899999999999999999987753 345667888889


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+...|++++|...+++..+.. +.+...+..+...|.+.|++++|.+.|++..   ..+..+|..+...|.+.|++++|
T Consensus       134 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  212 (243)
T 2q7f_A          134 VLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKA  212 (243)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHH
Confidence            9999999999999999988764 3467788888999999999999999998775   23567889999999999998864

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.32  E-value=4.8e-11  Score=80.47  Aligned_cols=151  Identities=13%  Similarity=-0.040  Sum_probs=101.6

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~   87 (164)
                      +...+..+...+.+.|++++|.+++++..   ..+...+..+...+...|++++|...+++....+..| +...+..+..
T Consensus        70 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~  149 (252)
T 2ho1_A           70 SADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGL  149 (252)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHH
Confidence            45566666677777777777777777654   2355667777777777777777777777776533344 3445666667


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHHHHHhcCCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~  163 (164)
                      .+...|++++|...+++..+.. +.+...+..+...|.+.|++++|...|++..+   .+...+..+...|...|++++
T Consensus       150 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  227 (252)
T 2ho1_A          150 VSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDT  227 (252)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHH
Confidence            7777777777777777776654 33456677777777777777777777776542   244566667777777776554

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.32  E-value=1.3e-10  Score=74.24  Aligned_cols=150  Identities=11%  Similarity=-0.022  Sum_probs=124.4

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...+..+...+...|++++|...++...+   .+...+..+...+...|++++|...+++..+.. +.+...+..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            34566677788899999999999998863   467788888899999999999999999987653 33566788888999


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...|++++|.+.+++..+.. +.+...+..+...|.+.|++++|.+.+++..   ..+..+|..+...|...|++++|
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999988764 4567788888899999999999999998875   23567888899999999887654

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.31  E-value=7e-11  Score=84.67  Aligned_cols=150  Identities=15%  Similarity=0.034  Sum_probs=87.5

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc-ccHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK-FTFPFV   85 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~l   85 (164)
                      +.+...|..+...+.+.|++++|...|+++.  .| +...|..+..++.+.|++++|...|+++.+.  .|+. ..+..+
T Consensus        64 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l  141 (388)
T 1w3b_A           64 PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY--NPDLYCVRSDL  141 (388)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH--CTTCTHHHHHH
T ss_pred             CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHH
Confidence            3455666667777777777777777777654  23 3445666666677777777777777666553  2433 334445


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~  162 (164)
                      -..+...|++++|.+.++++.+.. +.+...|..+...|.+.|++++|...|+++.  .| +...|..+-..+...|+++
T Consensus       142 ~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~  220 (388)
T 1w3b_A          142 GNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFD  220 (388)
T ss_dssp             HHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTT
T ss_pred             HHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHH
Confidence            555566666666666666666543 2234566666666666666666666666553  22 2334444444444444444

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

Probab=99.29  E-value=6.3e-11  Score=78.21  Aligned_cols=148  Identities=10%  Similarity=-0.049  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhc-CChhHHHHHHHHHHHcCCCCC-cccHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTID-GSSLQALLLYNLMICNGFRPD-KFTFPFVIK   87 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~   87 (164)
                      ...+..+...+...|++++|.++++...   ..+...+..+...+... |++++|...+++..+.+..|+ ...+..+..
T Consensus        42 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~  121 (225)
T 2vq2_A           42 ELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGI  121 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHH
Confidence            4445555555555555555555555543   12344555555555555 556666665555554222222 234455555


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---C-CCcchHHHHHHHHHhcCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---V-RSVVSWTTMISGLAASGDL  161 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~-~~~~~~~~li~~~~~~g~~  161 (164)
                      .+...|++++|...+++..+.. +.+...+..+...|.+.|++++|.+.+++..   . .+...+..+...+...|+.
T Consensus       122 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (225)
T 2vq2_A          122 CSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNA  198 (225)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcH
Confidence            5555556666655555555443 2234455555555555566666655555543   1 2334444444444544443

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

Probab=99.28  E-value=1.4e-10  Score=77.26  Aligned_cols=149  Identities=17%  Similarity=0.041  Sum_probs=112.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhc-----------CChhHHHHHHHHHHHcCCCC
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTID-----------GSSLQALLLYNLMICNGFRP   77 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~~~p   77 (164)
                      +...+..+-..+.+.|++++|...|++..  .| +...+..+-..+...           |++++|...|++..+.  .|
T Consensus        38 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P  115 (217)
T 2pl2_A           38 DPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NP  115 (217)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CT
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--Cc
Confidence            46667777777888888888888888765  34 556777777778888           8888888888888764  35


Q ss_pred             -CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHH
Q 031208           78 -DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMIS  153 (164)
Q Consensus        78 -~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~  153 (164)
                       +...+..+-..+...|++++|...+++..+..  .+...+..+-..|...|++++|...|++..  .| +...+..+..
T Consensus       116 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~  193 (217)
T 2pl2_A          116 RYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYAS  193 (217)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHH
Confidence             45567777788888899999999999888877  677888888888999999999999998775  34 5678888888


Q ss_pred             HHHhcCCCCCC
Q 031208          154 GLAASGDLDAA  164 (164)
Q Consensus       154 ~~~~~g~~~~A  164 (164)
                      .+.+.|++++|
T Consensus       194 ~~~~~g~~~~A  204 (217)
T 2pl2_A          194 ALLLKGKAEEA  204 (217)
T ss_dssp             HHTC-------
T ss_pred             HHHHccCHHHH
Confidence            89999988876

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

Probab=99.27  E-value=2.4e-10  Score=75.40  Aligned_cols=152  Identities=7%  Similarity=-0.132  Sum_probs=126.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+...+...|++++|...|+...   ..+...|..+...+...|++++|...+++..+.. +.+...+..+...
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~   85 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWF   85 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            56678888889999999999999999875   2457788889999999999999999999997753 3356688888999


Q ss_pred             HHhc-cchhhHHHHHHHHHHhCCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCC
Q 031208           89 CIAS-LAIEKGKEVHGLAVKAGFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus        89 ~~~~-~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      +... |++++|...+++..+.+..| +...+..+...|.+.|++++|...|+++.  .| +...|..+...|.+.|++++
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  165 (225)
T 2vq2_A           86 LCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGD  165 (225)
T ss_dssp             HHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHH
Confidence            9999 99999999999988733334 36788888899999999999999998875  33 56788889999999998765


Q ss_pred             C
Q 031208          164 A  164 (164)
Q Consensus       164 A  164 (164)
                      |
T Consensus       166 A  166 (225)
T 2vq2_A          166 A  166 (225)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=99.27  E-value=2.2e-10  Score=73.92  Aligned_cols=151  Identities=13%  Similarity=0.038  Sum_probs=124.6

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      ++.+|..+=..+.+.|++++|.+.|++..  .| +...|..+-..+.+.|++++|...+.+..... +-+...+..+...
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~   82 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGSA   82 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHHH
Confidence            56678888889999999999999999875  34 67788889999999999999999999987653 2244566677788


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +...++++.+...+.+..+.. +.+...+..+-..|.+.|++++|.+.|++..  .| +..+|..+-..|.+.|++++|
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A  160 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEA  160 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHH
Confidence            888999999999999887764 4457788888899999999999999998775  33 667889999999999988765

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.25  E-value=1.2e-10  Score=78.61  Aligned_cols=151  Identities=11%  Similarity=-0.087  Sum_probs=127.3

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...+..+...+...|++++|..+|+...   ..+...+..+...+...|++++|.+.+++..+.. +.+...+..+...+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~  115 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHH
Confidence            5667788888999999999999999875   2467788999999999999999999999997753 33567888889999


Q ss_pred             HhccchhhHHHHHHHHHHhCCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...|++++|.+++++..+.+..| +...+..+...|.+.|++++|.+.|++..   ..+...|..+...|...|++++|
T Consensus       116 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999988743445 56788888899999999999999999875   23577889999999999987654

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

Probab=99.25  E-value=1.4e-10  Score=82.42  Aligned_cols=152  Identities=9%  Similarity=-0.078  Sum_probs=95.8

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--------------
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG--------------   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--------------   74 (164)
                      +..+|..+...+.+.|++++|...|++..  . .+..+|..+...+...|++++|...|+++.+..              
T Consensus        98 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~  177 (365)
T 4eqf_A           98 DAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSP  177 (365)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC--------
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccch
Confidence            56667777777777777777777777664  2 346667777777777777777777777765421              


Q ss_pred             ----------------------------CCC---CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           75 ----------------------------FRP---DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        75 ----------------------------~~p---~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                                                  ..|   +...+..+...+...|++++|...+++..+.. +.+..+|..+...
T Consensus       178 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  256 (365)
T 4eqf_A          178 GLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGAT  256 (365)
T ss_dssp             -----------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence                                        012   34455566666666666666666666665543 3345566666666


Q ss_pred             HHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          124 YLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      |.+.|++++|.+.|++..  .| +..+|..+...|.+.|++++|
T Consensus       257 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A  300 (365)
T 4eqf_A          257 LANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYREA  300 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHH
Confidence            666666666666666554  22 355666666666666666543

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

Probab=99.23  E-value=2.3e-10  Score=76.14  Aligned_cols=153  Identities=15%  Similarity=0.025  Sum_probs=128.0

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      +++...+..+-..+.+.|++++|...|++..+   .+...|..+-..+.+.|++++|...|++..+.. +-+...+..+-
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            56778888888899999999999999998653   467788888999999999999999999998753 23456788888


Q ss_pred             HHHHhc-----------cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--CCcchHHHHHH
Q 031208           87 KACIAS-----------LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--RSVVSWTTMIS  153 (164)
Q Consensus        87 ~~~~~~-----------~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~  153 (164)
                      ..+.+.           |++++|...+++..+.. +.+...+..+-..|...|++++|...|++..+  .+...|..+-.
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~  159 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALAE  159 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHHH
Confidence            999999           99999999999998774 34577888888999999999999999987642  56678888999


Q ss_pred             HHHhcCCCCCC
Q 031208          154 GLAASGDLDAA  164 (164)
Q Consensus       154 ~~~~~g~~~~A  164 (164)
                      .|...|++++|
T Consensus       160 ~~~~~g~~~~A  170 (217)
T 2pl2_A          160 LYLSMGRLDEA  170 (217)
T ss_dssp             HHHHHTCHHHH
T ss_pred             HHHHcCCHHHH
Confidence            99999988764

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.21  E-value=2.9e-11  Score=87.99  Aligned_cols=136  Identities=8%  Similarity=-0.060  Sum_probs=80.2

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      .+++.+.+.++.+|.+.|+++++.++++   .|+..+|..+-..|...|++++|...|..+         ..|..+..++
T Consensus        91 ~~~~~i~~~Li~~Y~Klg~l~e~e~f~~---~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L  158 (449)
T 1b89_A           91 ARESYVETELIFALAKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTL  158 (449)
T ss_dssp             ------------------CHHHHTTTTT---CC----------------CTTTHHHHHHHT---------TCHHHHHHHH
T ss_pred             CccchhHHHHHHHHHHhCCHHHHHHHHc---CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHH
Confidence            3456778888889999998888887775   477789999999999999999999999877         3788999999


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCCCCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+.|++++|.+.+..+      .++.+|..++.+|...|+++.|......+. ....-...++..|.+.|++++|
T Consensus       159 ~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-~~ad~l~~lv~~Yek~G~~eEa  226 (449)
T 1b89_A          159 VHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-VHADELEELINYYQDRGYFEEL  226 (449)
T ss_dssp             HTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-hCHhhHHHHHHHHHHCCCHHHH
Confidence            9999999998888877      367888999999999998888887777655 2222234578888888887654

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

Probab=99.21  E-value=1.2e-10  Score=78.43  Aligned_cols=153  Identities=10%  Similarity=-0.021  Sum_probs=122.9

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC--Cc--------HhHHHHHHHHHHhcCChhHHHHHHHHHHHcC------
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PH--------VFTWNLMIRALTIDGSSLQALLLYNLMICNG------   74 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~--------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~------   74 (164)
                      .+...+..+-..+...|++++|...++...+  |+        ...|..+-..+...|++++|...|++.....      
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  115 (258)
T 3uq3_A           36 KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTADIL  115 (258)
T ss_dssp             CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHH
T ss_pred             ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchhHHH
Confidence            6777888888899999999999999988762  21        5778888889999999999999999987632      


Q ss_pred             ------------------CCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHH
Q 031208           75 ------------------FRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRK  135 (164)
Q Consensus        75 ------------------~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~  135 (164)
                                        ..| +...+..+...+...|++++|...+++..+.. +.+...+..+...|.+.|++++|.+
T Consensus       116 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  194 (258)
T 3uq3_A          116 TKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIA  194 (258)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHH
Confidence                              223 34567777888889999999999999988765 4467788888999999999999999


Q ss_pred             HhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          136 MFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       136 ~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .|++..  .| +..+|..+...|.+.|++++|
T Consensus       195 ~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A  226 (258)
T 3uq3_A          195 DCNKAIEKDPNFVRAYIRKATAQIAVKEYASA  226 (258)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHH
Confidence            998775  33 567888888889888887654

>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=99.20  E-value=9.9e-10  Score=66.41  Aligned_cols=125  Identities=16%  Similarity=0.078  Sum_probs=106.2

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      .|..+...+...|++++|..+++.+.   ..+...+..+...+...|++++|...++++...+ +.+...+..+...+..
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            56777888999999999999999875   3467788888899999999999999999997754 3355678888899999


Q ss_pred             ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .|++++|.++++++.+.. +.+...+..+...|.+.|++++|.+.|+++.
T Consensus        82 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  130 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKAL  130 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            999999999999998765 3457788889999999999999999998764

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

Probab=99.19  E-value=2.1e-10  Score=79.75  Aligned_cols=147  Identities=10%  Similarity=0.045  Sum_probs=108.4

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccC----CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIR----CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      +|+...+..+...+...++.+.|.+.++.+.    .| +...+..+-..+...|++++|.+.+++      +.+...+..
T Consensus        62 ~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~  135 (291)
T 3mkr_A           62 APELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAM  135 (291)
T ss_dssp             CHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHH
Confidence            4566677777788888888888888888753    24 344555555777888888888888877      456677888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHH---HHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhc
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQ---STLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAAS  158 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~---~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~  158 (164)
                      +...+.+.|+.++|.+.++.+.+..  |+....   ..++..+...|++++|..+|+++.   ..+...|+.+..+|.+.
T Consensus       136 l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~  213 (291)
T 3mkr_A          136 TVQILLKLDRLDLARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQ  213 (291)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHc
Confidence            8888889999999999999888764  553221   223344445688999999998876   23667888899999999


Q ss_pred             CCCCCC
Q 031208          159 GDLDAA  164 (164)
Q Consensus       159 g~~~~A  164 (164)
                      |++++|
T Consensus       214 g~~~eA  219 (291)
T 3mkr_A          214 GRWEAA  219 (291)
T ss_dssp             TCHHHH
T ss_pred             CCHHHH
Confidence            988765

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.18  E-value=8.7e-10  Score=78.09  Aligned_cols=150  Identities=9%  Similarity=-0.090  Sum_probs=84.8

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-------------
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF-------------   75 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-------------   75 (164)
                      +..++..+...+.+.|+++.|.+.|+...   ..+..++..+...+...|++++|...++++.....             
T Consensus        97 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  176 (368)
T 1fch_A           97 HMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGA  176 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC------
T ss_pred             CHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHh
Confidence            45566667777777777777777777654   23566677777777777777777777777654321             


Q ss_pred             ----------------------------------CC---CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           76 ----------------------------------RP---DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        76 ----------------------------------~p---~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                                                        .|   +..++..+...+.+.|++++|...+++..+.. +.+...+.
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~  255 (368)
T 1fch_A          177 GGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWN  255 (368)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             hhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHH
Confidence                                              11   13344444555555555555555555554432 22344555


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLD  162 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~  162 (164)
                      .+...|.+.|++++|.+.|++..  .| +..+|..+...|.+.|+++
T Consensus       256 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~  302 (368)
T 1fch_A          256 KLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHR  302 (368)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHH
Confidence            55555555555555555555443  12 3445555555555555544

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

Probab=99.18  E-value=1.3e-10  Score=77.65  Aligned_cols=152  Identities=13%  Similarity=0.066  Sum_probs=111.7

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      .+...|..+-..+...|+++.|..+|++..+   .+...+..+...+...|++++|...+++..+.. +.+...+..+..
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   99 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGN   99 (243)
T ss_dssp             ---------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHH
Confidence            3456677777788899999999999998752   467888889999999999999999999997753 335678888899


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+...|++++|.+.+++..+.. +.+...+..+...|.+.|++++|...+++..   ..+...|..+...|.+.|++++|
T Consensus       100 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  178 (243)
T 2q7f_A          100 VYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEA  178 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999999998775 4567788889999999999999999999875   33677888999999999998764

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.17  E-value=1.1e-09  Score=77.50  Aligned_cols=120  Identities=13%  Similarity=0.021  Sum_probs=103.1

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      +..++..+...+.+.|++++|...|++..... +.+...+..+...+...|++++|...+++..+.. +.+...+..+..
T Consensus       216 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~  293 (368)
T 1fch_A          216 DPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGI  293 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            46788889999999999999999999997753 3356789999999999999999999999998764 456788999999


Q ss_pred             HHHhcCCchhHHHHhcccC--CC-C-----------cchHHHHHHHHHhcCCCCCC
Q 031208          123 LYLKCGDVDGGRKMFDKMR--VR-S-----------VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~--~~-~-----------~~~~~~li~~~~~~g~~~~A  164 (164)
                      .|.+.|++++|...|++..  .| +           ..+|..+..+|...|++++|
T Consensus       294 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  349 (368)
T 1fch_A          294 SCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY  349 (368)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhH
Confidence            9999999999999998875  12 2           57899999999999998865

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.15  E-value=6.7e-10  Score=77.35  Aligned_cols=121  Identities=11%  Similarity=-0.031  Sum_probs=51.0

Q ss_pred             HHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--------CCCCcccHHHHHH
Q 031208           19 LLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG--------FRPDKFTFPFVIK   87 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--------~~p~~~t~~~ll~   87 (164)
                      +...+...|++++|...++...+   .+...+..+...+...|++++|...+++..+..        .+.+...+..+..
T Consensus       165 l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~  244 (330)
T 3hym_B          165 IGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGH  244 (330)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHH
Confidence            33344444444444444443321   223344444444444444444444444443210        0112234444444


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      .+...|++++|...+++..+.. +.+...+..+...|.+.|++++|.+.|++.
T Consensus       245 ~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  296 (330)
T 3hym_B          245 VCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTA  296 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTT
T ss_pred             HHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            4444444444444444444332 123334444444444444444444444444

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.15  E-value=1e-09  Score=76.46  Aligned_cols=151  Identities=11%  Similarity=0.013  Sum_probs=100.6

Q ss_pred             CHHHHHHHHHHHhccC-CcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYG-KTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      +...|..+-..+...| +++.|...|++..+   .+...|..+...+...|++++|...|++..+.. +.+...+..+..
T Consensus        89 ~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~  167 (330)
T 3hym_B           89 NPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGL  167 (330)
T ss_dssp             STHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHH
Confidence            4556666666777777 77777777776542   244567777777777777777777777776543 223455666777


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC-----------C-CcchHHHHHHHH
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-----------R-SVVSWTTMISGL  155 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----------~-~~~~~~~li~~~  155 (164)
                      .+...|++++|...+++..+.. +.+...+..+...|.+.|++++|...|++...           | +..+|..+...|
T Consensus       168 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~  246 (330)
T 3hym_B          168 EYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVC  246 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHH
Confidence            7777777777777777776543 34456777777777777888777777765541           2 245777777777


Q ss_pred             HhcCCCCCC
Q 031208          156 AASGDLDAA  164 (164)
Q Consensus       156 ~~~g~~~~A  164 (164)
                      ...|++++|
T Consensus       247 ~~~g~~~~A  255 (330)
T 3hym_B          247 RKLKKYAEA  255 (330)
T ss_dssp             HHTTCHHHH
T ss_pred             HHhcCHHHH
Confidence            777776543

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.12  E-value=2.8e-09  Score=82.65  Aligned_cols=150  Identities=11%  Similarity=0.092  Sum_probs=131.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~   87 (164)
                      +...++.+=..+.+.|++++|.+.|++..  .| +...|..+-.+|.+.|++++|...|++..+.  .|+ ...|..+-.
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~   85 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            46788888999999999999999999876  34 5788999999999999999999999999774  464 568899999


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ++.+.|++++|.+.+++..+.. +-+...|+.+-..|.+.|++++|.+.|++..  .| +...|..+...|...|++++|
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A  164 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDY  164 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHH
Confidence            9999999999999999998764 3457789999999999999999999999875  44 567999999999999999875

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

Probab=99.10  E-value=3.7e-10  Score=80.18  Aligned_cols=146  Identities=10%  Similarity=-0.035  Sum_probs=117.4

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC--CC---cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR--CP---HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~--~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      +..+...+.+.|++++|..+|++..  .|   +..+|..+...+...|++++|...|++..+.. +.+..+|..+...+.
T Consensus       180 ~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~  258 (365)
T 4eqf_A          180 TRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLA  258 (365)
T ss_dssp             ---------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            4455778889999999999999886  23   57889999999999999999999999997753 345678999999999


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-------------CcchHHHHHHHH
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-------------SVVSWTTMISGL  155 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-------------~~~~~~~li~~~  155 (164)
                      ..|++++|...+++..+.. +.+...+..+...|.+.|++++|...|++..+  |             +..+|..+-.++
T Consensus       259 ~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  337 (365)
T 4eqf_A          259 NGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIAL  337 (365)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHH
Confidence            9999999999999998774 34578899999999999999999999998751  1             267899999999


Q ss_pred             HhcCCCCC
Q 031208          156 AASGDLDA  163 (164)
Q Consensus       156 ~~~g~~~~  163 (164)
                      ...|+.+.
T Consensus       338 ~~~g~~~~  345 (365)
T 4eqf_A          338 SLMDQPEL  345 (365)
T ss_dssp             HHHTCHHH
T ss_pred             HHcCcHHH
Confidence            88887653

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.09  E-value=4.6e-09  Score=72.97  Aligned_cols=151  Identities=11%  Similarity=-0.034  Sum_probs=91.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-------------
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF-------------   75 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-------------   75 (164)
                      +...+..+...+...|++++|...|++..   ..+...+..+...+...|++++|...+++......             
T Consensus        54 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  133 (327)
T 3cv0_A           54 REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQAD  133 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTTTC--------
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHH
Confidence            56667777777888888888888887765   23566777777777888888888877777654310             


Q ss_pred             -----------------------------------CCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHH
Q 031208           76 -----------------------------------RPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTL  120 (164)
Q Consensus        76 -----------------------------------~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  120 (164)
                                                         +.+...+..+...+...|++++|...+++..+.. +.+...+..+
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l  212 (327)
T 3cv0_A          134 VDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKL  212 (327)
T ss_dssp             ------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHH
Confidence                                               1123344444455555566666666665555443 2334555555


Q ss_pred             HHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCC
Q 031208          121 MDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       121 l~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~  163 (164)
                      ...|.+.|++++|...|++..   ..+..+|..+...|.+.|++++
T Consensus       213 ~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~  258 (327)
T 3cv0_A          213 GATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDL  258 (327)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHH
Confidence            566666666666666665543   1234455556666666665543

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

Probab=99.07  E-value=5.1e-09  Score=77.15  Aligned_cols=153  Identities=13%  Similarity=-0.012  Sum_probs=110.3

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-------
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-------   80 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-------   80 (164)
                      |+...|..+..++.+.|+++.|...++...  .| +...|..+..++.+.|++++|...|+++...+- ++..       
T Consensus        37 p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~~~  115 (514)
T 2gw1_A           37 EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEGLGKFADAMFDLSVLSLNGD-FNDASIEPMLE  115 (514)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSS-CCGGGTHHHHH
T ss_pred             ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CccchHHHHHH
Confidence            789999999999999999999999999875  34 567889999999999999999999999876541 1111       


Q ss_pred             ------------------------------------------------------------------------cHHHHHHH
Q 031208           81 ------------------------------------------------------------------------TFPFVIKA   88 (164)
Q Consensus        81 ------------------------------------------------------------------------t~~~ll~~   88 (164)
                                                                                              .+......
T Consensus       116 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (514)
T 2gw1_A          116 RNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLS  195 (514)
T ss_dssp             HHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHH
Confidence                                                                                    11111122


Q ss_pred             HH---hccchhhHHHHHHHHHH-----hCC--------CCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHH
Q 031208           89 CI---ASLAIEKGKEVHGLAVK-----AGF--------SRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTT  150 (164)
Q Consensus        89 ~~---~~~~~~~a~~~~~~m~~-----~g~--------~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~  150 (164)
                      +.   +.|++++|..+++++.+     ..-        +.+...+..+...|.+.|++++|..+|++..  .|+...|..
T Consensus       196 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~  275 (514)
T 2gw1_A          196 NLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPRVNSYIY  275 (514)
T ss_dssp             HHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCCHHHHHH
T ss_pred             HHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccHHHHHH
Confidence            22   26788888888888776     211        2234566677777888888888888887764  334667777


Q ss_pred             HHHHHHhcCCCCCC
Q 031208          151 MISGLAASGDLDAA  164 (164)
Q Consensus       151 li~~~~~~g~~~~A  164 (164)
                      +...|...|++++|
T Consensus       276 l~~~~~~~~~~~~A  289 (514)
T 2gw1_A          276 MALIMADRNDSTEY  289 (514)
T ss_dssp             HHHHHHTSSCCTTG
T ss_pred             HHHHHHHCCCHHHH
Confidence            77777777777764

>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=99.05  E-value=2.9e-09  Score=64.29  Aligned_cols=117  Identities=20%  Similarity=0.189  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL  125 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  125 (164)
                      .|..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|..+++++...+ +.+...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            56777888999999999999999997753 3356678888899999999999999999998775 445678888999999


Q ss_pred             hcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208          126 KCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +.|++++|.++|+++.   ..+..+|..+...|.+.|++++|
T Consensus        81 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  122 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEA  122 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHH
Confidence            9999999999999875   23567888899999999987654

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

Probab=99.05  E-value=1.8e-09  Score=72.56  Aligned_cols=152  Identities=14%  Similarity=0.012  Sum_probs=124.9

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCC----cccHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG--FRPD----KFTFPF   84 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~   84 (164)
                      ...+..+-..+...|++++|..+|+...+  .+...|..+-..+...|++++|...+++..+..  ..|+    ...+..
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            45677788899999999999999987642  667789999999999999999999999986632  1122    478888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhC------------------------CCC-chHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAG------------------------FSR-DMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g------------------------~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      +...+...|++++|...+++..+..                        ..| +...+..+...|.+.|++++|...|++
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  164 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTE  164 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            9999999999999999999988742                        233 456778888899999999999999998


Q ss_pred             cC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208          140 MR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       140 m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ..   ..+..+|..+...|.+.|++++|
T Consensus       165 a~~~~~~~~~~~~~l~~~~~~~~~~~~A  192 (258)
T 3uq3_A          165 MIKRAPEDARGYSNRAAALAKLMSFPEA  192 (258)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHhcCcccHHHHHHHHHHHHHhCCHHHH
Confidence            75   33677899999999999988754

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.04  E-value=1.5e-08  Score=64.57  Aligned_cols=129  Identities=11%  Similarity=-0.093  Sum_probs=111.3

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      .+..++..+...+...|++++|...++...   ..+...+..+...+...|++++|...+++..+.. +.+...+..+..
T Consensus        40 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~  118 (186)
T 3as5_A           40 FDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGV  118 (186)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHH
Confidence            357778888889999999999999999875   3467788888999999999999999999997753 345677888889


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+...|++++|...+++..+.. +.+...+..+...|.+.|++++|.+.+++..
T Consensus       119 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  171 (186)
T 3as5_A          119 ALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALPHFKKAN  171 (186)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999999999998775 4567888999999999999999999998765

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.03  E-value=1.7e-09  Score=75.13  Aligned_cols=140  Identities=7%  Similarity=-0.090  Sum_probs=119.1

Q ss_pred             HhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHH
Q 031208           23 CSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      +...|++++|..+++...   ..+...+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|.
T Consensus       148 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~  226 (327)
T 3cv0_A          148 FAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEAL  226 (327)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHH
Confidence            778899999999999875   2467889999999999999999999999997753 335678889999999999999999


Q ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-------------CcchHHHHHHHHHhcCCCCCC
Q 031208          100 EVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-------------SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       100 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-------------~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ..+++..+.. +.+...+..+...|.+.|++++|.+.|++..  .|             +..+|..+...|.+.|++++|
T Consensus       227 ~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  305 (327)
T 3cv0_A          227 DAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLV  305 (327)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHH
Confidence            9999998765 3467788999999999999999999998775  22             366889999999999987654

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

Probab=99.02  E-value=6e-09  Score=73.16  Aligned_cols=150  Identities=9%  Similarity=0.014  Sum_probs=112.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC----CcccHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP----DKFTFPF   84 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p----~~~t~~~   84 (164)
                      +..++..+-..+...|+++.|...|+...  .| +...|..+...+...|++++|...|++..+.  .|    +...+..
T Consensus        36 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~  113 (359)
T 3ieg_A           36 NYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQ  113 (359)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCcccChHHHHHH
Confidence            46677777788888888888888888765  23 5677888888888888888888888888764  34    2233333


Q ss_pred             H------------HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHH
Q 031208           85 V------------IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWT  149 (164)
Q Consensus        85 l------------l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~  149 (164)
                      +            ...+...|++++|..++++..+.. +.+...+..+...|.+.|++++|...+++...   .+..+|.
T Consensus       114 l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  192 (359)
T 3ieg_A          114 LVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFY  192 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            3            467788888888888888887664 34667788888888888888888888887652   3566788


Q ss_pred             HHHHHHHhcCCCCCC
Q 031208          150 TMISGLAASGDLDAA  164 (164)
Q Consensus       150 ~li~~~~~~g~~~~A  164 (164)
                      .+...|...|++++|
T Consensus       193 ~la~~~~~~~~~~~A  207 (359)
T 3ieg_A          193 KISTLYYQLGDHELS  207 (359)
T ss_dssp             HHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHcCCHHHH
Confidence            888888888876643

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

Probab=99.02  E-value=2.3e-09  Score=79.05  Aligned_cols=151  Identities=10%  Similarity=0.013  Sum_probs=120.7

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      +..++..+...+...|+++.|..+|+...  .|+...|..+...+...|++++|...+++..... +.+...+..+...+
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~  314 (514)
T 2gw1_A          236 LAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMN  314 (514)
T ss_dssp             HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHH
Confidence            45667777888888999999999998875  3557778888888899999999999999987653 33566788888889


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcCCCCCC
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...|++++|...+++..+.. +.+...+..+...|.+.|++++|..+|+++.   ..+..+|..+...|.+.|++++|
T Consensus       315 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  391 (514)
T 2gw1_A          315 FILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFDKA  391 (514)
T ss_dssp             HHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHHHH
Confidence            99999999999999888764 3456788888888899999999999988765   23567888888888888887653

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

Probab=99.00  E-value=5.1e-09  Score=73.51  Aligned_cols=150  Identities=13%  Similarity=-0.015  Sum_probs=123.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      |+..+..+-..+...|++++|...|+...  . .+...+..+-..+...|++++|...|++..+.. +-+...+..+...
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~   80 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHH
Confidence            45567778888999999999999999875  2 457788999999999999999999999997753 2255788899999


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCC----chHHHHHH------------HHHHHhcCCchhHHHHhcccC---CCCcchHH
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSR----DMFVQSTL------------MDLYLKCGDVDGGRKMFDKMR---VRSVVSWT  149 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~----~~~~~~~l------------l~~~~~~~~~~~a~~~~~~m~---~~~~~~~~  149 (164)
                      +...|++++|...+++..+..  |    +...+..+            ...+...|++++|.++|+++.   ..+...+.
T Consensus        81 ~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  158 (359)
T 3ieg_A           81 LLKQGKLDEAEDDFKKVLKSN--PSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRE  158 (359)
T ss_dssp             HHHHTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHH
Confidence            999999999999999987653  4    34444444            478889999999999999875   33667888


Q ss_pred             HHHHHHHhcCCCCCC
Q 031208          150 TMISGLAASGDLDAA  164 (164)
Q Consensus       150 ~li~~~~~~g~~~~A  164 (164)
                      .+...|...|++++|
T Consensus       159 ~~~~~~~~~~~~~~A  173 (359)
T 3ieg_A          159 LRAECFIKEGEPRKA  173 (359)
T ss_dssp             HHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHCCCHHHH
Confidence            999999999987654

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

Probab=98.99  E-value=1.8e-08  Score=68.43  Aligned_cols=137  Identities=9%  Similarity=-0.034  Sum_probs=94.5

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc--ccHHHHHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK--FTFPFVIKAC   89 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~~ll~~~   89 (164)
                      .+-..-..+.+.|+++.|..+|+...  .| +...+..+...+...|++++|...+++..+.+-.|+.  ..|..+-..+
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~   84 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKIL   84 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHH
Confidence            34445567777888888888888764  23 3446777777888888888888888888763322222  1267777888


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-CcchHHHHH
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMI  152 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li  152 (164)
                      ...|++++|...++...+.. +.+...+..+...|.+.|++++|.+.|++..+  | +...|..+-
T Consensus        85 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~  149 (272)
T 3u4t_A           85 MKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELG  149 (272)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHH
T ss_pred             HHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHH
Confidence            88888888888888877654 33456777788888888888888888877653  2 334454444

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

Probab=98.99  E-value=9.4e-09  Score=69.83  Aligned_cols=124  Identities=13%  Similarity=-0.082  Sum_probs=86.6

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +..++..+-..+...|++++|...|++..  . .+...|..+-..+...|++++|...|++..+.. +.+...+..+...
T Consensus        42 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~  120 (275)
T 1xnf_A           42 RAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIA  120 (275)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHH
Confidence            46667777778888888888888888765  2 356778888888888888888888888886642 2345677777888


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhc
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFD  138 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  138 (164)
                      +...|++++|...+++..+..  |+.......+..+.+.|++++|...++
T Consensus       121 ~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~  168 (275)
T 1xnf_A          121 LYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLK  168 (275)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHhcCHHHHHHHHH
Confidence            888888888888888877653  443333344444455566666666553

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=98.98  E-value=7.2e-09  Score=76.91  Aligned_cols=148  Identities=13%  Similarity=0.055  Sum_probs=113.8

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC--CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR--CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      ++..+-..+...|+++.|...|+...  .|+...|..+-..+...|++++|...|++..+.. +.+...+..+...+...
T Consensus       245 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~  323 (537)
T 3fp2_A          245 ALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFIL  323 (537)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhc
Confidence            45555567777888888888888775  4667778888888888888899988888887643 23456788888888888


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--C-CCcchHHHHHHHHHhcCCCCCC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--V-RSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~-~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      |++++|...+++..+.. +.+...+..+...|.+.|++++|.+.|++..  . .+...|..+...|...|++++|
T Consensus       324 ~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  397 (537)
T 3fp2_A          324 QDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTA  397 (537)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHH
Confidence            88888888888887764 3346678888888888888888888888765  2 3566888888888888877653

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

Probab=98.96  E-value=6.2e-09  Score=77.06  Aligned_cols=150  Identities=12%  Similarity=-0.006  Sum_probs=107.2

Q ss_pred             CHHHHHHHHHHHhccCCc-HHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKT-DHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~-~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      +...+..+-..+...|++ ++|.+.|++..  .| +...|..+-..|...|++++|...|++..+.  .|+...+..+-.
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~  178 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSM  178 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHH
Confidence            456666666777778888 88888887764  23 4667777777888888888888888887664  366667777777


Q ss_pred             HHHhc---------cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc--------CCchhHHHHhcccC--CC----C
Q 031208           88 ACIAS---------LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC--------GDVDGGRKMFDKMR--VR----S  144 (164)
Q Consensus        88 ~~~~~---------~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~--------~~~~~a~~~~~~m~--~~----~  144 (164)
                      .+...         |++++|.+.+++..+.. +.+...|..+-..|...        |++++|.+.|++..  .|    +
T Consensus       179 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  257 (474)
T 4abn_A          179 VLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSN  257 (474)
T ss_dssp             HHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGC
T ss_pred             HHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccC
Confidence            77777         78888888888777654 33466777777777777        77888887777654  23    5


Q ss_pred             cchHHHHHHHHHhcCCCCCC
Q 031208          145 VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       145 ~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...|..+-..|...|++++|
T Consensus       258 ~~~~~~lg~~~~~~g~~~~A  277 (474)
T 4abn_A          258 PDLHLNRATLHKYEESYGEA  277 (474)
T ss_dssp             HHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHH
Confidence            56777777777777776654

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

Probab=98.94  E-value=1.9e-08  Score=68.28  Aligned_cols=150  Identities=15%  Similarity=0.033  Sum_probs=118.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      .+..+|..+-..+...|++++|...|+...+  | +...|..+...+...|++++|...|++..+.  .|+.......+.
T Consensus        75 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~  152 (275)
T 1xnf_A           75 DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLY  152 (275)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHH
Confidence            3577888888899999999999999998762  3 5678888889999999999999999999774  466655666666


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCC-------cchHHHHHHHHHhcCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRS-------VVSWTTMISGLAASGD  160 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-------~~~~~~li~~~~~~g~  160 (164)
                      .+...|++++|...+++..... +++...+ .+...+...++.++|...+++....+       ..+|..+...|.+.|+
T Consensus       153 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~  230 (275)
T 1xnf_A          153 LAEQKLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGD  230 (275)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCC
Confidence            7778899999999998877654 3444444 47777888888888999888776432       4788888999999998


Q ss_pred             CCCC
Q 031208          161 LDAA  164 (164)
Q Consensus       161 ~~~A  164 (164)
                      +++|
T Consensus       231 ~~~A  234 (275)
T 1xnf_A          231 LDSA  234 (275)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7764

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.92  E-value=5.3e-08  Score=70.25  Aligned_cols=149  Identities=7%  Similarity=-0.041  Sum_probs=123.6

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCC-hhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGS-SLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      ...|..+-..+.+.|++++|...+++..  .| +...|+.+-..+...|+ +++|+..|++..+.. +-+...|..+-.+
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~~  175 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL  175 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            4567777788889999999999999876  34 57788889999999997 999999999998753 2255688888899


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHh-cCCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAA-SGDLDA  163 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~-~g~~~~  163 (164)
                      +...|++++|...+++..+.. +-+...|..+-.++.+.|++++|...|+++.  .| +...|+.+-..|.+ .|..++
T Consensus       176 ~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~e  253 (382)
T 2h6f_A          176 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDR  253 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchH
Confidence            999999999999999998875 4567888999999999999999999999876  33 67788888888888 555454

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

Probab=98.87  E-value=2.2e-08  Score=69.90  Aligned_cols=153  Identities=11%  Similarity=0.081  Sum_probs=117.3

Q ss_pred             CCC-CHHHHHHHHHHHhccCCcHHHHHHHhccCC--Cc-Hh-HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208            9 LSN-DQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PH-VF-TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus         9 ~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      +.| +...|..+...+.+.|+++.|..+|++..+  |+ .. .|..+...+.+.|++++|..+|++..+.. +++...|.
T Consensus        94 ~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~  172 (308)
T 2ond_A           94 LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYV  172 (308)
T ss_dssp             TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHH
T ss_pred             hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHH
Confidence            345 456899999999999999999999998763  43 33 79999999999999999999999998753 23333443


Q ss_pred             HHHHHHH-hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC-----C--CcchHHHHHHHH
Q 031208           84 FVIKACI-ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-----R--SVVSWTTMISGL  155 (164)
Q Consensus        84 ~ll~~~~-~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~--~~~~~~~li~~~  155 (164)
                      ....... ..|+.++|..+++...+.. +.+...|..++..+.+.|+.++|..+|++...     |  ....|...+..+
T Consensus       173 ~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~  251 (308)
T 2ond_A          173 TAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFE  251 (308)
T ss_dssp             HHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Confidence            3322222 3699999999999887653 34678889999999999999999999997753     2  345788888888


Q ss_pred             HhcCCCCC
Q 031208          156 AASGDLDA  163 (164)
Q Consensus       156 ~~~g~~~~  163 (164)
                      .+.|+.++
T Consensus       252 ~~~g~~~~  259 (308)
T 2ond_A          252 SNIGDLAS  259 (308)
T ss_dssp             HHHSCHHH
T ss_pred             HHcCCHHH
Confidence            88887654

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

Probab=98.87  E-value=9.8e-09  Score=75.99  Aligned_cols=150  Identities=11%  Similarity=-0.053  Sum_probs=124.9

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CCcHhHHHHHHHHHHhc---------CChhHHHHHHHHHHHcCCCCCcc
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPHVFTWNLMIRALTID---------GSSLQALLLYNLMICNGFRPDKF   80 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~---------~~~~~a~~~~~~m~~~~~~p~~~   80 (164)
                      +...|..+-..|.+.|++++|...|++..  .|+...+..+-..+...         |++++|...|++..+.. +-+..
T Consensus       136 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~  214 (474)
T 4abn_A          136 LVEAWNQLGEVYWKKGDVTSAHTCFSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGR  214 (474)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHH
Confidence            47788999999999999999999999875  57778888888899999         99999999999997753 23567


Q ss_pred             cHHHHHHHHHhc--------cchhhHHHHHHHHHHhCCC---CchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-Ccc
Q 031208           81 TFPFVIKACIAS--------LAIEKGKEVHGLAVKAGFS---RDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVV  146 (164)
Q Consensus        81 t~~~ll~~~~~~--------~~~~~a~~~~~~m~~~g~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~  146 (164)
                      .|..+-.++...        |++++|...+++..+.. +   .+...|..+-..|.+.|++++|.+.|++..  .| +..
T Consensus       215 ~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~  293 (474)
T 4abn_A          215 SWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPE  293 (474)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHH
Confidence            888888999888        99999999999998864 2   367889999999999999999999999875  34 455


Q ss_pred             hHHHHHHHHHhcCCCCC
Q 031208          147 SWTTMISGLAASGDLDA  163 (164)
Q Consensus       147 ~~~~li~~~~~~g~~~~  163 (164)
                      .+..+-..+...|++++
T Consensus       294 a~~~l~~~~~~lg~~~e  310 (474)
T 4abn_A          294 PQQREQQLLEFLSRLTS  310 (474)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            67777777776665543

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=98.86  E-value=4.4e-08  Score=72.67  Aligned_cols=131  Identities=9%  Similarity=-0.079  Sum_probs=113.8

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      ..|+..++..+-..+...|+++.|...|+...   ..+..+|..+...+...|++++|...|++..+.. +.+...+..+
T Consensus       272 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l  350 (537)
T 3fp2_A          272 LHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQL  350 (537)
T ss_dssp             HCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHH
T ss_pred             cCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence            35667888889999999999999999999875   2467789999999999999999999999998753 3346788899


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ...+...|++++|...+++..+.. +.+...+..+...|.+.|++++|.+.|++..
T Consensus       351 a~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~  405 (537)
T 3fp2_A          351 ACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAK  405 (537)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            999999999999999999998775 4457788999999999999999999999875

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.85  E-value=1.7e-07  Score=62.27  Aligned_cols=147  Identities=7%  Similarity=-0.100  Sum_probs=117.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC---C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR---C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFV   85 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~l   85 (164)
                      .|+..+...-..+.+.|++++|...|+...   . ++...+..+-.++...|++++|...|++..+.  .| +...+..+
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l   82 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGK   82 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHH
Confidence            356777778888999999999999999765   2 67777777888999999999999999999875  35 45678888


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCch-------HHHHHHHHHHHhcCCchhHHHHhcccCC--CC---cchHHHHHH
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDM-------FVQSTLMDLYLKCGDVDGGRKMFDKMRV--RS---VVSWTTMIS  153 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~-------~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~~---~~~~~~li~  153 (164)
                      -..+...|++++|...+++..+.. +.+.       ..|..+-..+.+.|++++|.+.|++..+  |+   ...|..+-.
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~  161 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGV  161 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            999999999999999999998764 2233       4577777888899999999999998763  33   346666666


Q ss_pred             HHHhcCC
Q 031208          154 GLAASGD  160 (164)
Q Consensus       154 ~~~~~g~  160 (164)
                      .|...|+
T Consensus       162 ~~~~~~~  168 (228)
T 4i17_A          162 LFYNNGA  168 (228)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6655443

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.84  E-value=2.8e-07  Score=60.37  Aligned_cols=125  Identities=12%  Similarity=-0.089  Sum_probs=106.1

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccch
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAI   95 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~   95 (164)
                      +..+-..+...|++++|...|++...|+...|..+-..+...|++++|...|++..+.. +.+...+..+-..+...|++
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~   87 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKY   87 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccH
Confidence            44556677889999999999999988899999999999999999999999999987753 33566888899999999999


Q ss_pred             hhHHHHHHHHHHhCC--------------CC-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           96 EKGKEVHGLAVKAGF--------------SR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~--------------~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ++|.+.+++..+..-              .| ....+..+-..|.+.|++++|.+.|+...
T Consensus        88 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  148 (213)
T 1hh8_A           88 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALAT  148 (213)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            999999999887531              11 23678888899999999999999998765

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

Probab=98.84  E-value=3e-07  Score=58.96  Aligned_cols=129  Identities=12%  Similarity=-0.059  Sum_probs=109.6

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|+++.|...+....   ..+...+..+-..+...++++.+...+.+..... +-+...+..+-..
T Consensus        38 ~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~  116 (184)
T 3vtx_A           38 NVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLV  116 (184)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHH
Confidence            56778888889999999999999999875   3456677777788899999999999999987643 3356678888999


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      +.+.|++++|.+.+++..+.. +.+...|..+-..|.+.|++++|.+.|++..+
T Consensus       117 ~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  169 (184)
T 3vtx_A          117 YDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKKALE  169 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            999999999999999998775 45678899999999999999999999998753

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.84  E-value=2.5e-09  Score=72.67  Aligned_cols=130  Identities=15%  Similarity=0.069  Sum_probs=104.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC----------C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc------C
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC----------P-HVFTWNLMIRALTIDGSSLQALLLYNLMICN------G   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~   74 (164)
                      ...++..+-..+...|++++|...+++...          | ...++..+-..+...|++++|...|.+....      .
T Consensus        42 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~  121 (283)
T 3edt_B           42 VATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGK  121 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCC
Confidence            466788888899999999999999987651          2 3457888899999999999999999998653      1


Q ss_pred             CCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHh------CCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           75 FRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKA------GFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        75 ~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -.| ....+..+...+...|++++|...+++..+.      +-.| ...++..+...|.+.|++++|.++|++..
T Consensus       122 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l  196 (283)
T 3edt_B          122 FHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEIL  196 (283)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            122 3567888889999999999999999988765      2123 35678888999999999999999887654

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

Probab=98.84  E-value=6.1e-09  Score=71.84  Aligned_cols=130  Identities=14%  Similarity=0.036  Sum_probs=103.5

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC----------C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc------C
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC----------P-HVFTWNLMIRALTIDGSSLQALLLYNLMICN------G   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~   74 (164)
                      ...++..+-..+...|++++|...+++...          | ....+..+...+...|++++|...+++..+.      +
T Consensus        68 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~  147 (311)
T 3nf1_A           68 VATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGK  147 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCC
Confidence            456677888899999999999999987641          2 2456888888999999999999999998653      2


Q ss_pred             CCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHh------CCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           75 FRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKA------GFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        75 ~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -.| ....+..+...+...|++++|..++++..+.      +..| ....+..+...|.+.|++++|.+.|++..
T Consensus       148 ~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  222 (311)
T 3nf1_A          148 DHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEIL  222 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            223 3456788889999999999999999988765      2233 35578888899999999999999987765

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

Probab=98.81  E-value=1.1e-08  Score=70.49  Aligned_cols=153  Identities=12%  Similarity=-0.007  Sum_probs=121.5

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC----------C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc------C
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC----------P-HVFTWNLMIRALTIDGSSLQALLLYNLMICN------G   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~   74 (164)
                      +..++..+-..+...|++++|..+|++..+          | ....+..+-..+...|++++|...+++....      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            467788888899999999999999998753          1 2356788888999999999999999998653      2


Q ss_pred             CCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHh------CCCC-chHHHHHHHHHHHhcCCchhHHHHhcccCC----
Q 031208           75 FRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKA------GFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMRV----  142 (164)
Q Consensus        75 ~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----  142 (164)
                      -.| ....+..+...+...|++++|...+++..+.      +-.| ....+..+...|.+.|++++|.++|++...    
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~  185 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQT  185 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            223 3467888899999999999999999988764      3223 356778888999999999999999987642    


Q ss_pred             ---C----CcchHHHHHHHHHhcCCCCCC
Q 031208          143 ---R----SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       143 ---~----~~~~~~~li~~~~~~g~~~~A  164 (164)
                         +    ...++..+...|...|++++|
T Consensus       186 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A  214 (311)
T 3nf1_A          186 KLGPDDPNVAKTKNNLASCYLKQGKFKQA  214 (311)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HhCCCCHHHHHHHHHHHHHHHHcCCHHHH
Confidence               1    345788889999999988764

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

Probab=98.80  E-value=6e-08  Score=67.15  Aligned_cols=153  Identities=14%  Similarity=-0.026  Sum_probs=120.4

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      ++.+...+..+-..+...|+++.|...|++..  .| +...+..+-..+...|++++|...+++....  .|+.......
T Consensus       113 lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~  190 (287)
T 3qou_A          113 LPREEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLV  190 (287)
T ss_dssp             SCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHH
T ss_pred             cCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHH
Confidence            44455566667778889999999999999875  34 6678888899999999999999999998654  3554322222


Q ss_pred             -HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCC---cchHHHHHHHHHhcC
Q 031208           86 -IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRS---VVSWTTMISGLAASG  159 (164)
Q Consensus        86 -l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~---~~~~~~li~~~~~~g  159 (164)
                       ...+...++.+.|...+++..... +.+...+..+-..|...|++++|...|.++.  .|+   ...+..+...|...|
T Consensus       191 ~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g  269 (287)
T 3qou_A          191 AQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALG  269 (287)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHC
T ss_pred             HHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcC
Confidence             233567778888999898887765 4567888999999999999999999999886  342   668999999999999


Q ss_pred             CCCCC
Q 031208          160 DLDAA  164 (164)
Q Consensus       160 ~~~~A  164 (164)
                      +.++|
T Consensus       270 ~~~~a  274 (287)
T 3qou_A          270 TGDAL  274 (287)
T ss_dssp             TTCHH
T ss_pred             CCCcH
Confidence            88764

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

Probab=98.78  E-value=1.9e-07  Score=65.13  Aligned_cols=151  Identities=11%  Similarity=0.005  Sum_probs=116.6

Q ss_pred             CCHHHHHHHHHHHh-------ccCCc-------HHHHHHHhccCC---C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 031208           11 NDQLLVRKLLDLCS-------FYGKT-------DHALLVFSQIRC---P-HVFTWNLMIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus        11 ~~~~~~~~li~~~~-------~~~~~-------~~a~~~~~~~~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      -+...|..+...+.       +.|++       ++|..+|++...   | +...|..+...+.+.|++++|..+|++..+
T Consensus        48 ~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  127 (308)
T 2ond_A           48 HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA  127 (308)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            45667777777665       35886       899999997643   4 556899999999999999999999999987


Q ss_pred             cCCCCCcc--cHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHH-hcCCchhHHHHhcccC--CC-Ccc
Q 031208           73 NGFRPDKF--TFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL-KCGDVDGGRKMFDKMR--VR-SVV  146 (164)
Q Consensus        73 ~~~~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~-~~~~~~~a~~~~~~m~--~~-~~~  146 (164)
                        +.|+..  .|..+...+.+.|++++|..++++..+.. +++...|........ ..|+.+.|..+|+...  .| +..
T Consensus       128 --~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~  204 (308)
T 2ond_A          128 --IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPE  204 (308)
T ss_dssp             --SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHH
T ss_pred             --ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHH
Confidence              456543  78899999999999999999999988754 234444543333322 3699999999999875  23 667


Q ss_pred             hHHHHHHHHHhcCCCCCC
Q 031208          147 SWTTMISGLAASGDLDAA  164 (164)
Q Consensus       147 ~~~~li~~~~~~g~~~~A  164 (164)
                      .|..++..+.+.|++++|
T Consensus       205 ~~~~~~~~~~~~g~~~~A  222 (308)
T 2ond_A          205 YVLAYIDYLSHLNEDNNT  222 (308)
T ss_dssp             HHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHHCCCHHHH
Confidence            889999999998887654

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.77  E-value=3.4e-07  Score=62.44  Aligned_cols=139  Identities=12%  Similarity=-0.112  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHHhc----cCCcHHHHHHHhccCC-CcHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208           13 QLLVRKLLDLCSF----YGKTDHALLVFSQIRC-PHVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        13 ~~~~~~li~~~~~----~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      ...+..+-..+..    .+++++|...|++..+ .+...+..+-..|..    .+++++|...|++..+.+   +...+.
T Consensus        38 ~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~  114 (273)
T 1ouv_A           38 NSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCA  114 (273)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHH
Confidence            3444445555555    6666666666665432 344555555555666    666666666666665543   444555


Q ss_pred             HHHHHHHh----ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh----cCCchhHHHHhcccCCC-CcchHHHHHHH
Q 031208           84 FVIKACIA----SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK----CGDVDGGRKMFDKMRVR-SVVSWTTMISG  154 (164)
Q Consensus        84 ~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~-~~~~~~~li~~  154 (164)
                      .+-..|..    .+++++|...+++..+.+   +...+..+-..|.+    .+++++|...|++..+. +...+..+-..
T Consensus       115 ~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~  191 (273)
T 1ouv_A          115 SLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNM  191 (273)
T ss_dssp             HHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            55555665    666666666666666544   33444555555555    66666666666654422 34455555555


Q ss_pred             HHh
Q 031208          155 LAA  157 (164)
Q Consensus       155 ~~~  157 (164)
                      |..
T Consensus       192 ~~~  194 (273)
T 1ouv_A          192 YHH  194 (273)
T ss_dssp             HHH
T ss_pred             HHc
Confidence            555

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

Probab=98.77  E-value=4e-07  Score=54.00  Aligned_cols=93  Identities=13%  Similarity=0.014  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      ..+..+...+...|+++.|.+++++..   ..+...+..+...+...|++++|...++++.+.. +.+...+..+...+.
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~   88 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHH
Confidence            334444444555555555555554433   1233444444444555555555555555544321 123334444444445


Q ss_pred             hccchhhHHHHHHHHHH
Q 031208           91 ASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~  107 (164)
                      ..|++++|...+++..+
T Consensus        89 ~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHH
Confidence            55555555555544443

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.76  E-value=9.5e-07  Score=60.20  Aligned_cols=147  Identities=10%  Similarity=-0.115  Sum_probs=118.1

Q ss_pred             CHHHHHHHHHHHhc----cCCcHHHHHHHhccCC-CcHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCcccH
Q 031208           12 DQLLVRKLLDLCSF----YGKTDHALLVFSQIRC-PHVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFRPDKFTF   82 (164)
Q Consensus        12 ~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~   82 (164)
                      +...+..+-..+..    .+++++|...|++..+ .+...+..+-..|..    .+++++|...|++..+.+   +...+
T Consensus        73 ~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~  149 (273)
T 1ouv_A           73 YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGC  149 (273)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHH
Confidence            56677777778888    9999999999998653 467778888888888    999999999999998865   45566


Q ss_pred             HHHHHHHHh----ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh----cCCchhHHHHhcccCCC-CcchHHHHHH
Q 031208           83 PFVIKACIA----SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK----CGDVDGGRKMFDKMRVR-SVVSWTTMIS  153 (164)
Q Consensus        83 ~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~-~~~~~~~li~  153 (164)
                      ..+-..+..    .++.++|...+++..+.+   +...+..+-..|.+    .+++++|.+.|++..+. +...+..+-.
T Consensus       150 ~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~l~~  226 (273)
T 1ouv_A          150 TILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGA  226 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            677777777    899999999999988764   35677778888888    99999999999876533 4567777778


Q ss_pred             HHHh----cCCCCCC
Q 031208          154 GLAA----SGDLDAA  164 (164)
Q Consensus       154 ~~~~----~g~~~~A  164 (164)
                      .|..    .+++++|
T Consensus       227 ~~~~g~~~~~~~~~A  241 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQA  241 (273)
T ss_dssp             HHHTTSSSSCCSTTH
T ss_pred             HHHcCCCcccCHHHH
Confidence            8887    7777765

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

Probab=98.75  E-value=1.4e-07  Score=64.06  Aligned_cols=151  Identities=11%  Similarity=-0.036  Sum_probs=117.0

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC--Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      +...+..+...+...|++++|...++...+  ++    ...|..+-..+...|++++|...|++..+.. +.+...+..+
T Consensus        36 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l  114 (272)
T 3u4t_A           36 SPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQI  114 (272)
T ss_dssp             CSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHH
Confidence            345788888899999999999999997653  22    2348888899999999999999999997753 3355788999


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCC--
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGD--  160 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~--  160 (164)
                      ...+...|++++|...+++..+.. +.+...+..+...+...+++++|.+.|++..  .| +...|..+...+...|+  
T Consensus       115 ~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~  193 (272)
T 3u4t_A          115 GSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKADSSFVKVLELKPNIYIGYLWRARANAAQDPDT  193 (272)
T ss_dssp             HHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTC
T ss_pred             HHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcch
Confidence            999999999999999999887652 3345566666624445569999999999876  33 45677778888887777  


Q ss_pred             -CCCC
Q 031208          161 -LDAA  164 (164)
Q Consensus       161 -~~~A  164 (164)
                       +++|
T Consensus       194 ~~~~A  198 (272)
T 3u4t_A          194 KQGLA  198 (272)
T ss_dssp             SSCTT
T ss_pred             hhHHH
Confidence             5554

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

Probab=98.74  E-value=7.4e-07  Score=52.82  Aligned_cols=113  Identities=13%  Similarity=0.057  Sum_probs=91.7

Q ss_pred             HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           44 VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        44 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      ...|..+...+...|++++|...+.+..... +.+...+..+...+...|++++|..+++++.+.. +.+...+..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            5677888889999999999999999997653 3356678888999999999999999999998765 4567788899999


Q ss_pred             HHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhc
Q 031208          124 YLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAAS  158 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~  158 (164)
                      |.+.|++++|...|+++.  .| +...+..+-..+.+.
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~  124 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQKQ  124 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhc
Confidence            999999999999999875  33 445555555555443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.74  E-value=2.1e-07  Score=58.23  Aligned_cols=136  Identities=11%  Similarity=-0.004  Sum_probs=106.0

Q ss_pred             HHhccCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhh
Q 031208           22 LCSFYGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEK   97 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~   97 (164)
                      .+...|+++.|...+.....  | +...+-.+-..|.+.|++++|.+.|++..+.  .| +...|..+-..+.+.|++++
T Consensus         6 ~~~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~   83 (150)
T 4ga2_A            6 MRRSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEENTDK   83 (150)
T ss_dssp             -CCCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCchHH
Confidence            34567788999998887764  2 2344556777899999999999999999775  35 56788899999999999999


Q ss_pred             HHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHh-cccC--CC-CcchHHHHHHHHHhcCC
Q 031208           98 GKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMF-DKMR--VR-SVVSWTTMISGLAASGD  160 (164)
Q Consensus        98 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~-~~m~--~~-~~~~~~~li~~~~~~g~  160 (164)
                      |...+++..+.. +-+...+..+-..|.+.|+.++|.+.| ++..  .| +..+|...-..+...|+
T Consensus        84 A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           84 AVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            999999998774 345778888999999999998877654 6543  44 66677777777777765

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

Probab=98.74  E-value=6.5e-07  Score=53.51  Aligned_cols=115  Identities=6%  Similarity=-0.192  Sum_probs=62.1

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      ..+..+-..+...|++++|...|++..... +.+...+..+...+...|++++|...++...+.. +.+...+..+...|
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~   90 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHH
Confidence            344445555555666666666666654432 2234455555555566666666666666555442 22344555555566


Q ss_pred             HhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCC
Q 031208          125 LKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDL  161 (164)
Q Consensus       125 ~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~  161 (164)
                      .+.|++++|...|++..  .| +...+..+...+.+.|++
T Consensus        91 ~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTC
T ss_pred             HHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcC
Confidence            66666666666665543  22 344555555555555554

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.73  E-value=2.2e-07  Score=59.52  Aligned_cols=145  Identities=14%  Similarity=-0.008  Sum_probs=108.6

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH--H
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC--I   90 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~--~   90 (164)
                      +...-..+.+.|+++.|...|++..+   .+...+..+-..+...|++++|...|++....  .|+.. +..+...+  .
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~--~p~~~-~~~~~~~~~~~   85 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLE--YQDNS-YKSLIAKLELH   85 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG--GCCHH-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc--cCChH-HHHHHHHHHHH
Confidence            44556678889999999999999873   35678888889999999999999999998654  34332 22222211  2


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCC---cchHHHHHHHHHhcCCCCCC
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRS---VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~---~~~~~~li~~~~~~g~~~~A  164 (164)
                      ..+....+...+++..+.. +.+...+..+-..+.+.|++++|...|++..  .|+   ...+..+...|...|+.++|
T Consensus        86 ~~~~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A  163 (176)
T 2r5s_A           86 QQAAESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAI  163 (176)
T ss_dssp             HHHTSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHH
T ss_pred             hhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcH
Confidence            2233445678888877664 3357888889999999999999999999875  332   45889999999999998764

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

Probab=98.73  E-value=2.8e-07  Score=64.40  Aligned_cols=128  Identities=11%  Similarity=0.006  Sum_probs=97.3

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCC-----CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-----Cc
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-----DK   79 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-----~~   79 (164)
                      +++..+...+-.++...|++++|.+++.....     -+...+..++..+.+.|+++.|.+.+++|.+.  .|     +.
T Consensus        97 ~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d  174 (310)
T 3mv2_B           97 QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDN  174 (310)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--Cccccccch
Confidence            45666666777788899999999999998732     35678889999999999999999999999774  56     24


Q ss_pred             ccHHHHHHH--HHhcc--chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           80 FTFPFVIKA--CIASL--AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        80 ~t~~~ll~~--~~~~~--~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+...+..+  ....|  +..+|..+|+++...  .|+...-..++.++.+.|++++|.+.++.+.
T Consensus       175 ~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~  238 (310)
T 3mv2_B          175 EMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            455556655  33334  899999999998654  3553344455558999999999999997653

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.66  E-value=5.8e-07  Score=64.83  Aligned_cols=146  Identities=12%  Similarity=0.012  Sum_probs=113.4

Q ss_pred             CHHHHHHHHHHHhccCC-cHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGK-TDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~-~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      +..+|+.+-..+.+.|+ +++|...|++..  .| +...|..+-.++...|++++|+..|++..+.. +-+...|..+-.
T Consensus       130 ~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~  208 (382)
T 2h6f_A          130 NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQW  208 (382)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHH
Confidence            46778888888888996 999999999876  33 66788888888999999999999999987743 235667888888


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh-cCCchhH-----HHHhcccC--CC-CcchHHHHHHHHHhc
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK-CGDVDGG-----RKMFDKMR--VR-SVVSWTTMISGLAAS  158 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~-~~~~~~a-----~~~~~~m~--~~-~~~~~~~li~~~~~~  158 (164)
                      ++.+.|++++|...++++.+.. +-+...|+.+-..|.+ .|..++|     .+.|++..  .| +...|+.+-..+...
T Consensus       209 ~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~  287 (382)
T 2h6f_A          209 VIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDR  287 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTT
T ss_pred             HHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHcc
Confidence            8899999999999999988775 3467788888888888 6665777     36666554  33 566777777777776


Q ss_pred             C
Q 031208          159 G  159 (164)
Q Consensus       159 g  159 (164)
                      |
T Consensus       288 g  288 (382)
T 2h6f_A          288 G  288 (382)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.66  E-value=2.4e-07  Score=69.85  Aligned_cols=128  Identities=11%  Similarity=-0.063  Sum_probs=103.2

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|++++|.+.+++..+   .+...|..+-..+...|++++|...|++..+.. +-+...+..+-..
T Consensus        22 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~  100 (568)
T 2vsy_A           22 DFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHA  100 (568)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            466777788888889999999999987653   356778888888899999999999999987653 2345678888888


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc---CCchhHHHHhcccC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC---GDVDGGRKMFDKMR  141 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~---~~~~~a~~~~~~m~  141 (164)
                      +.+.|++++|.+.+++..+.. +.+...+..+...+.+.   |+.++|.+.+++..
T Consensus       101 ~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A          101 LEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence            999999999999999888764 34567788888888888   88999999888775

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

Probab=98.66  E-value=1.2e-06  Score=52.32  Aligned_cols=117  Identities=10%  Similarity=-0.066  Sum_probs=96.5

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+...|+++.|...|+...   ..+...|..+...+...|++++|...+.+..... +.+...+..+...
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~   89 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHH
Confidence            46677778888999999999999999865   2467788888999999999999999999997753 3346678888899


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCc
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV  130 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  130 (164)
                      +...|++++|...+++..+.. +.+...+..+...+.+.|++
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence            999999999999999998775 34566777777888777765

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

Probab=98.63  E-value=2.2e-06  Score=51.46  Aligned_cols=96  Identities=15%  Similarity=-0.063  Sum_probs=50.2

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|+++.|...|+....   .+...+..+-..+...|++++|...+++..+.. +.+...+..+...
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~   93 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHH
Confidence            344455555555556666666665555431   244455555555555566666666555554431 1233444555555


Q ss_pred             HHhccchhhHHHHHHHHHHh
Q 031208           89 CIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +.+.|++++|.+.+++..+.
T Consensus        94 ~~~~~~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKALDL  113 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHh
Confidence            55555555555555555443

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

Probab=98.62  E-value=1.4e-06  Score=52.28  Aligned_cols=117  Identities=9%  Similarity=-0.081  Sum_probs=95.4

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      .+...|..+-..+...|++++|...|++..... +.+...+..+...+...|++++|...+++..+.. +.+...+..+.
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la   91 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKA   91 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHH
Confidence            355678888889999999999999999997653 2356778888899999999999999999998764 34677888899


Q ss_pred             HHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCC
Q 031208          122 DLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGD  160 (164)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~  160 (164)
                      ..|.+.|++++|.+.|++..  .| +...+..+...+.+.|+
T Consensus        92 ~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  133 (133)
T 2lni_A           92 AALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYN  133 (133)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHTC
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhcC
Confidence            99999999999999999875  33 45677777777766553

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.62  E-value=7.1e-07  Score=68.94  Aligned_cols=146  Identities=10%  Similarity=-0.061  Sum_probs=119.3

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVI   86 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll   86 (164)
                      .+...+..+-..+.+.|++++|...|++..+   .+...|..+-.++...|++++|...|++..+.  .| +...+..+-
T Consensus       431 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~lg  508 (681)
T 2pzi_A          431 ESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDT--FPGELAPKLALA  508 (681)
T ss_dssp             TCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCSHHHHHHH
T ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHH
Confidence            3566788888899999999999999998763   46778888888999999999999999999775  35 566788899


Q ss_pred             HHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-CcchHHHHHHHHHhcCC
Q 031208           87 KACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMISGLAASGD  160 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~g~  160 (164)
                      .++.+.|++++ .+.+++..+.. +.+...|..+-..|.+.|++++|.+.|++..+  | +...|..+..++...|+
T Consensus       509 ~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          509 ATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            99999999999 99999998775 34577889999999999999999999999873  4 34567777777666554

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.61  E-value=1.8e-06  Score=53.96  Aligned_cols=126  Identities=10%  Similarity=-0.141  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...+..+-..+...|+++.|...|+...   ..+...|..+-..+...|++++|...+.+..... +.+...+..+...+
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~   91 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            3456667778888999999999999865   3467788888889999999999999999987753 33566788888999


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHH--HHHHHHHHhcCCchhHHHHhccc
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQ--STLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~--~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      ...|++++|...+++..+.. +.+...+  -.....+.+.|++++|.+.+...
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            99999999999999988764 2233444  33444477889999998888754

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

Probab=98.61  E-value=6e-07  Score=60.87  Aligned_cols=146  Identities=13%  Similarity=-0.025  Sum_probs=109.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC--Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC-cccHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGF-RPD-KFTFP   83 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~-~~t~~   83 (164)
                      +...+-..-..+.+.|++++|...|+....  |+    ...+..+-.++.+.|++++|...|++..+..- .|. ...+.
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~   93 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEY   93 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHH
Confidence            455666667788899999999999998863  43    56777888889999999999999999977531 112 23455


Q ss_pred             HHHHHHHh--------ccchhhHHHHHHHHHHhCCCCchHHH-----------------HHHHHHHHhcCCchhHHHHhc
Q 031208           84 FVIKACIA--------SLAIEKGKEVHGLAVKAGFSRDMFVQ-----------------STLMDLYLKCGDVDGGRKMFD  138 (164)
Q Consensus        84 ~ll~~~~~--------~~~~~~a~~~~~~m~~~g~~~~~~~~-----------------~~ll~~~~~~~~~~~a~~~~~  138 (164)
                      .+-.++..        .|++++|...+++..+.. +.+....                 ..+-..|.+.|++++|...|+
T Consensus        94 ~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  172 (261)
T 3qky_A           94 ERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY-PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYE  172 (261)
T ss_dssp             HHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC-TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHhcccccccchhHHHHHHHHHHHHHHC-cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            66677777        999999999999998764 2223333                 445778899999999999999


Q ss_pred             ccC--CCC----cchHHHHHHHHHhc
Q 031208          139 KMR--VRS----VVSWTTMISGLAAS  158 (164)
Q Consensus       139 ~m~--~~~----~~~~~~li~~~~~~  158 (164)
                      +..  .|+    ...+..+..+|...
T Consensus       173 ~~l~~~p~~~~~~~a~~~l~~~~~~~  198 (261)
T 3qky_A          173 AVFDAYPDTPWADDALVGAMRAYIAY  198 (261)
T ss_dssp             HHHHHCTTSTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCchHHHHHHHHHHHHHHh
Confidence            875  343    23566677777665

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.58  E-value=1.9e-06  Score=67.01  Aligned_cols=129  Identities=16%  Similarity=-0.005  Sum_probs=111.4

Q ss_pred             CC-CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHH
Q 031208           10 SN-DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPF   84 (164)
Q Consensus        10 ~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~   84 (164)
                      .| +...+..+-.++.+.|++++|...|++..  .| +...|..+-..+.+.|++++|.+.|++..+.  .| +...|..
T Consensus        39 ~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~  116 (723)
T 4gyw_A           39 FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI--NPAFADAHSN  116 (723)
T ss_dssp             CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHH
Confidence            45 46778888899999999999999999875  34 5778999999999999999999999999774  45 4568899


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +-..+.+.|++++|.+.+++..+.. +-+...+..+...|.+.|++++|.+.+++..
T Consensus       117 Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal  172 (723)
T 4gyw_A          117 LASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCDWTDYDERMKKLV  172 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCCTTHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhcccHHHHHHHHHHHH
Confidence            9999999999999999999998774 3457889999999999999999998887653

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

Probab=98.56  E-value=7.5e-07  Score=66.57  Aligned_cols=148  Identities=9%  Similarity=0.069  Sum_probs=114.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CCc--HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH--VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVI   86 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll   86 (164)
                      +...|..+...+.+.|+++.|..+|++..  .|+  ...|......+.+.|+.++|..+|++..+.  .|+ ...|....
T Consensus       320 ~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~--~~~~~~~~~~~a  397 (530)
T 2ooe_A          320 NMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED--ARTRHHVYVTAA  397 (530)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--TTCCTHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--cCCchHHHHHHH
Confidence            58889999999999999999999999875  343  357888888889999999999999999875  343 22222222


Q ss_pred             HH-HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC--C-C----cchHHHHHHHHHhc
Q 031208           87 KA-CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-S----VVSWTTMISGLAAS  158 (164)
Q Consensus        87 ~~-~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-~----~~~~~~li~~~~~~  158 (164)
                      .. +...|+.+.|..+|+...+.. +.+...|..+++.+.+.|+.++|..+|+....  | +    ...|...+.-....
T Consensus       398 ~~~~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~  476 (530)
T 2ooe_A          398 LMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNI  476 (530)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHS
T ss_pred             HHHHHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHc
Confidence            22 335899999999999887654 34578899999999999999999999998752  2 2    23787777777777


Q ss_pred             CCCC
Q 031208          159 GDLD  162 (164)
Q Consensus       159 g~~~  162 (164)
                      |+.+
T Consensus       477 G~~~  480 (530)
T 2ooe_A          477 GDLA  480 (530)
T ss_dssp             SCHH
T ss_pred             CCHH
Confidence            7654

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.55  E-value=1.8e-06  Score=59.63  Aligned_cols=146  Identities=7%  Similarity=-0.102  Sum_probs=106.8

Q ss_pred             HHHHHhccCCcHHHHHHHhccCC-----CcH---h-HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-Cc----ccHHH
Q 031208           19 LLDLCSFYGKTDHALLVFSQIRC-----PHV---F-TWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DK----FTFPF   84 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~~-----~~~---~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~----~t~~~   84 (164)
                      .+..+...|++++|.++++...+     |+.   . .+..+...+...+++++|...|.+........ +.    ..++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            36678889999999999987642     222   1 23345556677789999999999998743332 22    25888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHh-----CCCCc-hHHHHHHHHHHHhcCCchhHHHHhcccCC-----CC----cchHH
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKA-----GFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMRV-----RS----VVSWT  149 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~-----g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~  149 (164)
                      +-..|...|++++|...+++..+.     +..+. ..++..+...|.+.|++++|.+.+++..+     .+    ..+|.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            889999999999999999988742     22222 34788888999999999999999987651     11    45788


Q ss_pred             HHHHHHHhcCCC-CCC
Q 031208          150 TMISGLAASGDL-DAA  164 (164)
Q Consensus       150 ~li~~~~~~g~~-~~A  164 (164)
                      .+-..|.+.|+. ++|
T Consensus       241 ~lg~~~~~~g~~~~~A  256 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEI  256 (293)
T ss_dssp             HHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHhCCcHHHH
Confidence            888888888853 543

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.55  E-value=1.3e-06  Score=57.87  Aligned_cols=121  Identities=8%  Similarity=-0.084  Sum_probs=97.4

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      |...+...-..+...|++++|...|++..+..-+++...+..+-.++...|++++|...+++..+.. +.+...+..+-.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHHH
Confidence            4566777777889999999999999999876543677777778899999999999999999998764 346778889999


Q ss_pred             HHHhcCCchhHHHHhcccC--CC-Cc-------chHHHHHHHHHhcCCCCCC
Q 031208          123 LYLKCGDVDGGRKMFDKMR--VR-SV-------VSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~--~~-~~-------~~~~~li~~~~~~g~~~~A  164 (164)
                      .|.+.|++++|.+.|++..  .| +.       ..|..+-..+...|++++|
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A  136 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKA  136 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHH
Confidence            9999999999999999876  34 33       3466666777777776653

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

Probab=98.54  E-value=1.8e-06  Score=64.55  Aligned_cols=151  Identities=11%  Similarity=0.017  Sum_probs=115.1

Q ss_pred             CCHHHHHHHHHHHhc-------cCCcH-------HHHHHHhccCC---C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 031208           11 NDQLLVRKLLDLCSF-------YGKTD-------HALLVFSQIRC---P-HVFTWNLMIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus        11 ~~~~~~~~li~~~~~-------~~~~~-------~a~~~~~~~~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      -+...|......+.+       .|+++       .|..+|++..+   | +...|..+...+.+.|++++|..+|++..+
T Consensus       270 ~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~  349 (530)
T 2ooe_A          270 HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA  349 (530)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhC
Confidence            356777777777765       79987       89999998652   4 578899999999999999999999999987


Q ss_pred             cCCCCCc--ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH-HHHhcCCchhHHHHhcccC--CC-Ccc
Q 031208           73 NGFRPDK--FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD-LYLKCGDVDGGRKMFDKMR--VR-SVV  146 (164)
Q Consensus        73 ~~~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~-~~~~~~~~~~a~~~~~~m~--~~-~~~  146 (164)
                      .  .|+.  ..|......+.+.|+.+.|.++++...+.. +.+...|..... .+...|+.++|..+|+...  .| +..
T Consensus       350 ~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~  426 (530)
T 2ooe_A          350 I--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPE  426 (530)
T ss_dssp             S--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHH
T ss_pred             c--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHH
Confidence            4  5653  478888888889999999999999987642 112222322221 2346899999999999765  33 677


Q ss_pred             hHHHHHHHHHhcCCCCCC
Q 031208          147 SWTTMISGLAASGDLDAA  164 (164)
Q Consensus       147 ~~~~li~~~~~~g~~~~A  164 (164)
                      .|..++..+.+.|+.++|
T Consensus       427 ~~~~~~~~~~~~g~~~~A  444 (530)
T 2ooe_A          427 YVLAYIDYLSHLNEDNNT  444 (530)
T ss_dssp             HHHHHHHHHTTTTCHHHH
T ss_pred             HHHHHHHHHHhCCCHhhH
Confidence            899999988888887643

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.50  E-value=1.2e-06  Score=59.23  Aligned_cols=97  Identities=11%  Similarity=-0.030  Sum_probs=78.8

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC----------C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc------C
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC----------P-HVFTWNLMIRALTIDGSSLQALLLYNLMICN------G   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~   74 (164)
                      ...++..+-..+...|++++|...+++...          | ...++..+-..+...|++++|...+++....      +
T Consensus        84 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  163 (283)
T 3edt_B           84 VAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGP  163 (283)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCC
Confidence            456788888899999999999999987651          2 2456888888999999999999999998654      1


Q ss_pred             CCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           75 FRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        75 ~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      -.| ...++..+...+...|++++|..++++..+.
T Consensus       164 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          164 DDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            123 3457888899999999999999999988764

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.49  E-value=5.2e-06  Score=62.58  Aligned_cols=136  Identities=9%  Similarity=0.014  Sum_probs=99.3

Q ss_pred             cCCcHHHHHHHhccCC--C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHH
Q 031208           26 YGKTDHALLVFSQIRC--P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVH  102 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~  102 (164)
                      .|++++|...+++..+  | +...|..+-..+...|++++|.+.|++..+.. +-+...+..+-..+...|++++|.+.+
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4778899999988763  3 56788888899999999999999999997753 234668888899999999999999999


Q ss_pred             HHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhc---CCCCC
Q 031208          103 GLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAAS---GDLDA  163 (164)
Q Consensus       103 ~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~---g~~~~  163 (164)
                      ++..+.. +.+...+..+-..|.+.|++++|.+.|++..  .| +...+..+...|...   |+.++
T Consensus        81 ~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~  146 (568)
T 2vsy_A           81 QQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDV  146 (568)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHH
T ss_pred             HHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHH
Confidence            9998775 3457788899999999999999999999875  33 567888888999888   66544

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

Probab=98.48  E-value=8.1e-07  Score=61.51  Aligned_cols=150  Identities=14%  Similarity=-0.094  Sum_probs=112.2

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC-------Cc--HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-Ccc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC-------PH--VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-DKF   80 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~-------~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~   80 (164)
                      .|......|...|++++|.+.|.+...       +.  ..+|+.+-..|.+.|++++|...|++..+.    |-.+ -..
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  118 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            577777788889999999998886642       21  467888999999999999999999987542    2111 134


Q ss_pred             cHHHHHHHHHhc-cchhhHHHHHHHHHHhC--C-CC-c-hHHHHHHHHHHHhcCCchhHHHHhcccCC--CCc--c----
Q 031208           81 TFPFVIKACIAS-LAIEKGKEVHGLAVKAG--F-SR-D-MFVQSTLMDLYLKCGDVDGGRKMFDKMRV--RSV--V----  146 (164)
Q Consensus        81 t~~~ll~~~~~~-~~~~~a~~~~~~m~~~g--~-~~-~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~~~--~----  146 (164)
                      ++..+-..|... |++++|...+++..+..  . .+ . ..++..+...|.+.|++++|...|++...  |+.  .    
T Consensus       119 ~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  198 (292)
T 1qqe_A          119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSL  198 (292)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHH
Confidence            677888889986 99999999999877542  1 11 1 35688889999999999999999998652  221  1    


Q ss_pred             --hHHHHHHHHHhcCCCCCC
Q 031208          147 --SWTTMISGLAASGDLDAA  164 (164)
Q Consensus       147 --~~~~li~~~~~~g~~~~A  164 (164)
                        .|..+..+|...|++++|
T Consensus       199 ~~~~~~lg~~~~~~g~~~~A  218 (292)
T 1qqe_A          199 KDYFLKKGLCQLAATDAVAA  218 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHH
Confidence              466777788888887653

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.48  E-value=1.4e-06  Score=57.03  Aligned_cols=114  Identities=9%  Similarity=-0.089  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL  125 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  125 (164)
                      .+..+-..+...|++++|...|++.    +.|+...+..+...+...|++++|...+++..+.. +.+...+..+-..|.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHH
Confidence            3444566778899999999999877    46788889999999999999999999999998775 456778889999999


Q ss_pred             hcCCchhHHHHhcccCC--C-Cc----------------chHHHHHHHHHhcCCCCCC
Q 031208          126 KCGDVDGGRKMFDKMRV--R-SV----------------VSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~~--~-~~----------------~~~~~li~~~~~~g~~~~A  164 (164)
                      +.|++++|.+.|++..+  | +.                ..|..+-..|.+.|++++|
T Consensus        83 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  140 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKA  140 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHH
Confidence            99999999999987652  2 22                6788888899999887654

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.48  E-value=6.6e-07  Score=69.08  Aligned_cols=138  Identities=12%  Similarity=0.004  Sum_probs=115.2

Q ss_pred             hccCCcHHHHHHHhccC-----------CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           24 SFYGKTDHALLVFSQIR-----------CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        24 ~~~~~~~~a~~~~~~~~-----------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      ...|++++|.+.+++..           ..+...+..+-..+...|++++|...|++..+.. +-+...|..+-.++...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHc
Confidence            77899999999998765           2355678888889999999999999999997742 23556788888899999


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      |++++|.+.|++..+.. +.+...+..+-..|.+.|++++ .+.|++..  .| +...|..+-.+|.+.|++++|
T Consensus       481 g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A  553 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGA  553 (681)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHH
Confidence            99999999999998875 3456788889999999999999 99998765  34 667899999999999998764

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.47  E-value=1.6e-06  Score=55.19  Aligned_cols=117  Identities=9%  Similarity=0.049  Sum_probs=87.4

Q ss_pred             HhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH-HHhccch--h
Q 031208           23 CSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA-CIASLAI--E   96 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~-~~~~~~~--~   96 (164)
                      +...|+++.|...++...   ..+...|..+-..+...|++++|...|++..+.. +.+...+..+... +...|++  +
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhhccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchH
Confidence            345677778877777654   2466788888889999999999999999987643 2245566666667 6788888  9


Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +|...+++..+.. +.+...+..+...|.+.|++++|...|++..
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al  142 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVM  142 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            9999999988764 3456778888889999999999999998765

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.46  E-value=5.1e-06  Score=55.21  Aligned_cols=148  Identities=10%  Similarity=-0.044  Sum_probs=101.7

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc----cH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF----TF   82 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----t~   82 (164)
                      ...+-.+-..+.+.|++++|...|+.+..  |+    ...+..+..++.+.|++++|...|++..+..  |+..    .+
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~--P~~~~~~~a~   81 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN--PTHPNIDYVM   81 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCcHHHHH
Confidence            33455556678888999999999998762  43    2466677788899999999999999987643  4332    22


Q ss_pred             HHHHHHHHh------------------ccchhhHHHHHHHHHHhCCCCc-hHHH-----------------HHHHHHHHh
Q 031208           83 PFVIKACIA------------------SLAIEKGKEVHGLAVKAGFSRD-MFVQ-----------------STLMDLYLK  126 (164)
Q Consensus        83 ~~ll~~~~~------------------~~~~~~a~~~~~~m~~~g~~~~-~~~~-----------------~~ll~~~~~  126 (164)
                      -.+-.++..                  .|+.++|...++++.+..  |+ ...+                 -.+-..|.+
T Consensus        82 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~  159 (225)
T 2yhc_A           82 YMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY--PNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTE  159 (225)
T ss_dssp             HHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC--cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            223333332                  568888999998887653  33 2222                 234456788


Q ss_pred             cCCchhHHHHhcccC--CCCc----chHHHHHHHHHhcCCCCCC
Q 031208          127 CGDVDGGRKMFDKMR--VRSV----VSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       127 ~~~~~~a~~~~~~m~--~~~~----~~~~~li~~~~~~g~~~~A  164 (164)
                      .|+++.|...|+++.  .|+.    ..+..+..+|.+.|++++|
T Consensus       160 ~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A  203 (225)
T 2yhc_A          160 RGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQA  203 (225)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHH
Confidence            899999999998876  3432    4677888888888887654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.44  E-value=5.4e-07  Score=58.37  Aligned_cols=130  Identities=11%  Similarity=-0.062  Sum_probs=88.5

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC---------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCC-C--
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC---------PHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GFRP-D--   78 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p-~--   78 (164)
                      ...++..+-..+...|+++.|...+++...         .....+..+-..+...|++++|...+++..+. .-.+ +  
T Consensus        25 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  104 (203)
T 3gw4_A           25 ASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPL  104 (203)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHH
T ss_pred             HHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHH
Confidence            456677777778888888888888876542         12345667777788888888888888876432 0112 1  


Q ss_pred             --cccHHHHHHHHHhccchhhHHHHHHHHHHhC---CCCc--hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           79 --KFTFPFVIKACIASLAIEKGKEVHGLAVKAG---FSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        79 --~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g---~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                        ...+..+-..+...|++++|...+++.....   -.+.  ..++..+-..|.+.|++++|.+.+++..
T Consensus       105 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  174 (203)
T 3gw4_A          105 AASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRAR  174 (203)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence              2346667777888888888888888765421   1111  2345667777888888888888888777

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.44  E-value=1e-06  Score=63.03  Aligned_cols=152  Identities=11%  Similarity=-0.013  Sum_probs=116.0

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CC-CCC
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GF-RPD   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~-~p~   78 (164)
                      ..+++.+-..|...|++++|...|++..+     ++    ..++..+-..|...|++++|...|++..+.    +. +..
T Consensus       184 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~  263 (383)
T 3ulq_A          184 LQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSL  263 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhH
Confidence            34667777888999999999999987652     22    246778888899999999999999998652    33 334


Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHh----CCCCchHHHHHHHHHHHhcCC---chhHHHHhcccCCC--CcchHH
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKA----GFSRDMFVQSTLMDLYLKCGD---VDGGRKMFDKMRVR--SVVSWT  149 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~~~~~~~ll~~~~~~~~---~~~a~~~~~~m~~~--~~~~~~  149 (164)
                      ..++..+-..+.+.|++++|...+++..+.    +-......+..+-..|...|+   +++|..++++...+  ....+.
T Consensus       264 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~  343 (383)
T 3ulq_A          264 PQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAI  343 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            567888899999999999999999987653    222223345677788888888   88999999988643  334777


Q ss_pred             HHHHHHHhcCCCCCC
Q 031208          150 TMISGLAASGDLDAA  164 (164)
Q Consensus       150 ~li~~~~~~g~~~~A  164 (164)
                      .+-..|...|++++|
T Consensus       344 ~la~~y~~~g~~~~A  358 (383)
T 3ulq_A          344 DVAKYYHERKNFQKA  358 (383)
T ss_dssp             HHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHCCCHHHH
Confidence            888899999988764

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.42  E-value=2.2e-06  Score=53.56  Aligned_cols=116  Identities=5%  Similarity=-0.063  Sum_probs=89.4

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      ..|..+-..+...|++++|...|.+..+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+...|
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            456777778899999999999999987753 3356778888899999999999999999988775 44677888889999


Q ss_pred             HhcCCchhHHHHhcccC--CC-CcchHHHHHH--HHHhcCCCC
Q 031208          125 LKCGDVDGGRKMFDKMR--VR-SVVSWTTMIS--GLAASGDLD  162 (164)
Q Consensus       125 ~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~--~~~~~g~~~  162 (164)
                      .+.|++++|.+.|++..  .| +...+..+-.  .+.+.|+++
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~  134 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFE  134 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999875  33 3344433333  355555544

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

Probab=98.42  E-value=2.6e-06  Score=55.97  Aligned_cols=105  Identities=10%  Similarity=0.046  Sum_probs=68.7

Q ss_pred             HHHHhccCCcHHHHHHHhccC--CCc-HhHHHH----------------HHHHHHhcCChhHHHHHHHHHHHcCCCCCcc
Q 031208           20 LDLCSFYGKTDHALLVFSQIR--CPH-VFTWNL----------------MIRALTIDGSSLQALLLYNLMICNGFRPDKF   80 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~--~~~-~~~~~~----------------li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~   80 (164)
                      -..+...|+++.|...|+...  .|+ ...|..                +-..+.+.|++++|...|++..+.. +-+..
T Consensus        11 g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~   89 (208)
T 3urz_A           11 VSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA-PNNVD   89 (208)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHH
Confidence            345567788888888887765  342 334444                6667777888888888888876642 22455


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                      .+..+-..+...|++++|...+++..+.. +.+...+..+-..|..
T Consensus        90 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~  134 (208)
T 3urz_A           90 CLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYL  134 (208)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            67777777788888888888888777654 2344555555555433

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

Probab=98.42  E-value=3.4e-06  Score=58.34  Aligned_cols=129  Identities=9%  Similarity=-0.115  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhc-CChhHHHHHHHHHHHcCCCC-C---
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTID-GSSLQALLLYNLMICNGFRP-D---   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~p-~---   78 (164)
                      ..+|+.+-..|.+.|++++|...+++..+     .+    ..+++.+-..|... |++++|...|++..+..... +   
T Consensus        77 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~  156 (292)
T 1qqe_A           77 GNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVAL  156 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHH
Confidence            46788888899999999999999887652     12    35788888889986 99999999999986531111 1   


Q ss_pred             -cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCch------HHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           79 -KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDM------FVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        79 -~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~------~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                       ..++..+-..+.+.|++++|...+++..+.......      ..+..+..++...|+++.|...|++..
T Consensus       157 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  226 (292)
T 1qqe_A          157 SNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQ  226 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             246788889999999999999999999876432222      156777788999999999999999876

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

Probab=98.42  E-value=5.7e-06  Score=57.85  Aligned_cols=131  Identities=9%  Similarity=0.027  Sum_probs=97.0

Q ss_pred             HHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHH
Q 031208           32 ALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        32 a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  107 (164)
                      |...|++..   .++..++-.+-.++...|++++|++++.+-...+-.+ +...+..++..+.+.|+.+.|.+.++.|.+
T Consensus        85 a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~  164 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTN  164 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            556666554   2455555678888999999999999999986655322 445677889999999999999999999987


Q ss_pred             hCCCC-----chHHHHHHHHH--HHhcC--CchhHHHHhcccCCC--CcchHHHHHHHHHhcCCCCCC
Q 031208          108 AGFSR-----DMFVQSTLMDL--YLKCG--DVDGGRKMFDKMRVR--SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       108 ~g~~~-----~~~~~~~ll~~--~~~~~--~~~~a~~~~~~m~~~--~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .  .|     +..+...|..+  ....|  +..+|..+|+++.+.  +..+...++.++.+.|++++|
T Consensus       165 ~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eA  230 (310)
T 3mv2_B          165 A--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEA  230 (310)
T ss_dssp             H--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHH
T ss_pred             c--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHH
Confidence            6  46     35566666655  33334  899999999998743  323455666688899988765

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

Probab=98.42  E-value=6.4e-06  Score=51.63  Aligned_cols=121  Identities=7%  Similarity=-0.049  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCCC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRCP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      .+...+.+.+...+.++.+.++     .| +...+..+-..+.+.|++++|...|++..... +-+...|..+-.++...
T Consensus        10 ~~~~~l~~~~~~~~~l~~al~l-----~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~   83 (151)
T 3gyz_A           10 SISTAVIDAINSGATLKDINAI-----PDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIK   83 (151)
T ss_dssp             HHHHHHHHHHHTSCCTGGGCCS-----CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCCCHHHHhCC-----CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHH
Confidence            3445555555544444333221     23 34456666667778888888888888877643 22456677777788888


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |++++|...+++..+.. +.+...|..+-.+|.+.|++++|...|+...
T Consensus        84 g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al  131 (151)
T 3gyz_A           84 EQFQQAADLYAVAFALG-KNDYTPVFHTGQCQLRLKAPLKAKECFELVI  131 (151)
T ss_dssp             TCHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            88888888888877664 3356677777788888888888888887664

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.39  E-value=4.7e-06  Score=49.72  Aligned_cols=94  Identities=11%  Similarity=-0.013  Sum_probs=43.7

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC--CCC----cccHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF--RPD----KFTFPFV   85 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~--~p~----~~t~~~l   85 (164)
                      .+..+-..+...|+++.|...|+...   ..+...+..+-..+...|++++|...+++......  .++    ...+..+
T Consensus         6 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l   85 (131)
T 1elr_A            6 KEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHH
Confidence            34444445555555555555555433   12334444444455555555555555555433210  111    3344444


Q ss_pred             HHHHHhccchhhHHHHHHHHHHh
Q 031208           86 IKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      ...+...|++++|.+.+++..+.
T Consensus        86 a~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           86 GNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHh
Confidence            44555555555555555554443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.39  E-value=4.4e-06  Score=59.11  Aligned_cols=126  Identities=12%  Similarity=-0.001  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CCc----------------HhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH----------------VFTWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~----------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      ...+..+-..+.+.|+++.|...|++..  .|+                ...|..+-.++.+.|++++|...|++..+..
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  226 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD  226 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            4566777778889999999999998765  233                4788888889999999999999999987753


Q ss_pred             CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhH-HHHhccc
Q 031208           75 FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGG-RKMFDKM  140 (164)
Q Consensus        75 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a-~~~~~~m  140 (164)
                       +.+...|..+-.++...|++++|...+++..+.. +.+...+..+-..+.+.|+.++| ..+|+.|
T Consensus       227 -p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  291 (336)
T 1p5q_A          227 -SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANM  291 (336)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             3356788888899999999999999999988764 34567788888888888998888 3455544

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.39  E-value=1e-05  Score=66.45  Aligned_cols=135  Identities=10%  Similarity=0.083  Sum_probs=85.7

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      +..+|..+-.++.+.|++++|.+-|.+.  .|...|..+..++.+.|++++|.+.|..-++..  ++....+.+.-+|++
T Consensus      1104 ~p~vWsqLAKAql~~G~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAK 1179 (1630)
T 1xi4_A         1104 EPAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAK 1179 (1630)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHh
Confidence            4667888888888999999999988654  566777788999999999999999998766544  332223347777777


Q ss_pred             ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCCC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~~  162 (164)
                      .+++++...+.+       .++...|..+-+.|...|+++.|..+|...     ..|..+...|.+.|+++
T Consensus      1180 l~rleele~fI~-------~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA-----~ny~rLA~tLvkLge~q 1238 (1630)
T 1xi4_A         1180 TNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQ 1238 (1630)
T ss_pred             hcCHHHHHHHHh-------CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh-----hHHHHHHHHHHHhCCHH
Confidence            766664443321       233334444555555555555555555553     24444444444444443

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

Probab=98.37  E-value=2e-05  Score=47.64  Aligned_cols=93  Identities=5%  Similarity=-0.006  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                      +...=..+.+.|++++|.+.|++..+.. +.+...|..+-.++.+.|++++|...+++..+.. +.+...|..+-.+|..
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~   93 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVA   93 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHH
Confidence            3334444555566666666665554432 2234455555555555666666666665555443 2334455555555566


Q ss_pred             cCCchhHHHHhcccC
Q 031208          127 CGDVDGGRKMFDKMR  141 (164)
Q Consensus       127 ~~~~~~a~~~~~~m~  141 (164)
                      .|++++|.+.|++..
T Consensus        94 ~~~~~~A~~~~~~al  108 (126)
T 4gco_A           94 MREWSKAQRAYEDAL  108 (126)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH
Confidence            666666666655443

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.37  E-value=2.2e-05  Score=45.74  Aligned_cols=94  Identities=11%  Similarity=-0.099  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL  125 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  125 (164)
                      .+..+...+...|++++|...|++..... +.+...+..+...+...|++++|...+++..+.. +.+...+..+...|.
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~   83 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALE   83 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            44445555556666666666666655432 2234455555556666666666666666655543 223455555666666


Q ss_pred             hcCCchhHHHHhcccC
Q 031208          126 KCGDVDGGRKMFDKMR  141 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~  141 (164)
                      +.|++++|.+.|++..
T Consensus        84 ~~~~~~~A~~~~~~~~   99 (118)
T 1elw_A           84 FLNRFEEAKRTYEEGL   99 (118)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHH
Confidence            6666666666665543

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.33  E-value=1.5e-05  Score=49.64  Aligned_cols=90  Identities=11%  Similarity=-0.110  Sum_probs=43.2

Q ss_pred             HHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc
Q 031208           17 RKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL   93 (164)
Q Consensus        17 ~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~   93 (164)
                      ..+-..+.+.|++++|...|+...  . .+...|..+-.++...|++++|...|++..... +-+...+..+-.++...|
T Consensus        25 ~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g  103 (148)
T 2vgx_A           25 YSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQXG  103 (148)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcC
Confidence            333444445555555555555443  1 234444444445555555555555555554421 113334444455555555


Q ss_pred             chhhHHHHHHHHHH
Q 031208           94 AIEKGKEVHGLAVK  107 (164)
Q Consensus        94 ~~~~a~~~~~~m~~  107 (164)
                      ++++|...++...+
T Consensus       104 ~~~~A~~~~~~al~  117 (148)
T 2vgx_A          104 ELAEAESGLFLAQE  117 (148)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            55555555554443

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.31  E-value=3.2e-05  Score=45.03  Aligned_cols=97  Identities=12%  Similarity=-0.079  Sum_probs=81.3

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+...+...|+++.|...|+...  . .+...+..+-..+...|++++|...+++..+.. +.+...+..+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   81 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            34567778888999999999999999875  3 467788888889999999999999999997753 2356678888899


Q ss_pred             HHhccchhhHHHHHHHHHHhC
Q 031208           89 CIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +...|++++|...+++..+..
T Consensus        82 ~~~~~~~~~A~~~~~~~~~~~  102 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLKHE  102 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHhhHHHHHHHHHHHHHcC
Confidence            999999999999999887653

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.30  E-value=4.3e-06  Score=57.78  Aligned_cols=149  Identities=7%  Similarity=-0.123  Sum_probs=107.6

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC---CCcH------hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC---CC--ccc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR---CPHV------FTWNLMIRALTIDGSSLQALLLYNLMICNGFR---PD--KFT   81 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~---~~~~------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---p~--~~t   81 (164)
                      +...+..+...|++++|.+.++...   ..+.      ..+..+...+...|++++|...+.+.......   +.  ..+
T Consensus        78 l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 2qfc_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            3445667788999999999887543   1111      22334455567788999999999998653211   11  347


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHH---hC-CCC--chHHHHHHHHHHHhcCCchhHHHHhcccCC--C-------Ccc
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVK---AG-FSR--DMFVQSTLMDLYLKCGDVDGGRKMFDKMRV--R-------SVV  146 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~---~g-~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~-------~~~  146 (164)
                      |+.+-..|...|++++|...+++..+   .. -.+  ...++..+...|.+.|++++|...+++...  +       -..
T Consensus       158 ~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~  237 (293)
T 2qfc_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQ  237 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHH
Confidence            88888999999999999999998873   21 111  125888889999999999999999987641  1       145


Q ss_pred             hHHHHHHHHHhcCCCCCC
Q 031208          147 SWTTMISGLAASGDLDAA  164 (164)
Q Consensus       147 ~~~~li~~~~~~g~~~~A  164 (164)
                      +|..+-..|.+.|++++|
T Consensus       238 ~~~~lg~~y~~~g~~~~A  255 (293)
T 2qfc_A          238 LYYQRGECLRKLEYEEAE  255 (293)
T ss_dssp             HHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHcCCcHHH
Confidence            788888899999988764

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

Probab=98.30  E-value=1.8e-05  Score=48.57  Aligned_cols=89  Identities=12%  Similarity=-0.017  Sum_probs=41.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                      +-..+.+.|++++|...|++..... +.+...|..+-.++.+.|++++|...++...... +.+...+..+-.+|...|+
T Consensus        24 ~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~  101 (142)
T 2xcb_A           24 LGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGD  101 (142)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCC
Confidence            3344445555555555555544321 1133344444445555555555555555554443 2233444444455555555


Q ss_pred             chhHHHHhccc
Q 031208          130 VDGGRKMFDKM  140 (164)
Q Consensus       130 ~~~a~~~~~~m  140 (164)
                      +++|.+.|+..
T Consensus       102 ~~~A~~~~~~a  112 (142)
T 2xcb_A          102 LDGAESGFYSA  112 (142)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555555443

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

Probab=98.30  E-value=5.7e-05  Score=46.02  Aligned_cols=94  Identities=12%  Similarity=-0.163  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CCc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CPH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      ...+..+-..+.+.|+++.|...|+...  .|+    ...|..+-..+...|++++|...+++..+.. +.+...+..+.
T Consensus        28 ~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a  106 (148)
T 2dba_A           28 VEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRRS  106 (148)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHHH
Confidence            3344444444445555555555554433  232    3344444444445555555555554443321 11233344444


Q ss_pred             HHHHhccchhhHHHHHHHHHH
Q 031208           87 KACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~  107 (164)
                      .++...|++++|...+++..+
T Consensus       107 ~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          107 QALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHH
Confidence            444444555555555544443

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.30  E-value=2.2e-06  Score=55.73  Aligned_cols=136  Identities=6%  Similarity=-0.114  Sum_probs=74.0

Q ss_pred             HHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC--------------cccHH
Q 031208           22 LCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF-RPD--------------KFTFP   83 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~--------------~~t~~   83 (164)
                      .....|+++.+.+.|+.-..   .....+..+-..+...|++++|...|++.....- .|+              ...+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (198)
T 2fbn_A           13 GRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNL   92 (198)
T ss_dssp             ---------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHH
Confidence            34445555555555553321   1233455555666677777777777777655321 110              14556


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhc
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAAS  158 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~  158 (164)
                      .+-.++.+.|++++|...++...+.. +.+...+..+-.+|...|++++|...|++..  .| +...+..+...+...
T Consensus        93 ~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~  169 (198)
T 2fbn_A           93 NLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKL  169 (198)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHH
Confidence            66666777777777777777766653 3345666666677777777777777776654  23 344455554444433

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

Probab=98.28  E-value=1e-05  Score=46.86  Aligned_cols=93  Identities=11%  Similarity=-0.036  Sum_probs=47.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCC--chHHHHHHHHHH
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSR--DMFVQSTLMDLY  124 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~--~~~~~~~ll~~~  124 (164)
                      |..+-..+...|++++|...|++..+.. +.+...+..+-..+...|++++|...+++..+.. +.  +...+..+...|
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~   86 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADAL   86 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHH
Confidence            3344444555555555555555554432 1233344455555555555555555555555442 12  344555555555


Q ss_pred             Hhc-CCchhHHHHhcccC
Q 031208          125 LKC-GDVDGGRKMFDKMR  141 (164)
Q Consensus       125 ~~~-~~~~~a~~~~~~m~  141 (164)
                      .+. |++++|.+.|+...
T Consensus        87 ~~~~~~~~~A~~~~~~~~  104 (112)
T 2kck_A           87 RYIEGKEVEAEIAEARAK  104 (112)
T ss_dssp             TTCSSCSHHHHHHHHHHG
T ss_pred             HHHhCCHHHHHHHHHHHh
Confidence            556 66666666555543

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.28  E-value=6.4e-06  Score=58.87  Aligned_cols=152  Identities=9%  Similarity=-0.088  Sum_probs=114.0

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCCc
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRPDK   79 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~~   79 (164)
                      ..+++.+-..|...|+++.|.+.|++..+     ++    ..++..+-..|...|++++|...|.+....    +-+...
T Consensus       182 ~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~  261 (378)
T 3q15_A          182 IQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLP  261 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHH
Confidence            45666777788999999999999887642     22    246777888899999999999999998651    223336


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCC----CCchHHHHHHHHHHHhcCC---chhHHHHhcccCCC--CcchHHH
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGF----SRDMFVQSTLMDLYLKCGD---VDGGRKMFDKMRVR--SVVSWTT  150 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~----~~~~~~~~~ll~~~~~~~~---~~~a~~~~~~m~~~--~~~~~~~  150 (164)
                      .++..+-..+.+.|++++|...+++..+..-    +.....+..+-..|...++   +.+|...+++....  ....+..
T Consensus       262 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~  341 (378)
T 3q15_A          262 KVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARS  341 (378)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHH
Confidence            6788888999999999999999998876532    2234456666677777888   88889888876532  2346677


Q ss_pred             HHHHHHhcCCCCCC
Q 031208          151 MISGLAASGDLDAA  164 (164)
Q Consensus       151 li~~~~~~g~~~~A  164 (164)
                      +-..|...|++++|
T Consensus       342 la~~y~~~g~~~~A  355 (378)
T 3q15_A          342 AAAVFESSCHFEQA  355 (378)
T ss_dssp             HHHHHHHTTCHHHH
T ss_pred             HHHHHHHCCCHHHH
Confidence            88888888887654

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.28  E-value=3.3e-05  Score=46.67  Aligned_cols=95  Identities=7%  Similarity=-0.140  Sum_probs=51.4

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|+++.|...|+...  . .+...|..+-..+...|++++|...+++..+.. +.+...+..+-.+
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~   86 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQC   86 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHHH
Confidence            34455555555566666666666665543  1 234455555555566666666666666554432 1233445555555


Q ss_pred             HHhccchhhHHHHHHHHHH
Q 031208           89 CIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~  107 (164)
                      +...|++++|...+++..+
T Consensus        87 ~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           87 QLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHH
Confidence            5566666666666555543

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

Probab=98.28  E-value=4.6e-05  Score=52.59  Aligned_cols=127  Identities=10%  Similarity=0.018  Sum_probs=101.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHHHHHH-HHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTWNLMI-RALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li-~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|++++|...++....  |+........ ..+...++.++|...+++..... +.+...+..+-..
T Consensus       150 ~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~  228 (287)
T 3qou_A          150 NGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQ  228 (287)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHH
Confidence            566788888899999999999999999873  6554333322 23667788889999999987753 3356788889999


Q ss_pred             HHhccchhhHHHHHHHHHHhCCC-CchHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFS-RDMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      +...|++++|...+.+..+..-. .+...+..+...|...|+.++|...|++
T Consensus       229 l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~  280 (287)
T 3qou_A          229 LHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXYRR  280 (287)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            99999999999999999887522 2367899999999999999999887764

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.28  E-value=3.5e-05  Score=47.94  Aligned_cols=113  Identities=11%  Similarity=-0.095  Sum_probs=88.0

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKAC   89 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~   89 (164)
                      ..+-.+-..|.+.|++++|.+.|++..  . .+...|..+-..+.+.|++++|...|++..+.  .| +...+..+-..+
T Consensus        32 ~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~  109 (150)
T 4ga2_A           32 IKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELL  109 (150)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHH
Confidence            344456678999999999999999875  3 46788999999999999999999999999874  46 456788888999


Q ss_pred             HhccchhhHHHH-HHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 031208           90 IASLAIEKGKEV-HGLAVKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus        90 ~~~~~~~~a~~~-~~~m~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                      .+.|+.+++.+. ++...+.. +-+..+|...-..+.+.|+
T Consensus       110 ~~~~~~~~aa~~~~~~al~l~-P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A          110 CKNDVTDGRAKYWVERAAKLF-PGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHCSSSSHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTCCC
T ss_pred             HHcCChHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCc
Confidence            999999876655 57776653 3356677766666665554

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

Probab=98.27  E-value=4.4e-05  Score=46.54  Aligned_cols=109  Identities=12%  Similarity=-0.030  Sum_probs=88.2

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD----KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQ  117 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~  117 (164)
                      .+...+..+-..+...|++++|...|++..+.  .|+    ...+..+...+...|++++|...+++..+.. +.+...+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  102 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKAL  102 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHH
Confidence            45677888888999999999999999999874  466    5678888889999999999999999988764 3457788


Q ss_pred             HHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHH
Q 031208          118 STLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMIS  153 (164)
Q Consensus       118 ~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~  153 (164)
                      ..+...|.+.|++++|...|++..  .| +...+..+..
T Consensus       103 ~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~  141 (148)
T 2dba_A          103 YRRSQALEKLGRLDQAVLDLQRCVSLEPKNKVFQEALRN  141 (148)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHH
Confidence            888899999999999999999875  34 3344444333

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.27  E-value=3e-05  Score=46.40  Aligned_cols=89  Identities=9%  Similarity=-0.015  Sum_probs=40.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                      +-..+.+.|++++|...|++..+.. +.+...|..+-.++.+.|++++|...+++..+.. +.+...|..+-.+|...|+
T Consensus        10 ~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~   87 (126)
T 3upv_A           10 EGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKE   87 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhC
Confidence            3334444455555555555443321 1123344444444455555555555555444432 2223444444444555555


Q ss_pred             chhHHHHhccc
Q 031208          130 VDGGRKMFDKM  140 (164)
Q Consensus       130 ~~~a~~~~~~m  140 (164)
                      +++|...|++.
T Consensus        88 ~~~A~~~~~~a   98 (126)
T 3upv_A           88 YASALETLDAA   98 (126)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555554443

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.27  E-value=4.6e-05  Score=48.50  Aligned_cols=126  Identities=13%  Similarity=-0.015  Sum_probs=94.1

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC--CcHhHHHHHHHH-HHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC--PHVFTWNLMIRA-LTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~   87 (164)
                      +...+..+-..+.+.|++++|...++....  |+...+..+... +...+...++...+++..+.  .| +...+..+-.
T Consensus        39 ~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~--~P~~~~~~~~la~  116 (176)
T 2r5s_A           39 RGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAA--NPDNFELACELAV  116 (176)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHH--STTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHHHHHHHHHHHHhhcccchHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            466788888899999999999999999863  443333222111 22223344578888888764  45 4677888899


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCC-chHHHHHHHHHHHhcCCchhHHHHhcc
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDK  139 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~  139 (164)
                      .+...|++++|...+++..+..-.+ +...+..+...|...|+.++|...|++
T Consensus       117 ~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~  169 (176)
T 2r5s_A          117 QYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRR  169 (176)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHH
Confidence            9999999999999999988764222 356888999999999999999988875

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.26  E-value=5e-06  Score=58.82  Aligned_cols=133  Identities=14%  Similarity=-0.046  Sum_probs=103.8

Q ss_pred             CCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----------------cccHHHHHH
Q 031208           27 GKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD----------------KFTFPFVIK   87 (164)
Q Consensus        27 ~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----------------~~t~~~ll~   87 (164)
                      ++++.|...|+...  .| +...|..+-..+.+.|++++|...|++..+..  |+                ...|..+-.
T Consensus       127 ~~~~~A~~~~~~a~~~~p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~  204 (336)
T 1p5q_A          127 KSFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSFSNEEAQKAQALRLASHLNLAM  204 (336)
T ss_dssp             EEEECCCCGGGCCHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCCCSHHHHHHHHHHHHHHHHHHH
T ss_pred             eecccccchhcCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccCChHHHHHHHHHHHHHHHHHHH
Confidence            34445555554433  23 45678888888999999999999999997753  44                378888999


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~  162 (164)
                      ++.+.|++++|...+++..+.. +.+...+..+-.+|.+.|++++|...|++..  .| +...+..+-..+.+.|+.+
T Consensus       205 ~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~  281 (336)
T 1p5q_A          205 CHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQL  281 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998875 4567888999999999999999999999875  34 5567777777777666544

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

Probab=98.26  E-value=5.4e-05  Score=45.68  Aligned_cols=100  Identities=10%  Similarity=-0.087  Sum_probs=82.7

Q ss_pred             CCCC-HHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208            9 LSND-QLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus         9 ~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      +.|+ ...+...=..+.+.|++++|.+.|++..  . .+...|..+-.++.+.|++++|...|++..+.. +.+...|..
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~   86 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIR   86 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHH
Confidence            3443 3455566678899999999999999865  3 467889999999999999999999999997753 334568888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +-.++...|++++|.+.+++..+..
T Consensus        87 lg~~~~~~~~~~~A~~~~~~al~l~  111 (126)
T 4gco_A           87 KAACLVAMREWSKAQRAYEDALQVD  111 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            9999999999999999999998764

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

Probab=98.25  E-value=1.5e-05  Score=46.16  Aligned_cols=97  Identities=13%  Similarity=-0.095  Sum_probs=81.6

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC--CcccHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP--DKFTFPFVI   86 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~t~~~ll   86 (164)
                      +...+..+-..+.+.|++++|...|++..   ..+...|..+-..+...|++++|...|++..+.. +.  +...+..+.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~   83 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKA   83 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHH
Confidence            45667778888999999999999999865   3467788888899999999999999999998753 22  466788888


Q ss_pred             HHHHhc-cchhhHHHHHHHHHHhC
Q 031208           87 KACIAS-LAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        87 ~~~~~~-~~~~~a~~~~~~m~~~g  109 (164)
                      ..+.+. |++++|.+.++......
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           84 DALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             HHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             HHHHHHhCCHHHHHHHHHHHhhcc
Confidence            999999 99999999999987664

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

Probab=98.25  E-value=2.2e-05  Score=49.21  Aligned_cols=100  Identities=16%  Similarity=0.016  Sum_probs=83.9

Q ss_pred             CCC-CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208            9 LSN-DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus         9 ~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      +.| +...+..+-..+.+.|++++|...|+...  .| +...|..+-.++...|++++|...|++..+.. +-+...|..
T Consensus        31 l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~  109 (151)
T 3gyz_A           31 IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFH  109 (151)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHH
Confidence            344 34456666778889999999999999876  34 67889999999999999999999999998753 235678888


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +-.++.+.|++++|...++...+..
T Consensus       110 lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          110 TGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999998875

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

Probab=98.24  E-value=2.9e-05  Score=48.79  Aligned_cols=96  Identities=10%  Similarity=-0.029  Sum_probs=65.7

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|++++|...|++..  . .+...|..+-.++.+.|++++|...|++..+.. +-+...|..+-.+
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   88 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34556666667777777777777777654  2 355667777777777777777777777776543 2235566677777


Q ss_pred             HHhccchhhHHHHHHHHHHh
Q 031208           89 CIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +...|++++|...+++..+.
T Consensus        89 ~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHh
Confidence            77777777777777776654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.23  E-value=7.8e-06  Score=58.23  Aligned_cols=150  Identities=12%  Similarity=-0.038  Sum_probs=113.1

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC-
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRPD-   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~-   78 (164)
                      ..++..+-..+...|++++|...+++..+     ++    ..++..+-..+...|++++|...+++....    +-.+. 
T Consensus       187 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  266 (406)
T 3sf4_A          187 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE  266 (406)
T ss_dssp             HHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHH
Confidence            34677777889999999999999987652     22    237888888999999999999999997542    11111 


Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHhC----CCC-chHHHHHHHHHHHhcCCchhHHHHhcccCC-------C--C
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKAG----FSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-------R--S  144 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-------~--~  144 (164)
                      ..++..+...+...|++++|...+++..+..    -.+ ...++..+-..|.+.|++++|.+.|++..+       +  .
T Consensus       267 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  346 (406)
T 3sf4_A          267 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGE  346 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcch
Confidence            4577888899999999999999999876532    111 155777888899999999999999887641       1  2


Q ss_pred             cchHHHHHHHHHhcCCCC
Q 031208          145 VVSWTTMISGLAASGDLD  162 (164)
Q Consensus       145 ~~~~~~li~~~~~~g~~~  162 (164)
                      ..++..+...|...|+..
T Consensus       347 ~~~~~~l~~~~~~~g~~~  364 (406)
T 3sf4_A          347 LTARLNLSDLQMVLGLSY  364 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTS
T ss_pred             hHHHHHHHHHHHHhhHhH
Confidence            457777778887777654

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.22  E-value=1.1e-05  Score=66.41  Aligned_cols=134  Identities=11%  Similarity=0.095  Sum_probs=100.8

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC--CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR--CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      -|...|..+...+.+.|++++|.+++....  .++....+.+..+|++.+++++...+.    .   .|+...|..+-..
T Consensus      1132 dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele~fI----~---~~n~ad~~~iGd~ 1204 (1630)
T 1xi4_A         1132 DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFI----N---GPNNAHIQQVGDR 1204 (1630)
T ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHHH----h---CCCHHHHHHHHHH
Confidence            456778889999999999999999997644  234334445888999998888644332    2   3555677778899


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHhcCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~g~~~  162 (164)
                      |...|++++|..+|...         ..|..+...|.+.|+++.|.+.+++..  +..+|.-+-.+|...|++.
T Consensus      1205 le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~--n~~aWkev~~acve~~Ef~ 1267 (1630)
T 1xi4_A         1205 CYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKEFR 1267 (1630)
T ss_pred             HHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhC--CHHHHHHHHHHHhhhhHHH
Confidence            99999999999999884         488999999999999999999998775  3456655555555444443

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.21  E-value=6.3e-06  Score=57.42  Aligned_cols=148  Identities=11%  Similarity=-0.073  Sum_probs=86.4

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-Ccc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-DKF   80 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~   80 (164)
                      .|......|...|++++|...|.+...     .+    ..+|+.+-..|.+.|++++|...|++....    |-.+ -..
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  117 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAM  117 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            455556666777777777777665431     11    245666677777777777777777765432    1111 123


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHhC----CCC-chHHHHHHHHHHHhcCCchhHHHHhcccCC-----CC----cc
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKAG----FSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-----RS----VV  146 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~~----~~  146 (164)
                      ++..+-..|.. |++++|...+++.....    -.+ ...++..+-..|.+.|++++|.+.|++...     ++    ..
T Consensus       118 ~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (307)
T 2ifu_A          118 ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYK  196 (307)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHH
Confidence            55566666666 77777777777655421    101 134566667777777777777777776541     11    12


Q ss_pred             hHHHHHHHHHhcCCCCC
Q 031208          147 SWTTMISGLAASGDLDA  163 (164)
Q Consensus       147 ~~~~li~~~~~~g~~~~  163 (164)
                      .+..+...+...|++++
T Consensus       197 ~~~~~g~~~~~~g~~~~  213 (307)
T 2ifu_A          197 KCIAQVLVQLHRADYVA  213 (307)
T ss_dssp             HHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHcCCHHH
Confidence            44455555555566543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.20  E-value=1.1e-06  Score=63.01  Aligned_cols=151  Identities=12%  Similarity=0.024  Sum_probs=111.9

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC---------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-Cc
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC---------PHVFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-DK   79 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~---------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~   79 (164)
                      .++..+-..+...|++++|...+++...         .....+..+-..+...|++++|...+++....    +-.| ..
T Consensus        87 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  166 (411)
T 4a1s_A           87 AIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEG  166 (411)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHH
Confidence            4677788888899999999998887642         23356788888899999999999999987543    1112 23


Q ss_pred             ccHHHHHHHHHhccc-----------------hhhHHHHHHHHHHh----CCCC-chHHHHHHHHHHHhcCCchhHHHHh
Q 031208           80 FTFPFVIKACIASLA-----------------IEKGKEVHGLAVKA----GFSR-DMFVQSTLMDLYLKCGDVDGGRKMF  137 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~-----------------~~~a~~~~~~m~~~----g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~  137 (164)
                      ..+..+-..+...|+                 +++|...+++..+.    +-.+ ....+..+...|...|++++|.+.|
T Consensus       167 ~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  246 (411)
T 4a1s_A          167 RALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHH  246 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHH
Confidence            477788888899999                 89998888876542    2212 2347777888899999999999999


Q ss_pred             cccCC-----CC----cchHHHHHHHHHhcCCCCCC
Q 031208          138 DKMRV-----RS----VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       138 ~~m~~-----~~----~~~~~~li~~~~~~g~~~~A  164 (164)
                      ++...     ++    ..+|..+...|...|++++|
T Consensus       247 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  282 (411)
T 4a1s_A          247 QERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDA  282 (411)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHH
Confidence            87652     11    23778888888888887654

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.20  E-value=3.6e-05  Score=45.72  Aligned_cols=112  Identities=11%  Similarity=-0.015  Sum_probs=87.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCC--CCc----hHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGF--SRD----MFVQS  118 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~----~~~~~  118 (164)
                      ..|..+-..+...|++++|...|.+..... +.+...+..+...+...|++++|...+++.....-  .++    ...+.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            457777888999999999999999997753 34566788888999999999999999998876531  122    67888


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC--CCCcchHHHHHHHHHh
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTMISGLAA  157 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~li~~~~~  157 (164)
                      .+...|.+.|++++|.+.|+...  .|+...+..+-.....
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~  124 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKI  124 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            88999999999999999999875  4555555555544443

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.19  E-value=5.1e-05  Score=45.82  Aligned_cols=98  Identities=10%  Similarity=-0.023  Sum_probs=84.3

Q ss_pred             CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           42 PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      .+...|..+-..+...|++++|...|.+..... +.+...+..+-..+...|++++|...++...+.. +.+...+..+-
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            466788888889999999999999999987753 3356788888999999999999999999998875 34677888999


Q ss_pred             HHHHhcCCchhHHHHhcccC
Q 031208          122 DLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..|.+.|++++|...|++..
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~  104 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAY  104 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHH
Confidence            99999999999999998775

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.17  E-value=3.1e-06  Score=60.34  Aligned_cols=152  Identities=13%  Similarity=-0.021  Sum_probs=114.1

Q ss_pred             HHHHHHHHHHHhccCC--------------------cHHHHHHHhccCC-----C----cHhHHHHHHHHHHhcCChhHH
Q 031208           13 QLLVRKLLDLCSFYGK--------------------TDHALLVFSQIRC-----P----HVFTWNLMIRALTIDGSSLQA   63 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~--------------------~~~a~~~~~~~~~-----~----~~~~~~~li~~~~~~~~~~~a   63 (164)
                      ..++..+-..+...|+                    ++.|.+.++....     +    ...++..+-..+...|++++|
T Consensus       127 ~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  206 (406)
T 3sf4_A          127 ARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDA  206 (406)
T ss_dssp             HHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHH
T ss_pred             HHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHH
Confidence            3467777778888999                    8888888876541     1    234678888889999999999


Q ss_pred             HHHHHHHHHcCC-CCC----cccHHHHHHHHHhccchhhHHHHHHHHHHh----CCCCc-hHHHHHHHHHHHhcCCchhH
Q 031208           64 LLLYNLMICNGF-RPD----KFTFPFVIKACIASLAIEKGKEVHGLAVKA----GFSRD-MFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        64 ~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~-~~~~~~ll~~~~~~~~~~~a  133 (164)
                      ...+++..+... .++    ..++..+...+...|++++|...+++....    +-.+. ..++..+...|.+.|++++|
T Consensus       207 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  286 (406)
T 3sf4_A          207 VIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKA  286 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHH
Confidence            999999854311 122    237888889999999999999999987643    21111 45778888999999999999


Q ss_pred             HHHhcccCC-----CC----cchHHHHHHHHHhcCCCCCC
Q 031208          134 RKMFDKMRV-----RS----VVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       134 ~~~~~~m~~-----~~----~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+.|++...     .+    ..++..+-..|...|++++|
T Consensus       287 ~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  326 (406)
T 3sf4_A          287 IDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQA  326 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHH
Confidence            999987652     12    45788888888888887654

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.15  E-value=4.6e-05  Score=47.30  Aligned_cols=97  Identities=7%  Similarity=-0.079  Sum_probs=81.9

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      +...+..+-..+...|++++|...|++..... +.+...|..+-.++...|++++|...+++..... +.+...+..+-.
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~   97 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAE   97 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHH
Confidence            44567777788899999999999999997753 3366677888889999999999999999998775 345678888899


Q ss_pred             HHHhcCCchhHHHHhcccC
Q 031208          123 LYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~  141 (164)
                      +|...|++++|.+.|+...
T Consensus        98 ~~~~~g~~~~A~~~~~~al  116 (148)
T 2vgx_A           98 CLLQXGELAEAESGLFLAQ  116 (148)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            9999999999999999775

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.15  E-value=3.6e-06  Score=58.13  Aligned_cols=152  Identities=9%  Similarity=-0.020  Sum_probs=110.7

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC---------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC----
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC---------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF-RPD----   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~---------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----   78 (164)
                      ...+..+-..+...|+++.|...+++...         .....+..+-..+...|++++|...+.+..+..- .++    
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  122 (338)
T 3ro2_A           43 SAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGE  122 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHH
Confidence            35677888889999999999999887541         1245677888889999999999999998754211 112    


Q ss_pred             cccHHHHHHHHHhccc--------------------hhhHHHHHHHHHHh----CCCC-chHHHHHHHHHHHhcCCchhH
Q 031208           79 KFTFPFVIKACIASLA--------------------IEKGKEVHGLAVKA----GFSR-DMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~--------------------~~~a~~~~~~m~~~----g~~~-~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      ..++..+...+...|+                    +++|...+++....    +-.+ ....+..+...|...|++++|
T Consensus       123 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  202 (338)
T 3ro2_A          123 ARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDA  202 (338)
T ss_dssp             HHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHH
Confidence            2377778888888999                    88898888776532    2122 234677788888999999999


Q ss_pred             HHHhcccCC-----C----CcchHHHHHHHHHhcCCCCCC
Q 031208          134 RKMFDKMRV-----R----SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       134 ~~~~~~m~~-----~----~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+.+++..+     +    ...++..+...|...|++++|
T Consensus       203 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  242 (338)
T 3ro2_A          203 VIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  242 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHH
Confidence            999887651     1    123777788888888877653

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

Probab=98.14  E-value=3.2e-05  Score=52.25  Aligned_cols=127  Identities=8%  Similarity=-0.097  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--C---c-HhHHHHHHHHHHh--------cCChhHHHHHHHHHHHcCCCCC
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--P---H-VFTWNLMIRALTI--------DGSSLQALLLYNLMICNGFRPD   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~---~-~~~~~~li~~~~~--------~~~~~~a~~~~~~m~~~~~~p~   78 (164)
                      ...+..+-..+.+.|+++.|...|+...+  |   + ...+..+-.++..        .|++++|...|++.....  |+
T Consensus        52 ~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~  129 (261)
T 3qky_A           52 ADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PN  129 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TT
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cC
Confidence            56677778889999999999999998762  3   2 3455666667777        999999999999997753  43


Q ss_pred             -cccH-----------------HHHHHHHHhccchhhHHHHHHHHHHhCCC-C-chHHHHHHHHHHHhc----------C
Q 031208           79 -KFTF-----------------PFVIKACIASLAIEKGKEVHGLAVKAGFS-R-DMFVQSTLMDLYLKC----------G  128 (164)
Q Consensus        79 -~~t~-----------------~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~-~~~~~~~ll~~~~~~----------~  128 (164)
                       ....                 -.+-..+.+.|++++|...+++..+..-. + ....+..+..+|.+.          |
T Consensus       130 ~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~  209 (261)
T 3qky_A          130 HELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPE  209 (261)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccc
Confidence             3333                 34577889999999999999999876411 1 345677777788766          8


Q ss_pred             CchhHHHHhcccC
Q 031208          129 DVDGGRKMFDKMR  141 (164)
Q Consensus       129 ~~~~a~~~~~~m~  141 (164)
                      ++++|...|+++.
T Consensus       210 ~~~~A~~~~~~~~  222 (261)
T 3qky_A          210 RYRRAVELYERLL  222 (261)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH
Confidence            8899999999886

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.14  E-value=1.7e-05  Score=58.75  Aligned_cols=117  Identities=10%  Similarity=-0.126  Sum_probs=90.4

Q ss_pred             HHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh
Q 031208           20 LDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      -..+.+.|++++|.+.|++..  . .+...|..+-.++.+.|++++|.+.+++..+.. +-+...+..+-.++.+.|+++
T Consensus        13 g~~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           13 ANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             SSSTTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence            345667899999999999875  3 457889999999999999999999999998753 235568888899999999999


Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHH--HHhcCCchhHHHHhc
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDL--YLKCGDVDGGRKMFD  138 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~--~~~~~~~~~a~~~~~  138 (164)
                      +|.+.+++..+.. +.+...+..+-.+  +.+.|++++|.+.++
T Consensus        92 eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           92 AALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999988764 2233455555444  888899999999998

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.14  E-value=0.00012  Score=43.59  Aligned_cols=95  Identities=14%  Similarity=-0.102  Sum_probs=80.4

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...|..+-..+.+.|++++|...|++..  . .+...|..+-.++.+.|++++|...|++..+.. +-+...|..+-.++
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   82 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            4556677778899999999999999875  3 467889999999999999999999999997753 23456788889999


Q ss_pred             HhccchhhHHHHHHHHHHh
Q 031208           90 IASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~  108 (164)
                      ...|++++|...+++..+.
T Consensus        83 ~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           83 IAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHh
Confidence            9999999999999988765

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.13  E-value=2.7e-06  Score=58.80  Aligned_cols=152  Identities=13%  Similarity=0.003  Sum_probs=110.3

Q ss_pred             HHHHHHHHHHHhccCC--------------------cHHHHHHHhccCC-----C----cHhHHHHHHHHHHhcCChhHH
Q 031208           13 QLLVRKLLDLCSFYGK--------------------TDHALLVFSQIRC-----P----HVFTWNLMIRALTIDGSSLQA   63 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~--------------------~~~a~~~~~~~~~-----~----~~~~~~~li~~~~~~~~~~~a   63 (164)
                      ..++..+-..+...|+                    ++.|...+++...     +    ....+..+-..+...|++++|
T Consensus       123 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  202 (338)
T 3ro2_A          123 ARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDA  202 (338)
T ss_dssp             HHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHH
Confidence            3366777778888888                    8888888876531     1    234677788888999999999


Q ss_pred             HHHHHHHHHcCC-CCC----cccHHHHHHHHHhccchhhHHHHHHHHHHhC----CCC-chHHHHHHHHHHHhcCCchhH
Q 031208           64 LLLYNLMICNGF-RPD----KFTFPFVIKACIASLAIEKGKEVHGLAVKAG----FSR-DMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        64 ~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~-~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      ...+++..+... .++    ..++..+...+...|++++|...+++.....    ..+ ...++..+...|...|++++|
T Consensus       203 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  282 (338)
T 3ro2_A          203 VIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKA  282 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHH
Confidence            999998754211 111    2367788888999999999999998776431    111 145677788889999999999


Q ss_pred             HHHhcccCC-----C----CcchHHHHHHHHHhcCCCCCC
Q 031208          134 RKMFDKMRV-----R----SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       134 ~~~~~~m~~-----~----~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ...+++...     .    ...++..+...|.+.|++++|
T Consensus       283 ~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  322 (338)
T 3ro2_A          283 IDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQA  322 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence            999887641     1    134777888888888887654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.13  E-value=1.7e-05  Score=51.21  Aligned_cols=141  Identities=9%  Similarity=-0.061  Sum_probs=102.8

Q ss_pred             hccCCcHHHHH---HHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHH----cCCCC-CcccHHHHHHHHHhccch
Q 031208           24 SFYGKTDHALL---VFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMIC----NGFRP-DKFTFPFVIKACIASLAI   95 (164)
Q Consensus        24 ~~~~~~~~a~~---~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~p-~~~t~~~ll~~~~~~~~~   95 (164)
                      ...|++++|.+   ++..-+......+..+-..+...|++++|...+++...    .+..| ....+..+-..+...|++
T Consensus         3 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~   82 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNW   82 (203)
T ss_dssp             ----CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             cccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCH
Confidence            45789999999   66553334567888888899999999999999999855    22222 345778888899999999


Q ss_pred             hhHHHHHHHHHHh----CCCC--chHHHHHHHHHHHhcCCchhHHHHhcccCC-----CC----cchHHHHHHHHHhcCC
Q 031208           96 EKGKEVHGLAVKA----GFSR--DMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-----RS----VVSWTTMISGLAASGD  160 (164)
Q Consensus        96 ~~a~~~~~~m~~~----g~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~g~  160 (164)
                      ++|...+++....    +-.|  ....+..+-..+...|++++|.+.+++...     .+    ..++..+-..|...|+
T Consensus        83 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~  162 (203)
T 3gw4_A           83 DAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKN  162 (203)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcC
Confidence            9999999877653    2122  245677888899999999999999887641     12    2346777888888888


Q ss_pred             CCCC
Q 031208          161 LDAA  164 (164)
Q Consensus       161 ~~~A  164 (164)
                      +++|
T Consensus       163 ~~~A  166 (203)
T 3gw4_A          163 LLEA  166 (203)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

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

Probab=98.13  E-value=6.1e-05  Score=46.20  Aligned_cols=95  Identities=13%  Similarity=-0.145  Sum_probs=78.8

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKAC   89 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   89 (164)
                      ...+..+-..+.+.|++++|...|+...  .| +...|..+-.++...|++++|...|++..... +-+...+..+-.++
T Consensus        18 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   96 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHH
Confidence            3445555667889999999999999875  34 67788888889999999999999999997753 33556778888999


Q ss_pred             HhccchhhHHHHHHHHHHh
Q 031208           90 IASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~  108 (164)
                      ...|++++|...++...+.
T Consensus        97 ~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            9999999999999988765

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.13  E-value=1.7e-06  Score=62.04  Aligned_cols=149  Identities=10%  Similarity=-0.014  Sum_probs=112.2

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC--CCc-H----hHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-CcccHH
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR--CPH-V----FTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-DKFTFP   83 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~--~~~-~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~t~~   83 (164)
                      +..+-..+...|++++|...|++..  .|+ .    ..|..+-..+...|++++|...+++..+.    +-.| ....+.
T Consensus        51 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  130 (411)
T 4a1s_A           51 LALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSG  130 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHH
Confidence            3445557788999999999999875  233 2    46888888899999999999999987542    2122 345778


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHh----CCC-CchHHHHHHHHHHHhcCC-----------------chhHHHHhcccC
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKA----GFS-RDMFVQSTLMDLYLKCGD-----------------VDGGRKMFDKMR  141 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~----g~~-~~~~~~~~ll~~~~~~~~-----------------~~~a~~~~~~m~  141 (164)
                      .+-..+...|++++|...+++..+.    +-. .....+..+-..|...|+                 +++|.+.+++..
T Consensus       131 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al  210 (411)
T 4a1s_A          131 NLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENL  210 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHH
Confidence            8889999999999999999887654    211 234577888889999999                 999988887654


Q ss_pred             C-------C--CcchHHHHHHHHHhcCCCCCC
Q 031208          142 V-------R--SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       142 ~-------~--~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +       +  ...+|..+-..|...|++++|
T Consensus       211 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  242 (411)
T 4a1s_A          211 KLMRDLGDRGAQGRACGNLGNTYYLLGDFQAA  242 (411)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCChHHH
Confidence            1       1  234788888888888887654

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.12  E-value=6.3e-05  Score=48.72  Aligned_cols=125  Identities=8%  Similarity=-0.069  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC--C-c----------------HhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC--P-H----------------VFTWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~----------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      ..+..+-..+.+.|++++|...|++...  | +                ...|..+-.++.+.|++++|...+++..+..
T Consensus        39 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~  118 (198)
T 2fbn_A           39 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID  118 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            3455666778889999999999997652  1 2                2678888888999999999999999997752


Q ss_pred             CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHH-HHhccc
Q 031208           75 FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGR-KMFDKM  140 (164)
Q Consensus        75 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~-~~~~~m  140 (164)
                       +.+...+..+-.++...|++++|...+++..+.. +.+...+..+...+.+.++.+++. ..|..|
T Consensus       119 -p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  183 (198)
T 2fbn_A          119 -KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKKDKLTFGGM  183 (198)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC---------
T ss_pred             -cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             3356678888899999999999999999988764 335667777777777777776666 444444

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

Probab=98.12  E-value=5.9e-05  Score=49.42  Aligned_cols=129  Identities=13%  Similarity=0.033  Sum_probs=90.7

Q ss_pred             HHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccc
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLA   94 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~   94 (164)
                      +-..+.+.|++++|...|++..  .| +...|..+-..+...|++++|...|++..+.  .| +...+..+-..+...|.
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~  137 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAE  137 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhH
Confidence            7778889999999999999876  34 6788999999999999999999999999875  35 45677777777766554


Q ss_pred             h--hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcchHHHH
Q 031208           95 I--EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVVSWTTM  151 (164)
Q Consensus        95 ~--~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~~~~~l  151 (164)
                      .  ..+...+....  ...|....+...-.++...|++++|...|++..  .|+......+
T Consensus       138 ~~~~~~~~~~~~~~--~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l  196 (208)
T 3urz_A          138 QEKKKLETDYKKLS--SPTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHh--CCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            3  33444444432  222323333444555667899999999999876  4555444443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.10  E-value=4.6e-05  Score=52.59  Aligned_cols=128  Identities=5%  Similarity=-0.184  Sum_probs=94.6

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC--CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--cccHHHHHHHHHh
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR--CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD--KFTFPFVIKACIA   91 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~   91 (164)
                      .-.....+...|++++|.++|+...  .|+....-.+-..+.+.+++++|+..|+...... .|.  ...+..+-.++..
T Consensus       105 ~LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~  183 (282)
T 4f3v_A          105 TMGFAACEAAQGNYADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAAN  183 (282)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHH
Confidence            3445667888999999999999987  4544344444457899999999999998554321 111  2256667788999


Q ss_pred             ccchhhHHHHHHHHHHhCCCCc--hHHHHHHHHHHHhcCCchhHHHHhcccC--CCC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRD--MFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRS  144 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~  144 (164)
                      .|++++|...+++.......|.  .......-.++.+.|+.++|..+|+++.  .|+
T Consensus       184 LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~  240 (282)
T 4f3v_A          184 LALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE  240 (282)
T ss_dssp             TTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc
Confidence            9999999999999874433253  3355666777889999999999999886  555

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.08  E-value=0.00017  Score=51.08  Aligned_cols=149  Identities=10%  Similarity=-0.018  Sum_probs=103.3

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC----------Cc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC--C--Ccc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC----------PH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFR--P--DKF   80 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~----------~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--p--~~~   80 (164)
                      +..+-..+...|+++.|...+++...          |. ...+..+-..+...|++++|...+++.......  +  ...
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  175 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  175 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHH
Confidence            45556678889999999998887641          22 234566777888999999999999998653221  1  124


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-hHHHH-----HHHHHHHhcCCchhHHHHhcccCCCC-------cch
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-MFVQS-----TLMDLYLKCGDVDGGRKMFDKMRVRS-------VVS  147 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~-----~ll~~~~~~~~~~~a~~~~~~m~~~~-------~~~  147 (164)
                      ++..+...+...|++++|...+++.....-.++ ...+.     .....+...|+.++|...+++...++       ...
T Consensus       176 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  255 (373)
T 1hz4_A          176 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  255 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHH
Confidence            567778888999999999999998875422221 11122     23345778999999999998876432       124


Q ss_pred             HHHHHHHHHhcCCCCCC
Q 031208          148 WTTMISGLAASGDLDAA  164 (164)
Q Consensus       148 ~~~li~~~~~~g~~~~A  164 (164)
                      +..+...+...|++++|
T Consensus       256 ~~~la~~~~~~g~~~~A  272 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPA  272 (373)
T ss_dssp             HHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHcCCHHHH
Confidence            56677788888876643

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

Probab=98.08  E-value=0.00014  Score=45.52  Aligned_cols=97  Identities=18%  Similarity=0.036  Sum_probs=83.7

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      +...|..+-..+.+.|++++|...|++..+.. +-+...|..+-.++.+.|++++|...+++..+.. +.+...|..+-.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            45667778888999999999999999997753 2366788889999999999999999999998875 345788899999


Q ss_pred             HHHhcCCchhHHHHhcccC
Q 031208          123 LYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~  141 (164)
                      .|.+.|++++|.+.|++..
T Consensus        88 ~~~~~g~~~~A~~~~~~al  106 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGI  106 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHH
Confidence            9999999999999999875

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.07  E-value=8.4e-05  Score=53.04  Aligned_cols=148  Identities=9%  Similarity=-0.048  Sum_probs=105.2

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc-----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CC---
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH-----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFR-PD---   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~---   78 (164)
                      ..++..+-..+...|+++.|...+++..+     ++     ..+++.+-..|...|++++|...|.+.....-. ++   
T Consensus       143 a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  222 (383)
T 3ulq_A          143 AEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQL  222 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHH
Confidence            45677777788889999988888876541     22     346777778889999999999999887542111 11   


Q ss_pred             -cccHHHHHHHHHhccchhhHHHHHHHHHHh----CC-CCchHHHHHHHHHHHhcCCchhHHHHhcccCC-------C-C
Q 031208           79 -KFTFPFVIKACIASLAIEKGKEVHGLAVKA----GF-SRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV-------R-S  144 (164)
Q Consensus        79 -~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-------~-~  144 (164)
                       ..++..+-..|...|++++|...+++..+.    +. +....++..+-..|.+.|++++|.+.+++...       + .
T Consensus       223 ~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  302 (383)
T 3ulq_A          223 MGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIY  302 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHH
Confidence             146778888899999999999999887762    33 33466788888899999999999998887641       1 1


Q ss_pred             cchHHHHHHHHHhcCC
Q 031208          145 VVSWTTMISGLAASGD  160 (164)
Q Consensus       145 ~~~~~~li~~~~~~g~  160 (164)
                      ...+..+-..|...|+
T Consensus       303 ~~~~~~l~~~~~~~~~  318 (383)
T 3ulq_A          303 LSEFEFLKSLYLSGPD  318 (383)
T ss_dssp             HHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHhCCCc
Confidence            1234555555555554

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.06  E-value=1.8e-05  Score=58.66  Aligned_cols=109  Identities=7%  Similarity=-0.020  Sum_probs=88.7

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      .+.+.|++++|.+.|++..+.  .| +...|..+-.++.+.|++++|.+.+++..+.. +.+...+..+-.+|.+.|+++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence            456789999999999999775  35 46788899999999999999999999998764 345778889999999999999


Q ss_pred             hHHHHhcccC--CC-CcchHHHHHHH--HHhcCCCCCC
Q 031208          132 GGRKMFDKMR--VR-SVVSWTTMISG--LAASGDLDAA  164 (164)
Q Consensus       132 ~a~~~~~~m~--~~-~~~~~~~li~~--~~~~g~~~~A  164 (164)
                      +|.+.|++..  .| +...+..+-.+  +.+.|++++|
T Consensus        92 eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A  129 (477)
T 1wao_1           92 AALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERA  129 (477)
T ss_dssp             HHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999875  33 44566666555  7777877766

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.06  E-value=0.00011  Score=50.67  Aligned_cols=151  Identities=7%  Similarity=0.073  Sum_probs=101.2

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHh---HHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCCc----c
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVF---TWNLMIRALTIDGSSLQALLLYNLMICNG-FRPDK----F   80 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~----~   80 (164)
                      ..|+..+...+...+.-.-     ..++..-...+..   .+...+..+...|++++|...+++..... ..|+.    .
T Consensus        42 ~~~~~~~l~~i~~~l~~~~-----~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~  116 (293)
T 3u3w_A           42 VYPSMDILQGIAAKLQIPI-----IHFYEVLIYSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQ  116 (293)
T ss_dssp             CCCCHHHHHHHHHHHTCCT-----HHHHHTTTSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhCcCH-----HHHhCCCCCCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHH
Confidence            4566666666655544221     2233333333333   33344677899999999999999987632 12221    1


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHhCCC-Cc----hHHHHHHHHHHHhcCCchhHHHHhcccCC------C----Cc
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKAGFS-RD----MFVQSTLMDLYLKCGDVDGGRKMFDKMRV------R----SV  145 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~------~----~~  145 (164)
                      .+..+...+...+++++|...+++..+.... ++    ..+++.+-..|...|++++|...|++..+      .    ..
T Consensus       117 ~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (293)
T 3u3w_A          117 WQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDV  196 (293)
T ss_dssp             HHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHH
T ss_pred             HHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHH
Confidence            2334566667778999999999999874322 22    23688899999999999999999987751      1    23


Q ss_pred             chHHHHHHHHHhcCCCCCC
Q 031208          146 VSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       146 ~~~~~li~~~~~~g~~~~A  164 (164)
                      .+|..+-..|.+.|++++|
T Consensus       197 ~~~~nlg~~y~~~~~y~~A  215 (293)
T 3u3w_A          197 KVRYNHAKALYLDSRYEES  215 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHH
Confidence            4788888999999988764

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

Probab=98.05  E-value=0.00031  Score=41.73  Aligned_cols=84  Identities=10%  Similarity=-0.046  Sum_probs=37.5

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCc----ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc---hHHHHHHHHHHHh
Q 031208           54 LTIDGSSLQALLLYNLMICNGFRPDK----FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD---MFVQSTLMDLYLK  126 (164)
Q Consensus        54 ~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~ll~~~~~  126 (164)
                      +...|++++|...|++..+..  |+.    ..+..+-.++.+.|++++|...++...+.. +.+   ...+..+-.+|.+
T Consensus        12 ~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~la~~~~~   88 (129)
T 2xev_A           12 ALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY-PTHDKAAGGLLKLGLSQYG   88 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTSTTHHHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHHHHH
Confidence            344455555555555544321  211    133344444455555555555555544432 111   2334444444555


Q ss_pred             cCCchhHHHHhccc
Q 031208          127 CGDVDGGRKMFDKM  140 (164)
Q Consensus       127 ~~~~~~a~~~~~~m  140 (164)
                      .|++++|...|++.
T Consensus        89 ~g~~~~A~~~~~~~  102 (129)
T 2xev_A           89 EGKNTEAQQTLQQV  102 (129)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH
Confidence            55555555555444

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

Probab=98.04  E-value=5.3e-06  Score=49.29  Aligned_cols=82  Identities=10%  Similarity=-0.065  Sum_probs=45.8

Q ss_pred             cCCcHHHHHHHhccCC-----C-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHH
Q 031208           26 YGKTDHALLVFSQIRC-----P-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~-----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      .|++++|...|++..+     | +...|..+-..+...|++++|...|++..+.. +-+...+..+-.++...|++++|.
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHH
Confidence            4556666666665432     2 22445556666666677777777776665542 123445555666666666777766


Q ss_pred             HHHHHHHHh
Q 031208          100 EVHGLAVKA  108 (164)
Q Consensus       100 ~~~~~m~~~  108 (164)
                      ..+++....
T Consensus        82 ~~~~~al~~   90 (117)
T 3k9i_A           82 ELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            666665543

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.04  E-value=4.5e-05  Score=46.89  Aligned_cols=128  Identities=13%  Similarity=0.002  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-C
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-D   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~   78 (164)
                      ..++..+-..+...|++++|...+++...     ++    ..++..+-..+...|++++|...+++....    +-.+ .
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~   88 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHH
Confidence            34567777788899999999999987652     22    146778888899999999999999997542    1111 1


Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHh----CCCC-chHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKA----GFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      ...+..+-..+...|++++|...+++..+.    +..+ ....+..+...|...|++++|.+.+++.
T Consensus        89 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  155 (164)
T 3ro3_A           89 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  155 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            346777788889999999999999877643    2111 2456777888899999999999988764

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

Probab=98.02  E-value=8.1e-05  Score=44.53  Aligned_cols=87  Identities=7%  Similarity=-0.080  Sum_probs=44.4

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      ..+.+.|++++|...|++..+.. +-+...|..+-.++...|+.++|...+++..+.. +.+...+..+...|.+.|+++
T Consensus        25 ~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~~g~~~  102 (121)
T 1hxi_A           25 LSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNAN  102 (121)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence            34455555555555555554431 1133444445555555555555555555555443 223444555555555555555


Q ss_pred             hHHHHhccc
Q 031208          132 GGRKMFDKM  140 (164)
Q Consensus       132 ~a~~~~~~m  140 (164)
                      +|...|++.
T Consensus       103 ~A~~~~~~a  111 (121)
T 1hxi_A          103 AALASLRAW  111 (121)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=97.98  E-value=0.00015  Score=56.16  Aligned_cols=151  Identities=10%  Similarity=0.045  Sum_probs=105.2

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCC-------------C------------cHhHHHHHHHHHHhcCChhHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC-------------P------------HVFTWNLMIRALTIDGSSLQAL   64 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------------~------------~~~~~~~li~~~~~~~~~~~a~   64 (164)
                      +.+...|-..+...-+.|+++.|.++|+....             |            ....|...+....+.|..+.|.
T Consensus       375 P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR  454 (679)
T 4e6h_A          375 PNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASR  454 (679)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHH
Confidence            44566677778888889999999999988752             3            1236777787778888999999


Q ss_pred             HHHHHHHHc-CCCCCcccHHHHHHHHHhc-cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC
Q 031208           65 LLYNLMICN-GFRPDKFTFPFVIKACIAS-LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        65 ~~~~~m~~~-~~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      .+|.+..+. +. +....|......-.+. ++.+.|.++|+...+. ++-+...+...++.....|+.+.|..+|+....
T Consensus       455 ~vf~~A~~~~~~-~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~  532 (679)
T 4e6h_A          455 KIFGKCRRLKKL-VTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSID  532 (679)
T ss_dssp             HHHHHHHHTGGG-SCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcCC-CChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            999998765 21 1222332222222233 4588999999988776 344566777888888888999999999998663


Q ss_pred             C------CcchHHHHHHHHHhcCCCC
Q 031208          143 R------SVVSWTTMISGLAASGDLD  162 (164)
Q Consensus       143 ~------~~~~~~~li~~~~~~g~~~  162 (164)
                      .      ....|...+.--.+.|+.+
T Consensus       533 ~~~~~~~~~~lw~~~~~fE~~~G~~~  558 (679)
T 4e6h_A          533 KISDSHLLKMIFQKVIFFESKVGSLN  558 (679)
T ss_dssp             TSSSTTHHHHHHHHHHHHHHHTCCSH
T ss_pred             hcCCHHHHHHHHHHHHHHHHHcCCHH
Confidence            2      2356777777666666653

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.97  E-value=0.00022  Score=49.07  Aligned_cols=123  Identities=9%  Similarity=-0.066  Sum_probs=92.6

Q ss_pred             HHHHHHhccCCcHHHHHHHhccCC-------Cc--HhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCC-----cccH
Q 031208           18 KLLDLCSFYGKTDHALLVFSQIRC-------PH--VFTWNLMIRALTIDGSSLQALLLYNLMICN-GFRPD-----KFTF   82 (164)
Q Consensus        18 ~li~~~~~~~~~~~a~~~~~~~~~-------~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~-----~~t~   82 (164)
                      .+...+...|++++|...+++...       +.  ..+|+.+-..|...|++++|...|++.... ...|+     ..++
T Consensus       120 ~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~  199 (293)
T 2qfc_A          120 YVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVR  199 (293)
T ss_dssp             HHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHH
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHH
Confidence            344566778899999999876531       22  347888899999999999999999998621 11233     1578


Q ss_pred             HHHHHHHHhccchhhHHHHHHHHHHhC----CCC-chHHHHHHHHHHHhcCCchhH-HHHhccc
Q 031208           83 PFVIKACIASLAIEKGKEVHGLAVKAG----FSR-DMFVQSTLMDLYLKCGDVDGG-RKMFDKM  140 (164)
Q Consensus        83 ~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~-~~~~~~~ll~~~~~~~~~~~a-~~~~~~m  140 (164)
                      ..+-..|...|++++|...+++..+..    ... -..+|..+-..|.+.|+.++| ...+++.
T Consensus       200 ~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          200 YNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            888999999999999999999876532    111 256788888999999999999 6666653

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.97  E-value=0.00034  Score=44.24  Aligned_cols=98  Identities=6%  Similarity=0.023  Sum_probs=81.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHH-HHhcCCh--hHHHHHHHHHHHcCCCCCcccHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRA-LTIDGSS--LQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~-~~~~~~~--~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      .+...|..+-..+...|+++.|...|+...+   .+...+..+-.. +...|++  ++|...|++..+.. +-+...+..
T Consensus        42 ~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~  120 (177)
T 2e2e_A           42 QNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRAMIDKALALD-SNEITALML  120 (177)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhC-CCcHHHHHH
Confidence            3567888888899999999999999998762   466677777777 7789998  99999999997753 224567778


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +...+...|++++|...+++..+..
T Consensus       121 la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A          121 LASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhhC
Confidence            8899999999999999999988764

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

Probab=97.95  E-value=6.6e-05  Score=43.49  Aligned_cols=96  Identities=13%  Similarity=0.001  Sum_probs=67.1

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-------hH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-------MF  115 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-------~~  115 (164)
                      +...|..+-..+...|++++|...|++..+.. +.+...+..+-.++.+.|++++|...+++..+.  .|+       ..
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~   79 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTAEHVAIRSK   79 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSSTTSHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCccHHHHHHH
Confidence            34556666777778888888888888876642 234566777777888888888888888877654  343       44


Q ss_pred             HHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          116 VQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       116 ~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+..+-.++...|+.+.|.+.|++++
T Consensus        80 ~~~~~~~~~~~~~~~~~a~~~~~~~~  105 (111)
T 2l6j_A           80 LQYRLELAQGAVGSVQIPVVEVDELP  105 (111)
T ss_dssp             HHHHHHHHHHHHHCCCCCSSSSSSCS
T ss_pred             HHHHHHHHHHHHHhHhhhHhHHHHhH
Confidence            55566667777777777777777664

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.94  E-value=0.00011  Score=52.32  Aligned_cols=129  Identities=11%  Similarity=-0.112  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc-----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH-----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-   77 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-   77 (164)
                      ..++..+-..|...|+++.|...+++...     ++     ..+++.+-..|...|++++|.+.|.+..+.    +-.+ 
T Consensus       141 a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~  220 (378)
T 3q15_A          141 AEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRF  220 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHH
Confidence            45666777788899999888888776541     11     346777888889999999999999887542    1111 


Q ss_pred             CcccHHHHHHHHHhccchhhHHHHHHHHHHh----CCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           78 DKFTFPFVIKACIASLAIEKGKEVHGLAVKA----GFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        78 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ...++..+-..+...|++++|...+++....    +-+....++..+-..|.+.|++++|...+++..
T Consensus       221 ~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  288 (378)
T 3q15_A          221 IAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGL  288 (378)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            1246777888889999999999999887761    323346677888889999999999999888654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.94  E-value=0.00032  Score=51.15  Aligned_cols=152  Identities=6%  Similarity=-0.104  Sum_probs=88.0

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHh-------------------cCChhHHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTI-------------------DGSSLQALLLYNL   69 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~-------------------~~~~~~a~~~~~~   69 (164)
                      +..++..+-..+.+.|+++.|...+++..  .| +..++..+-..|..                   .+..+.|...+++
T Consensus       246 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  325 (472)
T 4g1t_A          246 VTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKK  325 (472)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            34445555556666666666666666543  23 23333333222221                   1123445555555


Q ss_pred             HHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchH--HHHHHHH-HHHhcCCchhHHHHhcccC-----
Q 031208           70 MICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMF--VQSTLMD-LYLKCGDVDGGRKMFDKMR-----  141 (164)
Q Consensus        70 m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~--~~~~ll~-~~~~~~~~~~a~~~~~~m~-----  141 (164)
                      ..... +.+...+..+-..+...|++++|...+++..+....+...  .+..+.. .+...|+.++|...|++..     
T Consensus       326 a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~  404 (472)
T 4g1t_A          326 ADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQK  404 (472)
T ss_dssp             HHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCC
T ss_pred             HhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcc
Confidence            54332 2345567778888899999999999999888765433321  2222222 2346788888887776532     


Q ss_pred             ---------------------CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          142 ---------------------VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       142 ---------------------~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                                           .| +..+|+.+-..|...|++++|
T Consensus       405 ~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A  449 (472)
T 4g1t_A          405 SREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQA  449 (472)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC--
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence                                 12 566888888888888888876

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.93  E-value=0.00025  Score=52.45  Aligned_cols=109  Identities=14%  Similarity=0.021  Sum_probs=49.3

Q ss_pred             cCCcHHHHHHHhccC-CCcHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh----ccchh
Q 031208           26 YGKTDHALLVFSQIR-CPHVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA----SLAIE   96 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~~~~~   96 (164)
                      .++++.|...|++.. ..+...+..|-..|..    .+++++|...|++..+.|   +...+..+-..|..    .++.+
T Consensus        56 ~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~  132 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKA  132 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             CcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHH
Confidence            455555555555433 2334444444444444    455555555555554433   22233333344444    44555


Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHh----cCCchhHHHHhccc
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLK----CGDVDGGRKMFDKM  140 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m  140 (164)
                      +|..++++..+.|   +...+..|-..|..    .++.++|.++|++.
T Consensus       133 ~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a  177 (490)
T 2xm6_A          133 ESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKA  177 (490)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            5555555544433   22233333333433    34444454444433

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.93  E-value=6.2e-05  Score=52.36  Aligned_cols=128  Identities=6%  Similarity=-0.088  Sum_probs=94.7

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC-------CCc--HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-C
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR-------CPH--VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFRP-D   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~-------~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~   78 (164)
                      ..+|+.+-..|.+.|++++|...|++..       .+.  ..++..+-..|.. |++++|...|++....    +-.+ .
T Consensus        76 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~  154 (307)
T 2ifu_A           76 AKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQA  154 (307)
T ss_dssp             HHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHH
Confidence            3467777788889999999988887653       222  3567777778888 9999999999987542    1111 1


Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHh----CCCCc-hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKA----GFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..++..+-..+.+.|++++|...+++..+.    +..+. ...+..+...+...|+++.|...|++..
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            356778889999999999999999988753    22122 2256666777888899999999998765

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.92  E-value=0.00021  Score=43.01  Aligned_cols=88  Identities=15%  Similarity=0.072  Sum_probs=39.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhC--CCCc----hHHHHHHHH
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAG--FSRD----MFVQSTLMD  122 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~----~~~~~~ll~  122 (164)
                      +=..+.+.|++++|+..|++..+.  .| +...|..+-.+|.+.|++++|.+.+++..+..  ..++    ..+|..+-.
T Consensus        14 lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~   91 (127)
T 4gcn_A           14 LGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGN   91 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHH
Confidence            334444555555555555554432  22 23344444455555555555555555443321  0010    123334444


Q ss_pred             HHHhcCCchhHHHHhcc
Q 031208          123 LYLKCGDVDGGRKMFDK  139 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~  139 (164)
                      .|...|++++|.+.|++
T Consensus        92 ~~~~~~~~~~A~~~~~k  108 (127)
T 4gcn_A           92 AFQKQNDLSLAVQWFHR  108 (127)
T ss_dssp             HHHHTTCHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHH
Confidence            45555555555555544

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.92  E-value=0.00044  Score=41.59  Aligned_cols=103  Identities=9%  Similarity=-0.014  Sum_probs=78.3

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCC----cccHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG--FRPD----KFTFPF   84 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~   84 (164)
                      ..+..+=..+.+.|++++|...|++..  . .+...|..+-.+|.+.|++++|+..+++..+..  ..++    ..+|..
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            345566678889999999999999865  3 467788889999999999999999999986532  1111    124556


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      +-.++...|++++|.+.+++....  .|+..+..
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~  120 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVK  120 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHH
Confidence            667788889999999999988765  45554443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.90  E-value=4.9e-05  Score=56.00  Aligned_cols=60  Identities=13%  Similarity=0.045  Sum_probs=28.8

Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      ..|..+-.++.+.|++++|...+++..+.. +.+...|..+-.+|.+.|++++|...|++.
T Consensus       318 ~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~a  377 (457)
T 1kt0_A          318 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKV  377 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            344444445555555555555555544432 223444444445555555555555555443

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.86  E-value=0.00058  Score=50.46  Aligned_cols=121  Identities=9%  Similarity=-0.047  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHhc----cCCcHHHHHHHhccCC-CcHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208           14 LLVRKLLDLCSF----YGKTDHALLVFSQIRC-PHVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        14 ~~~~~li~~~~~----~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      ..+..+-..|..    .++.++|...|++..+ .+...+..|-..|..    .+++++|...|++....|   +...+..
T Consensus        76 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~  152 (490)
T 2xm6_A           76 PAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQS  152 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            334444444444    5566666666665432 234444444444444    456666666666655443   2233334


Q ss_pred             HHHHHHh----ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh----cCCchhHHHHhccc
Q 031208           85 VIKACIA----SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK----CGDVDGGRKMFDKM  140 (164)
Q Consensus        85 ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m  140 (164)
                      +-..|..    .++.++|.+.++...+.|   +...+..|-..|..    .++.++|.++|++.
T Consensus       153 Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a  213 (490)
T 2xm6_A          153 MGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKS  213 (490)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHH
Confidence            4444443    445555555555555443   33344444444444    45555555555543

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.85  E-value=0.00027  Score=50.69  Aligned_cols=119  Identities=7%  Similarity=-0.118  Sum_probs=86.0

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC-------------------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC-------------------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF   75 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~-------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   75 (164)
                      .+..+-..+.+.|++++|...|++..+                   .+...|..+-.++.+.|++++|...+++..+.. 
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-  303 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  303 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-
Confidence            355666677888899888888886543                   234567777788888889999998888887643 


Q ss_pred             CCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHH
Q 031208           76 RPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRK  135 (164)
Q Consensus        76 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~  135 (164)
                      +-+...+..+-.++...|++++|...+++..+.. +.+...+..+-..+.+.++.+++.+
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            2245677777888888888999988888887664 2355666666677766666666544

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.84  E-value=2.5e-05  Score=48.06  Aligned_cols=120  Identities=13%  Similarity=0.012  Sum_probs=88.2

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CC----cccHHHHHHHHHhccchhhHHHHHHHHHHhC----CCC-ch
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFR-PD----KFTFPFVIKACIASLAIEKGKEVHGLAVKAG----FSR-DM  114 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~-~~  114 (164)
                      .++..+-..+...|++++|...+++..+..-. ++    ...+..+-..+...|++++|...+++..+..    -.+ ..
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   89 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEA   89 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHH
Confidence            45677777889999999999999997543211 11    1467788889999999999999999876531    111 14


Q ss_pred             HHHHHHHHHHHhcCCchhHHHHhcccCC-----C----CcchHHHHHHHHHhcCCCCCC
Q 031208          115 FVQSTLMDLYLKCGDVDGGRKMFDKMRV-----R----SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       115 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~----~~~~~~~li~~~~~~g~~~~A  164 (164)
                      ..+..+-..|...|++++|.+.+++...     .    ...++..+-..|...|++++|
T Consensus        90 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  148 (164)
T 3ro3_A           90 QSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQA  148 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHH
Confidence            5677778889999999999999887641     1    234677788888888887653

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

Probab=97.82  E-value=0.00095  Score=39.56  Aligned_cols=90  Identities=9%  Similarity=-0.089  Sum_probs=72.8

Q ss_pred             HHHHHHhccCCcHHHHHHHhccC--CCcH----hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----cccHHHHHH
Q 031208           18 KLLDLCSFYGKTDHALLVFSQIR--CPHV----FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD----KFTFPFVIK   87 (164)
Q Consensus        18 ~li~~~~~~~~~~~a~~~~~~~~--~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~   87 (164)
                      .+-..+.+.|++++|...|+...  .|+.    ..+..+-..+.+.|++++|...|++.....  |+    ...+..+-.
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~   84 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGL   84 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHH
Confidence            34556778999999999999875  3433    367777788999999999999999997753  43    345677888


Q ss_pred             HHHhccchhhHHHHHHHHHHhC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ++...|++++|...+++..+..
T Consensus        85 ~~~~~g~~~~A~~~~~~~~~~~  106 (129)
T 2xev_A           85 SQYGEGKNTEAQQTLQQVATQY  106 (129)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC
Confidence            9999999999999999998764

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.81  E-value=0.00026  Score=52.17  Aligned_cols=126  Identities=9%  Similarity=0.010  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC--C-c---------------HhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC--P-H---------------VFTWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~---------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      ...+..+-..+.+.|+++.|...|++..+  | +               ...|..+-.++.+.|++++|...+++..+..
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  347 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD  347 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            34566677788899999999999997652  3 2               5788888999999999999999999997753


Q ss_pred             CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHH-Hhccc
Q 031208           75 FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRK-MFDKM  140 (164)
Q Consensus        75 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~-~~~~m  140 (164)
                       +.+...|..+-.+|...|++++|...+++..+.. +.+...+..+-..+.+.++.+++.+ ++..|
T Consensus       348 -p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          348 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQISMCQKKAKEHNERDRRIYANM  412 (457)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             -CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             3356678888999999999999999999988653 2345678888888888888877653 44444

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.80  E-value=0.00094  Score=44.10  Aligned_cols=124  Identities=9%  Similarity=-0.107  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--CCcHh----HHHHHHHHHH------------------hcCChhHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--CPHVF----TWNLMIRALT------------------IDGSSLQALLLYNL   69 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~----~~~~li~~~~------------------~~~~~~~a~~~~~~   69 (164)
                      ..+..+-.++.+.|++++|...|++..  .|+..    .+-.+-.++.                  ..|++++|...|++
T Consensus        42 ~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  121 (225)
T 2yhc_A           42 QVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSK  121 (225)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHH
Confidence            567777889999999999999999875  24321    2222222332                  25789999999999


Q ss_pred             HHHcCCCCCcc-cH-----------------HHHHHHHHhccchhhHHHHHHHHHHhCCCCc----hHHHHHHHHHHHhc
Q 031208           70 MICNGFRPDKF-TF-----------------PFVIKACIASLAIEKGKEVHGLAVKAGFSRD----MFVQSTLMDLYLKC  127 (164)
Q Consensus        70 m~~~~~~p~~~-t~-----------------~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~ll~~~~~~  127 (164)
                      ..+.  .|+.. ..                 -.+-..+.+.|++++|...++++.+..  |+    ...+..+..+|.+.
T Consensus       122 ~l~~--~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~  197 (225)
T 2yhc_A          122 LVRG--YPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQM  197 (225)
T ss_dssp             HHTT--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHT
T ss_pred             HHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHc
Confidence            9875  35432 22                 134456788999999999999998764  33    35678889999999


Q ss_pred             CCchhHHHHhcccC
Q 031208          128 GDVDGGRKMFDKMR  141 (164)
Q Consensus       128 ~~~~~a~~~~~~m~  141 (164)
                      |+.++|.+.++.+.
T Consensus       198 g~~~~A~~~~~~l~  211 (225)
T 2yhc_A          198 QMNAQAEKVAKIIA  211 (225)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHH
Confidence            99999999998765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.78  E-value=0.00035  Score=49.50  Aligned_cols=149  Identities=14%  Similarity=0.128  Sum_probs=102.8

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC-----CcH----hHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCC--CC-
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC-----PHV----FTWNLMIRALTIDGSSLQALLLYNLMICN----GFR--PD-   78 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~--p~-   78 (164)
                      +++.+-..+...|+++.|...+++...     ++.    .++..+-..+...|++++|...+++....    +-.  |. 
T Consensus        55 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~  134 (373)
T 1hz4_A           55 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMH  134 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHH
Confidence            345555677889999999999987652     222    23556667788999999999999987542    222  22 


Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHhCCC--C--chHHHHHHHHHHHhcCCchhHHHHhcccC----CCCc-chHH
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFS--R--DMFVQSTLMDLYLKCGDVDGGRKMFDKMR----VRSV-VSWT  149 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~--~--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~----~~~~-~~~~  149 (164)
                      ...+..+-..+...|++++|...+++.....-.  +  ....+..+...+...|++++|...+++..    .++. ..|.
T Consensus       135 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~  214 (373)
T 1hz4_A          135 EFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWI  214 (373)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHH
Confidence            235566778889999999999999988765321  1  23467778888999999999999998754    2222 2222


Q ss_pred             H-----HHHHHHhcCCCCC
Q 031208          150 T-----MISGLAASGDLDA  163 (164)
Q Consensus       150 ~-----li~~~~~~g~~~~  163 (164)
                      .     ....+...|++++
T Consensus       215 ~~~~~~~~~~~~~~g~~~~  233 (373)
T 1hz4_A          215 SNANKVRVIYWQMTGDKAA  233 (373)
T ss_dssp             HHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHCCCHHH
Confidence            2     2234667777654

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.77  E-value=0.00092  Score=43.84  Aligned_cols=143  Identities=13%  Similarity=-0.037  Sum_probs=106.0

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC-CcHhHHHHHHHHHHhcC----ChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC-PHVFTWNLMIRALTIDG----SSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~~----~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      -++..+..+=..|...+++++|...|++..+ .+...+..|=..|.. +    ++++|...|++..+.|   +...+..|
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~~~L   91 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGEIVL   91 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHHHHH
Confidence            3566777777788889999999999998763 456666666666666 6    8999999999987654   44456666


Q ss_pred             HHHHHh----ccchhhHHHHHHHHHHhCCC-CchHHHHHHHHHHHh----cCCchhHHHHhcccC-C-CCcchHHHHHHH
Q 031208           86 IKACIA----SLAIEKGKEVHGLAVKAGFS-RDMFVQSTLMDLYLK----CGDVDGGRKMFDKMR-V-RSVVSWTTMISG  154 (164)
Q Consensus        86 l~~~~~----~~~~~~a~~~~~~m~~~g~~-~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~-~-~~~~~~~~li~~  154 (164)
                      -..|..    .+++++|..++++..+.|.. .+...+..|-..|..    .++.++|..+|++.. . .+...+..|-..
T Consensus        92 g~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~a~~~Lg~~  171 (212)
T 3rjv_A           92 ARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLSRTGYAEYWAGMM  171 (212)
T ss_dssp             HHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTSCTTHHHHHHHHH
T ss_pred             HHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            666766    77899999999988776521 126677778888887    788999999998764 2 455666666666


Q ss_pred             HHh
Q 031208          155 LAA  157 (164)
Q Consensus       155 ~~~  157 (164)
                      |..
T Consensus       172 y~~  174 (212)
T 3rjv_A          172 FQQ  174 (212)
T ss_dssp             HHH
T ss_pred             HHc
Confidence            654

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

Probab=97.77  E-value=0.00014  Score=41.97  Aligned_cols=85  Identities=8%  Similarity=-0.080  Sum_probs=67.8

Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCC-------cchHH
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRS-------VVSWT  149 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~-------~~~~~  149 (164)
                      ...+..+-..+...|++++|...+++..+.. +.+...+..+-.+|.+.|++++|.+.|++..  .|+       ...+.
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~   82 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSKLQY   82 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence            4456677888999999999999999998774 3467788889999999999999999999865  343       44666


Q ss_pred             HHHHHHHhcCCCCCC
Q 031208          150 TMISGLAASGDLDAA  164 (164)
Q Consensus       150 ~li~~~~~~g~~~~A  164 (164)
                      .+-.++...|++++|
T Consensus        83 ~~~~~~~~~~~~~~a   97 (111)
T 2l6j_A           83 RLELAQGAVGSVQIP   97 (111)
T ss_dssp             HHHHHHHHHHCCCCC
T ss_pred             HHHHHHHHHHhHhhh
Confidence            677777777777654

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.77  E-value=0.00039  Score=47.76  Aligned_cols=96  Identities=8%  Similarity=-0.109  Sum_probs=80.2

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+.+.|++++|...|+...  .| +...|..+-..+.+.|++++|...+++..+.. +-+...+..+-.+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            45667777888999999999999999875  34 67888888999999999999999999987642 2345678888899


Q ss_pred             HHhccchhhHHHHHHHHHHh
Q 031208           89 CIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +...|++++|...+++..+.
T Consensus        82 ~~~~g~~~~A~~~~~~al~l  101 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYSL  101 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            99999999999999988764

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

Probab=97.76  E-value=0.00039  Score=41.47  Aligned_cols=91  Identities=10%  Similarity=-0.047  Sum_probs=75.9

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHh
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIA   91 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~   91 (164)
                      +-.+-..+.+.|++++|...|+...  .| +...|..+-.++...|++++|...|++..+.  .| +...+..+-.++..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            4445567888999999999999876  34 6778888888999999999999999998775  35 45678888899999


Q ss_pred             ccchhhHHHHHHHHHHh
Q 031208           92 SLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~  108 (164)
                      .|++++|...+++..+.
T Consensus        98 ~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           98 EHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            99999999999988753

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

Probab=97.76  E-value=0.00016  Score=53.91  Aligned_cols=119  Identities=13%  Similarity=-0.022  Sum_probs=91.8

Q ss_pred             HhccCCcHHHHHHHhccC----------CCcH-hHHHHHHHHHHhcCChhHHHHHHHHHHH---cCCCCC----cccHHH
Q 031208           23 CSFYGKTDHALLVFSQIR----------CPHV-FTWNLMIRALTIDGSSLQALLLYNLMIC---NGFRPD----KFTFPF   84 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~----------~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p~----~~t~~~   84 (164)
                      +...|++++|..++++..          .|++ .+++.|...|...|++++|..++++...   .-+.|+    ..+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            457899999998887654          1433 5799999999999999999999999743   223333    357889


Q ss_pred             HHHHHHhccchhhHHHHHHHHHHh-----CC-CCc-hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKA-----GF-SRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~-----g~-~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      |-..|...|++++|..++++..+-     |- .|+ ..+.+.+-.++...+.+..|..++..+.
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~  462 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMR  462 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999876542     31 233 3455677788888899999999998876

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

Probab=97.73  E-value=0.00065  Score=42.34  Aligned_cols=93  Identities=12%  Similarity=0.022  Sum_probs=50.1

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCC---------------------cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCP---------------------HVFTWNLMIRALTIDGSSLQALLLYNLMICN   73 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~---------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   73 (164)
                      .+...=..+.+.|+++.|...|+.....                     +...|..+-.++.+.|++++|...+++..+.
T Consensus        13 ~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~   92 (162)
T 3rkv_A           13 ALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKR   92 (162)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhc
Confidence            3444444555666666666666553310                     1234555555556666666666666665543


Q ss_pred             CCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           74 GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        74 ~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      . +.+...|..+-.++...|++++|...++...+.
T Consensus        93 ~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           93 E-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             S-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             C-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            2 223445555556666666666666666655544

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.70  E-value=0.0007  Score=46.48  Aligned_cols=62  Identities=8%  Similarity=-0.174  Sum_probs=51.2

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSLQALLLYNLMICN   73 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   73 (164)
                      +...|..+-..+.+.|++++|...++...+   .+...+..+-.++...|++++|...|++..+.
T Consensus        37 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  101 (281)
T 2c2l_A           37 VAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL  101 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            567778888888899999999999988663   35677888888899999999999999887653

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

Probab=97.68  E-value=0.00031  Score=41.40  Aligned_cols=101  Identities=16%  Similarity=0.083  Sum_probs=74.1

Q ss_pred             hcCChhHHHHHHHHHHHcC--CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhH
Q 031208           56 IDGSSLQALLLYNLMICNG--FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGG  133 (164)
Q Consensus        56 ~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  133 (164)
                      ..|++++|...|++..+.+  -+-+...+..+-..+...|++++|...+++..+.. +-+...+..+-.+|.+.|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHH
Confidence            4688999999999998754  12245678888899999999999999999998875 34577888889999999999999


Q ss_pred             HHHhcccC--CC---CcchHHHHHHHHHh
Q 031208          134 RKMFDKMR--VR---SVVSWTTMISGLAA  157 (164)
Q Consensus       134 ~~~~~~m~--~~---~~~~~~~li~~~~~  157 (164)
                      ...|++..  .|   +...|...+..|.+
T Consensus        81 ~~~~~~al~~~p~~~~~~~~~~ai~~~~~  109 (117)
T 3k9i_A           81 VELLLKIIAETSDDETIQSYKQAILFYAD  109 (117)
T ss_dssp             HHHHHHHHHHHCCCHHHHHTHHHHHHHTT
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHHH
Confidence            99998765  22   33445555555543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.65  E-value=0.0024  Score=46.54  Aligned_cols=128  Identities=11%  Similarity=-0.008  Sum_probs=83.9

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC-----------CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-----C
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR-----------CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICN-----G   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~-----------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~   74 (164)
                      ....||.+-..+...|+.++|.+.|++..           .| ...+|+.+-..|...|++++|...+++..+-     +
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            35678888888899999999999887642           12 3568888999999999999999999887531     1


Q ss_pred             -CCCC-cccHHHHHHHHHhc--cchhhHHHHHHHHHHhCCCCchHHHHHHHHH---HHhcCCchhHHHHhccc
Q 031208           75 -FRPD-KFTFPFVIKACIAS--LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL---YLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        75 -~~p~-~~t~~~ll~~~~~~--~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~---~~~~~~~~~a~~~~~~m  140 (164)
                       ..++ ..++..+-.++...  +++++|...|++..+.. +.+...+..+...   +...++.++|.+.+++.
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~a  201 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQA  201 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence             1121 23444444444443  46889999998887654 2233344433333   33456666677666544

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

Probab=97.64  E-value=0.00023  Score=50.34  Aligned_cols=125  Identities=11%  Similarity=-0.050  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--CCcHh------------------HHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--CPHVF------------------TWNLMIRALTIDGSSLQALLLYNLMICN   73 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~------------------~~~~li~~~~~~~~~~~a~~~~~~m~~~   73 (164)
                      ..+..+-..+.+.|+++.|...|++..  .|+..                  .|..+-.++.+.|++++|...+++..+.
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  259 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTE  259 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            345555667777888888888888754  34332                  5666677777778888888888777654


Q ss_pred             CCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHH-HHhcCCchhHHHHhcccC
Q 031208           74 GFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDL-YLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        74 ~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~-~~~~~~~~~a~~~~~~m~  141 (164)
                      . +.+...|..+-.++...|++++|...+++..+.  .|+ ...+..+... ....+..+.+..+|..|.
T Consensus       260 ~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l  326 (338)
T 2if4_A          260 E-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALYQKQKEMYKGIF  326 (338)
T ss_dssp             C-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------------------------
T ss_pred             C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            2 224556777777777788888888777776543  232 3333333333 223345556666666654

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.61  E-value=0.00012  Score=52.59  Aligned_cols=115  Identities=5%  Similarity=-0.099  Sum_probs=88.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHc--------------CCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICN--------------GFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~--------------~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ..+..+-..+.+.|++++|...|++..+.              ...| +...|..+-.++.+.|++++|...+++..+..
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            34677778889999999999999998651              0223 45678888899999999999999999998754


Q ss_pred             CCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCC
Q 031208          110 FSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGD  160 (164)
Q Consensus       110 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~  160 (164)
                       +.+...+..+-.+|.+.|++++|.+.|++..  .| +...+..+-..+...++
T Consensus       304 -p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~  356 (370)
T 1ihg_A          304 -PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKA  356 (370)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             -chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence             3457788888999999999999999999875  34 45566666665555443

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

Probab=97.53  E-value=0.0027  Score=39.49  Aligned_cols=94  Identities=6%  Similarity=-0.020  Sum_probs=76.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHc-------CC---------CC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICN-------GF---------RP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~-------~~---------~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +...-..+.+.|++++|...|.+....       .-         .| +...|..+-.++.+.|++++|...++...+..
T Consensus        14 ~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~   93 (162)
T 3rkv_A           14 LRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE   93 (162)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            344556778899999999999998653       00         12 23578888899999999999999999998875


Q ss_pred             CCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          110 FSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       110 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                       +.+...|..+-.+|...|++++|...|+...
T Consensus        94 -p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al  124 (162)
T 3rkv_A           94 -ETNEKALFRRAKARIAAWKLDEAEEDLKLLL  124 (162)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -CcchHHHHHHHHHHHHHhcHHHHHHHHHHHH
Confidence             4567888999999999999999999999875

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

Probab=97.52  E-value=0.0028  Score=34.86  Aligned_cols=78  Identities=12%  Similarity=0.019  Sum_probs=44.5

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      ..|..+-..+...|++++|...|++..+.. +.+...+..+-..+.+.|++++|...+++..+.. +.+...+..+-..+
T Consensus        10 ~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~   87 (91)
T 1na3_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAK   87 (91)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            445555556666777777777777665532 2234455566666667777777777776666543 22333444444433

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.44  E-value=0.0061  Score=39.84  Aligned_cols=127  Identities=9%  Similarity=-0.108  Sum_probs=94.7

Q ss_pred             CHHHHHHHHHHHhccC----CcHHHHHHHhccCC-CcHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCC-CCccc
Q 031208           12 DQLLVRKLLDLCSFYG----KTDHALLVFSQIRC-PHVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFR-PDKFT   81 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~----~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~-p~~~t   81 (164)
                      ++..+..+=..|.. +    ++++|.++|++..+ .+...+..|-..|..    .+++++|...|++..+.|.. .+...
T Consensus        49 ~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a  127 (212)
T 3rjv_A           49 DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDA  127 (212)
T ss_dssp             CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHH
T ss_pred             CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHH
Confidence            45556666666766 6    89999999998764 466677777777766    78999999999999876532 01556


Q ss_pred             HHHHHHHHHh----ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc-C-----CchhHHHHhcccC
Q 031208           82 FPFVIKACIA----SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC-G-----DVDGGRKMFDKMR  141 (164)
Q Consensus        82 ~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-~-----~~~~a~~~~~~m~  141 (164)
                      +..|-..|..    .++.++|..++++..+.+  .+...+..|-..|.+. |     +.++|.++|+...
T Consensus       128 ~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~--~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~  195 (212)
T 3rjv_A          128 QMLLGLIYASGVHGPEDDVKASEYFKGSSSLS--RTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSC  195 (212)
T ss_dssp             HHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS--CTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHH
Confidence            7777777877    789999999999988762  3344566666677653 3     8999999998765

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

Probab=97.42  E-value=0.0013  Score=38.45  Aligned_cols=64  Identities=5%  Similarity=-0.079  Sum_probs=40.8

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  107 (164)
                      +...|..+-..+...|++++|...|++..+.. +.+...|..+-.++...|+.++|...+++..+
T Consensus        18 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           18 NMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45566666666777777777777777765532 22344566666667777777777777766654

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

Probab=97.38  E-value=0.0013  Score=46.47  Aligned_cols=94  Identities=13%  Similarity=0.082  Sum_probs=78.5

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc------------------cHHHHHHHHHhccchhhHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF------------------TFPFVIKACIASLAIEKGKEVHGLAV  106 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~------------------t~~~ll~~~~~~~~~~~a~~~~~~m~  106 (164)
                      ..+..+-..+.+.|++++|...|++....  .|+..                  .|..+-.++.+.|++++|...++...
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al  257 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVL  257 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44666677788899999999999997653  34432                  67788889999999999999999998


Q ss_pred             HhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          107 KAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       107 ~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +.. +.+...|..+-.+|...|++++|...|++..
T Consensus       258 ~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al  291 (338)
T 2if4_A          258 TEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQ  291 (338)
T ss_dssp             HHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTT
T ss_pred             HhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            764 3467889999999999999999999999886

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.36  E-value=0.0011  Score=47.80  Aligned_cols=127  Identities=9%  Similarity=-0.053  Sum_probs=92.8

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC-----CcH---h-HHHHHHHHHHhcCChhHHHHHHHHHHH----cCCCCC-cc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC-----PHV---F-TWNLMIRALTIDGSSLQALLLYNLMIC----NGFRPD-KF   80 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~---~-~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~p~-~~   80 (164)
                      .+..+...|.+.|++++|.+++.....     ++.   . +.+.+=..+...|+.+.+..++.+...    .+..+. ..
T Consensus        57 al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  136 (434)
T 4b4t_Q           57 SILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHS  136 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHH
Confidence            467788899999999999999987752     221   1 222222333456889999999988743    233332 34


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHHh--CCC--C-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVKA--GFS--R-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~--~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ++..+...+...|++++|..++++....  +..  + ....+..+...|...|++++|..++++..
T Consensus       137 ~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al  202 (434)
T 4b4t_Q          137 LSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAAR  202 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence            6778889999999999999999987653  221  1 24578888999999999999999987654

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

Probab=97.35  E-value=0.0011  Score=38.00  Aligned_cols=84  Identities=14%  Similarity=0.035  Sum_probs=55.1

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhC-CCCchHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAG-FSRDMFVQSTLM  121 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~ll  121 (164)
                      +...|..+-..+...|++++|...|++..+.. +-+...|..+-.++...|++++|.+.+++..+.. -.++......+.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~l~   84 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSELQ   84 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHHHH
Confidence            45567777777888888888888888876643 2245567777788888888888888887766432 123444444444


Q ss_pred             HHHHhc
Q 031208          122 DLYLKC  127 (164)
Q Consensus       122 ~~~~~~  127 (164)
                      ..+.+.
T Consensus        85 ~~l~~~   90 (100)
T 3ma5_A           85 DAKLKA   90 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHc
Confidence            444433

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

Probab=97.31  E-value=0.0025  Score=35.10  Aligned_cols=80  Identities=14%  Similarity=0.054  Sum_probs=62.6

Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHH
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGL  155 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~  155 (164)
                      ...+..+-..+...|++++|...+++..+.. +.+...+..+-..|.+.|++++|...|++..  .| +...+..+-..+
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~   87 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAK   87 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            3456677788899999999999999998765 3456788888999999999999999998765  33 555666666666


Q ss_pred             HhcC
Q 031208          156 AASG  159 (164)
Q Consensus       156 ~~~g  159 (164)
                      .+.|
T Consensus        88 ~~~g   91 (91)
T 1na3_A           88 QKQG   91 (91)
T ss_dssp             HHHC
T ss_pred             HhcC
Confidence            5543

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=97.28  E-value=0.0022  Score=49.74  Aligned_cols=150  Identities=5%  Similarity=0.010  Sum_probs=104.7

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHH-HHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC---------CCC
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHAL-LVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNG---------FRP   77 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~-~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---------~~p   77 (164)
                      -+...|-.....+...|+.+.|. +++++..  .| +...|-..+...-+.|+++.|.++|++.....         -.|
T Consensus       341 ~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p  420 (679)
T 4e6h_A          341 FAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDP  420 (679)
T ss_dssp             TCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHST
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccC
Confidence            35666777777777788888996 9998765  34 55567777778888999999999999987631         014


Q ss_pred             C------------cccHHHHHHHHHhccchhhHHHHHHHHHHh-C-CCCchHHHHHHHHHHHh-cCCchhHHHHhcccCC
Q 031208           78 D------------KFTFPFVIKACIASLAIEKGKEVHGLAVKA-G-FSRDMFVQSTLMDLYLK-CGDVDGGRKMFDKMRV  142 (164)
Q Consensus        78 ~------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g-~~~~~~~~~~ll~~~~~-~~~~~~a~~~~~~m~~  142 (164)
                      +            ...|...++...+.|+.+.|.++|+...+. + ..+...+..+.+.  .+ .++.+.|..+|+...+
T Consensus       421 ~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE--~~~~~d~e~Ar~ife~~Lk  498 (679)
T 4e6h_A          421 TNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIE--YHISKDTKTACKVLELGLK  498 (679)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHH--HTTTSCCHHHHHHHHHHHH
T ss_pred             cchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHH--HHhCCCHHHHHHHHHHHHH
Confidence            2            235777788888889999999999998876 3 2233344334443  33 3558999999997762


Q ss_pred             ---CCcchHHHHHHHHHhcCCCC
Q 031208          143 ---RSVVSWTTMISGLAASGDLD  162 (164)
Q Consensus       143 ---~~~~~~~~li~~~~~~g~~~  162 (164)
                         .+...|...+.-....|+.+
T Consensus       499 ~~p~~~~~w~~y~~fe~~~~~~~  521 (679)
T 4e6h_A          499 YFATDGEYINKYLDFLIYVNEES  521 (679)
T ss_dssp             HHTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HCCCchHHHHHHHHHHHhCCCHH
Confidence               24556666666666666543

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.26  E-value=0.0069  Score=38.10  Aligned_cols=93  Identities=10%  Similarity=-0.075  Sum_probs=68.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--------c-----ccHHHHHHHHHhccchhhHHHHHHHHHHh-----
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPD--------K-----FTFPFVIKACIASLAIEKGKEVHGLAVKA-----  108 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--------~-----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----  108 (164)
                      +...-..+.+.|++++|...|++..+.  .|+        .     ..|..+-.++.+.|++++|...++...+.     
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            334445567778888888888887653  233        1     26777788888889999999988888765     


Q ss_pred             CCCCc-hHHH----HHHHHHHHhcCCchhHHHHhcccC
Q 031208          109 GFSRD-MFVQ----STLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       109 g~~~~-~~~~----~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+.|+ ...|    ...-.++...|++++|...|++..
T Consensus        92 e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAl  129 (159)
T 2hr2_A           92 ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  129 (159)
T ss_dssp             CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHH
Confidence            12453 5567    777888999999999999998764

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

Probab=97.17  E-value=0.0055  Score=34.90  Aligned_cols=60  Identities=18%  Similarity=0.079  Sum_probs=35.2

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMI   71 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   71 (164)
                      +...+..+-..+.+.|++++|...|++..  .| +...|..+-.+|...|++++|...|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34455555556666666666666666554  22 34455566666666666666666666554

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

Probab=97.10  E-value=0.0038  Score=36.32  Aligned_cols=78  Identities=12%  Similarity=0.002  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           62 QALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        62 ~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .|...|++..+.. +.+...+..+-..+...|++++|...+++..+.. +.+...|..+-..|.+.|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4455555554432 2234456666666677777777777777666553 2345566666666777777777777776554

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.10  E-value=0.032  Score=38.96  Aligned_cols=136  Identities=5%  Similarity=-0.045  Sum_probs=98.0

Q ss_pred             CCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChh--HHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc------h
Q 031208           27 GKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSL--QALLLYNLMICNGFRPDKFTFPFVIKACIASLA------I   95 (164)
Q Consensus        27 ~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~--~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~------~   95 (164)
                      ++++++.++++.+.   ..|-..|+.---.+.+.+.++  ++++.++++.+.. +-|-..|+.-...+.+.+.      +
T Consensus       124 ~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~~~~  202 (306)
T 3dra_A          124 FDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATDNTI  202 (306)
T ss_dssp             CCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchhhhH
Confidence            78888988888876   357778888777788888888  9999999998754 2355566666666666665      7


Q ss_pred             hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchh-HHHHhcccCC------CCcchHHHHHHHHHhcCCCCCC
Q 031208           96 EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDG-GRKMFDKMRV------RSVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~-a~~~~~~m~~------~~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +++.+.++...... +-|...|+-+-..+.+.|+... +..+..+..+      ++...+..+...|.+.|+.++|
T Consensus       203 ~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A  277 (306)
T 3dra_A          203 DEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNES  277 (306)
T ss_dssp             HHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHH
Confidence            77888888877765 4577888888888888777444 4456655432      2557788888888877776543

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.09  E-value=0.00064  Score=49.02  Aligned_cols=144  Identities=6%  Similarity=-0.148  Sum_probs=100.0

Q ss_pred             HHHhccCCcHHHHHHHhccCC--Cc------------------HhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCc
Q 031208           21 DLCSFYGKTDHALLVFSQIRC--PH------------------VFTWNLMIRALTIDGSSLQALLLYNLMICN-GFRPDK   79 (164)
Q Consensus        21 ~~~~~~~~~~~a~~~~~~~~~--~~------------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~   79 (164)
                      ..+.+.|++++|.+.|....+  |+                  ...+..+...|...|++++|.+.+.+.... +..++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            456778999999999987641  11                  124677889999999999999999987542 112222


Q ss_pred             c----cHHHHHHHHHhccchhhHHHHHHHHHH----hCCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC--------C
Q 031208           80 F----TFPFVIKACIASLAIEKGKEVHGLAVK----AGFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR--------V  142 (164)
Q Consensus        80 ~----t~~~ll~~~~~~~~~~~a~~~~~~m~~----~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--------~  142 (164)
                      .    ..+.+-..+...|+.+.+..++.+...    .+..+ ...++..+...|...|++++|..++++..        .
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~  171 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDK  171 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCS
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccc
Confidence            1    122222233445788899988887654    23233 24577888999999999999999988654        1


Q ss_pred             C-CcchHHHHHHHHHhcCCCCCC
Q 031208          143 R-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       143 ~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      + ...+|..+...|...|++++|
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~A  194 (434)
T 4b4t_Q          172 PSLVDVHLLESKVYHKLRNLAKS  194 (434)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCcHHHH
Confidence            1 235788889999999887654

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.98  E-value=0.0032  Score=46.18  Aligned_cols=62  Identities=8%  Similarity=-0.073  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHH---cCCCC---C-cccHHHHHHHHHhccchhhHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMIC---NGFRP---D-KFTFPFVIKACIASLAIEKGKEVHGLAV  106 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p---~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~  106 (164)
                      .+++.|..+|...|++++|..++++...   .-+.|   + ..+++.|-..|...|++++|..++++..
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            3456666666666666666666665532   11112   1 1345555566666666666666555443

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

Probab=96.95  E-value=0.0074  Score=44.98  Aligned_cols=89  Identities=11%  Similarity=-0.015  Sum_probs=69.9

Q ss_pred             HHHhcCChhHHHHHHHHHHH---cCCCCC----cccHHHHHHHHHhccchhhHHHHHHHHHHh-----C-CCCc-hHHHH
Q 031208           53 ALTIDGSSLQALLLYNLMIC---NGFRPD----KFTFPFVIKACIASLAIEKGKEVHGLAVKA-----G-FSRD-MFVQS  118 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~---~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----g-~~~~-~~~~~  118 (164)
                      .+...|++++|..++++...   .-+.|+    ..+++.|...|...|++++|..++++...-     | -.|+ ..+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            45678999999999988743   223343    357899999999999999999999977642     2 2333 56788


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .|-..|...|++++|..++++..
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al  420 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAY  420 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHH
Confidence            99999999999999999888654

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.87  E-value=0.04  Score=38.02  Aligned_cols=109  Identities=6%  Similarity=-0.206  Sum_probs=79.2

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCC-Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc--ccHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRC-PH----VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK--FTFP   83 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~   83 (164)
                      |+....-.+-..+.+.+++++|...|+.... |+    ...+-.+=.++...|++++|+..|++.......|..  ....
T Consensus       133 p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~  212 (282)
T 4f3v_A          133 SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAW  212 (282)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHH
T ss_pred             CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHH
Confidence            4333444445588899999999999997653 32    235666777889999999999999999854432542  2445


Q ss_pred             HHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           84 FVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        84 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      ..-.++.+.|+.++|..+|+++....  |+...+..|.
T Consensus       213 ~~glaL~~lGr~deA~~~l~~a~a~~--P~~~~~~aL~  248 (282)
T 4f3v_A          213 YLAMARRSQGNESAAVALLEWLQTTH--PEPKVAAALK  248 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHS--CCHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHHh
Confidence            56678889999999999999999874  5544444443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.84  E-value=0.0098  Score=43.65  Aligned_cols=135  Identities=13%  Similarity=-0.011  Sum_probs=73.6

Q ss_pred             HHHHHHHHHhccC---CcHHHHHHHhccC---CCcHhHHHHHHHHHHhc----CChhHHHHHHHHHHHcCCCCCcccHHH
Q 031208           15 LVRKLLDLCSFYG---KTDHALLVFSQIR---CPHVFTWNLMIRALTID----GSSLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        15 ~~~~li~~~~~~~---~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      .+..+-..|.+.|   +.++|.+.|+...   .++...+..+-..|...    +++++|...|++.. .|   +...+..
T Consensus       178 a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~~  253 (452)
T 3e4b_A          178 CYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWVS  253 (452)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHHH
T ss_pred             HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHHH
Confidence            4555555555666   6666666666543   23333333344444333    46677777777665 22   2333333


Q ss_pred             HHHH-H--HhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcC-----CchhHHHHhcccCCCCcchHHHHHHHHH
Q 031208           85 VIKA-C--IASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCG-----DVDGGRKMFDKMRVRSVVSWTTMISGLA  156 (164)
Q Consensus        85 ll~~-~--~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~-----~~~~a~~~~~~m~~~~~~~~~~li~~~~  156 (164)
                      +-.. +  ...++.++|..++++..+.|   +...+..|-..|. .|     +.++|.++|++....+...+..|-..|.
T Consensus       254 Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa~g~~~A~~~Lg~~y~  329 (452)
T 3e4b_A          254 LAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAVGREVAADYYLGQIYR  329 (452)
T ss_dssp             HHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4333 2  34667777777777776665   3344445555554 44     7777777777766224445555555554


Q ss_pred             h
Q 031208          157 A  157 (164)
Q Consensus       157 ~  157 (164)
                      .
T Consensus       330 ~  330 (452)
T 3e4b_A          330 R  330 (452)
T ss_dssp             T
T ss_pred             C
Confidence            4

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.83  E-value=0.0085  Score=43.93  Aligned_cols=86  Identities=16%  Similarity=0.126  Sum_probs=68.2

Q ss_pred             hcCChhHHHHHHHHHHH---cCCCCCc----ccHHHHHHHHHhccchhhHHHHHHHHHHh-----C-CCCc-hHHHHHHH
Q 031208           56 IDGSSLQALLLYNLMIC---NGFRPDK----FTFPFVIKACIASLAIEKGKEVHGLAVKA-----G-FSRD-MFVQSTLM  121 (164)
Q Consensus        56 ~~~~~~~a~~~~~~m~~---~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----g-~~~~-~~~~~~ll  121 (164)
                      ..|++++|..++++...   .-+.|+.    .+++.|..+|...|++++|..++++...-     | -.|+ ..+++.|-
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            45789999999998743   3344442    67899999999999999999999987642     2 2343 46788999


Q ss_pred             HHHHhcCCchhHHHHhcccC
Q 031208          122 DLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..|...|++++|..++++..
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHH
Confidence            99999999999999988754

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.81  E-value=0.087  Score=38.61  Aligned_cols=29  Identities=7%  Similarity=0.048  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHhcC---ChhHHHHHHHHHHHcC
Q 031208           46 TWNLMIRALTIDG---SSLQALLLYNLMICNG   74 (164)
Q Consensus        46 ~~~~li~~~~~~~---~~~~a~~~~~~m~~~~   74 (164)
                      .+..|-..|.+.|   +.++|+..|++..+.|
T Consensus       178 a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g  209 (452)
T 3e4b_A          178 CYVELATVYQKKQQPEQQAELLKQMEAGVSRG  209 (452)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC
Confidence            4444444444444   4444444444444433

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=96.80  E-value=0.008  Score=37.80  Aligned_cols=94  Identities=14%  Similarity=-0.114  Sum_probs=73.9

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC--Cc--------H-----hHHHHHHHHHHhcCChhHHHHHHHHHHHc-----C
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC--PH--------V-----FTWNLMIRALTIDGSSLQALLLYNLMICN-----G   74 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~--~~--------~-----~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~   74 (164)
                      .+...-..+.+.|++++|...|++..+  |+        .     ..|+.+-.++.+.|++++|+..+++..+.     .
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e   92 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE   92 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcccc
Confidence            344455667789999999999997652  33        2     38888889999999999999999998763     2


Q ss_pred             CCCCc-ccH----HHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           75 FRPDK-FTF----PFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        75 ~~p~~-~t~----~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +.|+. ..|    ...-.++...|++++|...|++..+.
T Consensus        93 ~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel  131 (159)
T 2hr2_A           93 LNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  131 (159)
T ss_dssp             TTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            25754 456    67778889999999999999988753

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

Probab=96.78  E-value=0.013  Score=42.99  Aligned_cols=92  Identities=14%  Similarity=0.013  Sum_probs=71.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHc---CCCCCc----ccHHHHHHHHHhccchhhHHHHHHHHHHh-----C-CCCc-hH
Q 031208           50 MIRALTIDGSSLQALLLYNLMICN---GFRPDK----FTFPFVIKACIASLAIEKGKEVHGLAVKA-----G-FSRD-MF  115 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~---~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----g-~~~~-~~  115 (164)
                      .+..+.+.|++++|..++++....   -+.|+.    .+++.+...|...|++++|..++++...-     | ..|+ ..
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            355677889999999999998642   233432    57888999999999999999999977642     2 2343 46


Q ss_pred             HHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          116 VQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       116 ~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +++.|-..|...|++++|..++++..
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            78889999999999999999888764

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.70  E-value=0.04  Score=42.95  Aligned_cols=100  Identities=13%  Similarity=0.056  Sum_probs=57.7

Q ss_pred             cCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHH
Q 031208           26 YGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLA  105 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  105 (164)
                      .|+++.|.++.+.+  .+...|..+-..+.+.++++.|.+.|.++..         |..+...+...++.+...++-+..
T Consensus       665 ~~~~~~A~~~~~~~--~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a  733 (814)
T 3mkq_A          665 VGQLTLARDLLTDE--SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDA  733 (814)
T ss_dssp             HTCHHHHHHHHTTC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHhh--CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHH
Confidence            34444444444333  3445677777777777777777777776642         344555555555555555554444


Q ss_pred             HHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC
Q 031208          106 VKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus       106 ~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      ...|      -++....+|.+.|++++|.+++.++.+
T Consensus       734 ~~~~------~~~~A~~~~~~~g~~~~a~~~~~~~~~  764 (814)
T 3mkq_A          734 ETTG------KFNLAFNAYWIAGDIQGAKDLLIKSQR  764 (814)
T ss_dssp             HHTT------CHHHHHHHHHHHTCHHHHHHHHHHTTC
T ss_pred             HHcC------chHHHHHHHHHcCCHHHHHHHHHHcCC
Confidence            4443      234455566667777777777777663

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

Probab=96.69  E-value=0.013  Score=42.85  Aligned_cols=89  Identities=13%  Similarity=-0.067  Sum_probs=69.5

Q ss_pred             HHHHHhccCCcHHHHHHHhccCC----------Cc-HhHHHHHHHHHHhcCChhHHHHHHHHHHH---cCCCCC----cc
Q 031208           19 LLDLCSFYGKTDHALLVFSQIRC----------PH-VFTWNLMIRALTIDGSSLQALLLYNLMIC---NGFRPD----KF   80 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~~----------~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p~----~~   80 (164)
                      .+..+.+.|++++|..++++...          |+ ..+++.+...|...|++++|..++++...   .-+.|+    ..
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            35566778999999999876531          22 35789999999999999999999998753   212232    25


Q ss_pred             cHHHHHHHHHhccchhhHHHHHHHHHH
Q 031208           81 TFPFVIKACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        81 t~~~ll~~~~~~~~~~~a~~~~~~m~~  107 (164)
                      +++.|-..|...|++++|..++++..+
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            788899999999999999999987654

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

Probab=96.66  E-value=0.019  Score=32.14  Aligned_cols=57  Identities=14%  Similarity=0.017  Sum_probs=40.4

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ..+.+.|++++|...|++..+.. +.+.. .+..+-.++...|++++|.+.+++..+..
T Consensus         8 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            8 KELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            35567788888888888876642 22344 66677777788888888888888877664

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=96.32  E-value=0.017  Score=36.24  Aligned_cols=93  Identities=9%  Similarity=-0.108  Sum_probs=52.1

Q ss_pred             ccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCCh----------hHHHHHHHHHHHcCCCCC-cccHHHHHHHHH
Q 031208           25 FYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSS----------LQALLLYNLMICNGFRPD-KFTFPFVIKACI   90 (164)
Q Consensus        25 ~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~----------~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~   90 (164)
                      +.+++++|.+.++...  .| +...|+.+=.++...+++          ++|...|++..+.  .|+ ...|..+-.+|.
T Consensus        14 r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~ay~   91 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYT   91 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHH
Confidence            4455666666666554  23 555555555555555543          4666666666553  343 345666666666


Q ss_pred             hcc-----------chhhHHHHHHHHHHhCCCCchHHHHHHH
Q 031208           91 ASL-----------AIEKGKEVHGLAVKAGFSRDMFVQSTLM  121 (164)
Q Consensus        91 ~~~-----------~~~~a~~~~~~m~~~g~~~~~~~~~~ll  121 (164)
                      ..|           ++++|.+.|++..+.  .|+...|...+
T Consensus        92 ~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al  131 (158)
T 1zu2_A           92 SFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSL  131 (158)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            553           666677766666654  35544444333

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.30  E-value=0.019  Score=34.83  Aligned_cols=107  Identities=9%  Similarity=-0.064  Sum_probs=70.8

Q ss_pred             CCcHHHHHHHhccCC-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh----ccchhhHHHH
Q 031208           27 GKTDHALLVFSQIRC-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA----SLAIEKGKEV  101 (164)
Q Consensus        27 ~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~  101 (164)
                      +++++|.+.|++..+ .+....  +=..|...+.+++|.+.|++..+.|   +...+..|-..|..    .++.++|..+
T Consensus         9 ~d~~~A~~~~~~aa~~g~~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~   83 (138)
T 1klx_A            9 KDLKKAIQYYVKACELNEMFGC--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQY   83 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTCTTHH--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCHhhh--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHHHH
Confidence            456677777776542 222333  4444555566777888888887664   34455566666666    6788888888


Q ss_pred             HHHHHHhCCCCchHHHHHHHHHHHh----cCCchhHHHHhcccC
Q 031208          102 HGLAVKAGFSRDMFVQSTLMDLYLK----CGDVDGGRKMFDKMR  141 (164)
Q Consensus       102 ~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~  141 (164)
                      ++...+.|   +...+..|-..|..    .++.++|.++|+...
T Consensus        84 ~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa  124 (138)
T 1klx_A           84 YSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKAC  124 (138)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHH
Confidence            88887765   34556666677777    788888888887654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=95.95  E-value=0.17  Score=37.73  Aligned_cols=103  Identities=11%  Similarity=0.135  Sum_probs=60.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc-chhhHHHHHHHHHHhCCCCchHHHHHHHHHHH
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL-AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL  125 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  125 (164)
                      |-..+....+.+..+.|..+|.+. +.. .++...|......-...+ +.+.|..+|+...+.- +-+...+...++...
T Consensus       289 w~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~-~~~~~~~~~yid~e~  365 (493)
T 2uy1_A          289 RINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKH-PDSTLLKEEFFLFLL  365 (493)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-CCCHHHHHHHHHHHH
Confidence            333344444566788888888888 211 112222322111112223 6888999999887653 223445666778778


Q ss_pred             hcCCchhHHHHhcccCCCCcchHHHHHH
Q 031208          126 KCGDVDGGRKMFDKMRVRSVVSWTTMIS  153 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~~~~~li~  153 (164)
                      +.|+.+.|..+|+.... ....|...+.
T Consensus       366 ~~~~~~~aR~l~er~~k-~~~lw~~~~~  392 (493)
T 2uy1_A          366 RIGDEENARALFKRLEK-TSRMWDSMIE  392 (493)
T ss_dssp             HHTCHHHHHHHHHHSCC-BHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH-HHHHHHHHHH
Confidence            88999999999988742 3334444443

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

Probab=95.95  E-value=0.078  Score=29.48  Aligned_cols=56  Identities=16%  Similarity=0.077  Sum_probs=47.2

Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchH-HHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMF-VQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ....+.+.|++++|...+++..+.. +.+.. .+..+-.+|.+.|++++|.+.|++..
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al   62 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAI   62 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4556788999999999999998774 33556 88888899999999999999999875

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=95.89  E-value=0.13  Score=38.98  Aligned_cols=149  Identities=8%  Similarity=-0.068  Sum_probs=106.7

Q ss_pred             HHHHHHHHHHHhccCC----------cHHHHHHHhccC--C-CcHhHHHHHHHHHHhcC--ChhHHHHHHHHHHHcCCCC
Q 031208           13 QLLVRKLLDLCSFYGK----------TDHALLVFSQIR--C-PHVFTWNLMIRALTIDG--SSLQALLLYNLMICNGFRP   77 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~----------~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p   77 (164)
                      ..+|+.-=..+.+.|+          ++++.+.++.+.  . .+-.+|+.--..+.+.+  +++++++.++++.+.. +-
T Consensus        63 ~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d-~~  141 (567)
T 1dce_A           63 ATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ER  141 (567)
T ss_dssp             HHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhc-cc
Confidence            3455554444555555          788888888876  2 46678888888888888  6799999999998753 33


Q ss_pred             CcccHHHHHHHHHhcc-chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc--------------CCchhHHHHhcccC-
Q 031208           78 DKFTFPFVIKACIASL-AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC--------------GDVDGGRKMFDKMR-  141 (164)
Q Consensus        78 ~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~--------------~~~~~a~~~~~~m~-  141 (164)
                      |-..|+.--..+.+.| ..+++.+.++++.+.. .-+...|+..-..+.+.              +.++++.+.+++.. 
T Consensus       142 N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~  220 (567)
T 1dce_A          142 NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFF  220 (567)
T ss_dssp             CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHh
Confidence            5667777777778888 7888888888887654 34677788777666653              44577777776554 


Q ss_pred             -CC-CcchHHHHHHHHHhcCCCCC
Q 031208          142 -VR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       142 -~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                       .| |...|+.+--.+.+.++.++
T Consensus       221 ~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          221 TDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             HCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             hCCCCccHHHHHHHHHhcCCCccc
Confidence             34 77888888777777776543

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

Probab=95.81  E-value=0.19  Score=36.04  Aligned_cols=142  Identities=6%  Similarity=-0.002  Sum_probs=93.1

Q ss_pred             hhcCCCCHHHHHHHHHHHhc-----cCCcHHHHHHHhccC--CCc-HhHHHHHHHHHH----hcC-ChhHHHH---HHHH
Q 031208            6 RYGLSNDQLLVRKLLDLCSF-----YGKTDHALLVFSQIR--CPH-VFTWNLMIRALT----IDG-SSLQALL---LYNL   69 (164)
Q Consensus         6 ~~g~~~~~~~~~~li~~~~~-----~~~~~~a~~~~~~~~--~~~-~~~~~~li~~~~----~~~-~~~~a~~---~~~~   69 (164)
                      ..+.+.+...|...+.+...     ..+..+|..+|++..  .|+ ...|..+-.+|.    ... .......   -+..
T Consensus       187 ~~~~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a  266 (372)
T 3ly7_A          187 QKILPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDN  266 (372)
T ss_dssp             HHHSCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             hccCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHH
Confidence            34567788889998876654     234578999999876  464 334443333332    111 1111111   1121


Q ss_pred             HHH-cCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CCCcc
Q 031208           70 MIC-NGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VRSVV  146 (164)
Q Consensus        70 m~~-~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~~~~  146 (164)
                      ... ..-+.+...|..+...+...|++++|...+++....+  |+...|..+-..+.-.|+.++|.+.|++..  +|...
T Consensus       267 ~~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~  344 (372)
T 3ly7_A          267 IVTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGAN  344 (372)
T ss_dssp             HHTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHH
T ss_pred             HHhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcC
Confidence            111 1224566777777777777899999999999999886  787777777788889999999999998765  56555


Q ss_pred             hHH
Q 031208          147 SWT  149 (164)
Q Consensus       147 ~~~  149 (164)
                      +|.
T Consensus       345 t~~  347 (372)
T 3ly7_A          345 TLY  347 (372)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            543

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=95.74  E-value=0.31  Score=34.00  Aligned_cols=145  Identities=7%  Similarity=0.019  Sum_probs=76.4

Q ss_pred             HHHHHHHHHhccC--CcHHHHHHHhccC--CC-cHhHHHHHHHHH----Hhc---CChhHHHHHHHHHHHcCCCCCcccH
Q 031208           15 LVRKLLDLCSFYG--KTDHALLVFSQIR--CP-HVFTWNLMIRAL----TID---GSSLQALLLYNLMICNGFRPDKFTF   82 (164)
Q Consensus        15 ~~~~li~~~~~~~--~~~~a~~~~~~~~--~~-~~~~~~~li~~~----~~~---~~~~~a~~~~~~m~~~~~~p~~~t~   82 (164)
                      +|+.--..+...|  +++++.++++.+.  .| +..+|+.--..+    ...   +++++++.+++++.+.. +-|-..|
T Consensus        69 aWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW  147 (306)
T 3dra_A           69 IWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVW  147 (306)
T ss_dssp             HHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHH
Confidence            3444444444455  6666666666554  22 223343322222    333   56666666666665532 2244555


Q ss_pred             HHHHHHHHhccchh--hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC------chhHHHHhcccC--C-CCcchHHHH
Q 031208           83 PFVIKACIASLAIE--KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD------VDGGRKMFDKMR--V-RSVVSWTTM  151 (164)
Q Consensus        83 ~~ll~~~~~~~~~~--~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~------~~~a~~~~~~m~--~-~~~~~~~~l  151 (164)
                      +.--..+.+.+..+  ++.++++.+.+.. .-|-..|+.--....+.+.      ++++.+.+++..  . .|...|+.+
T Consensus       148 ~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~  226 (306)
T 3dra_A          148 SYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNYL  226 (306)
T ss_dssp             HHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             HHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCCCCccHHHHH
Confidence            55555555566665  6666666666554 2344555544444444444      555666665443  2 256666666


Q ss_pred             HHHHHhcCCC
Q 031208          152 ISGLAASGDL  161 (164)
Q Consensus       152 i~~~~~~g~~  161 (164)
                      -..+.+.|+.
T Consensus       227 ~~ll~~~~~~  236 (306)
T 3dra_A          227 LGIHERFDRS  236 (306)
T ss_dssp             HHHHHHTTCC
T ss_pred             HHHHHhcCCC
Confidence            6666655553

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=95.66  E-value=0.36  Score=34.33  Aligned_cols=100  Identities=6%  Similarity=-0.063  Sum_probs=45.6

Q ss_pred             CcHHHHHHHhccCC---CcHhHHHHHHHHHHhcCChh--------HHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc--
Q 031208           28 KTDHALLVFSQIRC---PHVFTWNLMIRALTIDGSSL--------QALLLYNLMICNGFRPDKFTFPFVIKACIASLA--   94 (164)
Q Consensus        28 ~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~--------~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~--   94 (164)
                      +++++.++++.+.+   .|-..|+.---.+.+.+.++        ++++.+.++.+.. +-|...|+-.-..+.+.++  
T Consensus       140 ~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~  218 (349)
T 3q7a_A          140 DPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAE  218 (349)
T ss_dssp             CCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCC
T ss_pred             ChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccc
Confidence            45555555555442   23444444333333333333        5555555554432 2233344444444444443  


Q ss_pred             -----hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC
Q 031208           95 -----IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus        95 -----~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                           ++++.+.+.+..... +-|...|+-+-..+.+.|+
T Consensus       219 ~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          219 TSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             cchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC
Confidence                 344555555444433 2345555555444444443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.59  E-value=0.24  Score=31.67  Aligned_cols=104  Identities=16%  Similarity=0.217  Sum_probs=55.2

Q ss_pred             HHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHH
Q 031208           20 LDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      ++...+.|+++.|.++-+.+  .+...|..|-......|+++-|.+.|.+..         .|..+.--|.-.|+.+...
T Consensus        12 F~LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~---------D~~~L~~Ly~~tg~~e~L~   80 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQH---------SFDKLSFLYLVTGDVNKLS   80 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT---------CHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhC---------CHHHHHHHHHHhCCHHHHH
Confidence            34455677777777776554  345567777777777777777766666553         2344444445555554444


Q ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208          100 EVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus       100 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      .+-+.....|      -++.....+.-.|+++++.++|.+.
T Consensus        81 kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~  115 (177)
T 3mkq_B           81 KMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEG  115 (177)
T ss_dssp             HHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHC
Confidence            4433333333      1233333344444444444444433

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.57  E-value=0.12  Score=32.23  Aligned_cols=78  Identities=14%  Similarity=-0.055  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc---chhhHHHHHHHHHHhCCCC--chHHHHHHHHHHHhcCCchhHHHH
Q 031208           62 QALLLYNLMICNGFRPDKFTFPFVIKACIASL---AIEKGKEVHGLAVKAGFSR--DMFVQSTLMDLYLKCGDVDGGRKM  136 (164)
Q Consensus        62 ~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~g~~~--~~~~~~~ll~~~~~~~~~~~a~~~  136 (164)
                      .+.+-|.+....|. ++..+--.+-.++++++   +++++..++++..+.. .|  +....-.|--+|.+.|++++|.+.
T Consensus        16 ~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y   93 (152)
T 1pc2_A           16 KFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKY   93 (152)
T ss_dssp             HHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHH
Confidence            34444555444443 45555555666677766   5667888888777765 24  223333334455788888888888


Q ss_pred             hcccC
Q 031208          137 FDKMR  141 (164)
Q Consensus       137 ~~~m~  141 (164)
                      ++.+.
T Consensus        94 ~~~lL   98 (152)
T 1pc2_A           94 VRGLL   98 (152)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87765

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.54  E-value=0.00086  Score=49.80  Aligned_cols=141  Identities=9%  Similarity=0.040  Sum_probs=110.5

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhc
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIAS   92 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   92 (164)
                      +.+|..|-.+..+.+++.+|.+-|-+  ..|...|..+|.+..+.|.+++-+..+...++..-.|.+.  +.|+-+|++.
T Consensus        54 p~VWs~LgkAqL~~~~v~eAIdsyIk--A~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~ID--teLi~ayAk~  129 (624)
T 3lvg_A           54 PAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVE--TELIFALAKT  129 (624)
T ss_dssp             CCCSSSHHHHTTTSSSCTTTTTSSCC--CSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTTT--HHHHHHHHTS
T ss_pred             ccHHHHHHHHHHccCchHHHHHHHHh--CCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccH--HHHHHHHHhh
Confidence            45688888888888888888766543  4455667888999999999999999888777665555555  5899999999


Q ss_pred             cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC------------------------CCcchH
Q 031208           93 LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV------------------------RSVVSW  148 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~------------------------~~~~~~  148 (164)
                      ++..+.++++.       .|+..-...+-+-|...|.++.|.-+|..+.+                        .+..||
T Consensus       130 ~rL~elEefl~-------~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktW  202 (624)
T 3lvg_A          130 NRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTW  202 (624)
T ss_dssp             CSSSTTTSTTS-------CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSH
T ss_pred             CcHHHHHHHHc-------CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHH
Confidence            99876555443       47777777888889999999999888887752                        267899


Q ss_pred             HHHHHHHHhcCCCCCC
Q 031208          149 TTMISGLAASGDLDAA  164 (164)
Q Consensus       149 ~~li~~~~~~g~~~~A  164 (164)
                      .-+-.+|...++|..|
T Consensus       203 KeV~~ACvd~~EfrLA  218 (624)
T 3lvg_A          203 KEVCFACVDGKEFRLA  218 (624)
T ss_dssp             HHHTHHHHHSCTTTTT
T ss_pred             HHHHHHHhCchHHHHH
Confidence            9999999999998765

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=95.49  E-value=0.054  Score=33.98  Aligned_cols=98  Identities=6%  Similarity=-0.136  Sum_probs=68.8

Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccch----------hhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           55 TIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAI----------EKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        55 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~----------~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      .+.+.+++|...+++..+.. +-+...|..+-.++...+++          ++|...+++..+.. +.+...|..+-.+|
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld-P~~~~A~~~LG~ay   90 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAY   90 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC-cCcHHHHHHHHHHH
Confidence            44566788888888887643 23555666666677776654          58888888888775 33566788888888


Q ss_pred             HhcC-----------CchhHHHHhcccC--CCCcchHHHHHHH
Q 031208          125 LKCG-----------DVDGGRKMFDKMR--VRSVVSWTTMISG  154 (164)
Q Consensus       125 ~~~~-----------~~~~a~~~~~~m~--~~~~~~~~~li~~  154 (164)
                      ...|           ++++|.+.|++..  +|+...|...+..
T Consensus        91 ~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~al~~  133 (158)
T 1zu2_A           91 TSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHhcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            7664           7899999998776  6666666655544

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=95.43  E-value=0.22  Score=37.07  Aligned_cols=120  Identities=11%  Similarity=0.067  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCCCc--HhHHH--HHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRCPH--VFTWN--LMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKA   88 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~--~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~   88 (164)
                      .+|...+...-+.++++.|..+|+....|+  ...|.  +.+.. ...++++.|..+|+...+.-  |+ ...+...++.
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~~~~~v~i~~A~lE~-~~~~d~~~ar~ife~al~~~--~~~~~~~~~yid~  363 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIEY-YATGSRATPYNIFSSGLLKH--PDSTLLKEEFFLF  363 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHTTSCCCHHHHHHHHHHHH-HHHCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhhCCCCChHHHHHHHHHHH-HHCCChHHHHHHHHHHHHHC--CCCHHHHHHHHHH
Confidence            557777777777888999999999885343  23332  22222 22347999999999987652  43 3334556677


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..+.|+.+.|..+++..     ......|...++.=...|+.+.+..++++..
T Consensus       364 e~~~~~~~~aR~l~er~-----~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~  411 (493)
T 2uy1_A          364 LLRIGDEENARALFKRL-----EKTSRMWDSMIEYEFMVGSMELFRELVDQKM  411 (493)
T ss_dssp             HHHHTCHHHHHHHHHHS-----CCBHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            77889999999999986     2357888888888888899998888777654

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.28  E-value=0.12  Score=29.59  Aligned_cols=63  Identities=13%  Similarity=-0.065  Sum_probs=46.0

Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHhC------CCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKAG------FSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g------~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ...+-.|-..+.+.+++..|...+++..+.-      -.+...++..|..+|.+.|+++.|...+++..
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al   73 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLL   73 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            3345566677777788888888887766531      13456778888888899999999998888765

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.99  E-value=0.17  Score=28.45  Aligned_cols=64  Identities=9%  Similarity=0.067  Sum_probs=36.4

Q ss_pred             cHhHHHHHHHHHHhcCC---hhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           43 HVFTWNLMIRALTIDGS---SLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      |...+..+-.++...++   .++|..++++..+.  .|+ ......+-..+.+.|++++|...|+.+.+.
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            33444444444433333   56777777776653  343 334445556666777777777777776654

>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=94.85  E-value=0.26  Score=35.51  Aligned_cols=72  Identities=8%  Similarity=-0.068  Sum_probs=57.7

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHH-----hCCCCchHHHHHH
Q 031208           48 NLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVK-----AGFSRDMFVQSTL  120 (164)
Q Consensus        48 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~-----~g~~~~~~~~~~l  120 (164)
                      ..++..+...|+++++...+....... +.++..+..+|.++.+.|+..+|.+.|+...+     .|+.|+..+-...
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~  251 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALN  251 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            445667778899999999999886542 55888999999999999999999999987654     4999987654433

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=94.47  E-value=0.88  Score=32.39  Aligned_cols=146  Identities=8%  Similarity=0.003  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHhccC-CcHHHHHHHhccC--C-CcHhHHHHHHHHHHhc-C-ChhHHHHHHHHHHHcCCCCCcccHHHHH
Q 031208           13 QLLVRKLLDLCSFYG-KTDHALLVFSQIR--C-PHVFTWNLMIRALTID-G-SSLQALLLYNLMICNGFRPDKFTFPFVI   86 (164)
Q Consensus        13 ~~~~~~li~~~~~~~-~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~-~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll   86 (164)
                      ..+|+.--..+...| .++++..+++.+.  . .+-.+|+.--..+.+. + ++++++++++++.+.. +-|-..|+---
T Consensus        88 ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~d-pkNy~AW~~R~  166 (349)
T 3q7a_A           88 YTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPD-PKNYHTWAYLH  166 (349)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            334555444445555 4777777777664  2 3455666655555554 5 6777777777776532 22445565555


Q ss_pred             HHHHhccchh--------hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC-------chhHHHHhcccC--CC-CcchH
Q 031208           87 KACIASLAIE--------KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD-------VDGGRKMFDKMR--VR-SVVSW  148 (164)
Q Consensus        87 ~~~~~~~~~~--------~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~-------~~~a~~~~~~m~--~~-~~~~~  148 (164)
                      ..+.+.+..+        ++.+..+.+.+.. .-|...|+..-..+.+.+.       ++++.+.+++..  .| |...|
T Consensus       167 wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW  245 (349)
T 3q7a_A          167 WLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAW  245 (349)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHH
Confidence            5555555555        7777777777665 3456677777666666665       456666665543  33 66777


Q ss_pred             HHHHHHHHhcCC
Q 031208          149 TTMISGLAASGD  160 (164)
Q Consensus       149 ~~li~~~~~~g~  160 (164)
                      +.+-..+.+.|+
T Consensus       246 ~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          246 NYLRGFLKHFSL  257 (349)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHhcCC
Confidence            766555555544

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=94.46  E-value=1.2  Score=33.84  Aligned_cols=132  Identities=14%  Similarity=0.003  Sum_probs=98.6

Q ss_pred             ccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCC----------hhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh
Q 031208           25 FYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGS----------SLQALLLYNLMICNGFRPDKFTFPFVIKACIA   91 (164)
Q Consensus        25 ~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   91 (164)
                      .....++|.+.++.+.  .| +...|+.-=..+...++          ++++++.++++.+.. +-+...|..--..+.+
T Consensus        41 ~~~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~  119 (567)
T 1dce_A           41 AGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSR  119 (567)
T ss_dssp             TTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            3445567888888876  34 44567665555555555          899999999998753 3355688888888888


Q ss_pred             cc--chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcC-CchhHHHHhcccCCC---CcchHHHHHHHHHhc
Q 031208           92 SL--AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCG-DVDGGRKMFDKMRVR---SVVSWTTMISGLAAS  158 (164)
Q Consensus        92 ~~--~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~-~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~  158 (164)
                      .+  +++++.++++.+.+.. +-+-..|+.---...+.| .++++.+.++++.+.   |...|+..-..+.+.
T Consensus       120 l~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l  191 (567)
T 1dce_A          120 LPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQL  191 (567)
T ss_dssp             CSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhh
Confidence            89  6699999999999876 456778887777777888 889999999888743   667888776666653

>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=94.30  E-value=0.12  Score=29.80  Aligned_cols=64  Identities=6%  Similarity=0.059  Sum_probs=47.4

Q ss_pred             ChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           59 SSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        59 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      +.=++.+-++.+-...+.|++....+.+++|.+.+++..|.++++-++..- .+...+|..+++-
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHHH
Confidence            445677777777778888888888888888888888888888888776432 3335567777653

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

Probab=94.14  E-value=0.47  Score=34.07  Aligned_cols=74  Identities=7%  Similarity=-0.080  Sum_probs=60.1

Q ss_pred             CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           41 CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        41 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      ..+...|..+-..+...|++++|...+++....+  |+...|..+-..+.-.|+.++|.+.+++....  .|...+|.
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~  347 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLY  347 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHH
Confidence            3566777777777777899999999999998875  88777777788889999999999999988876  46655543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=93.96  E-value=1.5  Score=34.61  Aligned_cols=125  Identities=14%  Similarity=0.089  Sum_probs=78.2

Q ss_pred             HHHHHHHHHhccCC-cHHHHHHHhccC--CCcHhH-H-HHHHHHHHhcCC-hhHHHHHHHHHHH------cCCCCCcccH
Q 031208           15 LVRKLLDLCSFYGK-TDHALLVFSQIR--CPHVFT-W-NLMIRALTIDGS-SLQALLLYNLMIC------NGFRPDKFTF   82 (164)
Q Consensus        15 ~~~~li~~~~~~~~-~~~a~~~~~~~~--~~~~~~-~-~~li~~~~~~~~-~~~a~~~~~~m~~------~~~~p~~~t~   82 (164)
                      ....++..+...|+ .+.|.++|+.+.  .|...+ + ..++..+.+.++ --+|..++.+..+      ....+.....
T Consensus       250 L~~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          250 LMYSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            44555565665666 477999999876  343222 2 333333333332 2245555555432      1223322111


Q ss_pred             -------HHHH----HHHHhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           83 -------PFVI----KACIASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        83 -------~~ll----~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                             ..|+    +-|...|+++.|.++-++....  .|+ -.+|-.|..+|.+.|+++.|+-.++.++
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~--aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTEL--ALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhc--CchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                   1133    3455679999999999988765  465 6799999999999999999999999886

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=93.84  E-value=0.52  Score=36.71  Aligned_cols=83  Identities=13%  Similarity=0.005  Sum_probs=55.0

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      .+...|..+-..+.+.++++.|.+.|..+...     ..+...+...++.+....+-+.....|      -++....++.
T Consensus       679 ~~~~~W~~la~~al~~~~~~~A~~~y~~~~d~-----~~l~~l~~~~~~~~~~~~~~~~a~~~~------~~~~A~~~~~  747 (814)
T 3mkq_A          679 SAEMKWRALGDASLQRFNFKLAIEAFTNAHDL-----ESLFLLHSSFNNKEGLVTLAKDAETTG------KFNLAFNAYW  747 (814)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCH-----HHHHHHHHHTTCHHHHHHHHHHHHHTT------CHHHHHHHHH
T ss_pred             CcHhHHHHHHHHHHHcCCHHHHHHHHHHccCh-----hhhHHHHHHcCCHHHHHHHHHHHHHcC------chHHHHHHHH
Confidence            46788999999999999999999999988753     334444555666665555544444443      3344555555


Q ss_pred             hccchhhHHHHHHH
Q 031208           91 ASLAIEKGKEVHGL  104 (164)
Q Consensus        91 ~~~~~~~a~~~~~~  104 (164)
                      +.|++++|.+++.+
T Consensus       748 ~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          748 IAGDIQGAKDLLIK  761 (814)
T ss_dssp             HHTCHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHH
Confidence            56666666555543

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=93.80  E-value=0.6  Score=28.02  Aligned_cols=89  Identities=9%  Similarity=-0.111  Sum_probs=70.2

Q ss_pred             HHHHHhccCCcHHHHHHHhccC-CCcHhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh--
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR-CPHVFTWNLMIRALTI----DGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA--   91 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~--   91 (164)
                      +=..|...+.++.|.+.|++.. ..+...+..|=..|..    .+++++|...|++-.+.|   +...+..|-..|..  
T Consensus        31 lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~  107 (138)
T 1klx_A           31 LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGK  107 (138)
T ss_dssp             HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTS
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCC
Confidence            4456666677888999999765 4577777777777777    789999999999998775   34556667777777  


Q ss_pred             --ccchhhHHHHHHHHHHhCC
Q 031208           92 --SLAIEKGKEVHGLAVKAGF  110 (164)
Q Consensus        92 --~~~~~~a~~~~~~m~~~g~  110 (164)
                        .++.++|..+++...+.|.
T Consensus       108 g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A          108 GVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             SSCCCHHHHHHHHHHHHHTTC
T ss_pred             CCCcCHHHHHHHHHHHHHCCC
Confidence              7899999999999888774

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=93.50  E-value=1.4  Score=31.15  Aligned_cols=136  Identities=9%  Similarity=-0.053  Sum_probs=93.9

Q ss_pred             CCHHHHHHHHHHHhccC--CcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCC-hhHHHHHHHHHHHcCCCCCcccHHH
Q 031208           11 NDQLLVRKLLDLCSFYG--KTDHALLVFSQIR---CPHVFTWNLMIRALTIDGS-SLQALLLYNLMICNGFRPDKFTFPF   84 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~--~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~t~~~   84 (164)
                      -+..+|+----.+.+.+  .++.+..+++.+.   ..|-..|+.---.....|. ++++++.+.++.+.. +-|...|+.
T Consensus       106 Kny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-p~N~SAW~~  184 (331)
T 3dss_A          106 KSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHY  184 (331)
T ss_dssp             TCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-SCCHHHHHH
T ss_pred             CCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-CCCHHHHHH
Confidence            36666766656666666  4788999888876   3577888887777788888 589999999998754 335556666


Q ss_pred             HHHHHHhc--------------cchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc-----------CCchhHHHHhcc
Q 031208           85 VIKACIAS--------------LAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC-----------GDVDGGRKMFDK  139 (164)
Q Consensus        85 ll~~~~~~--------------~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-----------~~~~~a~~~~~~  139 (164)
                      ....+.+.              +.++++.+.+....... +-|...|+-+-..+.+.           +.++++.+.+++
T Consensus       185 R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~e  263 (331)
T 3dss_A          185 RSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKE  263 (331)
T ss_dssp             HHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHH
Confidence            65555544              45677888888877665 45677777665555554           346777777777


Q ss_pred             cC--CCCcchHH
Q 031208          140 MR--VRSVVSWT  149 (164)
Q Consensus       140 m~--~~~~~~~~  149 (164)
                      +.  +||. .|.
T Consensus       264 lle~~pd~-~w~  274 (331)
T 3dss_A          264 LQELEPEN-KWC  274 (331)
T ss_dssp             HHHHCTTC-HHH
T ss_pred             HHhhCccc-chH
Confidence            76  5654 343

>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=93.20  E-value=0.67  Score=26.72  Aligned_cols=57  Identities=5%  Similarity=0.044  Sum_probs=32.5

Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC---CCcchHHHHHH
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV---RSVVSWTTMIS  153 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~  153 (164)
                      +..+-+..+....+.|++.+..+.+.+|.|.+++..|.++|+.++.   ....+|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~lq   87 (109)
T 1v54_E           28 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   87 (109)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHHH
Confidence            3444444444555666666666666666666666666666665551   12334555544

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=93.16  E-value=0.33  Score=35.00  Aligned_cols=66  Identities=15%  Similarity=0.193  Sum_probs=54.2

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHH-----cCCCCCccc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMIC-----NGFRPDKFT   81 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~t   81 (164)
                      ...++..+...|+.++|........  .| +...|..+|.++.+.|+..+|++.|++..+     .|+.|+..+
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 HTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            3445667778999999988877765  34 778999999999999999999999999744     599998865

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=93.02  E-value=0.17  Score=39.78  Aligned_cols=116  Identities=9%  Similarity=-0.016  Sum_probs=70.2

Q ss_pred             HHHHHHHHHhcCC-hhHHHHHHHHHHHcCCCCCccc--HHHHHHHHHhccch-hhHHHHHHHHHHh------CCCCchH-
Q 031208           47 WNLMIRALTIDGS-SLQALLLYNLMICNGFRPDKFT--FPFVIKACIASLAI-EKGKEVHGLAVKA------GFSRDMF-  115 (164)
Q Consensus        47 ~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~t--~~~ll~~~~~~~~~-~~a~~~~~~m~~~------g~~~~~~-  115 (164)
                      ...++.-+...++ .+.|.++|+++....  |...+  ...++....+.++- -+|.+++.+..+.      ...+... 
T Consensus       251 ~~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~  328 (754)
T 4gns_B          251 MYSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDAD  328 (754)
T ss_dssp             HHHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccc
Confidence            3455555666666 588999999997753  43322  22333333333322 2344444443321      2222111 


Q ss_pred             ----------HHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          116 ----------VQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       116 ----------~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                                .-+.-.+.+...|+++.|+++-++..  .| +-.+|-.|..+|.+.|++|.|
T Consensus       329 ~~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~A  390 (754)
T 4gns_B          329 SARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKA  390 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHH
Confidence                      11222345567899999999998876  45 567999999999999999865

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.76  E-value=1  Score=27.71  Aligned_cols=129  Identities=12%  Similarity=0.081  Sum_probs=86.6

Q ss_pred             HHHHHHHHH--HhccCCcHHHHHHHhccCC-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CC--------------
Q 031208           14 LLVRKLLDL--CSFYGKTDHALLVFSQIRC-PHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GF--------------   75 (164)
Q Consensus        14 ~~~~~li~~--~~~~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~--------------   75 (164)
                      .+...||++  ..-.|.+++..++..+... .+..-||-+|.-....-+=+-.+++++.+-.. .+              
T Consensus         6 el~kkLmeAK~~ildG~v~qGveii~k~~~ssni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C~~   85 (172)
T 1wy6_A            6 EIIRKLMDAKKFLLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGV   85 (172)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHcCCCCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHHHH
Confidence            345556654  3347888888888887663 45556666666666666666666666665331 11              


Q ss_pred             --CCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC
Q 031208           76 --RPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR  143 (164)
Q Consensus        76 --~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  143 (164)
                        ..+..-+...++.....|+.++..++...+.. +.+|++...-.+-.+|.+.|+..+|.+++.+.-++
T Consensus        86 ~~n~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~k  154 (172)
T 1wy6_A           86 INNTLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKK  154 (172)
T ss_dssp             HTTCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HhcchHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHh
Confidence              12333456667777888888888888888654 33677888888889999999999999998876533

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.51  E-value=1.1  Score=27.54  Aligned_cols=83  Identities=10%  Similarity=-0.123  Sum_probs=62.1

Q ss_pred             cCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHH
Q 031208           26 YGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLA  105 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  105 (164)
                      +|.+....+.+-.+- .+...++..++.....|.-|+-.+++.++.. +.+|++...-.+..+|.+.|+..++.+++.+.
T Consensus        74 C~NlKrVi~C~~~~n-~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~A  151 (172)
T 1wy6_A           74 CQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEA  151 (172)
T ss_dssp             CSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            344444444443332 3344567788889999999999999999744 34677777788999999999999999999999


Q ss_pred             HHhCC
Q 031208          106 VKAGF  110 (164)
Q Consensus       106 ~~~g~  110 (164)
                      -+.|+
T Consensus       152 C~kG~  156 (172)
T 1wy6_A          152 CKKGE  156 (172)
T ss_dssp             HHTTC
T ss_pred             HHhhh
Confidence            99986

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=92.48  E-value=0.78  Score=25.65  Aligned_cols=77  Identities=14%  Similarity=0.099  Sum_probs=55.5

Q ss_pred             CCCHHHHHHHHHHHhccCC---cHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHH
Q 031208           10 SNDQLLVRKLLDLCSFYGK---TDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFP   83 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~---~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   83 (164)
                      +.|+..+..+-.++...++   .++|..++++..  .| +......+-..+.+.|++++|...|+++.+..  |+.....
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~--p~~~~~~   80 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN--DPNLDRV   80 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC--CTTCCHH
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCccHH
Confidence            4566777777776654443   799999999876  34 56677777788899999999999999998764  3333344


Q ss_pred             HHHHH
Q 031208           84 FVIKA   88 (164)
Q Consensus        84 ~ll~~   88 (164)
                      .+...
T Consensus        81 ~i~~~   85 (93)
T 3bee_A           81 TIIES   85 (93)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

>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=92.43  E-value=0.32  Score=29.65  Aligned_cols=63  Identities=6%  Similarity=0.075  Sum_probs=40.4

Q ss_pred             ChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           59 SSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        59 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      +.=+..+-++.+....+.|++......+++|-+.+|+..|.++++-++..- .+...+|..+++
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~lq  130 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ  130 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHHH
Confidence            333555556666666777777777777777777777777777777665332 334556666655

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=92.35  E-value=1.4  Score=28.15  Aligned_cols=111  Identities=10%  Similarity=0.133  Sum_probs=78.1

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      -+...|..|-+.....|+++-|.+.|.....     +..+.-.|.-.|+.+....+-+.-...|      -++..+..+.
T Consensus        32 ~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D-----~~~L~~Ly~~tg~~e~L~kla~iA~~~g------~~n~af~~~l  100 (177)
T 3mkq_B           32 NDSITWERLIQEALAQGNASLAEMIYQTQHS-----FDKLSFLYLVTGDVNKLSKMQNIAQTRE------DFGSMLLNTF  100 (177)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC-----HHHHHHHHHHHTCHHHHHHHHHHHHHTT------CHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC-----HHHHHHHHHHhCCHHHHHHHHHHHHHCc------cHHHHHHHHH
Confidence            3677899999999999999999999999885     4445556677788777666555555554      6788888899


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      -.|+++++.+++.+   .|..|..      .-.....|..+.|.++.+++.
T Consensus       101 ~lGdv~~~i~lL~~---~~r~~eA------~~~A~t~g~~~~a~~~~~~~~  142 (177)
T 3mkq_B          101 YNNSTKERSSIFAE---GGSLPLA------YAVAKANGDEAAASAFLEQAE  142 (177)
T ss_dssp             HHTCHHHHHHHHHH---TTCHHHH------HHHHHHTTCHHHHHHHHHHTT
T ss_pred             HcCCHHHHHHHHHH---CCChHHH------HHHHHHcCcHHHHHHHHHHhC
Confidence            99999999888754   3432211      111222566667777776553

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=92.30  E-value=2  Score=29.87  Aligned_cols=92  Identities=12%  Similarity=0.042  Sum_probs=69.3

Q ss_pred             cHHHHHHHhccC--CCc---HhHHHHHHHHHHhc-----CChhHHHHHHHHHHHcCCCC--CcccHHHHHHHHHhc-cch
Q 031208           29 TDHALLVFSQIR--CPH---VFTWNLMIRALTID-----GSSLQALLLYNLMICNGFRP--DKFTFPFVIKACIAS-LAI   95 (164)
Q Consensus        29 ~~~a~~~~~~~~--~~~---~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p--~~~t~~~ll~~~~~~-~~~   95 (164)
                      ...|...+++..  .|+   ...|+.+-..|.+.     |+.+.|...|++-.+-  .|  +..++...-..++.. |+.
T Consensus       179 l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~L--nP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRY--CSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHH--CCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHh--CCCCCchHHHHHHHHHHHhcCCH
Confidence            355555555554  355   56899999999984     9999999999999884  46  366777778888884 999


Q ss_pred             hhHHHHHHHHHHhCCC--CchHHHHHHHH
Q 031208           96 EKGKEVHGLAVKAGFS--RDMFVQSTLMD  122 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~~--~~~~~~~~ll~  122 (164)
                      +++.+.+++.......  |+....+.+-+
T Consensus       257 ~~a~~~L~kAL~a~p~~~P~~~lan~~~q  285 (301)
T 3u64_A          257 AGFDEALDRALAIDPESVPHNKLLVILSQ  285 (301)
T ss_dssp             HHHHHHHHHHHHCCGGGCSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCChhHHHHHHH
Confidence            9999999999887655  66655555544

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=92.18  E-value=3.1  Score=34.48  Aligned_cols=142  Identities=9%  Similarity=0.108  Sum_probs=90.4

Q ss_pred             HHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-------------------
Q 031208           18 KLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-------------------   78 (164)
Q Consensus        18 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-------------------   78 (164)
                      .++..+.+.+..+.+.++..-.......+| .+-.++...|++++|.+.|.+.-. |+..+                   
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~~~~~~~~y-l~g~~~L~~ge~~~A~~~F~kaa~-~~~~~~~l~~~~~~~~~~~~~~~~  894 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWLNSDPIAVY-LKALIYLKSKEAVKAVRCFKTTSL-VLYSHTSQFAVLREFQEIAEKYHH  894 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHSCCCHHHHH-HHHHHHHHTTCHHHHHHHHHTCCC-SCTTCCCSCSSHHHHHHHHHTTTS
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccCCcHHHH-HHHHHHHhcCCHHHHHHHHHHHhh-hhcccchhhhhhcccccccccccc
Confidence            355566677777777776655544333333 333456788999999999976521 11110                   


Q ss_pred             ----cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc----hHHHHHHHHHHHhcCCchhHHHHhcccCCC--CcchH
Q 031208           79 ----KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD----MFVQSTLMDLYLKCGDVDGGRKMFDKMRVR--SVVSW  148 (164)
Q Consensus        79 ----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--~~~~~  148 (164)
                          ..=|..++..+-+.+.++.+.++-....+..-..+    ...|..+++.+...|++++|...+-.++.+  -....
T Consensus       895 ~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r~~cL  974 (1139)
T 4fhn_B          895 QNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPLKKSCL  974 (1139)
T ss_dssp             CCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSCHHHH
T ss_pred             cccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHHHHHH
Confidence                01256677777888888888877766655432211    236888899999999999998888666532  12356


Q ss_pred             HHHHHHHHhcCCC
Q 031208          149 TTMISGLAASGDL  161 (164)
Q Consensus       149 ~~li~~~~~~g~~  161 (164)
                      ..+|...+..|+.
T Consensus       975 r~LV~~lce~~~~  987 (1139)
T 4fhn_B          975 LDFVNQLTKQGKI  987 (1139)
T ss_dssp             HHHHHHHHHHCCH
T ss_pred             HHHHHHHHhCCCh
Confidence            6677777766654

>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=91.48  E-value=1.5  Score=26.77  Aligned_cols=59  Identities=5%  Similarity=0.012  Sum_probs=46.3

Q ss_pred             hhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHH
Q 031208           96 EKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISG  154 (164)
Q Consensus        96 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~  154 (164)
                      -+..+-+..+....+.|++.+..+.+.+|-|.+++..|.++|+.++   .+...+|..+++-
T Consensus        70 wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~lqE  131 (152)
T 2y69_E           70 WELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQE  131 (152)
T ss_dssp             HHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHHHH
Confidence            3455556666667788999999999999999999999999999887   2344567777764

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=91.23  E-value=1.2  Score=25.19  Aligned_cols=62  Identities=5%  Similarity=-0.077  Sum_probs=38.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcC------CCCCcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICNG------FRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~~------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +-.|=..+.+.++++.|...|++..+.-      -.+....+..+..++.+.|+++.|...+++..+.
T Consensus         8 c~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            8 CFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            3344555666777777777777654321      1123345666677777777777777777777654

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=89.40  E-value=1.5  Score=26.24  Aligned_cols=77  Identities=10%  Similarity=-0.105  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhh---HHHHHHHHHHhCCCC--chHHHHHHHHHHHhcCCchhHHHHh
Q 031208           63 ALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEK---GKEVHGLAVKAGFSR--DMFVQSTLMDLYLKCGDVDGGRKMF  137 (164)
Q Consensus        63 a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~---a~~~~~~m~~~g~~~--~~~~~~~ll~~~~~~~~~~~a~~~~  137 (164)
                      +.+-|.+....|. |+..+---+..++.++....+   +..+++++.+.+ .|  .....-.|--++.|.|++++|.+.+
T Consensus        20 ~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~   97 (126)
T 1nzn_A           20 FEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYV   97 (126)
T ss_dssp             HHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            3334444333332 444444445556666655444   667777666554 23  2222223344567777777777777


Q ss_pred             cccC
Q 031208          138 DKMR  141 (164)
Q Consensus       138 ~~m~  141 (164)
                      +.+.
T Consensus        98 ~~lL  101 (126)
T 1nzn_A           98 RGLL  101 (126)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7665

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=87.22  E-value=6.1  Score=27.85  Aligned_cols=123  Identities=7%  Similarity=-0.082  Sum_probs=87.8

Q ss_pred             cHHHHHHHhccC--C-CcHhHHHHHHHHHHhcC--ChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc-hhhHHHHH
Q 031208           29 TDHALLVFSQIR--C-PHVFTWNLMIRALTIDG--SSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLA-IEKGKEVH  102 (164)
Q Consensus        29 ~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~-~~~a~~~~  102 (164)
                      ++++..+++.+.  . .+-.+|+.--..+.+.+  .+++++.+++++.+.. +-|-..|+.--..+...|. .+++.+.+
T Consensus        90 l~~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~  168 (331)
T 3dss_A           90 VKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFT  168 (331)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHH
Confidence            567777777665  3 36678888777777777  4899999999998753 3366677777777778887 58899999


Q ss_pred             HHHHHhCCCCchHHHHHHHHHHHhc--------------CCchhHHHHhcccC--CC-CcchHHHHHH
Q 031208          103 GLAVKAGFSRDMFVQSTLMDLYLKC--------------GDVDGGRKMFDKMR--VR-SVVSWTTMIS  153 (164)
Q Consensus       103 ~~m~~~g~~~~~~~~~~ll~~~~~~--------------~~~~~a~~~~~~m~--~~-~~~~~~~li~  153 (164)
                      +.+.+.. +-|...|+..-..+.+.              +.++++.+.++...  .| |...|+-+--
T Consensus       169 ~~~I~~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~  235 (331)
T 3dss_A          169 DSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRW  235 (331)
T ss_dssp             HHHHHHC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            9998876 45677787766666554              34667777777654  44 6677765433

>2ion_A PDCD4, programmed cell death 4, PDCD4; alpha-helical, antitumor protein; 1.57A {Mus musculus} SCOP: a.118.1.14 PDB: 2ios_A 2iol_A

Probab=86.72  E-value=4  Score=25.24  Aligned_cols=67  Identities=15%  Similarity=0.145  Sum_probs=47.0

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCCc---HhHHHHHHHHHHhcCC--hhHHHHHHHHHHHcCCCCCccc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCPH---VFTWNLMIRALTIDGS--SLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      ..+.++.-|...|+.++|...++.+..|.   ..+...+..++-+.++  -+.+..++..+...|+-+....
T Consensus        11 ki~~lL~EY~~~~D~~EA~~cl~EL~~p~f~~e~V~~~i~~alE~~~~~~re~~~~LL~~L~~~~~is~~q~   82 (152)
T 2ion_A           11 EIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQM   82 (152)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcCHHHH
Confidence            35678888999999999999999998663   3445555556555332  4567778888877665555443

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=86.59  E-value=3.1  Score=23.91  Aligned_cols=57  Identities=9%  Similarity=0.046  Sum_probs=35.9

Q ss_pred             hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHH
Q 031208           95 IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMIS  153 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~  153 (164)
                      .++|..+-+.+...+.  .+.+--+-+..+...|++++|..+.+...-||...|-++-.
T Consensus        22 HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce   78 (115)
T 2uwj_G           22 HEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE   78 (115)
T ss_dssp             HHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH
Confidence            4566666666655543  33333344455667777777777777777777777766644

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=86.31  E-value=3.3  Score=23.87  Aligned_cols=57  Identities=14%  Similarity=0.158  Sum_probs=30.5

Q ss_pred             hhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHH
Q 031208           95 IEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMIS  153 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~  153 (164)
                      .++|..+-+.+...+.  .+.+--+-+..+...|++++|..+.+...-||...|-++-.
T Consensus        23 HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce   79 (116)
T 2p58_C           23 HEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE   79 (116)
T ss_dssp             HHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH
Confidence            3455555555554442  33333333444555666666666666666666666655543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=86.13  E-value=4.4  Score=25.12  Aligned_cols=69  Identities=9%  Similarity=-0.037  Sum_probs=43.5

Q ss_pred             CcHhHHHHHHHHHHhcC---ChhHHHHHHHHHHHcCCCC--CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc
Q 031208           42 PHVFTWNLMIRALTIDG---SSLQALLLYNLMICNGFRP--DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD  113 (164)
Q Consensus        42 ~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~  113 (164)
                      ++..+.-.+-.++++.+   +.+++..++++..+.. .|  +...+=.+--++.+.|+++.|.+.++.+.+.  +|+
T Consensus        30 ~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~i--eP~  103 (152)
T 1pc2_A           30 VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQ  103 (152)
T ss_dssp             CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH--CTT
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCC
Confidence            44544444455667766   5668888888876654 23  1222233445668888888888888888776  454

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=86.00  E-value=3.4  Score=23.76  Aligned_cols=53  Identities=11%  Similarity=-0.044  Sum_probs=33.6

Q ss_pred             HHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           20 LDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      +..+...|++++|..+.+.+..||...|-.|-  -.+.|..+.+..-+.++..+|
T Consensus        46 ~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALc--e~rlGl~s~le~rL~~la~sg   98 (115)
T 2uwj_G           46 ISSLANQGRYQEALAFAHGNPWPALEPWFALC--EWHLGLGAALDRRLAGLGGSS   98 (115)
T ss_dssp             HHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHH--HHHTTCHHHHHHHHHHHHTCS
T ss_pred             HHHHHcchhHHHHHHhcCCCCCchHHHHHHHH--HHhcccHHHHHHHHHHHHhCC
Confidence            34455677777777777777777777775442  346666666666666666555

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.81  E-value=8.4  Score=28.08  Aligned_cols=93  Identities=11%  Similarity=-0.047  Sum_probs=60.0

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCC------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCCcccHHHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRC------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNG-FRPDKFTFPFVIK   87 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~ll~   87 (164)
                      +...+-+.+.+.|+++.|.+.+.++..      .-...+-.+|..+...+++..+...+.+....- -.++...-+ -++
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~-~lk  211 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRN-RYK  211 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHH-HHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHH-HHH
Confidence            455677788888888888888888762      334567777888888888888888888874321 112222111 122


Q ss_pred             H-----HHhccchhhHHHHHHHHHHh
Q 031208           88 A-----CIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        88 ~-----~~~~~~~~~a~~~~~~m~~~  108 (164)
                      .     +...+++..|.+.|-+....
T Consensus       212 ~~~gl~~l~~r~f~~Aa~~f~e~~~t  237 (429)
T 4b4t_R          212 TYYGIHCLAVRNFKEAAKLLVDSLAT  237 (429)
T ss_dssp             HHHHHGGGGTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhChHHHHHHHHHHHhcc
Confidence            2     23456788887777766544

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=85.23  E-value=3.8  Score=23.61  Aligned_cols=52  Identities=13%  Similarity=0.001  Sum_probs=30.3

Q ss_pred             HHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 031208           21 DLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNG   74 (164)
Q Consensus        21 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   74 (164)
                      ..+...|++++|..+.+.+..||...|-.|-  -.+.|..+.+..-+.++..+|
T Consensus        48 sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALc--e~rlGl~s~le~rL~~la~sg   99 (116)
T 2p58_C           48 SSLMNRGDYASALQQGNKLAYPDLEPWLALC--EYRLGLGSALESRLNRLARSQ   99 (116)
T ss_dssp             HHHHHTTCHHHHHHHHTTSCCGGGHHHHHHH--HHHHTCHHHHHHHHHHHTTCC
T ss_pred             HHHHcchhHHHHHHhcCCCCCchHHHHHHHH--HHhcccHHHHHHHHHHHHhCC
Confidence            3455566666666666666666666664442  245555555555555555544

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A

Probab=84.25  E-value=4.9  Score=24.03  Aligned_cols=65  Identities=15%  Similarity=0.167  Sum_probs=45.8

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCCCc---HhHHHHHHHHHHhcCC--hhHHHHHHHHHHHcCCCCCcc
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRCPH---VFTWNLMIRALTIDGS--SLQALLLYNLMICNGFRPDKF   80 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~~~~p~~~   80 (164)
                      .+.++.-|...|+.++|...++.+..|.   ..+...+..++-+.++  .+.+..++..+...|+-+...
T Consensus        10 i~~ll~EY~~~~D~~Ea~~cl~eL~~p~f~~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~~~~~is~~q   79 (129)
T 2nsz_A           10 IDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQ   79 (129)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcCHHH
Confidence            5678888888999999999999988663   2445555556555432  467778888887766555443

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=83.88  E-value=7.3  Score=27.10  Aligned_cols=109  Identities=13%  Similarity=0.010  Sum_probs=72.8

Q ss_pred             HHHHHHhccCCCc--HhHHHHHHHHH-Hhc--CC------hhHHHHHHHHHHHcCCCCC---cccHHHHHHHHHh-----
Q 031208           31 HALLVFSQIRCPH--VFTWNLMIRAL-TID--GS------SLQALLLYNLMICNGFRPD---KFTFPFVIKACIA-----   91 (164)
Q Consensus        31 ~a~~~~~~~~~~~--~~~~~~li~~~-~~~--~~------~~~a~~~~~~m~~~~~~p~---~~t~~~ll~~~~~-----   91 (164)
                      .-.+.+......+  ...|..++.+- +..  |.      ...|...+++..+  +.|+   -..|.++-..|.+     
T Consensus       139 ~~~~~l~~~~~~dve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAle--LDP~~~~GsA~~~LG~lY~~vPp~~  216 (301)
T 3u64_A          139 RLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACD--LWPSYQEGAVWNVLTKFYAAAPESF  216 (301)
T ss_dssp             HHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHH--HCTTHHHHHHHHHHHHHHHHSCTTT
T ss_pred             hHHHHHHHcCccccHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHH--hCCCcccCHHHHHHHHHHHhCCCcc
Confidence            3344444444333  34566655543 332  32      3455555555544  4566   3467888888888     


Q ss_pred             ccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhc-CCchhHHHHhcccC
Q 031208           92 SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKC-GDVDGGRKMFDKMR  141 (164)
Q Consensus        92 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-~~~~~a~~~~~~m~  141 (164)
                      .|+.++|.+.|++..+-+-.-+..++...-+.+++. |+.+.+.+.+++..
T Consensus       217 gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL  267 (301)
T 3u64_A          217 GGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRAL  267 (301)
T ss_dssp             TCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            499999999999998875222477888888888885 99999999999875

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.45  E-value=8.4  Score=28.08  Aligned_cols=95  Identities=8%  Similarity=-0.098  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--cccHHHHHHHHHhccchhhHHHHHHHHHHh-CCCCchHHHHHH--
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPD--KFTFPFVIKACIASLAIEKGKEVHGLAVKA-GFSRDMFVQSTL--  120 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~l--  120 (164)
                      +...+-..|.+.|+.+.|.+.|.++......+.  ...+-.+++.+...+++..+.......... .-.++...-+.+  
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            345677788899999999999999976543333  356777889999999999999999887543 112222222211  


Q ss_pred             --HHHHHhcCCchhHHHHhccc
Q 031208          121 --MDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus       121 --l~~~~~~~~~~~a~~~~~~m  140 (164)
                        .-.+...+++..|.+.|-+.
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~  234 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDS  234 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHH
Confidence              11123467888888777654

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=82.80  E-value=10  Score=26.79  Aligned_cols=132  Identities=16%  Similarity=0.016  Sum_probs=74.8

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHH----HHHHHcCCCCCcccHHHHHHHHH
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLY----NLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~----~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      .|.++..-|.+.+++++|.+++-.-           ...+.+.|....+-++-    +-..+.++++|..+..-|+..+.
T Consensus        37 ~~RTi~~Ry~~~k~y~eAidLL~~G-----------A~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~~  105 (336)
T 3lpz_A           37 ETRLVAARYSKQGNWAAAVDILASV-----------SQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCLR  105 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHH-----------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            4555666666666666666654321           22345556655544443    44456777888777777777776


Q ss_pred             hccchh-hHHHHHHHH----HHhCC--CCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHh
Q 031208           91 ASLAIE-KGKEVHGLA----VKAGF--SRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAA  157 (164)
Q Consensus        91 ~~~~~~-~a~~~~~~m----~~~g~--~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~  157 (164)
                      ....-+ .-..+++.+    .+.|-  .-++.....+-..|.+.+++.+|..-|=--..++...+..++.-+..
T Consensus       106 ~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~ilg~~~s~~~~a~mL~ew~~  179 (336)
T 3lpz_A          106 LFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLVLGTKESPEVLARMEYEWYK  179 (336)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHTTSCTTHHHHHHHHHHHHHH
T ss_pred             hCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHhcCCchHHHHHHHHHHHHH
Confidence            655321 222333333    33442  23567777888888999999998887732122223555444444433

>2d2s_A Exocyst complex component EXO84; tethering complex, EXO84P, endocytosis/exocytosis complex; 2.85A {Saccharomyces cerevisiae} SCOP: a.118.17.2

Probab=82.45  E-value=8.7  Score=25.62  Aligned_cols=89  Identities=9%  Similarity=-0.031  Sum_probs=53.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHH--cCCCC----CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHH
Q 031208           49 LMIRALTIDGSSLQALLLYNLMIC--NGFRP----DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMD  122 (164)
Q Consensus        49 ~li~~~~~~~~~~~a~~~~~~m~~--~~~~p----~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  122 (164)
                      --++.+....++++|++++++.+.  .++++    ........++.-.....-..+..+.+++..   .++...-...+.
T Consensus        23 deLDv~IA~r~feeAv~lle~~~~~l~~~~~~~~~~~~~~~~~l~~ki~eR~~~L~~~L~~~l~~---~~~~~~~r~~v~   99 (235)
T 2d2s_A           23 EEIDIELARLRFESAVETLLDIESQLEDLSERISDEELMLLNLISLKIEQRREAISSKLSQSILS---SNEIVHLKSGTE   99 (235)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHT---CSSHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHhCcccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHh---cCCHHHHHHHHH
Confidence            346677778888888888887743  22332    112333344444555555556666666632   455555666677


Q ss_pred             HHHhcCCchhHHHHhccc
Q 031208          123 LYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m  140 (164)
                      ...+.|+.++|.++|=+.
T Consensus       100 ~L~rLg~~~~A~~lfL~~  117 (235)
T 2d2s_A          100 NMIKLGLPEQALDLFLQN  117 (235)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHHHCCChhHHHHHHHHH
Confidence            788888888888877544

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=82.19  E-value=7  Score=24.37  Aligned_cols=101  Identities=14%  Similarity=-0.011  Sum_probs=48.5

Q ss_pred             CHHHHHHHHHHHhccCCc------HHHHHHHhccC---CCcH----hHHHHHHHH---HHhcCChhHHHHHHHHHHHcCC
Q 031208           12 DQLLVRKLLDLCSFYGKT------DHALLVFSQIR---CPHV----FTWNLMIRA---LTIDGSSLQALLLYNLMICNGF   75 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~------~~a~~~~~~~~---~~~~----~~~~~li~~---~~~~~~~~~a~~~~~~m~~~~~   75 (164)
                      |..+|=..+...-+.|++      +...++|++..   .|+.    ..|.-|---   +-..++++.|.++|+.+...+-
T Consensus        12 ~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~hK   91 (161)
T 4h7y_A           12 NPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCK   91 (161)
T ss_dssp             SHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhH
Confidence            566666666666666776      55556665432   1211    111111111   1222566777777777654311


Q ss_pred             CCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc
Q 031208           76 RPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD  113 (164)
Q Consensus        76 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~  113 (164)
                      +. ...|..-..-=.+.|+...|.+++......+-.|.
T Consensus        92 kF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~  128 (161)
T 4h7y_A           92 KF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPL  128 (161)
T ss_dssp             TB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCH
T ss_pred             HH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcH
Confidence            11 11222222222445666677777766665553333

>3ltj_A Alpharep-4; protein engineering, heat-like repeat, protein binding; 1.80A {Synthetic}

Probab=81.38  E-value=7.9  Score=24.39  Aligned_cols=139  Identities=9%  Similarity=-0.041  Sum_probs=71.6

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACI   90 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   90 (164)
                      +|..+-...+..+.+.+..+....+.+.+..+|...-...+.++++.+..+.. ..+.++..   .++...-...+.++.
T Consensus        26 ~~~~vr~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~~L~~~~~~~~~-~~L~~~l~---d~~~~vr~~a~~aL~  101 (201)
T 3ltj_A           26 DSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDERAV-EPLIKALK---DEDGWVRQSAAVALG  101 (201)
T ss_dssp             SCHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGGGH-HHHHHHTT---CSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHHHH-HHHHHHHc---CCCHHHHHHHHHHHH
Confidence            45555555566666666655566666666666666655666666666655333 33333332   255555556666666


Q ss_pred             hccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCCCcchHHHHHHHHHh
Q 031208           91 ASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVRSVVSWTTMISGLAA  157 (164)
Q Consensus        91 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~  157 (164)
                      +.++.+....+.+.+    -.++..+-...+.+..+.+..+....+.+-+..++..+-...+.++.+
T Consensus       102 ~~~~~~~~~~L~~~l----~d~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~A~~aL~~  164 (201)
T 3ltj_A          102 QIGDERAVEPLIKAL----KDEDWFVRIAAAFALGEIGDERAVEPLIKALKDEDGWVRQSAADALGE  164 (201)
T ss_dssp             HHCCGGGHHHHHHHT----TCSSHHHHHHHHHHHHHHTCGGGHHHHHHHTTCSSHHHHHHHHHHHHH
T ss_pred             HhCcHHHHHHHHHHH----cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            666544333333322    135555555556666666654433333333334444333444444433

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=80.90  E-value=7.2  Score=23.67  Aligned_cols=63  Identities=10%  Similarity=0.043  Sum_probs=47.6

Q ss_pred             HHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           68 NLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        68 ~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      +.+.+.|++++..= ..++..+...+..-.|.++++.+.+.+-..+..|.-..|+.+...|-+.
T Consensus        11 ~~l~~~g~r~T~qR-~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   73 (145)
T 2fe3_A           11 ETLKETGVRITPQR-HAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVK   73 (145)
T ss_dssp             HHHHHTTCCCCHHH-HHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHcCCCCCHHH-HHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEE
Confidence            44677888877643 4667777777777889999999988776677777777888888777654

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=80.41  E-value=7.2  Score=23.36  Aligned_cols=62  Identities=10%  Similarity=0.018  Sum_probs=46.5

Q ss_pred             HHHHcCCCCCcccHHHHHHHHHhcc-chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           69 LMICNGFRPDKFTFPFVIKACIASL-AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        69 ~m~~~~~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      .+.+.|++++..= ..++..+...+ ..-.|.++++.+.+.+-..+..|.-.-|+.+...|-+.
T Consensus         8 ~l~~~g~r~T~qR-~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   70 (136)
T 1mzb_A            8 ELRKAGLKVTLPR-VKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVV   70 (136)
T ss_dssp             HHHHTTCCCCHHH-HHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHCCCCCCHHH-HHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEE
Confidence            4677888877643 45677777766 67789999999988876777777777888888777655

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A

Probab=80.12  E-value=4.2  Score=24.30  Aligned_cols=68  Identities=7%  Similarity=0.045  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc--chhhHHHHHHHHHHhCCCCch
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL--AIEKGKEVHGLAVKAGFSRDM  114 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~--~~~~a~~~~~~m~~~g~~~~~  114 (164)
                      ..+.++.-|...|+.++|...++++..-.+. .......+..++-+.+  ..+....++..+.+.|+-+..
T Consensus         9 ki~~ll~EY~~~~D~~Ea~~cl~eL~~p~f~-~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~~~~~is~~   78 (129)
T 2nsz_A            9 EIDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITID   78 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhCCCccH-HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcCHH
Confidence            4567888899999999999999998532111 1233344444555443  235567777777777754443

---

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	164
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.16
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.01
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.84
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.66
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.58
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.48
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.47
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.39
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.32
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.22
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.2
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.16
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.15
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.14
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.13
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.11
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.09
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.9
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.88
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.83
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.83
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.73
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.72
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.71
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.68
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.63
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.57
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.53
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.48
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.48
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.46
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.45
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.43
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.39
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.1
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.09
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.09
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.95
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.89
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.85
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.76
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.6
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.37
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.37
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.96
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	95.63
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	95.58
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	95.28
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.04
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	94.98
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	94.18
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.9
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	93.9
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.5
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.31
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	92.73
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	86.52
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	85.43
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	85.37
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	83.21
d1u9pa1	36	Arc repressor {Salmonella bacteriophage P22 [TaxId	82.89

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=1.1e-09  Score=75.73  Aligned_cols=151  Identities=12%  Similarity=0.032  Sum_probs=108.0

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      +...+..+-..+...|++++|...++...   ..+...+..+-..+.+.|++++|...|++..+.. +-+...+..+...
T Consensus       202 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  280 (388)
T d1w3ba_         202 FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANA  280 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHH
T ss_pred             cHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34566677777778888888888777654   3455666777777788888888888888876642 2234567777778


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      +...|+.++|.+.++...... +.+...+..+...|.+.|++++|.+.|++..  .| +..+|..+-..|.+.|++++|
T Consensus       281 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A  358 (388)
T d1w3ba_         281 LKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEA  358 (388)
T ss_dssp             HHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHH
T ss_pred             HHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            888888888888887776554 4556677777778888888888888887654  33 455677777788888877654

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=8.3e-09  Score=71.22  Aligned_cols=148  Identities=14%  Similarity=0.044  Sum_probs=122.8

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      .+...+..+-..+.+.|++++|...|++..  . .+..+|..+-..+...|++++|.+.++...... +.+...+..+..
T Consensus       235 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  313 (388)
T d1w3ba_         235 NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLAN  313 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHH
Confidence            456667778889999999999999999764  3 456788899999999999999999999987653 456678888999


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCC
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGD  160 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~  160 (164)
                      .+.+.|++++|...+++..+.. +.+...+..+-..|.+.|++++|.+.|++..  .| +...|..+-..|.+.|+
T Consensus       314 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         314 IKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            9999999999999999887543 2346678888999999999999999999765  44 56688999898888775

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=7.1e-08  Score=65.64  Aligned_cols=152  Identities=11%  Similarity=-0.052  Sum_probs=110.2

Q ss_pred             CHHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--------------
Q 031208           12 DQLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNG--------------   74 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--------------   74 (164)
                      +...|..+-..+...|+++.|...|++..  .| +...|..+...+...|++++|.+.+.+.....              
T Consensus        52 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  131 (323)
T d1fcha_          52 HMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGA  131 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC------
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhh
Confidence            46678888888888999999998888765  23 56677778888888888888888887764321              


Q ss_pred             ---------------------------------CCC---CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           75 ---------------------------------FRP---DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        75 ---------------------------------~~p---~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                                                       ..|   +...+..+-..+...|++++|...+++..... +-+...|.
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~  210 (323)
T d1fcha_         132 GGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWN  210 (323)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             hhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchh
Confidence                                             112   22344555666777788888888888877654 23466777


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .+-..|.+.|++++|.+.|++..  .| +..+|..+-..|.+.|++++|
T Consensus       211 ~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A  259 (323)
T d1fcha_         211 KLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREA  259 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             hhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHH
Confidence            77888888888888888888764  33 556777888888888877654

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.66  E-value=2e-07  Score=63.38  Aligned_cols=150  Identities=10%  Similarity=0.078  Sum_probs=111.6

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccCC--C--cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIRC--P--HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFV   85 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   85 (164)
                      +.+...|........+.|+.+.|..+|+....  |  ....|...+....+.|+.+.|.++|.+..+.+. .+...|...
T Consensus        96 p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~-~~~~~~~~~  174 (308)
T d2onda1          96 KKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTA  174 (308)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CcHHHHHHH
Confidence            33566788888888899999999999998642  3  245789999999999999999999999877542 233333333


Q ss_pred             HH-HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC-----CC--CcchHHHHHHHHHh
Q 031208           86 IK-ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR-----VR--SVVSWTTMISGLAA  157 (164)
Q Consensus        86 l~-~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~-----~~--~~~~~~~li~~~~~  157 (164)
                      .. -+...|+.+.|..+++...+.. +.+...|...++...+.|+++.|..+|++..     .|  ....|...+.--..
T Consensus       175 a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~  253 (308)
T d2onda1         175 ALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESN  253 (308)
T ss_dssp             HHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHH
Confidence            22 2344578999999999998763 4567889999999999999999999999753     12  22467777665556


Q ss_pred             cCCC
Q 031208          158 SGDL  161 (164)
Q Consensus       158 ~g~~  161 (164)
                      .|+.
T Consensus       254 ~G~~  257 (308)
T d2onda1         254 IGDL  257 (308)
T ss_dssp             HSCH
T ss_pred             cCCH
Confidence            5654

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=6e-07  Score=60.91  Aligned_cols=142  Identities=17%  Similarity=0.152  Sum_probs=111.6

Q ss_pred             HHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchh
Q 031208           21 DLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        21 ~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~   96 (164)
                      ..+.+.|++++|...|+...  .| +..+|..+-..+...|++++|...|.+..+.  .| +...+..+...+...|+++
T Consensus        27 ~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~  104 (323)
T d1fcha_          27 LRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLEL--KPDNQTALMALAVSFTNESLQR  104 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcc--cccccccccccccccccccccc
Confidence            35778999999999999875  34 5778999999999999999999999998764  35 4567777888899999999


Q ss_pred             hHHHHHHHHHHhC-----------------------------------------------C---CCchHHHHHHHHHHHh
Q 031208           97 KGKEVHGLAVKAG-----------------------------------------------F---SRDMFVQSTLMDLYLK  126 (164)
Q Consensus        97 ~a~~~~~~m~~~g-----------------------------------------------~---~~~~~~~~~ll~~~~~  126 (164)
                      +|.+.+++.....                                               .   .++...+..+-..+.+
T Consensus       105 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~  184 (323)
T d1fcha_         105 QACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNL  184 (323)
T ss_dssp             HHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHH
T ss_pred             ccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHH
Confidence            9888877665321                                               0   1234556667778888


Q ss_pred             cCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCCCCC
Q 031208          127 CGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDLDAA  164 (164)
Q Consensus       127 ~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~~~A  164 (164)
                      .|++++|...|++..  .| +..+|..+-..|.+.|++++|
T Consensus       185 ~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A  225 (323)
T d1fcha_         185 SGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEA  225 (323)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhhhhcccccccccccccccchhhhhhcccccccchhH
Confidence            999999999998764  33 567888888999999988764

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=5.5e-06  Score=56.45  Aligned_cols=147  Identities=5%  Similarity=-0.054  Sum_probs=113.5

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcC-ChhHHHHHHHHHHHcCCCCCcccHHHHHHH
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDG-SSLQALLLYNLMICNGFRPDKFTFPFVIKA   88 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   88 (164)
                      ...++-+-..+.+.+..++|..++++..  .| +...|+..-.++...+ ++++|+..+++..+.. +-+..+|..+-..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~  121 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHH
Confidence            4455566667778889999999999876  34 5567887777777766 5899999999987643 2356688888888


Q ss_pred             HHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHHHHhcCCC
Q 031208           89 CIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISGLAASGDL  161 (164)
Q Consensus        89 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~g~~  161 (164)
                      +.+.|++++|...++.+.+.. +.+...|..+...+.+.|++++|.+.|++..  .| +...|+.+-..+.+.+..
T Consensus       122 ~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~  196 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGY  196 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCS
T ss_pred             HHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHcccc
Confidence            999999999999999988764 4567888899999999999999999998876  33 566777766666665554

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=1.2e-05  Score=50.86  Aligned_cols=125  Identities=13%  Similarity=-0.074  Sum_probs=99.9

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLA   94 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~   94 (164)
                      .|+. -..+...|+++.|.+.|+....|+..+|..+=.++...|++++|.+.|++..+.. +-+...|..+-.++.+.|+
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~   85 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   85 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhcc
Confidence            3443 3355679999999999999988999999989999999999999999999998743 2345688888899999999


Q ss_pred             hhhHHHHHHHHHHhC------------CC--Cc-hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           95 IEKGKEVHGLAVKAG------------FS--RD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        95 ~~~a~~~~~~m~~~g------------~~--~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +++|...|++.....            ..  ++ ..++..+-.+|.+.|++++|.+.|....
T Consensus        86 ~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~  147 (192)
T d1hh8a_          86 YDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALAT  147 (192)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999999999876531            11  11 2345566778999999999999998664

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.39  E-value=2.1e-06  Score=58.20  Aligned_cols=134  Identities=12%  Similarity=0.010  Sum_probs=100.7

Q ss_pred             cHHHHHHHhccC----CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHH
Q 031208           29 TDHALLVFSQIR----CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGL  104 (164)
Q Consensus        29 ~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  104 (164)
                      .+.|..+|++..    ..+...|........+.|+++.|..+|+++...........|...+..+.+.|+++.|.++++.
T Consensus        80 ~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~  159 (308)
T d2onda1          80 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  159 (308)
T ss_dssp             HHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            467888888753    2355678888888899999999999999998753222234688999999999999999999999


Q ss_pred             HHHhCCCCchHHHHHHHH-HHHhcCCchhHHHHhcccCC---CCcchHHHHHHHHHhcCCCCC
Q 031208          105 AVKAGFSRDMFVQSTLMD-LYLKCGDVDGGRKMFDKMRV---RSVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       105 m~~~g~~~~~~~~~~ll~-~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~g~~~~  163 (164)
                      ..+.+- .+...|-.... -+...|+.+.|..+|+.+..   .+...|...+.-+.+.|++++
T Consensus       160 al~~~~-~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~  221 (308)
T d2onda1         160 AREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNN  221 (308)
T ss_dssp             HHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHhCC-CcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHH
Confidence            876652 23333433333 24456899999999998873   356789999998888888764

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.32  E-value=9.7e-06  Score=47.01  Aligned_cols=88  Identities=11%  Similarity=-0.073  Sum_probs=60.3

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           52 RALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      ..+.+.|++++|...|++..+.. +-+...|..+-.++.+.|++++|...+....+.. +.+...|..+-.+|.+.|+++
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHH
Confidence            34566677777777777776542 2344567777777777777777777777777664 445666777777777777777


Q ss_pred             hHHHHhcccC
Q 031208          132 GGRKMFDKMR  141 (164)
Q Consensus       132 ~a~~~~~~m~  141 (164)
                      +|...|++..
T Consensus        89 ~A~~~~~~a~   98 (117)
T d1elwa_          89 EAKRTYEEGL   98 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            7777777654

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.22  E-value=1.6e-05  Score=48.45  Aligned_cols=89  Identities=11%  Similarity=-0.152  Sum_probs=74.9

Q ss_pred             HHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh
Q 031208           20 LDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      =..|.+.|+++.|...|++..   ..+...|..+-..+...|++++|...|.+..+.. +-+...|..+..++...|+++
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~   95 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFR   95 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHH
Confidence            346778999999999999876   3467788888899999999999999999997753 334568888999999999999


Q ss_pred             hHHHHHHHHHHhC
Q 031208           97 KGKEVHGLAVKAG  109 (164)
Q Consensus        97 ~a~~~~~~m~~~g  109 (164)
                      +|...+++..+..
T Consensus        96 eA~~~~~~a~~~~  108 (159)
T d1a17a_          96 AALRDYETVVKVK  108 (159)
T ss_dssp             HHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999998775

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.20  E-value=1.3e-05  Score=50.34  Aligned_cols=97  Identities=8%  Similarity=-0.123  Sum_probs=81.3

Q ss_pred             CCCHHHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHH
Q 031208           10 SNDQLLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFV   85 (164)
Q Consensus        10 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~l   85 (164)
                      +|+...+...=..+.+.|+++.|...|++..  . .+...|..+-.+|.+.|++++|...|.+..+  +.| +...|..+
T Consensus         1 ~~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~l   78 (201)
T d2c2la1           1 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFFL   78 (201)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHHH
Confidence            4667777777778999999999999998765  3 4677888899999999999999999999976  456 45678889


Q ss_pred             HHHHHhccchhhHHHHHHHHHHh
Q 031208           86 IKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      -.++.+.|++++|...+++..+.
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh
Confidence            99999999999999999987653

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.16  E-value=5.1e-05  Score=49.36  Aligned_cols=94  Identities=15%  Similarity=-0.081  Sum_probs=78.3

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHH
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKAC   89 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~   89 (164)
                      .++..+=..|.+.|++++|...|++..  . .+..+|..+-.++.+.|++++|...|++..+.  .| +...+..+-..+
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~  115 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIAL  115 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH--HhhhhhhHHHHHHHH
Confidence            355555668888999999999999876  3 46778999999999999999999999999874  35 455778888899


Q ss_pred             HhccchhhHHHHHHHHHHhC
Q 031208           90 IASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ...|++++|...++...+..
T Consensus       116 ~~~g~~~~A~~~~~~al~~~  135 (259)
T d1xnfa_         116 YYGGRDKLAQDDLLAFYQDD  135 (259)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhhHHHHHHHHHHHHhhc
Confidence            99999999999999888764

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.15  E-value=2.1e-05  Score=49.41  Aligned_cols=95  Identities=9%  Similarity=-0.053  Sum_probs=60.4

Q ss_pred             cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCC-chHHHHHHH
Q 031208           43 HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSR-DMFVQSTLM  121 (164)
Q Consensus        43 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll  121 (164)
                      +.......=..+.+.|++++|...|.+..... +-+...|..+-.+|.+.|+++.|...++...+.  .| +...|..+-
T Consensus         3 ~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~lg   79 (201)
T d2c2la1           3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLG   79 (201)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHHH
Confidence            33334444456667777777777777765542 234556666677777777777777777776543  34 355666677


Q ss_pred             HHHHhcCCchhHHHHhccc
Q 031208          122 DLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m  140 (164)
                      .+|.+.|++++|...|++.
T Consensus        80 ~~~~~l~~~~~A~~~~~~a   98 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRA   98 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHH
Confidence            7777777777777777654

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.14  E-value=6.5e-05  Score=50.96  Aligned_cols=143  Identities=8%  Similarity=-0.037  Sum_probs=97.5

Q ss_pred             CHHHHHHHHHHHhccC-CcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHH
Q 031208           12 DQLLVRKLLDLCSFYG-KTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIK   87 (164)
Q Consensus        12 ~~~~~~~li~~~~~~~-~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   87 (164)
                      +...|+..-..+...| ++++|...++...  . .+..+|..+-..+.+.|++++|+..++++.+.. +-+...|..+..
T Consensus        76 ~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~  154 (315)
T d2h6fa1          76 NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQW  154 (315)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHH
Confidence            3446666666666665 4788888888765  2 456788888888888899999999988887642 335678888888


Q ss_pred             HHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCC------chhHHHHhcccC--CC-CcchHHHHHHHHH
Q 031208           88 ACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGD------VDGGRKMFDKMR--VR-SVVSWTTMISGLA  156 (164)
Q Consensus        88 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~------~~~a~~~~~~m~--~~-~~~~~~~li~~~~  156 (164)
                      .+.+.|++++|.+.++...+.. +.+...|+.+-..+.+.+.      +++|.+.+....  .| +...|+.+-..+.
T Consensus       155 ~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~  231 (315)
T d2h6fa1         155 VIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQ  231 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHT
T ss_pred             HHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHH
Confidence            8888888888888888888765 3345566666555555555      345555555443  33 4555555544443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=2e-05  Score=48.02  Aligned_cols=89  Identities=7%  Similarity=-0.035  Sum_probs=77.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCc
Q 031208           51 IRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDV  130 (164)
Q Consensus        51 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  130 (164)
                      =..|.+.|++++|...|++..+.. +-+...|..+-..+...|++++|...++...+.. +.+...|..+..+|...|++
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~   94 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKF   94 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCH
Confidence            446789999999999999998754 3356788888999999999999999999998875 45668899999999999999


Q ss_pred             hhHHHHhcccC
Q 031208          131 DGGRKMFDKMR  141 (164)
Q Consensus       131 ~~a~~~~~~m~  141 (164)
                      ++|...|++..
T Consensus        95 ~eA~~~~~~a~  105 (159)
T d1a17a_          95 RAALRDYETVV  105 (159)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999876

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.11  E-value=1.3e-05  Score=46.13  Aligned_cols=84  Identities=8%  Similarity=-0.035  Sum_probs=58.0

Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           53 ALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      .+.+.|++++|...|++.....  | +...|..+-.++.+.|++++|...++...+.. +.+...+..+-..|...|+++
T Consensus        25 ~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~  101 (112)
T d1hxia_          25 SMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNAN  101 (112)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHH
Confidence            4566777777777777776542  4 45566667777777777777777777766654 334667777777777777777


Q ss_pred             hHHHHhcc
Q 031208          132 GGRKMFDK  139 (164)
Q Consensus       132 ~a~~~~~~  139 (164)
                      +|.+.|++
T Consensus       102 ~A~~~l~~  109 (112)
T d1hxia_         102 AALASLRA  109 (112)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77777664

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=5e-05  Score=43.85  Aligned_cols=92  Identities=13%  Similarity=-0.072  Sum_probs=78.1

Q ss_pred             HHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh
Q 031208           20 LDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      =..+.+.|++++|..+|++..  . .+...|..+-.++.+.|++++|...+.+..+.. +.+...|..+-.++...|+++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHH
Confidence            346778999999999999875  3 467789999999999999999999999998754 446678899999999999999


Q ss_pred             hHHHHHHHHHHhCCCCch
Q 031208           97 KGKEVHGLAVKAGFSRDM  114 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~  114 (164)
                      +|...++...+.  .|+.
T Consensus        89 ~A~~~~~~a~~~--~p~~  104 (117)
T d1elwa_          89 EAKRTYEEGLKH--EANN  104 (117)
T ss_dssp             HHHHHHHHHHTT--CTTC
T ss_pred             HHHHHHHHHHHh--CCCC
Confidence            999999998865  4543

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.90  E-value=4.9e-05  Score=43.56  Aligned_cols=86  Identities=9%  Similarity=-0.060  Sum_probs=73.4

Q ss_pred             HHHHhccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh
Q 031208           20 LDLCSFYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE   96 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~   96 (164)
                      -..+.+.|++++|...|++..  .| +...|..+-.++.+.|++++|...|++..+.. +-+...+..+-..|...|+.+
T Consensus        23 g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~  101 (112)
T d1hxia_          23 GLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNAN  101 (112)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHH
Confidence            446778999999999999876  35 67889999999999999999999999987753 335678888999999999999


Q ss_pred             hHHHHHHHHH
Q 031208           97 KGKEVHGLAV  106 (164)
Q Consensus        97 ~a~~~~~~m~  106 (164)
                      +|.+.+++..
T Consensus       102 ~A~~~l~~~l  111 (112)
T d1hxia_         102 AALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998753

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.88  E-value=0.00021  Score=46.34  Aligned_cols=94  Identities=7%  Similarity=-0.122  Sum_probs=79.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      .+|..+=..|.+.|++++|...|++..+.  .| +..+|..+-.++.+.|++++|...|++..+.. +.+...+..+...
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~  114 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIA  114 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-hhhhhhHHHHHHH
Confidence            45666667889999999999999999874  45 55688899999999999999999999998875 3346678888899


Q ss_pred             HHhcCCchhHHHHhcccC
Q 031208          124 YLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~  141 (164)
                      |...|++++|...|+...
T Consensus       115 ~~~~g~~~~A~~~~~~al  132 (259)
T d1xnfa_         115 LYYGGRDKLAQDDLLAFY  132 (259)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            999999999999998765

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=4.8e-05  Score=44.40  Aligned_cols=90  Identities=12%  Similarity=-0.032  Sum_probs=37.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhcc---chhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHH
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASL---AIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYL  125 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~  125 (164)
                      +++.+...+++++|.+.|++....+ +.+..++..+-.++.+.+   +.++|..++++.....-.|+ ...+..+-.+|.
T Consensus         5 l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~   83 (122)
T d1nzna_           5 VLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNY   83 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHH
Confidence            3444444445555555555544422 122333334444444322   22234444444433321121 113334444444


Q ss_pred             hcCCchhHHHHhccc
Q 031208          126 KCGDVDGGRKMFDKM  140 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m  140 (164)
                      +.|++++|.+.|++.
T Consensus        84 ~~g~~~~A~~~~~~a   98 (122)
T d1nzna_          84 RLKEYEKALKYVRGL   98 (122)
T ss_dssp             HTTCHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHH
Confidence            555555555555444

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=0.00079  Score=42.12  Aligned_cols=118  Identities=8%  Similarity=-0.122  Sum_probs=89.4

Q ss_pred             CCCCHHHHHHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-----------
Q 031208            9 LSNDQLLVRKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGSSLQALLLYNLMICNG-----------   74 (164)
Q Consensus         9 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----------   74 (164)
                      .+|++.+|.-+=..+.+.|++++|.+.|++..   ..+...|..+-.++.+.|++++|..-|++.....           
T Consensus        32 ~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~  111 (192)
T d1hh8a_          32 QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKIL  111 (192)
T ss_dssp             SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGG
T ss_pred             CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHh
Confidence            46788888888889999999999999999876   3467788889999999999999999999976431           


Q ss_pred             -CCCCc---ccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Q 031208           75 -FRPDK---FTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLK  126 (164)
Q Consensus        75 -~~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  126 (164)
                       .....   .++..+-.++.+.|++++|.+.+....+....+........+..+.+
T Consensus       112 ~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~~~~~~Al~~~~~  167 (192)
T d1hh8a_         112 GLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWK  167 (192)
T ss_dssp             TBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHHHHHHHHHHT
T ss_pred             hhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHh
Confidence             11111   23445667889999999999999988776655555555555554443

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.73  E-value=6.1e-05  Score=50.34  Aligned_cols=128  Identities=13%  Similarity=-0.082  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCC-CCc
Q 031208           14 LLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALTIDGSSLQALLLYNLMICN----GFR-PDK   79 (164)
Q Consensus        14 ~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~-p~~   79 (164)
                      ..|...-..|...|++++|.+.|.+...     .+    ..+|..+-.+|.+.|++++|.+.+++....    |.. ...
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  117 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHH
Confidence            3577778888889999999999987652     12    357888889999999999999999986432    211 113


Q ss_pred             ccHHHHHHHHH-hccchhhHHHHHHHHHHh----CCCC-chHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           80 FTFPFVIKACI-ASLAIEKGKEVHGLAVKA----GFSR-DMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        80 ~t~~~ll~~~~-~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .++..+...|. ..|+++.|.+.+++..+.    +-.+ -..++..+...|.+.|++++|.+.|++..
T Consensus       118 ~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~  185 (290)
T d1qqea_         118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLI  185 (290)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHH
Confidence            44555556664 469999999999876542    2222 13467788899999999999999998865

>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=97.72  E-value=0.00026  Score=44.02  Aligned_cols=104  Identities=11%  Similarity=-0.055  Sum_probs=79.7

Q ss_pred             CHHHHHHHHH---HHhccCCcHHHHHHHhccCC-------------------------CcHhHHHHHHHHHHhcCChhHH
Q 031208           12 DQLLVRKLLD---LCSFYGKTDHALLVFSQIRC-------------------------PHVFTWNLMIRALTIDGSSLQA   63 (164)
Q Consensus        12 ~~~~~~~li~---~~~~~~~~~~a~~~~~~~~~-------------------------~~~~~~~~li~~~~~~~~~~~a   63 (164)
                      |...|.....   .....|++++|...|..-..                         .....+..+...+.+.|++++|
T Consensus         7 D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~A   86 (179)
T d2ff4a2           7 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAV   86 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHH
Confidence            4444555443   56678999999888776431                         0124577788889999999999


Q ss_pred             HHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHH-----hCCCCchHH
Q 031208           64 LLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVK-----AGFSRDMFV  116 (164)
Q Consensus        64 ~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~-----~g~~~~~~~  116 (164)
                      ...+++..+.. +-+...|..++.++.+.|+..+|.+.|++..+     .|+.|+..+
T Consensus        87 l~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          87 IAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            99999997753 44778999999999999999999999998744     589998755

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.71  E-value=0.00012  Score=42.68  Aligned_cols=102  Identities=9%  Similarity=-0.065  Sum_probs=77.1

Q ss_pred             HHHHHHHhccCCcHHHHHHHhccC---CCcHhHHHHHHHHHHhcCC---hhHHHHHHHHHHHcCCCCCc-ccHHHHHHHH
Q 031208           17 RKLLDLCSFYGKTDHALLVFSQIR---CPHVFTWNLMIRALTIDGS---SLQALLLYNLMICNGFRPDK-FTFPFVIKAC   89 (164)
Q Consensus        17 ~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~   89 (164)
                      ..+++.+...+++++|.+.|+...   ..+..++..+-.++.+.++   .++|..+|++.......|+. ..+..+-.+|
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            457788888999999999999876   2466677777777777554   45699999998775533432 3667788999


Q ss_pred             HhccchhhHHHHHHHHHHhCCCCchHHHHHH
Q 031208           90 IASLAIEKGKEVHGLAVKAGFSRDMFVQSTL  120 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  120 (164)
                      .+.|++++|.+.+++..+.  .|+-.-...+
T Consensus        83 ~~~g~~~~A~~~~~~aL~~--~P~~~~A~~l  111 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQT--EPQNNQAKEL  111 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHHh--CcCCHHHHHH
Confidence            9999999999999999886  4664443333

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.68  E-value=0.00071  Score=41.45  Aligned_cols=89  Identities=12%  Similarity=-0.048  Sum_probs=63.8

Q ss_pred             HHHHhccCCcHHHHHHHhccCC-----C-------------cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCccc
Q 031208           20 LDLCSFYGKTDHALLVFSQIRC-----P-------------HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFT   81 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~~-----~-------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   81 (164)
                      =..+.+.|+++.|...|.....     +             ...+|+-+-.+|.+.|++++|...+++..... +-+...
T Consensus        20 G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a   98 (170)
T d1p5qa1          20 GTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKG   98 (170)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhh
Confidence            3467788888888888875531     0             12345556677788888888888888877643 225667


Q ss_pred             HHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           82 FPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        82 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      +..+-.++...|++++|...+++..+..
T Consensus        99 ~~~~g~~~~~~g~~~~A~~~~~~al~l~  126 (170)
T d1p5qa1          99 LSRRGEAHLAVNDFELARADFQKVLQLY  126 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            7777788888888888888888887653

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=0.00021  Score=41.77  Aligned_cols=91  Identities=11%  Similarity=-0.002  Sum_probs=65.1

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhC---CCCc---hHHHHHHHHH
Q 031208           50 MIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAG---FSRD---MFVQSTLMDL  123 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g---~~~~---~~~~~~ll~~  123 (164)
                      +=..+.+.|++++|+..|.+..+.+ +.+...+..+-.+|.+.|++++|.+.+++..+..   ..+.   ..+|..+-..
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~   88 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNS   88 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHH
Confidence            3346777888888888888887653 2356677778888888888888888888876532   1111   2356667777


Q ss_pred             HHhcCCchhHHHHhcccC
Q 031208          124 YLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~  141 (164)
                      +...+++++|.+.|+.-.
T Consensus        89 ~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          89 YFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHH
Confidence            788888999988887643

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.57  E-value=0.0019  Score=38.65  Aligned_cols=55  Identities=9%  Similarity=0.012  Sum_probs=25.4

Q ss_pred             HHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhccc
Q 031208           85 VIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKM  140 (164)
Q Consensus        85 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  140 (164)
                      +..+|.+.|++++|...++...+.. +.+...|..+..+|...|++++|...|+..
T Consensus        73 la~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~a  127 (153)
T d2fbna1          73 LATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKA  127 (153)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHH
Confidence            4444444444544444444444432 223444444444444555555555444443

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.53  E-value=0.0012  Score=40.16  Aligned_cols=105  Identities=6%  Similarity=-0.137  Sum_probs=65.0

Q ss_pred             HHHHHHhccCCcHHHHHHHhccCC-------------------CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC
Q 031208           18 KLLDLCSFYGKTDHALLVFSQIRC-------------------PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD   78 (164)
Q Consensus        18 ~li~~~~~~~~~~~a~~~~~~~~~-------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~   78 (164)
                      ..-..+.+.|+++.|...|++..+                   .+...|..+-.++.+.|++++|+..+.+..+.. +.+
T Consensus        32 ~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~  110 (169)
T d1ihga1          32 NIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSN  110 (169)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhh
Confidence            344556677888888777765421                   122345555666777777777777777776542 224


Q ss_pred             cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHH
Q 031208           79 KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLY  124 (164)
Q Consensus        79 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  124 (164)
                      ...|..+-.++...|++++|.+.++...+.. +.+......+-.+.
T Consensus       111 ~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-p~n~~~~~~l~~~~  155 (169)
T d1ihga1         111 TKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVK  155 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            4566777777777777777777777777653 22344444444433

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.48  E-value=0.0007  Score=41.47  Aligned_cols=88  Identities=18%  Similarity=0.103  Sum_probs=65.6

Q ss_pred             HHHhcCChhHHHHHHHHHHHcC-CCC-------------CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHH
Q 031208           53 ALTIDGSSLQALLLYNLMICNG-FRP-------------DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQS  118 (164)
Q Consensus        53 ~~~~~~~~~~a~~~~~~m~~~~-~~p-------------~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  118 (164)
                      .+.+.|++++|...|.+....- ..+             ...+|+-+..+|.+.|++++|...++...+.. +.++..+.
T Consensus        22 ~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~~  100 (170)
T d1p5qa1          22 VYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLS  100 (170)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhhH
Confidence            4566778888888887765421 001             12466677788888999999999998888775 44677888


Q ss_pred             HHHHHHHhcCCchhHHHHhcccC
Q 031208          119 TLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       119 ~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+-.+|...|++++|...|++..
T Consensus       101 ~~g~~~~~~g~~~~A~~~~~~al  123 (170)
T d1p5qa1         101 RRGEAHLAVNDFELARADFQKVL  123 (170)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHH
Confidence            88888999999999999998875

>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=97.48  E-value=0.0016  Score=40.30  Aligned_cols=89  Identities=11%  Similarity=-0.029  Sum_probs=73.0

Q ss_pred             HHHHhcCChhHHHHHHHHHHHc--CCC-CCc------------------ccHHHHHHHHHhccchhhHHHHHHHHHHhCC
Q 031208           52 RALTIDGSSLQALLLYNLMICN--GFR-PDK------------------FTFPFVIKACIASLAIEKGKEVHGLAVKAGF  110 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~--~~~-p~~------------------~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~  110 (164)
                      ......|++++|.+.|.+-...  |-. ++.                  ..+..+...+.+.|++++|...++...+.. 
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~al~~~-   97 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEH-   97 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhC-
Confidence            4568889999999999998653  211 111                  245677888999999999999999998876 


Q ss_pred             CCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          111 SRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       111 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      +-++..|..++.+|.+.|+.++|.+.|++..
T Consensus        98 P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~  128 (179)
T d2ff4a2          98 PYREPLWTQLITAYYLSDRQSDALGAYRRVK  128 (179)
T ss_dssp             TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            5689999999999999999999999999863

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.46  E-value=0.0015  Score=43.35  Aligned_cols=145  Identities=8%  Similarity=-0.112  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccCC-----Cc----HhHHHHHHHHHH-hcCChhHHHHHHHHHHH----cCCCCC
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIRC-----PH----VFTWNLMIRALT-IDGSSLQALLLYNLMIC----NGFRPD   78 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~-~~~~~~~a~~~~~~m~~----~~~~p~   78 (164)
                      ..+|..+-.+|.+.|++++|.+.++....     .+    ...+..+...|- ..|++++|.+.+.+...    .+-++.
T Consensus        77 a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~  156 (290)
T d1qqea_          77 GNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVAL  156 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhh
Confidence            35677788889999999999999887541     12    344555665664 46999999999998743    222221


Q ss_pred             -cccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-----h-HHHHHHHHHHHhcCCchhHHHHhcccCCCC-------
Q 031208           79 -KFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-----M-FVQSTLMDLYLKCGDVDGGRKMFDKMRVRS-------  144 (164)
Q Consensus        79 -~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-----~-~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-------  144 (164)
                       ..++..+...+...|++++|...+++.........     . ..+......+...|+++.|.+.|++..+-+       
T Consensus       157 ~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sr  236 (290)
T d1qqea_         157 SNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSR  236 (290)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC--------
T ss_pred             hhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchH
Confidence             34577788999999999999999999876532211     1 223445556778899999999999886322       


Q ss_pred             -cchHHHHHHHHHh
Q 031208          145 -VVSWTTMISGLAA  157 (164)
Q Consensus       145 -~~~~~~li~~~~~  157 (164)
                       ......++.++..
T Consensus       237 e~~~l~~l~~a~~~  250 (290)
T d1qqea_         237 ESNFLKSLIDAVNE  250 (290)
T ss_dssp             -HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence             1234556666544

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.45  E-value=0.0062  Score=40.87  Aligned_cols=147  Identities=12%  Similarity=-0.009  Sum_probs=99.9

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccC--CCcHh-HHHH---HHHHHHh-------cCChhHHHHHHHHHHHcCCCCCcccH
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIR--CPHVF-TWNL---MIRALTI-------DGSSLQALLLYNLMICNGFRPDKFTF   82 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~-~~~~---li~~~~~-------~~~~~~a~~~~~~m~~~~~~p~~~t~   82 (164)
                      +..++....+.+..++|.+++++..  .|+.. .|+.   ++.....       .|++++|+.+++...+.. +-+...|
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~  110 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTW  110 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHH
Confidence            4444444444555689999999875  56543 3433   2333333       345788999999987643 2244556


Q ss_pred             HHHHHHHHhcc--chhhHHHHHHHHHHhCCCCchHHHHHHH-HHHHhcCCchhHHHHhcccCC--C-CcchHHHHHHHHH
Q 031208           83 PFVIKACIASL--AIEKGKEVHGLAVKAGFSRDMFVQSTLM-DLYLKCGDVDGGRKMFDKMRV--R-SVVSWTTMISGLA  156 (164)
Q Consensus        83 ~~ll~~~~~~~--~~~~a~~~~~~m~~~g~~~~~~~~~~ll-~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~  156 (164)
                      ..+..++...+  +.+++...+....+.. +++...+.... ..+...+..+.|...++...+  | +...|+.+-..+.
T Consensus       111 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~  189 (334)
T d1dcea1         111 HHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLP  189 (334)
T ss_dssp             HHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHH
T ss_pred             HHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            66666666665  4788999999888764 34455555444 566678999999999998873  3 6678888999999


Q ss_pred             hcCCCCCC
Q 031208          157 ASGDLDAA  164 (164)
Q Consensus       157 ~~g~~~~A  164 (164)
                      +.|++++|
T Consensus       190 ~~~~~~~A  197 (334)
T d1dcea1         190 QLHPQPDS  197 (334)
T ss_dssp             HHSCCCCS
T ss_pred             HhcCHHHH
Confidence            99998875

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.43  E-value=0.00046  Score=40.23  Aligned_cols=91  Identities=9%  Similarity=-0.043  Sum_probs=69.9

Q ss_pred             HHHHHhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CC-----cccHHHHHHHH
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFR-PD-----KFTFPFVIKAC   89 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~-----~~t~~~ll~~~   89 (164)
                      +=..+.+.|++++|...|++..  . .+...|..+-.+|.+.|++++|...+.+..+..-. +.     ..+|..+-..+
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~   89 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSY   89 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHH
Confidence            3356888999999999999876  3 46788999999999999999999999998653211 11     12455566677


Q ss_pred             HhccchhhHHHHHHHHHHhC
Q 031208           90 IASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        90 ~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ...+++++|...+.......
T Consensus        90 ~~~~~~~~A~~~~~kal~~~  109 (128)
T d1elra_          90 FKEEKYKDAIHFYNKSLAEH  109 (128)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC
T ss_pred             HHhCCHHHHHHHHHHHHhcC
Confidence            77889999999998876653

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.39  E-value=0.0017  Score=38.89  Aligned_cols=90  Identities=8%  Similarity=-0.116  Sum_probs=72.6

Q ss_pred             HHHHHhccCCcHHHHHHHhccC--------CC-----------cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc
Q 031208           19 LLDLCSFYGKTDHALLVFSQIR--------CP-----------HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK   79 (164)
Q Consensus        19 li~~~~~~~~~~~a~~~~~~~~--------~~-----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   79 (164)
                      -=..+.+.|++..|...|....        .+           ...+|+.+-.+|.+.|++++|++.+.+..... +.+.
T Consensus        23 ~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~  101 (153)
T d2fbna1          23 EGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNV  101 (153)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-chhh
Confidence            3356778899999999887643        11           12456778888999999999999999987753 3466


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ..|..+..++...|++++|...++...+..
T Consensus       102 ka~~~~g~~~~~lg~~~~A~~~~~~al~l~  131 (153)
T d2fbna1         102 KALYKLGVANMYFGFLEEAKENLYKAASLN  131 (153)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             hhhHHhHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            799999999999999999999999988774

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.10  E-value=0.0069  Score=36.66  Aligned_cols=92  Identities=10%  Similarity=-0.050  Sum_probs=65.2

Q ss_pred             HHHHHHHHhccCCcHHHHHHHhccCC-------C-----------cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 031208           16 VRKLLDLCSFYGKTDHALLVFSQIRC-------P-----------HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRP   77 (164)
Q Consensus        16 ~~~li~~~~~~~~~~~a~~~~~~~~~-------~-----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   77 (164)
                      +...=..+.+.|+++.|...|+....       .           ....|+-+-.+|.+.|++++|+..+++..... +.
T Consensus        18 ~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~   96 (168)
T d1kt1a1          18 VKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SA   96 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-cc
Confidence            44445567778888888888876431       1           11234455566788888888888888887643 34


Q ss_pred             CcccHHHHHHHHHhccchhhHHHHHHHHHHh
Q 031208           78 DKFTFPFVIKACIASLAIEKGKEVHGLAVKA  108 (164)
Q Consensus        78 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  108 (164)
                      +...|..+..++...|++++|...++...+.
T Consensus        97 ~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          97 NEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5667777888888888888888888887764

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.09  E-value=0.0065  Score=36.80  Aligned_cols=91  Identities=13%  Similarity=0.050  Sum_probs=70.6

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHc---CCCC-----------CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchH
Q 031208           50 MIRALTIDGSSLQALLLYNLMICN---GFRP-----------DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMF  115 (164)
Q Consensus        50 li~~~~~~~~~~~a~~~~~~m~~~---~~~p-----------~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~  115 (164)
                      .-..+.+.|++++|...|++....   ...+           ....|+-+-.+|.+.|++++|...++...+.. +.+..
T Consensus        21 ~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~   99 (168)
T d1kt1a1          21 KGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEK   99 (168)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHH
Confidence            345677889999999998876431   1111           12456667788899999999999999988765 55778


Q ss_pred             HHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          116 VQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       116 ~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .|..+..+|...|++++|.+.|+...
T Consensus       100 a~~~~~~~~~~l~~~~~A~~~~~~al  125 (168)
T d1kt1a1         100 GLYRRGEAQLLMNEFESAKGDFEKVL  125 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            88888999999999999999999876

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.09  E-value=0.0038  Score=37.87  Aligned_cols=107  Identities=6%  Similarity=-0.077  Sum_probs=78.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHc--------------CCCC-CcccHHHHHHHHHhccchhhHHHHHHHHHHhCCC
Q 031208           47 WNLMIRALTIDGSSLQALLLYNLMICN--------------GFRP-DKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFS  111 (164)
Q Consensus        47 ~~~li~~~~~~~~~~~a~~~~~~m~~~--------------~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~  111 (164)
                      +...-..+.+.|++++|+..|.+..+.              .+.| +...|..+-.++.+.|++++|...+.+..+.. +
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p  108 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-P  108 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-T
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-h
Confidence            334455677889999999998876431              1122 33456667788899999999999999988764 4


Q ss_pred             CchHHHHHHHHHHHhcCCchhHHHHhcccC--CC-CcchHHHHHHH
Q 031208          112 RDMFVQSTLMDLYLKCGDVDGGRKMFDKMR--VR-SVVSWTTMISG  154 (164)
Q Consensus       112 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~  154 (164)
                      .+...|..+-.+|.+.|++++|.+.|+...  .| |...+..+-..
T Consensus       109 ~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~~~~l~~~  154 (169)
T d1ihga1         109 SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKV  154 (169)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            567889999999999999999999999775  33 44444444433

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=96.95  E-value=0.0027  Score=42.15  Aligned_cols=122  Identities=11%  Similarity=0.019  Sum_probs=85.3

Q ss_pred             HHHHhccCCcHHHHHHHhccC--CCc------HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC----cccHHHHH
Q 031208           20 LDLCSFYGKTDHALLVFSQIR--CPH------VFTWNLMIRALTIDGSSLQALLLYNLMICNGF-RPD----KFTFPFVI   86 (164)
Q Consensus        20 i~~~~~~~~~~~a~~~~~~~~--~~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~t~~~ll   86 (164)
                      -..+...|++++|..++++..  .|+      ...++.+-..+...|++++|...|++..+... .++    ...+..+.
T Consensus        19 A~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~   98 (366)
T d1hz4a_          19 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQS   98 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHH
Confidence            446678999999999998753  222      24566777888999999999999998754211 111    23455666


Q ss_pred             HHHHhccchhhHHHHHHHHHHh----CCCC--c-hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           87 KACIASLAIEKGKEVHGLAVKA----GFSR--D-MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        87 ~~~~~~~~~~~a~~~~~~m~~~----g~~~--~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..+...|++..+...+.+....    +...  . ...+..+-..+...|+++.+...+....
T Consensus        99 ~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~  160 (366)
T d1hz4a_          99 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGI  160 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHH
Confidence            7788889999999888876542    2111  1 2345556678888999999988887654

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=96.89  E-value=0.0067  Score=40.13  Aligned_cols=151  Identities=13%  Similarity=0.042  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHhccCCcHHHHHHHhccC-------C-C--cHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCc---
Q 031208           13 QLLVRKLLDLCSFYGKTDHALLVFSQIR-------C-P--HVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDK---   79 (164)
Q Consensus        13 ~~~~~~li~~~~~~~~~~~a~~~~~~~~-------~-~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~---   79 (164)
                      ...+......+...++...+...+....       . +  ....+..+...+...|+++.|...+.+........+.   
T Consensus       172 ~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  251 (366)
T d1hz4a_         172 LQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQ  251 (366)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHH
Confidence            3344444555666677666666554432       1 1  1234566666778889999999988887543322222   


Q ss_pred             ccHHHHHHHHHhccchhhHHHHHHHHHH----hCCCCc-hHHHHHHHHHHHhcCCchhHHHHhcccC---CC--------
Q 031208           80 FTFPFVIKACIASLAIEKGKEVHGLAVK----AGFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR---VR--------  143 (164)
Q Consensus        80 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~----~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~--------  143 (164)
                      ..+..+...+...|++++|...+++...    .+..|+ ...+..+-..|.+.|++++|.+.+++..   ++        
T Consensus       252 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~~~  331 (366)
T d1hz4a_         252 GQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFV  331 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHHHH
Confidence            3445567888999999999999987753    244444 3466677788999999999999988653   11        


Q ss_pred             -CcchHHHHHHHHHhcCCCCC
Q 031208          144 -SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       144 -~~~~~~~li~~~~~~g~~~~  163 (164)
                       .......++..+...++.++
T Consensus       332 ~~~~~~~~~~~~l~~~~~l~e  352 (366)
T d1hz4a_         332 IEGEAMAQQLRQLIQLNTLPE  352 (366)
T ss_dssp             TTHHHHHHHHHHHHHTTCSCH
T ss_pred             HHHHHHHHHHHHHHhcCCChH
Confidence             11234445555666665543

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.85  E-value=0.011  Score=40.29  Aligned_cols=146  Identities=14%  Similarity=0.045  Sum_probs=70.0

Q ss_pred             CCHHHHHHHHHHHhccCCcHHHHHHHhccCCCcHhHHHHHHHHHHhcCChhHHHHHHHHH--------------------
Q 031208           11 NDQLLVRKLLDLCSFYGKTDHALLVFSQIRCPHVFTWNLMIRALTIDGSSLQALLLYNLM--------------------   70 (164)
Q Consensus        11 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m--------------------   70 (164)
                      ||..-...+.+.|.+.|.++.|..+|..+..     |..++..+.+.++++.|++.+.+.                    
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d-----~~rl~~~~v~l~~~~~avd~~~k~~~~~~~k~~~~~l~~~~e~~   86 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN-----FGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFR   86 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC-----HHHHHHHHHTTTCHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC-----HHHHHHHHHhhccHHHHHHHHHHcCCHHHHHHHHHHHHhCcHHH
Confidence            4555555556666677777777777776653     222222222222222222222211                    


Q ss_pred             ----HHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCCC---
Q 031208           71 ----ICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRVR---  143 (164)
Q Consensus        71 ----~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---  143 (164)
                          ...+...+......++..|-..|.+++...+++..... -..+...++-++..|++.+. ++..+.++....+   
T Consensus        87 la~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~-~kl~e~l~~~s~~y~~  164 (336)
T d1b89a_          87 LAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP-QKMREHLELFWSRVNI  164 (336)
T ss_dssp             HHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH-HHHHHHHHHHSTTSCH
T ss_pred             HHHHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh-HHHHHHHHhccccCCH
Confidence                11123334445567778888888888888777766432 24566778888888887653 3444444433211   


Q ss_pred             --------CcchHHHHHHHHHhcCCCCC
Q 031208          144 --------SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       144 --------~~~~~~~li~~~~~~g~~~~  163 (164)
                              ...-|.-++--|.+.|++++
T Consensus       165 ~k~~~~c~~~~l~~elv~Ly~~~~~~~~  192 (336)
T d1b89a_         165 PKVLRAAEQAHLWAELVFLYDKYEEYDN  192 (336)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHcCChHHHHHHHHhcCCHHH
Confidence                    23356666667777666653

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.76  E-value=0.014  Score=39.59  Aligned_cols=121  Identities=14%  Similarity=-0.010  Sum_probs=60.0

Q ss_pred             cCCCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC----CCCcccHHHHHHHHHhccchhhHHHHHHHHHH-------
Q 031208           39 IRCPHVFTWNLMIRALTIDGSSLQALLLYNLMICNGF----RPDKFTFPFVIKACIASLAIEKGKEVHGLAVK-------  107 (164)
Q Consensus        39 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~----~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~-------  107 (164)
                      +..||..--..+..-|-+.|.++.|..+|..+...+-    --....|...+....+.+..+.-..+...+.+       
T Consensus         9 l~~~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d~~rl~~~~v~l~~~~~avd~~~k~~~~~~~k~~~~~l~~~~e~~la   88 (336)
T d1b89a_           9 INGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLA   88 (336)
T ss_dssp             TTCC----------------CTTTHHHHHHHTTCHHHHHHHHHTTTCHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HcCCCcCCHHHHHHHHHHCCCHHHHHHHHHhCCCHHHHHHHHHhhccHHHHHHHHHHcCCHHHHHHHHHHHHhCcHHHHH
Confidence            3356655555566667777777777777775432100    00111234444444444433332222222221       


Q ss_pred             ----hCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcC
Q 031208          108 ----AGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASG  159 (164)
Q Consensus       108 ----~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g  159 (164)
                          .+...+......++..|-..|.++....+++...   ..+...++-++..|++.+
T Consensus        89 ~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_          89 QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhC
Confidence                1223455556788999999999999999998653   345567888999998765

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.60  E-value=0.00052  Score=45.34  Aligned_cols=117  Identities=15%  Similarity=0.026  Sum_probs=73.3

Q ss_pred             HhccCCcHHHHHHHhccC--C-CcHhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcc-cHHHHHHHHHhccchhhH
Q 031208           23 CSFYGKTDHALLVFSQIR--C-PHVFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKF-TFPFVIKACIASLAIEKG   98 (164)
Q Consensus        23 ~~~~~~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll~~~~~~~~~~~a   98 (164)
                      ..+.|++++|...+++..  + .|...+..+...++..|++++|...|+...+.  .|+.. .+..+-..+...+..+++
T Consensus         6 aL~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~~~~~~l~~ll~a~~~~~~a   83 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHhccccHHH
Confidence            346799999999999875  3 47789999999999999999999999999774  46443 222222222222222211


Q ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           99 KEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        99 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..-...-...+-.++..........+.+.|+.++|.+++++..
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~  126 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIE  126 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            1100000000111223344445567788899999999988764

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.37  E-value=0.0025  Score=41.97  Aligned_cols=107  Identities=15%  Similarity=-0.038  Sum_probs=69.4

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCchh
Q 031208           54 LTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYLKCGDVDG  132 (164)
Q Consensus        54 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~  132 (164)
                      ..+.|++++|...+++-.+.. +-|...+..+...++..|++++|.+.++...+..  |+ ...+..+-..+...+..++
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~--P~~~~~~~~l~~ll~a~~~~~~   82 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLF--PEYLPGASQLRHLVKAAQARKD   82 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHhccccHH
Confidence            356799999999999998763 4466899999999999999999999999998764  54 4444444444444444333


Q ss_pred             HHHHhccc---CCC-CcchHHHHHHHHHhcCCCCC
Q 031208          133 GRKMFDKM---RVR-SVVSWTTMISGLAASGDLDA  163 (164)
Q Consensus       133 a~~~~~~m---~~~-~~~~~~~li~~~~~~g~~~~  163 (164)
                      +..-...-   .+| +...+......+.+.|+.++
T Consensus        83 a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~  117 (264)
T d1zbpa1          83 FAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQ  117 (264)
T ss_dssp             HTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHH
Confidence            32222211   122 22333444555666666554

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.37  E-value=0.037  Score=32.75  Aligned_cols=96  Identities=10%  Similarity=0.013  Sum_probs=66.0

Q ss_pred             HHHHH--HHHHHhcCChhHHHHHHHHHHHcC-CCCC----------cccHHHHHHHHHhccchhhHHHHHHHHHHh----
Q 031208           46 TWNLM--IRALTIDGSSLQALLLYNLMICNG-FRPD----------KFTFPFVIKACIASLAIEKGKEVHGLAVKA----  108 (164)
Q Consensus        46 ~~~~l--i~~~~~~~~~~~a~~~~~~m~~~~-~~p~----------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----  108 (164)
                      +|..+  -..+...|++++|+..|++..+-. -.|+          ...|+.+-.+|.+.|++++|...+++..+.    
T Consensus         9 a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~   88 (156)
T d2hr2a1           9 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   88 (156)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccccc
Confidence            45555  334556788999999888875411 1122          245777888889999999999888877642    


Q ss_pred             -CCCCc-----hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          109 -GFSRD-----MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       109 -g~~~~-----~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                       ...++     ...++.+-.+|.+.|++++|...|++..
T Consensus        89 ~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          89 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence             11221     2245667788999999999999988754

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=95.96  E-value=0.034  Score=32.95  Aligned_cols=94  Identities=15%  Similarity=-0.092  Sum_probs=69.1

Q ss_pred             HHHHHH--HHHHhccCCcHHHHHHHhccCC-----Cc----------HhHHHHHHHHHHhcCChhHHHHHHHHHHHc---
Q 031208           14 LLVRKL--LDLCSFYGKTDHALLVFSQIRC-----PH----------VFTWNLMIRALTIDGSSLQALLLYNLMICN---   73 (164)
Q Consensus        14 ~~~~~l--i~~~~~~~~~~~a~~~~~~~~~-----~~----------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---   73 (164)
                      .+|..+  -..+.+.|++++|...|++..+     |+          ...|+.+-.+|.+.|++++|..-+++....   
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~   87 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR   87 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc
Confidence            455655  3455567999999998887641     21          356888899999999999999999997542   


Q ss_pred             --CCCCCc-----ccHHHHHHHHHhccchhhHHHHHHHHHH
Q 031208           74 --GFRPDK-----FTFPFVIKACIASLAIEKGKEVHGLAVK  107 (164)
Q Consensus        74 --~~~p~~-----~t~~~ll~~~~~~~~~~~a~~~~~~m~~  107 (164)
                        ...++.     ..+..+-.+|...|++++|...|++..+
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence              112221     2456677889999999999999998664

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=95.63  E-value=0.028  Score=33.05  Aligned_cols=66  Identities=8%  Similarity=-0.166  Sum_probs=30.4

Q ss_pred             ccCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhc----------CChhHHHHHHHHHHHcCCCC-CcccHHHHHHHHH
Q 031208           25 FYGKTDHALLVFSQIR--CP-HVFTWNLMIRALTID----------GSSLQALLLYNLMICNGFRP-DKFTFPFVIKACI   90 (164)
Q Consensus        25 ~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~----------~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~   90 (164)
                      +.+.+++|...|+...  .| |...+..+=.++...          +.+++|...|++..+.  .| +..+|..+-.+|.
T Consensus         9 r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l--~P~~~~a~~~lG~~y~   86 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYT   86 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHh--cchhhHHHhhHHHHHH
Confidence            3444566666666553  23 333444433333322          2334555555555442  23 2334544545554


Q ss_pred             hc
Q 031208           91 AS   92 (164)
Q Consensus        91 ~~   92 (164)
                      ..
T Consensus        87 ~~   88 (145)
T d1zu2a1          87 SF   88 (145)
T ss_dssp             HH
T ss_pred             Hc
Confidence            43

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.58  E-value=0.011  Score=39.54  Aligned_cols=114  Identities=10%  Similarity=-0.067  Sum_probs=79.7

Q ss_pred             cCCcHHHHHHHhccC--CC-cHhHHHHHHHHHHhcC--ChhHHHHHHHHHHHcCCCCCcccHHHHH-HHHHhccchhhHH
Q 031208           26 YGKTDHALLVFSQIR--CP-HVFTWNLMIRALTIDG--SSLQALLLYNLMICNGFRPDKFTFPFVI-KACIASLAIEKGK   99 (164)
Q Consensus        26 ~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t~~~ll-~~~~~~~~~~~a~   99 (164)
                      .|++++|..+++...  .| +...|..+-.++...+  ++++|...+.+..+.. +++...+...+ ..+...+..+.|.
T Consensus        86 ~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al  164 (334)
T d1dcea1          86 AALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEEL  164 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHH
Confidence            344677888888764  33 5667777766666665  4789999999987752 23344444333 5666778899999


Q ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208          100 EVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus       100 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      ..++...+.. +-+...|+.+-..+.+.|++++|...+....
T Consensus       165 ~~~~~~i~~~-p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~  205 (334)
T d1dcea1         165 AFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPE  205 (334)
T ss_dssp             HHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSCCSSCH
T ss_pred             HHHHHHHHcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHhH
Confidence            9998877664 3457788888888889998888766665443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.28  E-value=0.03  Score=39.89  Aligned_cols=110  Identities=6%  Similarity=-0.173  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYL  125 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  125 (164)
                      .+..+-..+.+.|+.+.|...+....+..  | ..++..+-+.+...+++++|...+.+..+.. +-+...|+.|-..|.
T Consensus       122 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~--~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~  197 (497)
T d1ya0a1         122 KSSQLGIISNKQTHTSAIVKPQSSSCSYI--C-QHCLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAILAS  197 (497)
T ss_dssp             ---------------------CCHHHHHH--H-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHHHHH
T ss_pred             HHHHhHHHHHhCCCHHHHHHHHHHHhCCC--H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            34444444445555555554444432211  1 1244555566666677777777777666553 334456677777777


Q ss_pred             hcCCchhHHHHhcccC---CCCcchHHHHHHHHHhcC
Q 031208          126 KCGDVDGGRKMFDKMR---VRSVVSWTTMISGLAASG  159 (164)
Q Consensus       126 ~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~g  159 (164)
                      ..|+..+|...|.+-.   .|-..++..|...|.+..
T Consensus       198 ~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         198 SKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             HTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHHT
T ss_pred             HcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhh
Confidence            7777777766665432   344455666665555443

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.04  E-value=0.067  Score=28.77  Aligned_cols=58  Identities=9%  Similarity=0.052  Sum_probs=34.6

Q ss_pred             HHHHhcCChhHHHHHHHHHHHc---C--CCCC-cccHHHHHHHHHhccchhhHHHHHHHHHHhC
Q 031208           52 RALTIDGSSLQALLLYNLMICN---G--FRPD-KFTFPFVIKACIASLAIEKGKEVHGLAVKAG  109 (164)
Q Consensus        52 ~~~~~~~~~~~a~~~~~~m~~~---~--~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g  109 (164)
                      ..+.+.|++++|...|++..+.   .  ..++ ..++..+-.++.+.|++++|...+++..+..
T Consensus        13 ~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_          13 KVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            3456667777777776665331   1  1111 2356666777777777777777777766653

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.98  E-value=0.037  Score=39.38  Aligned_cols=104  Identities=8%  Similarity=-0.174  Sum_probs=65.1

Q ss_pred             HHhccCCcHHHHHHHhccCCCc-HhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-cccHHHHHHHHHhccchhhHH
Q 031208           22 LCSFYGKTDHALLVFSQIRCPH-VFTWNLMIRALTIDGSSLQALLLYNLMICNGFRPD-KFTFPFVIKACIASLAIEKGK   99 (164)
Q Consensus        22 ~~~~~~~~~~a~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~   99 (164)
                      .+.+.|+.+.|...+.....++ ...+..+-..+...+++++|...|.+..+.  .|+ ...|+.+-..+...|+..+|.
T Consensus       129 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~  206 (497)
T d1ya0a1         129 ISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTI  206 (497)
T ss_dssp             --------------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHH
Confidence            3344445555544444332222 235566677788889999999999998764  464 468899999999999999998


Q ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHhcC
Q 031208          100 EVHGLAVKAGFSRDMFVQSTLMDLYLKCG  128 (164)
Q Consensus       100 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~  128 (164)
                      ..+.+..... +|....+..|...|.+..
T Consensus       207 ~~y~ral~~~-~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         207 FYYCRSIAVK-FPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             HHHHHHHSSS-BCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCC-CCCHHHHHHHHHHHHHhh
Confidence            8888776554 566777777777776544

>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=94.18  E-value=0.062  Score=29.36  Aligned_cols=64  Identities=6%  Similarity=0.045  Sum_probs=47.3

Q ss_pred             ChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           59 SSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        59 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      +.=++.+-++.+-...+.|++....+.+++|.+-+++..|.++++-.+.. +.++...|..+++-
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilqe   84 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE   84 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHHH
Confidence            44466677777777888888888888888888888888888888877633 23445577766653

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.90  E-value=0.28  Score=28.28  Aligned_cols=118  Identities=9%  Similarity=0.037  Sum_probs=82.4

Q ss_pred             hccCCcHHHHHHHhccC-CCcHhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCC----------------CCcccHHHH
Q 031208           24 SFYGKTDHALLVFSQIR-CPHVFTWNLMIRALTIDGSSLQALLLYNLMICN-GFR----------------PDKFTFPFV   85 (164)
Q Consensus        24 ~~~~~~~~a~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~----------------p~~~t~~~l   85 (164)
                      ...|.+++..++..+.. ..+..-||-+|.-....-+-+..+.+++..-.. .+.                .+..-+...
T Consensus        13 ildG~ve~Gveii~k~~~ss~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~n~~se~vdlA   92 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNTLNEHVNKA   92 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTCCCHHHHHH
T ss_pred             HHhhhHHhHHHHHHHHcccCCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHhcchHHHHHHH
Confidence            34677788888877765 345666777777767777777777777666332 111                222335566


Q ss_pred             HHHHHhccchhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccCC
Q 031208           86 IKACIASLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMRV  142 (164)
Q Consensus        86 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  142 (164)
                      ++...+.|+-+...++...+.+++ +|++...-.+-.+|-+-|...++.+++.+.-+
T Consensus        93 Ld~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe  148 (161)
T d1wy6a1          93 LDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACK  148 (161)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            788888888888888888877766 67777778888899999999999988876543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=93.90  E-value=0.13  Score=29.91  Aligned_cols=98  Identities=7%  Similarity=-0.100  Sum_probs=63.2

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHh----------ccchhhHHHHHHHHHHhCCCCchHHHHHHHHH
Q 031208           54 LTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIA----------SLAIEKGKEVHGLAVKAGFSRDMFVQSTLMDL  123 (164)
Q Consensus        54 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----------~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  123 (164)
                      |-+.+.+++|...|+...+.. +-+...+..+-.++..          .+.+++|...+++..+.. +.+...|..+-.+
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHH
Confidence            345566888888888887643 2244455555555543          355688888888887764 3456677777777


Q ss_pred             HHhcC-----------CchhHHHHhcccC--CCCcchHHHHHH
Q 031208          124 YLKCG-----------DVDGGRKMFDKMR--VRSVVSWTTMIS  153 (164)
Q Consensus       124 ~~~~~-----------~~~~a~~~~~~m~--~~~~~~~~~li~  153 (164)
                      |...|           .++.|.+.|+...  .|+...|..-+.
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~  127 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLE  127 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHH
Confidence            76544           3577888888765  565555554443

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.50  E-value=0.25  Score=26.36  Aligned_cols=27  Identities=22%  Similarity=0.228  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHH
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMIC   72 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~   72 (164)
                      +++.+-.++.+.|++++|.+.+++..+
T Consensus        48 ~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_          48 VLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            344444455555555555555555443

>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=93.31  E-value=0.29  Score=26.64  Aligned_cols=57  Identities=5%  Similarity=0.042  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCchhHHHHhcccC---CCCcchHHHHHH
Q 031208           97 KGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVDGGRKMFDKMR---VRSVVSWTTMIS  153 (164)
Q Consensus        97 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~  153 (164)
                      +..+-+..+....+.|++.+..+.+.+|.|.+++..|.++|+.++   ..+...|..+++
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yilq   83 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            344444444455566777777777777777777777777777665   223445555544

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=92.73  E-value=0.46  Score=27.36  Aligned_cols=66  Identities=14%  Similarity=-0.034  Sum_probs=54.3

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchhhHHHHHHHHHHhCCC
Q 031208           45 FTWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIEKGKEVHGLAVKAGFS  111 (164)
Q Consensus        45 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~  111 (164)
                      .-++..++...+.|+-++-.++++++.+.+ .|++...-.+-.+|-+.|+..++.+++.+.-+.|+.
T Consensus        87 e~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          87 EHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            446777888999999999999999976644 566666778889999999999999999999988863

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.52  E-value=0.45  Score=27.03  Aligned_cols=48  Identities=13%  Similarity=-0.020  Sum_probs=27.9

Q ss_pred             cchhhHHHHHHHHHHhCCCCc-hHHHHHHHHHHHhcCCchhHHHHhcccC
Q 031208           93 LAIEKGKEVHGLAVKAGFSRD-MFVQSTLMDLYLKCGDVDGGRKMFDKMR  141 (164)
Q Consensus        93 ~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  141 (164)
                      .+++.|..++++..+.+ +.+ ...+-.|--+|.+.|++++|.+.++...
T Consensus        52 ~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L  100 (124)
T d2pqrb1          52 NDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLF  100 (124)
T ss_dssp             HHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            34566777777766543 112 2233344445667777777777777665

>d2nsza1 a.118.1.14 (A:322-450) Programmed cell death 4, PDCD4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Programmed cell death 4, PDCD4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.43  E-value=0.88  Score=25.91  Aligned_cols=68  Identities=6%  Similarity=0.013  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCcccHHHHHHHHHhccchh--hHHHHHHHHHHhCCCCch
Q 031208           46 TWNLMIRALTIDGSSLQALLLYNLMICNGFRPDKFTFPFVIKACIASLAIE--KGKEVHGLAVKAGFSRDM  114 (164)
Q Consensus        46 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~~~~~--~a~~~~~~m~~~g~~~~~  114 (164)
                      -...++.-|...++.++|...++++...... ....+..+..+.-+.+.-.  .+..++..+...|+-+..
T Consensus         9 k~~~ll~EY~~~~D~~Ea~~~l~eL~~p~~~-~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~~~~~is~~   78 (129)
T d2nsza1           9 EIDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITID   78 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCchhh-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHCCCCCHH
Confidence            4577899999999999999999998532222 2334444445554544432  356688888877754443

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.37  E-value=2  Score=24.32  Aligned_cols=62  Identities=10%  Similarity=0.023  Sum_probs=48.8

Q ss_pred             HHHHcCCCCCcccHHHHHHHHHhcc-chhhHHHHHHHHHHhCCCCchHHHHHHHHHHHhcCCch
Q 031208           69 LMICNGFRPDKFTFPFVIKACIASL-AIEKGKEVHGLAVKAGFSRDMFVQSTLMDLYLKCGDVD  131 (164)
Q Consensus        69 ~m~~~~~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  131 (164)
                      ++++.|++++. .-..++..+.... ..-.|.++++.+.+.+..++..|.-.-|+.+...|-+.
T Consensus         6 ~Lr~~GlR~T~-qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~   68 (134)
T d1mzba_           6 ELRKAGLKVTL-PRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVV   68 (134)
T ss_dssp             HHHHTTCCCCH-HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHcCCCCCH-HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEE
Confidence            47888998887 4467888887764 47889999999999988888887777788888777654

>d2nsza1 a.118.1.14 (A:322-450) Programmed cell death 4, PDCD4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Programmed cell death 4, PDCD4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.21  E-value=2.6  Score=23.83  Aligned_cols=66  Identities=17%  Similarity=0.176  Sum_probs=47.7

Q ss_pred             HHHHHHHHHhccCCcHHHHHHHhccCCCc---HhHHHHHHHHHHhcCCh--hHHHHHHHHHHHcCCCCCcc
Q 031208           15 LVRKLLDLCSFYGKTDHALLVFSQIRCPH---VFTWNLMIRALTIDGSS--LQALLLYNLMICNGFRPDKF   80 (164)
Q Consensus        15 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~~~~--~~a~~~~~~m~~~~~~p~~~   80 (164)
                      -...++.-|...|+.++|...++++..|.   ...+..+..+.-+.+.-  +.+..++..+...|+.+...
T Consensus         9 k~~~ll~EY~~~~D~~Ea~~~l~eL~~p~~~~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~~~~~is~~~   79 (129)
T d2nsza1           9 EIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQ   79 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            36788999999999999999999998654   34455555555555544  34577999998887655543

>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=82.89  E-value=0.54  Score=19.41  Aligned_cols=24  Identities=21%  Similarity=0.239  Sum_probs=16.5

Q ss_pred             HHhCCCCchHHHHHHHHHHHhcCC
Q 031208          106 VKAGFSRDMFVQSTLMDLYLKCGD  129 (164)
Q Consensus       106 ~~~g~~~~~~~~~~ll~~~~~~~~  129 (164)
                      .++|...+..+|..++..+-+.|+
T Consensus        12 eeng~s~ns~iy~~vmes~kkegr   35 (36)
T d1u9pa1          12 EENGRSVNSEIYQRVMESFKKEGR   35 (36)
T ss_dssp             HHHTCCHHHHHHHHHHHHHHHTTC
T ss_pred             HHcCcchhHHHHHHHHHHHHHccC
Confidence            356677777777777777766665