Citrus Sinensis ID: 045511

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------21
Protein Sequence
MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM
Secondary Structure (PSIPRED)
cEEccHHHHHcccccccHHHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHHHcccccccEEHHHHHHHHHHHHcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHcccccccEEEHHHHHHHHHccccHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccEEEccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEHHHHHHHHHHHcccHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEHHHHHHHcc
Coil and Loop (DISEMBL)
mfvnglkslkptlsFKQLNQIHAQIIKIPQPHILNTLLKLLTqsstpqnaiplynkmlncpssynhyTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISglskcgfhkeAIDMFcgidvkpnaNTLVSVLSACSslgsrklgKAIHAHSLRnlnenniildnavldfm
Flexible Loop (DISEMBL)
mfvnglkslkptLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAhslrnlnenniildnavldfm
Low Complexity Region (SEG)
MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM
Disordered region (IsUnstruct)
***********TLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL***
Disordered Region (DISOPRED)
MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM
Disordered Region (DISEMBL)
MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM
Disordered Region (DISPRO)
MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	209	2.2.26 [Sep-21-2011]
Q9LUJ2	842	Pentatricopeptide repeat-	yes	no	0.837	0.207	0.335	9e-26
Q9SZK1	559	Pentatricopeptide repeat-	no	no	0.794	0.296	0.358	2e-25
Q9SJG6	559	Pentatricopeptide repeat-	no	no	0.846	0.316	0.323	8e-24
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.861	0.290	0.288	2e-21
P93011	583	Pentatricopeptide repeat-	no	no	0.875	0.313	0.279	3e-21
A8MQA3	595	Pentatricopeptide repeat-	no	no	0.885	0.310	0.309	4e-21
Q9LN01	741	Pentatricopeptide repeat-	no	no	0.885	0.249	0.292	4e-21
Q9LTV8	694	Pentatricopeptide repeat-	no	no	0.789	0.237	0.331	2e-20
Q9C6T2	606	Pentatricopeptide repeat-	no	no	0.875	0.301	0.278	3e-20
Q9M9E2	866	Pentatricopeptide repeat-	no	no	0.669	0.161	0.368	5e-20

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

 Score =  116 bits (291), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 60/179 (33%), Positives = 109/179 (60%), Gaps = 4/179 (2%)

Query: 33  ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHV 92
           + N+L++    S     AI L+ +M+N   S + YTF   L AC+ + A   G++IH  +
Sbjct: 101 MYNSLIRGYASSGLCNEAILLFLRMMNSGISPDKYTFPFGLSACAKSRAKGNGIQIHGLI 160

Query: 93  IKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAI 152
           +K G+  D+F+QNSL+HFY    ++ SA ++F+ +   +VV+WT++I G ++  F K+A+
Sbjct: 161 VKMGYAKDLFVQNSLVHFYAECGELDSARKVFDEMSERNVVSWTSMICGYARRDFAKDAV 220

Query: 153 DMFCGI----DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
           D+F  +    +V PN+ T+V V+SAC+ L   + G+ ++A    +  E N ++ +A++D
Sbjct: 221 DLFFRMVRDEEVTPNSVTMVCVISACAKLEDLETGEKVYAFIRNSGIEVNDLMVSALVD 279

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZK1|PP355_ARATH Pentatricopeptide repeat-containing protein At4g38010 OS=Arabidopsis thaliana GN=PCMP-E45 PE=3 SV=1

 Score =  115 bits (287), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/173 (35%), Positives = 94/173 (54%)

Query: 35  NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIK 94
           NTLL        P+  I  Y   ++   S + +TF    KAC      ++G +IH  V K
Sbjct: 75  NTLLSSYAVCDKPRVTIFAYKTFVSNGFSPDMFTFPPVFKACGKFSGIREGKQIHGIVTK 134

Query: 95  YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDM 154
            G   DI++QNSL+HFY    +  +A ++F  +   DVV+WT II+G ++ G +KEA+D 
Sbjct: 135 MGFYDDIYVQNSLVHFYGVCGESRNACKVFGEMPVRDVVSWTGIITGFTRTGLYKEALDT 194

Query: 155 FCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
           F  +DV+PN  T V VL +   +G   LGK IH   L+  +  ++   NA++D
Sbjct: 195 FSKMDVEPNLATYVCVLVSSGRVGCLSLGKGIHGLILKRASLISLETGNALID 247

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (274), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 69/213 (32%), Positives = 109/213 (51%), Gaps = 36/213 (16%)

Query: 31  PHILNTLLKLLTQSSTPQNAIPLYNKML-NCPS-SYNHYTFTQALKACSLAHAHQKGLEI 88
           P + NT+++  ++SS P+ AI ++  ML + PS      T+    KA       + G ++
Sbjct: 89  PFVWNTIIRGFSRSSFPEMAISIFIDMLCSSPSVKPQRLTYPSVFKAYGRLGQARDGRQL 148

Query: 89  HAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGF- 147
           H  VIK G   D FI+N++LH YVT   +  A +IF  ++  DVV W ++I G +KCG  
Sbjct: 149 HGMVIKEGLEDDSFIRNTMLHMYVTCGCLIEAWRIFLGMIGFDVVAWNSMIMGFAKCGLI 208

Query: 148 ------------------------------HKEAIDMFCGI---DVKPNANTLVSVLSAC 174
                                          K+A+DMF  +   DVKP+  T+VS+L+AC
Sbjct: 209 DQAQNLFDEMPQRNGVSWNSMISGFVRNGRFKDALDMFREMQEKDVKPDGFTMVSLLNAC 268

Query: 175 SSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
           + LG+ + G+ IH + +RN  E N I+  A++D
Sbjct: 269 AYLGASEQGRWIHEYIVRNRFELNSIVVTALID 301

Arabidopsis thaliana (taxid: 3702)

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

 Score =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 64/222 (28%), Positives = 112/222 (50%), Gaps = 42/222 (18%)

Query: 22  HAQII----KIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACS 77
           +AQI+      P   + N +++  + S  P+ ++ LY +ML   + +N YTF   LKACS
Sbjct: 67  YAQIVFDGFDRPDTFLWNLMIRGFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACS 126

Query: 78  LAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPD------ 131
              A ++  +IHA + K G+ +D++  NSL++ Y    +   AH +F+ +  PD      
Sbjct: 127 NLSAFEETTQIHAQITKLGYENDVYAVNSLINSYAVTGNFKLAHLLFDRIPEPDDVSWNS 186

Query: 132 -------------------------VVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPN 163
                                     ++WTT+ISG  +   +KEA+ +F  +   DV+P+
Sbjct: 187 VIKGYVKAGKMDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPD 246

Query: 164 ANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAV 205
             +L + LSAC+ LG+ + GK IH++    LN+  I +D+ +
Sbjct: 247 NVSLANALSACAQLGALEQGKWIHSY----LNKTRIRMDSVL 284

Arabidopsis thaliana (taxid: 3702)

>sp|P93011|PP182_ARATH Pentatricopeptide repeat-containing protein At2g33760 OS=Arabidopsis thaliana GN=PCMP-H6 PE=3 SV=1

 Score =  101 bits (252), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 101/186 (54%), Gaps = 3/186 (1%)

Query: 26  IKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG 85
           + +P   + N+++K  ++   P + +  Y +ML+   S ++YTFT  +K+C+   A + G
Sbjct: 67  VPLPDDFLFNSVIKSTSKLRLPLHCVAYYRRMLSSNVSPSNYTFTSVIKSCADLSALRIG 126

Query: 86  LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKC 145
             +H H +  G   D ++Q +L+ FY    D+  A Q+F+ +    +V W +++SG  + 
Sbjct: 127 KGVHCHAVVSGFGLDTYVQAALVTFYSKCGDMEGARQVFDRMPEKSIVAWNSLVSGFEQN 186

Query: 146 GFHKEAIDMFCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILD 202
           G   EAI +F  +     +P++ T VS+LSAC+  G+  LG  +H + +    + N+ L 
Sbjct: 187 GLADEAIQVFYQMRESGFEPDSATFVSLLSACAQTGAVSLGSWVHQYIISEGLDLNVKLG 246

Query: 203 NAVLDF 208
            A+++ 
Sbjct: 247 TALINL 252

Arabidopsis thaliana (taxid: 3702)

>sp|A8MQA3|PP330_ARATH Pentatricopeptide repeat-containing protein At4g21065 OS=Arabidopsis thaliana GN=PCMP-H28 PE=2 SV=2

 Score =  101 bits (251), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 61/197 (30%), Positives = 113/197 (57%), Gaps = 12/197 (6%)

Query: 18  LNQIHAQIIKIPQP---HILNTLLKLLTQSSTPQNAIPLYNKM-LNCPSSYNHYTFTQAL 73
           ++  H    KI +P    I NTL++   +     +A  LY +M ++     + +T+   +
Sbjct: 69  MSYAHKVFSKIEKPINVFIWNTLIRGYAEIGNSISAFSLYREMRVSGLVEPDTHTYPFLI 128

Query: 74  KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVV 133
           KA +     + G  IH+ VI+ G    I++QNSLLH Y    D+ SA+++F+ +   D+V
Sbjct: 129 KAVTTMADVRLGETIHSVVIRSGFGSLIYVQNSLLHLYANCGDVASAYKVFDKMPEKDLV 188

Query: 134 TWTTIISGLSKCGFHKEAIDMFCGID---VKPNANTLVSVLSACSSLGSRKLGKAIHAHS 190
            W ++I+G ++ G  +EA+ ++  ++   +KP+  T+VS+LSAC+ +G+  LGK +H + 
Sbjct: 189 AWNSVINGFAENGKPEEALALYTEMNSKGIKPDGFTIVSLLSACAKIGALTLGKRVHVYM 248

Query: 191 L-----RNLNENNIILD 202
           +     RNL+ +N++LD
Sbjct: 249 IKVGLTRNLHSSNVLLD 265

Arabidopsis thaliana (taxid: 3702)

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

 Score =  101 bits (251), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 114/219 (52%), Gaps = 34/219 (15%)

Query: 24  QIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQ 83
           + I+ P   I NT+ +    SS P +A+ LY  M++     N YTF   LK+C+ + A +
Sbjct: 92  KTIQEPNLLIWNTMFRGHALSSDPVSALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFK 151

Query: 84  KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFN------------------ 125
           +G +IH HV+K G   D+++  SL+  YV    +  AH++F+                  
Sbjct: 152 EGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKVFDKSPHRDVVSYTALIKGYA 211

Query: 126 -------------SVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANTLVS 169
                         +   DVV+W  +ISG ++ G +KEA+++F  +   +V+P+ +T+V+
Sbjct: 212 SRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVT 271

Query: 170 VLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDF 208
           V+SAC+  GS +LG+ +H     +   +N+ + NA++D 
Sbjct: 272 VVSACAQSGSIELGRQVHLWIDDHGFGSNLKIVNALIDL 310

Arabidopsis thaliana (taxid: 3702)

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

 Score = 99.4 bits (246), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 57/172 (33%), Positives = 98/172 (56%), Gaps = 7/172 (4%)

Query: 28  IPQPHIL--NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG 85
           +P+P I   N +++  ++++  Q+A+ +Y+ M     S + +TF   LKACS     Q G
Sbjct: 79  LPRPQIFPWNAIIRGYSRNNHFQDALLMYSNMQLARVSPDSFTFPHLLKACSGLSHLQMG 138

Query: 86  LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPD--VVTWTTIISGLS 143
             +HA V + G   D+F+QN L+  Y   + + SA  +F  +  P+  +V+WT I+S  +
Sbjct: 139 RFVHAQVFRLGFDADVFVQNGLIALYAKCRRLGSARTVFEGLPLPERTIVSWTAIVSAYA 198

Query: 144 KCGFHKEAIDMFC---GIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR 192
           + G   EA+++F     +DVKP+   LVSVL+A + L   K G++IHA  ++
Sbjct: 199 QNGEPMEALEIFSQMRKMDVKPDWVALVSVLNAFTCLQDLKQGRSIHASVVK 250

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C6T2|PPR68_ARATH Pentatricopeptide repeat-containing protein At1g31920 OS=Arabidopsis thaliana GN=PCMP-H11 PE=2 SV=1

 Score = 98.6 bits (244), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 102/187 (54%), Gaps = 4/187 (2%)

Query: 26  IKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG 85
           I  P     NT+++      + + A+  YN+M+   +  +++T+   LKAC+   + ++G
Sbjct: 92  IDDPCTFDFNTMIRGYVNVMSFEEALCFYNEMMQRGNEPDNFTYPCLLKACTRLKSIREG 151

Query: 86  LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKC 145
            +IH  V K G   D+F+QNSL++ Y    ++  +  +F  +      +W++++S  +  
Sbjct: 152 KQIHGQVFKLGLEADVFVQNSLINMYGRCGEMELSSAVFEKLESKTAASWSSMVSARAGM 211

Query: 146 GFHKEAIDMFCGI----DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIIL 201
           G   E + +F G+    ++K   + +VS L AC++ G+  LG +IH   LRN++E NII+
Sbjct: 212 GMWSECLLLFRGMCSETNLKAEESGMVSALLACANTGALNLGMSIHGFLLRNISELNIIV 271

Query: 202 DNAVLDF 208
             +++D 
Sbjct: 272 QTSLVDM 278

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M9E2|PPR45_ARATH Pentatricopeptide repeat-containing protein At1g15510, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H73 PE=2 SV=1

 Score = 97.8 bits (242), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 53/144 (36%), Positives = 84/144 (58%), Gaps = 4/144 (2%)

Query: 50  AIPLYNKMLNCPS-SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL 108
           A+ LY++ML       + YTF   L+ C       +G E+H HV++YG+  DI + N+L+
Sbjct: 179 AMCLYHRMLWVGGVKPDVYTFPCVLRTCGGIPDLARGKEVHVHVVRYGYELDIDVVNALI 238

Query: 109 HFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFC---GIDVKPNAN 165
             YV   D+ SA  +F+ +   D+++W  +ISG  + G   E +++F    G+ V P+  
Sbjct: 239 TMYVKCGDVKSARLLFDRMPRRDIISWNAMISGYFENGMCHEGLELFFAMRGLSVDPDLM 298

Query: 166 TLVSVLSACSSLGSRKLGKAIHAH 189
           TL SV+SAC  LG R+LG+ IHA+
Sbjct: 299 TLTSVISACELLGDRRLGRDIHAY 322

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	209
449442521	517	PREDICTED: pentatricopeptide repeat-cont	0.928	0.375	0.610	6e-65
296083914	541	unnamed protein product [Vitis vinifera]	0.952	0.367	0.558	6e-53
357446587	528	Pentatricopeptide repeat-containing prot	0.933	0.369	0.553	5e-48
217074958	515	unknown [Medicago truncatula] gi|3885214	0.746	0.302	0.605	7e-48
449476231	472	PREDICTED: pentatricopeptide repeat-cont	0.665	0.294	0.641	7e-48
356555244	521	PREDICTED: pentatricopeptide repeat-cont	0.923	0.370	0.497	4e-45
147788829	725	hypothetical protein VITISV_018159 [Viti	0.660	0.190	0.598	2e-42
297741134	573	unnamed protein product [Vitis vinifera]	0.909	0.331	0.350	2e-28
225469326	590	PREDICTED: pentatricopeptide repeat-cont	0.909	0.322	0.350	2e-28
225463844	617	PREDICTED: pentatricopeptide repeat-cont	0.961	0.325	0.322	2e-27

>gi|449442521|ref|XP_004139030.1| PREDICTED: pentatricopeptide repeat-containing protein At1g08070-like isoform 1 [Cucumis sativus] gi|449442523|ref|XP_004139031.1| PREDICTED: pentatricopeptide repeat-containing protein At1g08070-like isoform 2 [Cucumis sativus]

 Score =  252 bits (644), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 124/203 (61%), Positives = 152/203 (74%)

Query: 6   LKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN 65
           LK LKP++S  Q  QIHA+++  P+PHI N LL  L  S  P+N + LYN+ML  PSS+N
Sbjct: 3   LKPLKPSISIAQFTQIHAKLLTNPKPHIFNPLLGSLVNSIFPENGLFLYNQMLRYPSSHN 62

Query: 66  HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFN 125
           H+TFT ALKAC   H  QKGLEIHAH+IK GHL DIFIQNSLLHFY+   D+ SA  IF+
Sbjct: 63  HFTFTYALKACCFLHQTQKGLEIHAHLIKSGHLSDIFIQNSLLHFYILDGDVSSASLIFD 122

Query: 126 SVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKA 185
           S+  PDVV+WT+IISGLSK GF KEA+  F  ++V+PN+ TLV+ LSACSSL   KLGKA
Sbjct: 123 SIPDPDVVSWTSIISGLSKLGFEKEALSKFLSMNVRPNSTTLVTALSACSSLRCLKLGKA 182

Query: 186 IHAHSLRNLNENNIILDNAVLDF 208
           IH   +R LNE N+IL+NA+LDF
Sbjct: 183 IHGLRMRTLNEENVILENALLDF 205

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083914|emb|CBI24302.3| unnamed protein product [Vitis vinifera]

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 114/204 (55%), Positives = 144/204 (70%), Gaps = 5/204 (2%)

Query: 6   LKSLKPTLSFKQLNQIHAQIIKIPQPH-ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY 64
           LK   PT +  QLNQIHA ++K  +P  I NTLL  L+    PQ+A+ LYN+M+   +S+
Sbjct: 19  LKHPIPTCTLNQLNQIHAHLLKTHKPPLIFNTLLPSLS----PQDALLLYNQMVLHRTSH 74

Query: 65  NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIF 124
           NH+TFT AL A S  HA  K LEIHA  IK GH  DIFIQN+LLH YV   +   A  +F
Sbjct: 75  NHFTFTHALIASSSLHALHKTLEIHARAIKSGHYSDIFIQNTLLHSYVVENNFVFAKSVF 134

Query: 125 NSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGK 184
            S+  PDVV+WT+IISGLSKCGF +EAI  F  +DVKPN +TLVSV+SAC  L + + GK
Sbjct: 135 KSISSPDVVSWTSIISGLSKCGFDEEAIGEFLSMDVKPNTSTLVSVVSACCGLRAVRFGK 194

Query: 185 AIHAHSLRNLNENNIILDNAVLDF 208
           AIH +SLR+++ +NIILDNA+LDF
Sbjct: 195 AIHGYSLRSMDGDNIILDNALLDF 218

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446587|ref|XP_003593569.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355482617|gb|AES63820.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  196 bits (498), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 114/206 (55%), Positives = 146/206 (70%), Gaps = 11/206 (5%)

Query: 9   LKPTLSFKQLNQI----HAQIIKIPQPHILNTLLKLLTQSSTPQNAI-PLYNKMLNCPSS 63
           +KP    + LNQI      QII  P P +LN  LKLL++S     A   L N+ML+C SS
Sbjct: 1   MKP----QNLNQIAKLSQFQIIN-PNPQLLNQNLKLLSKSHDNVKAFFNLCNQMLSCSSS 55

Query: 64  YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQI 123
           +NHYTFT ALKAC   HAH KGLEIHA +IK GH+ D FI+N+LL+FY++  D+ SA ++
Sbjct: 56  HNHYTFTHALKACCSYHAHAKGLEIHARLIKSGHIFDGFIKNTLLYFYLSSNDVVSATRV 115

Query: 124 FNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLG 183
           F S+  PDVV+WT++ISGLSKCGF  EAI+ F  I+VKPNA TLVS +SACSS+G+ K G
Sbjct: 116 FKSIPSPDVVSWTSLISGLSKCGFETEAIEAFSSINVKPNALTLVSAISACSSIGAIKFG 175

Query: 184 KAIHAHSLRNLN-ENNIILDNAVLDF 208
           KAIHA+ L++L  + NI+  NA LD 
Sbjct: 176 KAIHAYGLKSLMIDGNIVFYNAALDL 201

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074958|gb|ACJ85839.1| unknown [Medicago truncatula] gi|388521431|gb|AFK48777.1| unknown [Medicago truncatula]

 Score =  196 bits (497), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 95/157 (60%), Positives = 122/157 (77%), Gaps = 1/157 (0%)

Query: 53  LYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV 112
           L N+ML+C SS+NHYTFT ALKAC   HAH KGLEIHA +IK GH+ D FI+N+LL+FY+
Sbjct: 45  LCNQMLSCSSSHNHYTFTHALKACCSYHAHAKGLEIHARLIKSGHIFDGFIKNTLLYFYL 104

Query: 113 TVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLS 172
           +  D+ SA ++F S+  PDVV+WT++ISGLSKCGF  EAI+ F  I+VKPNA TLVS +S
Sbjct: 105 SSNDVVSATRVFKSIPSPDVVSWTSLISGLSKCGFETEAIEAFSSINVKPNALTLVSAIS 164

Query: 173 ACSSLGSRKLGKAIHAHSLRNLN-ENNIILDNAVLDF 208
           ACSS+G+ K GKAIHA+ L++L  + NI+  NA LD 
Sbjct: 165 ACSSIGAIKFGKAIHAYGLKSLMIDGNIVFYNAALDL 201

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449476231|ref|XP_004154679.1| PREDICTED: pentatricopeptide repeat-containing protein At1g08070-like, partial [Cucumis sativus]

 Score =  196 bits (497), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 95/148 (64%), Positives = 114/148 (77%)

Query: 61  PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSA 120
           P S+NH+TFT ALKAC   H  QKGLEIHAH+IK GHL DIFIQNSLLHFY+   D+ SA
Sbjct: 13  PISHNHFTFTYALKACCFLHQTQKGLEIHAHLIKSGHLSDIFIQNSLLHFYILDGDVSSA 72

Query: 121 HQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSR 180
             IF+S+  PDVV+WT+IISGLSK GF KEA+  F  ++V+PN+ TLV+ LS CSSL   
Sbjct: 73  SLIFDSIPDPDVVSWTSIISGLSKLGFEKEALSKFLSMNVRPNSTTLVTALSTCSSLRCL 132

Query: 181 KLGKAIHAHSLRNLNENNIILDNAVLDF 208
           KLGKAIH   +R LNE N+IL+NA+LDF
Sbjct: 133 KLGKAIHGLRMRTLNEENVILENALLDF 160

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555244|ref|XP_003545944.1| PREDICTED: pentatricopeptide repeat-containing protein At1g08070-like [Glycine max]

 Score =  186 bits (473), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 137/207 (66%), Gaps = 14/207 (6%)

Query: 13  LSFKQLNQI----HAQIIKIPQPHILNTLLKLLTQSSTPQNAI-PLYNKMLNCPSSYNHY 67
           +  + LNQI      Q+I  P P  LN LL  LT S   QNA   LYN++L+ P S+NHY
Sbjct: 1   MKVQNLNQIAIRAQQQLITNPNPQFLNPLLSQLTNS---QNAFFDLYNQILSHPFSHNHY 57

Query: 68  TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV 127
           TFT AL+AC   H+  K LEIHAH++K GH  D+F+QNSLLHFY+   D+ SA  +F S+
Sbjct: 58  TFTHALRACYSHHSRSKALEIHAHLVKSGHYLDLFLQNSLLHFYLAHNDVVSASNLFRSI 117

Query: 128 VFPDVVTWTTIISGLSKCGFHKEAIDMFCGID-----VKPNANTLVSVLSACSSLGSRKL 182
             PDVV+WT+++SGL+K GF  +A+  F  ++     V+PNA TLV+ L ACSSLG+  L
Sbjct: 118 PSPDVVSWTSLVSGLAKSGFEAQALHHFTNMNAKPKIVRPNAATLVAALCACSSLGALGL 177

Query: 183 GKAIHAHSLRNL-NENNIILDNAVLDF 208
           GK+ HA+ LR L  + N+I DNAVL+ 
Sbjct: 178 GKSAHAYGLRMLIFDGNVIFDNAVLEL 204

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147788829|emb|CAN73311.1| hypothetical protein VITISV_018159 [Vitis vinifera]

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 88/147 (59%), Positives = 109/147 (74%)

Query: 62  SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAH 121
           +S+NH+TFT AL A S  HA  K LEIHA  IK GH  DIFIQN+LLH YV   +   A 
Sbjct: 6   TSHNHFTFTHALIASSSLHALHKTLEIHARAIKSGHYSDIFIQNTLLHSYVVENNXVFAK 65

Query: 122 QIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRK 181
            +F S+  PDVV+WT+IISGLSKCGF +EAI  F  +DVKPN +TLVSV+SAC  L + +
Sbjct: 66  SVFKSISSPDVVSWTSIISGLSKCGFDEEAIGEFLSMDVKPNTSTLVSVVSACCGLRAVR 125

Query: 182 LGKAIHAHSLRNLNENNIILDNAVLDF 208
            GKAIH +SLR+++ +NIILDNA+LDF
Sbjct: 126 FGKAIHGYSLRSMDGDNIILDNALLDF 152

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741134|emb|CBI31865.3| unnamed protein product [Vitis vinifera]

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/194 (35%), Positives = 106/194 (54%), Gaps = 4/194 (2%)

Query: 14  SFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQAL 73
           +F  LNQ    +  +P     NTL+     S TP+ A  +Y +++      + YTF   L
Sbjct: 57  AFDFLNQTDLHVGTLP----YNTLIAAYASSCTPKAAFLVYGRIVGNGFVPDMYTFPVVL 112

Query: 74  KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVV 133
           KAC+     Q+G ++H   +K G L D+++QNSLLHFY        A ++F+ ++  DVV
Sbjct: 113 KACTKFLGVQEGEQVHGVAVKMGFLCDLYVQNSLLHFYSVCGKWGGAGRVFDEMLVRDVV 172

Query: 134 TWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN 193
           +WT +ISG  + G   EAI++F  +DV PN  T VSVL AC  +G   +GK +H    + 
Sbjct: 173 SWTGLISGYVRTGLFDEAINLFLKMDVVPNVATFVSVLVACGRMGYLSMGKGVHGLVYKR 232

Query: 194 LNENNIILDNAVLD 207
                +++ NA++D
Sbjct: 233 AFGIGLVVGNALVD 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225469326|ref|XP_002268072.1| PREDICTED: pentatricopeptide repeat-containing protein At4g38010-like [Vitis vinifera]

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/194 (35%), Positives = 106/194 (54%), Gaps = 4/194 (2%)

Query: 14  SFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQAL 73
           +F  LNQ    +  +P     NTL+     S TP+ A  +Y +++      + YTF   L
Sbjct: 57  AFDFLNQTDLHVGTLPY----NTLIAAYASSCTPKAAFLVYGRIVGNGFVPDMYTFPVVL 112

Query: 74  KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVV 133
           KAC+     Q+G ++H   +K G L D+++QNSLLHFY        A ++F+ ++  DVV
Sbjct: 113 KACTKFLGVQEGEQVHGVAVKMGFLCDLYVQNSLLHFYSVCGKWGGAGRVFDEMLVRDVV 172

Query: 134 TWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN 193
           +WT +ISG  + G   EAI++F  +DV PN  T VSVL AC  +G   +GK +H    + 
Sbjct: 173 SWTGLISGYVRTGLFDEAINLFLKMDVVPNVATFVSVLVACGRMGYLSMGKGVHGLVYKR 232

Query: 194 LNENNIILDNAVLD 207
                +++ NA++D
Sbjct: 233 AFGIGLVVGNALVD 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463844|ref|XP_002265179.1| PREDICTED: pentatricopeptide repeat-containing protein At1g08070-like [Vitis vinifera]

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 126/248 (50%), Gaps = 47/248 (18%)

Query: 6   LKSLKPTLSFKQLNQIHAQIIK-IPQPHILNTL-------------------LKLLTQSS 45
           L +L+   S K L QIHA IIK +P P    T+                   L LL Q  
Sbjct: 26  LSTLQTCKSIKGLKQIHASIIKTMPSPDAQLTISTRLSALCAQSLPIDPRYALSLLAQLR 85

Query: 46  TPQNAIPLYNKMLNCPSSYNH---------------------YTFTQALKACSLAHAHQK 84
           TP   +PLYN ++   ++ N+                     YT    LKAC+ + A ++
Sbjct: 86  TPN--LPLYNAIIRGLATSNNDSIEGLVVYKQMLSKGIVPDNYTIPFVLKACAESRAVRE 143

Query: 85  GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSK 144
           G E+H   IK G   D+++ N+L+  Y     I SA ++F++    D+V+WTT+I G  K
Sbjct: 144 GEEVHGQAIKMGLASDVYVSNTLMRMYAVCDVIRSARKVFDTSPQRDLVSWTTMIQGYVK 203

Query: 145 CGFHKEAIDMF---CGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNEN-NII 200
            GF +E + +F   CG +++ +  TLV VLS+C+ LG  +LG+ +H + +RN N N ++ 
Sbjct: 204 MGFAREGVGLFFEMCGENLQADGMTLVIVLSSCARLGDLRLGRKLHRYIIRNSNVNLDVF 263

Query: 201 LDNAVLDF 208
           + NA++D 
Sbjct: 264 VGNALVDM 271

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	209
TAIR|locus:2121055	559	AT4G38010 "AT4G38010" [Arabido	0.827	0.309	0.358	1.8e-23
TAIR|locus:4010713895	595	AT4G21065 "AT4G21065" [Arabido	0.885	0.310	0.309	6.7e-21
TAIR|locus:2057574	583	AT2G33760 [Arabidopsis thalian	0.928	0.332	0.276	1.1e-20
TAIR|locus:2034456	606	AT1G31920 [Arabidopsis thalian	0.827	0.285	0.282	1.6e-20
TAIR|locus:2151501	697	AT5G46460 [Arabidopsis thalian	0.928	0.278	0.276	6.9e-20
TAIR|locus:2025946	638	CRR28 "CHLORORESPIRATORY REDUC	0.985	0.322	0.287	1.6e-19
TAIR|locus:2063771	689	AT2G03380 [Arabidopsis thalian	0.794	0.240	0.319	2e-19
TAIR|locus:2196583	866	ECB2 "EARLY CHLOROPLAST BIOGEN	0.669	0.161	0.368	3.5e-19
TAIR|locus:2040565	501	AT2G36730 [Arabidopsis thalian	0.933	0.389	0.295	6.2e-19
TAIR|locus:2122551	834	AT4G39530 [Arabidopsis thalian	0.669	0.167	0.317	6.8e-19

TAIR|locus:2121055 AT4G38010 "AT4G38010" [Arabidopsis thaliana (taxid:3702)]

 Score = 277 (102.6 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 62/173 (35%), Positives = 94/173 (54%)

Query:    35 NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIK 94
             NTLL        P+  I  Y   ++   S + +TF    KAC      ++G +IH  V K
Sbjct:    75 NTLLSSYAVCDKPRVTIFAYKTFVSNGFSPDMFTFPPVFKACGKFSGIREGKQIHGIVTK 134

Query:    95 YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDM 154
              G   DI++QNSL+HFY    +  +A ++F  +   DVV+WT II+G ++ G +KEA+D 
Sbjct:   135 MGFYDDIYVQNSLVHFYGVCGESRNACKVFGEMPVRDVVSWTGIITGFTRTGLYKEALDT 194

Query:   155 FCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
             F  +DV+PN  T V VL +   +G   LGK IH   L+  +  ++   NA++D
Sbjct:   195 FSKMDVEPNLATYVCVLVSSGRVGCLSLGKGIHGLILKRASLISLETGNALID 247

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:4010713895 AT4G21065 "AT4G21065" [Arabidopsis thaliana (taxid:3702)]

 Score = 254 (94.5 bits), Expect = 6.7e-21, P = 6.7e-21
 Identities = 61/197 (30%), Positives = 113/197 (57%)

Query:    18 LNQIHAQIIKIPQP---HILNTLLKLLTQSSTPQNAIPLYNKM-LNCPSSYNHYTFTQAL 73
             ++  H    KI +P    I NTL++   +     +A  LY +M ++     + +T+   +
Sbjct:    69 MSYAHKVFSKIEKPINVFIWNTLIRGYAEIGNSISAFSLYREMRVSGLVEPDTHTYPFLI 128

Query:    74 KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVV 133
             KA +     + G  IH+ VI+ G    I++QNSLLH Y    D+ SA+++F+ +   D+V
Sbjct:   129 KAVTTMADVRLGETIHSVVIRSGFGSLIYVQNSLLHLYANCGDVASAYKVFDKMPEKDLV 188

Query:   134 TWTTIISGLSKCGFHKEAIDMFCGID---VKPNANTLVSVLSACSSLGSRKLGKAIHAHS 190
              W ++I+G ++ G  +EA+ ++  ++   +KP+  T+VS+LSAC+ +G+  LGK +H + 
Sbjct:   189 AWNSVINGFAENGKPEEALALYTEMNSKGIKPDGFTIVSLLSACAKIGALTLGKRVHVYM 248

Query:   191 L-----RNLNENNIILD 202
             +     RNL+ +N++LD
Sbjct:   249 IKVGLTRNLHSSNVLLD 265

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2057574 AT2G33760 [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 1.1e-20, P = 1.1e-20
 Identities = 55/199 (27%), Positives = 106/199 (53%)

Query:    14 SFKQLNQIHAQIIKIPQPH--ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQ 71
             S + +   H   + +P P   + N+++K  ++   P + +  Y +ML+   S ++YTFT 
Sbjct:    53 SARAIAYTHLLFLSVPLPDDFLFNSVIKSTSKLRLPLHCVAYYRRMLSSNVSPSNYTFTS 112

Query:    72 ALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPD 131
              +K+C+   A + G  +H H +  G   D ++Q +L+ FY    D+  A Q+F+ +    
Sbjct:   113 VIKSCADLSALRIGKGVHCHAVVSGFGLDTYVQAALVTFYSKCGDMEGARQVFDRMPEKS 172

Query:   132 VVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHA 188
             +V W +++SG  + G   EAI +F  +     +P++ T VS+LSAC+  G+  LG  +H 
Sbjct:   173 IVAWNSLVSGFEQNGLADEAIQVFYQMRESGFEPDSATFVSLLSACAQTGAVSLGSWVHQ 232

Query:   189 HSLRNLNENNIILDNAVLD 207
             + +    + N+ L  A+++
Sbjct:   233 YIISEGLDLNVKLGTALIN 251

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2034456 AT1G31920 [Arabidopsis thaliana (taxid:3702)]

 Score = 237 (88.5 bits), Expect = 1.6e-20, Sum P(2) = 1.6e-20
 Identities = 50/177 (28%), Positives = 100/177 (56%)

Query:    35 NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIK 94
             NT+++      + + A+  YN+M+   +  +++T+   LKAC+   + ++G +IH  V K
Sbjct:   101 NTMIRGYVNVMSFEEALCFYNEMMQRGNEPDNFTYPCLLKACTRLKSIREGKQIHGQVFK 160

Query:    95 YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDM 154
              G   D+F+QNSL++ Y    ++  +  +F  +      +W++++S  +  G   E + +
Sbjct:   161 LGLEADVFVQNSLINMYGRCGEMELSSAVFEKLESKTAASWSSMVSARAGMGMWSECLLL 220

Query:   155 FCGI----DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
             F G+    ++K   + +VS L AC++ G+  LG +IH   LRN++E NII+  +++D
Sbjct:   221 FRGMCSETNLKAEESGMVSALLACANTGALNLGMSIHGFLLRNISELNIIVQTSLVD 277

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:2151501 AT5G46460 [Arabidopsis thaliana (taxid:3702)]

 Score = 246 (91.7 bits), Expect = 6.9e-20, P = 6.9e-20
 Identities = 55/199 (27%), Positives = 106/199 (53%)

Query:    13 LSFKQLNQIHAQIIKIPQPHILN--TLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFT 70
             L F +++       ++P  ++++  T++  L Q+     A+ L+  ML C        FT
Sbjct:   170 LQFGKVDDALKLFKQMPGKNVISWTTMICGLDQNERSGEALDLFKNMLRCCIKSTSRPFT 229

Query:    71 QALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFP 130
               + AC+ A A   G+++H  +IK G L++ ++  SL+ FY   K I  + ++F+  V  
Sbjct:   230 CVITACANAPAFHMGIQVHGLIIKLGFLYEEYVSASLITFYANCKRIGDSRKVFDEKVHE 289

Query:   131 DVVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIH 187
              V  WT ++SG S    H++A+ +F G+    + PN +T  S L++CS+LG+   GK +H
Sbjct:   290 QVAVWTALLSGYSLNKKHEDALSIFSGMLRNSILPNQSTFASGLNSCSALGTLDWGKEMH 349

Query:   188 AHSLRNLNENNIILDNAVL 206
               +++   E +  + N+++
Sbjct:   350 GVAVKLGLETDAFVGNSLV 368

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 242 (90.2 bits), Expect = 1.6e-19, P = 1.6e-19
 Identities = 62/216 (28%), Positives = 113/216 (52%)

Query:     1 MFVNGLKSLKPTLSFKQLNQIHAQIIKIPQ--PHILNTLLKLLTQS-STPQNAIPLYNKM 57
             +F+ G K L+ + SF  +N        I      + NTL++      S  + A  LY KM
Sbjct:    83 LFLYG-KILQLSSSFSDVNYAFRVFDSIENHSSFMWNTLIRACAHDVSRKEEAFMLYRKM 141

Query:    58 LNC-PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD 116
             L    SS + +TF   LKAC+      +G ++H  ++K+G   D+++ N L+H Y +   
Sbjct:   142 LERGESSPDKHTFPFVLKACAYIFGFSEGKQVHCQIVKHGFGGDVYVNNGLIHLYGSCGC 201

Query:   117 IFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGID--VKPNANTLVSVLSAC 174
             +  A ++F+ +    +V+W ++I  L + G +  A+ +F  +    +P+  T+ SVLSAC
Sbjct:   202 LDLARKVFDEMPERSLVSWNSMIDALVRFGEYDSALQLFREMQRSFEPDGYTMQSVLSAC 261

Query:   175 SSLGSRKLGKAIHAHSLRNLNEN---NIILDNAVLD 207
             + LGS  LG   HA  LR  + +   ++++ N++++
Sbjct:   262 AGLGSLSLGTWAHAFLLRKCDVDVAMDVLVKNSLIE 297

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:2063771 AT2G03380 [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 2.0e-19, Sum P(2) = 2.0e-19
 Identities = 55/172 (31%), Positives = 87/172 (50%)

Query:    42 TQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI 101
             T + +   A+ L+ KM       N  T    L  C L    + G  +H   IK G + D 
Sbjct:   319 THNGSVNEALSLFQKMKGVEIKPNCVTIASVLSGCGLIENLELGRSVHGLSIKVG-IWDT 377

Query:   102 FIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGID-- 159
              + N+L+H Y        A  +F      D+V W +IISG S+ G   EA+ +F  ++  
Sbjct:   378 NVANALVHMYAKCYQNRDAKYVFEMESEKDIVAWNSIISGFSQNGSIHEALFLFHRMNSE 437

Query:   160 -VKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN--LNENNIILDNAVLDF 208
              V PN  T+ S+ SAC+SLGS  +G ++HA+S++   L  +++ +  A+LDF
Sbjct:   438 SVTPNGVTVASLFSACASLGSLAVGSSLHAYSVKLGFLASSSVHVGTALLDF 489

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 241 (89.9 bits), Expect = 3.5e-19, P = 3.5e-19
 Identities = 53/144 (36%), Positives = 84/144 (58%)

Query:    50 AIPLYNKMLNCPS-SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL 108
             A+ LY++ML       + YTF   L+ C       +G E+H HV++YG+  DI + N+L+
Sbjct:   179 AMCLYHRMLWVGGVKPDVYTFPCVLRTCGGIPDLARGKEVHVHVVRYGYELDIDVVNALI 238

Query:   109 HFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFC---GIDVKPNAN 165
               YV   D+ SA  +F+ +   D+++W  +ISG  + G   E +++F    G+ V P+  
Sbjct:   239 TMYVKCGDVKSARLLFDRMPRRDIISWNAMISGYFENGMCHEGLELFFAMRGLSVDPDLM 298

Query:   166 TLVSVLSACSSLGSRKLGKAIHAH 189
             TL SV+SAC  LG R+LG+ IHA+
Sbjct:   299 TLTSVISACELLGDRRLGRDIHAY 322

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

GO:0040007 "growth" evidence=IMP

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

TAIR|locus:2040565 AT2G36730 [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 6.2e-19, Sum P(2) = 6.2e-19
 Identities = 60/203 (29%), Positives = 101/203 (49%)

Query:     8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHY 67
             SL   L+F +   +H+       P   N L +  + S +P  +I +Y++M       N  
Sbjct:    58 SLAKDLAFARTLLLHSSD---STPSTWNMLSRGYSSSDSPVESIWVYSEMKRRGIKPNKL 114

Query:    68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV 127
             TF   LKAC+       G +I   V+K+G   D+++ N+L+H Y T K    A ++F+ +
Sbjct:   115 TFPFLLKACASFLGLTAGRQIQVEVLKHGFDFDVYVGNNLIHLYGTCKKTSDARKVFDEM 174

Query:   128 VFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVK---PNANTLVSVLSACSSLGSRKLGK 184
                +VV+W +I++ L + G      + FC +  K   P+  T+V +LSAC   G+  LGK
Sbjct:   175 TERNVVSWNSIMTALVENGKLNLVFECFCEMIGKRFCPDETTMVVLLSACG--GNLSLGK 232

Query:   185 AIHAHSLRNLNENNIILDNAVLD 207
              +H+  +    E N  L  A++D
Sbjct:   233 LVHSQVMVRELELNCRLGTALVD 255

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2122551 AT4G39530 [Arabidopsis thaliana (taxid:3702)]

 Score = 238 (88.8 bits), Expect = 6.8e-19, P = 6.8e-19
 Identities = 46/145 (31%), Positives = 88/145 (60%)

Query:    67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNS 126
             Y  +  L ACS+    + G +IHAH+++YG   D  + N L+  YV    + +AH++FN 
Sbjct:   250 YILSTVLSACSILPFLEGGKQIHAHILRYGLEMDASLMNVLIDSYVKCGRVIAAHKLFNG 309

Query:   127 VVFPDVVTWTTIISGLSKCGFHKEAIDMFCGID---VKPNANTLVSVLSACSSLGSRKLG 183
             +   ++++WTT++SG  +   HKEA+++F  +    +KP+     S+L++C+SL +   G
Sbjct:   310 MPNKNIISWTTLLSGYKQNALHKEAMELFTSMSKFGLKPDMYACSSILTSCASLHALGFG 369

Query:   184 KAIHAHSLR-NLNENNIILDNAVLD 207
               +HA++++ NL  N+  + N+++D
Sbjct:   370 TQVHAYTIKANLG-NDSYVTNSLID 393

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: GSVIVG00017291001 SubName- Full=Chromosome chr6 scaffold_15, whole genome shotgun sequence; (555 aa) (Vitis vinifera)

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	209
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-24
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	7e-23
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-21
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-14
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-13
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-13
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	6e-11
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-07
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-05
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-04

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

 Score =  100 bits (250), Expect = 2e-24
 Identities = 47/146 (32%), Positives = 82/146 (56%), Gaps = 3/146 (2%)

Query: 50  AIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH 109
           A+ LY++ML      + YTF   L+ C       +G E+HAHV+++G   D+ + N+L+ 
Sbjct: 171 ALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALIT 230

Query: 110 FYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFC---GIDVKPNANT 166
            YV   D+ SA  +F+ +   D ++W  +ISG  + G   E +++F     + V P+  T
Sbjct: 231 MYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMT 290

Query: 167 LVSVLSACSSLGSRKLGKAIHAHSLR 192
           + SV+SAC  LG  +LG+ +H + ++
Sbjct: 291 ITSVISACELLGDERLGREMHGYVVK 316

Length = 857

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

 Score = 95.3 bits (237), Expect = 7e-23
 Identities = 53/165 (32%), Positives = 87/165 (52%), Gaps = 6/165 (3%)

Query: 47  PQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNS 106
           P  A+  Y  M     S +  T    L AC+       G+++H    + G +  + + N+
Sbjct: 370 PDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANA 429

Query: 107 LLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHK--EAIDMF--CGIDVKP 162
           L+  Y   K I  A ++F+++   DV++WT+II+GL     ++  EA+  F    + +KP
Sbjct: 430 LIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGL--RLNNRCFEALIFFRQMLLTLKP 487

Query: 163 NANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
           N+ TL++ LSAC+ +G+   GK IHAH LR     +  L NA+LD
Sbjct: 488 NSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLD 532

Length = 857

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

 Score = 89.9 bits (223), Expect = 5e-21
 Identities = 46/158 (29%), Positives = 84/158 (53%), Gaps = 3/158 (1%)

Query: 53  LYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV 112
           L+  M       +  T T  + AC L    + G E+H +V+K G   D+ + NSL+  Y+
Sbjct: 275 LFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYL 334

Query: 113 TVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGID---VKPNANTLVS 169
           ++     A ++F+ +   D V+WT +ISG  K G   +A++ +  ++   V P+  T+ S
Sbjct: 335 SLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIAS 394

Query: 170 VLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
           VLSAC+ LG   +G  +H  + R    + +++ NA+++
Sbjct: 395 VLSACACLGDLDVGVKLHELAERKGLISYVVVANALIE 432

Length = 857

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

 Score = 70.6 bits (173), Expect = 2e-14
 Identities = 43/117 (36%), Positives = 59/117 (50%), Gaps = 4/117 (3%)

Query: 65  NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIF 124
           N  T   AL AC+   A   G EIHAHV++ G   D F+ N+LL  YV    +  A   F
Sbjct: 488 NSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF 547

Query: 125 NSVVFPDVVTWTTIISGLSKCGFHKEAIDMF---CGIDVKPNANTLVSVLSACSSLG 178
           NS    DVV+W  +++G    G    A+++F       V P+  T +S+L ACS  G
Sbjct: 548 NSHE-KDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSG 603

Length = 857

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

 Score = 68.7 bits (168), Expect = 1e-13
 Identities = 40/177 (22%), Positives = 80/177 (45%), Gaps = 3/177 (1%)

Query: 35  NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIK 94
            T++  L  +   + A  L+ +M    S     TF   L+A +   + + G ++H  V+K
Sbjct: 193 GTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLK 252

Query: 95  YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDM 154
            G + D F+  +L+  Y    DI  A  +F+ +     V W ++++G +  G+ +EA+ +
Sbjct: 253 TGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCL 312

Query: 155 F---CGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDF 208
           +       V  +  T   ++   S L   +  K  HA  +R     +I+ + A++D 
Sbjct: 313 YYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDL 369

Length = 697

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

 Score = 67.2 bits (164), Expect = 4e-13
 Identities = 36/178 (20%), Positives = 78/178 (43%), Gaps = 3/178 (1%)

Query: 32  HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAH 91
           H  N+ L+ L      + A+ L   M       +   +    + C    A ++G  + + 
Sbjct: 52  HDSNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSR 111

Query: 92  VIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEA 151
            +       + + N++L  +V   ++  A  +F  +   D+ +W  ++ G +K G+  EA
Sbjct: 112 ALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEA 171

Query: 152 IDMFCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL 206
           + ++  +    V+P+  T   VL  C  +     G+ +HAH +R   E ++ + NA++
Sbjct: 172 LCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALI 229

Length = 857

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

 Score = 60.7 bits (147), Expect = 6e-11
 Identities = 41/146 (28%), Positives = 70/146 (47%), Gaps = 11/146 (7%)

Query: 48  QNAIPLYNKMLNCPSSYNHYTFTQALKACS----LAHAHQKGLEIHAHVIKYGHLHDIFI 103
           + A+ LY +M +   S + +TF+  ++  S    L HA Q     HA +I+ G   DI  
Sbjct: 307 EEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQA----HAGLIRTGFPLDIVA 362

Query: 104 QNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMF---CGIDV 160
             +L+  Y     +  A  +F+ +   ++++W  +I+G    G   +A++MF       V
Sbjct: 363 NTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGV 422

Query: 161 KPNANTLVSVLSACSSLGSRKLGKAI 186
            PN  T ++VLSAC   G  + G  I
Sbjct: 423 APNHVTFLAVLSACRYSGLSEQGWEI 448

Length = 697

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

 Score = 49.9 bits (119), Expect = 3e-07
 Identities = 36/153 (23%), Positives = 69/153 (45%), Gaps = 3/153 (1%)

Query: 58  LNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI 117
             CP +    T+   ++AC    + +    ++ HV   G   D ++ N +L  +V    +
Sbjct: 115 AGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGML 174

Query: 118 FSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMF---CGIDVKPNANTLVSVLSAC 174
             A ++F+ +   ++ +W TII GL   G ++EA  +F             T V +L A 
Sbjct: 175 IDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRAS 234

Query: 175 SSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD 207
           + LGS + G+ +H   L+     +  +  A++D
Sbjct: 235 AGLGSARAGQQLHCCVLKTGVVGDTFVSCALID 267

Length = 697

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

 Score = 44.3 bits (106), Expect = 7e-07
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 130 PDVVTWTTIISGLSKCGFHKEAIDMF---CGIDVKPNANTLVSVLSAC 174
           PDVVT+ T+I G  K G  +EA+ +F       +KPN  T   ++   
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|205109 pfam12854, PPR_1, PPR repeat

 Score = 39.6 bits (94), Expect = 3e-05
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 128 VFPDVVTWTTIISGLSKCGFHKEAIDMF 155
           + PDVVT+ T+I GL + G   EA+++ 
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELL 30

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 37.0 bits (87), Expect = 2e-04
 Identities = 10/23 (43%), Positives = 17/23 (73%)

Query: 133 VTWTTIISGLSKCGFHKEAIDMF 155
           VT+ ++ISG  K G  +EA+++F
Sbjct: 1   VTYNSLISGYCKAGKLEEALELF 23

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

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

 Score = 37.0 bits (87), Expect = 3e-04
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 100 DIFIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDVVTWTTIISGLSK 144
           D+   N+L+  Y     +  A ++FN +    + P+V T++ +I GL K
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	209
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
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.67
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.67
PF13041	50	PPR_2: PPR repeat family	99.63
PF13041	50	PPR_2: PPR repeat family	99.6
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.46
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.44
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.39
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.28
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.25
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.18
PF12854	34	PPR_1: PPR repeat	99.18
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.18
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.14
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.12
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.11
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.1
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.06
PF12854	34	PPR_1: PPR repeat	99.05
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.01
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.99
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.89
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.88
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.85
PRK12370	553	invasion protein regulator; Provisional	98.79
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.78
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.74
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.73
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.73
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.73
PRK12370	553	invasion protein regulator; Provisional	98.7
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.68
PRK11189	296	lipoprotein NlpI; Provisional	98.68
PRK14574	822	hmsH outer membrane protein; Provisional	98.67
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.66
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.65
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.65
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.64
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.62
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.59
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.56
PRK14574	822	hmsH outer membrane protein; Provisional	98.54
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.53
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.45
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.44
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.42
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.41
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.4
KOG1129	478	consensus TPR repeat-containing protein [General f	98.38
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.37
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.37
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.35
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.34
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.34
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.29
KOG2003	840	consensus TPR repeat-containing protein [General f	98.28
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.23
PRK11189	296	lipoprotein NlpI; Provisional	98.2
KOG1126	638	consensus DNA-binding cell division cycle control	98.2
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.2
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.19
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.19
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.18
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.17
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.15
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.14
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.12
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.12
KOG1129	478	consensus TPR repeat-containing protein [General f	98.12
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.11
KOG2003	840	consensus TPR repeat-containing protein [General f	98.1
PRK15359	144	type III secretion system chaperone protein SscB;	98.1
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.08
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.06
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.05
KOG1126	638	consensus DNA-binding cell division cycle control	98.03
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.99
PRK15359	144	type III secretion system chaperone protein SscB;	97.98
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.97
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.96
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.94
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.93
KOG2076	895	consensus RNA polymerase III transcription factor	97.93
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.92
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.91
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.91
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.9
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.89
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.88
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.88
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.85
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.83
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.83
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.83
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.83
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.79
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.78
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.73
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.72
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.7
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.69
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.69
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.67
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.63
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.59
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.58
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.57
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.56
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.55
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.52
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.52
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.5
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.48
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.46
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.45
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.45
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.44
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.43
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.41
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.4
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.39
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.36
KOG2076	895	consensus RNA polymerase III transcription factor	97.31
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.29
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.29
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.28
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.28
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.22
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.21
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.18
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.14
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.13
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.12
PF12688	120	TPR_5: Tetratrico peptide repeat	97.12
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.11
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.11
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.03
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.01
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.01
PLN02789	320	farnesyltranstransferase	96.96
KOG3941	406	consensus Intermediate in Toll signal transduction	96.93
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.91
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.91
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.9
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.87
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.87
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.82
PRK04841	903	transcriptional regulator MalT; Provisional	96.78
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.77
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.74
PRK04841	903	transcriptional regulator MalT; Provisional	96.72
KOG1125	579	consensus TPR repeat-containing protein [General f	96.69
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.64
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.6
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.59
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.57
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.56
KOG2047	835	consensus mRNA splicing factor [RNA processing and	96.53
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.46
PF12688	120	TPR_5: Tetratrico peptide repeat	96.45
KOG2376	652	consensus Signal recognition particle, subunit Srp	96.35
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.34
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.32
PRK14720	906	transcript cleavage factor/unknown domain fusion p	96.31
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.3
KOG3941	406	consensus Intermediate in Toll signal transduction	96.27
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.21
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.17
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	96.17
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.14
KOG0553	304	consensus TPR repeat-containing protein [General f	96.13
PLN02789	320	farnesyltranstransferase	96.12
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.11
PRK10803	263	tol-pal system protein YbgF; Provisional	96.08
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	96.07
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.05
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.04
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.03
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	95.94
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	95.92
PRK10803	263	tol-pal system protein YbgF; Provisional	95.84
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.78
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.77
PF13371	73	TPR_9: Tetratricopeptide repeat	95.77
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	95.7
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	95.61
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.61
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.51
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	95.51
COG4700	251	Uncharacterized protein conserved in bacteria cont	95.31
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	95.27
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	95.21
PF13371	73	TPR_9: Tetratricopeptide repeat	95.08
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.01
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	94.99
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	94.98
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.96
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	94.78
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	94.77
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	94.68
KOG0553	304	consensus TPR repeat-containing protein [General f	94.59
KOG2376	652	consensus Signal recognition particle, subunit Srp	94.36
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	94.34
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	94.32
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.28
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.14
PF13762	145	MNE1: Mitochondrial splicing apparatus component	93.96
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.96
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	93.94
KOG1125	579	consensus TPR repeat-containing protein [General f	93.85
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	93.82
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.81
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	93.79
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.72
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	93.56
KOG4570	418	consensus Uncharacterized conserved protein [Funct	93.26
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.1
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.08
KOG4570	418	consensus Uncharacterized conserved protein [Funct	93.06
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	92.87
PF13929	292	mRNA_stabil: mRNA stabilisation	92.72
KOG4555	175	consensus TPR repeat-containing protein [Function	92.6
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	92.37
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	92.28
PF13929	292	mRNA_stabil: mRNA stabilisation	92.25
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	92.01
KOG2610	491	consensus Uncharacterized conserved protein [Funct	91.97
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	91.94
PRK15331	165	chaperone protein SicA; Provisional	91.76
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	91.38
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	91.38
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	91.31
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	91.29
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	91.24
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	91.23
PF13762	145	MNE1: Mitochondrial splicing apparatus component	91.19
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	91.06
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	91.02
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	90.96
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.94
smart00638	574	LPD_N Lipoprotein N-terminal Domain.	90.94
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	90.64
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	90.58
COG4105	254	ComL DNA uptake lipoprotein [General function pred	90.39
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	90.32
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	90.31
PF13512	142	TPR_18: Tetratricopeptide repeat	90.3
PF13428	44	TPR_14: Tetratricopeptide repeat	90.16
PRK15331	165	chaperone protein SicA; Provisional	90.1
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	89.93
PF13512	142	TPR_18: Tetratricopeptide repeat	89.74
KOG2610	491	consensus Uncharacterized conserved protein [Funct	89.58
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	89.48
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	89.47
PF13428	44	TPR_14: Tetratricopeptide repeat	89.37
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	89.3
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	89.27
COG3898	531	Uncharacterized membrane-bound protein [Function u	88.63
cd08819	88	CARD_MDA5_2 Caspase activation and recruitment dom	88.5
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	88.49
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.39
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	88.15
COG0457	291	NrfG FOG: TPR repeat [General function prediction	88.14
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	87.39
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	87.38
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	87.17
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	86.99
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	86.72
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	86.57
COG3898	531	Uncharacterized membrane-bound protein [Function u	86.12
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	85.98
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	85.61
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	85.57
PF13431	34	TPR_17: Tetratricopeptide repeat	85.48
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	85.42
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	85.39
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	84.88
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	84.71
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	84.37
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	84.34
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	84.33
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	83.99
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	83.61
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	83.33
cd08326	84	CARD_CASP9 Caspase activation and recruitment doma	82.99
KOG4567	370	consensus GTPase-activating protein [General funct	82.28
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	82.24
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	81.61
PHA02875	413	ankyrin repeat protein; Provisional	81.57
PF01347	618	Vitellogenin_N: Lipoprotein amino terminal region;	81.4
COG4455	273	ImpE Protein of avirulence locus involved in tempe	81.03
COG4105	254	ComL DNA uptake lipoprotein [General function pred	80.78
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	80.74
PRK10564	303	maltose regulon periplasmic protein; Provisional	80.72
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	80.68
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	80.6
COG3118	304	Thioredoxin domain-containing protein [Posttransla	80.11

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

Probab=100.00  E-value=3.6e-41  Score=288.94  Aligned_cols=204  Identities=20%  Similarity=0.310  Sum_probs=196.4

Q ss_pred             Chhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc
Q 045511            1 MFVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA   79 (209)
Q Consensus         1 ~li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~   79 (209)
                      +||+++ +.|+.++|.+.|+++     ..+|+.+||++|.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|++.
T Consensus       264 ~Li~~y~k~g~~~~A~~vf~~m-----~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~  338 (697)
T PLN03081        264 ALIDMYSKCGDIEDARCVFDGM-----PEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRL  338 (697)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhC-----CCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence            367888 899999999888877     34799999999999999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      |+++.|.++++.|.+.|+.||..+||+||++|++.|++++|.++|++|.+||..+||+||.+|++.|+.++|.++|++| 
T Consensus       339 g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~  418 (697)
T PLN03081        339 ALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMI  418 (697)
T ss_pred             cchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             --CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH-hccCCCchhHhHhhhcC
Q 045511          159 --DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR-NLNENNIILDNAVLDFM  209 (209)
Q Consensus       159 --~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~p~~~~~~~li~~y  209 (209)
                        |+.||..||+++|.+|++.|++++|.++|+.|.+ .|+.|+..+|+++|++|
T Consensus       419 ~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l  472 (697)
T PLN03081        419 AEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELL  472 (697)
T ss_pred             HhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHH
Confidence              9999999999999999999999999999999976 69999999999999875

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.9e-39  Score=283.68  Aligned_cols=207  Identities=13%  Similarity=0.147  Sum_probs=107.6

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH   80 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~   80 (209)
                      ||+++ +.|+.+.+.+.+.++.+.. ..||..+||.+|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|
T Consensus       478 LI~~y~k~G~vd~A~~vf~eM~~~G-v~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G  556 (1060)
T PLN03218        478 LISTCAKSGKVDAMFEVFHEMVNAG-VEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSG  556 (1060)
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCC
Confidence            34444 4555555555555544432 235555555555555555555555555555555555555555555555555555


Q ss_pred             cHHHHHHHHHHHHH--hccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC----CCcHhHHHHHHHHHHhCCChHHHHHH
Q 045511           81 AHQKGLEIHAHVIK--YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV----FPDVVTWTTIISGLSKCGFHKEAIDM  154 (209)
Q Consensus        81 ~~~~a~~~~~~m~~--~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~g~~~~a~~~  154 (209)
                      ++++|.++|++|.+  .|+.||..+|++||.+|++.|++++|.++|++|.    .|+..+||++|.+|++.|++++|.++
T Consensus       557 ~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~l  636 (1060)
T PLN03218        557 AVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSI  636 (1060)
T ss_pred             CHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHH
Confidence            55555555555543  3445555555555555555555555555555552    24445555555555555555555555


Q ss_pred             HhhC---CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          155 FCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       155 ~~~m---~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                      |++|   |+.||..||+++|.+|++.|++++|.+++..|.+.|+.|+..+|++||++|
T Consensus       637 f~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay  694 (1060)
T PLN03218        637 YDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGAC  694 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            5555   555555555555555555555555555555555555555555555555443

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.4e-39  Score=283.06  Aligned_cols=206  Identities=15%  Similarity=0.188  Sum_probs=151.7

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH   80 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~   80 (209)
                      ||+++ +.|+.++|.+.+.++.+.. ..|+..+||.+|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|
T Consensus       585 LI~ay~k~G~ldeA~elf~~M~e~g-i~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G  663 (1060)
T PLN03218        585 LMKACANAGQVDRAKEVYQMIHEYN-IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAG  663 (1060)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcC-CCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Confidence            45556 6666666666666665543 346667777777777777777777777777777777777777777777777777


Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc----CCCcHhHHHHHHHHHHhCCChHHHHHHHh
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDVVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      ++++|.++|+.|.+.|+.||..+|++||.+|++.|++++|.++|++|    ..||..+||+||.+|++.|++++|.++|+
T Consensus       664 ~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~  743 (1060)
T PLN03218        664 DLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLS  743 (1060)
T ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            77777777777777777777777777777777777777777777777    35777777777777777777777777777


Q ss_pred             hC---CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhc
Q 045511          157 GI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDF  208 (209)
Q Consensus       157 ~m---~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~  208 (209)
                      +|   |+.||..||+.+|.+|++.|++++|.+++.+|.+.|+.||..+|++||.+
T Consensus       744 eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIgl  798 (1060)
T PLN03218        744 EMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGL  798 (1060)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            77   77777777777777777777777777777777777777777777777653

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.4e-38  Score=278.32  Aligned_cols=204  Identities=24%  Similarity=0.385  Sum_probs=196.9

Q ss_pred             Chhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc
Q 045511            1 MFVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA   79 (209)
Q Consensus         1 ~li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~   79 (209)
                      +|++++ +.|+.++|.+.|+++     ..||..+||++|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.
T Consensus       227 ~Li~~y~k~g~~~~A~~lf~~m-----~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~  301 (857)
T PLN03077        227 ALITMYVKCGDVVSARLVFDRM-----PRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELL  301 (857)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcC-----CCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhc
Confidence            367778 888888888888877     35899999999999999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      |+++.+.+++..|.+.|+.||..+||+||.+|++.|++++|+++|++|..||..+||++|.+|++.|++++|+++|++| 
T Consensus       302 g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~  381 (857)
T PLN03077        302 GDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALME  381 (857)
T ss_pred             CChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             --CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          159 --DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       159 --~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                        |+.||..||+++|.+|++.|+++.|.++++.|.+.|+.|+..+|++||++|
T Consensus       382 ~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y  434 (857)
T PLN03077        382 QDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMY  434 (857)
T ss_pred             HhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHH
Confidence              999999999999999999999999999999999999999999999999986

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

Probab=100.00  E-value=1.7e-38  Score=272.40  Aligned_cols=203  Identities=20%  Similarity=0.292  Sum_probs=192.9

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH   80 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~   80 (209)
                      |++++ +.|+.+.|.+.|+++.     .||..+||++|.+|++.|++++|.++|++|.+.|+.||..||+.++.+|++.|
T Consensus       164 Li~~y~k~g~~~~A~~lf~~m~-----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~  238 (697)
T PLN03081        164 VLLMHVKCGMLIDARRLFDEMP-----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLG  238 (697)
T ss_pred             HHHHHhcCCCHHHHHHHHhcCC-----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCC
Confidence            56677 7888888888887773     48999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC--
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI--  158 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--  158 (209)
                      ..+.+.+++..+.+.|+.||..+||+||++|++.|++++|.++|++|+++|..+||+||.+|++.|++++|.++|++|  
T Consensus       239 ~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~  318 (697)
T PLN03081        239 SARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRD  318 (697)
T ss_pred             cHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999999  


Q ss_pred             -CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          159 -DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       159 -~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                       |+.||..||+++|++|++.|++++|.+++..|.+.|+.||..+|++||++|
T Consensus       319 ~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y  370 (697)
T PLN03081        319 SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLY  370 (697)
T ss_pred             cCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHH
Confidence             999999999999999999999999999999999999999999999999987

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=5.8e-38  Score=274.53  Aligned_cols=203  Identities=25%  Similarity=0.444  Sum_probs=195.3

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH   80 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~   80 (209)
                      |+.++ +.|+.+.|.+.|.++.     .||..+||++|.+|++.|++++|.++|++|...|+.||..||+.+|++|++.+
T Consensus       127 li~~~~~~g~~~~A~~~f~~m~-----~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~  201 (857)
T PLN03077        127 MLSMFVRFGELVHAWYVFGKMP-----ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIP  201 (857)
T ss_pred             HHHHHHhCCChHHHHHHHhcCC-----CCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCcc
Confidence            56667 7888888888887773     48999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC--
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI--  158 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--  158 (209)
                      +++.+.+++..|.+.|+.||..+||+||.+|++.|++++|.++|++|++||..+||++|.+|++.|++++|+++|.+|  
T Consensus       202 ~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~  281 (857)
T PLN03077        202 DLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRE  281 (857)
T ss_pred             chhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999999  


Q ss_pred             -CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          159 -DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       159 -~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                       |+.||..||+.+|++|++.|+.+.+.+++..|.+.|+.||..+||+||++|
T Consensus       282 ~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y  333 (857)
T PLN03077        282 LSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMY  333 (857)
T ss_pred             cCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHH
Confidence             999999999999999999999999999999999999999999999999876

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.67  E-value=4.8e-15  Score=119.55  Aligned_cols=195  Identities=12%  Similarity=0.064  Sum_probs=107.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH----HHHHHHHHHHhccccH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH----YTFTQALKACSLAHAH   82 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~   82 (209)
                      +.++.+.|.+.+.++.+.  ..++..+++.+...+.+.|++++|.+.++.+.+.+..++.    ..|..+...+.+.|++
T Consensus       119 ~~g~~~~A~~~~~~~l~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~  196 (389)
T PRK11788        119 KAGLLDRAEELFLQLVDE--GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDL  196 (389)
T ss_pred             HCCCHHHHHHHHHHHHcC--CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCH
Confidence            556666666666665543  2234456666666666666666666666666554422211    1234444555566666


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc--HhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD--VVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ++|.+.|+.+.+.. +.+...+..+...|.+.|++++|.++|+++.  .|+  ..+++.+..+|...|++++|...++++
T Consensus       197 ~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  275 (389)
T PRK11788        197 DAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRA  275 (389)
T ss_pred             HHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            66666666665543 2234455555566666666666666666553  222  234555566666666666666666665


Q ss_pred             -CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          159 -DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       159 -~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                       ...|+...+..+...+.+.|++++|..++..+.+.  .|+..+++.++
T Consensus       276 ~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~  322 (389)
T PRK11788        276 LEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLL  322 (389)
T ss_pred             HHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHH
Confidence             44555555555556666666666666666555444  45555554443

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.67  E-value=4.9e-15  Score=119.49  Aligned_cols=165  Identities=10%  Similarity=-0.010  Sum_probs=83.6

Q ss_pred             HHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC
Q 045511           35 NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV  114 (209)
Q Consensus        35 ~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  114 (209)
                      ..+...+.+.|++++|...|+++.+.. +.+...+..+...+.+.|++++|.++++.+.+.+......+++.+...|.+.
T Consensus       184 ~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~  262 (389)
T PRK11788        184 CELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQAL  262 (389)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHc
Confidence            344444455555555555555555432 1223344445555555555555555555555443222233455555555555


Q ss_pred             CChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhcc---ccchhHHHHHHH
Q 045511          115 KDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSS---LGSRKLGKAIHA  188 (209)
Q Consensus       115 g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~---~g~~~~a~~~~~  188 (209)
                      |++++|.+.++++.  .|+...+..+...+.+.|++++|..+|.++ ...|+..++..++..+..   .|+.+++..+++
T Consensus       263 g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~  342 (389)
T PRK11788        263 GDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLR  342 (389)
T ss_pred             CCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHH
Confidence            55555555555542  244444455555555555555555555554 445555555555554432   335555555555


Q ss_pred             HHHHhccCCCch
Q 045511          189 HSLRNLNENNII  200 (209)
Q Consensus       189 ~~~~~~~~p~~~  200 (209)
                      .+.+.++.|++.
T Consensus       343 ~~~~~~~~~~p~  354 (389)
T PRK11788        343 DLVGEQLKRKPR  354 (389)
T ss_pred             HHHHHHHhCCCC
Confidence            555555555543

>PF13041 PPR_2: PPR repeat family

Probab=99.63  E-value=4.9e-16  Score=88.37  Aligned_cols=50  Identities=18%  Similarity=0.267  Sum_probs=29.3

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL   78 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~   78 (209)
                      ||+.+||++|.+|++.|++++|.++|++|.+.|++||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            45555555555555555555555555555555555555555555555543

>PF13041 PPR_2: PPR repeat family

Probab=99.60  E-value=3e-15  Score=85.08  Aligned_cols=50  Identities=16%  Similarity=0.190  Sum_probs=48.5

Q ss_pred             CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           64 YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        64 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      ||+.+|+++|.+|++.|++++|.++|++|.+.|++||..||+.+|++|+|
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

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

Probab=99.46  E-value=7.9e-12  Score=109.83  Aligned_cols=61  Identities=10%  Similarity=0.084  Sum_probs=24.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVI   93 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~   93 (209)
                      ..|..+...+.+.|++++|...|+++.+.+ +.+...+..+...+.+.|++++|.++++.+.
T Consensus       602 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  662 (899)
T TIGR02917       602 EAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRAL  662 (899)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            344444444444444444444444443321 1122333334444444444444444444433

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=99.44  E-value=1.5e-11  Score=108.05  Aligned_cols=198  Identities=12%  Similarity=0.016  Sum_probs=149.2

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      .++ +.++.+++...+.++.+..  +.+...+..+...+.+.|++++|...|+++.+.. +.+..++..+...+...|++
T Consensus       609 ~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~  685 (899)
T TIGR02917       609 RAQLAAGDLNKAVSSFKKLLALQ--PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRT  685 (899)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCH
Confidence            344 5677777777777666543  2345678888888888999999999998887753 34567888888888888999


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC--
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI--  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--  158 (209)
                      ++|.++++.+.+.+ +.+...+..+...+.+.|++++|.+.|..+.  .|+..++..+...+.+.|++++|.+.+..+  
T Consensus       686 ~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~  764 (899)
T TIGR02917       686 ESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLK  764 (899)
T ss_pred             HHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99998888888775 5566778888888888888888888888873  355567777888888888888888888887  


Q ss_pred             CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          159 DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       159 ~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                      ..+.+...+..+...|...|+.++|.+.|+.+.+.. .+++..++.+.
T Consensus       765 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~  811 (899)
T TIGR02917       765 THPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLA  811 (899)
T ss_pred             hCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            334455677778888888888888888888887764 33455555443

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

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.39  E-value=1.3e-11  Score=96.96  Aligned_cols=161  Identities=20%  Similarity=0.265  Sum_probs=134.0

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      .+..+|.++|.++|+-.+.++|.+++++-.....+.+..+||.+|.+-.-.    ...+++.+|....+.||..|+|+++
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~----~~K~Lv~EMisqkm~Pnl~TfNalL  280 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYS----VGKKLVAEMISQKMTPNLFTFNALL  280 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhh----ccHHHHHHHHHhhcCCchHhHHHHH
Confidence            355999999999999999999999999999988999999999999887443    3378899999999999999999999


Q ss_pred             HHHHhCCChhhHHH----HHHhc----CCCcHhHHHHHHHHHHhCCChHH-HHHHHhhC-------CCCC----CHHhHH
Q 045511          109 HFYVTVKDIFSAHQ----IFNSV----VFPDVVTWTTIISGLSKCGFHKE-AIDMFCGI-------DVKP----NANTLV  168 (209)
Q Consensus       109 ~~~~~~g~~~~a~~----~~~~~----~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~m-------~~~p----~~~t~~  168 (209)
                      ++..+.|.++.|.+    ++.+|    ++|...+|.-+|.-+++.++..+ +..+..++       .++|    |...|.
T Consensus       281 ~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~  360 (625)
T KOG4422|consen  281 SCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQ  360 (625)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHH
Confidence            99999999887655    45555    57999999999999999998754 44444444       3333    456788


Q ss_pred             HHHHHhccccchhHHHHHHHHHHHh
Q 045511          169 SVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       169 ~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +.+..|.+..|.+.|+++...+...
T Consensus       361 ~AM~Ic~~l~d~~LA~~v~~ll~tg  385 (625)
T KOG4422|consen  361 SAMSICSSLRDLELAYQVHGLLKTG  385 (625)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcC
Confidence            8899999999999999998766443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.28  E-value=2.9e-10  Score=89.56  Aligned_cols=112  Identities=11%  Similarity=0.118  Sum_probs=66.4

Q ss_pred             CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc----CCCcHhHHHHHHH
Q 045511           65 NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDVVTWTTIIS  140 (209)
Q Consensus        65 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----~~~~~~~~~~li~  140 (209)
                      +..||++||.++|+--..+.|.+++++-.....+.+..++|.+|.+-.-.-+    .++..+|    ..||..|||++++
T Consensus       206 T~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL~  281 (625)
T KOG4422|consen  206 TDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALLS  281 (625)
T ss_pred             CchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHHH
Confidence            4455666666666666666666666666655556666666666654333322    4444444    3466666666666


Q ss_pred             HHHhCCChHHH----HHHHhhC---CCCCCHHhHHHHHHHhccccch
Q 045511          141 GLSKCGFHKEA----IDMFCGI---DVKPNANTLVSVLSACSSLGSR  180 (209)
Q Consensus       141 ~~~~~g~~~~a----~~~~~~m---~~~p~~~t~~~li~~~~~~g~~  180 (209)
                      +.++.|+++.|    .+++.+|   |+.|+..+|..+|+.+++.++.
T Consensus       282 c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp  328 (625)
T KOG4422|consen  282 CAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDP  328 (625)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCc
Confidence            66666665543    3455555   6666666666666666666655

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

Probab=99.25  E-value=1.4e-10  Score=98.13  Aligned_cols=182  Identities=11%  Similarity=0.019  Sum_probs=124.2

Q ss_pred             hHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCC------------------------CCCHHHHHHH
Q 045511           17 QLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPS------------------------SYNHYTFTQA   72 (209)
Q Consensus        17 ~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~------------------------~p~~~t~~~l   72 (209)
                      -|...++..+..|+..+|..+|.-||..|+.+.|- +|.-|+-..+                        .|...||..+
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~L   89 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNL   89 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHH
Confidence            45666677788899999999999999999999998 8777754333                        4677788888


Q ss_pred             HHHHhccccHHHHHHH---HHHHHHh----cc-----------------CccHhHHHHHHHHHHhCCChhhHHHHHH---
Q 045511           73 LKACSLAHAHQKGLEI---HAHVIKY----GH-----------------LHDIFIQNSLLHFYVTVKDIFSAHQIFN---  125 (209)
Q Consensus        73 l~~~~~~~~~~~a~~~---~~~m~~~----g~-----------------~~~~~~~~~ll~~~~~~g~~~~a~~~~~---  125 (209)
                      +.+|...||+...+.+   +..+..+    |+                 -||..   +.+.-....|.++.+.+++.   
T Consensus        90 l~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~---n~illlv~eglwaqllkll~~~P  166 (1088)
T KOG4318|consen   90 LKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAE---NAILLLVLEGLWAQLLKLLAKVP  166 (1088)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHH---HHHHHHHHHHHHHHHHHHHhhCC
Confidence            8888888876542222   2122111    11                 11111   11111122222222222221   


Q ss_pred             -------------hc------------------CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC---CCCCCHHhHHHHH
Q 045511          126 -------------SV------------------VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANTLVSVL  171 (209)
Q Consensus       126 -------------~~------------------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m---~~~p~~~t~~~li  171 (209)
                                   .+                  ..++..+|.+++++-..+|+.+.|..++.+|   |+..+.+-|..+|
T Consensus       167 vsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl  246 (1088)
T KOG4318|consen  167 VSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLL  246 (1088)
T ss_pred             cccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhh
Confidence                         11                  1377888888888888888888888888888   8888888888888


Q ss_pred             HHhccccchhHHHHHHHHHHHhccCCCchhHhHh
Q 045511          172 SACSSLGSRKLGKAIHAHSLRNLNENNIILDNAV  205 (209)
Q Consensus       172 ~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  205 (209)
                      -+   .++...++.++..|...|+.|+..|+..-
T Consensus       247 ~g---~~~~q~~e~vlrgmqe~gv~p~seT~ady  277 (1088)
T KOG4318|consen  247 LG---INAAQVFEFVLRGMQEKGVQPGSETQADY  277 (1088)
T ss_pred             hc---CccchHHHHHHHHHHHhcCCCCcchhHHH
Confidence            77   77888888888888888888888887643

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

Probab=99.18  E-value=2.2e-10  Score=88.68  Aligned_cols=181  Identities=15%  Similarity=0.171  Sum_probs=88.8

Q ss_pred             hhccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHHHHHHHHHHHhccccHHH
Q 045511            6 LKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~   84 (209)
                      +..+++++|.+.+....+..   ++...+..++..+.+.++++++.++++...... .+++...|..+-..+.+.|+.++
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~---~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~  164 (280)
T PF13429_consen   88 LQDGDPEEALKLAEKAYERD---GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDK  164 (280)
T ss_dssp             ---------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHH
T ss_pred             cccccccccccccccccccc---cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHH
Confidence            35566666666665554432   455666677777777777777777777766433 34566667777777777777777


Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV  160 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~  160 (209)
                      |.+.++...+.. +-|....+.++..+...|+.+++.+++...   ...|...+..+-.+|...|+.++|...|.+. ..
T Consensus       165 A~~~~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~  243 (280)
T PF13429_consen  165 ALRDYRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKL  243 (280)
T ss_dssp             HHHHHHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccc
Confidence            877777777654 334667777777777777777766666555   2244556677777777777888887777777 44


Q ss_pred             CC-CHHhHHHHHHHhccccchhHHHHHHHHH
Q 045511          161 KP-NANTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       161 ~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      .| |..+...+..++...|+.++|.++....
T Consensus       244 ~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  244 NPDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             STT-HHHHHHHHHHHT---------------
T ss_pred             ccccccccccccccccccccccccccccccc
Confidence            44 5566677777777777777777776654

>PF12854 PPR_1: PPR repeat

Probab=99.18  E-value=3.5e-11  Score=62.16  Aligned_cols=32  Identities=22%  Similarity=0.392  Sum_probs=23.3

Q ss_pred             ccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           96 GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        96 g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      |+.||..|||+||++||+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            56777777777777777777777777777766

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.18  E-value=5.8e-09  Score=77.38  Aligned_cols=160  Identities=12%  Similarity=0.026  Sum_probs=78.9

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+..+...+.+.|++++|.+.+++..+.. +.+...+..+...+...|+++.|.+.++...+.. +.+...+..+...+
T Consensus        32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~  109 (234)
T TIGR02521        32 KIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFL  109 (234)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            444445555555555555555555554432 1223444555555555555555555555555443 22334455555555


Q ss_pred             HhCCChhhHHHHHHhcCC-----CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHH
Q 045511          112 VTVKDIFSAHQIFNSVVF-----PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~  184 (209)
                      ...|++++|.+.+++..+     .....+..+-..+...|++++|...|.+. ...|+ ...+..+...+...|++++|.
T Consensus       110 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  189 (234)
T TIGR02521       110 CQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDAR  189 (234)
T ss_pred             HHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHH
Confidence            555555555555555421     11223444445555555555555555555 32332 234444555555555555555


Q ss_pred             HHHHHHHHh
Q 045511          185 AIHAHSLRN  193 (209)
Q Consensus       185 ~~~~~~~~~  193 (209)
                      +.++...+.
T Consensus       190 ~~~~~~~~~  198 (234)
T TIGR02521       190 AYLERYQQT  198 (234)
T ss_pred             HHHHHHHHh
Confidence            555554443

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.14  E-value=1.6e-08  Score=75.04  Aligned_cols=184  Identities=9%  Similarity=-0.036  Sum_probs=147.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      ..++.+++...+.+..+..  +.+...+..+...+...|++++|.+.+++..+.+. .+...+..+...+...|++++|.
T Consensus        43 ~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~~~~g~~~~A~  119 (234)
T TIGR02521        43 EQGDLEVAKENLDKALEHD--PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNP-NNGDVLNNYGTFLCQQGKYEQAM  119 (234)
T ss_pred             HCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcccHHHHH
Confidence            6778888888888776653  22457888888999999999999999999987642 35567788888899999999999


Q ss_pred             HHHHHHHHhcc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC
Q 045511           87 EIHAHVIKYGH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK  161 (209)
Q Consensus        87 ~~~~~m~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~  161 (209)
                      +.++...+... ......+..+-..+...|++++|.+.+++...   .+...+..+...+...|++++|.+.+++. ...
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  199 (234)
T TIGR02521       120 QQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQTY  199 (234)
T ss_pred             HHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999987542 23455777888899999999999999988732   34667888899999999999999999998 433


Q ss_pred             C-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 P-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      | +...+..+...+...|+.+.|..+.+.+.+.
T Consensus       200 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       200 NQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            4 4566777788888999999999988776543

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

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.12  E-value=1e-08  Score=88.18  Aligned_cols=152  Identities=14%  Similarity=0.092  Sum_probs=82.8

Q ss_pred             HHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhh-
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFS-  119 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~-  119 (209)
                      +.+.|++++|...++.+.+..-.++...+..+..++.+.|++++|...++...+.. +.+...+..+-..|...|++++ 
T Consensus       187 l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA  265 (656)
T PRK15174        187 FLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREA  265 (656)
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhh
Confidence            44555555555555555443322333333444455555666666666666655543 2334555556666666666654 


Q ss_pred             ---HHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          120 ---AHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       120 ---a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                         |...|++..  .| +...+..+...+...|++++|...+++. ...|+. .....+-..+...|++++|.+.+..+.
T Consensus       266 ~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al  345 (656)
T PRK15174        266 KLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLA  345 (656)
T ss_pred             HHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence               555555542  12 3445666666666666666666666666 444443 334445555566666666666666555


Q ss_pred             Hh
Q 045511          192 RN  193 (209)
Q Consensus       192 ~~  193 (209)
                      +.
T Consensus       346 ~~  347 (656)
T PRK15174        346 RE  347 (656)
T ss_pred             Hh
Confidence            43

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

Probab=99.11  E-value=2.4e-10  Score=88.46  Aligned_cols=148  Identities=15%  Similarity=0.091  Sum_probs=55.2

Q ss_pred             cCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhc-cCccHhHHHHHHHHHHhCCChhhHH
Q 045511           43 QSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYG-HLHDIFIQNSLLHFYVTVKDIFSAH  121 (209)
Q Consensus        43 ~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~g~~~~a~  121 (209)
                      ..+++++|.++++...+..  ++...+..++..+.+.++++.+.++++...+.. .+.+...|..+-..+.+.|+.++|.
T Consensus        89 ~~~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~  166 (280)
T PF13429_consen   89 QDGDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKAL  166 (280)
T ss_dssp             -------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHH
T ss_pred             ccccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            4444444444443332221  333444444555555555555555555544322 2334445555555555555555555


Q ss_pred             HHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          122 QIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       122 ~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      +++++..  .| |....+.++..+...|+.+++.+++...  ....|...+..+-.++...|+.++|...+....+
T Consensus       167 ~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~  242 (280)
T PF13429_consen  167 RDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALK  242 (280)
T ss_dssp             HHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccc
Confidence            5555541  23 2444555555555555555555555444  2223333444555555555555555555555444

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.10  E-value=1.3e-08  Score=87.61  Aligned_cols=183  Identities=11%  Similarity=0.018  Sum_probs=115.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|...+.++.+..  +.+...+..+...+.+.|+.++|...++.+......+ ...+.. +..+...|++++|.
T Consensus       122 ~~g~~~~Ai~~l~~Al~l~--P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~-~~~l~~~g~~~eA~  197 (656)
T PRK15174        122 KSKQYATVADLAEQAWLAF--SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIAT-CLSFLNKSRLPEDH  197 (656)
T ss_pred             HcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHH-HHHHHHcCCHHHHH
Confidence            4555566665555555442  1233566666666777777777777776665433211 122222 23356667777777


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHH----HHHHHhhC-
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKE----AIDMFCGI-  158 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~----a~~~~~~m-  158 (209)
                      ..++.+.+....++...+..+...+.+.|+.++|.+.+++..+   .+...+..+-..+...|++++    |...|.+. 
T Consensus       198 ~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al  277 (656)
T PRK15174        198 DLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHAL  277 (656)
T ss_pred             HHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHH
Confidence            7777666554333344445556677777788888777777632   345666777777888888775    67777777 


Q ss_pred             CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          159 DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       159 ~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ...|+. ..+..+...+...|++++|...++...+.
T Consensus       278 ~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l  313 (656)
T PRK15174        278 QFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLAT  313 (656)
T ss_pred             hhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            666654 46777778888888888888888877665

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

Probab=99.06  E-value=1.2e-09  Score=92.58  Aligned_cols=150  Identities=15%  Similarity=0.046  Sum_probs=108.1

Q ss_pred             HHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc------------------------CccHhHHHHH
Q 045511           52 PLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH------------------------LHDIFIQNSL  107 (209)
Q Consensus        52 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~------------------------~~~~~~~~~l  107 (209)
                      .++-.+...|+.||.+||..+|..||..|+.+.|. +|..|.-+..                        .|.+-||++|
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~L   89 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNL   89 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHH
Confidence            46778999999999999999999999999999998 8887764432                        2567799999


Q ss_pred             HHHHHhCCChhh---HHHHHHhcC-------------------------CCcHhHHHHHHHHHHhCCChHHHHHHH----
Q 045511          108 LHFYVTVKDIFS---AHQIFNSVV-------------------------FPDVVTWTTIISGLSKCGFHKEAIDMF----  155 (209)
Q Consensus       108 l~~~~~~g~~~~---a~~~~~~~~-------------------------~~~~~~~~~li~~~~~~g~~~~a~~~~----  155 (209)
                      ..+|...||+..   .++.+..+.                         -||..   +.+.-....|.|+.+.++.    
T Consensus        90 l~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~---n~illlv~eglwaqllkll~~~P  166 (1088)
T KOG4318|consen   90 LKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAE---NAILLLVLEGLWAQLLKLLAKVP  166 (1088)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHH---HHHHHHHHHHHHHHHHHHHhhCC
Confidence            999999998654   333222210                         02211   1122222223333332222    


Q ss_pred             ------------hhC------------------CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHh
Q 045511          156 ------------CGI------------------DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAV  205 (209)
Q Consensus       156 ------------~~m------------------~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  205 (209)
                                  +.+                  + .|+..+|..++++..-+|+.+.|..++..|++.|+..+.+-|-.|
T Consensus       167 vsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e-~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpL  245 (1088)
T KOG4318|consen  167 VSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVE-APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPL  245 (1088)
T ss_pred             cccccchHHHHHHHhccCCchHHHHHHHHHHhhc-CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhh
Confidence                        222                  3 599999999999999999999999999999999999988866655


Q ss_pred             h
Q 045511          206 L  206 (209)
Q Consensus       206 i  206 (209)
                      +
T Consensus       246 l  246 (1088)
T KOG4318|consen  246 L  246 (1088)
T ss_pred             h
Confidence            4

>PF12854 PPR_1: PPR repeat

Probab=99.05  E-value=2.8e-10  Score=58.73  Aligned_cols=33  Identities=9%  Similarity=0.120  Sum_probs=24.6

Q ss_pred             CCCCCCHHHHHHHHHHHhccccHHHHHHHHHHH
Q 045511           60 CPSSYNHYTFTQALKACSLAHAHQKGLEIHAHV   92 (209)
Q Consensus        60 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m   92 (209)
                      .|+.||..||+++|.++|+.|++++|.++|++|
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            367777777777777777777777777777776

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

Probab=99.01  E-value=5.2e-08  Score=83.45  Aligned_cols=159  Identities=9%  Similarity=-0.036  Sum_probs=136.2

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC-HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN-HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      ..|+.+-..+...|++++|...|++..+.  .|+ ...|..+-..+...|++++|...|+...+.. +.+..+|..+-..
T Consensus       332 ~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~  408 (615)
T TIGR00990       332 IALNLRGTFKCLKGKHLEALADLSKSIEL--DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQL  408 (615)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            67888888888999999999999998875  354 5678888888999999999999999998764 4557889999999


Q ss_pred             HHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHH
Q 045511          111 YVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKA  185 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~  185 (209)
                      +...|++++|.+.|++..  .| +...+..+-..+.+.|++++|+..|++. ...|+ ...++.+-..+...|++++|..
T Consensus       409 ~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~  488 (615)
T TIGR00990       409 HFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIE  488 (615)
T ss_pred             HHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHH
Confidence            999999999999999883  23 5677788889999999999999999998 55665 5678888899999999999999


Q ss_pred             HHHHHHHh
Q 045511          186 IHAHSLRN  193 (209)
Q Consensus       186 ~~~~~~~~  193 (209)
                      .|+...+.
T Consensus       489 ~~~~Al~l  496 (615)
T TIGR00990       489 KFDTAIEL  496 (615)
T ss_pred             HHHHHHhc
Confidence            99987665

>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=98.99  E-value=7.4e-08  Score=82.53  Aligned_cols=147  Identities=15%  Similarity=0.041  Sum_probs=84.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC-cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      ..++.++|...+.++.+..   |+ ...|..+-..+...|++++|...|++..+.. +-+...|..+-..+...|++++|
T Consensus       343 ~~g~~~eA~~~~~kal~l~---P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A  418 (615)
T TIGR00990       343 LKGKHLEALADLSKSIELD---PRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQA  418 (615)
T ss_pred             HcCCHHHHHHHHHHHHHcC---CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            3455555555555544432   33 2455566666666667777777666665542 22345566666666666666666


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ...|+...+.. +.+...+..+-..+.+.|++++|...|++..  .| +...|+.+-..+...|++++|...|++.
T Consensus       419 ~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~A  493 (615)
T TIGR00990       419 GKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTA  493 (615)
T ss_pred             HHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            66666665543 2334555556666666666666666666552  12 3455556666666666666666666654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.89  E-value=2e-07  Score=83.01  Aligned_cols=157  Identities=6%  Similarity=-0.047  Sum_probs=79.5

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      +..+...+.+.|+.++|...+++..+.+ +++...+..+.......|++++|...++...+..  |+...|..+-..+.+
T Consensus       545 ~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~~l~~  621 (987)
T PRK09782        545 LLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--PSANAYVARATIYRQ  621 (987)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHH
Confidence            3334444445555555555555554432 1111222222222333355555555555555432  345555555566666


Q ss_pred             CCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHH
Q 045511          114 VKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       114 ~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      .|+.++|.+.+++..  .| +...++.+-..+...|++++|+..|.+. ...|+. ..+..+-.++...|++++|+..++
T Consensus       622 lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~  701 (987)
T PRK09782        622 RHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYAR  701 (987)
T ss_pred             CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            666666666665552  22 3445555555566666666666666555 444433 345555555566666666666665


Q ss_pred             HHHHh
Q 045511          189 HSLRN  193 (209)
Q Consensus       189 ~~~~~  193 (209)
                      ...+.
T Consensus       702 ~Al~l  706 (987)
T PRK09782        702 LVIDD  706 (987)
T ss_pred             HHHhc
Confidence            55433

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.88  E-value=3.6e-07  Score=81.41  Aligned_cols=183  Identities=10%  Similarity=0.009  Sum_probs=137.8

Q ss_pred             chhccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHH
Q 045511            5 GLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         5 ~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~   84 (209)
                      ++..+++.+|...+.+.....   |+....-.+...+.+.|++++|...|+++...  +|+...+..+..++.+.|++++
T Consensus       486 ~l~~~~~~eAi~a~~~Al~~~---Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~e  560 (987)
T PRK09782        486 CYRDTLPGVALYAWLQAEQRQ---PDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAA  560 (987)
T ss_pred             HHHhCCcHHHHHHHHHHHHhC---CchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHH
Confidence            333356666776666665543   55433223344446899999999999998654  4555556667778889999999


Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK  161 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~  161 (209)
                      |.+.++...+.. +.+...+..+...+.+.|++++|...+++..  .|+...|..+-..+.+.|++++|...|.+. ...
T Consensus       561 A~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~  639 (987)
T PRK09782        561 RDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALELE  639 (987)
T ss_pred             HHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            999999998765 3333344444445556699999999999884  477888999999999999999999999999 777


Q ss_pred             CCHH-hHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PNAN-TLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~~~-t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |+.. .+..+-.++...|+.++|.+.+....+.
T Consensus       640 Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l  672 (987)
T PRK09782        640 PNNSNYQAALGYALWDSGDIAQSREMLERAHKG  672 (987)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            8664 5666777888999999999999988775

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.85  E-value=3.8e-07  Score=80.04  Aligned_cols=185  Identities=12%  Similarity=0.073  Sum_probs=141.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC---CHHHHHHHHHHHhccccH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY---NHYTFTQALKACSLAHAH   82 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p---~~~t~~~ll~~~~~~~~~   82 (209)
                      ..++.++|...+.++.+.....|+. ..+  +-..+...|++++|...|++..+..-..   .......+..++...|++
T Consensus       249 ~~g~~~eA~~~~~~ll~~~~~~P~~a~~~--la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~  326 (765)
T PRK10049        249 ARDRYKDVISEYQRLKAEGQIIPPWAQRW--VASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENY  326 (765)
T ss_pred             HhhhHHHHHHHHHHhhccCCCCCHHHHHH--HHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccH
Confidence            5566677777777776653322332 222  4668889999999999999987643111   134566777788999999


Q ss_pred             HHHHHHHHHHHHhcc-----------Ccc---HhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           83 QKGLEIHAHVIKYGH-----------LHD---IFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~-----------~~~---~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      ++|.++++.+.+...           .|+   ...+..+...+...|+.++|+++++++.   ..+...+..+...+...
T Consensus       327 ~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~  406 (765)
T PRK10049        327 PGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQAR  406 (765)
T ss_pred             HHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhc
Confidence            999999999987631           123   2355677788999999999999999983   23577888999999999


Q ss_pred             CChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          146 GFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       146 g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |++++|++.+++. ...||. ..+......+...|++++|+.+++.+.+.
T Consensus       407 g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        407 GWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             CCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            9999999999999 778875 45556666788999999999999998876

>PRK12370 invasion protein regulator; Provisional

Probab=98.79  E-value=6.5e-07  Score=75.80  Aligned_cols=174  Identities=11%  Similarity=-0.063  Sum_probs=124.1

Q ss_pred             CcchHhHHHHHHHHhhCC-CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHH
Q 045511           12 TLSFKQLNQIHAQIIKIP-QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHA   90 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~   90 (209)
                      .+|...+.++.+.   .| +...+..+-..+...|++++|...|++..+.+ +.+...+..+-..+...|++++|...++
T Consensus       321 ~~A~~~~~~Al~l---dP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~  396 (553)
T PRK12370        321 IKAKEHAIKATEL---DHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTIN  396 (553)
T ss_pred             HHHHHHHHHHHhc---CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            3444444444433   34 44777777778889999999999999998865 2345677778888999999999999999


Q ss_pred             HHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511           91 HVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus        91 ~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      ...+.... +...+..+...+...|++++|...+.+..   .| +...+..+-..+...|+.++|...+.++ ...|+..
T Consensus       397 ~Al~l~P~-~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~  475 (553)
T PRK12370        397 ECLKLDPT-RAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGL  475 (553)
T ss_pred             HHHhcCCC-ChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhH
Confidence            99876522 22333344445667899999999998763   24 3455677778888999999999999998 5566654


Q ss_pred             h-HHHHHHHhccccchhHHHHHHHHHHH
Q 045511          166 T-LVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       166 t-~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      + .+.+...+...|+  ++...++.+.+
T Consensus       476 ~~~~~l~~~~~~~g~--~a~~~l~~ll~  501 (553)
T PRK12370        476 IAVNLLYAEYCQNSE--RALPTIREFLE  501 (553)
T ss_pred             HHHHHHHHHHhccHH--HHHHHHHHHHH
Confidence            4 4445556677774  67776666544

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.78  E-value=3.2e-07  Score=74.58  Aligned_cols=60  Identities=23%  Similarity=0.249  Sum_probs=40.2

Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          132 VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       132 ~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      .....++-..+.+.|+|++|.+.|... ...|+..+|..+-..+.+.|+.++|.+.++.-.
T Consensus       328 ~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        328 PLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334555566666777777777777766 666777777777777777777777776666543

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.74  E-value=9.5e-07  Score=80.86  Aligned_cols=184  Identities=14%  Similarity=0.098  Sum_probs=128.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCC-CCHHHHHH------------HH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSS-YNHYTFTQ------------AL   73 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-p~~~t~~~------------ll   73 (209)
                      ..++.++|...+.++.+..+  .+...+..+-..+.+.|++++|...|++..+..-. ++...+..            .-
T Consensus       281 ~~g~~~~A~~~l~~aL~~~P--~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g  358 (1157)
T PRK11447        281 DSGQGGKAIPELQQAVRANP--KDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQG  358 (1157)
T ss_pred             HCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHH
Confidence            66777888888877777531  25577788888888888888888888888764421 11111211            12


Q ss_pred             HHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--Cc-HhHHH--------------
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PD-VVTWT--------------  136 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~-~~~~~--------------  136 (209)
                      ..+.+.|++++|.+.|+...+.. +.+...+..+-..+...|++++|++.|++..+  |+ ...+.              
T Consensus       359 ~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~~~~~~~A  437 (1157)
T PRK11447        359 DAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYRQQSPEKA  437 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHH
Confidence            34567788888888888887764 34556777778888888888888888877631  22 22222              


Q ss_pred             ----------------------------HHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHH
Q 045511          137 ----------------------------TIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       137 ----------------------------~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~  186 (209)
                                                  .+...+...|++++|.+.|++. ...|+. ..+..+...+.+.|++++|...
T Consensus       438 ~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~  517 (1157)
T PRK11447        438 LAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADAL  517 (1157)
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence                                        2233455678999999999888 667754 4566777888899999999999


Q ss_pred             HHHHHHh
Q 045511          187 HAHSLRN  193 (209)
Q Consensus       187 ~~~~~~~  193 (209)
                      ++.+.+.
T Consensus       518 l~~al~~  524 (1157)
T PRK11447        518 MRRLAQQ  524 (1157)
T ss_pred             HHHHHHc
Confidence            9988764

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.73  E-value=1.4e-06  Score=79.69  Aligned_cols=185  Identities=14%  Similarity=0.009  Sum_probs=127.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      ..++.++|.+.+.++.+..+.  +...+..+...+.+.|++++|...+++..+..- -+...+..+...+...++.++|.
T Consensus       473 ~~g~~~eA~~~~~~Al~~~P~--~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P-~~~~~~~a~al~l~~~~~~~~Al  549 (1157)
T PRK11447        473 NQGKWAQAAELQRQRLALDPG--SVWLTYRLAQDLRQAGQRSQADALMRRLAQQKP-NDPEQVYAYGLYLSGSDRDRAAL  549 (1157)
T ss_pred             HCCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHhCCCHHHHH
Confidence            567777888878777765422  345677788889999999999999999876431 12222222222333444444444


Q ss_pred             HHHHHHHHh---------------------------------------ccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           87 EIHAHVIKY---------------------------------------GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        87 ~~~~~m~~~---------------------------------------g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ..++.+...                                       ..+.+...+..+-..+.+.|+.++|.+.|++.
T Consensus       550 ~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~a  629 (1157)
T PRK11447        550 AHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRV  629 (1157)
T ss_pred             HHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444332111                                       12345556677888888889999999998887


Q ss_pred             C--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          128 V--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       128 ~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .  .| +...+..+...|...|++++|.+.++.. ...|+. .+...+-.++...|++++|.++++.+.+..
T Consensus       630 l~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~  701 (1157)
T PRK11447        630 LTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQA  701 (1157)
T ss_pred             HHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhC
Confidence            3  23 5778888889999999999999999888 666654 445566677778899999999999887653

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.73  E-value=1.2e-08  Score=52.79  Aligned_cols=33  Identities=24%  Similarity=0.349  Sum_probs=24.6

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN   65 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~   65 (209)
                      +||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            677777777777777777777777777777776

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.

>TIGR00540 hemY_coli hemY protein

Probab=98.73  E-value=4.8e-07  Score=73.80  Aligned_cols=118  Identities=13%  Similarity=0.024  Sum_probs=51.9

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHH---hccccHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKAC---SLAHAHQK   84 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~---~~~~~~~~   84 (209)
                      .++.+.|...+..+.+..+.  +..+...+...+.+.|++++|.+++..+.+.+..++...-..-..+.   ...+..+.
T Consensus       166 ~~~~~~Al~~l~~l~~~~P~--~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~  243 (409)
T TIGR00540       166 QNELHAARHGVDKLLEMAPR--HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADE  243 (409)
T ss_pred             CCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44444444444444444311  22455555666666666666666666666554322111111111111   11111111


Q ss_pred             HHHHHHHHHHhcc---CccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           85 GLEIHAHVIKYGH---LHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        85 a~~~~~~m~~~g~---~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ..+.+..+.+...   +.+...+-.+...+...|+.++|.+++++.
T Consensus       244 ~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~  289 (409)
T TIGR00540       244 GIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDG  289 (409)
T ss_pred             CHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHH
Confidence            1122222222211   124555556666666667777776666554

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.

>PRK12370 invasion protein regulator; Provisional

Probab=98.70  E-value=3e-06  Score=71.82  Aligned_cols=147  Identities=11%  Similarity=-0.091  Sum_probs=114.0

Q ss_pred             CCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHH
Q 045511           45 STPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIF  124 (209)
Q Consensus        45 g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~  124 (209)
                      ++.++|...+++..+.+ +-+...+..+-..+...|++++|...|+...+.. +.+...+..+-..+...|++++|...+
T Consensus       318 ~~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~  395 (553)
T PRK12370        318 NAMIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTI  395 (553)
T ss_pred             hHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            45789999999988864 2355677777778889999999999999998876 445678888899999999999999999


Q ss_pred             HhcC--CCcH-hHHHHHHHHHHhCCChHHHHHHHhhC-C-CCCCHH-hHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          125 NSVV--FPDV-VTWTTIISGLSKCGFHKEAIDMFCGI-D-VKPNAN-TLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       125 ~~~~--~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m-~-~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ++..  .|+. ..+..+...+...|++++|...+.+. . ..|+.. .+..+-.++...|+.++|.+.+..+...
T Consensus       396 ~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~  470 (553)
T PRK12370        396 NECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ  470 (553)
T ss_pred             HHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc
Confidence            9983  3432 23334455577789999999999887 3 346554 4566667778999999999999876544

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.68  E-value=2.5e-06  Score=74.96  Aligned_cols=184  Identities=10%  Similarity=-0.022  Sum_probs=132.9

Q ss_pred             CcchHhHHHHHHHHhhCCCcc-cHH----HHHHHHHcCCCccchHHHHHHhhhCCCC-CCHHHHHHHHHHHhccccHHHH
Q 045511           12 TLSFKQLNQIHAQIIKIPQPH-ILN----TLLKLLTQSSTPQNAIPLYNKMLNCPSS-YNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p~~~-~~~----~li~~~~~~g~~~~a~~l~~~m~~~g~~-p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +.|.+.++.+.+.....|+.. .+.    ..+..+...|+.++|...|+.+.+.+-+ |+. .-..+-.++...|++++|
T Consensus       213 d~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A  291 (765)
T PRK10049        213 DRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKA  291 (765)
T ss_pred             HHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHH
Confidence            345555556655544444432 111    1134556779999999999999987632 432 222246689999999999


Q ss_pred             HHHHHHHHHhccCc---cHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-------------c---HhHHHHHHHHHHh
Q 045511           86 LEIHAHVIKYGHLH---DIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-------------D---VVTWTTIISGLSK  144 (209)
Q Consensus        86 ~~~~~~m~~~g~~~---~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-------------~---~~~~~~li~~~~~  144 (209)
                      ...|+.+.+.....   .......+..++...|++++|.++++.+.+  |             +   ...+..+...+..
T Consensus       292 ~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~  371 (765)
T PRK10049        292 QSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKY  371 (765)
T ss_pred             HHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHH
Confidence            99999987654211   134567778889999999999999998832  2             2   2345667788899


Q ss_pred             CCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHhccCCC
Q 045511          145 CGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENN  198 (209)
Q Consensus       145 ~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~  198 (209)
                      .|++++|++.++++ ...|+. ..+..+...+...|++++|++.++...+.  .|+
T Consensus       372 ~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l--~Pd  425 (765)
T PRK10049        372 SNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAEVL--EPR  425 (765)
T ss_pred             cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh--CCC
Confidence            99999999999999 555644 56788888889999999999999988775  355

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.68  E-value=4.9e-06  Score=65.01  Aligned_cols=162  Identities=10%  Similarity=-0.100  Sum_probs=86.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|..+-..+.+.|+.++|...|++..+.. +.+...|..+-..+...|+++.|.+.|+...+.. +-+..+|..+-..+
T Consensus        65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l  142 (296)
T PRK11189         65 QLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAYLNRGIAL  142 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            345555555566666666666666665543 1234556666666666666666666666665533 22344555555666


Q ss_pred             HhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCC------------------------
Q 045511          112 VTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPN------------------------  163 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~------------------------  163 (209)
                      ...|++++|.+.|+...  .|+..........+...+++++|...|.+.  ...|+                        
T Consensus       143 ~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~~~~~~~~lg~~~~~~~~~~~~  222 (296)
T PRK11189        143 YYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQAKENLKQRYEKLDKEQWGWNIVEFYLGKISEETLMERLK  222 (296)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhCCccccHHHHHHHHccCCCHHHHHHHHH
Confidence            66666666666665542  222111111111122334455555555332  11111                        


Q ss_pred             -------------HHhHHHHHHHhccccchhHHHHHHHHHHHhcc
Q 045511          164 -------------ANTLVSVLSACSSLGSRKLGKAIHAHSLRNLN  195 (209)
Q Consensus       164 -------------~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~  195 (209)
                                   ..+|.-+-..+...|++++|...|+...+.+.
T Consensus       223 ~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        223 AGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             hcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence                         12455556666777888888888887776653

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.67  E-value=2e-06  Score=75.36  Aligned_cols=186  Identities=10%  Similarity=0.054  Sum_probs=140.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCC-----CCCCHHHHHHHHHHHhcccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCP-----SSYNHYTFTQALKACSLAHA   81 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-----~~p~~~t~~~ll~~~~~~~~   81 (209)
                      ++++..++.+.++.+.......|+. +--.+.++|...+++++|..+|+......     ..++......|..++...++
T Consensus       304 ~r~r~~~vi~~y~~l~~~~~~~P~y-~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~  382 (822)
T PRK14574        304 VRHQTADLIKEYEAMEAEGYKMPDY-ARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQ  382 (822)
T ss_pred             HhhhHHHHHHHHHHhhhcCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhccc
Confidence            5555556666666665554444544 55678899999999999999999986643     23344556889999999999


Q ss_pred             HHHHHHHHHHHHHhcc-----------Ccc--H-hHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh
Q 045511           82 HQKGLEIHAHVIKYGH-----------LHD--I-FIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK  144 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~-----------~~~--~-~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~  144 (209)
                      +++|..+++.+.+...           .||  - ..+..+...+...|+..+|++.++++.   .-|......+-+.+..
T Consensus       383 ~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~  462 (822)
T PRK14574        383 LDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLA  462 (822)
T ss_pred             HHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence            9999999999987321           122  1 244566777889999999999999983   2477888899999999


Q ss_pred             CCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          145 CGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       145 ~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .|.+.+|++.++.. .+.|+. .+......++...|++.+|+.+.+.+.+.
T Consensus       463 Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~  513 (822)
T PRK14574        463 RDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQMELLTDDVISR  513 (822)
T ss_pred             cCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence            99999999999777 777765 56677788888899999998888666444

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.66  E-value=2.7e-08  Score=51.28  Aligned_cols=32  Identities=22%  Similarity=0.378  Sum_probs=16.7

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCC
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY   64 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p   64 (209)
                      +||.+|.+|++.|+++.|.++|++|++.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            45555555555555555555555555555444

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.65  E-value=3.4e-08  Score=51.08  Aligned_cols=34  Identities=12%  Similarity=0.129  Sum_probs=25.6

Q ss_pred             hHHHHHHHhccccchhHHHHHHHHHHHhccCCCc
Q 045511          166 TLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNI  199 (209)
Q Consensus       166 t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~  199 (209)
                      ||+++|++|++.|++++|.++|.+|.+.|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            6777777777777777777777777777777763

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.

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

Probab=98.65  E-value=4.6e-07  Score=74.96  Aligned_cols=152  Identities=14%  Similarity=0.168  Sum_probs=69.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      .++..+-..|-..|.+|.|.+.|++..+.  .|+- ..|+.|-.++-..|++.+|.+.+...+.-. +.-..+.+.|-..
T Consensus       287 ~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~-p~hadam~NLgni  363 (966)
T KOG4626|consen  287 VAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLC-PNHADAMNNLGNI  363 (966)
T ss_pred             hhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            34444444444445555555555544442  2221 345555555555555555555555544432 1223344555555


Q ss_pred             HHhCCChhhHHHHHHhcC--CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHH
Q 045511          111 YVTVKDIFSAHQIFNSVV--FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKA  185 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~  185 (209)
                      |...|.+++|.++|...-  .|. ....|.|-..|-+.|++++|+.-|++. .++|+. ..|+-+-+.|-..|+.+.|.+
T Consensus       364 ~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q  443 (966)
T KOG4626|consen  364 YREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQ  443 (966)
T ss_pred             HHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHH
Confidence            555555555555554431  122 223444555555555555555555544 444443 234444444444444444433


Q ss_pred             H
Q 045511          186 I  186 (209)
Q Consensus       186 ~  186 (209)
                      -
T Consensus       444 ~  444 (966)
T KOG4626|consen  444 C  444 (966)
T ss_pred             H
Confidence            3

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

Probab=98.64  E-value=4.7e-06  Score=65.48  Aligned_cols=191  Identities=12%  Similarity=0.082  Sum_probs=148.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC-------HHHHHHHHHHHhcc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN-------HYTFTQALKACSLA   79 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~-------~~t~~~ll~~~~~~   79 (209)
                      ..++...|...+.++.+..+  .++.........|.+.|++..+..++..|.+.|+--|       ..+|..++.-....
T Consensus       165 ~~~d~~aA~~~v~~ll~~~p--r~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~  242 (400)
T COG3071         165 NRRDYPAARENVDQLLEMTP--RHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDD  242 (400)
T ss_pred             hCCCchhHHHHHHHHHHhCc--CChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhcc
Confidence            56667777777888777643  3557888999999999999999999999999986443       34577777777777


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--------------------------------
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--------------------------------  127 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--------------------------------  127 (209)
                      +..+.-...++...++ .+.++..-.+++.-+...|+.++|.++..+.                                
T Consensus       243 ~~~~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l  321 (400)
T COG3071         243 NGSEGLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWL  321 (400)
T ss_pred             ccchHHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHH
Confidence            7666666666666544 3556667777888888888888888877443                                


Q ss_pred             --CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCch
Q 045511          128 --VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNII  200 (209)
Q Consensus       128 --~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~  200 (209)
                        ..-+.-.+.+|=..|.+++.|.+|.+.|+.- ..+|+..+|+.+-.++.+.|+.++|.++.++....-..|+..
T Consensus       322 ~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~~~  397 (400)
T COG3071         322 KQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPNLP  397 (400)
T ss_pred             HhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCCCc
Confidence              0123456778888899999999999999987 999999999999999999999999999999877665555543

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

Probab=98.62  E-value=4e-07  Score=59.28  Aligned_cols=80  Identities=10%  Similarity=-0.011  Sum_probs=70.2

Q ss_pred             HHHHHHHHcCCCccchHHHHHHhhhCCC-CCCHHHHHHHHHHHhccc--------cHHHHHHHHHHHHHhccCccHhHHH
Q 045511           35 NTLLKLLTQSSTPQNAIPLYNKMLNCPS-SYNHYTFTQALKACSLAH--------AHQKGLEIHAHVIKYGHLHDIFIQN  105 (209)
Q Consensus        35 ~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~m~~~g~~~~~~~~~  105 (209)
                      ..-|..|...+++.....+|+.+++.|+ .|++.+|+.++.+.++..        ++.....+++.|+..+++|+..+||
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            4567777788999999999999999999 999999999999987763        3456778899999999999999999


Q ss_pred             HHHHHHHhC
Q 045511          106 SLLHFYVTV  114 (209)
Q Consensus       106 ~ll~~~~~~  114 (209)
                      .++..+.+.
T Consensus       109 ivl~~Llkg  117 (120)
T PF08579_consen  109 IVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHh
Confidence            999988764

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

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.59  E-value=7e-08  Score=49.66  Aligned_cols=33  Identities=15%  Similarity=0.203  Sum_probs=28.1

Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHHHHhccCC
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHSLRNLNEN  197 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  197 (209)
                      .||+.+|++|++.|+++.|.++|++|.+.|++|
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            578888888888888888888888888888877

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.56  E-value=3.7e-06  Score=68.43  Aligned_cols=193  Identities=7%  Similarity=-0.008  Sum_probs=146.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-------HHHHHHHHHHhcc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-------YTFTQALKACSLA   79 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-------~t~~~ll~~~~~~   79 (209)
                      ..++.+.|...+.++.+..+..|...-.-  ...+.+.|++++|..++..+.+.+..++.       .+|..++......
T Consensus       165 ~~g~~~~Al~~l~~~~~~~P~~~~al~ll--~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~  242 (398)
T PRK10747        165 ARNENHAARHGVDKLLEVAPRHPEVLRLA--EQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMAD  242 (398)
T ss_pred             HCCCHHHHHHHHHHHHhcCCCCHHHHHHH--HHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            68899999999999988876666664433  24557779999999999999998765332       2445555555555


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--CcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      .+.+...++++.+.+. .+.++.....+...+...|+.++|.+++++.-+  ++..  -.++.+....++.+++....+.
T Consensus       243 ~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~~~~--l~~l~~~l~~~~~~~al~~~e~  319 (398)
T PRK10747        243 QGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQYDER--LVLLIPRLKTNNPEQLEKVLRQ  319 (398)
T ss_pred             cCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHH--HHHHHhhccCCChHHHHHHHHH
Confidence            6667777777776544 356788999999999999999999999988733  3432  2345666677999999999988


Q ss_pred             C-CCCCCHH-hHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          158 I-DVKPNAN-TLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       158 m-~~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                      . ...|+.. ....+-+.|.+.|++++|.+.|+...+.  .|+...+..|-
T Consensus       320 ~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La  368 (398)
T PRK10747        320 QIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLA  368 (398)
T ss_pred             HHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHH
Confidence            8 6677665 5778888999999999999999988876  57776655443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.54  E-value=8.3e-06  Score=71.62  Aligned_cols=172  Identities=10%  Similarity=0.051  Sum_probs=121.1

Q ss_pred             hhccCCCcchHhHHHHHHHHhhCCCc--ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC-CHHHHHHH--HHHHhccc
Q 045511            6 LKSLKPTLSFKQLNQIHAQIIKIPQP--HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY-NHYTFTQA--LKACSLAH   80 (209)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~~~~~p~~--~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-~~~t~~~l--l~~~~~~~   80 (209)
                      ++.|+...|...+.++.+..   |+.  ..+ .++..+...|+.++|...+++..    .| +...+..+  ...+...|
T Consensus        45 ~r~Gd~~~Al~~L~qaL~~~---P~~~~av~-dll~l~~~~G~~~~A~~~~eka~----~p~n~~~~~llalA~ly~~~g  116 (822)
T PRK14574         45 ARAGDTAPVLDYLQEESKAG---PLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQ----SSMNISSRGLASAARAYRNEK  116 (822)
T ss_pred             HhCCCHHHHHHHHHHHHhhC---ccchhhHH-HHHHHHHHcCCcHHHHHHHHHhc----cCCCCCHHHHHHHHHHHHHcC
Confidence            46777777777777776654   443  233 77888888899999998888887    23 22333333  45777788


Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--CcHhHHHHHHHHHHh--CCChHHHHHHHh
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PDVVTWTTIISGLSK--CGFHKEAIDMFC  156 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~~~--~g~~~~a~~~~~  156 (209)
                      +++.|.++|+.+.+.. +-++..+..+...+...++.++|.+.+.+...  |+...+  +..++..  .++..+|++.++
T Consensus       117 dyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~--l~layL~~~~~~~~~AL~~~e  193 (822)
T PRK14574        117 RWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNY--MTLSYLNRATDRNYDALQASS  193 (822)
T ss_pred             CHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHH--HHHHHHHHhcchHHHHHHHHH
Confidence            9999999999888775 34466667778888888999999999888854  554455  3334444  455555888888


Q ss_pred             hC-CCCCC-HHhHHHHHHHhccccchhHHHHHHH
Q 045511          157 GI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       157 ~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      ++ ...|+ ...+..+..+..+.|-...|.++..
T Consensus       194 kll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~  227 (822)
T PRK14574        194 EAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAK  227 (822)
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            88 66675 4566777888888888877776644

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

Probab=98.53  E-value=5.4e-06  Score=63.72  Aligned_cols=190  Identities=12%  Similarity=0.146  Sum_probs=117.1

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCc------ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHH
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQP------HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALK   74 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~------~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~   74 (209)
                      |-+.+ ++|..++|.+..+.+.+    .||.      .+.-.|-.-|..+|-+|+|.++|..+.++|- .-.....-++.
T Consensus        75 LGnLfRsRGEvDRAIRiHQ~L~~----spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~  149 (389)
T COG2956          75 LGNLFRSRGEVDRAIRIHQTLLE----SPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLN  149 (389)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhc----CCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHH
Confidence            34455 56666666554444433    3544      3444555556677777777777777777653 23345666777


Q ss_pred             HHhccccHHHHHHHHHHHHHhccCccHh----HHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHH-HHHHhCCC
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHLHDIF----IQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTII-SGLSKCGF  147 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~----~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li-~~~~~~g~  147 (209)
                      .|-...++++|.++-+.+.+.+-.+..+    -|--|-..+....+++.|..++.+.-  .|+.+=-++++ +.....|+
T Consensus       150 IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~  229 (389)
T COG2956         150 IYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGD  229 (389)
T ss_pred             HHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccc
Confidence            7777777777777777666655333321    23334444445567777777776652  23322223333 56667788


Q ss_pred             hHHHHHHHhhC-CCCCCH--HhHHHHHHHhccccchhHHHHHHHHHHHhccC
Q 045511          148 HKEAIDMFCGI-DVKPNA--NTLVSVLSACSSLGSRKLGKAIHAHSLRNLNE  196 (209)
Q Consensus       148 ~~~a~~~~~~m-~~~p~~--~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  196 (209)
                      ++.|.+.+... ...|+-  .+...+..+|...|+.++....+..+.+....
T Consensus       230 y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g  281 (389)
T COG2956         230 YQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTG  281 (389)
T ss_pred             hHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCC
Confidence            88888888877 555554  45677788888888888888887776665433

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.45  E-value=2e-05  Score=65.33  Aligned_cols=185  Identities=12%  Similarity=0.089  Sum_probs=138.8

Q ss_pred             hccCCCcchHhHHHHHHHHh----h-CCCc-ccHHHHHHHHHcCCCccchHHHHHHhhh-----CC-CCCCH-HHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQII----K-IPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLN-----CP-SSYNH-YTFTQAL   73 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~----~-~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~g-~~p~~-~t~~~ll   73 (209)
                      ..++.++|...+..+...+.    . .|.+ .+++.|-..|.+.|++++|...+++..+     .| ..|.+ .-++.+.
T Consensus       253 ~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~  332 (508)
T KOG1840|consen  253 SLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELA  332 (508)
T ss_pred             HhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHH
Confidence            56777888877777777653    1 1222 7788888899999999999888877643     22 22333 3366677


Q ss_pred             HHHhccccHHHHHHHHHHHHHh---ccCcc----HhHHHHHHHHHHhCCChhhHHHHHHhcCC----------C-cHhHH
Q 045511           74 KACSLAHAHQKGLEIHAHVIKY---GHLHD----IFIQNSLLHFYVTVKDIFSAHQIFNSVVF----------P-DVVTW  135 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~---g~~~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~~----------~-~~~~~  135 (209)
                      ..|+..+++++|..++....+.   -+.++    ..+++.|-..|.+.|++.+|++++.+..+          + ....+
T Consensus       333 ~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l  412 (508)
T KOG1840|consen  333 AILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPL  412 (508)
T ss_pred             HHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHH
Confidence            7788899999999988755433   12222    45899999999999999999999988721          1 13467


Q ss_pred             HHHHHHHHhCCChHHHHHHHhhC--------CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          136 TTIISGLSKCGFHKEAIDMFCGI--------DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       136 ~~li~~~~~~g~~~~a~~~~~~m--------~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      +-|-..|.+.+++++|.++|.+-        .-.|+. .+|..|...|...|+++.|.++...+.
T Consensus       413 ~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  413 NQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            78888999999999999888776        223444 689999999999999999999988664

>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=98.44  E-value=6.8e-07  Score=69.37  Aligned_cols=146  Identities=12%  Similarity=0.110  Sum_probs=108.2

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHh---HHHHHHHHHHhCCC
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIF---IQNSLLHFYVTVKD  116 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~---~~~~ll~~~~~~g~  116 (209)
                      .+...|++++|+++++.-      .+.......+..+.+.++++.|.+.++.|.+..  .|..   ...+.+..+.....
T Consensus       111 i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~~l~qLa~awv~l~~g~e~  182 (290)
T PF04733_consen  111 ILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQID--EDSILTQLAEAWVNLATGGEK  182 (290)
T ss_dssp             HHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHHHHHHHHHhCchh
Confidence            345678888888877542      466778889999999999999999999998754  3432   33444555555567


Q ss_pred             hhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccch-hHHHHHHHHH
Q 045511          117 IFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSR-KLGKAIHAHS  190 (209)
Q Consensus       117 ~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~-~~a~~~~~~~  190 (209)
                      +.+|.-+|+++.+   ++..+.|.+..++...|++++|.+++.+. ...| |..|..-+|..+...|+. +.+.+.++++
T Consensus       183 ~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL  262 (290)
T PF04733_consen  183 YQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQL  262 (290)
T ss_dssp             CCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            9999999999843   57788899999999999999999999887 4444 445777778888888877 7788888887


Q ss_pred             HHh
Q 045511          191 LRN  193 (209)
Q Consensus       191 ~~~  193 (209)
                      ++.
T Consensus       263 ~~~  265 (290)
T PF04733_consen  263 KQS  265 (290)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            765

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

>TIGR00540 hemY_coli hemY protein

Probab=98.42  E-value=4.4e-05  Score=62.41  Aligned_cols=154  Identities=13%  Similarity=0.054  Sum_probs=91.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcc--cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPH--ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~--~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~   84 (209)
                      +.|+.+.+.+.+.+..+..   |+..  .--.....+.+.|+.+.|...++.+.+.+ +-+...+..+...+...|++++
T Consensus       130 ~~g~~~~A~~~l~~a~~~~---p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~  205 (409)
T TIGR00540       130 QRGDEARANQHLEEAAELA---GNDNILVEIARTRILLAQNELHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQA  205 (409)
T ss_pred             HCCCHHHHHHHHHHHHHhC---CcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHH
Confidence            4456666666666654433   4442  22224666667788888888888777764 2244567777777788888888


Q ss_pred             HHHHHHHHHHhccCccHhH-------HHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHH
Q 045511           85 GLEIHAHVIKYGHLHDIFI-------QNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDM  154 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~-------~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~  154 (209)
                      +.+.+..+.+.+..++...       +..++..-......+...+++...++   .+...+-.+...+...|+.++|.++
T Consensus       206 a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~  285 (409)
T TIGR00540       206 LDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEI  285 (409)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHH
Confidence            8888888877764332221       11112111222233444555555543   3667777777888888888888777


Q ss_pred             HhhC-CCCCCH
Q 045511          155 FCGI-DVKPNA  164 (209)
Q Consensus       155 ~~~m-~~~p~~  164 (209)
                      +.+. ...||.
T Consensus       286 l~~~l~~~pd~  296 (409)
T TIGR00540       286 IFDGLKKLGDD  296 (409)
T ss_pred             HHHHHhhCCCc
Confidence            7776 433443

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

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

Probab=98.41  E-value=3.8e-05  Score=64.06  Aligned_cols=180  Identities=13%  Similarity=0.137  Sum_probs=143.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccccHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAHAHQK   84 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~   84 (209)
                      ..|..+-|...+.+..+.   .|+- ..||.|-.++-..|++.+|.+.|.+....  .|+. .+.+.+-..+...|.++.
T Consensus       298 eqG~ldlAI~~Ykral~~---~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l--~p~hadam~NLgni~~E~~~~e~  372 (966)
T KOG4626|consen  298 EQGLLDLAIDTYKRALEL---QPNFPDAYNNLANALKDKGSVTEAVDCYNKALRL--CPNHADAMNNLGNIYREQGKIEE  372 (966)
T ss_pred             ccccHHHHHHHHHHHHhc---CCCchHHHhHHHHHHHhccchHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhccchH
Confidence            456666666666655553   4554 78999999999999999999999988874  3443 678888899999999999


Q ss_pred             HHHHHHHHHHhccCcc-HhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC-C
Q 045511           85 GLEIHAHVIKYGHLHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI-D  159 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m-~  159 (209)
                      |..+|....+-  .|. ....|.|-..|-.+|++++|...+.+..  +|+ ..+|+.+=..|-..|+.+.|.+.+.+. .
T Consensus       373 A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~  450 (966)
T KOG4626|consen  373 ATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQ  450 (966)
T ss_pred             HHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHh
Confidence            99999887764  344 4678999999999999999999998873  465 457888888888889999999988887 7


Q ss_pred             CCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          160 VKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       160 ~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +.|.. ..++-+-..+-..|+..+|.+-++...+-
T Consensus       451 ~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLkl  485 (966)
T KOG4626|consen  451 INPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKL  485 (966)
T ss_pred             cCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHcc
Confidence            77766 47888888888999999999888876654

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

Probab=98.40  E-value=2.6e-07  Score=46.34  Aligned_cols=29  Identities=14%  Similarity=0.234  Sum_probs=18.3

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCC
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCP   61 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g   61 (209)
                      +||++|++|++.|++++|.++|++|.+.|
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.

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

Probab=98.38  E-value=5.1e-06  Score=64.07  Aligned_cols=186  Identities=12%  Similarity=0.068  Sum_probs=122.4

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHH-HHHHHHhcc
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFT-QALKACSLA   79 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~-~ll~~~~~~   79 (209)
                      +.+|+ +.|.+.+|.++++...+.+   |-+.+|-.|-..|.+-.++..|+.+|.+-.+.  -|..+||- -+-..+-..
T Consensus       229 ~gkCylrLgm~r~AekqlqssL~q~---~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  229 MGKCYLRLGMPRRAEKQLQSSLTQF---PHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHhcChhhhHHHHHHHhhcC---CchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHHH
Confidence            45677 8999999998887776654   77788888999999999999999998876653  35555543 344555566


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHh
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      ++.+++.++++...+.. +.++....++-.+|.-.++++.|++++.++-   -.+...|+.+--+|...+++|.++.-|.
T Consensus       304 ~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~  382 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQ  382 (478)
T ss_pred             HhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHH
Confidence            77777888887777654 4556666667777777777777777777652   2344455555555555555554444333


Q ss_pred             hC--------------------------------------CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          157 GI--------------------------------------DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       157 ~m--------------------------------------~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +.                                      .-.| +...++-+--.-.+.|+.+.|+.+++-..+.
T Consensus       383 RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  383 RALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             HHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhh
Confidence            33                                      1112 2345555555556677777777777665444

>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=98.37  E-value=6.8e-06  Score=63.83  Aligned_cols=160  Identities=10%  Similarity=0.075  Sum_probs=105.3

Q ss_pred             CCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHH-HHHHHhccccHHHHHHHHHHHHHhccCccHhHHHH
Q 045511           28 IPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQ-ALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNS  106 (209)
Q Consensus        28 ~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~-ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  106 (209)
                      .|.......+...+...++-+.+..-+++....+..++..++.. .-..+...|++++|.+++..-      .+......
T Consensus        63 ~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al  136 (290)
T PF04733_consen   63 SPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLAL  136 (290)
T ss_dssp             SCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHH
T ss_pred             ChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHH
Confidence            34555555554444433455556655555544444333333333 334556779999888887532      45667778


Q ss_pred             HHHHHHhCCChhhHHHHHHhcCCC--cHh---HHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccc
Q 045511          107 LLHFYVTVKDIFSAHQIFNSVVFP--DVV---TWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGS  179 (209)
Q Consensus       107 ll~~~~~~g~~~~a~~~~~~~~~~--~~~---~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~  179 (209)
                      .+..|.+.++++.|.+.++.|.+.  |..   ...+.+..+.-.+.+.+|..+|+++  ...++..+.+.+..+....|+
T Consensus       137 ~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~  216 (290)
T PF04733_consen  137 AVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGH  216 (290)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCC
Confidence            899999999999999999999653  322   2233334333345799999999999  667888999999999999999


Q ss_pred             hhHHHHHHHHHHHh
Q 045511          180 RKLGKAIHAHSLRN  193 (209)
Q Consensus       180 ~~~a~~~~~~~~~~  193 (209)
                      +++|++++....+.
T Consensus       217 ~~eAe~~L~~al~~  230 (290)
T PF04733_consen  217 YEEAEELLEEALEK  230 (290)
T ss_dssp             HHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999886543

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

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

Probab=98.37  E-value=0.00011  Score=54.04  Aligned_cols=182  Identities=12%  Similarity=-0.012  Sum_probs=117.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +.|....|.+.++++.+.-   |+. .+|..+-..|-+.|..+.|.+-|++..+... -+....|..=..+|..|++++|
T Consensus        47 ~~gd~~~A~~nlekAL~~D---Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p-~~GdVLNNYG~FLC~qg~~~eA  122 (250)
T COG3063          47 QQGDYAQAKKNLEKALEHD---PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAP-NNGDVLNNYGAFLCAQGRPEEA  122 (250)
T ss_pred             HCCCHHHHHHHHHHHHHhC---cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCC-CccchhhhhhHHHHhCCChHHH
Confidence            4555555555555555542   333 6777777777777777777777777766431 2335556666666777777777


Q ss_pred             HHHHHHHHHhccCcc-HhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHHHHHhhC--C
Q 045511           86 LEIHAHVIKYGHLHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAIDMFCGI--D  159 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m--~  159 (209)
                      ...|+......--+. ..+|.++.-+..+.|+.+.|+..|.+--+  | ...+.-.+..-....|++-.|...++..  +
T Consensus       123 ~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~  202 (250)
T COG3063         123 MQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQR  202 (250)
T ss_pred             HHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhc
Confidence            777777766543333 35777777777777777777777776522  2 2345556666677777777777777777  4


Q ss_pred             CCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          160 VKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       160 ~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ..++..+.-.-|+--.+.||.+.+.+.=..+.+
T Consensus       203 ~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r  235 (250)
T COG3063         203 GGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQR  235 (250)
T ss_pred             ccccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            447777777777777777777766665444433

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.35  E-value=4.9e-05  Score=57.17  Aligned_cols=160  Identities=15%  Similarity=0.063  Sum_probs=117.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH----HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccH--hHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH----YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI--FIQN  105 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~--~~~~  105 (209)
                      ..+-.+...+.+.|++++|...|++.....  |+.    ..+..+-.++.+.|++++|...++.+.+.......  .++.
T Consensus        34 ~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~  111 (235)
T TIGR03302        34 EELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYY  111 (235)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHH
Confidence            566677778889999999999999987743  332    46677778889999999999999999876532111  1344


Q ss_pred             HHHHHHHhC--------CChhhHHHHHHhcC--CCcH-hHH-----------------HHHHHHHHhCCChHHHHHHHhh
Q 045511          106 SLLHFYVTV--------KDIFSAHQIFNSVV--FPDV-VTW-----------------TTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       106 ~ll~~~~~~--------g~~~~a~~~~~~~~--~~~~-~~~-----------------~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      .+-.++...        |+.++|.+.|+.+.  .|+. ..+                 -.+-..+.+.|++++|...|.+
T Consensus       112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~  191 (235)
T TIGR03302       112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFET  191 (235)
T ss_pred             HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            444455443        77889999998873  2332 111                 1344667889999999999999


Q ss_pred             C-CCCCC----HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          158 I-DVKPN----ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       158 m-~~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      . ...|+    ...+..+..++.+.|++++|...++.+..+
T Consensus       192 al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       192 VVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            8 44333    467889999999999999999998887665

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).

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

Probab=98.34  E-value=5.1e-07  Score=45.25  Aligned_cols=31  Identities=13%  Similarity=0.040  Sum_probs=22.4

Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHHHHhcc
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHSLRNLN  195 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~  195 (209)
                      +||+++|++|++.|++++|.+++++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            3677777777777777777777777777664

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.

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

Probab=98.34  E-value=9.2e-05  Score=54.53  Aligned_cols=165  Identities=12%  Similarity=-0.018  Sum_probs=136.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      .+.-.|--+|.+.|+...|..-+++..+..- -+..+|..+-..|-+.|..+.|.+-|+...+.. +-+-.+.|+.=-.+
T Consensus        36 ~arlqLal~YL~~gd~~~A~~nlekAL~~DP-s~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FL  113 (250)
T COG3063          36 KARLQLALGYLQQGDYAQAKKNLEKALEHDP-SYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFL  113 (250)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHH
Confidence            4566777889999999999999999999752 355889999999999999999999999888764 34556889999999


Q ss_pred             HhCCChhhHHHHHHhcC-CCc----HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHH
Q 045511          112 VTVKDIFSAHQIFNSVV-FPD----VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~-~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~  184 (209)
                      |..|++++|.+.|+... .|+    ..+|..+--+..+.|+.+.|...|++- ...|+. .+.-.+.+...+.|++-.|.
T Consensus       114 C~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar  193 (250)
T COG3063         114 CAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPAR  193 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHH
Confidence            99999999999999873 343    457888888888999999999999988 556654 57778888888999999999


Q ss_pred             HHHHHHHHhccCCCc
Q 045511          185 AIHAHSLRNLNENNI  199 (209)
Q Consensus       185 ~~~~~~~~~~~~p~~  199 (209)
                      .+++.....+- ++.
T Consensus       194 ~~~~~~~~~~~-~~A  207 (250)
T COG3063         194 LYLERYQQRGG-AQA  207 (250)
T ss_pred             HHHHHHHhccc-ccH
Confidence            99988766654 443

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

Probab=98.29  E-value=0.00012  Score=58.35  Aligned_cols=182  Identities=9%  Similarity=-0.028  Sum_probs=108.9

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHH---HHHHHhccccHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQ---ALKACSLAHAHQ   83 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~---ll~~~~~~~~~~   83 (209)
                      .++++.+.+.+....+.....++. .........+...|++++|.+++++..+.. +.|...+..   ........+..+
T Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~~~~~~~~~~~~~~~   97 (355)
T cd05804          19 GGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKLHLGAFGLGDFSGMRD   97 (355)
T ss_pred             cCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHhHHHHHhcccccCch
Confidence            345566555566665555443333 112222334456788888988888877653 223333332   111112234444


Q ss_pred             HHHHHHHHHHHhccCcc-HhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           84 KGLEIHAHVIKYGHLHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        84 ~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      .+.+.+..  ..+..|+ ......+-..+...|++++|.+.+++..   ..+...+..+-..+...|++++|...+.+. 
T Consensus        98 ~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l  175 (355)
T cd05804          98 HVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWR  175 (355)
T ss_pred             hHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhh
Confidence            45544443  1112233 3344555667788888999988888873   234566777788888889999998888877 


Q ss_pred             CCC---CCH--HhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          159 DVK---PNA--NTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       159 ~~~---p~~--~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ...   |+.  ..|..+...+...|++++|..+++....
T Consensus       176 ~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         176 DTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             hccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            332   232  2345667777888899999888887643

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.

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

Probab=98.28  E-value=0.0001  Score=59.51  Aligned_cols=167  Identities=15%  Similarity=0.240  Sum_probs=93.8

Q ss_pred             cCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHH
Q 045511            9 LKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEI   88 (209)
Q Consensus         9 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~   88 (209)
                      ++.++|+..|..++....  -+..+.-.+.+.|-...+...|.+++.+.... ++-|...++.+-..|-+.|+-..|.+.
T Consensus       538 ~~ldeald~f~klh~il~--nn~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~  614 (840)
T KOG2003|consen  538 GNLDEALDCFLKLHAILL--NNAEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQC  614 (840)
T ss_pred             cCHHHHHHHHHHHHHHHH--hhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhh
Confidence            334444444444443321  23344444444454555555555555333221 233445566666666666666666555


Q ss_pred             HHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHhHHHHHH-HHHHhCCChHHHHHHHhhC--CCCCC
Q 045511           89 HAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVVTWTTII-SGLSKCGFHKEAIDMFCGI--DVKPN  163 (209)
Q Consensus        89 ~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~~~~~li-~~~~~~g~~~~a~~~~~~m--~~~p~  163 (209)
                      +-+--+. ++-|..+..=|-..|....-.+.|..+|++.  .+|+..-|-.|| +++.+.|++.+|+++|+..  .+.-|
T Consensus       615 ~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfped  693 (840)
T KOG2003|consen  615 HYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPED  693 (840)
T ss_pred             hhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccc
Confidence            4332221 3445555555556666666666677777654  567777777777 4445577888888888777  55556


Q ss_pred             HHhHHHHHHHhccccc
Q 045511          164 ANTLVSVLSACSSLGS  179 (209)
Q Consensus       164 ~~t~~~li~~~~~~g~  179 (209)
                      .....-+.+.|...|.
T Consensus       694 ldclkflvri~~dlgl  709 (840)
T KOG2003|consen  694 LDCLKFLVRIAGDLGL  709 (840)
T ss_pred             hHHHHHHHHHhccccc
Confidence            6666667777766653

>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=98.23  E-value=1e-05  Score=59.06  Aligned_cols=100  Identities=8%  Similarity=0.065  Sum_probs=84.1

Q ss_pred             HhhCCCcccHHHHHHHHHcC-----CCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc----------------ccHH
Q 045511           25 IIKIPQPHILNTLLKLLTQS-----STPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA----------------HAHQ   83 (209)
Q Consensus        25 ~~~~p~~~~~~~li~~~~~~-----g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~----------------~~~~   83 (209)
                      .....+..+|..+|..|.+.     |.++-....++.|.+-|+.-|..+|+.||..+=+.                .+.+
T Consensus        41 ~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~  120 (228)
T PF06239_consen   41 PGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQE  120 (228)
T ss_pred             hhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHH
Confidence            34557789999999999864     78888888999999999999999999999998653                3467


Q ss_pred             HHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh-hhHHHHH
Q 045511           84 KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI-FSAHQIF  124 (209)
Q Consensus        84 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~-~~a~~~~  124 (209)
                      .+.+++++|...|+-||..++..|++.+++.+.. ....++.
T Consensus       121 c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rmm  162 (228)
T PF06239_consen  121 CAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRMM  162 (228)
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHHH
Confidence            8999999999999999999999999999988764 3344443

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

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.20  E-value=0.0003  Score=54.98  Aligned_cols=146  Identities=13%  Similarity=-0.030  Sum_probs=110.5

Q ss_pred             CCccchHHHHHHhhhCC-CCCC--HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHH
Q 045511           45 STPQNAIPLYNKMLNCP-SSYN--HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAH  121 (209)
Q Consensus        45 g~~~~a~~l~~~m~~~g-~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~  121 (209)
                      ++.+.+..-+.++.... +.|+  ...|...-..+.+.|+.+.|...|+...+.. +.+...|+.+-..+...|++++|.
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~  118 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAY  118 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            44455666666666532 3333  2456666677889999999999999988865 446789999999999999999999


Q ss_pred             HHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          122 QIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       122 ~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      ..|+...  .| +..+|..+-..+...|++++|.+.|+.. ...|+..........+...++.++|.+.+....
T Consensus       119 ~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        119 EAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            9999883  34 4678888888899999999999999998 777766433333333456778999999997654

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

Probab=98.20  E-value=2.2e-05  Score=65.43  Aligned_cols=160  Identities=11%  Similarity=0.042  Sum_probs=94.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCC------------------------------CCCCHHHHHHH---HHHHhc
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCP------------------------------SSYNHYTFTQA---LKACSL   78 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g------------------------------~~p~~~t~~~l---l~~~~~   78 (209)
                      .+|.++=+.|.-.++.+.|++.|++..+.+                              +..|...|+++   -..|.+
T Consensus       422 esWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~K  501 (638)
T KOG1126|consen  422 ESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLK  501 (638)
T ss_pred             HHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheec
Confidence            666666666666666666666666654422                              12344444443   334566


Q ss_pred             cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHH
Q 045511           79 AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMF  155 (209)
Q Consensus        79 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~  155 (209)
                      .++++.|+..|+...+-+ +.+.+..-.+...+-+.|+.++|.+++++..   ..|...-=-....+...+++++|+..+
T Consensus       502 qek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~L  580 (638)
T KOG1126|consen  502 QEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQEL  580 (638)
T ss_pred             cchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHH
Confidence            666666666666666544 3455566666666667777777777777652   223333223344455567777777777


Q ss_pred             hhC-CCCCCHH-hHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          156 CGI-DVKPNAN-TLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       156 ~~m-~~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      .++ .+.|+.. .|..+-+.|-+.|+.+.|..=|.-+.+
T Consensus       581 EeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  581 EELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             HHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            777 6666553 466666677777777776665554433

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

Probab=98.20  E-value=2.3e-05  Score=63.58  Aligned_cols=128  Identities=15%  Similarity=0.168  Sum_probs=96.4

Q ss_pred             hHHHHHHHHhhC--CCcccHHHHHHHHHcCCCccchHHHHHHhhhC--CCCCCHHHHHHHHHHHhccccHHHHHHHHHHH
Q 045511           17 QLNQIHAQIIKI--PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNC--PSSYNHYTFTQALKACSLAHAHQKGLEIHAHV   92 (209)
Q Consensus        17 ~~~~~~~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~--g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m   92 (209)
                      .+..+.+.+...  -+......+++.+.+..+++++..++.+.+..  ....-..|.++++..|.+.|..+.+.+++..=
T Consensus        50 ~~~~l~~k~~~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~  129 (429)
T PF10037_consen   50 LYSELDKKFERKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNR  129 (429)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhCh
Confidence            344555555333  23367788888888888899999998888775  33333456679999999999999999999999


Q ss_pred             HHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC----CCcHhHHHHHHHHHHh
Q 045511           93 IKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV----FPDVVTWTTIISGLSK  144 (209)
Q Consensus        93 ~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~li~~~~~  144 (209)
                      ...|+-||..++|.||+.+.+.|++..|.++...|.    -.+..++.-.+.+|.+
T Consensus       130 ~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~  185 (429)
T PF10037_consen  130 LQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYK  185 (429)
T ss_pred             hhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHH
Confidence            999999999999999999999999999999998872    1333444444444433

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

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

Probab=98.19  E-value=0.00039  Score=55.01  Aligned_cols=168  Identities=7%  Similarity=0.003  Sum_probs=137.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|-.-..+--+.|+.+.+-.++.+..+.--.++...+-+........|+.+.|.+-++...+.+ +.++........+|
T Consensus       119 l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~-pr~~~vlrLa~r~y  197 (400)
T COG3071         119 LAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEMT-PRHPEVLRLALRAY  197 (400)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhC-cCChHHHHHHHHHH
Confidence            34444445555679999999999999886445677777778888889999999999999998877 56788899999999


Q ss_pred             HhCCChhhHHHHHHhcCC-----------CcHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhcccc
Q 045511          112 VTVKDIFSAHQIFNSVVF-----------PDVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLG  178 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~~-----------~~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g  178 (209)
                      .+.|++.+...++..+.+           .-..+|+.++.-....+..+.-...|+..  ..+-+...-.+++.-+.+.|
T Consensus       198 ~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~  277 (400)
T COG3071         198 IRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLG  277 (400)
T ss_pred             HHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcC
Confidence            999999999999999843           22468999999888888888777888887  56666777777888899999


Q ss_pred             chhHHHHHHHHHHHhccCCCch
Q 045511          179 SRKLGKAIHAHSLRNLNENNII  200 (209)
Q Consensus       179 ~~~~a~~~~~~~~~~~~~p~~~  200 (209)
                      +.+.|.++..+-.+++..|+..
T Consensus       278 ~~~~A~~~i~~~Lk~~~D~~L~  299 (400)
T COG3071         278 DHDEAQEIIEDALKRQWDPRLC  299 (400)
T ss_pred             ChHHHHHHHHHHHHhccChhHH
Confidence            9999999999999998888743

>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=98.19  E-value=8.3e-05  Score=59.99  Aligned_cols=121  Identities=19%  Similarity=0.209  Sum_probs=97.2

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      .-..|+..+...++++.|..+|+++.+..  |++  ...+.+.+...++-.+|.+++.+..+.. +.+......-...|.
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl  245 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLL  245 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            34556666667899999999999999876  554  4457777777777788888888887653 456777777888899


Q ss_pred             hCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          113 TVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +.++.+.|.++..+..  .| +..+|..|..+|...|+++.|+-.++.+
T Consensus       246 ~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  246 SKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             hcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence            9999999999999884  35 4569999999999999999999998888

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

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.18  E-value=9.3e-05  Score=55.65  Aligned_cols=151  Identities=15%  Similarity=0.129  Sum_probs=108.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCC-CCH-HHHHHHHHHHhcc----
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSS-YNH-YTFTQALKACSLA----   79 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-p~~-~t~~~ll~~~~~~----   79 (209)
                      +.++.+.|...+.++....+..|.. .++..+-..+.+.|++++|...++++.+..-. |.. .++..+-..+...    
T Consensus        45 ~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~  124 (235)
T TIGR03302        45 DSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRV  124 (235)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccc
Confidence            7788888888888887765333322 46777888999999999999999999875421 111 1233333333332    


Q ss_pred             ----ccHHHHHHHHHHHHHhccCccHhHH-----------------HHHHHHHHhCCChhhHHHHHHhcCC--C----cH
Q 045511           80 ----HAHQKGLEIHAHVIKYGHLHDIFIQ-----------------NSLLHFYVTVKDIFSAHQIFNSVVF--P----DV  132 (209)
Q Consensus        80 ----~~~~~a~~~~~~m~~~g~~~~~~~~-----------------~~ll~~~~~~g~~~~a~~~~~~~~~--~----~~  132 (209)
                          |+.+.|.+.|+.+.+.... +...+                 -.+-..|.+.|++++|...+.....  |    ..
T Consensus       125 ~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  203 (235)
T TIGR03302       125 DRDQTAAREAFEAFQELIRRYPN-SEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATE  203 (235)
T ss_pred             cCCHHHHHHHHHHHHHHHHHCCC-ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchH
Confidence                7888999999999876422 11121                 1345568889999999999988732  2    35


Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..+..+...+...|++++|...++.+
T Consensus       204 ~a~~~l~~~~~~lg~~~~A~~~~~~l  229 (235)
T TIGR03302       204 EALARLVEAYLKLGLKDLAQDAAAVL  229 (235)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            68899999999999999999999887

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).

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

Probab=98.17  E-value=0.00034  Score=51.37  Aligned_cols=144  Identities=11%  Similarity=0.046  Sum_probs=88.1

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~  117 (209)
                      +..|...|+++.+....+.+...    . .       .+...++.+++...++...+.. +.|...|..|-..|...|++
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~~----~-~-------~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~   89 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLADP----L-H-------QFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDY   89 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhCc----c-c-------cccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCH
Confidence            34566677776665444332211    0 0       1112445555555566555554 55667777777777777888


Q ss_pred             hhHHHHHHhcC---CCcHhHHHHHHHHH-HhCCC--hHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHH
Q 045511          118 FSAHQIFNSVV---FPDVVTWTTIISGL-SKCGF--HKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       118 ~~a~~~~~~~~---~~~~~~~~~li~~~-~~~g~--~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      ++|...|++..   ..+...+..+-.++ ...|+  .++|.+++++. ...|+. ..+..+-..+.+.|++++|...|+.
T Consensus        90 ~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~  169 (198)
T PRK10370         90 DNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQK  169 (198)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            88877777762   23555666666653 45565  47777777777 555533 5566666667777788888877777


Q ss_pred             HHHhc
Q 045511          190 SLRNL  194 (209)
Q Consensus       190 ~~~~~  194 (209)
                      +.+..
T Consensus       170 aL~l~  174 (198)
T PRK10370        170 VLDLN  174 (198)
T ss_pred             HHhhC
Confidence            76653

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.15  E-value=7.2e-05  Score=62.09  Aligned_cols=165  Identities=12%  Similarity=0.118  Sum_probs=123.6

Q ss_pred             CCc-ccHHHHHHHHHcCCCccchHHHHHHhhhC-----C-CCCCHHHHH-HHHHHHhccccHHHHHHHHHHHHHhc---c
Q 045511           29 PQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNC-----P-SSYNHYTFT-QALKACSLAHAHQKGLEIHAHVIKYG---H   97 (209)
Q Consensus        29 p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----g-~~p~~~t~~-~ll~~~~~~~~~~~a~~~~~~m~~~g---~   97 (209)
                      |.. .+...+-..|...|+++.|..+++.-.+.     | ..|.+.+.- .+-..|...+++++|..+|+.++.--   .
T Consensus       196 P~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~  275 (508)
T KOG1840|consen  196 PERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVF  275 (508)
T ss_pred             chHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhc
Confidence            444 67777999999999999999999887653     2 124443332 35567888899999999999887542   1


Q ss_pred             ---Ccc-HhHHHHHHHHHHhCCChhhHHHHHHhcC----------CCcH-hHHHHHHHHHHhCCChHHHHHHHhhC----
Q 045511           98 ---LHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVV----------FPDV-VTWTTIISGLSKCGFHKEAIDMFCGI----  158 (209)
Q Consensus        98 ---~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~----------~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m----  158 (209)
                         .|. ..+++.|-..|.+.|++++|+..+++..          .|.+ ..++.+...++..+++++|..+++..    
T Consensus       276 G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~  355 (508)
T KOG1840|consen  276 GEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIY  355 (508)
T ss_pred             CCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHH
Confidence               222 3578888889999999999988887651          2333 35677778888899999999998876    


Q ss_pred             --CCCC---CH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          159 --DVKP---NA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       159 --~~~p---~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                        -..+   +. .+++.+-..|...|++++|++++....+.
T Consensus       356 ~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~  396 (508)
T KOG1840|consen  356 LDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQI  396 (508)
T ss_pred             HhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH
Confidence              1222   22 58999999999999999999999966443

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

Probab=98.14  E-value=5.3e-05  Score=61.50  Aligned_cols=118  Identities=10%  Similarity=0.081  Sum_probs=89.9

Q ss_pred             CCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh--ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC----CCcHh
Q 045511           60 CPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY--GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV----FPDVV  133 (209)
Q Consensus        60 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~----~~~~~  133 (209)
                      .+.+.+...+.++++.+....+++.+..++-.....  ....-..|..++|+.|.+.|..+.+..++..=.    -||..
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            445667788888888888888888888887777755  233334555688888888888888888887653    38888


Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC---CCCCCHHhHHHHHHHhccc
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANTLVSVLSACSSL  177 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m---~~~p~~~t~~~li~~~~~~  177 (209)
                      +||.+|..+.+.|++..|.++...|   +...+..|+.-.+.+|.+-
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            8888888888888888888888888   5556667777667776654

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 [].

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.12  E-value=0.0003  Score=60.98  Aligned_cols=137  Identities=10%  Similarity=0.053  Sum_probs=103.3

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      ++..+-.|-....+.|..++|..+++...+  +.||. .....+...+.+.+++++|....+..++.. +-+....+.+-
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            357777777888888888999988888887  44554 556677778888888888888888888765 44556777777


Q ss_pred             HHHHhCCChhhHHHHHHhcCC--Cc-HhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHH
Q 045511          109 HFYVTVKDIFSAHQIFNSVVF--PD-VVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVS  169 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~  169 (209)
                      .++...|+.++|..+|++...  |+ ..++..+-.++-..|+.++|...|...  ...|...-|+-
T Consensus       162 ~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~  227 (694)
T PRK15179        162 KSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTR  227 (694)
T ss_pred             HHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHH
Confidence            788888899999888888843  33 567777778888888888888888887  44444444443

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

Probab=98.12  E-value=0.00019  Score=53.77  Aligned_cols=116  Identities=9%  Similarity=-0.030  Sum_probs=53.1

Q ss_pred             HHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCC
Q 045511           70 TQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCG  146 (209)
Q Consensus        70 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g  146 (209)
                      +...+...+.|++..|...+.+...-. ++|...||.+--+|-+.|++++|..-|.+..   ..+....|.|--.|.-.|
T Consensus       104 ~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~g  182 (257)
T COG5010         104 AAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRG  182 (257)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcC
Confidence            334455555555555555554444332 4445555555555555555555555554431   123334444444444455


Q ss_pred             ChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHH
Q 045511          147 FHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       147 ~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~  186 (209)
                      +.+.|..++..-  .-.-|...-.-+--+-...|+++.|+.+
T Consensus       183 d~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i  224 (257)
T COG5010         183 DLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDI  224 (257)
T ss_pred             CHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhh
Confidence            555555555444  1111333333333344444555555444

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

Probab=98.12  E-value=1.6e-05  Score=61.37  Aligned_cols=156  Identities=10%  Similarity=0.049  Sum_probs=101.8

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccH-HHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHIL-NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA   81 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~-~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~   81 (209)
                      +++ +--+|..|+..+.+-.+.+   |-.++| .-.-+.+-..++.++|.++|++..+.. +.++.....+-..|--.++
T Consensus       264 kvY~ridQP~~AL~~~~~gld~f---P~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~  339 (478)
T KOG1129|consen  264 KVYQRIDQPERALLVIGEGLDSF---PFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNN  339 (478)
T ss_pred             HHHHHhccHHHHHHHHhhhhhcC---CchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCC
Confidence            344 4556666777777766665   333333 334444555677788888887776643 2355666666666677777


Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc----------------------------------
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV----------------------------------  127 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----------------------------------  127 (209)
                      ++-|...+..+++.|+ .++..|+++--+|.-.+++|-+..-|.+.                                  
T Consensus       340 PE~AlryYRRiLqmG~-~speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcf  418 (478)
T KOG1129|consen  340 PEMALRYYRRILQMGA-QSPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCF  418 (478)
T ss_pred             hHHHHHHHHHHHHhcC-CChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHH
Confidence            7888888888887773 45666666666666665555555444322                                  


Q ss_pred             -----CC-CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH
Q 045511          128 -----VF-PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       128 -----~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                           .. .+...+|.|--.-.+.|++++|..+++.. .+.|+.
T Consensus       419 rlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~~P~m  462 (478)
T KOG1129|consen  419 RLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSVMPDM  462 (478)
T ss_pred             HHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhhCccc
Confidence                 11 23467888887788999999999999887 666765

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

Probab=98.11  E-value=0.00022  Score=55.13  Aligned_cols=196  Identities=12%  Similarity=0.066  Sum_probs=103.1

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccH---HHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-H--HHHHHHHHHhcccc
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHIL---NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-Y--TFTQALKACSLAHA   81 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~---~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~--t~~~ll~~~~~~~~   81 (209)
                      +-+++.|...|.++.+.     |+.+|   =+|=+.|-+.|..|+|+.+-+.+.++.-.+.. .  ..--+-.=|...|-
T Consensus        48 s~Q~dKAvdlF~e~l~~-----d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl  122 (389)
T COG2956          48 SNQPDKAVDLFLEMLQE-----DPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGL  122 (389)
T ss_pred             hcCcchHHHHHHHHHhc-----CchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhh
Confidence            44556666666665552     22222   23344455556666666666666554211111 1  11122333455566


Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcH--------hHHHHHHHHHHhCCChHHHHH
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDV--------VTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~--------~~~~~li~~~~~~g~~~~a~~  153 (209)
                      ++.|+++|..+.+.| ..-....--|+..|-...++++|.++-.+....+.        ..|--+-..+....+++.|..
T Consensus       123 ~DRAE~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~  201 (389)
T COG2956         123 LDRAEDIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARE  201 (389)
T ss_pred             hhHHHHHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHH
Confidence            666666666665543 23344555666666666666666666555432221        233334444445566777777


Q ss_pred             HHhhC-CCCCCHHhHH-HHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          154 MFCGI-DVKPNANTLV-SVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       154 ~~~~m-~~~p~~~t~~-~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                      ++.+. ...|+.+--+ .+-+.....|+++.|.+.++.+.+.+...-+.+-..|..+|
T Consensus       202 ~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y  259 (389)
T COG2956         202 LLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECY  259 (389)
T ss_pred             HHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHH
Confidence            77665 4444433222 23344567788888888888777776554444555554443

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

Probab=98.10  E-value=0.00016  Score=58.37  Aligned_cols=192  Identities=13%  Similarity=0.075  Sum_probs=137.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ..|..+.|...+.+....     |.    ..||+=+. +-..|++++|++.|-+++.- +.-++..+--+.+.|-...+.
T Consensus       502 ~ngd~dka~~~ykeal~n-----dasc~ealfniglt-~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~  574 (840)
T KOG2003|consen  502 ANGDLDKAAEFYKEALNN-----DASCTEALFNIGLT-AEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDP  574 (840)
T ss_pred             ecCcHHHHHHHHHHHHcC-----chHHHHHHHHhccc-HHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCH
Confidence            345555555555554331     22    22333222 44568888888888766542 224566777777788888888


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      ..|.+++.+... -++.|+.+.+-|-..|-+.|+-..|.+++-+--   ..|..+..=|-.-|....-+++++..|.+. 
T Consensus       575 aqaie~~~q~~s-lip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaa  653 (840)
T KOG2003|consen  575 AQAIELLMQANS-LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA  653 (840)
T ss_pred             HHHHHHHHHhcc-cCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            888888755433 256788999999999999999999999876542   246666666777778888899999999998 


Q ss_pred             CCCCCHHhHHHHHHHhc-cccchhHHHHHHHHHHHhccCCCchhHhHhhh
Q 045511          159 DVKPNANTLVSVLSACS-SLGSRKLGKAIHAHSLRNLNENNIILDNAVLD  207 (209)
Q Consensus       159 ~~~p~~~t~~~li~~~~-~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~  207 (209)
                      -++|+..-|..+|..|. +.|++.+|.+++....+. +.-|.....-|++
T Consensus       654 liqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvr  702 (840)
T KOG2003|consen  654 LIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVR  702 (840)
T ss_pred             hcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHH
Confidence            89999999999999986 689999999999887654 4445555444443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.10  E-value=8.3e-05  Score=51.72  Aligned_cols=92  Identities=9%  Similarity=-0.049  Sum_probs=45.1

Q ss_pred             HHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChH
Q 045511           73 LKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHK  149 (209)
Q Consensus        73 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~  149 (209)
                      -..+...|++++|...|+...+.. +.+...|..+-..+.+.|++++|...|+....   .+...+..+-.++...|+++
T Consensus        31 g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~g~~~  109 (144)
T PRK15359         31 GYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMMGEPG  109 (144)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHH
Confidence            344445555555555555544433 23444555555555555555555555555421   23444445555555555555


Q ss_pred             HHHHHHhhC-CCCCCHH
Q 045511          150 EAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       150 ~a~~~~~~m-~~~p~~~  165 (209)
                      +|...|+.. ...|+..
T Consensus       110 eAi~~~~~Al~~~p~~~  126 (144)
T PRK15359        110 LAREAFQTAIKMSYADA  126 (144)
T ss_pred             HHHHHHHHHHHhCCCCh
Confidence            555555554 4444443

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

Probab=98.08  E-value=0.00011  Score=50.12  Aligned_cols=99  Identities=9%  Similarity=-0.032  Sum_probs=56.8

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      ...+...+.+.|++++|.+.|+...+.+ +.+...+..+-..+.+.|++++|..+++...   ..+...+..+-..|...
T Consensus        20 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~   98 (135)
T TIGR02552        20 IYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLAL   98 (135)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHc
Confidence            4444455556666666666666665544 3355566666666666666666666665552   22344455555566666


Q ss_pred             CChHHHHHHHhhC-CCCCCHHhHH
Q 045511          146 GFHKEAIDMFCGI-DVKPNANTLV  168 (209)
Q Consensus       146 g~~~~a~~~~~~m-~~~p~~~t~~  168 (209)
                      |++++|...|++. ...|+...+.
T Consensus        99 g~~~~A~~~~~~al~~~p~~~~~~  122 (135)
T TIGR02552        99 GEPESALKALDLAIEICGENPEYS  122 (135)
T ss_pred             CCHHHHHHHHHHHHHhccccchHH
Confidence            6666666666665 5555554443

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

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

Probab=98.06  E-value=0.00045  Score=48.04  Aligned_cols=125  Identities=10%  Similarity=0.002  Sum_probs=82.0

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHH--HHHHHhccccHHHHHHHHHHHHHhccCccH--hHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQ--ALKACSLAHAHQKGLEIHAHVIKYGHLHDI--FIQNSL  107 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~--ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~--~~~~~l  107 (209)
                      ..|..++..+ ..++.+.+...++.+.+..-.-.......  +-..+...|++++|...|+...+....|+.  ...-.|
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            4566666666 37777888888888877542111122222  335667778888888888888877633332  244556


Q ss_pred             HHHHHhCCChhhHHHHHHhcCCC--cHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          108 LHFYVTVKDIFSAHQIFNSVVFP--DVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       108 l~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      -..+...|++++|...++....+  ....+...=..|.+.|++++|...|..
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            67778888888888888776432  334455555778888888888887754

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

Probab=98.05  E-value=0.00029  Score=63.61  Aligned_cols=176  Identities=9%  Similarity=0.016  Sum_probs=95.6

Q ss_pred             HHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhC-CCCCC---------------------------------
Q 045511           21 IHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNC-PSSYN---------------------------------   65 (209)
Q Consensus        21 ~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~-g~~p~---------------------------------   65 (209)
                      ..+.....||. ..|-..|..+.+.++.+.|.++.++.... ++.-.                                 
T Consensus      1447 ferlvrssPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy 1526 (1710)
T KOG1070|consen 1447 FERLVRSSPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY 1526 (1710)
T ss_pred             HHHHHhcCCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh
Confidence            33333344666 77888888888888888888888777543 11111                                 


Q ss_pred             ---HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc----CC-CcHhHHHH
Q 045511           66 ---HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV----VF-PDVVTWTT  137 (209)
Q Consensus        66 ---~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----~~-~~~~~~~~  137 (209)
                         ...|..|...|.+.+..++|-++++.|.++- .....+|......+.++++-+.|.+++.+.    ++ .......-
T Consensus      1527 cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF-~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~Isk 1605 (1710)
T KOG1070|consen 1527 CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKF-GQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISK 1605 (1710)
T ss_pred             cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHh-cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHH
Confidence               1223444444444555555555555555442 244455555555555555555555555443    11 12223333


Q ss_pred             HHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCC
Q 045511          138 IISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNEN  197 (209)
Q Consensus       138 li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  197 (209)
                      .+..-.+.|+.+++..+|...  .-+--...|+..|..-.++|+.+.++.+|+++...++.|
T Consensus      1606 fAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1606 FAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            333344555555555555554  222233456666666666666666666666666665554

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

Probab=98.03  E-value=0.00011  Score=61.29  Aligned_cols=178  Identities=12%  Similarity=0.028  Sum_probs=110.4

Q ss_pred             hccCCCcchHhHHHHHHHHhh-CCCcccHHHHHHHHHcCCCcc-chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIK-IPQPHILNTLLKLLTQSSTPQ-NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~-~p~~~~~~~li~~~~~~g~~~-~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~   84 (209)
                      .-+..+.+.+.|..+++..+- ..+..+|++.+..+-+.-.+. .|..+.+.++     -...||.++=+.|.-+++.+.
T Consensus       365 El~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~-----~sPesWca~GNcfSLQkdh~~  439 (638)
T KOG1126|consen  365 ELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDP-----NSPESWCALGNCFSLQKDHDT  439 (638)
T ss_pred             HHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCC-----CCcHHHHHhcchhhhhhHHHH
Confidence            555666677777777776422 235599999998765532221 2333333332     345899999999999999999


Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHH---HHHHHhCCChHHHHHHHhhC-CC
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTI---ISGLSKCGFHKEAIDMFCGI-DV  160 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l---i~~~~~~g~~~~a~~~~~~m-~~  160 (209)
                      |.+.|+...+-. +....+|+.+=+=+....++|.|++.|+.....|...||+.   -..|.+.++++.|+--|+.. .+
T Consensus       440 Aik~f~RAiQld-p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~I  518 (638)
T KOG1126|consen  440 AIKCFKRAIQLD-PRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEI  518 (638)
T ss_pred             HHHHHHHhhccC-CccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcC
Confidence            999998877643 22566777777777777777777777776655554444443   34455556666665555555 44


Q ss_pred             CCCH-HhHHHHHHHhccccchhHHHHHHHHH
Q 045511          161 KPNA-NTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       161 ~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      .|.. +....+-..+.+.|+.++|.++++..
T Consensus       519 NP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A  549 (638)
T KOG1126|consen  519 NPSNSVILCHIGRIQHQLKRKDKALQLYEKA  549 (638)
T ss_pred             CccchhHHhhhhHHHHHhhhhhHHHHHHHHH
Confidence            4432 33444444444555555555555543

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

Probab=97.99  E-value=0.0003  Score=56.81  Aligned_cols=120  Identities=14%  Similarity=0.133  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHH
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLS  143 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~  143 (209)
                      .-...+++.+...++++.|.++|+.+.+..  |+.  .-.|.+.+...++-.+|.+++++...   .+....+.-...|.
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl  245 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLL  245 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            445667788888899999999999998875  554  44588888888999999999988732   35666666678899


Q ss_pred             hCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHH
Q 045511          144 KCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      +.++++.|+.+.++. ...|+. .+|..|.++|...|+++.|...+.-+
T Consensus       246 ~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  246 SKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             hcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence            999999999999999 888877 59999999999999999999888754

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=97.98  E-value=0.00028  Score=49.09  Aligned_cols=94  Identities=9%  Similarity=-0.082  Sum_probs=79.4

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhc
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACS  175 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~  175 (209)
                      +..+..+-..+...|++++|...|+...   ..+...|..+-..+.+.|++++|...|++. ...| +..++..+-.++.
T Consensus        24 p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~  103 (144)
T PRK15359         24 PETVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLK  103 (144)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHH
Confidence            3345567778899999999999999873   346788899999999999999999999999 6666 5577888888899


Q ss_pred             cccchhHHHHHHHHHHHhc
Q 045511          176 SLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       176 ~~g~~~~a~~~~~~~~~~~  194 (209)
                      ..|+.++|...++...+..
T Consensus       104 ~~g~~~eAi~~~~~Al~~~  122 (144)
T PRK15359        104 MMGEPGLAREAFQTAIKMS  122 (144)
T ss_pred             HcCCHHHHHHHHHHHHHhC
Confidence            9999999999999887763

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

Probab=97.97  E-value=0.00016  Score=56.09  Aligned_cols=141  Identities=15%  Similarity=0.201  Sum_probs=108.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      .+|..+|..+-+.+..+.|..+|.+.++.+ +...+....+.|..+ ..++.+.|..+|+...+. +..+...|...++.
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 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            468899999999999999999999998754 345555555555443 346677899999998876 57788899999999


Q ss_pred             HHhCCChhhHHHHHHhcCC--C----cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHh
Q 045511          111 YVTVKDIFSAHQIFNSVVF--P----DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSAC  174 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~~--~----~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~  174 (209)
                      +.+.|+.+.|+.+|++...  +    ....|...+.-=.+.|+++.+..+.+++ ..-|+...+..+++-|
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPEDNSLELFSDRY  150 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTTS-HHHHHHCCT
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhhHHHHHHHHh
Confidence            9999999999999998843  2    3458999999999999999999999998 6666666666666655

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.

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

Probab=97.96  E-value=0.00041  Score=50.97  Aligned_cols=122  Identities=10%  Similarity=0.090  Sum_probs=94.9

Q ss_pred             CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH-HHhCCC--hhhH
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF-YVTVKD--IFSA  120 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~-~~~~g~--~~~a  120 (209)
                      .++.+++...++...+.+ +.|...|..+-..+...|+++.|...|+...+.. +-+...+..+-.+ +...|+  .++|
T Consensus        52 ~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            455566666676666654 3577889999999999999999999999888865 4467777777776 467777  5999


Q ss_pred             HHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhH
Q 045511          121 HQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTL  167 (209)
Q Consensus       121 ~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~  167 (209)
                      .+++++..  .| +..++..+-..+...|++++|...|+++  ...|+..-+
T Consensus       130 ~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~~~~r~  181 (198)
T PRK10370        130 REMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKVLDLNSPRVNRT  181 (198)
T ss_pred             HHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCccHH
Confidence            99999883  23 6778888889999999999999999999  445555444

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

Probab=97.94  E-value=9.2e-05  Score=54.19  Aligned_cols=30  Identities=7%  Similarity=0.000  Sum_probs=20.7

Q ss_pred             chhHHHHHHHHHHHhccCCCchhHhHhhhc
Q 045511          179 SRKLGKAIHAHSLRNLNENNIILDNAVLDF  208 (209)
Q Consensus       179 ~~~~a~~~~~~~~~~~~~p~~~~~~~li~~  208 (209)
                      +.+-|.++++.|..+|+.||..|+..|++.
T Consensus       118 Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~i  147 (228)
T PF06239_consen  118 QQECAIDLLEQMENNGVMPDKETEQMLLNI  147 (228)
T ss_pred             HHHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            445667777777777777777777777654

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

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

Probab=97.93  E-value=0.0011  Score=53.69  Aligned_cols=178  Identities=7%  Similarity=0.010  Sum_probs=122.7

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCC-cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      ++..+.|..-|+.+.+..   |. ...|+.+=+-|...++...|.+-+++..+-+ +.|-..|--+=++|.-.+.+.-|.
T Consensus       343 r~eHEKAv~YFkRALkLN---p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaL  418 (559)
T KOG1155|consen  343 RSEHEKAVMYFKRALKLN---PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYAL  418 (559)
T ss_pred             HHhHHHHHHHHHHHHhcC---cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHH
Confidence            444555555555555442   33 3677777777777778788888777777653 346777777788888888887787


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-----
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-----  158 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-----  158 (209)
                      -.|+...+-. +-|...|.+|-.+|.+.++.++|.+.|....   +.+...+..+-+.|-+-++.++|-..|..-     
T Consensus       419 yYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~  497 (559)
T KOG1155|consen  419 YYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSE  497 (559)
T ss_pred             HHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            7777776643 5577899999999999999999999998873   345578888888898888888887777654     


Q ss_pred             --CC-CCCH-HhHHHHHHHhccccchhHHHHHHHHH
Q 045511          159 --DV-KPNA-NTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       159 --~~-~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                        |. .|.. .....|-..+.+.+++++|.......
T Consensus       498 ~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~  533 (559)
T KOG1155|consen  498 LEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLV  533 (559)
T ss_pred             hhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence              33 3322 22223444456667777766654433

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

Probab=97.93  E-value=0.0003  Score=60.78  Aligned_cols=184  Identities=12%  Similarity=0.109  Sum_probs=135.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCC-------------------------
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCP-------------------------   61 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-------------------------   61 (209)
                      ...+.+.|.+.+...........+...+|++...+.+..+++.+......+...-                         
T Consensus       292 ~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~  371 (895)
T KOG2076|consen  292 THNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVG  371 (895)
T ss_pred             HhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCC
Confidence            3444566677777766655555666889999999999999999999988887621                         


Q ss_pred             --CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc--CccHhHHHHHHHHHHhCCChhhHHHHHHhcCC----CcHh
Q 045511           62 --SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH--LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF----PDVV  133 (209)
Q Consensus        62 --~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~----~~~~  133 (209)
                        +.++... -.++-++.+....+..+-+.....+..+  .-++..|.-+..+|...|.+.+|.++|..+..    .+..
T Consensus       372 ~~~s~~l~v-~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~  450 (895)
T KOG2076|consen  372 KELSYDLRV-IRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAF  450 (895)
T ss_pred             CCCCccchh-HhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchh
Confidence              2233333 1222333445555556666666666663  34566899999999999999999999999832    3577


Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHH-hHHHHHHHhccccchhHHHHHHHHHH
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI-DVKPNAN-TLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      .|=-+-.+|-..|.++.|.+.|... ...|+.. .-.+|-..+.+.|+.++|.+++..+.
T Consensus       451 vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  451 VWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             hhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            8999999999999999999999998 7777653 34455556778999999999998753

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

Probab=97.92  E-value=0.00053  Score=54.72  Aligned_cols=145  Identities=10%  Similarity=0.020  Sum_probs=90.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHH----cCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLT----QSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAH   80 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~----~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~   80 (209)
                      ..++.+++.+.+.++.+..   |+. ..++. ...+.    ..+..+.+.+.++.  ..+..|+. .....+-..+...|
T Consensus        55 ~~g~~~~A~~~~~~~l~~~---P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G  128 (355)
T cd05804          55 IAGDLPKALALLEQLLDDY---PRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAG  128 (355)
T ss_pred             HcCCHHHHHHHHHHHHHHC---CCcHHHHHH-hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcC
Confidence            4566666766666666543   333 34332 11222    23444455555443  11222332 34445556677888


Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-----CcH--hHHHHHHHHHHhCCChHHHHH
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----PDV--VTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~~~--~~~~~li~~~~~~g~~~~a~~  153 (209)
                      ++++|...++...+.. +.+...+..+-..|...|++++|...+++..+     ++.  ..|-.+...+...|++++|..
T Consensus       129 ~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~  207 (355)
T cd05804         129 QYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALA  207 (355)
T ss_pred             CHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHH
Confidence            8888888888888765 44566778888888888888888888877632     222  234466777888888888888


Q ss_pred             HHhhC
Q 045511          154 MFCGI  158 (209)
Q Consensus       154 ~~~~m  158 (209)
                      .|++.
T Consensus       208 ~~~~~  212 (355)
T cd05804         208 IYDTH  212 (355)
T ss_pred             HHHHH
Confidence            88886

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.

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

Probab=97.91  E-value=0.00051  Score=55.54  Aligned_cols=147  Identities=14%  Similarity=0.124  Sum_probs=99.0

Q ss_pred             HcCCCccchHHHHHHhhhCCC--CCCHHHHHHHHH-------------------------------HHhccccHHHHHHH
Q 045511           42 TQSSTPQNAIPLYNKMLNCPS--SYNHYTFTQALK-------------------------------ACSLAHAHQKGLEI   88 (209)
Q Consensus        42 ~~~g~~~~a~~l~~~m~~~g~--~p~~~t~~~ll~-------------------------------~~~~~~~~~~a~~~   88 (209)
                      -...+++.|..+|+++.++..  .-|..+|+.++-                               .|+-.++.+.|...
T Consensus       273 y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~Y  352 (559)
T KOG1155|consen  273 YNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMY  352 (559)
T ss_pred             hhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHH
Confidence            356899999999999988752  125566665543                               33344567888888


Q ss_pred             HHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc-------------------------------------CCCc
Q 045511           89 HAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV-------------------------------------VFPD  131 (209)
Q Consensus        89 ~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~-------------------------------------~~~~  131 (209)
                      |+..++-+ +-....|+.+-+=|....+...|.+-++..                                     ...|
T Consensus       353 FkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnD  431 (559)
T KOG1155|consen  353 FKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPND  431 (559)
T ss_pred             HHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCc
Confidence            88877755 334567777777777777766666666433                                     1235


Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHH
Q 045511          132 VVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       132 ~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      ...|.+|=.+|.+.++.++|+..|++.  .-..+...+..+-+.+.+.++.++|.+.+..
T Consensus       432 sRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek  491 (559)
T KOG1155|consen  432 SRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEK  491 (559)
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            667777777777777777777777776  3334556777777777777777777776663

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

Probab=97.91  E-value=0.0038  Score=46.91  Aligned_cols=126  Identities=12%  Similarity=0.031  Sum_probs=107.2

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      |...-+.+.....++|++.+|...|++...-. ++|..+|+.+=-+|.+.|+++.|..-|.+..+-- .-++...|+|-.
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 DRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQLGRFDEARRAYRQALELA-PNEPSIANNLGM  176 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHH
Confidence            33456668889999999999999999987753 5788999999999999999999999998888753 446788999999


Q ss_pred             HHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          110 FYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      .|.-+|+.+.|+.++..-   +..|...-..+.......|++++|..+-..
T Consensus       177 s~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~  227 (257)
T COG5010         177 SLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQ  227 (257)
T ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhccc
Confidence            999999999999999876   334778888888899999999999988765

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

Probab=97.90  E-value=0.00078  Score=54.70  Aligned_cols=136  Identities=13%  Similarity=0.095  Sum_probs=99.4

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc-HhHHHHHHHHHHhCCChh
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD-IFIQNSLLHFYVTVKDIF  118 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~g~~~  118 (209)
                      .....|+.++|+..++.+... .+-|..-.......+.+.++.++|.+-++.+....  |+ ....-++-.+|.+.|++.
T Consensus       315 ~~~~~~~~d~A~~~l~~L~~~-~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~--P~~~~l~~~~a~all~~g~~~  391 (484)
T COG4783         315 QTYLAGQYDEALKLLQPLIAA-QPDNPYYLELAGDILLEANKAKEAIERLKKALALD--PNSPLLQLNLAQALLKGGKPQ  391 (484)
T ss_pred             HHHHhcccchHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CCccHHHHHHHHHHHhcCChH
Confidence            355678888888888887764 33455666677778888888888888888887653  44 566777778888888888


Q ss_pred             hHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          119 SAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       119 ~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +|.++++.-.   .-|...|..|-.+|...|+..++..-..+.               +...|+++.|.+.+....+.
T Consensus       392 eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~---------------~~~~G~~~~A~~~l~~A~~~  454 (484)
T COG4783         392 EAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEG---------------YALAGRLEQAIIFLMRASQQ  454 (484)
T ss_pred             HHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHH---------------HHhCCCHHHHHHHHHHHHHh
Confidence            8888888763   236778888888888888888888777774               22445666666665555444

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

Probab=97.89  E-value=0.00018  Score=47.12  Aligned_cols=86  Identities=15%  Similarity=0.103  Sum_probs=60.0

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhcc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCC
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCG  146 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g  146 (209)
                      |-...|..|...+++..+..+|+.+++.|+ .|++.+||.++.+.+++.--.++                       -.+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~-----------------------ie~   83 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSED-----------------------IEN   83 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchh-----------------------HHH
Confidence            344556667777999999999999999999 99999999999998887422100                       011


Q ss_pred             ChHHHHHHHhhC---CCCCCHHhHHHHHHHhcc
Q 045511          147 FHKEAIDMFCGI---DVKPNANTLVSVLSACSS  176 (209)
Q Consensus       147 ~~~~a~~~~~~m---~~~p~~~t~~~li~~~~~  176 (209)
                      .+-..+.+|+.|   +++|+..||+.++....+
T Consensus        84 kl~~LLtvYqDiL~~~lKP~~etYnivl~~Llk  116 (120)
T PF08579_consen   84 KLTNLLTVYQDILSNKLKPNDETYNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHH
Confidence            223344555555   677777777777766543

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 [, , ].

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

Probab=97.88  E-value=0.00023  Score=62.02  Aligned_cols=190  Identities=15%  Similarity=0.102  Sum_probs=127.9

Q ss_pred             CcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCC-CCCHHHHHHHHHHHhc------------
Q 045511           12 TLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SYNHYTFTQALKACSL------------   78 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p~~~t~~~ll~~~~~------------   78 (209)
                      .++...+.+......  .++..++.+=..+.+...+..|.+-|+...+.-. .+|..+.-.|=+.|..            
T Consensus       547 ~ea~~~lk~~l~~d~--~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~  624 (1018)
T KOG2002|consen  547 YEASLLLKDALNIDS--SNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKE  624 (1018)
T ss_pred             HHHHHHHHHHHhccc--CCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHH
Confidence            334444444433322  2334444455566666666677766655554432 2444444444343322            


Q ss_pred             cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCC---cHhHHHHHHHHHHhCCChHHHHHHH
Q 045511           79 AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFP---DVVTWTTIISGLSKCGFHKEAIDMF  155 (209)
Q Consensus        79 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~  155 (209)
                      .+..+.|.++|+..++.. +.|...-|.+--.++.+|++.+|..+|.++.+.   ...+|-.+-++|...|++..|+++|
T Consensus       625 kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmY  703 (1018)
T KOG2002|consen  625 KKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMY  703 (1018)
T ss_pred             HHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHH
Confidence            134577888888888765 668888899999999999999999999998653   3467888899999999999999999


Q ss_pred             hhC----CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhH
Q 045511          156 CGI----DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNA  204 (209)
Q Consensus       156 ~~m----~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~  204 (209)
                      ...    .-.-+.....-|-+++.+.|.+.+|.+.+-..+.....-....||.
T Consensus       704 e~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~  756 (1018)
T KOG2002|consen  704 ENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNL  756 (1018)
T ss_pred             HHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHH
Confidence            877    5445667888889999999999999988765555443333344443

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

Probab=97.88  E-value=0.001  Score=51.53  Aligned_cols=126  Identities=13%  Similarity=0.091  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH-HHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHH
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF-YVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGL  142 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~-~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~  142 (209)
                      .+|..++...-+.+..+.|..+|...++.+ ..+..+|-..-.. |.-.++.+.|.++|+...   ..+...|...+.-+
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 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            468899999999999999999999998654 2233444443333 233467777999999873   35778899999999


Q ss_pred             HhCCChHHHHHHHhhC-CCCCCH----HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          143 SKCGFHKEAIDMFCGI-DVKPNA----NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       143 ~~~g~~~~a~~~~~~m-~~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ...|+.+.|..+|.+. ..-|..    ..|...++.-.+.|+++.+..+..++.+.
T Consensus        81 ~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   81 IKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            9999999999999998 334444    48999999999999999999999888765

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.

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

Probab=97.85  E-value=0.002  Score=44.71  Aligned_cols=122  Identities=17%  Similarity=0.047  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--HhHHHHHHHHHHhCCChhhHHHHHHhcCC--CcH----hHHHHH
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PDV----VTWTTI  138 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~~----~~~~~l  138 (209)
                      ..|..++..+ ..++...+...++.+.+......  ....-.+-..+...|++++|...|+....  |+.    ...-.+
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            4566667766 47888999999999988752221  22333455788899999999999998832  332    344556


Q ss_pred             HHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHH
Q 045511          139 ISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      ...+...|++++|+..+... +-......+...-..+.+.|+.++|...|+.
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            78889999999999999886 3333445566677778999999999999875

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.83  E-value=0.0021  Score=55.88  Aligned_cols=131  Identities=11%  Similarity=0.008  Sum_probs=111.2

Q ss_pred             CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHH
Q 045511           62 SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTI  138 (209)
Q Consensus        62 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~l  138 (209)
                      ...+...+-.|-....+.|++++|+.+++...+.. +-+......+...+.+.+++++|....++.-  .| +....+.+
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~-Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~  160 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRF-PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLE  160 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHH
Confidence            34568889999999999999999999999998864 3456788899999999999999999999983  35 45667777


Q ss_pred             HHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          139 ISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      -.++.+.|++++|..+|++. ...|+ ..++..+-.++.+.|+.++|...|....+.
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            89999999999999999999 44455 578888999999999999999999987555

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

Probab=97.83  E-value=0.00086  Score=45.71  Aligned_cols=95  Identities=13%  Similarity=0.119  Sum_probs=81.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      .....+...+.+.|+.++|...|+.....+ +.+...+..+-..+.+.|+++.|...++...+.+ +.+...+..+-..|
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~   95 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECL   95 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHH
Confidence            556677788889999999999999998765 3467888888889999999999999999887765 55677888888899


Q ss_pred             HhCCChhhHHHHHHhcC
Q 045511          112 VTVKDIFSAHQIFNSVV  128 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~  128 (209)
                      ...|+.++|.+.|+...
T Consensus        96 ~~~g~~~~A~~~~~~al  112 (135)
T TIGR02552        96 LALGEPESALKALDLAI  112 (135)
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            99999999999998874

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

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

Probab=97.83  E-value=0.00045  Score=60.95  Aligned_cols=119  Identities=11%  Similarity=0.042  Sum_probs=80.5

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH--------------
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH--------------   66 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~--------------   66 (209)
                      |+..+ ..++++++.+...+..+.++..+....|...  .+.+.++.+++..+  .+... +..+.              
T Consensus        37 Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~--l~~q~~~~~~~~lv--~~l~~-~~~~~~~~~ve~~~~~i~~  111 (906)
T PRK14720         37 LIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGI--LSLSRRPLNDSNLL--NLIDS-FSQNLKWAIVEHICDKILL  111 (906)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHH--HHHhhcchhhhhhh--hhhhh-cccccchhHHHHHHHHHHh
Confidence            45566 6777777777777655555333333333333  55666666666555  22221 11222              


Q ss_pred             -----HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           67 -----YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        67 -----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                           ..+-.+-.+|-+.|+.+++..+++.+++.. +.|+.+.|.+-..|... ++++|++++.+.
T Consensus       112 ~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KA  175 (906)
T PRK14720        112 YGENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKA  175 (906)
T ss_pred             hhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHH
Confidence                 455566677777799999999999999887 77889999999999999 999999888654

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

Probab=97.83  E-value=0.0027  Score=57.75  Aligned_cols=145  Identities=10%  Similarity=0.063  Sum_probs=102.2

Q ss_pred             CccchHHHHHHhhhCCCCCC-HHHHHHHHHHHhccccHHHHHHHHHHHHHh-ccCc---cHhHHHHHHHHHHhCCChhhH
Q 045511           46 TPQNAIPLYNKMLNCPSSYN-HYTFTQALKACSLAHAHQKGLEIHAHVIKY-GHLH---DIFIQNSLLHFYVTVKDIFSA  120 (209)
Q Consensus        46 ~~~~a~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~---~~~~~~~ll~~~~~~g~~~~a  120 (209)
                      ..+.|.++-+..+..   || ...|-..|..+...++++.|.++.+..+.. ++.-   -..+|.++++.-..-|.-+..
T Consensus      1440 ~pesaeDferlvrss---PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl 1516 (1710)
T KOG1070|consen 1440 APESAEDFERLVRSS---PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESL 1516 (1710)
T ss_pred             CCcCHHHHHHHHhcC---CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHH
Confidence            444555555555442   44 466888888899999999999998887754 1211   134777777777777877888


Q ss_pred             HHHHHhcCC-Cc-HhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          121 HQIFNSVVF-PD-VVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       121 ~~~~~~~~~-~~-~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .++|++..+ -| ...|..|..-|.+.+..++|-++++.|  .+.-....|...+..+.+..+.+.|..++.+.+++
T Consensus      1517 ~kVFeRAcqycd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~ 1593 (1710)
T KOG1070|consen 1517 KKVFERACQYCDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKS 1593 (1710)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh
Confidence            888888754 23 456777888888888888888888888  44445567777777777777777777777765544

>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=97.79  E-value=0.00037  Score=43.22  Aligned_cols=87  Identities=15%  Similarity=0.083  Sum_probs=34.7

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      +...+.+.|++++|...+++..+... .+...+..+...+...++++.|.+.++...+.. +.+..++..+...+...|+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   83 (100)
T cd00189           6 LGNLYYKLGDYDEALEYYEKALELDP-DNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGK   83 (100)
T ss_pred             HHHHHHHHhcHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHh
Confidence            33334444444444444444433221 112333334444444444444444444443332 1122333444444444444


Q ss_pred             hhhHHHHHH
Q 045511          117 IFSAHQIFN  125 (209)
Q Consensus       117 ~~~a~~~~~  125 (209)
                      .++|.+.+.
T Consensus        84 ~~~a~~~~~   92 (100)
T cd00189          84 YEEALEAYE   92 (100)
T ss_pred             HHHHHHHHH
Confidence            444444443

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

Probab=97.78  E-value=0.0034  Score=51.11  Aligned_cols=160  Identities=15%  Similarity=0.105  Sum_probs=120.0

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +...+...+.+......-..+..++.+-.+.+  -..--|...+..| ..|.++.|+..++.+...- +-|+.-+.....
T Consensus       273 ~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~--~~aa~YG~A~~~~-~~~~~d~A~~~l~~L~~~~-P~N~~~~~~~~~  348 (484)
T COG4783         273 DFQLARARIRAKYEALPNQQAADLLAKRSKRG--GLAAQYGRALQTY-LAGQYDEALKLLQPLIAAQ-PDNPYYLELAGD  348 (484)
T ss_pred             cHHHHHHHHHHHhccccccchHHHHHHHhCcc--chHHHHHHHHHHH-HhcccchHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            34666677776666655555554544444321  2334577766665 7789999999999977653 567778888889


Q ss_pred             HHHhCCChhhHHHHHHhcC--CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHH
Q 045511          110 FYVTVKDIFSAHQIFNSVV--FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~  184 (209)
                      .+.+.++..+|.+.++++.  .|+ ...+-.+-.+|.+.|++.+|..++++-  ..+-|...|..|-++|...|+..++.
T Consensus       349 i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~  428 (484)
T COG4783         349 ILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEAL  428 (484)
T ss_pred             HHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHH
Confidence            9999999999999999984  355 455666778999999999999999998  55557789999999999999999988


Q ss_pred             HHHHHHHHh
Q 045511          185 AIHAHSLRN  193 (209)
Q Consensus       185 ~~~~~~~~~  193 (209)
                      .-..+....
T Consensus       429 ~A~AE~~~~  437 (484)
T COG4783         429 LARAEGYAL  437 (484)
T ss_pred             HHHHHHHHh
Confidence            887766443

>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=97.73  E-value=0.0036  Score=52.56  Aligned_cols=182  Identities=12%  Similarity=0.138  Sum_probs=99.5

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHh----c--c
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACS----L--A   79 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~----~--~   79 (209)
                      ..|+.++|++.+..-...   .+|. ......-..+.+.|+.++|..+|+.+.+.+  |+...|-..+..+.    .  .
T Consensus        16 e~g~~~~AL~~L~~~~~~---I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g~~~~~~~   90 (517)
T PF12569_consen   16 EAGDYEEALEHLEKNEKQ---ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALGLQLQLSD   90 (517)
T ss_pred             HCCCHHHHHHHHHhhhhh---CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHhhhccccc
Confidence            566777777666543332   2444 556677777778888888888888888866  56666555555554    1  1


Q ss_pred             ccHHHHHHHHHHHHHhccC------------------------------cc-HhHHHHHHHHHHhCCChhhHHHHHHhc-
Q 045511           80 HAHQKGLEIHAHVIKYGHL------------------------------HD-IFIQNSLLHFYVTVKDIFSAHQIFNSV-  127 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~------------------------------~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~-  127 (209)
                      ...+...++++.+.+.-..                              -+ +.+++.|-..|......+-..+++... 
T Consensus        91 ~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~  170 (517)
T PF12569_consen   91 EDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYV  170 (517)
T ss_pred             ccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHH
Confidence            1334444444444332100                              00 223333333333333333333333222 


Q ss_pred             -----------------CCCcHhHH--HHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHH
Q 045511          128 -----------------VFPDVVTW--TTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       128 -----------------~~~~~~~~--~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~  186 (209)
                                       ..|+...|  .-+-..|-..|++++|++..++. ...|+. ..|..--+.+-+.|++++|.+.
T Consensus       171 ~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~  250 (517)
T PF12569_consen  171 NSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEA  250 (517)
T ss_pred             HhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence                             01333233  44445566677777777777766 666664 4566666666677777777776


Q ss_pred             HHHHHHh
Q 045511          187 HAHSLRN  193 (209)
Q Consensus       187 ~~~~~~~  193 (209)
                      .+..++.
T Consensus       251 ~~~Ar~L  257 (517)
T PF12569_consen  251 MDEAREL  257 (517)
T ss_pred             HHHHHhC
Confidence            6655443

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 [], [].

>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=97.72  E-value=0.0072  Score=50.81  Aligned_cols=163  Identities=15%  Similarity=0.091  Sum_probs=117.4

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhC----C----------CCCCH--HHHHHHHHHHhccccHHHHHHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNC----P----------SSYNH--YTFTQALKACSLAHAHQKGLEIHAHVI   93 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g----------~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~   93 (209)
                      -+..|+.|-..|....+.+-..+++......    |          -+|..  +++.-+-..|-..|++++|.+.++...
T Consensus       142 vPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI  221 (517)
T PF12569_consen  142 VPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAI  221 (517)
T ss_pred             CchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3467777777777666666666666665432    1          12443  355666777788999999999999888


Q ss_pred             HhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC---CCCCCHHh-
Q 045511           94 KYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANT-  166 (209)
Q Consensus        94 ~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m---~~~p~~~t-  166 (209)
                      +.. +..+..|..--+.|-+.|++++|.+.++..+.   .|...-+-..+-+.++|+.++|.+++...   +..|-... 
T Consensus       222 ~ht-Pt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~  300 (517)
T PF12569_consen  222 EHT-PTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLN  300 (517)
T ss_pred             hcC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHH
Confidence            764 33367888888999999999999999988754   46778888899999999999999998887   33332211 


Q ss_pred             ---H----HHHHHHhccccchhHHHHHHHHHHHh
Q 045511          167 ---L----VSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       167 ---~----~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                         +    +-.-.+|.+.|++..|..-|..+.+.
T Consensus       301 ~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k~  334 (517)
T PF12569_consen  301 DMQCMWFETECAEAYLRQGDYGLALKRFHAVLKH  334 (517)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence               1    33356677889999888877766544

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 [], [].

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

Probab=97.70  E-value=0.0019  Score=48.81  Aligned_cols=109  Identities=12%  Similarity=0.013  Sum_probs=49.2

Q ss_pred             HHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh----CCC
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT----VKD  116 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~g~  116 (209)
                      |+..|++++|++..+..      -+......=+..+.+..+++.|++.++.|.+..   +..|.+-|-.++.+    .+.
T Consensus       118 ~~~~~~~deAl~~~~~~------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~id---ed~tLtQLA~awv~la~ggek  188 (299)
T KOG3081|consen  118 YMHDGDFDEALKALHLG------ENLEAAALNVQILLKMHRFDLAEKELKKMQQID---EDATLTQLAQAWVKLATGGEK  188 (299)
T ss_pred             hhcCCChHHHHHHHhcc------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHHhccchh
Confidence            34445555555554431      122222233333344445555555555554432   23333333333322    234


Q ss_pred             hhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          117 IFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       117 ~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +.+|.=+|++|.+   |+..+-|-...++...|++++|..++.+.
T Consensus       189 ~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~ea  233 (299)
T KOG3081|consen  189 IQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEA  233 (299)
T ss_pred             hhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHH
Confidence            5555555555533   44444445555555555555555555554

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.69  E-value=0.0012  Score=47.23  Aligned_cols=85  Identities=13%  Similarity=0.075  Sum_probs=57.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC--HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN--HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..|..+-..+.+.|++++|...|++..+.+..++  ...+..+-..+.+.|+++.|...++...+.. +.+...+..+..
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~  114 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHH
Confidence            5566667777778888888888887776442222  3567777777788888888888887777653 224556666666


Q ss_pred             HHHhCCCh
Q 045511          110 FYVTVKDI  117 (209)
Q Consensus       110 ~~~~~g~~  117 (209)
                      .|...|+.
T Consensus       115 ~~~~~g~~  122 (172)
T PRK02603        115 IYHKRGEK  122 (172)
T ss_pred             HHHHcCCh
Confidence            67666664

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.69  E-value=0.0012  Score=51.91  Aligned_cols=162  Identities=10%  Similarity=0.062  Sum_probs=103.6

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHH-----hccccHHHHHHHHHHHHHhccCc------------
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKAC-----SLAHAHQKGLEIHAHVIKYGHLH------------   99 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~-----~~~~~~~~a~~~~~~m~~~g~~~------------   99 (209)
                      |+-.+.+.+++.+|..+.+++..  ..|-......++.+-     .....+.-|.+.|...-+++..-            
T Consensus       291 L~iYyL~q~dVqeA~~L~Kdl~P--ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~  368 (557)
T KOG3785|consen  291 LIIYYLNQNDVQEAISLCKDLDP--TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASY  368 (557)
T ss_pred             heeeecccccHHHHHHHHhhcCC--CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHH
Confidence            44557788888888888766543  334444433333332     22234556777777776666432            


Q ss_pred             --------cHhHHHHHHHH---------------HHhCCChhhHHHHHHhcCCC---cHhHHHHHH-HHHHhCCChHHHH
Q 045511          100 --------DIFIQNSLLHF---------------YVTVKDIFSAHQIFNSVVFP---DVVTWTTII-SGLSKCGFHKEAI  152 (209)
Q Consensus       100 --------~~~~~~~ll~~---------------~~~~g~~~~a~~~~~~~~~~---~~~~~~~li-~~~~~~g~~~~a~  152 (209)
                              |+.+|-.-|.+               ++..|++.+|+++|-.++.|   |..+|-+++ ++|.+.|.++.|+
T Consensus       369 fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW  448 (557)
T KOG3785|consen  369 FFLSFQFDDVLTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAW  448 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHH
Confidence                    23344433443               44457788999999888654   566776655 8899999999999


Q ss_pred             HHHhhCCCCCCHHh-HHHHHHHhccccchhHHHHHHHHHHHhccCCCchhH
Q 045511          153 DMFCGIDVKPNANT-LVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILD  202 (209)
Q Consensus       153 ~~~~~m~~~p~~~t-~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  202 (209)
                      +++-.+.-..+..+ ...+-+.|.+.+.+--|...|+++...  .|++.-|
T Consensus       449 ~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~l--DP~pEnW  497 (557)
T KOG3785|consen  449 DMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEIL--DPTPENW  497 (557)
T ss_pred             HHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHcc--CCCcccc
Confidence            99888733333333 444556788888888888888877665  5555444

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

Probab=97.67  E-value=0.0034  Score=47.45  Aligned_cols=137  Identities=12%  Similarity=0.097  Sum_probs=101.6

Q ss_pred             HHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCc
Q 045511           52 PLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPD  131 (209)
Q Consensus        52 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~  131 (209)
                      ++.+.+......-|......-...|+..|++++|++....    |  .+......=+..+.+..+++-|++-++.|.+.|
T Consensus        94 ~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~----~--~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~id  167 (299)
T KOG3081|consen   94 SLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHL----G--ENLEAAALNVQILLKMHRFDLAEKELKKMQQID  167 (299)
T ss_pred             HHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhc----c--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            4455555555555544455556678899999999888654    2  233344444567788899999999999998754


Q ss_pred             -HhHHHHHHHH----HHhCCChHHHHHHHhhC-C-CCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          132 -VVTWTTIISG----LSKCGFHKEAIDMFCGI-D-VKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       132 -~~~~~~li~~----~~~~g~~~~a~~~~~~m-~-~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                       ..+.+-|..+    ....+.+.+|+-+|.+| + ..|+..+.+....++...|++++|+.++.....+.
T Consensus       168 ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd  237 (299)
T KOG3081|consen  168 EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKD  237 (299)
T ss_pred             hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhcc
Confidence             3444444444    44456789999999999 4 89999999999999999999999999999887764

>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=97.63  E-value=0.00089  Score=41.43  Aligned_cols=89  Identities=10%  Similarity=0.035  Sum_probs=71.1

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      +..+...+...|+++.|...++...+.. +.+...+..+...+...|++++|.+.++...   ..+..++..+...+...
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHH
Confidence            4556667778899999999999887764 3344778888889999999999999998763   23446788888899999


Q ss_pred             CChHHHHHHHhhC
Q 045511          146 GFHKEAIDMFCGI  158 (209)
Q Consensus       146 g~~~~a~~~~~~m  158 (209)
                      |+++.|...+.+.
T Consensus        82 ~~~~~a~~~~~~~   94 (100)
T cd00189          82 GKYEEALEAYEKA   94 (100)
T ss_pred             HhHHHHHHHHHHH
Confidence            9999999988775

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

Probab=97.59  E-value=0.0047  Score=50.45  Aligned_cols=183  Identities=12%  Similarity=0.065  Sum_probs=128.5

Q ss_pred             hccCCCcchHhHHHHHHHHhhCC-----CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIP-----QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAH   80 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p-----~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~   80 (209)
                      +-++-++..+.+..++..+....     +...|--.+..=.++.++..|..++++....  -|-+ ..|-..+..=-..|
T Consensus        78 kYaqwEesq~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~--lPRVdqlWyKY~ymEE~Lg  155 (677)
T KOG1915|consen   78 KYAQWEESQKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI--LPRVDQLWYKYIYMEEMLG  155 (677)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh--cchHHHHHHHHHHHHHHhc
Confidence            44555555555666655553333     3355555666777888888888888877653  2333 44555666666778


Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ++..|.++|+...+  ..|+...|++.|+.=.+-..++.|..+++..  ..|++.+|--..+-=-++|+...+..+|...
T Consensus       156 Ni~gaRqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~VyerA  233 (677)
T KOG1915|consen  156 NIAGARQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYERA  233 (677)
T ss_pred             ccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            88999999887765  4689999999999999999999999999887  4688888888888888888888888888776


Q ss_pred             ----CC-CCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          159 ----DV-KPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       159 ----~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                          |- .-+...|.++-.--.+...++.|.-++....++
T Consensus       234 ie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~  273 (677)
T KOG1915|consen  234 IEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH  273 (677)
T ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence                21 122334455544445567778888888776655

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

Probab=97.58  E-value=0.006  Score=48.15  Aligned_cols=85  Identities=15%  Similarity=0.154  Sum_probs=72.9

Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchh
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRK  181 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~  181 (209)
                      .+.+.-|.-+...|+...|.++-.+..=|+..-|-..|.+|+..++|++-.++.+.   +-+++-|..++.+|.+.|...
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s---kKsPIGyepFv~~~~~~~~~~  254 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS---KKSPIGYEPFVEACLKYGNKK  254 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC---CCCCCChHHHHHHHHHCCCHH
Confidence            35666678888999999999999999889999999999999999999998887665   445688999999999999988


Q ss_pred             HHHHHHHH
Q 045511          182 LGKAIHAH  189 (209)
Q Consensus       182 ~a~~~~~~  189 (209)
                      +|..+...
T Consensus       255 eA~~yI~k  262 (319)
T PF04840_consen  255 EASKYIPK  262 (319)
T ss_pred             HHHHHHHh
Confidence            88877665

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

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

Probab=97.57  E-value=0.00049  Score=43.03  Aligned_cols=78  Identities=12%  Similarity=0.057  Sum_probs=40.6

Q ss_pred             cccHHHHHHHHHHHHHhcc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHH
Q 045511           79 AHAHQKGLEIHAHVIKYGH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMF  155 (209)
Q Consensus        79 ~~~~~~a~~~~~~m~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~  155 (209)
                      .|+++.|..+++.+.+... .++...+-.+-.+|.+.|++++|.++++...  ..+....-.+-.+|.+.|++++|++.|
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l   81 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKAL   81 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            3556666666666665543 1233444446666666666666666665521  112222223345666666666666665


Q ss_pred             h
Q 045511          156 C  156 (209)
Q Consensus       156 ~  156 (209)
                      .
T Consensus        82 ~   82 (84)
T PF12895_consen   82 E   82 (84)
T ss_dssp             H
T ss_pred             h
Confidence            4

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.56  E-value=0.0022  Score=42.33  Aligned_cols=91  Identities=14%  Similarity=0.053  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccC--ccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc----HhHHHHHH
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHL--HDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD----VVTWTTII  139 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~--~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~----~~~~~~li  139 (209)
                      ++-.....+.+.|++++|.+.|+.+.+....  .....+..+...+.+.|++++|.+.|+...  .|+    ...+..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            3444455555666666666666666554311  112344556666666666666666666552  122    23445555


Q ss_pred             HHHHhCCChHHHHHHHhhC
Q 045511          140 SGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       140 ~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..+.+.|++++|...+.++
T Consensus        84 ~~~~~~~~~~~A~~~~~~~  102 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQV  102 (119)
T ss_pred             HHHHHhCChHHHHHHHHHH
Confidence            5556666666666666665

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.

>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=97.55  E-value=0.0011  Score=44.89  Aligned_cols=80  Identities=14%  Similarity=0.067  Sum_probs=60.6

Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhc-------------------CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC--
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSV-------------------VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI--  158 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~-------------------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--  158 (209)
                      |..++.++|.++++.|+++...++++..                   ..|+..+..+++.+|+..|++..|+++.+..  
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            4567888899999999999888888655                   0266777788888888888888888777777  


Q ss_pred             --CCCCCHHhHHHHHHHhccccc
Q 045511          159 --DVKPNANTLVSVLSACSSLGS  179 (209)
Q Consensus       159 --~~~p~~~t~~~li~~~~~~g~  179 (209)
                        ++..+..+|..|++-+...-+
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHHhcC
Confidence              766677778888777655444

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=97.52  E-value=0.0038  Score=41.19  Aligned_cols=94  Identities=13%  Similarity=-0.024  Sum_probs=50.3

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCC--CCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC--ccHhHHHHHHH
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPS--SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL--HDIFIQNSLLH  109 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~--~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~--~~~~~~~~ll~  109 (209)
                      +-.+...+.+.|++++|.+.|+.+.+..-  ......+-.+...+.+.|+++.|.+.|+...+....  ....++..+..
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~   84 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGM   84 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHH
Confidence            44445555566666666666666654321  011234444555566666666666666665543211  11344555555


Q ss_pred             HHHhCCChhhHHHHHHhc
Q 045511          110 FYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~  127 (209)
                      .+.+.|+.++|.+.++++
T Consensus        85 ~~~~~~~~~~A~~~~~~~  102 (119)
T TIGR02795        85 SLQELGDKEKAKATLQQV  102 (119)
T ss_pred             HHHHhCChHHHHHHHHHH
Confidence            666666666666666655

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

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

Probab=97.52  E-value=0.0021  Score=51.61  Aligned_cols=98  Identities=7%  Similarity=0.040  Sum_probs=59.3

Q ss_pred             HhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHH
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAI  152 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~  152 (209)
                      ....|+++.|.+.|+..++.. +.+...|..+-.+|.+.|++++|...++...+   .+...|..+-.+|...|++++|.
T Consensus        12 a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~eA~   90 (356)
T PLN03088         12 AFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTAK   90 (356)
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCHHHHH
Confidence            345566666666666666544 33455666666666666777777666666522   24455666666666677777777


Q ss_pred             HHHhhC-CCCCCHHhHHHHHHHh
Q 045511          153 DMFCGI-DVKPNANTLVSVLSAC  174 (209)
Q Consensus       153 ~~~~~m-~~~p~~~t~~~li~~~  174 (209)
                      ..|++. .+.|+.......+..|
T Consensus        91 ~~~~~al~l~P~~~~~~~~l~~~  113 (356)
T PLN03088         91 AALEKGASLAPGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHH
Confidence            777666 5566655555444444

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

Probab=97.50  E-value=0.0039  Score=55.25  Aligned_cols=134  Identities=13%  Similarity=0.055  Sum_probs=64.1

Q ss_pred             hhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHH
Q 045511           26 IKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQN  105 (209)
Q Consensus        26 ~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  105 (209)
                      ....|+..|--+|....+.|.+++-.+.+.-.++..-.|.+.  +.+|-+|++.+++.+.++++       ..||..-..
T Consensus      1128 ikadDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi-------~gpN~A~i~ 1198 (1666)
T KOG0985|consen 1128 IKADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFI-------AGPNVANIQ 1198 (1666)
T ss_pred             HhcCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHh-------cCCCchhHH
Confidence            333444555555555555555555555544444433333333  34455555555554444433       234444444


Q ss_pred             HHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhcc
Q 045511          106 SLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSS  176 (209)
Q Consensus       106 ~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~  176 (209)
                      .+-+-|...|.++.|.-+|.     ++..|.-+...+...|++..|.+.-+.   .-+..||..+--+|..
T Consensus      1199 ~vGdrcf~~~~y~aAkl~y~-----~vSN~a~La~TLV~LgeyQ~AVD~aRK---Ans~ktWK~VcfaCvd 1261 (1666)
T KOG0985|consen 1199 QVGDRCFEEKMYEAAKLLYS-----NVSNFAKLASTLVYLGEYQGAVDAARK---ANSTKTWKEVCFACVD 1261 (1666)
T ss_pred             HHhHHHhhhhhhHHHHHHHH-----HhhhHHHHHHHHHHHHHHHHHHHHhhh---ccchhHHHHHHHHHhc
Confidence            44444444455555544444     344566666666666666655544433   2233344444444433

>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=97.48  E-value=0.0011  Score=39.34  Aligned_cols=60  Identities=10%  Similarity=0.153  Sum_probs=36.2

Q ss_pred             ccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTI  138 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~l  138 (209)
                      +.|++++|.+.|+.+.+.. +-+...+-.+..+|.+.|++++|.++++.+.  .|+...|..+
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l   64 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQL   64 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            4566777777777766654 3355566667777777777777777777663  3443444433

...

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

Probab=97.46  E-value=0.0062  Score=49.77  Aligned_cols=149  Identities=12%  Similarity=0.104  Sum_probs=121.5

Q ss_pred             cCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHH
Q 045511           43 QSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQ  122 (209)
Q Consensus        43 ~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~  122 (209)
                      ..+++.+|.++|++..... .-++..|-..+..=.+...+..|..+++.....= +.-...|--.+.+=-..|++..|.+
T Consensus        85 sq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~l-PRVdqlWyKY~ymEE~LgNi~gaRq  162 (677)
T KOG1915|consen   85 SQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTIL-PRVDQLWYKYIYMEEMLGNIAGARQ  162 (677)
T ss_pred             hHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhc-chHHHHHHHHHHHHHHhcccHHHHH
Confidence            4677888999999988755 3466666667777788888888999988776542 2222455556666667899999999


Q ss_pred             HHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          123 IFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       123 ~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +|+.-.  +|+...|++.|+.=.+-+.++.|..+|.+. -+.|+..+|--..+--.++|....+..++....+.
T Consensus       163 iferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~  236 (677)
T KOG1915|consen  163 IFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYERAIEF  236 (677)
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            999864  699999999999999999999999999999 78899999998888889999999999999876544

>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=97.45  E-value=0.002  Score=43.60  Aligned_cols=27  Identities=11%  Similarity=0.169  Sum_probs=20.4

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHh
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKM   57 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m   57 (209)
                      ..++.++|.++++.|+++....+++..
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~   28 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSV   28 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHh
Confidence            456777888888888888887777655

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

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

Probab=97.45  E-value=0.0032  Score=52.15  Aligned_cols=164  Identities=13%  Similarity=0.043  Sum_probs=109.1

Q ss_pred             CCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccccHHHHHHH
Q 045511           10 KPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAHAHQKGLEI   88 (209)
Q Consensus        10 ~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~   88 (209)
                      ..+.|..-+..+-+.++..--+..|-.  --|.+.++.+.|.+.|.+...  +-|+. ..++-+=-..-..+.+.+|..+
T Consensus       361 EhdQAmaaY~tAarl~~G~hlP~LYlg--mey~~t~n~kLAe~Ff~~A~a--i~P~Dplv~~Elgvvay~~~~y~~A~~~  436 (611)
T KOG1173|consen  361 EHDQAMAAYFTAARLMPGCHLPSLYLG--MEYMRTNNLKLAEKFFKQALA--IAPSDPLVLHELGVVAYTYEEYPEALKY  436 (611)
T ss_pred             hHHHHHHHHHHHHHhccCCcchHHHHH--HHHHHhccHHHHHHHHHHHHh--cCCCcchhhhhhhheeehHhhhHHHHHH
Confidence            334444444444444433222233322  235667788888888766554  44543 3333333333346778888888


Q ss_pred             HHHHHHhc--cC----ccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           89 HAHVIKYG--HL----HDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        89 ~~~m~~~g--~~----~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      |+..++.-  +.    .-..+++.|-+.|.+.+..++|...++..   ...+..+++++--.|...|+++.|.+.|++- 
T Consensus       437 f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL  516 (611)
T KOG1173|consen  437 FQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKAL  516 (611)
T ss_pred             HHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence            87666221  11    12346888889999999999999999876   5678888889888889999999999999888 


Q ss_pred             CCCCCHHhHHHHHHHhccc
Q 045511          159 DVKPNANTLVSVLSACSSL  177 (209)
Q Consensus       159 ~~~p~~~t~~~li~~~~~~  177 (209)
                      .++||..+.+.+++.+...
T Consensus       517 ~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  517 ALKPDNIFISELLKLAIED  535 (611)
T ss_pred             hcCCccHHHHHHHHHHHHh
Confidence            9999998888888866543

>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=97.44  E-value=0.001  Score=39.58  Aligned_cols=60  Identities=15%  Similarity=0.176  Sum_probs=44.0

Q ss_pred             HhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHH
Q 045511          112 VTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVL  171 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li  171 (209)
                      .+.|++++|.++|+.+.  .| +...+-.+..+|.+.|++++|.+++.++ ...|+...|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            46788888888888872  23 5666677888888888888888888888 7777766665544

...

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

Probab=97.43  E-value=0.028  Score=44.41  Aligned_cols=125  Identities=14%  Similarity=0.093  Sum_probs=61.2

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      .+.+..|.-+...|+...|.++-.+.+   + ||..-|-.-+.+++..+++++.+++-..      +-++.-|.-.+..|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fk---v-~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~  247 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFK---V-PDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEAC  247 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcC---C-cHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHH
Confidence            344444555555555555555544332   2 5555555556666666665544443211      12345555555556


Q ss_pred             HhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhc
Q 045511          112 VTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACS  175 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~  175 (209)
                      .+.|+..+|.++...++      +.--+..|.+.|++.+|.+.-.+   .-|......+.+.|.
T Consensus       248 ~~~~~~~eA~~yI~k~~------~~~rv~~y~~~~~~~~A~~~A~~---~kd~~~L~~i~~~~~  302 (319)
T PF04840_consen  248 LKYGNKKEASKYIPKIP------DEERVEMYLKCGDYKEAAQEAFK---EKDIDLLKQILKRCP  302 (319)
T ss_pred             HHCCCHHHHHHHHHhCC------hHHHHHHHHHCCCHHHHHHHHHH---cCCHHHHHHHHHHCC
Confidence            66666656655555532      23444555555555555444333   223344444444443

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.41  E-value=0.0045  Score=44.08  Aligned_cols=61  Identities=7%  Similarity=0.005  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCc--cHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLH--DIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~--~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ..|..+...+...|++++|...|+........+  ...++..+-..|...|+.++|.+.++..
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~A   98 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQA   98 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444444555555566666666666555432221  1235555556666666666666666554

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

Probab=97.40  E-value=0.0067  Score=49.66  Aligned_cols=180  Identities=8%  Similarity=0.025  Sum_probs=112.6

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLE   87 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~   87 (209)
                      .|.+..+..-++.........+  ..|--+-..|.+..+.++.+..|+...+-+- -|..+|..--+...-.++++.|..
T Consensus       339 ~g~~~~a~~d~~~~I~l~~~~~--~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp-~n~dvYyHRgQm~flL~q~e~A~a  415 (606)
T KOG0547|consen  339 KGDSLGAQEDFDAAIKLDPAFN--SLYIKRAAAYADENQSEKMWKDFNKAEDLDP-ENPDVYYHRGQMRFLLQQYEEAIA  415 (606)
T ss_pred             cCCchhhhhhHHHHHhcCcccc--hHHHHHHHHHhhhhccHHHHHHHHHHHhcCC-CCCchhHhHHHHHHHHHHHHHHHH
Confidence            3455556666666655543322  2266677778888888888888887777542 244556665566666677777777


Q ss_pred             HHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC
Q 045511           88 IHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN  163 (209)
Q Consensus        88 ~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~  163 (209)
                      =|+...+-. +-++..|--+.-+.-|.+.+++++..|++...  | ....||-.-..+...++++.|.+.|+.. .+.|+
T Consensus       416 DF~Kai~L~-pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~  494 (606)
T KOG0547|consen  416 DFQKAISLD-PENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPR  494 (606)
T ss_pred             HHHHHhhcC-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccc
Confidence            777766543 23455666666666677888888888887732  4 3567777788888888888888888766 44444


Q ss_pred             -------HHhH-HHHHHHhccccchhHHHHHHHHHH
Q 045511          164 -------ANTL-VSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       164 -------~~t~-~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                             ..++ +--+-.....+++..|.++++...
T Consensus       495 ~~~~~v~~~plV~Ka~l~~qwk~d~~~a~~Ll~KA~  530 (606)
T KOG0547|consen  495 EHLIIVNAAPLVHKALLVLQWKEDINQAENLLRKAI  530 (606)
T ss_pred             cccccccchhhhhhhHhhhchhhhHHHHHHHHHHHH
Confidence                   1111 111222234566666666665443

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

Probab=97.39  E-value=0.0058  Score=50.04  Aligned_cols=178  Identities=11%  Similarity=0.069  Sum_probs=123.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC-CHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY-NHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      ...++++.++.|..+.+.-+.-|  .+|..--....-.+++++|..=|++.....  | ++..|.-+--+.-+.+.++++
T Consensus       372 d~~~~~~~~~~F~~A~~ldp~n~--dvYyHRgQm~flL~q~e~A~aDF~Kai~L~--pe~~~~~iQl~~a~Yr~~k~~~~  447 (606)
T KOG0547|consen  372 DENQSEKMWKDFNKAEDLDPENP--DVYYHRGQMRFLLQQYEEAIADFQKAISLD--PENAYAYIQLCCALYRQHKIAES  447 (606)
T ss_pred             hhhccHHHHHHHHHHHhcCCCCC--chhHhHHHHHHHHHHHHHHHHHHHHHhhcC--hhhhHHHHHHHHHHHHHHHHHHH
Confidence            45566666777777776654434  455444444555568888888888887743  4 334555555555677889999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--Cc-------H--hHHHHHHHHHHhCCChHHHHHH
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PD-------V--VTWTTIISGLSKCGFHKEAIDM  154 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~-------~--~~~~~li~~~~~~g~~~~a~~~  154 (209)
                      +..|++.+++ ++.-+..||-.-..+...++++.|.+.|+...+  |+       .  ..--.++-.- =.+++..|.++
T Consensus       448 m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~L  525 (606)
T KOG0547|consen  448 MKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENL  525 (606)
T ss_pred             HHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhc-hhhhHHHHHHH
Confidence            9999998876 466678899888999999999999999987632  22       1  1111111111 23788889999


Q ss_pred             HhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHH
Q 045511          155 FCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       155 ~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      +... .+.|-. ..|.+|-..-...|+.++|.++|+.-
T Consensus       526 l~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEks  563 (606)
T KOG0547|consen  526 LRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKS  563 (606)
T ss_pred             HHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            8887 666644 57888888888899999999998843

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.36  E-value=0.0095  Score=42.60  Aligned_cols=82  Identities=12%  Similarity=0.105  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--HhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIIS  140 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~  140 (209)
                      ...|..+-..+...|++++|...|+...+....+.  ...+..+-..+.+.|++++|.+.+.+..+  | +...+..+..
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~  114 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHH
Confidence            34566667777788899999998888876543332  45778888888888888888888887632  2 4555666666


Q ss_pred             HHHhCCC
Q 045511          141 GLSKCGF  147 (209)
Q Consensus       141 ~~~~~g~  147 (209)
                      .+...|+
T Consensus       115 ~~~~~g~  121 (172)
T PRK02603        115 IYHKRGE  121 (172)
T ss_pred             HHHHcCC
Confidence            6666665

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

Probab=97.31  E-value=0.013  Score=51.17  Aligned_cols=156  Identities=14%  Similarity=0.153  Sum_probs=117.9

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCC--CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSS--YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV  114 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  114 (209)
                      ++-++......+....+.......++.  -+..-|--+..++...|++.+|..+|..+......-+...|=.+-.+|...
T Consensus       383 l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l  462 (895)
T KOG2076|consen  383 LMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMEL  462 (895)
T ss_pred             HhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHH
Confidence            334455666666666677777777744  455678889999999999999999999999887777788999999999999


Q ss_pred             CChhhHHHHHHhcCC--Cc-HhHHHHHHHHHHhCCChHHHHHHHhhC-----------CCCCCHHhHHHHHHHhccccch
Q 045511          115 KDIFSAHQIFNSVVF--PD-VVTWTTIISGLSKCGFHKEAIDMFCGI-----------DVKPNANTLVSVLSACSSLGSR  180 (209)
Q Consensus       115 g~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~g~~~~a~~~~~~m-----------~~~p~~~t~~~li~~~~~~g~~  180 (209)
                      |..++|.+.|+....  |+ ...--+|-..+-+.|++++|.+++..|           +..|+...--.....+...|+.
T Consensus       463 ~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~  542 (895)
T KOG2076|consen  463 GEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKR  542 (895)
T ss_pred             hhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhH
Confidence            999999999999843  42 334445556778899999999999997           3445665555566667777887


Q ss_pred             hHHHHHHHHHHH
Q 045511          181 KLGKAIHAHSLR  192 (209)
Q Consensus       181 ~~a~~~~~~~~~  192 (209)
                      ++=..+-..|..
T Consensus       543 E~fi~t~~~Lv~  554 (895)
T KOG2076|consen  543 EEFINTASTLVD  554 (895)
T ss_pred             HHHHHHHHHHHH
Confidence            765555555443

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

Probab=97.29  E-value=0.027  Score=46.89  Aligned_cols=175  Identities=12%  Similarity=0.012  Sum_probs=121.1

Q ss_pred             CCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHH--------------------------------
Q 045511           29 PQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKA--------------------------------   75 (209)
Q Consensus        29 p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~--------------------------------   75 (209)
                      |+. .+|-++-..|.-.|+..+|.+.|.+...-+-... ..|-..-..                                
T Consensus       309 P~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fg-paWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlg  387 (611)
T KOG1173|consen  309 PSKALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFG-PAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLG  387 (611)
T ss_pred             CCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCcccc-HHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHH
Confidence            544 7888887777778888888888877654321100 111111111                                


Q ss_pred             --HhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--------C-C-cHhHHHHHHHHHH
Q 045511           76 --CSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--------F-P-DVVTWTTIISGLS  143 (209)
Q Consensus        76 --~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--------~-~-~~~~~~~li~~~~  143 (209)
                        |.+.+.++.|.++|.+..... +-|+.+.+-+--.....+.+.+|..+|....        + + -..+++.|=..|.
T Consensus       388 mey~~t~n~kLAe~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~R  466 (611)
T KOG1173|consen  388 MEYMRTNNLKLAEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYR  466 (611)
T ss_pred             HHHHHhccHHHHHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHH
Confidence              244466777777776665432 3456777777767777888999999987652        1 1 2346788889999


Q ss_pred             hCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhh
Q 045511          144 KCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD  207 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~  207 (209)
                      +.+.+++|+..|+.-  -.+-|..|++++--.+...|+++.|.+.|...  ..+.|+-.+.+.+++
T Consensus       467 kl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKa--L~l~p~n~~~~~lL~  530 (611)
T KOG1173|consen  467 KLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKA--LALKPDNIFISELLK  530 (611)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHH--HhcCCccHHHHHHHH
Confidence            999999999999988  44457788888888888999999999988654  356777766666654

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.29  E-value=0.0072  Score=43.00  Aligned_cols=93  Identities=12%  Similarity=-0.018  Sum_probs=68.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC--CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY--NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..|..+...+...|++++|...|++.......|  ...+|..+-..+...|++++|.+.++...+.. +....+++.+..
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~  114 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHH
Confidence            667778888888999999999999997654222  23578888899999999999999999888653 333455666666


Q ss_pred             HHH-------hCCChhhHHHHHH
Q 045511          110 FYV-------TVKDIFSAHQIFN  125 (209)
Q Consensus       110 ~~~-------~~g~~~~a~~~~~  125 (209)
                      .+.       +.|++++|...++
T Consensus       115 i~~~~~~~~~~~g~~~~A~~~~~  137 (168)
T CHL00033        115 ICHYRGEQAIEQGDSEIAEAWFD  137 (168)
T ss_pred             HHHHhhHHHHHcccHHHHHHHHH
Confidence            666       6666665544443

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

Probab=97.28  E-value=0.00051  Score=42.95  Aligned_cols=81  Identities=15%  Similarity=0.140  Sum_probs=57.2

Q ss_pred             CCCccchHHHHHHhhhCCC-CCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHH
Q 045511           44 SSTPQNAIPLYNKMLNCPS-SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQ  122 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~  122 (209)
                      .|+++.|..+++++.+... .|+...+-.+-.++.+.|+++.|.++++. .+.+. .+....-.+-.+|.+.|++++|.+
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            5788899999999988653 12444555578888999999999999988 33332 223333355788899999999999


Q ss_pred             HHHh
Q 045511          123 IFNS  126 (209)
Q Consensus       123 ~~~~  126 (209)
                      ++++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            8875

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.28  E-value=0.025  Score=47.73  Aligned_cols=59  Identities=12%  Similarity=0.051  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      ..|.++--.....|++++|...+++. .+.|+...|..+-+.+...|+.++|.+.+....
T Consensus       421 ~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~  480 (517)
T PRK10153        421 RIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAF  480 (517)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44444444444456666666666665 555555556666666666666666666655543

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.22  E-value=0.029  Score=42.29  Aligned_cols=151  Identities=14%  Similarity=0.124  Sum_probs=81.0

Q ss_pred             cchhccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHH
Q 045511            4 NGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQ   83 (209)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~   83 (209)
                      .++-.++...|..-+.++...|+..+.+.-..++.  +-..|+.++|.++++.+.+.+ +-|.++|..=+-..-..|+--
T Consensus        61 AAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~--lEa~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l  137 (289)
T KOG3060|consen   61 AALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAML--LEATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNL  137 (289)
T ss_pred             HHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHH--HHHhhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcH
Confidence            34445556666666666666664433332222211  123466677777777776665 345555555444444455555


Q ss_pred             HHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHhH-HHHHHHHHHhC---CChHHHHHHHhh
Q 045511           84 KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVVT-WTTIISGLSKC---GFHKEAIDMFCG  157 (209)
Q Consensus        84 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~~-~~~li~~~~~~---g~~~~a~~~~~~  157 (209)
                      +|.+-+....+. +.-|...|.-+-..|...|+++.|--+++++  .+|.... |-.+-..+.-.   .+.+.+...|.+
T Consensus       138 ~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~  216 (289)
T KOG3060|consen  138 EAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYER  216 (289)
T ss_pred             HHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            555555555554 3556677777777777777777777777776  3443322 22232222222   234455566655


Q ss_pred             C
Q 045511          158 I  158 (209)
Q Consensus       158 m  158 (209)
                      -
T Consensus       217 a  217 (289)
T KOG3060|consen  217 A  217 (289)
T ss_pred             H
Confidence            4

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

Probab=97.21  E-value=0.0067  Score=51.77  Aligned_cols=157  Identities=8%  Similarity=0.011  Sum_probs=92.9

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhc-cC--c---------
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYG-HL--H---------   99 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~--~---------   99 (209)
                      .-|..+|.+|+..|+.+.|..+..+..+  -+||..-|..+.......--++.|.++.+..-.+. ..  +         
T Consensus       425 emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs  502 (777)
T KOG1128|consen  425 EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFS  502 (777)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHH
Confidence            5678888889999988888888877776  35888888888888877777777877776543220 00  0         


Q ss_pred             ---------------cHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CC
Q 045511          100 ---------------DIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DV  160 (209)
Q Consensus       100 ---------------~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~  160 (209)
                                     -..+|=.+=.+..+.++++.|.+.|..-.  +| +...||.+-.+|.+.|+-.+|...+++- ..
T Consensus       503 ~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKc  582 (777)
T KOG1128|consen  503 EADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKC  582 (777)
T ss_pred             HHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhc
Confidence                           01112222222233344555555555442  23 3456666666666666666666666665 11


Q ss_pred             -CCCHHhHHHHHHHhccccchhHHHHHHHHH
Q 045511          161 -KPNANTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       161 -~p~~~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                       .-+-..|.-.+-...+.|.+++|.+.+.++
T Consensus       583 n~~~w~iWENymlvsvdvge~eda~~A~~rl  613 (777)
T KOG1128|consen  583 NYQHWQIWENYMLVSVDVGEFEDAIKAYHRL  613 (777)
T ss_pred             CCCCCeeeechhhhhhhcccHHHHHHHHHHH
Confidence             112233444444555666666666666654

>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=97.18  E-value=0.0026  Score=44.15  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC--------CCCCCHHh
Q 045511          103 IQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI--------DVKPNANT  166 (209)
Q Consensus       103 ~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--------~~~p~~~t  166 (209)
                      +...++..+...|++++|.++.....   ..|...|-.+|.+|...|+...|.+.|+++        |+.|+..|
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            44555555666666666666666652   234556666666666666666666666665        66666554

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

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

Probab=97.14  E-value=0.006  Score=53.58  Aligned_cols=193  Identities=15%  Similarity=0.098  Sum_probs=126.9

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHH-cCCCccchHHHHHHhhhCC-CCCCHHHHHHHHHHHhccccHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLT-QSSTPQNAIPLYNKMLNCP-SSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~-~~g~~~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      -++.+.|.+.+.++....   |..+..-.-+.+++ ..++..+|..+++...+.+ -.|++.+  .+=..+.+...+..|
T Consensus       509 l~~~~~A~e~Yk~Ilkeh---p~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~ars--l~G~~~l~k~~~~~a  583 (1018)
T KOG2002|consen  509 LHDTEVAEEMYKSILKEH---PGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARS--LLGNLHLKKSEWKPA  583 (1018)
T ss_pred             hhhhhHHHHHHHHHHHHC---chhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHH--HHHHHHHhhhhhccc
Confidence            345555555565555543   65544443333333 3467778888888877654 4455543  333456666677777


Q ss_pred             HHHHHHHHHhc-cCccHhHHHHHHHHHHhC------------CChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChH
Q 045511           86 LEIHAHVIKYG-HLHDIFIQNSLLHFYVTV------------KDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHK  149 (209)
Q Consensus        86 ~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~------------g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~  149 (209)
                      .+-|....+.- ..+|+.+.-+|-+.|...            +..+.|.++|.+.-   ..|...=|-+-..++..|+++
T Consensus       584 ~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~  663 (1018)
T KOG2002|consen  584 KKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFS  663 (1018)
T ss_pred             ccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCch
Confidence            77777666543 235666666666655432            45778888988773   357788888889999999999


Q ss_pred             HHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh-ccCCCchhHhHh
Q 045511          150 EAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN-LNENNIILDNAV  205 (209)
Q Consensus       150 ~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~p~~~~~~~l  205 (209)
                      +|..+|...  ...-+..+|--+-.+|...|++..|.++|+...+. .-+-++.+-+.|
T Consensus       664 ~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~L  722 (1018)
T KOG2002|consen  664 EARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYL  722 (1018)
T ss_pred             HHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHH
Confidence            999999998  22234456777888899999999999999965554 433344443333

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.13  E-value=0.027  Score=42.80  Aligned_cols=140  Identities=12%  Similarity=0.096  Sum_probs=107.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH--
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH--  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~--  109 (209)
                      .+-+.++..+.-.|.+.-..+++++..+.+-+-+..-.+.+...-.+.|+.+.+...|+...+..-..|..+.+.++.  
T Consensus       178 ~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  178 RVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhh
Confidence            344666666677788888889999998877677888889999999999999999999998887665666666665554  


Q ss_pred             ---HHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHH
Q 045511          110 ---FYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVL  171 (209)
Q Consensus       110 ---~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li  171 (209)
                         .|.-.+++.+|...|++++.   .|...-|.-.-++...|+..+|.+....| ...|...+-++++
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~~~l~es~~  326 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPRHYLHESVL  326 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCccchhhhHH
Confidence               45556788999999988854   35566666666666789999999999999 7777776655443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.12  E-value=0.0032  Score=54.05  Aligned_cols=104  Identities=12%  Similarity=0.095  Sum_probs=71.7

Q ss_pred             hccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHh
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      .....+..|..+++.+....  .-..-|..+-+-|+..|+++.|+++|-+-     ..++--|..|.++|+|++|.++-.
T Consensus       743 i~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~-----~~~~dai~my~k~~kw~da~kla~  815 (1636)
T KOG3616|consen  743 IGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA-----DLFKDAIDMYGKAGKWEDAFKLAE  815 (1636)
T ss_pred             hhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc-----chhHHHHHHHhccccHHHHHHHHH
Confidence            34445566666666665443  23445788888999999999999999753     236677888999999999998887


Q ss_pred             hC-CCCCCHHhHHHHHHHhccccchhHHHHHH
Q 045511          157 GI-DVKPNANTLVSVLSACSSLGSRKLGKAIH  187 (209)
Q Consensus       157 ~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~  187 (209)
                      +. |-......|-+--.-.-+.|++.+|++++
T Consensus       816 e~~~~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  816 ECHGPEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             HhcCchhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            76 55545555655555555666666666654

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.12  E-value=0.017  Score=38.78  Aligned_cols=105  Identities=11%  Similarity=0.014  Sum_probs=62.0

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCC--HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCc--cHhHHHHHHHHHHhC
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYN--HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLH--DIFIQNSLLHFYVTV  114 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~--~~~~~~~ll~~~~~~  114 (209)
                      .++-..|+.++|..+|++-...|+...  ...+--+-+.+...|++++|..+++........+  +....-.+-.++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~   88 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYNL   88 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHC
Confidence            345566788888888888877776544  2345555666677788888888887776543110  112222233356667


Q ss_pred             CChhhHHHHHHhcCCCcHhHHHHHHHHHH
Q 045511          115 KDIFSAHQIFNSVVFPDVVTWTTIISGLS  143 (209)
Q Consensus       115 g~~~~a~~~~~~~~~~~~~~~~~li~~~~  143 (209)
                      |+.++|.+.+-....++...|.--|..|+
T Consensus        89 gr~~eAl~~~l~~la~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   89 GRPKEALEWLLEALAETLPRYRRAIRFYA  117 (120)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777765543344444444444443

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

Probab=97.11  E-value=0.096  Score=44.80  Aligned_cols=180  Identities=14%  Similarity=0.061  Sum_probs=110.9

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      .|....+...+.++.+..   |+. ..|=.-+..-..+.++++|..+|.+-..  ..|+...|-.-+..---.+..++|.
T Consensus       597 agdv~~ar~il~~af~~~---pnseeiwlaavKle~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~  671 (913)
T KOG0495|consen  597 AGDVPAARVILDQAFEAN---PNSEEIWLAAVKLEFENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEAL  671 (913)
T ss_pred             cCCcHHHHHHHHHHHHhC---CCcHHHHHHHHHHhhccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHH
Confidence            445555555555555443   333 5666666666677777777777766655  3356666665555555566677777


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHHHHHhhC--CCC
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAIDMFCGI--DVK  161 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~  161 (209)
                      +++++.++.- +.=...|-.+-..+-..++++.|.+.|..=.+  | ....|-.+.+.=-+.|++-+|..++++-  .-.
T Consensus       672 rllEe~lk~f-p~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNP  750 (913)
T KOG0495|consen  672 RLLEEALKSF-PDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNP  750 (913)
T ss_pred             HHHHHHHHhC-CchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCC
Confidence            7766665542 22234555555566666666666666654322  3 3445666666666677778888888776  223


Q ss_pred             CCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      -|...|-..|+.-.+.|+.+.|+.+.....+.
T Consensus       751 k~~~lwle~Ir~ElR~gn~~~a~~lmakALQe  782 (913)
T KOG0495|consen  751 KNALLWLESIRMELRAGNKEQAELLMAKALQE  782 (913)
T ss_pred             CcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            35567777788888888888888777665554

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.11  E-value=0.0092  Score=45.29  Aligned_cols=160  Identities=13%  Similarity=0.005  Sum_probs=104.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHH--HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYT--FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t--~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..|.. ...+.+.|++++|.+.|+.+...-..+....  .-.+..++-+.++++.|...++...+.-......-|...+.
T Consensus        34 ~~Y~~-A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~  112 (243)
T PRK10866         34 EIYAT-AQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMR  112 (243)
T ss_pred             HHHHH-HHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHH
Confidence            44444 4445678999999999999988542222111  12455777889999999999999988754433445555555


Q ss_pred             HHHh-----------------CCCh---hhHHHHHHhcCC--CcH------h-----HH-------HHHHHHHHhCCChH
Q 045511          110 FYVT-----------------VKDI---FSAHQIFNSVVF--PDV------V-----TW-------TTIISGLSKCGFHK  149 (209)
Q Consensus       110 ~~~~-----------------~g~~---~~a~~~~~~~~~--~~~------~-----~~-------~~li~~~~~~g~~~  149 (209)
                      +.+.                 ..+.   .+|.+.|+.+.+  |+.      .     .-       -.+.+-|.+.|.+.
T Consensus       113 g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~  192 (243)
T PRK10866        113 GLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYV  192 (243)
T ss_pred             HHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchH
Confidence            5441                 1122   344455555421  221      1     11       12346688899999


Q ss_pred             HHHHHHhhC-----CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          150 EAIDMFCGI-----DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       150 ~a~~~~~~m-----~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      .|..-|+.+     +.+......-.++++|...|..++|..+.+.+..
T Consensus       193 AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~  240 (243)
T PRK10866        193 AVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIAA  240 (243)
T ss_pred             HHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence            998888888     4444556788899999999999999988776643

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

Probab=97.03  E-value=0.13  Score=44.00  Aligned_cols=154  Identities=8%  Similarity=-0.015  Sum_probs=61.8

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      +|+.--..|.+.+.++-|..+|....+. ++-+...|......=-..|..++.+.+|+.....- +.....|--..+.+-
T Consensus       518 tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake~w  595 (913)
T KOG0495|consen  518 TWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKEKW  595 (913)
T ss_pred             HHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHHH
Confidence            3333333333444444444444443332 11222333333333333344444444444443331 223333444444444


Q ss_pred             hCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHH
Q 045511          113 TVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      ..|++..|..+++..-+  | +...|-+-++....+..++.|..+|... ...|+...|.--++.---.++.++|.++++
T Consensus       596 ~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA~rllE  675 (913)
T KOG0495|consen  596 KAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEALRLLE  675 (913)
T ss_pred             hcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHHHHH
Confidence            44555555444444311  1 2334444444444444444444444444 444444444333333333344444444443

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

Probab=97.01  E-value=0.016  Score=46.64  Aligned_cols=87  Identities=9%  Similarity=-0.020  Sum_probs=65.3

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChh
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIF  118 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~  118 (209)
                      ......|++++|...|++..+.+- -+...|..+-.++.+.|++++|...++..++.. +.+...|..+-.+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLDP-NNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHH
Confidence            345567888888888888877542 345667777778888888888888888887764 345667777888888888888


Q ss_pred             hHHHHHHhc
Q 045511          119 SAHQIFNSV  127 (209)
Q Consensus       119 ~a~~~~~~~  127 (209)
                      +|...|++.
T Consensus        88 eA~~~~~~a   96 (356)
T PLN03088         88 TAKAALEKG   96 (356)
T ss_pred             HHHHHHHHH
Confidence            888888776

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

Probab=97.01  E-value=0.064  Score=45.65  Aligned_cols=153  Identities=10%  Similarity=0.103  Sum_probs=94.6

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhC-CCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNC-PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVK  115 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~-g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g  115 (209)
                      ....+.+.|++......|++.... .+.--...|...+......+-++-+.+++...++    .++..-+.-|..+++.+
T Consensus       108 Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk----~~P~~~eeyie~L~~~d  183 (835)
T KOG2047|consen  108 YLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLK----VAPEAREEYIEYLAKSD  183 (835)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHh----cCHHHHHHHHHHHHhcc
Confidence            333344445555555555444332 1122224455556666666666666677666654    23445777788888888


Q ss_pred             ChhhHHHHHHhcC----------CCcHhHHHHHHHHHHhCCChHH---HHHHHhhC-CCCCCHH--hHHHHHHHhccccc
Q 045511          116 DIFSAHQIFNSVV----------FPDVVTWTTIISGLSKCGFHKE---AIDMFCGI-DVKPNAN--TLVSVLSACSSLGS  179 (209)
Q Consensus       116 ~~~~a~~~~~~~~----------~~~~~~~~~li~~~~~~g~~~~---a~~~~~~m-~~~p~~~--t~~~li~~~~~~g~  179 (209)
                      +.++|-+.+....          +.+-..|+-+-...+++.+.-.   ...+++.+ +.-||..  .|++|-+.|.+.|.
T Consensus       184 ~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~  263 (835)
T KOG2047|consen  184 RLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGL  263 (835)
T ss_pred             chHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhh
Confidence            8888888877662          2345567766666666554332   44556665 6667764  57888888888888


Q ss_pred             hhHHHHHHHHHHHh
Q 045511          180 RKLGKAIHAHSLRN  193 (209)
Q Consensus       180 ~~~a~~~~~~~~~~  193 (209)
                      +++|..++.+..+.
T Consensus       264 ~ekarDvyeeai~~  277 (835)
T KOG2047|consen  264 FEKARDVYEEAIQT  277 (835)
T ss_pred             hHHHHHHHHHHHHh
Confidence            88888888876555

>PLN02789 farnesyltranstransferase

Probab=96.96  E-value=0.13  Score=40.74  Aligned_cols=182  Identities=6%  Similarity=-0.024  Sum_probs=108.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCC-CccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc--HH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSS-TPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA--HQ   83 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~--~~   83 (209)
                      +..+.++|+....++.+..+.  +..+|+.--..+.+.| ++++++..++++.+.+. -+..+|+.--..+.+.|+  .+
T Consensus        49 ~~e~serAL~lt~~aI~lnP~--~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~np-knyqaW~~R~~~l~~l~~~~~~  125 (320)
T PLN02789         49 SDERSPRALDLTADVIRLNPG--NYTVWHFRRLCLEALDADLEEELDFAEDVAEDNP-KNYQIWHHRRWLAEKLGPDAAN  125 (320)
T ss_pred             cCCCCHHHHHHHHHHHHHCch--hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCC-cchHHhHHHHHHHHHcCchhhH
Confidence            455666667666666655321  3356665555555666 57888888888887653 233455544333444454  25


Q ss_pred             HHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhC---CCh----HHHHH
Q 045511           84 KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKC---GFH----KEAID  153 (209)
Q Consensus        84 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~---g~~----~~a~~  153 (209)
                      .+.++++.+.+.. +-|-.+|+..--.+.+.|+++++.+.++++.+   .|..+|+-....+.+.   |..    ++.++
T Consensus       126 ~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~  204 (320)
T PLN02789        126 KELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRSPLLGGLEAMRDSELK  204 (320)
T ss_pred             HHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHhccccccccccHHHHHH
Confidence            6677777777665 56778888888888888889999998888843   4556666555444443   222    34555


Q ss_pred             HHhhC-CCCCCH-HhHHHHHHHhccc----cchhHHHHHHHHHHH
Q 045511          154 MFCGI-DVKPNA-NTLVSVLSACSSL----GSRKLGKAIHAHSLR  192 (209)
Q Consensus       154 ~~~~m-~~~p~~-~t~~~li~~~~~~----g~~~~a~~~~~~~~~  192 (209)
                      ..... ...|+- ..|+-+-..+...    +...+|..++....+
T Consensus       205 y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~  249 (320)
T PLN02789        205 YTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS  249 (320)
T ss_pred             HHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc
Confidence            55444 455544 4555555555442    333446666555444

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

Probab=96.93  E-value=0.0057  Score=46.80  Aligned_cols=99  Identities=6%  Similarity=0.020  Sum_probs=78.6

Q ss_pred             CCcccHHHHHHHHHc-----CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc----------------ccHHHHHH
Q 045511           29 PQPHILNTLLKLLTQ-----SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA----------------HAHQKGLE   87 (209)
Q Consensus        29 p~~~~~~~li~~~~~-----~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~----------------~~~~~a~~   87 (209)
                      .|-.+|-+.+..|..     .+.++-....++.|++-|+.-|..+|+.||+.+-+.                .+-+.+..
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~  144 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIK  144 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHH
Confidence            345667666666653     467777888899999999999999999999988554                34578999


Q ss_pred             HHHHHHHhccCccHhHHHHHHHHHHhCCCh-hhHHHHHHhc
Q 045511           88 IHAHVIKYGHLHDIFIQNSLLHFYVTVKDI-FSAHQIFNSV  127 (209)
Q Consensus        88 ~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~-~~a~~~~~~~  127 (209)
                      ++++|...|+.||..+--.|++.+.+.+.. .+..++.--|
T Consensus       145 vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWm  185 (406)
T KOG3941|consen  145 VLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWM  185 (406)
T ss_pred             HHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhh
Confidence            999999999999999999999999998764 3444444444

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.91  E-value=0.046  Score=43.35  Aligned_cols=131  Identities=11%  Similarity=0.078  Sum_probs=94.5

Q ss_pred             HHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHH-HHHHHHHHh
Q 045511           35 NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQ-NSLLHFYVT  113 (209)
Q Consensus        35 ~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~-~~ll~~~~~  113 (209)
                      .++.+.+.-..++++++..++..+.-=..-|.+-|+ +.++.+..|.+.+|+++|-.+..-.+ .|..+| .-|-++|++
T Consensus       363 QsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~i-kn~~~Y~s~LArCyi~  440 (557)
T KOG3785|consen  363 QSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEI-KNKILYKSMLARCYIR  440 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhh-hhhHHHHHHHHHHHHh
Confidence            445566666778899998888887765555555554 56788889999999999876654433 345555 556679999


Q ss_pred             CCChhhHHHHHHhcCCCc-HhH-HHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhH
Q 045511          114 VKDIFSAHQIFNSVVFPD-VVT-WTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTL  167 (209)
Q Consensus       114 ~g~~~~a~~~~~~~~~~~-~~~-~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~  167 (209)
                      ++.++.|+.++-.+..|. .++ .-.+..-|.+.+.+--|-..|+.+ -..|+..-|
T Consensus       441 nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~pEnW  497 (557)
T KOG3785|consen  441 NKKPQLAWDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTPENW  497 (557)
T ss_pred             cCCchHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCcccc
Confidence            999999999999986653 333 333446777888888888888888 667766543

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.91  E-value=0.059  Score=45.53  Aligned_cols=140  Identities=14%  Similarity=0.030  Sum_probs=96.6

Q ss_pred             hCCCcccHHHHHHHHHcCC-----CccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhcc--------ccHHHHHHHHHHH
Q 045511           27 KIPQPHILNTLLKLLTQSS-----TPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLA--------HAHQKGLEIHAHV   92 (209)
Q Consensus        27 ~~p~~~~~~~li~~~~~~g-----~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~--------~~~~~a~~~~~~m   92 (209)
                      ...+...|..++.+.....     +.+.|..+|++..+.  .||- ..|..+..++...        .++..+.+..+..
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a  410 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNI  410 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHh
Confidence            3356689999999866432     366899999999885  3653 4444433333221        1222333333332


Q ss_pred             HHh-ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHH
Q 045511           93 IKY-GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLV  168 (209)
Q Consensus        93 ~~~-g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~  168 (209)
                      ... ....+..+|..+--.....|++++|...+++..  .|+...|..+-+.+...|+.++|.+.|.+. .+.|...||-
T Consensus       411 ~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt~~  490 (517)
T PRK10153        411 VALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENTLY  490 (517)
T ss_pred             hhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCchHH
Confidence            222 233455778777666777899999999999983  478889999999999999999999999887 7788777764

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.90  E-value=0.046  Score=42.38  Aligned_cols=161  Identities=9%  Similarity=-0.020  Sum_probs=96.8

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHH-HHHHHH
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNS-LLHFYV  112 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~-ll~~~~  112 (209)
                      +++++..+.+..++++|.+++..-.++.- .+....+.+-..|-...++..|-+.++++....  |...-|.. --.++-
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~p-~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~--P~~~qYrlY~AQSLY   89 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERSP-RSRAGLSLLGYCYYRLQEFALAAECYEQLGQLH--PELEQYRLYQAQSLY   89 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--hHHHHHHHHHHHHHH
Confidence            45555556666666666666655555431 244555555555556666666666665554432  22211111 011222


Q ss_pred             hC----------------------------------CChhhHHHHHHhcC-CCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          113 TV----------------------------------KDIFSAHQIFNSVV-FPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       113 ~~----------------------------------g~~~~a~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      +.                                  +++..+..+.++.+ +.+..+.+..-....+.|+++.|.+-|+.
T Consensus        90 ~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqa  169 (459)
T KOG4340|consen   90 KACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQA  169 (459)
T ss_pred             HhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHH
Confidence            33                                  44444444444443 23444444444556789999999999998


Q ss_pred             C----CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCc
Q 045511          158 I----DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNI  199 (209)
Q Consensus       158 m----~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~  199 (209)
                      .    |..| ...|+..+..| +.|+.+.|....+++.++|+.-.+
T Consensus       170 AlqvsGyqp-llAYniALaHy-~~~qyasALk~iSEIieRG~r~HP  213 (459)
T KOG4340|consen  170 ALQVSGYQP-LLAYNLALAHY-SSRQYASALKHISEIIERGIRQHP  213 (459)
T ss_pred             HHhhcCCCc-hhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCC
Confidence            8    6665 46788888777 568899999999999999876544

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.87  E-value=0.052  Score=42.08  Aligned_cols=155  Identities=15%  Similarity=0.095  Sum_probs=101.0

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhC-CCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCc-----------
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNC-PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLH-----------   99 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~-g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-----------   99 (209)
                      .+.+..-....+.|+.+.|.+-|+...+- |..|- ..|+..+..| +.|+.+.|.+...++.++|++.           
T Consensus       145 d~~in~gCllykegqyEaAvqkFqaAlqvsGyqpl-lAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~te  222 (459)
T KOG4340|consen  145 DGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPL-LAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTE  222 (459)
T ss_pred             chhccchheeeccccHHHHHHHHHHHHhhcCCCch-hHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceec
Confidence            34444444455788999999988888775 45544 6788877665 5678888999999999888641           


Q ss_pred             --cH--------hHHHHHHH-------HHHhCCChhhHHHHHHhcCC-----CcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          100 --DI--------FIQNSLLH-------FYVTVKDIFSAHQIFNSVVF-----PDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       100 --~~--------~~~~~ll~-------~~~~~g~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                        |+        ..-+.++.       .+.+.|+.+.|.+.+-.|+.     .|.+|.+.+.-.-. .+++.+..+-++=
T Consensus       223 giDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqF  301 (459)
T KOG4340|consen  223 GIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQF  301 (459)
T ss_pred             cCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHH
Confidence              21        11233333       34566899999999999953     46667666543332 2333333333332


Q ss_pred             C-CCCCC-HHhHHHHHHHhccccchhHHHHHHHH
Q 045511          158 I-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       158 m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      + ++.|= ..||..++-.||+..-++.|-.++.+
T Consensus       302 LL~~nPfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  302 LLQQNPFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             HHhcCCCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            3 45553 36888888888888888888888764

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

Probab=96.87  E-value=0.06  Score=47.24  Aligned_cols=117  Identities=12%  Similarity=0.106  Sum_probs=88.5

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      .+++...|++...++.+.++..|-..++.+++  +.|.|+.++|..+++.....+.. |..|...+-..|...+..+++.
T Consensus        21 d~~qfkkal~~~~kllkk~Pn~~~a~vLkaLs--l~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~   97 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKKHPNALYAKVLKALS--LFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAV   97 (932)
T ss_pred             hhHHHHHHHHHHHHHHHHCCCcHHHHHHHHHH--HHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHH
Confidence            45666677777777777664433334444433  35889999999999998887765 8899999999999999999999


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChh----hHHHHHHhcC
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIF----SAHQIFNSVV  128 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~----~a~~~~~~~~  128 (209)
                      .+|+...+.  .|+......+..+|.|.+++.    .|.+++...+
T Consensus        98 ~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~p  141 (932)
T KOG2053|consen   98 HLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKNFP  141 (932)
T ss_pred             HHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            999988765  467888888888888887654    4566665554

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

Probab=96.82  E-value=0.0061  Score=42.24  Aligned_cols=70  Identities=13%  Similarity=0.089  Sum_probs=52.7

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHH-----HhccCCCchhH
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSL-----RNLNENNIILD  202 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~-----~~~~~p~~~~~  202 (209)
                      .+...++..+...|++++|......+ ...| |...|..+|.++...|+...|.++|..+.     +.|+.|++.+-
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            45667778888999999999999999 6666 56789999999999999999999999653     34999988764

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

>PRK04841 transcriptional regulator MalT; Provisional

Probab=96.78  E-value=0.12  Score=46.72  Aligned_cols=186  Identities=7%  Similarity=-0.080  Sum_probs=115.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCC-----Cc--ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH----HHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIP-----QP--HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH----YTFTQALKA   75 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p-----~~--~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~----~t~~~ll~~   75 (209)
                      ..++.+++...+.++.+.....+     ..  .....+-..+...|++++|...+++....--..+.    ...+.+-..
T Consensus       421 ~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~  500 (903)
T PRK04841        421 SQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEV  500 (903)
T ss_pred             HCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHH
Confidence            34555666666665544432211     11  11122223445789999999999987653111121    234555556


Q ss_pred             HhccccHHHHHHHHHHHHHhccC---c--cHhHHHHHHHHHHhCCChhhHHHHHHhcCC-------C----cHhHHHHHH
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHL---H--DIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-------P----DVVTWTTII  139 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~---~--~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-------~----~~~~~~~li  139 (209)
                      +...|+++.|...+.......-.   +  -..++..+-..+...|++++|...+++..+       +    ....+..+-
T Consensus       501 ~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la  580 (903)
T PRK04841        501 HHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRA  580 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHH
Confidence            67889999999998877643211   1  123556667778899999999998876511       1    123344555


Q ss_pred             HHHHhCCChHHHHHHHhhC-----CCCCC--HHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          140 SGLSKCGFHKEAIDMFCGI-----DVKPN--ANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       140 ~~~~~~g~~~~a~~~~~~m-----~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ..+...|++++|...+.+.     ...|.  ..++..+-......|+++.|.+.+.....
T Consensus       581 ~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~  640 (903)
T PRK04841        581 QLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLEN  640 (903)
T ss_pred             HHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6677789999999988876     22222  23444455567788999999998887644

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.77  E-value=0.038  Score=40.71  Aligned_cols=173  Identities=14%  Similarity=0.045  Sum_probs=81.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +.|+..+|.+.|..+...++..|-. .+.=.+..++-+.|+++.|...+++..+.-..-...-+...+.+.+........
T Consensus        17 ~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~~~~~~~   96 (203)
T PF13525_consen   17 QQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYYKQIPGI   96 (203)
T ss_dssp             HCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHhCccc
Confidence            5566666666666666665443332 344445556666666666666666655432111112233333333222211111


Q ss_pred             HHHHHHHHHhc---cCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC
Q 045511           86 LEIHAHVIKYG---HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK  161 (209)
Q Consensus        86 ~~~~~~m~~~g---~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~  161 (209)
                      .     ..+..   ..--...+..++.-|=.+....+|.+.+..+...=...--.+.+-|.+.|.+..|..-|+.+ .--
T Consensus        97 ~-----~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~la~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~y  171 (203)
T PF13525_consen   97 L-----RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNRLAEHELYIARFYYKRGKYKAAIIRFQYVIENY  171 (203)
T ss_dssp             H------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHS
T ss_pred             h-----hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC
Confidence            0     00000   00012244455555555555555555544442211111122456788888888888888877 223


Q ss_pred             CCH----HhHHHHHHHhccccchhHHH
Q 045511          162 PNA----NTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       162 p~~----~t~~~li~~~~~~g~~~~a~  184 (209)
                      |++    ...-.++.++.+.|..+.+.
T Consensus       172 p~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  172 PDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             TTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             CCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            333    45677778888888776443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.74  E-value=0.16  Score=38.46  Aligned_cols=160  Identities=9%  Similarity=0.045  Sum_probs=116.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHH-HHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQA-LKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~l-l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      ..|..++-+....|+.+.|..-+++++.+-  |+..-...+ --.+-..|+.++|.++++.+++.. +.|.+++-.=+..
T Consensus        53 ~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAi  129 (289)
T KOG3060|consen   53 TLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLLEATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAI  129 (289)
T ss_pred             HHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHhhchhhHHHHHHHHhccC-cchhHHHHHHHHH
Confidence            677888888888999999999999988763  433221111 112234588999999999999887 7788888877777


Q ss_pred             HHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhH-HHHHHHhc---cccchhH
Q 045511          111 YVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTL-VSVLSACS---SLGSRKL  182 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~-~~li~~~~---~~g~~~~  182 (209)
                      .-..|.--+|.+-+.+.-   -.|...|.-+-.-|...|++++|.-.+.++ -+.|-...| ..+-..+.   ...+.+.
T Consensus       130 lka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~  209 (289)
T KOG3060|consen  130 LKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLEL  209 (289)
T ss_pred             HHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHH
Confidence            777787777766665542   258889999999999999999999999999 667766543 33333332   2345667


Q ss_pred             HHHHHHHHHHhc
Q 045511          183 GKAIHAHSLRNL  194 (209)
Q Consensus       183 a~~~~~~~~~~~  194 (209)
                      +...+....+..
T Consensus       210 arkyy~~alkl~  221 (289)
T KOG3060|consen  210 ARKYYERALKLN  221 (289)
T ss_pred             HHHHHHHHHHhC
Confidence            777777665554

>PRK04841 transcriptional regulator MalT; Provisional

Probab=96.72  E-value=0.13  Score=46.45  Aligned_cols=188  Identities=11%  Similarity=0.007  Sum_probs=120.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhC--CC----cccHHHHHHHHHcCCCccchHHHHHHhhhCC--CCC--CHHHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKI--PQ----PHILNTLLKLLTQSSTPQNAIPLYNKMLNCP--SSY--NHYTFTQALKAC   76 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~--p~----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g--~~p--~~~t~~~ll~~~   76 (209)
                      ..|+.+.+...+.+..+.....  ++    ...+..+-..+...|++++|...+++.....  ..+  ....+..+-...
T Consensus       543 ~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~  622 (903)
T PRK04841        543 AQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKIS  622 (903)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHH
Confidence            5677777777777766654321  11    1233444455667799999999988875421  112  233444455667


Q ss_pred             hccccHHHHHHHHHHHHHhccCcc-HhHH-----HHHHHHHHhCCChhhHHHHHHhcCCCc---H----hHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHLHD-IFIQ-----NSLLHFYVTVKDIFSAHQIFNSVVFPD---V----VTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~~~-~~~~-----~~ll~~~~~~g~~~~a~~~~~~~~~~~---~----~~~~~li~~~~  143 (209)
                      ...|+.+.|.+.++......-... ...+     ...+..+...|+.+.|.+++.....+.   .    ..+..+..++.
T Consensus       623 ~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~  702 (903)
T PRK04841        623 LARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQI  702 (903)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHH
Confidence            788999999999888754321111 1111     112344566899999999987764322   1    11345667888


Q ss_pred             hCCChHHHHHHHhhC-------CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          144 KCGFHKEAIDMFCGI-------DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-------~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ..|++++|...+.+.       |..++. .+...+-.++.+.|+.++|...+....+..
T Consensus       703 ~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        703 LLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            899999999998887       333332 456666677889999999999998776553

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

Probab=96.69  E-value=0.13  Score=43.16  Aligned_cols=108  Identities=19%  Similarity=0.198  Sum_probs=84.2

Q ss_pred             HHHHHHHHHHHH-HhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCC-cHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511           82 HQKGLEIHAHVI-KYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFP-DVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus        82 ~~~a~~~~~~m~-~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      +..+.++|-++. +.+..+|+.++..|=-.|--.|+++.|...|+..  .+| |...||-|=-.+++..+.++|++-|++
T Consensus       410 l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~r  489 (579)
T KOG1125|consen  410 LAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNR  489 (579)
T ss_pred             HHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHH
Confidence            344445544443 4444577778888888888999999999999987  445 677999999999999999999999999


Q ss_pred             C-CCCCCHH-h-HHHHHHHhccccchhHHHHHHHHH
Q 045511          158 I-DVKPNAN-T-LVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       158 m-~~~p~~~-t-~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      . .++|+-+ . || |--+|...|.+++|...|-..
T Consensus       490 ALqLqP~yVR~RyN-lgIS~mNlG~ykEA~~hlL~A  524 (579)
T KOG1125|consen  490 ALQLQPGYVRVRYN-LGISCMNLGAYKEAVKHLLEA  524 (579)
T ss_pred             HHhcCCCeeeeehh-hhhhhhhhhhHHHHHHHHHHH
Confidence            9 9999874 3 54 455678999999988776643

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.64  E-value=0.12  Score=35.52  Aligned_cols=88  Identities=13%  Similarity=0.099  Sum_probs=44.4

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      .....+|..+.+.+.......+++.+...|. .+....+.++..|++.+.- ...+.+..      ..+......+++.|
T Consensus         8 ~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~~~-~ll~~l~~------~~~~yd~~~~~~~c   79 (140)
T smart00299        8 IDVSEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYDPQ-KEIERLDN------KSNHYDIEKVGKLC   79 (140)
T ss_pred             CCHHHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHCHH-HHHHHHHh------ccccCCHHHHHHHH
Confidence            3445566666666666666666666655552 4555566666666554332 12222221      12233333455555


Q ss_pred             HhCCChhhHHHHHHhc
Q 045511          112 VTVKDIFSAHQIFNSV  127 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~  127 (209)
                      .+.+.++++.-++..+
T Consensus        80 ~~~~l~~~~~~l~~k~   95 (140)
T smart00299       80 EKAKLYEEAVELYKKD   95 (140)
T ss_pred             HHcCcHHHHHHHHHhh
Confidence            5555555555555554

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

Probab=96.60  E-value=0.32  Score=40.80  Aligned_cols=141  Identities=17%  Similarity=0.208  Sum_probs=76.7

Q ss_pred             cchHHHHHHhhhCC-CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCc-cHhHHHHHHHHHHhCCChhhHHHHHH
Q 045511           48 QNAIPLYNKMLNCP-SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLH-DIFIQNSLLHFYVTVKDIFSAHQIFN  125 (209)
Q Consensus        48 ~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~~~  125 (209)
                      +.....++++...- ..|+ -+|...|+...+..-++.|..+|....+.+..+ .+.++++++..||. ++.+-|.++|+
T Consensus       348 ~~~~~~~~~ll~~~~~~~t-Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFe  425 (656)
T KOG1914|consen  348 KKVHEIYNKLLKIEDIDLT-LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFE  425 (656)
T ss_pred             hhhHHHHHHHHhhhccCCc-eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHH
Confidence            34444444444332 3333 446666666666666666666666666665444 55666666666654 34555566654


Q ss_pred             hc-C-CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC---CCCCCH--HhHHHHHHHhccccchhHHHHHHHHH
Q 045511          126 SV-V-FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNA--NTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       126 ~~-~-~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m---~~~p~~--~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      -= . -+| ..--...++-+...++=..+..+|.+.   ++.||.  ..|..+|..-+.-||++-+..+-+++
T Consensus       426 LGLkkf~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~  498 (656)
T KOG1914|consen  426 LGLKKFGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRR  498 (656)
T ss_pred             HHHHhcCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            32 1 122 222244555555556666666666665   334433  45666666666666666666655544

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.59  E-value=0.22  Score=38.09  Aligned_cols=136  Identities=16%  Similarity=0.084  Sum_probs=99.2

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC----CCcHhHHHHHH---
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV----FPDVVTWTTII---  139 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~li---  139 (209)
                      ...+.++..+...+.+......+....+...+.++.....|.+.-...||.+.|...|++..    ..|..+++.++   
T Consensus       178 ~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  178 RVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhh
Confidence            44566777777788888899999999998878899999999999999999999999999663    23444444443   


Q ss_pred             --HHHHhCCChHHHHHHHhhC-CCCCCHHhH-H--HHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          140 --SGLSKCGFHKEAIDMFCGI-DVKPNANTL-V--SVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       140 --~~~~~~g~~~~a~~~~~~m-~~~p~~~t~-~--~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                        ..|.-++++..|...|.+. ...|....+ |  +++..  -.|+...|....+.|+..  .|.+.+-++++
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcll--Ylg~l~DAiK~~e~~~~~--~P~~~l~es~~  326 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLL--YLGKLKDALKQLEAMVQQ--DPRHYLHESVL  326 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHH--HHHHHHHHHHHHHHHhcc--CCccchhhhHH
Confidence              3455677899999999888 333333222 2  23333  458999999998888766  66666655543

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

Probab=96.57  E-value=0.0069  Score=35.58  Aligned_cols=49  Identities=6%  Similarity=-0.086  Sum_probs=20.3

Q ss_pred             hccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      .+.|++++|...|+...+.. +-+...+..+-.++...|++++|...|++
T Consensus         8 ~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~   56 (65)
T PF13432_consen    8 YQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYER   56 (65)
T ss_dssp             HHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34444444444444444433 22333444444444444444444444443

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

Probab=96.56  E-value=0.32  Score=40.78  Aligned_cols=147  Identities=10%  Similarity=0.094  Sum_probs=114.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      -+|..+|+.-.+..-++.|..+|.+..+.+..+ .+..++++|..+|. ++.+-|..+|+.=++. ..-++.--+..++.
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkk-f~d~p~yv~~Yldf  444 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKK-FGDSPEYVLKYLDF  444 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHh-cCCChHHHHHHHHH
Confidence            688999999999999999999999999999877 88999999999886 4567889998754433 23445556788999


Q ss_pred             HHhCCChhhHHHHHHhcCC------CcHhHHHHHHHHHHhCCChHHHHHHHhhC--C----CCCCHHhHHHHHHHhcccc
Q 045511          111 YVTVKDIFSAHQIFNSVVF------PDVVTWTTIISGLSKCGFHKEAIDMFCGI--D----VKPNANTLVSVLSACSSLG  178 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~g~~~~a~~~~~~m--~----~~p~~~t~~~li~~~~~~g  178 (209)
                      +...++-..++.+|+....      .....|+.+|.-=.+-|+...+.++-+++  -    ..|...+-..+++-|.-.+
T Consensus       445 L~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d  524 (656)
T KOG1914|consen  445 LSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILD  524 (656)
T ss_pred             HHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhcc
Confidence            9999999999999998832      24579999999999999999999998888  2    3333334444555554444


Q ss_pred             ch
Q 045511          179 SR  180 (209)
Q Consensus       179 ~~  180 (209)
                      ..
T Consensus       525 ~~  526 (656)
T KOG1914|consen  525 LY  526 (656)
T ss_pred             cc
Confidence            43

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

Probab=96.53  E-value=0.043  Score=46.65  Aligned_cols=166  Identities=12%  Similarity=0.159  Sum_probs=122.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.+........|+.+.+..+..-...+|...+....+.+-++-+..++++..+-    +...-+-.|..+++.+++++|-
T Consensus       114 ~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~L~~~d~~~eaa  189 (835)
T KOG2047|consen  114 KQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEYLAKSDRLDEAA  189 (835)
T ss_pred             hcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHHHHhccchHHHH
Confidence            445555555666666666555455689999999888889999999999999772    3344778888899999999999


Q ss_pred             HHHHHHHHhc------cCccHhHHHHHHHHHHhCCChh---hHHHHHHhcCC--Cc--HhHHHHHHHHHHhCCChHHHHH
Q 045511           87 EIHAHVIKYG------HLHDIFIQNSLLHFYVTVKDIF---SAHQIFNSVVF--PD--VVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        87 ~~~~~m~~~g------~~~~~~~~~~ll~~~~~~g~~~---~a~~~~~~~~~--~~--~~~~~~li~~~~~~g~~~~a~~  153 (209)
                      +.+..++...      -+.+-..|+.+.+...++.+..   ....++..+..  +|  -..|++|.+-|.+.|++++|.+
T Consensus       190 ~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarD  269 (835)
T KOG2047|consen  190 QRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARD  269 (835)
T ss_pred             HHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            9888776432      2456678998888888876544   44555665532  44  4689999999999999999999


Q ss_pred             HHhhC-CCCCCHHhHHHHHHHhcc
Q 045511          154 MFCGI-DVKPNANTLVSVLSACSS  176 (209)
Q Consensus       154 ~~~~m-~~~p~~~t~~~li~~~~~  176 (209)
                      +|.+- .......-|+.+.++|+.
T Consensus       270 vyeeai~~v~tvrDFt~ifd~Ya~  293 (835)
T KOG2047|consen  270 VYEEAIQTVMTVRDFTQIFDAYAQ  293 (835)
T ss_pred             HHHHHHHhheehhhHHHHHHHHHH
Confidence            99886 334455567777777764

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

Probab=96.46  E-value=0.065  Score=43.85  Aligned_cols=144  Identities=13%  Similarity=0.137  Sum_probs=110.4

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..+|+.+|+...+..-++.|..+|-+..+.| +.+++..++++|..++. |+...|..+|+.=... ++-+..--+-.+.
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~  474 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK-FPDSTLYKEKYLL  474 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh-CCCchHHHHHHHH
Confidence            4788899999999999999999999999999 77899999999998865 5566688887643332 2333444577888


Q ss_pred             HHHhCCChhhHHHHHHhcCC---Cc--HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhcc
Q 045511          110 FYVTVKDIFSAHQIFNSVVF---PD--VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSS  176 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~~---~~--~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~  176 (209)
                      .+++.++-..|..+|+.-.+   .+  ...|..+|+-=..-|+...+..+=++| .+-|-..+...+..-|+-
T Consensus       475 fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQen~~evF~Sry~i  547 (660)
T COG5107         475 FLIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQENLIEVFTSRYAI  547 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCcHhHHHHHHHHHhh
Confidence            99999999999999986532   23  457889998888889988888777777 566666666666665543

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.45  E-value=0.094  Score=35.18  Aligned_cols=101  Identities=12%  Similarity=0.073  Sum_probs=70.2

Q ss_pred             HHHhccccHHHHHHHHHHHHHhccCcc--HhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc----HhHHHHHHHHHHhC
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYGHLHD--IFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD----VVTWTTIISGLSKC  145 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~----~~~~~~li~~~~~~  145 (209)
                      .++-..|+.++|..+|+...+.|....  ...+-.+-..|...|++++|..++++..  .|+    ....-.+-.++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~   88 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYNL   88 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHC
Confidence            345677999999999999999886654  3355567778889999999999998873  243    22222334577889


Q ss_pred             CChHHHHHHHhhCCCCCCHHhHHHHHHHhc
Q 045511          146 GFHKEAIDMFCGIDVKPNANTLVSVLSACS  175 (209)
Q Consensus       146 g~~~~a~~~~~~m~~~p~~~t~~~li~~~~  175 (209)
                      |++++|.+.+-.. +.++...|.--|..|+
T Consensus        89 gr~~eAl~~~l~~-la~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   89 GRPKEALEWLLEA-LAETLPRYRRAIRFYA  117 (120)
T ss_pred             CCHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            9999998887553 3334445555555553

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

Probab=96.35  E-value=0.062  Score=45.14  Aligned_cols=46  Identities=13%  Similarity=0.057  Sum_probs=21.5

Q ss_pred             hCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          113 TVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +.+..++|.+.++...+.+..+-..--..+.+.|++++|+.+|+.+
T Consensus        91 rlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L  136 (652)
T KOG2376|consen   91 RLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHL  136 (652)
T ss_pred             HcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            3445555555555433333333333334444555555555555554

>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=96.34  E-value=0.035  Score=32.85  Aligned_cols=60  Identities=12%  Similarity=0.036  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCC-ChhhHHHHHHh
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVK-DIFSAHQIFNS  126 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g-~~~~a~~~~~~  126 (209)
                      ..+|..+-..+...|+++.|...|+...+.. +.+...|..+-.+|.+.| ++++|.+.++.
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~   63 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEK   63 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHH
Confidence            3445555555566666666666666665543 334455666666666666 46666665554

...

>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=96.32  E-value=0.013  Score=35.74  Aligned_cols=55  Identities=18%  Similarity=0.195  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcC-------C--Cc-HhHHHHHHHHHHhCCChHHHHHHHh
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVV-------F--PD-VVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~--~~-~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      .+|+.+-..|...|++++|...|++..       .  |+ ..+++.+-..|...|++++|++.++
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~   70 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQ   70 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            345555555566666665555555431       0  11 2344444444444444444444443

...

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

Probab=96.31  E-value=0.35  Score=43.49  Aligned_cols=147  Identities=11%  Similarity=0.069  Sum_probs=103.2

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      .++-.+..+|-+.|+.+++...|+++.+.. +-|....|.+-..++.. ++++|.+.+....+.               |
T Consensus       117 ~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~---------------~  179 (906)
T PRK14720        117 LALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR---------------F  179 (906)
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH---------------H
Confidence            566777888888999999999999999987 46788899999999998 999999998877665               4


Q ss_pred             HhCCChhhHHHHHHhcCC-----------------------CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHh
Q 045511          112 VTVKDIFSAHQIFNSVVF-----------------------PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANT  166 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~~-----------------------~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t  166 (209)
                      ....++.++++++.++..                       .-+.++--+-..|-..++|+++..+++.+ ...| |...
T Consensus       180 i~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a  259 (906)
T PRK14720        180 IKKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKA  259 (906)
T ss_pred             HhhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhh
Confidence            555555555555555421                       22344455557778888999999999999 6665 4456


Q ss_pred             HHHHHHHhccccchhHHHHHHHHHHHhccCC
Q 045511          167 LVSVLSACSSLGSRKLGKAIHAHSLRNLNEN  197 (209)
Q Consensus       167 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  197 (209)
                      ..-++.+|.  +.+..-..+=+.++..|+.-
T Consensus       260 ~~~l~~~y~--~kY~~~~~~ee~l~~s~l~~  288 (906)
T PRK14720        260 REELIRFYK--EKYKDHSLLEDYLKMSDIGN  288 (906)
T ss_pred             HHHHHHHHH--HHccCcchHHHHHHHhcccc
Confidence            666776665  44433222323344445443

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

Probab=96.30  E-value=0.021  Score=33.47  Aligned_cols=54  Identities=13%  Similarity=0.067  Sum_probs=25.8

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIK   94 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~   94 (209)
                      .+.+.|++++|...|++..+.. +-+...+..+-..+...|++++|...|+...+
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3444555555555555555543 11334444444455555555555555555443

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

Probab=96.27  E-value=0.034  Score=42.76  Aligned_cols=89  Identities=4%  Similarity=0.015  Sum_probs=59.5

Q ss_pred             HHHHHhcC--CCcHhHHHHHHHHHHhC-----CChHHHHHHHhhC---CCCCCHHhHHHHHHHhccc-------------
Q 045511          121 HQIFNSVV--FPDVVTWTTIISGLSKC-----GFHKEAIDMFCGI---DVKPNANTLVSVLSACSSL-------------  177 (209)
Q Consensus       121 ~~~~~~~~--~~~~~~~~~li~~~~~~-----g~~~~a~~~~~~m---~~~p~~~t~~~li~~~~~~-------------  177 (209)
                      ++.|....  ++|..+|-..+..+...     ++++-....++.|   |+.-|..+|+.||+.+-+.             
T Consensus        54 e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~  133 (406)
T KOG3941|consen   54 EKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFL  133 (406)
T ss_pred             hhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHh
Confidence            44455543  45666666666555433     4555555555555   7777778887777776554             


Q ss_pred             ---cchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          178 ---GSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       178 ---g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                         .+-+-+..++++|..+|+.||..+-..||.++
T Consensus       134 HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~F  168 (406)
T KOG3941|consen  134 HYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAF  168 (406)
T ss_pred             hCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHh
Confidence               23456778889999999999988888777653

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.21  E-value=0.29  Score=35.48  Aligned_cols=103  Identities=11%  Similarity=-0.003  Sum_probs=57.6

Q ss_pred             CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-----CcHhHHH
Q 045511           62 SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----PDVVTWT  136 (209)
Q Consensus        62 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~~~~~~~  136 (209)
                      +.|++..--.+-.+....|+..+|...|++-...-+-.|....-.+-++....+++.+|...++.+-+     .+..+--
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~L  164 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHL  164 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchH
Confidence            34555555556666666666666666666665544555566666666666666666666666655511     1112222


Q ss_pred             HHHHHHHhCCChHHHHHHHhhC-CCCCCH
Q 045511          137 TIISGLSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       137 ~li~~~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      .+-+.|...|.+.+|+.-|... ..-|+.
T Consensus       165 l~aR~laa~g~~a~Aesafe~a~~~ypg~  193 (251)
T COG4700         165 LFARTLAAQGKYADAESAFEVAISYYPGP  193 (251)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHhCCCH
Confidence            4445566666666666666555 444444

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

Probab=96.17  E-value=0.052  Score=46.64  Aligned_cols=169  Identities=14%  Similarity=0.066  Sum_probs=110.4

Q ss_pred             hcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhC-----C-CC------------
Q 045511            3 VNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNC-----P-SS------------   63 (209)
Q Consensus         3 i~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----g-~~------------   63 (209)
                      |.|+ ..|+...|.....+..+   ..|+...|..+-+...+-.-++.|.++.+.....     | ..            
T Consensus       431 i~CY~~lg~~~kaeei~~q~le---k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~~h  507 (777)
T KOG1128|consen  431 ILCYLLLGQHGKAEEINRQELE---KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEADKH  507 (777)
T ss_pred             HHHHHHhcccchHHHHHHHHhc---CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHHHHH
Confidence            3455 55555555544444333   4578888888877776666666666666544321     1 00            


Q ss_pred             ---------CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc-HhHHHHHHHHHHhCCChhhHHHHHHhcCC---C
Q 045511           64 ---------YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVVF---P  130 (209)
Q Consensus        64 ---------p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~  130 (209)
                               .-..||=..=.+..+.++.+.+.+.|-....  ..|| ...||++=.+|.+.|+-.+|...+.+.-+   .
T Consensus       508 le~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~  585 (777)
T KOG1128|consen  508 LERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQ  585 (777)
T ss_pred             HHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCC
Confidence                     1112232233333455677777777766654  3455 56999999999999999999999988743   4


Q ss_pred             cHhHHHHHHHHHHhCCChHHHHHHHhhC----CCCCCHHhHHHHHHHhcc
Q 045511          131 DVVTWTTIISGLSKCGFHKEAIDMFCGI----DVKPNANTLVSVLSACSS  176 (209)
Q Consensus       131 ~~~~~~~li~~~~~~g~~~~a~~~~~~m----~~~p~~~t~~~li~~~~~  176 (209)
                      +...|-..+....+-|.+++|++.++++    ....|......++..-.+
T Consensus       586 ~w~iWENymlvsvdvge~eda~~A~~rll~~~~~~~d~~vl~~iv~~~~~  635 (777)
T KOG1128|consen  586 HWQIWENYMLVSVDVGEFEDAIKAYHRLLDLRKKYKDDEVLLIIVRTVLE  635 (777)
T ss_pred             CCeeeechhhhhhhcccHHHHHHHHHHHHHhhhhcccchhhHHHHHHHHh
Confidence            5567888888899999999999999999    222355555555555443

>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=96.17  E-value=0.0013  Score=45.53  Aligned_cols=83  Identities=12%  Similarity=0.087  Sum_probs=39.5

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      +|..+.+.+.+.....+++.+...+..-+....+.++..|++.++.+...++++       ..+..-...+++.|.+.|.
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            445555555555555555555555444445555555666655555444444443       1111223344444444444


Q ss_pred             hhhHHHHHHh
Q 045511          117 IFSAHQIFNS  126 (209)
Q Consensus       117 ~~~a~~~~~~  126 (209)
                      +++|.-++.+
T Consensus        86 ~~~a~~Ly~~   95 (143)
T PF00637_consen   86 YEEAVYLYSK   95 (143)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            4444444443

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.

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.14  E-value=0.14  Score=44.48  Aligned_cols=110  Identities=9%  Similarity=0.100  Sum_probs=68.6

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      .|.+-..+..+..|..+++.+.....  -..-|..+-..|+..|+++.|+++|-+         ...++-.|.+|.+.|+
T Consensus       738 aieaai~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e---------~~~~~dai~my~k~~k  806 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTE---------ADLFKDAIDMYGKAGK  806 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHh---------cchhHHHHHHHhcccc
Confidence            34455567777888888877776543  223366677777788888877777643         2345666777788888


Q ss_pred             hhhHHHHHHhcCCC--cHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          117 IFSAHQIFNSVVFP--DVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       117 ~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      +++|.++-.+...|  ....|-+-..-+-.+|++.+|.++|-.
T Consensus       807 w~da~kla~e~~~~e~t~~~yiakaedldehgkf~eaeqlyit  849 (1636)
T KOG3616|consen  807 WEDAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYIT  849 (1636)
T ss_pred             HHHHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeEE
Confidence            88777777766433  344454444445555555555544443

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

Probab=96.13  E-value=0.11  Score=40.23  Aligned_cols=143  Identities=14%  Similarity=0.096  Sum_probs=101.9

Q ss_pred             HHHHHHHhhCCCc---ccHHHHHHHHHcCCC-------ccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHH
Q 045511           19 NQIHAQIIKIPQP---HILNTLLKLLTQSST-------PQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEI   88 (209)
Q Consensus        19 ~~~~~~~~~~p~~---~~~~~li~~~~~~g~-------~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~   88 (209)
                      +.+...|...++.   ...+.++.++-+..+       ..+...+=++++.+|=            -..+.+++.+|.+.
T Consensus        36 qc~e~~f~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~e~~~~AE~LK~eGN------------~~m~~~~Y~eAv~k  103 (304)
T KOG0553|consen   36 QCLEAAFGFRRDDVDRAEGTTLLDSFESAERHPVEILTPEEDKALAESLKNEGN------------KLMKNKDYQEAVDK  103 (304)
T ss_pred             HHHHHHhCcchhhccccccccHHHHHHHhccCcccccChHhHHHHHHHHHHHHH------------HHHHhhhHHHHHHH
Confidence            3444445444433   444556666655544       1124444555555541            24677899999999


Q ss_pred             HHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH
Q 045511           89 HAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus        89 ~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      |.+.++-. +.|++-|..=-.+|++.|.++.|.+-.+....  | ...+|..|=.+|...|++++|.+.|++- .+.|+-
T Consensus       104 Y~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~aykKaLeldP~N  182 (304)
T KOG0553|consen  104 YTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIEAYKKALELDPDN  182 (304)
T ss_pred             HHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHHHHHhhhccCCCc
Confidence            99888764 56778888888999999999999888877643  3 3568999999999999999999999888 999999


Q ss_pred             HhHHHHHHHh
Q 045511          165 NTLVSVLSAC  174 (209)
Q Consensus       165 ~t~~~li~~~  174 (209)
                      .+|-.=|+..
T Consensus       183 e~~K~nL~~A  192 (304)
T KOG0553|consen  183 ESYKSNLKIA  192 (304)
T ss_pred             HHHHHHHHHH
Confidence            8887666554

>PLN02789 farnesyltranstransferase

Probab=96.12  E-value=0.51  Score=37.43  Aligned_cols=175  Identities=9%  Similarity=0.021  Sum_probs=118.2

Q ss_pred             CcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCc--cchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHH
Q 045511           12 TLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTP--QNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIH   89 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~--~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~   89 (209)
                      ++++..+.++.+..  +.+..+|+..-..+.+.|+.  +++..+++++.+.+- -|...|+..-.++.+.|+++++.+.+
T Consensus        89 ~eeL~~~~~~i~~n--pknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~  165 (320)
T PLN02789         89 EEELDFAEDVAEDN--PKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYC  165 (320)
T ss_pred             HHHHHHHHHHHHHC--CcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            45555555555442  23446777665555566653  677888988887653 47788888888888999999999999


Q ss_pred             HHHHHhccCccHhHHHHHHHHHHhC---CCh----hhHHHHHHhcC--C-CcHhHHHHHHHHHHhC----CChHHHHHHH
Q 045511           90 AHVIKYGHLHDIFIQNSLLHFYVTV---KDI----FSAHQIFNSVV--F-PDVVTWTTIISGLSKC----GFHKEAIDMF  155 (209)
Q Consensus        90 ~~m~~~g~~~~~~~~~~ll~~~~~~---g~~----~~a~~~~~~~~--~-~~~~~~~~li~~~~~~----g~~~~a~~~~  155 (209)
                      +.+++.. +.|...|+.....+.+.   |..    +++.....+..  . .|...|+-+-..+...    ++..+|.+.+
T Consensus       166 ~~~I~~d-~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~  244 (320)
T PLN02789        166 HQLLEED-VRNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVC  244 (320)
T ss_pred             HHHHHHC-CCchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHH
Confidence            9999886 45667777766655554   222    34555554442  2 4667888777777663    3345687888


Q ss_pred             hhC-CCCC-CHHhHHHHHHHhcccc------------------chhHHHHHHHHH
Q 045511          156 CGI-DVKP-NANTLVSVLSACSSLG------------------SRKLGKAIHAHS  190 (209)
Q Consensus       156 ~~m-~~~p-~~~t~~~li~~~~~~g------------------~~~~a~~~~~~~  190 (209)
                      .+. ...| +......++..|+...                  ..++|..+++.+
T Consensus       245 ~~~~~~~~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l  299 (320)
T PLN02789        245 LEVLSKDSNHVFALSDLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSEL  299 (320)
T ss_pred             HHhhcccCCcHHHHHHHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHH
Confidence            776 4444 5567888888887643                  236788888877

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.11  E-value=0.25  Score=33.80  Aligned_cols=124  Identities=12%  Similarity=0.136  Sum_probs=84.0

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCCh
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFH  148 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~  148 (209)
                      ...++..+.+.+........++.+.+.+ ..+....|.++..|++.+. .+..+.+..  ..+......+++.|-+.+.+
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~-~~ll~~l~~--~~~~yd~~~~~~~c~~~~l~   85 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDP-QKEIERLDN--KSNHYDIEKVGKLCEKAKLY   85 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCH-HHHHHHHHh--ccccCCHHHHHHHHHHcCcH
Confidence            4567777777788889999999888877 4778899999999998743 444455552  34555566688888888899


Q ss_pred             HHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhh
Q 045511          149 KEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD  207 (209)
Q Consensus       149 ~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~  207 (209)
                      +++..++.++|...+  ....+++   ..++++.|.++...-      .++..|..+++
T Consensus        86 ~~~~~l~~k~~~~~~--Al~~~l~---~~~d~~~a~~~~~~~------~~~~lw~~~~~  133 (140)
T smart00299       86 EEAVELYKKDGNFKD--AIVTLIE---HLGNYEKAIEYFVKQ------NNPELWAEVLK  133 (140)
T ss_pred             HHHHHHHHhhcCHHH--HHHHHHH---cccCHHHHHHHHHhC------CCHHHHHHHHH
Confidence            999999988743322  2223333   227788887776541      13445555554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.08  E-value=0.09  Score=40.42  Aligned_cols=93  Identities=16%  Similarity=0.116  Sum_probs=67.3

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcH----hHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC----HHhHHH
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDV----VTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN----ANTLVS  169 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~----~~t~~~  169 (209)
                      ...|+..+..+.+.|++++|...|+.+.  .|+.    ..+--+-..|...|++++|...|..+ ...|+    ...+-.
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~k  222 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFK  222 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHH
Confidence            3467777777677899999999998883  2432    35556668888899999999999888 44444    233333


Q ss_pred             HHHHhccccchhHHHHHHHHHHHh
Q 045511          170 VLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +...+...|+.++|..+++.+.+.
T Consensus       223 lg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        223 VGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            455566889999999999888776

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

Probab=96.07  E-value=0.16  Score=39.48  Aligned_cols=159  Identities=13%  Similarity=0.148  Sum_probs=86.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhh----CCCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHH----hccCcc--
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLN----CPSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIK----YGHLHD--  100 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~----~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~----~g~~~~--  100 (209)
                      ..|+..-..|-..|++++|...|.+...    .+-+. -...|......+-+. +++.|.+.++...+    .| .|+  
T Consensus        36 ~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G-~~~~a  113 (282)
T PF14938_consen   36 DLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAG-RFSQA  113 (282)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT--HHHH
T ss_pred             HHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcC-cHHHH
Confidence            4566666666677777777777766532    12111 123344444444333 66666666655443    23 222  


Q ss_pred             HhHHHHHHHHHHhC-CChhhHHHHHHhcC------C-C--cHhHHHHHHHHHHhCCChHHHHHHHhhC--------CCCC
Q 045511          101 IFIQNSLLHFYVTV-KDIFSAHQIFNSVV------F-P--DVVTWTTIISGLSKCGFHKEAIDMFCGI--------DVKP  162 (209)
Q Consensus       101 ~~~~~~ll~~~~~~-g~~~~a~~~~~~~~------~-~--~~~~~~~li~~~~~~g~~~~a~~~~~~m--------~~~p  162 (209)
                      ..++..+-..|-.. |++++|.+.|.+..      . +  -...+.-+...+.+.|++++|.++|.+.        ..++
T Consensus       114 A~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~  193 (282)
T PF14938_consen  114 AKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKY  193 (282)
T ss_dssp             HHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccch
Confidence            34666677777777 78887777776651      1 1  1345666677778888888888888776        1122


Q ss_pred             CHH--hHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          163 NAN--TLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       163 ~~~--t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +..  .+..+| ++...||+..|...++.....
T Consensus       194 ~~~~~~l~a~l-~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  194 SAKEYFLKAIL-CHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             HHHHHHHHHHH-HHHHTT-HHHHHHHHHHHGTT
T ss_pred             hHHHHHHHHHH-HHHHcCCHHHHHHHHHHHHhh
Confidence            332  223333 333457777777777765433

>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=96.05  E-value=0.029  Score=34.19  Aligned_cols=60  Identities=12%  Similarity=0.091  Sum_probs=45.8

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhc--cC---cc-HhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYG--HL---HD-IFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~---~~-~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      .+|+.+-..+...|++++|.+.|+...+..  ..   |+ ..+++.+-..|...|++++|++.+++
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~   71 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQK   71 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            567778888888888888888888776441  11   22 56788888999999999999998875

...

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.04  E-value=0.13  Score=36.02  Aligned_cols=82  Identities=9%  Similarity=-0.090  Sum_probs=43.9

Q ss_pred             HhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHH
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAI  152 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~  152 (209)
                      +...|++++|+.+|+.+..-. +-+..-|-.|-.++-..|++++|...|...   ...|...+=.+-.++...|+.+.|.
T Consensus        45 ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L~lG~~~~A~  123 (157)
T PRK15363         45 LMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYLACDNVCYAI  123 (157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCCHHHHH
Confidence            345566666666666555443 233444555555555566666666666554   1123444444455555666666666


Q ss_pred             HHHhhC
Q 045511          153 DMFCGI  158 (209)
Q Consensus       153 ~~~~~m  158 (209)
                      +-|+..
T Consensus       124 ~aF~~A  129 (157)
T PRK15363        124 KALKAV  129 (157)
T ss_pred             HHHHHH
Confidence            666554

>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=96.03  E-value=0.022  Score=33.80  Aligned_cols=57  Identities=19%  Similarity=0.216  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhcccc-chhHHHHHHHHH
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLG-SRKLGKAIHAHS  190 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g-~~~~a~~~~~~~  190 (209)
                      .|..+-..+...|++++|+..|.+. .+.|+. ..|..+-.++...| ++++|.+.++..
T Consensus         5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    5 AWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             HHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            3444444444445555555444444 333322 23444444444444 444444444443

...

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

Probab=95.94  E-value=0.72  Score=37.60  Aligned_cols=30  Identities=20%  Similarity=0.198  Sum_probs=19.2

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhh
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLN   59 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~   59 (209)
                      |++....+-..+...|+.++|...|+.-..
T Consensus       231 NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~  260 (564)
T KOG1174|consen  231 NEHLMMALGKCLYYNGDYFQAEDIFSSTLC  260 (564)
T ss_pred             cHHHHHHHhhhhhhhcCchHHHHHHHHHhh
Confidence            445566666666666666666666666555

>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=95.92  E-value=0.0037  Score=43.21  Aligned_cols=85  Identities=12%  Similarity=0.158  Sum_probs=63.1

Q ss_pred             HHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHH
Q 045511           71 QALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKE  150 (209)
Q Consensus        71 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  150 (209)
                      .+++.+.+.+.++....+++.+...+...+....+.++..|++.++.+..++++.....   .-...++..+-+.|.+++
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~   88 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEE   88 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHH
Confidence            35667777888888888999998877677899999999999999998999999885432   333455666666666666


Q ss_pred             HHHHHhhC
Q 045511          151 AIDMFCGI  158 (209)
Q Consensus       151 a~~~~~~m  158 (209)
                      +.-++.++
T Consensus        89 a~~Ly~~~   96 (143)
T PF00637_consen   89 AVYLYSKL   96 (143)
T ss_dssp             HHHHHHCC
T ss_pred             HHHHHHHc
Confidence            66666666

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=95.84  E-value=0.2  Score=38.51  Aligned_cols=100  Identities=12%  Similarity=0.032  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--HhHHHHHHHHHHhCCChhhHHHHHHhcCC--Cc----HhHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PD----VVTWTT  137 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~----~~~~~~  137 (209)
                      ...|...+....+.|++++|...|+.+.+.-....  ...+--+-..|...|++++|...|..+..  |+    ...+-.
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~k  222 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFK  222 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHH
Confidence            35577777666777999999999999987652211  24666777888999999999999998842  32    233334


Q ss_pred             HHHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511          138 IISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       138 li~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      +...+...|++++|..+|+++ ...|+..
T Consensus       223 lg~~~~~~g~~~~A~~~~~~vi~~yP~s~  251 (263)
T PRK10803        223 VGVIMQDKGDTAKAKAVYQQVIKKYPGTD  251 (263)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCcCCH
Confidence            456677889999999999887 4445543

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

Probab=95.78  E-value=0.25  Score=40.61  Aligned_cols=127  Identities=17%  Similarity=0.190  Sum_probs=101.2

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhc-cCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHhHH-HHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYG-HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVVTW-TTIISG  141 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~~~-~~li~~  141 (209)
                      ...|...|++..+..-++.|..+|....+.| +.+++.+++++|..++. |+..-|.++|+-=  .-||...| +-.+.-
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~f  475 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLKFPDSTLYKEKYLLF  475 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            4678889999999999999999999999999 78899999999998875 5677788888653  23555444 567778


Q ss_pred             HHhCCChHHHHHHHhhC--CCCCC--HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          142 LSKCGFHKEAIDMFCGI--DVKPN--ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m--~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +.+.++-+.|..+|..-  .+.-+  ...|..+|..-+.-|++..+..+-+++...
T Consensus       476 Li~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~  531 (660)
T COG5107         476 LIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL  531 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH
Confidence            88899999999999855  34444  468999999999999998887776665443

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.77  E-value=0.3  Score=38.25  Aligned_cols=120  Identities=10%  Similarity=0.066  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHh--CC----ChhhHHHHHHhcC-------CCcHhHHHHHHHHHHhCCCh
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT--VK----DIFSAHQIFNSVV-------FPDVVTWTTIISGLSKCGFH  148 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~--~g----~~~~a~~~~~~~~-------~~~~~~~~~li~~~~~~g~~  148 (209)
                      ++....+++.|.+.|+..+..+|-+..-....  ..    ....|..+++.|.       .++-.++.+++..  ..++.
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            34566667777777777776655543333332  11    2456677777773       2455566666554  33333


Q ss_pred             H----HHHHHHhhC---CCCCCHH--hHHHHHHHhccccc--hhHHHHHHHHHHHhccCCCchhHh
Q 045511          149 K----EAIDMFCGI---DVKPNAN--TLVSVLSACSSLGS--RKLGKAIHAHSLRNLNENNIILDN  203 (209)
Q Consensus       149 ~----~a~~~~~~m---~~~p~~~--t~~~li~~~~~~g~--~~~a~~~~~~~~~~~~~p~~~~~~  203 (209)
                      +    .++.+|+.+   |+..+..  ..+.++..+....+  ..++.++++.+.+.|+++...+|.
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp  221 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYP  221 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCcccccccc
Confidence            2    345555555   5555433  34444444433332  346677777777777777666554

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.77  E-value=0.047  Score=32.68  Aligned_cols=14  Identities=14%  Similarity=0.325  Sum_probs=5.2

Q ss_pred             ccHHHHHHHHHHHH
Q 045511           80 HAHQKGLEIHAHVI   93 (209)
Q Consensus        80 ~~~~~a~~~~~~m~   93 (209)
                      ++++.|.++++.+.
T Consensus         9 ~~~~~A~~~~~~~l   22 (73)
T PF13371_consen    9 EDYEEALEVLERAL   22 (73)
T ss_pred             CCHHHHHHHHHHHH
Confidence            33333333333333

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=95.70  E-value=0.18  Score=35.42  Aligned_cols=79  Identities=13%  Similarity=0.071  Sum_probs=33.8

Q ss_pred             HhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHH
Q 045511          112 VTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~  186 (209)
                      ...|++++|+++|.-..  .| +..-|-.|--++-..|++++|+..|... -+.||. ..+-.+-.++...|+.+.|++-
T Consensus        46 y~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L~lG~~~~A~~a  125 (157)
T PRK15363         46 MEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYLACDNVCYAIKA  125 (157)
T ss_pred             HHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCCHHHHHHH
Confidence            34455555555554441  12 2223333333444444555555555444 333322 3333344444444555555544


Q ss_pred             HHHH
Q 045511          187 HAHS  190 (209)
Q Consensus       187 ~~~~  190 (209)
                      |+..
T Consensus       126 F~~A  129 (157)
T PRK15363        126 LKAV  129 (157)
T ss_pred             HHHH
Confidence            4433

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

Probab=95.61  E-value=0.19  Score=40.72  Aligned_cols=148  Identities=9%  Similarity=0.006  Sum_probs=74.6

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHH-HHHHHhC-CC
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSL-LHFYVTV-KD  116 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l-l~~~~~~-g~  116 (209)
                      +.+.+.|+++.|.=.|+...... +-+..+|.-++..|...|++.+|.-.-.+..+. ++.+..+.+.+ -..+.-. ..
T Consensus       342 ~lL~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~  419 (564)
T KOG1174|consen  342 RLLIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRM  419 (564)
T ss_pred             HHHHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchh
Confidence            34455666666666666655421 124466666666666666666655443333222 22334444333 1222222 12


Q ss_pred             hhhHHHHHHhc--CCCc-HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHH
Q 045511          117 IFSAHQIFNSV--VFPD-VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       117 ~~~a~~~~~~~--~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      -++|.+++++-  .+|+ ....+.+...+...|..++++.++.+- -..||...-+.+-....-...+.++.+.|.
T Consensus       420 rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~  495 (564)
T KOG1174|consen  420 REKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYY  495 (564)
T ss_pred             HHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            34555555554  2233 334455555556666666666666555 455555555555555555555555544443

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

Probab=95.61  E-value=0.25  Score=38.34  Aligned_cols=91  Identities=12%  Similarity=0.074  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccC-----ccHh-HHHHHHHHHHhCCChhhHHHHHHhcCC--C------cHh
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHL-----HDIF-IQNSLLHFYVTVKDIFSAHQIFNSVVF--P------DVV  133 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-----~~~~-~~~~ll~~~~~~g~~~~a~~~~~~~~~--~------~~~  133 (209)
                      ++..+...+.+.|++++|.++|+.....-..     .+.. .+-..+-++...||+..|.+.+++...  |      ...
T Consensus       157 ~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~  236 (282)
T PF14938_consen  157 CLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYK  236 (282)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHH
Confidence            3445555666667777777777666544321     1221 222333355556677777777666521  1      123


Q ss_pred             HHHHHHHHHHhC--CChHHHHHHHhhC
Q 045511          134 TWTTIISGLSKC--GFHKEAIDMFCGI  158 (209)
Q Consensus       134 ~~~~li~~~~~~--g~~~~a~~~~~~m  158 (209)
                      .-..||.++-..  ..++.++.-|+.+
T Consensus       237 ~~~~l~~A~~~~D~e~f~~av~~~d~~  263 (282)
T PF14938_consen  237 FLEDLLEAYEEGDVEAFTEAVAEYDSI  263 (282)
T ss_dssp             HHHHHHHHHHTT-CCCHHHHCHHHTTS
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHccc
Confidence            445555555332  2344555555555

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

Probab=95.51  E-value=0.2  Score=44.17  Aligned_cols=127  Identities=17%  Similarity=0.162  Sum_probs=93.5

Q ss_pred             HcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHH--hccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhh
Q 045511           42 TQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKAC--SLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFS  119 (209)
Q Consensus        42 ~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~--~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~  119 (209)
                      ...+++..|.+....+.+.-  || ..|..+++++  .+.|+.++|..+++....-+. .|..|...+..+|-..|..++
T Consensus        20 ld~~qfkkal~~~~kllkk~--Pn-~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~-~D~~tLq~l~~~y~d~~~~d~   95 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKKH--PN-ALYAKVLKALSLFRLGKGDEALKLLEALYGLKG-TDDLTLQFLQNVYRDLGKLDE   95 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHHC--CC-cHHHHHHHHHHHHHhcCchhHHHHHhhhccCCC-CchHHHHHHHHHHHHHhhhhH
Confidence            34567788888887776642  55 4577777776  577899999988888776553 388999999999999999999


Q ss_pred             HHHHHHhcC--CCcHhHHHHHHHHHHhCCChHH----HHHHHhhCCCCCCHHhHHHHHHHh
Q 045511          120 AHQIFNSVV--FPDVVTWTTIISGLSKCGFHKE----AIDMFCGIDVKPNANTLVSVLSAC  174 (209)
Q Consensus       120 a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~----a~~~~~~m~~~p~~~t~~~li~~~  174 (209)
                      |..+++...  .|+......+..+|.+.+++.+    |.++++..  .-+...|-++++..
T Consensus        96 ~~~~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~--pk~~yyfWsV~Sli  154 (932)
T KOG2053|consen   96 AVHLYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYKNF--PKRAYYFWSVISLI  154 (932)
T ss_pred             HHHHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--CcccchHHHHHHHH
Confidence            999999984  4776677777888888887764    56666653  33345555555544

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

Probab=95.51  E-value=1.9  Score=39.32  Aligned_cols=72  Identities=14%  Similarity=0.203  Sum_probs=59.1

Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhc
Q 045511          132 VVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDF  208 (209)
Q Consensus       132 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~  208 (209)
                      ...|+-+-++-.+.|.+.+|.+-|-+   .-|...|.-+++.+.+.|++++-...+.+.++..-+|.+.  +.||-+
T Consensus      1104 p~vWsqlakAQL~~~~v~dAieSyik---adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~A 1175 (1666)
T KOG0985|consen 1104 PAVWSQLAKAQLQGGLVKDAIESYIK---ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFA 1175 (1666)
T ss_pred             hHHHHHHHHHHHhcCchHHHHHHHHh---cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHH
Confidence            45788999999999999999888866   4567889999999999999999999998888887777754  344433

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=95.31  E-value=0.75  Score=33.45  Aligned_cols=145  Identities=13%  Similarity=0.127  Sum_probs=100.9

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLE   87 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~   87 (209)
                      ...|++.+   .++.+.+...|++..=-.|-.++.+.|+..+|...|++-..--+.-|....-.+-++....+++..+..
T Consensus        69 ~ldP~R~~---Rea~~~~~~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~  145 (251)
T COG4700          69 KLDPERHL---REATEELAIAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQ  145 (251)
T ss_pred             hcChhHHH---HHHHHHHhhchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHH
Confidence            44444444   555556666688877777888999999999999999998876666777878888888888899999999


Q ss_pred             HHHHHHHhcc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHH
Q 045511           88 IHAHVIKYGH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMF  155 (209)
Q Consensus        88 ~~~~m~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~  155 (209)
                      .++.+-+... ..++.+.-.+-+.|...|..++|+.-|+...  -|+...---.-..+++.|+.+++..-+
T Consensus       146 tLe~l~e~~pa~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~ar~~Y~e~La~qgr~~ea~aq~  216 (251)
T COG4700         146 TLEDLMEYNPAFRSPDGHLLFARTLAAQGKYADAESAFEVAISYYPGPQARIYYAEMLAKQGRLREANAQY  216 (251)
T ss_pred             HHHHHhhcCCccCCCCchHHHHHHHHhcCCchhHHHHHHHHHHhCCCHHHHHHHHHHHHHhcchhHHHHHH
Confidence            9998877651 1122334455677888899999999888763  244433333334455666666554333

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

Probab=95.27  E-value=0.45  Score=30.74  Aligned_cols=60  Identities=13%  Similarity=0.063  Sum_probs=43.0

Q ss_pred             chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           49 NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        49 ~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +..+-++.+....+.|+.....+.|++|.+.+++..|..+|+.++.+- .....+|..++.
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHH
Confidence            445567777888899999999999999999999999999999887553 222337777764

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=95.21  E-value=1.5  Score=39.09  Aligned_cols=154  Identities=10%  Similarity=-0.007  Sum_probs=80.6

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhC-CC--------CCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCc
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNC-PS--------SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLH   99 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-g~--------~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~   99 (209)
                      ....+|..+.+.|.+..++|-|.--+-.|... |.        .|+ .+=..+--.....|.+++|+.+|..-++.    
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            44567888888888887777666555555331 11        122 11112222224556777777776665543    


Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhcCCCc-HhHHHHHHHHHHhCCChHHHHHHHhhC--------------------
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPD-VVTWTTIISGLSKCGFHKEAIDMFCGI--------------------  158 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m--------------------  158 (209)
                           ..|=+.|-..|++++|.++-+.-.+-. ..||.....-+-..++.+.|++.|..-                    
T Consensus       830 -----DLlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~  904 (1416)
T KOG3617|consen  830 -----DLLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQ  904 (1416)
T ss_pred             -----HHHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHH
Confidence                 233345555666666665544321111 124444444444455555555444433                    


Q ss_pred             --CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          159 --DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       159 --~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                        ....|...|.+.-+.....|+.+.|..++...++
T Consensus       905 Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D  940 (1416)
T KOG3617|consen  905 YVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD  940 (1416)
T ss_pred             HHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh
Confidence              2223555566666666666777777666665433

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.08  E-value=0.1  Score=31.14  Aligned_cols=55  Identities=11%  Similarity=0.099  Sum_probs=25.9

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      .+.+.++++.|.+.++++...+. .+...+...-..+.+.|++++|.+.|+...+.
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELDP-DDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCc-ccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34445555555555555554321 13333444444445555555555555555443

>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=95.01  E-value=0.85  Score=32.47  Aligned_cols=134  Identities=11%  Similarity=0.012  Sum_probs=76.8

Q ss_pred             HHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCC--ChhhHHHHHHhcCC
Q 045511           52 PLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVK--DIFSAHQIFNSVVF  129 (209)
Q Consensus        52 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g--~~~~a~~~~~~~~~  129 (209)
                      +.++.+.+.|++|+...|..++..+.+.|++..    +..+.+.++-+|.......+-.+....  -.+-|..++.++. 
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~-   89 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG-   89 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh-
Confidence            445556667777777777777777777776543    344455555555555444443333321  1233333333322 


Q ss_pred             CcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          130 PDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       130 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                         ..+..+++.+...|++-+|.++.+..+ ..+......++.+....+|...-..++....+++
T Consensus        90 ---~~~~~iievLL~~g~vl~ALr~ar~~~-~~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~n  150 (167)
T PF07035_consen   90 ---TAYEEIIEVLLSKGQVLEALRYARQYH-KVDSVPARKFLEAAANSNDDQLFYAVFRFFEERN  150 (167)
T ss_pred             ---hhHHHHHHHHHhCCCHHHHHHHHHHcC-CcccCCHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence               235566666777888888887777641 1222333556777777777766666666655543

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

Probab=94.99  E-value=1.9  Score=37.05  Aligned_cols=94  Identities=12%  Similarity=-0.023  Sum_probs=45.4

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      +-|..+--.+-...++++|.+-|+.....+- -|...|.-+-..-++.|+++........+.+.. +.....|.....++
T Consensus        76 vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~-dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~  153 (700)
T KOG1156|consen   76 VCWHVLGLLQRSDKKYDEAIKCYRNALKIEK-DNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQ  153 (700)
T ss_pred             hhHHHHHHHHhhhhhHHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHH
Confidence            4444444444445666666666666655431 233444444333344444444444444443332 12234455555555


Q ss_pred             HhCCChhhHHHHHHhc
Q 045511          112 VTVKDIFSAHQIFNSV  127 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~  127 (209)
                      .-.|+...|..+.++.
T Consensus       154 ~L~g~y~~A~~il~ef  169 (700)
T KOG1156|consen  154 HLLGEYKMALEILEEF  169 (700)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            5556666665555544

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

Probab=94.98  E-value=0.63  Score=41.93  Aligned_cols=158  Identities=13%  Similarity=0.094  Sum_probs=94.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHH--HHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNS--LLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~--ll~  109 (209)
                      ..|+.|=..|+..-+..+|.+-|+...+-+- -+..........|+...+++.|..+.-.--+.. +.....+|-  .--
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFeLDa-tdaeaaaa~adtyae~~~we~a~~I~l~~~qka-~a~~~k~nW~~rG~  570 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFELDA-TDAEAAAASADTYAEESTWEEAFEICLRAAQKA-PAFACKENWVQRGP  570 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc-hhhhhHHHHHHHhhccccHHHHHHHHHHHhhhc-hHHHHHhhhhhccc
Confidence            5555566666655566666666666655432 344556666666677777766666621111111 001111222  222


Q ss_pred             HHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHH--hccccchhHH
Q 045511          110 FYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSA--CSSLGSRKLG  183 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~--~~~~g~~~~a  183 (209)
                      .|.+.++.-+|..-|...   ...|...|..+..+|.++|++.-|..+|.+. .++|+.. |..+-.+  -+..|++.++
T Consensus       571 yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~-y~~fk~A~~ecd~GkYkea  649 (1238)
T KOG1127|consen  571 YYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSK-YGRFKEAVMECDNGKYKEA  649 (1238)
T ss_pred             cccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhH-HHHHHHHHHHHHhhhHHHH
Confidence            344455555555555554   2246788999999999999999999999888 7777653 3333333  2467888888


Q ss_pred             HHHHHHHHH
Q 045511          184 KAIHAHSLR  192 (209)
Q Consensus       184 ~~~~~~~~~  192 (209)
                      ...++.+..
T Consensus       650 ld~l~~ii~  658 (1238)
T KOG1127|consen  650 LDALGLIIY  658 (1238)
T ss_pred             HHHHHHHHH
Confidence            888876643

>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=94.96  E-value=0.74  Score=31.48  Aligned_cols=66  Identities=14%  Similarity=0.106  Sum_probs=51.1

Q ss_pred             cHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccC
Q 045511          131 DVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNE  196 (209)
Q Consensus       131 ~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  196 (209)
                      +..-.+.-+..+..+|.-++-.++++++  .-+|+....-.+-.+|.+.|+..++.+++...-++|++
T Consensus        85 ~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   85 LSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             --HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            3445677888999999999999999887  56788899999999999999999999999999988864

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

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

Probab=94.78  E-value=0.9  Score=35.21  Aligned_cols=97  Identities=13%  Similarity=0.004  Sum_probs=63.0

Q ss_pred             CccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCC---ChHHHHHHHhhC-CCCCCHHh-HHH
Q 045511           98 LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCG---FHKEAIDMFCGI-DVKPNANT-LVS  169 (209)
Q Consensus        98 ~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g---~~~~a~~~~~~m-~~~p~~~t-~~~  169 (209)
                      +-|...|--|-..|...|+.+.|..-|.+..   .+|...+..+-.++..+.   ...++..+|+++ ...|+..+ ..-
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~l  232 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALSL  232 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHHH
Confidence            4466777777778888888888877777652   245555555555554433   244677777777 66665543 444


Q ss_pred             HHHHhccccchhHHHHHHHHHHHhc
Q 045511          170 VLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      +--.+...|++.+|...|+.|.+..
T Consensus       233 LA~~afe~g~~~~A~~~Wq~lL~~l  257 (287)
T COG4235         233 LAFAAFEQGDYAEAAAAWQMLLDLL  257 (287)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcC
Confidence            4455667778888888887777663

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=94.77  E-value=0.63  Score=29.78  Aligned_cols=60  Identities=13%  Similarity=0.058  Sum_probs=47.2

Q ss_pred             chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           49 NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        49 ~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ++.+-++.+....+.|+.....+.+++|.+.+++..|..+|+.++.+. ..+..+|..++.
T Consensus        25 e~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~-~~~~~~y~~~lq   84 (103)
T cd00923          25 ELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC-GAHKEIYPYILQ   84 (103)
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cCchhhHHHHHH
Confidence            456667777788899999999999999999999999999999887443 124557776664

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.

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=94.68  E-value=1.4  Score=33.44  Aligned_cols=76  Identities=12%  Similarity=0.136  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHH---HHHHHHHHhCCChhhHHHHHHhcCC--C--cHhHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQ---NSLLHFYVTVKDIFSAHQIFNSVVF--P--DVVTWTTI  138 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~---~~ll~~~~~~g~~~~a~~~~~~~~~--~--~~~~~~~l  138 (209)
                      ...|..-... ...|+++.|.+.|+.+...-... ....   -.+..+|.+.+++++|...+++..+  |  ....|--.
T Consensus        33 ~~~Y~~A~~~-~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y  110 (243)
T PRK10866         33 SEIYATAQQK-LQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLY  110 (243)
T ss_pred             HHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHH
Confidence            3445555554 56899999999999998865322 2332   3456788999999999999998832  2  23345455


Q ss_pred             HHHHH
Q 045511          139 ISGLS  143 (209)
Q Consensus       139 i~~~~  143 (209)
                      +.|.+
T Consensus       111 ~~g~~  115 (243)
T PRK10866        111 MRGLT  115 (243)
T ss_pred             HHHHh
Confidence            55544

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

Probab=94.59  E-value=0.6  Score=36.22  Aligned_cols=100  Identities=13%  Similarity=0.106  Sum_probs=75.8

Q ss_pred             HHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhH
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSA  120 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a  120 (209)
                      +.+++++.+|+..|.+..+-. +-|.+-|..=-.+|++.|..+.|.+--+.-++-. +....+|..|=.+|...|++++|
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            456789999999999998853 2366778888999999999988877655544432 22356899999999999999999


Q ss_pred             HHHHHhc--CCCcHhHHHHHHHHH
Q 045511          121 HQIFNSV--VFPDVVTWTTIISGL  142 (209)
Q Consensus       121 ~~~~~~~--~~~~~~~~~~li~~~  142 (209)
                      .+.|.+.  .+|+..+|-.=++..
T Consensus       169 ~~aykKaLeldP~Ne~~K~nL~~A  192 (304)
T KOG0553|consen  169 IEAYKKALELDPDNESYKSNLKIA  192 (304)
T ss_pred             HHHHHhhhccCCCcHHHHHHHHHH
Confidence            9999887  457766665555433

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

Probab=94.36  E-value=2.9  Score=35.65  Aligned_cols=154  Identities=16%  Similarity=0.201  Sum_probs=104.7

Q ss_pred             ccHHHHHHHHHcC--CCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHH--------HHHHhccCccH
Q 045511           32 HILNTLLKLLTQS--STPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHA--------HVIKYGHLHDI  101 (209)
Q Consensus        32 ~~~~~li~~~~~~--g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~--------~m~~~g~~~~~  101 (209)
                      ..+.+++..+.+.  .....+..++....+..-.-.....-+++......|+++.|.+++.        .+.+.+..  +
T Consensus       340 ~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~--P  417 (652)
T KOG2376|consen  340 SLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHL--P  417 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccC--h
Confidence            5566666655543  3456677776666554322223455566777788999999999998        44444444  4


Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcC------CCcHhHHHHHH----HHHHhCCChHHHHHHHhhC-C-CCCCHHhHHH
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVV------FPDVVTWTTII----SGLSKCGFHKEAIDMFCGI-D-VKPNANTLVS  169 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~------~~~~~~~~~li----~~~~~~g~~~~a~~~~~~m-~-~~p~~~t~~~  169 (209)
                      .+-.+++..+.+.++-+.|-.++++..      .+.....++++    ..-.+.|+-++|..+++++ . ..+|..+...
T Consensus       418 ~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d~~~l~~  497 (652)
T KOG2376|consen  418 GTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFNPNDTDLLVQ  497 (652)
T ss_pred             hHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCchHHHHHH
Confidence            455678888888888888888887652      23333334443    4445679999999999999 4 5678889999


Q ss_pred             HHHHhccccchhHHHHHHH
Q 045511          170 VLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       170 li~~~~~~g~~~~a~~~~~  188 (209)
                      ++.+|++. |+++|+.+-.
T Consensus       498 lV~a~~~~-d~eka~~l~k  515 (652)
T KOG2376|consen  498 LVTAYARL-DPEKAESLSK  515 (652)
T ss_pred             HHHHHHhc-CHHHHHHHhh
Confidence            99999765 5777777644

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.34  E-value=1.8  Score=37.80  Aligned_cols=92  Identities=14%  Similarity=0.136  Sum_probs=75.3

Q ss_pred             ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhc
Q 045511           96 GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACS  175 (209)
Q Consensus        96 g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~  175 (209)
                      |....-.+.+--+.-++..|+..+|.++-.+..-||-..|--=+.+++..++|++-+++-+.+  + +..-|..+..+|.
T Consensus       679 ~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAksk--k-sPIGy~PFVe~c~  755 (829)
T KOG2280|consen  679 GGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSK--K-SPIGYLPFVEACL  755 (829)
T ss_pred             ccccccCcHHHHHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhcc--C-CCCCchhHHHHHH
Confidence            334445567777888889999999999999999999999999999999999999998888885  2 2566777888888


Q ss_pred             cccchhHHHHHHHHH
Q 045511          176 SLGSRKLGKAIHAHS  190 (209)
Q Consensus       176 ~~g~~~~a~~~~~~~  190 (209)
                      +.|+.++|...+.+.
T Consensus       756 ~~~n~~EA~KYiprv  770 (829)
T KOG2280|consen  756 KQGNKDEAKKYIPRV  770 (829)
T ss_pred             hcccHHHHhhhhhcc
Confidence            888888888776543

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=94.32  E-value=2.3  Score=34.41  Aligned_cols=161  Identities=15%  Similarity=0.085  Sum_probs=97.7

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCC---CCCCHHHHHHHHHHHhc---cccHHHHHHHHHHHHHhccCccHhHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCP---SSYNHYTFTQALKACSL---AHAHQKGLEIHAHVIKYGHLHDIFIQNS  106 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g---~~p~~~t~~~ll~~~~~---~~~~~~a~~~~~~m~~~g~~~~~~~~~~  106 (209)
                      +.-.++-+|-...+++...++.+.|....   +.-....--....++-+   .|+.+.|.+++..+....-.+++.+|..
T Consensus       143 iv~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL  222 (374)
T PF13281_consen  143 IVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGL  222 (374)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHH
Confidence            33345556888999999999999998752   11122211223334445   8899999999999776666788888877


Q ss_pred             HHHHHHhC---------CChhhHHHHHHhc--CCCcHhH---HHHHHHHHHhCCC-hHHHHHH---HhhC----CC---C
Q 045511          107 LLHFYVTV---------KDIFSAHQIFNSV--VFPDVVT---WTTIISGLSKCGF-HKEAIDM---FCGI----DV---K  161 (209)
Q Consensus       107 ll~~~~~~---------g~~~~a~~~~~~~--~~~~~~~---~~~li~~~~~~g~-~~~a~~~---~~~m----~~---~  161 (209)
                      +-..|-..         ...+.|...|.+-  .+||..+   +-+|+........ -.+..++   +..+    |.   .
T Consensus       223 ~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~  302 (374)
T PF13281_consen  223 LGRIYKDLFLESNFTDRESLDKAIEWYRKGFEIEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKM  302 (374)
T ss_pred             HHHHHHHHHHHcCccchHHHHHHHHHHHHHHcCCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhcccccc
Confidence            77665432         2356677777655  3344332   2233332222111 1122222   2222    22   2


Q ss_pred             CCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .|-=-+.+++.++.-.|+.++|.+..+.|.+.
T Consensus       303 ~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  303 QDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            23335677889999999999999999998866

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

Probab=94.28  E-value=0.44  Score=36.84  Aligned_cols=73  Identities=10%  Similarity=0.083  Sum_probs=57.6

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC--------CCCCCHHhHHH
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI--------DVKPNANTLVS  169 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--------~~~p~~~t~~~  169 (209)
                      ..++..++..+...|+.+.+...+++..   .-+...|-.+|.+|.+.|+...|++.|+.+        |+.|...+...
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            4466777888888888888888888773   246778888888888888888888888877        88888877776


Q ss_pred             HHHH
Q 045511          170 VLSA  173 (209)
Q Consensus       170 li~~  173 (209)
                      ..+.
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            6666

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

Probab=94.14  E-value=0.35  Score=37.37  Aligned_cols=75  Identities=12%  Similarity=0.140  Sum_probs=63.7

Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHH-----hccCCCchhHhH
Q 045511          132 VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLR-----NLNENNIILDNA  204 (209)
Q Consensus       132 ~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~~~~  204 (209)
                      ..++..++..+...|+.+.+.+.++++ ...| |...|..++.+|.+.|+...|+..+..+.+     .|+.|.+.+...
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            457788999999999999999999999 5555 778999999999999999999999997755     488988876654


Q ss_pred             hh
Q 045511          205 VL  206 (209)
Q Consensus       205 li  206 (209)
                      ..
T Consensus       233 y~  234 (280)
T COG3629         233 YE  234 (280)
T ss_pred             HH
Confidence            43

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=93.96  E-value=0.94  Score=31.40  Aligned_cols=84  Identities=11%  Similarity=0.069  Sum_probs=67.0

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCC-----CCCHHHHHHHHHHHhcccc-HHHHHHHHHHHHHhccCccHhHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-----SYNHYTFTQALKACSLAHA-HQKGLEIHAHVIKYGHLHDIFIQN  105 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-----~p~~~t~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~  105 (209)
                      ...|.++...+..+++.....+++.+..-..     ..+..+|++++++.++... --.+..+|+.|++.+.++++.-|.
T Consensus        40 ~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~  119 (145)
T PF13762_consen   40 IFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYS  119 (145)
T ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            5678888888888999999998888854211     2456779999999977776 457888899999888899999999


Q ss_pred             HHHHHHHhCC
Q 045511          106 SLLHFYVTVK  115 (209)
Q Consensus       106 ~ll~~~~~~g  115 (209)
                      .+|.++.+-.
T Consensus       120 ~li~~~l~g~  129 (145)
T PF13762_consen  120 CLIKAALRGY  129 (145)
T ss_pred             HHHHHHHcCC
Confidence            9998887763

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.96  E-value=3.3  Score=34.78  Aligned_cols=151  Identities=10%  Similarity=0.032  Sum_probs=97.1

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCC-CCCCH-----HHHHHHHHHHhc----cccHHHHHHHHHHHHHhccCccHhHHHHH
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCP-SSYNH-----YTFTQALKACSL----AHAHQKGLEIHAHVIKYGHLHDIFIQNSL  107 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g-~~p~~-----~t~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  107 (209)
                      +....=.|+-+.+++++.+-.+.+ +.-..     -+|..++..++.    ..+.+.+.++++.+.++  -|+...|.-.
T Consensus       195 l~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lfl~~  272 (468)
T PF10300_consen  195 LSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALFLFF  272 (468)
T ss_pred             HhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHHHHH
Confidence            333344577788888877765533 33222     234555554444    34678899999999876  4666655433


Q ss_pred             H-HHHHhCCChhhHHHHHHhcC-------CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHh-cc
Q 045511          108 L-HFYVTVKDIFSAHQIFNSVV-------FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSAC-SS  176 (209)
Q Consensus       108 l-~~~~~~g~~~~a~~~~~~~~-------~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~-~~  176 (209)
                      - +.+...|++++|.+.|++..       +.....+--+.-.+....+|++|.+.|.++ .... +..+|.-+..+| ..
T Consensus       273 ~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~WSka~Y~Y~~a~c~~~  352 (468)
T PF10300_consen  273 EGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKWSKAFYAYLAAACLLM  352 (468)
T ss_pred             HHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhccccHHHHHHHHHHHHHHh
Confidence            3 35667899999999999652       223344445556678889999999999999 3333 344454444444 35


Q ss_pred             ccch-------hHHHHHHHHH
Q 045511          177 LGSR-------KLGKAIHAHS  190 (209)
Q Consensus       177 ~g~~-------~~a~~~~~~~  190 (209)
                      .|+.       ++|.+++..+
T Consensus       353 l~~~~~~~~~~~~a~~l~~~v  373 (468)
T PF10300_consen  353 LGREEEAKEHKKEAEELFRKV  373 (468)
T ss_pred             hccchhhhhhHHHHHHHHHHH
Confidence            6777       7888888765

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.

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

Probab=93.94  E-value=2.3  Score=33.00  Aligned_cols=108  Identities=11%  Similarity=0.042  Sum_probs=58.4

Q ss_pred             CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh---CCChhhHHHHHHhcC--CC-cHhHHHHH
Q 045511           65 NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT---VKDIFSAHQIFNSVV--FP-DVVTWTTI  138 (209)
Q Consensus        65 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~---~g~~~~a~~~~~~~~--~~-~~~~~~~l  138 (209)
                      |...|-.|=.+|...|+.+.|..-|..-.+-. .+|+..+..+-..+..   ..+..++.++|++..  +| |+.+-.-|
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~lL  233 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALSLL  233 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHHHH
Confidence            55666666666666666666666666555432 2333333333333222   224456666666663  22 34444555


Q ss_pred             HHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHH
Q 045511          139 ISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSA  173 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~  173 (209)
                      -..+...|++.+|...|..| ..-|.......+|..
T Consensus       234 A~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie~  269 (287)
T COG4235         234 AFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIER  269 (287)
T ss_pred             HHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHHH
Confidence            56666677777777777776 444444444444443

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

Probab=93.85  E-value=1.5  Score=37.14  Aligned_cols=110  Identities=13%  Similarity=0.088  Sum_probs=82.4

Q ss_pred             cchHHHHHHhh-hCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           48 QNAIPLYNKML-NCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        48 ~~a~~l~~~m~-~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      ....++|-++- +.+..+|......|=-.|-..|+++.+.+.|+..++-. +-|-.+||.|=..++...+.++|...|.+
T Consensus       411 ~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~r  489 (579)
T KOG1125|consen  411 AHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNR  489 (579)
T ss_pred             HHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHH
Confidence            34455555554 34545677777777777788899999999999998754 44678999999999999999999999998


Q ss_pred             cC--CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          127 VV--FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       127 ~~--~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..  +|+ +.+.-.|--+|.+.|.+++|...|-+.
T Consensus       490 ALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~A  524 (579)
T KOG1125|consen  490 ALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEA  524 (579)
T ss_pred             HHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHH
Confidence            83  465 334444555678899999988777554

>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=93.82  E-value=1.7  Score=30.97  Aligned_cols=116  Identities=9%  Similarity=0.024  Sum_probs=84.1

Q ss_pred             HhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHH
Q 045511           25 IIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQ  104 (209)
Q Consensus        25 ~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~  104 (209)
                      .+..|+...|..+|..+.+.|+..    .+..+...++.+|.......+-.+...  ...+.++=-+|.++=    ...+
T Consensus        23 ~~i~~~~~L~~lli~lLi~~~~~~----~L~qllq~~Vi~DSk~lA~~LLs~~~~--~~~~~Ql~lDMLkRL----~~~~   92 (167)
T PF07035_consen   23 HNIPVQHELYELLIDLLIRNGQFS----QLHQLLQYHVIPDSKPLACQLLSLGNQ--YPPAYQLGLDMLKRL----GTAY   92 (167)
T ss_pred             cCCCCCHHHHHHHHHHHHHcCCHH----HHHHHHhhcccCCcHHHHHHHHHhHcc--ChHHHHHHHHHHHHh----hhhH
Confidence            456688899999999999999854    555667778888888888777666543  334555544444331    1256


Q ss_pred             HHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHH
Q 045511          105 NSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKE  150 (209)
Q Consensus       105 ~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  150 (209)
                      ..++..+...|++-+|.++.......+...-..++.+-.+.+|...
T Consensus        93 ~~iievLL~~g~vl~ALr~ar~~~~~~~~~~~~fLeAA~~~~D~~l  138 (167)
T PF07035_consen   93 EEIIEVLLSKGQVLEALRYARQYHKVDSVPARKFLEAAANSNDDQL  138 (167)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCCcccCCHHHHHHHHHHcCCHHH
Confidence            7888999999999999999988755555556677888777777554

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.81  E-value=0.28  Score=40.33  Aligned_cols=96  Identities=9%  Similarity=-0.007  Sum_probs=69.1

Q ss_pred             ccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcH----hHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHH
Q 045511           99 HDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDV----VTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVL  171 (209)
Q Consensus        99 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li  171 (209)
                      .+...++.+-..|.+.|++++|...|++.  ..|+.    .+|..+-.+|...|+.++|++.+.+. .+.+  .-|..+.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALelsn--~~f~~i~  150 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDYN--LKFSTIL  150 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcc--hhHHHHH
Confidence            45678999999999999999999999986  34553    46999999999999999999999997 4321  1232221


Q ss_pred             HH--hccccchhHHHHHHHHHHHhccC
Q 045511          172 SA--CSSLGSRKLGKAIHAHSLRNLNE  196 (209)
Q Consensus       172 ~~--~~~~g~~~~a~~~~~~~~~~~~~  196 (209)
                      ..  +....+.....++++...+-|..
T Consensus       151 ~DpdL~plR~~pef~eLlee~rk~G~~  177 (453)
T PLN03098        151 NDPDLAPFRASPEFKELQEEARKGGED  177 (453)
T ss_pred             hCcchhhhcccHHHHHHHHHHHHhCCc
Confidence            11  11223445677788888877753

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.79  E-value=3.7  Score=36.02  Aligned_cols=114  Identities=11%  Similarity=-0.039  Sum_probs=79.4

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      -.--+.+.-+.-+..-|+..+|.++-.+.+-    ||-..|-.=+.+++..+++++-+++=+.+      .++.-|.-.+
T Consensus       682 f~dlSl~dTv~~li~~g~~k~a~ql~~~Fki----pdKr~~wLk~~aLa~~~kweeLekfAksk------ksPIGy~PFV  751 (829)
T KOG2280|consen  682 FVDLSLHDTVTTLILIGQNKRAEQLKSDFKI----PDKRLWWLKLTALADIKKWEELEKFAKSK------KSPIGYLPFV  751 (829)
T ss_pred             cccCcHHHHHHHHHHccchHHHHHHHHhcCC----cchhhHHHHHHHHHhhhhHHHHHHHHhcc------CCCCCchhHH
Confidence            3345667777778888888888887666653    78888888888888888887655543322      1256677778


Q ss_pred             HHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          109 HFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      ..|.+.|+.++|.+++.+.....     -...+|.+.|++.+|.++-.+
T Consensus       752 e~c~~~~n~~EA~KYiprv~~l~-----ekv~ay~~~~~~~eAad~A~~  795 (829)
T KOG2280|consen  752 EACLKQGNKDEAKKYIPRVGGLQ-----EKVKAYLRVGDVKEAADLAAE  795 (829)
T ss_pred             HHHHhcccHHHHhhhhhccCChH-----HHHHHHHHhccHHHHHHHHHH
Confidence            88888888888888888765322     455666677777666554433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.72  E-value=0.79  Score=37.81  Aligned_cols=64  Identities=9%  Similarity=0.049  Sum_probs=55.4

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH----HHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH----YTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      +...|+.+-.+|.+.|++++|...|++-.+.  .|+.    .+|..+-.+|.+.|++++|.+.++...+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3388999999999999999999999998874  4664    46899999999999999999999988875

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=93.56  E-value=3.2  Score=33.27  Aligned_cols=119  Identities=13%  Similarity=0.031  Sum_probs=74.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc-----------ccHH--HHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP-----------HILN--TLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQAL   73 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~-----------~~~~--~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll   73 (209)
                      +.|..+.|..-|.++....+..-..           ..|+  ..+....-+|+...|...+..+.+-. +.|...|..--
T Consensus       118 K~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Ra  196 (504)
T KOG0624|consen  118 KQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARA  196 (504)
T ss_pred             hcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHH
Confidence            6677777777777666553211011           2222  23344556789999999999888754 36778888888


Q ss_pred             HHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ++|...|++..|.+=+...-+-. .-|+.+.--+-..+-..|+.+.++...++.
T Consensus       197 kc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iREC  249 (504)
T KOG0624|consen  197 KCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIREC  249 (504)
T ss_pred             HHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            89999999888877666554433 233444444445555566666655555444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.26  E-value=0.53  Score=36.93  Aligned_cols=94  Identities=18%  Similarity=0.233  Sum_probs=68.5

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCC---CCCC--HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCP---SSYN--HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQ  104 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g---~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~  104 (209)
                      .+.+...++..-.+..+++++...+-+++...   ..|+  .+++..++.-|    +++.+.-++..-.+.|+-||.+++
T Consensus        63 s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllky----~pq~~i~~l~npIqYGiF~dqf~~  138 (418)
T KOG4570|consen   63 SSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLKY----DPQKAIYTLVNPIQYGIFPDQFTF  138 (418)
T ss_pred             ceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHcc----ChHHHHHHHhCcchhccccchhhH
Confidence            33566666666666778888888876665432   2333  33333333333    667888888888999999999999


Q ss_pred             HHHHHHHHhCCChhhHHHHHHhc
Q 045511          105 NSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       105 ~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +.+|+.+.+.+++.+|-++.-.|
T Consensus       139 c~l~D~flk~~n~~~aa~vvt~~  161 (418)
T KOG4570|consen  139 CLLMDSFLKKENYKDAASVVTEV  161 (418)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHH
Confidence            99999999999999988887665

>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=93.10  E-value=0.47  Score=32.41  Aligned_cols=65  Identities=12%  Similarity=0.153  Sum_probs=31.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH   97 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~   97 (209)
                      ...+..++.+.+.|+-+.-.++++++.+. -.++....-.+-.+|.+.|+..++.+++.+.-++|+
T Consensus        87 e~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   87 EYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            34445555555555555555555555432 234555555555666666666666666655555553

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

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=93.08  E-value=1.6  Score=30.82  Aligned_cols=50  Identities=4%  Similarity=-0.023  Sum_probs=27.2

Q ss_pred             hccccHHHHHHHHHHHHHhcc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcC
Q 045511           77 SLAHAHQKGLEIHAHVIKYGH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV  128 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~  128 (209)
                      .+.++.+.++.+++.+.--.. .|...++...  .++++|++.+|.++|+++.
T Consensus        21 l~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~--l~i~r~~w~dA~rlLr~l~   71 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVLRPEFPELDLFDGW--LHIVRGDWDDALRLLRELE   71 (160)
T ss_pred             HccCChHHHHHHHHHHHHhCCCchHHHHHHHH--HHHHhCCHHHHHHHHHHHh
Confidence            455666667777666654321 1112233322  3556677777777777763

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.06  E-value=2  Score=33.88  Aligned_cols=100  Identities=14%  Similarity=0.080  Sum_probs=68.1

Q ss_pred             HhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-CcH-----hHHHHHHHHHHhCCChHHHHHHHhhC---CCCCCH
Q 045511           94 KYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-PDV-----VTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNA  164 (209)
Q Consensus        94 ~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-~~~-----~~~~~li~~~~~~g~~~~a~~~~~~m---~~~p~~  164 (209)
                      ..|.+.+..+-..++..-....+++++...+-+++. |+.     .+-.+.++ ++-.-++++++.+...=   |+-||.
T Consensus        57 ~~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~ir-lllky~pq~~i~~l~npIqYGiF~dq  135 (418)
T KOG4570|consen   57 ERGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIR-LLLKYDPQKAIYTLVNPIQYGIFPDQ  135 (418)
T ss_pred             hcCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHH-HHHccChHHHHHHHhCcchhccccch
Confidence            345566667777777777777888888888877732 221     11122222 22344566777776554   999999


Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .|++.+|..+.+.+++..|.++...|....
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            999999999999999988888877665553

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

Probab=92.87  E-value=4.7  Score=34.85  Aligned_cols=164  Identities=11%  Similarity=0.078  Sum_probs=114.0

Q ss_pred             hcchhccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            3 VNGLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         3 i~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ++++..++....++..+++...++..+++.+.-.  -.+...|+.++|....+.-.+..+ -+.+.|+.+--.+....++
T Consensus        15 lk~yE~kQYkkgLK~~~~iL~k~~eHgeslAmkG--L~L~~lg~~~ea~~~vr~glr~d~-~S~vCwHv~gl~~R~dK~Y   91 (700)
T KOG1156|consen   15 LKCYETKQYKKGLKLIKQILKKFPEHGESLAMKG--LTLNCLGKKEEAYELVRLGLRNDL-KSHVCWHVLGLLQRSDKKY   91 (700)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHhCCccchhHHhcc--chhhcccchHHHHHHHHHHhccCc-ccchhHHHHHHHHhhhhhH
Confidence            3455566677778888888886655555433322  234566888999988877766544 5678888888788888899


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      ++|...|...+..+ +-|..+|--+--.-+..++++.........   .......|..+.-++.-.|++..|..+..+. 
T Consensus        92 ~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~  170 (700)
T KOG1156|consen   92 DEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFE  170 (700)
T ss_pred             HHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999888766 456667766555555566666555544443   3345678888888888899999999888888 


Q ss_pred             ---CCCCCHHhHHHH
Q 045511          159 ---DVKPNANTLVSV  170 (209)
Q Consensus       159 ---~~~p~~~t~~~l  170 (209)
                         .-.|+...|...
T Consensus       171 ~t~~~~~s~~~~e~s  185 (700)
T KOG1156|consen  171 KTQNTSPSKEDYEHS  185 (700)
T ss_pred             HhhccCCCHHHHHHH
Confidence               224666655443

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.72  E-value=1  Score=34.90  Aligned_cols=99  Identities=11%  Similarity=0.080  Sum_probs=74.2

Q ss_pred             CCcccHHHHHHHHHcC--CCccchHHHHHHhhhC-CCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh-ccCccHhHH
Q 045511           29 PQPHILNTLLKLLTQS--STPQNAIPLYNKMLNC-PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY-GHLHDIFIQ  104 (209)
Q Consensus        29 p~~~~~~~li~~~~~~--g~~~~a~~l~~~m~~~-g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~  104 (209)
                      .|..+...+++.+...  .....-.++.+-+... |-.++..+...+|..++..+++....++++.-... +...|...|
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            5667777777777762  2333444444444433 45678888899999999999999888888877655 667788899


Q ss_pred             HHHHHHHHhCCChhhHHHHHHhc
Q 045511          105 NSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       105 ~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ...|+.....|+..-..++.++=
T Consensus       242 ~~FI~li~~sgD~~~~~kiI~~G  264 (292)
T PF13929_consen  242 AEFIKLIVESGDQEVMRKIIDDG  264 (292)
T ss_pred             HHHHHHHHHcCCHHHHHHHhhCC
Confidence            99999999999999888888653

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=92.60  E-value=2.2  Score=29.25  Aligned_cols=87  Identities=11%  Similarity=0.151  Sum_probs=46.5

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH---HHHHhCCC
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL---HFYVTVKD  116 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll---~~~~~~g~  116 (209)
                      +++..|+++.|++.|.+-..- .+-....||.--.++.-+|+.++|.+-++...+-.-..+...+.+.+   ..|-..|+
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            345566666666666665543 22344566666666666666666666665555432222322222222   23445566


Q ss_pred             hhhHHHHHHhc
Q 045511          117 IFSAHQIFNSV  127 (209)
Q Consensus       117 ~~~a~~~~~~~  127 (209)
                      .+.|..-|+..
T Consensus       131 dd~AR~DFe~A  141 (175)
T KOG4555|consen  131 DDAARADFEAA  141 (175)
T ss_pred             hHHHHHhHHHH
Confidence            66666666543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.37  E-value=3.2  Score=31.83  Aligned_cols=89  Identities=17%  Similarity=0.029  Sum_probs=50.2

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccH---hHHHHHHHHHHhCCChhhHHHHHHhcCC------CcHhHHHHH
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI---FIQNSLLHFYVTVKDIFSAHQIFNSVVF------PDVVTWTTI  138 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~---~~~~~ll~~~~~~g~~~~a~~~~~~~~~------~~~~~~~~l  138 (209)
                      -|+..+..+ +.|++..|.+-|....+.. +-+.   ..+==|-.++...|++++|-.+|..+.+      +-..+.--+
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~Y-P~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl  221 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKY-PNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL  221 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcC-CCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH
Confidence            466666654 5555777777777666654 1111   1222355666667777777777666521      122334444


Q ss_pred             HHHHHhCCChHHHHHHHhhC
Q 045511          139 ISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m  158 (209)
                      -.+..+.|+.++|..+|+++
T Consensus       222 g~~~~~l~~~d~A~atl~qv  241 (262)
T COG1729         222 GVSLGRLGNTDEACATLQQV  241 (262)
T ss_pred             HHHHHHhcCHHHHHHHHHHH
Confidence            55556666666666666665

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=92.28  E-value=4.1  Score=35.42  Aligned_cols=88  Identities=10%  Similarity=-0.014  Sum_probs=64.7

Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHH-----------hHHH
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNAN-----------TLVS  169 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~-----------t~~~  169 (209)
                      .+...+-..+.+...+.-|-++|.+|.+     .-.++..+...++|.+|+.+-++. ...||.+           -|.-
T Consensus       748 e~l~~~a~ylk~l~~~gLAaeIF~k~gD-----~ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeE  822 (1081)
T KOG1538|consen  748 EPLLLCATYLKKLDSPGLAAEIFLKMGD-----LKSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEE  822 (1081)
T ss_pred             hHHHHHHHHHhhccccchHHHHHHHhcc-----HHHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHH
Confidence            3444555556666778888888887743     235677888899999999998888 6666654           2444


Q ss_pred             HHHHhccccchhHHHHHHHHHHHhc
Q 045511          170 VLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .=+++.++|+-.+|.++++++....
T Consensus       823 AqkAfhkAGr~~EA~~vLeQLtnna  847 (1081)
T KOG1538|consen  823 AQKAFHKAGRQREAVQVLEQLTNNA  847 (1081)
T ss_pred             HHHHHHHhcchHHHHHHHHHhhhhh
Confidence            5578899999999999998875553

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.25  E-value=4.4  Score=31.51  Aligned_cols=111  Identities=13%  Similarity=0.169  Sum_probs=53.8

Q ss_pred             ccchHHHHHHhhh-CCCCCCHHHHHHHHHHHhccc--cHHHHHHHHHHHH-HhccCccHhHHHHHHHHHHhCCChhhHHH
Q 045511           47 PQNAIPLYNKMLN-CPSSYNHYTFTQALKACSLAH--AHQKGLEIHAHVI-KYGHLHDIFIQNSLLHFYVTVKDIFSAHQ  122 (209)
Q Consensus        47 ~~~a~~l~~~m~~-~g~~p~~~t~~~ll~~~~~~~--~~~~a~~~~~~m~-~~g~~~~~~~~~~ll~~~~~~g~~~~a~~  122 (209)
                      +.+|+.+|+...- +.+.-|..+...+++......  .+..-.++.+.+. ..|-.++..+...+|..+++.+++..-.+
T Consensus       144 Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~  223 (292)
T PF13929_consen  144 VVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQ  223 (292)
T ss_pred             HHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHH
Confidence            3344444443222 234455566666666554411  2233333333333 12234555555555555566665555555


Q ss_pred             HHHhcC-----CCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          123 IFNSVV-----FPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       123 ~~~~~~-----~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      .++.-.     ..|...|..+|+.....|+..-...+..+
T Consensus       224 fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  224 FWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            555441     23455555555555555555555554433

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=92.01  E-value=1.1  Score=31.26  Aligned_cols=68  Identities=16%  Similarity=0.202  Sum_probs=33.5

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH   80 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~   80 (209)
                      ...+.++...+..++-..+..|...+|...+  +.+.|++++|..+|++..+.+.   ...|...+.++|-.-
T Consensus        23 ~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~~---~~p~~kAL~A~CL~a   90 (153)
T TIGR02561        23 SADPYDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSAG---APPYGKALLALCLNA   90 (153)
T ss_pred             cCCHHHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccCC---CchHHHHHHHHHHHh
Confidence            3444444444555544444444445554444  3455666666666666655431   123444555544443

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.97  E-value=5.4  Score=31.91  Aligned_cols=144  Identities=10%  Similarity=-0.078  Sum_probs=89.8

Q ss_pred             CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHH----HHHHHHHHhCCChhh
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQ----NSLLHFYVTVKDIFS  119 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~----~~ll~~~~~~g~~~~  119 (209)
                      .|+..+|-..++++.+. .+-|.-.+.-.=.+|.-.|+...-...++.+...- .+|...|    ..+--++...|-+++
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~w-n~dlp~~sYv~GmyaFgL~E~g~y~d  193 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKW-NADLPCYSYVHGMYAFGLEECGIYDD  193 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhcccc-CCCCcHHHHHHHHHHhhHHHhccchh
Confidence            45556666666666553 44566666666677777787777777777665431 2343322    223334556788888


Q ss_pred             HHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC------CCCCCHHhHHHHHHHhccccchhHHHHHHHH
Q 045511          120 AHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI------DVKPNANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       120 a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m------~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      |++.-++--   +.|...-++.-..+-..|++.++.++..+-      +--.-.+.|-..--.+...+.++.|+++|++
T Consensus       194 AEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~  272 (491)
T KOG2610|consen  194 AEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDR  272 (491)
T ss_pred             HHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHH
Confidence            888877763   345666677777777788888888777665      1111223444444455666888888888873

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=91.94  E-value=2.6  Score=37.65  Aligned_cols=52  Identities=6%  Similarity=-0.042  Sum_probs=31.7

Q ss_pred             HHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHH
Q 045511          136 TTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       136 ~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      -++++..|-.|+.++|-++-++   .-|....-.+-+.|...|++.+|..+|.+.
T Consensus       942 fs~VrI~C~qGk~~kAa~iA~e---sgd~AAcYhlaR~YEn~g~v~~Av~FfTrA  993 (1416)
T KOG3617|consen  942 FSMVRIKCIQGKTDKAARIAEE---SGDKAACYHLARMYENDGDVVKAVKFFTRA  993 (1416)
T ss_pred             hhheeeEeeccCchHHHHHHHh---cccHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            3444444555555555544444   335556666777777888888888777754

>PRK15331 chaperone protein SicA; Provisional

Probab=91.76  E-value=1.5  Score=31.02  Aligned_cols=79  Identities=9%  Similarity=-0.106  Sum_probs=32.1

Q ss_pred             ccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDM  154 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~  154 (209)
                      ..|++++|+.+|..+.-.+ ..+..-|..|-.++-..+++++|...|...   ...|...+--.-.+|...|+.+.|...
T Consensus        49 ~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~~A~~~  127 (165)
T PRK15331         49 NQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAKARQC  127 (165)
T ss_pred             HCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHHHHHH
Confidence            3444555555554444332 122223344444444444555555444332   111111222223344444555555554


Q ss_pred             Hhh
Q 045511          155 FCG  157 (209)
Q Consensus       155 ~~~  157 (209)
                      |..
T Consensus       128 f~~  130 (165)
T PRK15331        128 FEL  130 (165)
T ss_pred             HHH
Confidence            444

>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=91.38  E-value=6.1  Score=32.97  Aligned_cols=82  Identities=11%  Similarity=-0.019  Sum_probs=53.6

Q ss_pred             ccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhcccc
Q 045511           99 HDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLG  178 (209)
Q Consensus        99 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g  178 (209)
                      .+...|..|-+...+.|+++-|++.|.+..+     |+.|+-.|.-.|+.+.-.++-+.-   ...--++....++...|
T Consensus       345 ~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d-----~~~L~lLy~~~g~~~~L~kl~~~a---~~~~~~n~af~~~~~lg  416 (443)
T PF04053_consen  345 DDPEKWKQLGDEALRQGNIELAEECYQKAKD-----FSGLLLLYSSTGDREKLSKLAKIA---EERGDINIAFQAALLLG  416 (443)
T ss_dssp             STHHHHHHHHHHHHHTTBHHHHHHHHHHCT------HHHHHHHHHHCT-HHHHHHHHHHH---HHTT-HHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC-----ccccHHHHHHhCCHHHHHHHHHHH---HHccCHHHHHHHHHHcC
Confidence            4677899999999999999999999887643     566666777777776655554332   11122455556666678


Q ss_pred             chhHHHHHHH
Q 045511          179 SRKLGKAIHA  188 (209)
Q Consensus       179 ~~~~a~~~~~  188 (209)
                      +.++..+++.
T Consensus       417 d~~~cv~lL~  426 (443)
T PF04053_consen  417 DVEECVDLLI  426 (443)
T ss_dssp             -HHHHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            8887777754

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.

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=91.38  E-value=6.5  Score=31.61  Aligned_cols=175  Identities=8%  Similarity=-0.002  Sum_probs=100.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHH---HHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHH--HHHHhcccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTL---LKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQA--LKACSLAHA   81 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l---i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~l--l~~~~~~~~   81 (209)
                      .+++..+|+..+..+.+.     |+..|.++   -..|...|+...|+.=+.+..+  ++||-.. ..+  -..+.++|.
T Consensus        50 a~~Q~sDALt~yHaAve~-----dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVle--lKpDF~~-ARiQRg~vllK~Ge  121 (504)
T KOG0624|consen   50 ARGQLSDALTHYHAAVEG-----DPNNYQAIFRRATVYLAMGKSKAALQDLSRVLE--LKPDFMA-ARIQRGVVLLKQGE  121 (504)
T ss_pred             HhhhHHHHHHHHHHHHcC-----CchhHHHHHHHHHHHhhhcCCccchhhHHHHHh--cCccHHH-HHHHhchhhhhccc
Confidence            455555555554444332     33333332   3345556776767666666665  4566321 111  123467788


Q ss_pred             HHHHHHHHHHHHHhccCccH--------------hHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHh
Q 045511           82 HQKGLEIHAHVIKYGHLHDI--------------FIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSK  144 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~--------------~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~  144 (209)
                      ++.|+.=|+.+++.....+.              ...-..+..+...|+...|......+   ..+|...|-.=-.+|..
T Consensus       122 le~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~Wda~l~~~Rakc~i~  201 (504)
T KOG0624|consen  122 LEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPWDASLRQARAKCYIA  201 (504)
T ss_pred             HHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcchhHHHHHHHHHHHh
Confidence            88888888888766432111              11223445666678888887777666   33577777777788888


Q ss_pred             CCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHH
Q 045511          145 CGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       145 ~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      .|.+..|+.=++.. .+.. |+.++--+-..+...|+.+.+....++
T Consensus       202 ~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRE  248 (504)
T KOG0624|consen  202 EGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRE  248 (504)
T ss_pred             cCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            88888877666555 3332 334444455556666776665544443

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=91.31  E-value=4.1  Score=33.10  Aligned_cols=93  Identities=17%  Similarity=0.104  Sum_probs=70.5

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhcc
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSS  176 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~  176 (209)
                      ..++++|..+|.+.+++.+|.+.-+..   ..+|....=-==.+|...|+++.|+..|+.+ .+.|+....+.=|..|.+
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~  336 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQ  336 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            457888999999999999999988876   3455555444557888899999999999999 999988887776766653


Q ss_pred             -ccc-hhHHHHHHHHHHHh
Q 045511          177 -LGS-RKLGKAIHAHSLRN  193 (209)
Q Consensus       177 -~g~-~~~a~~~~~~~~~~  193 (209)
                       ... .++..++|..|-..
T Consensus       337 k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  337 KIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHhhc
Confidence             333 34557788877443

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=91.29  E-value=2.5  Score=35.00  Aligned_cols=130  Identities=13%  Similarity=-0.018  Sum_probs=68.6

Q ss_pred             cCCCccchHHHHHHhhhCCC-CC---C-HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH--HHhCC
Q 045511           43 QSSTPQNAIPLYNKMLNCPS-SY---N-HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF--YVTVK  115 (209)
Q Consensus        43 ~~g~~~~a~~l~~~m~~~g~-~p---~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~--~~~~g  115 (209)
                      +.+++.++.++|.+.-++-- .|   . ...-+.+|++|-. .+++..+..+....+..  | ...|-.|..+  +-+.+
T Consensus        18 kq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl-~nld~Me~~l~~l~~~~--~-~s~~l~LF~~L~~Y~~k   93 (549)
T PF07079_consen   18 KQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFL-NNLDLMEKQLMELRQQF--G-KSAYLPLFKALVAYKQK   93 (549)
T ss_pred             HHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHH-hhHHHHHHHHHHHHHhc--C-CchHHHHHHHHHHHHhh
Confidence            45777777777777755421 11   1 2334556666643 34555555555554332  1 2223333332  23556


Q ss_pred             ChhhHHHHHHhcCC------------------CcHhHHHHHHHHHHhCCChHHHHHHHhhC-------CCCCCHHhHHHH
Q 045511          116 DIFSAHQIFNSVVF------------------PDVVTWTTIISGLSKCGFHKEAIDMFCGI-------DVKPNANTLVSV  170 (209)
Q Consensus       116 ~~~~a~~~~~~~~~------------------~~~~~~~~li~~~~~~g~~~~a~~~~~~m-------~~~p~~~t~~~l  170 (209)
                      .+..|.+.+..-..                  +|..-=++.+.++...|++.++..++++|       ...-|..+|+.+
T Consensus        94 ~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~  173 (549)
T PF07079_consen   94 EYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRA  173 (549)
T ss_pred             hHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHH
Confidence            66777666643310                  12223355567777777777777777776       334566667665


Q ss_pred             HHHhcc
Q 045511          171 LSACSS  176 (209)
Q Consensus       171 i~~~~~  176 (209)
                      .-.+++
T Consensus       174 vlmlsr  179 (549)
T PF07079_consen  174 VLMLSR  179 (549)
T ss_pred             HHHHhH
Confidence            555443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

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

Probab=91.24  E-value=0.44  Score=24.25  Aligned_cols=22  Identities=5%  Similarity=-0.087  Sum_probs=9.6

Q ss_pred             HHHHHHhccccchhHHHHHHHH
Q 045511          168 VSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       168 ~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      ..+-+.|.+.|++++|.++++.
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            3344444444444444444444

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=91.23  E-value=6.2  Score=32.81  Aligned_cols=135  Identities=14%  Similarity=0.055  Sum_probs=86.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHH--hccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKAC--SLAH   80 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~--~~~~   80 (209)
                      +.++..++.+.|..+.......|-.    ...+-+|++|..+ +.+.....+....+..  | ...|-.+..+.  -+.+
T Consensus        18 kq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~~--~-~s~~l~LF~~L~~Y~~k   93 (549)
T PF07079_consen   18 KQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQF--G-KSAYLPLFKALVAYKQK   93 (549)
T ss_pred             HHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHhc--C-CchHHHHHHHHHHHHhh
Confidence            4455566666666666654333322    4456777887766 4566666665555532  3 23344444443  4667


Q ss_pred             cHHHHHHHHHHHHHh--ccCc------------cHhHHHHHHHHHHhCCChhhHHHHHHhcC--------CCcHhHHHHH
Q 045511           81 AHQKGLEIHAHVIKY--GHLH------------DIFIQNSLLHFYVTVKDIFSAHQIFNSVV--------FPDVVTWTTI  138 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~--g~~~------------~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--------~~~~~~~~~l  138 (209)
                      .++.|.+.+.-..+.  +-.|            |-..=+...+++++.|++.+++.++++|.        ..++.+||.+
T Consensus        94 ~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~  173 (549)
T PF07079_consen   94 EYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRA  173 (549)
T ss_pred             hHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHH
Confidence            888888888776655  3222            23334677889999999999999999882        3788899986


Q ss_pred             HHHHHhC
Q 045511          139 ISGLSKC  145 (209)
Q Consensus       139 i~~~~~~  145 (209)
                      +-.++++
T Consensus       174 vlmlsrS  180 (549)
T PF07079_consen  174 VLMLSRS  180 (549)
T ss_pred             HHHHhHH
Confidence            6655544

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=91.19  E-value=3.7  Score=28.50  Aligned_cols=93  Identities=12%  Similarity=0.154  Sum_probs=67.1

Q ss_pred             HHHHHhccCccH--hHHHHHHHHHHhCCChhhHHHHHHhcC---------CCcHhHHHHHHHHHHhCCChH-HHHHHHhh
Q 045511           90 AHVIKYGHLHDI--FIQNSLLHFYVTVKDIFSAHQIFNSVV---------FPDVVTWTTIISGLSKCGFHK-EAIDMFCG  157 (209)
Q Consensus        90 ~~m~~~g~~~~~--~~~~~ll~~~~~~g~~~~a~~~~~~~~---------~~~~~~~~~li~~~~~~g~~~-~a~~~~~~  157 (209)
                      .-|.+.+..++.  ...|+++.-....+++.....+++.+.         ..+...|++++++.+++.--. -+..+|+-
T Consensus        26 ~y~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~  105 (145)
T PF13762_consen   26 PYMQEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNF  105 (145)
T ss_pred             HHhhhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHH
Confidence            344555555554  356888888888888888887777762         246678999999997776633 35666666


Q ss_pred             C---CCCCCHHhHHHHHHHhccccchhH
Q 045511          158 I---DVKPNANTLVSVLSACSSLGSRKL  182 (209)
Q Consensus       158 m---~~~p~~~t~~~li~~~~~~g~~~~  182 (209)
                      |   +.+++..-|..+|++|.+.-..+.
T Consensus       106 Lk~~~~~~t~~dy~~li~~~l~g~~~~~  133 (145)
T PF13762_consen  106 LKKNDIEFTPSDYSCLIKAALRGYFHDS  133 (145)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHcCCCCcc
Confidence            6   788899999999999988755443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=91.06  E-value=4.8  Score=29.54  Aligned_cols=146  Identities=12%  Similarity=0.045  Sum_probs=74.3

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCC--CCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPS--SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~--~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      ..+.+.|++++|...|+.+...-.  +--....-.+..++-+.|+++.|...++.+.+.-......-+...+.+.+....
T Consensus        13 ~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~~~   92 (203)
T PF13525_consen   13 LEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYYKQ   92 (203)
T ss_dssp             HHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHh
Confidence            346678889999999999886421  112234456677788889999999999888876433333334444444432211


Q ss_pred             ----------hhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHH
Q 045511          117 ----------IFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       117 ----------~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~  186 (209)
                                ...+.+.        ...|..+|.-|=.+.-..+|......+.-.....-+. +.+.|.+.|.+.-|..-
T Consensus        93 ~~~~~~~~~D~~~~~~A--------~~~~~~li~~yP~S~y~~~A~~~l~~l~~~la~~e~~-ia~~Y~~~~~y~aA~~r  163 (203)
T PF13525_consen   93 IPGILRSDRDQTSTRKA--------IEEFEELIKRYPNSEYAEEAKKRLAELRNRLAEHELY-IARFYYKRGKYKAAIIR  163 (203)
T ss_dssp             HHHHH-TT---HHHHHH--------HHHHHHHHHH-TTSTTHHHHHHHHHHHHHHHHHHHHH-HHHHHHCTT-HHHHHHH
T ss_pred             CccchhcccChHHHHHH--------HHHHHHHHHHCcCchHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHcccHHHHHHH
Confidence                      1111111        2235566666666666666655544440010111111 23445555555555555


Q ss_pred             HHHHHHh
Q 045511          187 HAHSLRN  193 (209)
Q Consensus       187 ~~~~~~~  193 (209)
                      ++.+.++
T Consensus       164 ~~~v~~~  170 (203)
T PF13525_consen  164 FQYVIEN  170 (203)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555554

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=91.02  E-value=7.4  Score=31.63  Aligned_cols=153  Identities=12%  Similarity=0.096  Sum_probs=89.8

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCc------ccHHHHHHHHHc---CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQP------HILNTLLKLLTQ---SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL   78 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~------~~~~~li~~~~~---~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~   78 (209)
                      +.+....+..+-++.+.....|+.      .+--...-++-+   .|+.++|.+++.......-.++..||..+-..|-.
T Consensus       150 SyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GRIyKD  229 (374)
T PF13281_consen  150 SYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGRIYKD  229 (374)
T ss_pred             HhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHHHHHH
Confidence            334444444455555555444433      112233445556   89999999999996666666888888888766622


Q ss_pred             ---------cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC-hh---hHHHHH---Hhc--------CCCcHhH
Q 045511           79 ---------AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD-IF---SAHQIF---NSV--------VFPDVVT  134 (209)
Q Consensus        79 ---------~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~-~~---~a~~~~---~~~--------~~~~~~~  134 (209)
                               ...++.|.++|..--+.  .||..+--++...+.-.|. .+   +..++-   ...        ...+-.-
T Consensus       230 ~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~~dYWd  307 (374)
T PF13281_consen  230 LFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKMQDYWD  307 (374)
T ss_pred             HHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccccccccHHH
Confidence                     12355666666544332  3444333233333333443 22   222222   111        1246677


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhhC-CCCC
Q 045511          135 WTTIISGLSKCGFHKEAIDMFCGI-DVKP  162 (209)
Q Consensus       135 ~~~li~~~~~~g~~~~a~~~~~~m-~~~p  162 (209)
                      +.+++.+..-.|+.++|.+....| ...|
T Consensus       308 ~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~  336 (374)
T PF13281_consen  308 VATLLEASVLAGDYEKAIQAAEKAFKLKP  336 (374)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHhhcCC
Confidence            889999999999999999999998 4444

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

Probab=90.96  E-value=3.3  Score=37.68  Aligned_cols=127  Identities=13%  Similarity=-0.006  Sum_probs=84.3

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHH--HHHHhccccHHHHHHHHHHHHHhccCccHhHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQA--LKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSL  107 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~l--l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  107 (209)
                      +..++......|++..+++.|..+.-.--+. -+.....++..  =-.+...++...+...|+.-.+.. +-|...|..+
T Consensus       525 daeaaaa~adtyae~~~we~a~~I~l~~~qk-a~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gL  602 (1238)
T KOG1127|consen  525 DAEAAAASADTYAEESTWEEAFEICLRAAQK-APAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGL  602 (1238)
T ss_pred             hhhhHHHHHHHhhccccHHHHHHHHHHHhhh-chHHHHHhhhhhccccccCccchhhHHHHHHHHhcCC-chhHHHHHHH
Confidence            4588889999999999999999883222111 11111222222  223455667777777777776654 4567799999


Q ss_pred             HHHHHhCCChhhHHHHHHhcCCCcH-hHHHHHH--HHHHhCCChHHHHHHHhhC
Q 045511          108 LHFYVTVKDIFSAHQIFNSVVFPDV-VTWTTII--SGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       108 l~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~li--~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..+|.++|++..|.++|++....+. ..|....  -..|..|.+.++...+...
T Consensus       603 GeAY~~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~l~~i  656 (1238)
T KOG1127|consen  603 GEAYPESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLI  656 (1238)
T ss_pred             HHHHHhcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            9999999999999999988754222 1222222  2235678888888887776

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.94  E-value=2  Score=38.11  Aligned_cols=114  Identities=11%  Similarity=0.031  Sum_probs=54.2

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      +|.-|..+.+..+--..++.+.+.|+ .+...-..||.+|.+.++.+...++.+.-. .|..  ..-....+..+-+.+-
T Consensus       403 Vi~kfLdaq~IknLt~YLe~L~~~gl-a~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~sny  478 (933)
T KOG2114|consen  403 VIKKFLDAQRIKNLTSYLEALHKKGL-ANSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNY  478 (933)
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHHccc-ccchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhCh
Confidence            34444444444444445555555554 344444555666666665555444443332 1211  1112333444444444


Q ss_pred             hhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          117 IFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       117 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .++|+-+=..... +....++++.   ..+++++|++.+..+
T Consensus       479 l~~a~~LA~k~~~-he~vl~ille---~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  479 LDEAELLATKFKK-HEWVLDILLE---DLHNYEEALRYISSL  516 (933)
T ss_pred             HHHHHHHHHHhcc-CHHHHHHHHH---HhcCHHHHHHHHhcC
Confidence            4444443333221 3333344443   457788888888877

>smart00638 LPD_N Lipoprotein N-terminal Domain

Probab=90.94  E-value=9.7  Score=32.84  Aligned_cols=120  Identities=9%  Similarity=-0.051  Sum_probs=61.3

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc--cccHHHHHHHHHHHHHhccCccH-------
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL--AHAHQKGLEIHAHVIKYGHLHDI-------  101 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~--~~~~~~a~~~~~~m~~~g~~~~~-------  101 (209)
                      ...+..+++++...|......-+.+.+....+ ++...-..+..+...  .-..+....+++.+......+..       
T Consensus       340 ~~~r~~~~Dal~~~GT~~a~~~i~~~i~~~~~-~~~ea~~~~~~~~~~~~~Pt~~~l~~l~~l~~~~~~~~~~~l~~sa~  418 (574)
T smart00638      340 KKARRIFLDAVAQAGTPPALKFIKQWIKNKKI-TPLEAAQLLAVLPHTARYPTEEILKALFELAESPEVQKQPYLRESAL  418 (574)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhhhcCCHHHHHHHHHHhcCccccccHHHHHHHH
Confidence            45777788888888886555555555555444 333333334443333  33444444444444434444443       


Q ss_pred             hHHHHHHHHHHhCCCh------hhHHHHHHhc-----CCCcHhHHHHHHHHHHhCCChHHH
Q 045511          102 FIQNSLLHFYVTVKDI------FSAHQIFNSV-----VFPDVVTWTTIISGLSKCGFHKEA  151 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~------~~a~~~~~~~-----~~~~~~~~~~li~~~~~~g~~~~a  151 (209)
                      .++.++++-+|.....      ++..+.+.+.     .+.|..--...|+++++.|.....
T Consensus       419 l~~~~lv~~~c~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~LkaLGN~g~~~~i  479 (574)
T smart00638      419 LAYGSLVRRYCVNTPSCPDFVLEELLKYLHELLQQAVSKGDEEEIQLYLKALGNAGHPSSI  479 (574)
T ss_pred             HHHHHHHHHHhcCCCCCChhhHHHHHHHHHHHHHHHHhcCCchheeeHHHhhhccCChhHH
Confidence            4566677656655432      2232222221     122333335567777777775554

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=90.64  E-value=7  Score=30.72  Aligned_cols=122  Identities=16%  Similarity=0.178  Sum_probs=78.1

Q ss_pred             ccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc--c----ccHHHHHHHHHHHHHhcc---CccHhHHHHHHHHHHhCCCh
Q 045511           47 PQNAIPLYNKMLNCPSSYNHYTFTQALKACSL--A----HAHQKGLEIHAHVIKYGH---LHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        47 ~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~--~----~~~~~a~~~~~~m~~~g~---~~~~~~~~~ll~~~~~~g~~  117 (209)
                      +++...+++.|.+.|+.-+..+|-+.......  .    .....+.++|+.|++...   .++-.++..|+..  ...++
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            45677889999999999998888775444433  2    235678999999998863   4555677777665  33333


Q ss_pred             ----hhHHHHHHhcC-----CCcHhHHHHHHHHHHhCCC---hHHHHHHHhhC---CCCCCHHhHHHH
Q 045511          118 ----FSAHQIFNSVV-----FPDVVTWTTIISGLSKCGF---HKEAIDMFCGI---DVKPNANTLVSV  170 (209)
Q Consensus       118 ----~~a~~~~~~~~-----~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m---~~~p~~~t~~~l  170 (209)
                          +.++++|+.+.     +.|..-+-+-+-+++....   ..++.++++.+   |+++....|..+
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence                45566666652     3344444444444444333   33577777777   777766666544

>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=90.58  E-value=5  Score=28.89  Aligned_cols=58  Identities=5%  Similarity=-0.005  Sum_probs=26.9

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccH--hHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI--FIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~--~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      +..+...|++.|+.+.|.+.|..+.+....+..  ..+-.+|......+++..+.....+
T Consensus        39 ~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~k   98 (177)
T PF10602_consen   39 LEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEK   98 (177)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            444444455555555555555555444333322  2344444555555554444444433

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.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=90.39  E-value=6.6  Score=29.99  Aligned_cols=161  Identities=19%  Similarity=0.102  Sum_probs=109.9

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCC--CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCP--SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g--~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      .-|+.-+. -.+.|++++|.+.|+.+..+-  -+....+--.++.++-+.++++.|...++...+.-....-.-|-.-|.
T Consensus        36 ~LY~~g~~-~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~Ylk  114 (254)
T COG4105          36 ELYNEGLT-ELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLK  114 (254)
T ss_pred             HHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHH
Confidence            45555444 567899999999999998753  233557777888899999999999999998887654444455666666


Q ss_pred             HHHhC-------CChhhHHHHHHhc-------CC----CcHh----------H-H-HHHHHHHHhCCChHHHHHHHhhC-
Q 045511          110 FYVTV-------KDIFSAHQIFNSV-------VF----PDVV----------T-W-TTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus       110 ~~~~~-------g~~~~a~~~~~~~-------~~----~~~~----------~-~-~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      +++..       .|...+.+-|..+       |.    +|..          . + -.+-+-|.+.|.+..|..-+++| 
T Consensus       115 gLs~~~~i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~  194 (254)
T COG4105         115 GLSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVL  194 (254)
T ss_pred             HHHHhccCCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence            66543       3344445555444       11    2221          1 1 23347788999999999999999 


Q ss_pred             CCCCCH----HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          159 DVKPNA----NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       159 ~~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .--|++    ...-.+..+|...|-.++|...-+-+..+
T Consensus       195 e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         195 ENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             hccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            223333    45677788899999999888876655444

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

Probab=90.32  E-value=1.4  Score=28.53  Aligned_cols=71  Identities=14%  Similarity=0.087  Sum_probs=41.0

Q ss_pred             HHHHHHHHhCCChH--HHHHHHhhC---CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhh
Q 045511          136 TTIISGLSKCGFHK--EAIDMFCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD  207 (209)
Q Consensus       136 ~~li~~~~~~g~~~--~a~~~~~~m---~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~  207 (209)
                      ++=-..|....+.|  +..+-++.+   .+-|+.....+.+++|-+..|+..|.++|+-++.+ +.+....|.-+++
T Consensus        12 ~ary~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   12 DARYEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHH
T ss_pred             HHHHHHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHH
Confidence            33334444444333  344444444   88899999999999999999999999999776544 3333336665553

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 ....

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

Probab=90.31  E-value=0.6  Score=23.71  Aligned_cols=23  Identities=22%  Similarity=0.221  Sum_probs=10.0

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHh
Q 045511          104 QNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus       104 ~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      |+.|-..|.+.|++++|.+++++
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            34444444444444444444443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=90.30  E-value=2.1  Score=29.59  Aligned_cols=75  Identities=9%  Similarity=-0.042  Sum_probs=42.8

Q ss_pred             HHcCCCccchHHHHHHhhhCC--CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCC
Q 045511           41 LTQSSTPQNAIPLYNKMLNCP--SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVK  115 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g--~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g  115 (209)
                      ..+.|++++|.+.|+.+..+=  -+-....--.++.++-+.+++++|...++...+.....-.+-|-..+.|++.-.
T Consensus        20 ~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~~   96 (142)
T PF13512_consen   20 ALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYYE   96 (142)
T ss_pred             HHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHH
Confidence            345567777777777666542  111224445566666777777777777776666654333445555555554443

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=90.16  E-value=1.7  Score=23.12  Aligned_cols=23  Identities=4%  Similarity=-0.005  Sum_probs=9.7

Q ss_pred             HHHHHhccccHHHHHHHHHHHHH
Q 045511           72 ALKACSLAHAHQKGLEIHAHVIK   94 (209)
Q Consensus        72 ll~~~~~~~~~~~a~~~~~~m~~   94 (209)
                      +-.++...|++++|.++|+...+
T Consensus         7 la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    7 LARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            33344444444444444444443

>PRK15331 chaperone protein SicA; Provisional

Probab=90.10  E-value=2.2  Score=30.25  Aligned_cols=88  Identities=15%  Similarity=0.045  Sum_probs=52.1

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChh
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIF  118 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~  118 (209)
                      ..+-+.|++++|..+|+-+-..+. -|..-+-.|-..+-..++++.|...|......+ .-|+..+=-.-.+|...|+.+
T Consensus        45 y~~y~~Gk~~eA~~~F~~L~~~d~-~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-~~dp~p~f~agqC~l~l~~~~  122 (165)
T PRK15331         45 YEFYNQGRLDEAETFFRFLCIYDF-YNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-KNDYRPVFFTGQCQLLMRKAA  122 (165)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCc-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-cCCCCccchHHHHHHHhCCHH
Confidence            334567788888888877776442 222223333333344567777777776554443 233444444556777778888


Q ss_pred             hHHHHHHhcC
Q 045511          119 SAHQIFNSVV  128 (209)
Q Consensus       119 ~a~~~~~~~~  128 (209)
                      .|+..|....
T Consensus       123 ~A~~~f~~a~  132 (165)
T PRK15331        123 KARQCFELVN  132 (165)
T ss_pred             HHHHHHHHHH
Confidence            8887777653

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=89.93  E-value=3.4  Score=31.97  Aligned_cols=92  Identities=8%  Similarity=0.047  Sum_probs=66.8

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      +-.=|.+++..+++.++..+.-+--+..-+........-|-.|.+.+.+..+.++-...++..-..+..-|.++...|..
T Consensus        86 cvvGIQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl  165 (309)
T PF07163_consen   86 CVVGIQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLL  165 (309)
T ss_pred             hhhhHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHH
Confidence            34457788888899988887655544332333455666677789999999999998888776545555668888777766


Q ss_pred             C-----CChhhHHHHHH
Q 045511          114 V-----KDIFSAHQIFN  125 (209)
Q Consensus       114 ~-----g~~~~a~~~~~  125 (209)
                      +     |.+++|+++..
T Consensus       166 ~VLlPLG~~~eAeelv~  182 (309)
T PF07163_consen  166 HVLLPLGHFSEAEELVV  182 (309)
T ss_pred             HHHhccccHHHHHHHHh
Confidence            4     99999999873

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

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=89.74  E-value=3.2  Score=28.73  Aligned_cols=81  Identities=15%  Similarity=0.053  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhcc--CccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--Cc--HhHHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGH--LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PD--VVTWTTII  139 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~--~~~~~~li  139 (209)
                      ...|..-..+ .+.|++++|.+.|+.+..+-.  +-.....-.|+.+|.+.+++++|...+++..+  |+  ..-|--.+
T Consensus        11 ~~ly~~a~~~-l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~   89 (142)
T PF13512_consen   11 QELYQEAQEA-LQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYM   89 (142)
T ss_pred             HHHHHHHHHH-HHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            3444444444 477888888888888876631  12345666788888888888888888888732  21  24566666


Q ss_pred             HHHHhCCC
Q 045511          140 SGLSKCGF  147 (209)
Q Consensus       140 ~~~~~~g~  147 (209)
                      .|++.-..
T Consensus        90 ~gL~~~~~   97 (142)
T PF13512_consen   90 RGLSYYEQ   97 (142)
T ss_pred             HHHHHHHH
Confidence            66655433

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.58  E-value=9.5  Score=30.61  Aligned_cols=146  Identities=5%  Similarity=-0.054  Sum_probs=101.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhC-CCCCCH--HHHH--HHHHHHhcccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNC-PSSYNH--YTFT--QALKACSLAHA   81 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-g~~p~~--~t~~--~ll~~~~~~~~   81 (209)
                      -+|+..+|...++++.+.++  .|..+++-.=.+|.-+|+.+.-...+++.... +  ||.  .+|-  ..--++...|-
T Consensus       115 ~~g~~h~a~~~wdklL~d~P--tDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn--~dlp~~sYv~GmyaFgL~E~g~  190 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDDYP--TDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWN--ADLPCYSYVHGMYAFGLEECGI  190 (491)
T ss_pred             ccccccHHHHHHHHHHHhCc--hhhhhhhhhhhHHHhccchhhhhhHHHHhccccC--CCCcHHHHHHHHHHhhHHHhcc
Confidence            56777888888888877753  36688888889999999999999999888653 2  333  2332  33333456688


Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC----CcH----hHHHHHHHHHHhCCChHHHHH
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF----PDV----VTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~----~~~----~~~~~li~~~~~~g~~~~a~~  153 (209)
                      ++.|++.-+.-.+-+ +.|...-.+..+.+--+|++.++.+...+-..    .+.    --|+.- -.+...+.++.|++
T Consensus       191 y~dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~A-l~~iE~aeye~ale  268 (491)
T KOG2610|consen  191 YDDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTA-LFHIEGAEYEKALE  268 (491)
T ss_pred             chhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHH-HhhhcccchhHHHH
Confidence            888888777666654 55677778888888899999999998876532    111    112222 23445588999999


Q ss_pred             HHhhC
Q 045511          154 MFCGI  158 (209)
Q Consensus       154 ~~~~m  158 (209)
                      +|++=
T Consensus       269 IyD~e  273 (491)
T KOG2610|consen  269 IYDRE  273 (491)
T ss_pred             HHHHH
Confidence            99653

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

Probab=89.48  E-value=2.1  Score=35.84  Aligned_cols=70  Identities=11%  Similarity=-0.005  Sum_probs=40.4

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCC-CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc-HhHHHHHHH
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSS-YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD-IFIQNSLLH  109 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~  109 (209)
                      ++-+.|+.++|.+.+++|.+..-. -+......++.++...+.+.++..++....+...+.+ ..+|+..+-
T Consensus       268 CarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALL  339 (539)
T PF04184_consen  268 CARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALL  339 (539)
T ss_pred             HHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHH
Confidence            334557777777777777654311 2334566677777777777777777766654332222 345665443

The molecular function of this protein is uncertain.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.47  E-value=7.8  Score=29.79  Aligned_cols=90  Identities=20%  Similarity=0.283  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHhCCChhhHHHHHHhcCC--Cc----HhHHHHHHHHHHhCCChHHHHHHHhhC----CCCCCH-HhHHHHH
Q 045511          103 IQNSLLHFYVTVKDIFSAHQIFNSVVF--PD----VVTWTTIISGLSKCGFHKEAIDMFCGI----DVKPNA-NTLVSVL  171 (209)
Q Consensus       103 ~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~----~~~~~~li~~~~~~g~~~~a~~~~~~m----~~~p~~-~t~~~li  171 (209)
                      .|+.-+..| +.|++.+|+..|....+  |+    .-.+==|-.++...|++++|-.+|..+    +-.|-. .++--+-
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            688888765 55669999999988832  21    223334678999999999999999999    222222 4555566


Q ss_pred             HHhccccchhHHHHHHHHHHHh
Q 045511          172 SACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       172 ~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ....+.|+.++|..+|+.+.+.
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHH
Confidence            6677899999999999999877

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=89.37  E-value=0.94  Score=24.12  Aligned_cols=17  Identities=18%  Similarity=0.188  Sum_probs=6.2

Q ss_pred             HHHhCCChHHHHHHHhh
Q 045511          141 GLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       141 ~~~~~g~~~~a~~~~~~  157 (209)
                      .|.+.|++++|.++|++
T Consensus        10 ~~~~~G~~~~A~~~~~~   26 (44)
T PF13428_consen   10 AYRRLGQPDEAERLLRR   26 (44)
T ss_pred             HHHHcCCHHHHHHHHHH
Confidence            33333333333333333

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=89.30  E-value=4.2  Score=26.14  Aligned_cols=58  Identities=16%  Similarity=0.147  Sum_probs=41.8

Q ss_pred             hHHHHHHHhhC---CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          148 HKEAIDMFCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       148 ~~~a~~~~~~m---~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                      .-++.+-++.+   .+-|+.....+.+++|-+..|+..|..+++-++.+ +..+...|..++
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~l   83 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYIL   83 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHH
Confidence            33445555555   88899999999999999999999999999877633 222444565554

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.

>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=89.27  E-value=6.5  Score=28.30  Aligned_cols=96  Identities=10%  Similarity=0.059  Sum_probs=65.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH--HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH--YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..+..+...|++.|+.+.|.+.|.++.+....|..  ..+-.+|....-.+++..+...+......--.++.....+=++
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            78899999999999999999999999987665544  3456667777888898888888766654432222221111111


Q ss_pred             -----HHHhCCChhhHHHHHHhc
Q 045511          110 -----FYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       110 -----~~~~~g~~~~a~~~~~~~  127 (209)
                           .+...+++.+|-+.|-+.
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~  139 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDS  139 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHcc
Confidence                 123356777777776554

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.

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=88.63  E-value=12  Score=30.64  Aligned_cols=94  Identities=14%  Similarity=0.080  Sum_probs=45.8

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhc-----CCCcHh--HHHHHHHHHHh---CCChHHHHHHHhhC-CCCCCHHh-HH
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSV-----VFPDVV--TWTTIISGLSK---CGFHKEAIDMFCGI-DVKPNANT-LV  168 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~-----~~~~~~--~~~~li~~~~~---~g~~~~a~~~~~~m-~~~p~~~t-~~  168 (209)
                      ...+.+.+...|..|+++.|.++.+.-     .+++..  .--.|+.+-+.   .-+...|...-.+- .+.||.+. -.
T Consensus       188 ~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pdlvPaav  267 (531)
T COG3898         188 PWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVPAAV  267 (531)
T ss_pred             chHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCccchHHH
Confidence            455667777777777777777777643     122221  11122211111   11233333333222 44455432 22


Q ss_pred             HHHHHhccccchhHHHHHHHHHHHhc
Q 045511          169 SVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       169 ~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .--+++.+.|++.++-.+++.+=+..
T Consensus       268 ~AAralf~d~~~rKg~~ilE~aWK~e  293 (531)
T COG3898         268 VAARALFRDGNLRKGSKILETAWKAE  293 (531)
T ss_pred             HHHHHHHhccchhhhhhHHHHHHhcC
Confidence            23455666677777777766665553

>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat

Probab=88.50  E-value=4.3  Score=25.46  Aligned_cols=67  Identities=10%  Similarity=0.089  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHH
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  153 (209)
                      +.++++.+.+.|+ .+..-.+.+-..=-+.|+.+.|.++++.++ .....|+..++++-..|+.+.|.+
T Consensus        21 ~~~v~d~ll~~~i-lT~~d~e~I~aa~~~~g~~~~ar~LL~~L~-rg~~aF~~Fl~aLreT~~~~LA~e   87 (88)
T cd08819          21 TRDVCDKCLEQGL-LTEEDRNRIEAATENHGNESGARELLKRIV-QKEGWFSKFLQALRETEHHELARE   87 (88)
T ss_pred             HHHHHHHHHhcCC-CCHHHHHHHHHhccccCcHHHHHHHHHHhc-cCCcHHHHHHHHHHHcCchhhhhc
Confidence            5566777777773 223333333333346688888999998888 777888889998888888776643

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

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

Probab=88.49  E-value=2.7  Score=35.33  Aligned_cols=100  Identities=13%  Similarity=0.088  Sum_probs=77.5

Q ss_pred             HHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--Cc-HhHHHHHHHHHHhCCChHH
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PD-VVTWTTIISGLSKCGFHKE  150 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~g~~~~  150 (209)
                      ++.+..|+++.|...|-+-..-. ++|.+.|+.=..+|++.|++++|.+-=.+-++  |+ ...|+-.=-++.-.|++++
T Consensus        10 naa~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   10 NAAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDWAKGYSRKGAALFGLGDYEE   88 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCchhhHHHHhHHHHHhcccHHH
Confidence            34567899999999998887765 45888999999999999999998876665543  44 3478888888888999999


Q ss_pred             HHHHHhhC-CCCCCH-HhHHHHHHHh
Q 045511          151 AIDMFCGI-DVKPNA-NTLVSVLSAC  174 (209)
Q Consensus       151 a~~~~~~m-~~~p~~-~t~~~li~~~  174 (209)
                      |+.-|.+= ...||. ..++.+..++
T Consensus        89 A~~ay~~GL~~d~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   89 AILAYSEGLEKDPSNKQLKTGLAQAY  114 (539)
T ss_pred             HHHHHHHHhhcCCchHHHHHhHHHhh
Confidence            99999885 445544 4566666666

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

Probab=88.39  E-value=1.1  Score=23.08  Aligned_cols=25  Identities=16%  Similarity=0.114  Sum_probs=14.8

Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHh
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      .+++.|-..|...|++++|++++++
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~   27 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEE   27 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHH
Confidence            3556666666666666666666654

>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=88.15  E-value=5.3  Score=28.24  Aligned_cols=51  Identities=12%  Similarity=0.061  Sum_probs=22.9

Q ss_pred             cCCCccchHHHHHHhhhCC-CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           43 QSSTPQNAIPLYNKMLNCP-SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        43 ~~g~~~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      +.++.+++..++.-++-.. -.|...++..++  +...|++.+|..+|+.+.+.
T Consensus        22 ~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l--~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   22 RLGDPDDAEALLDALRVLRPEFPELDLFDGWL--HIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             ccCChHHHHHHHHHHHHhCCCchHHHHHHHHH--HHHhCCHHHHHHHHHHHhcc
Confidence            3445555555555554421 112222333322  23455555555555555443

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=88.14  E-value=7.3  Score=27.49  Aligned_cols=161  Identities=15%  Similarity=0.066  Sum_probs=94.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHH-HHhccccHHHHHHHHHHHHHhcc--CccHhHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALK-ACSLAHAHQKGLEIHAHVIKYGH--LHDIFIQNSLL  108 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~-~~~~~~~~~~a~~~~~~m~~~g~--~~~~~~~~~ll  108 (209)
                      ..+..........++...+...+.........+. ........ .+...|+++.+...+........  ......+....
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  174 (291)
T COG0457          96 EALLNLGLLLEALGKYEEALELLEKALALDPDPD-LAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALG  174 (291)
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCcc-hHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhh
Confidence            5555555666666677777777777766443331 22222222 66777888888888777754221  12333444444


Q ss_pred             HHHHhCCChhhHHHHHHhcCC---C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhH
Q 045511          109 HFYVTVKDIFSAHQIFNSVVF---P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKL  182 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~~---~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~  182 (209)
                      ..+...++.+.+...+.....   . ....+..+-..+...++++.+...+... ...|+ ...+..+...+...|..+.
T Consensus       175 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (291)
T COG0457         175 ALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEE  254 (291)
T ss_pred             hHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHH
Confidence            446677778888777777632   2 3456677777777777778887777777 55554 3333333333335556677


Q ss_pred             HHHHHHHHHHh
Q 045511          183 GKAIHAHSLRN  193 (209)
Q Consensus       183 a~~~~~~~~~~  193 (209)
                      +...+....+.
T Consensus       255 ~~~~~~~~~~~  265 (291)
T COG0457         255 ALEALEKALEL  265 (291)
T ss_pred             HHHHHHHHHHh
Confidence            76666655443

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=87.39  E-value=16  Score=30.72  Aligned_cols=125  Identities=10%  Similarity=0.091  Sum_probs=83.9

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCcc------HhHHHHHHHHHHhC----CChhhHHHHHHhcCC--CcHhHHH
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHD------IFIQNSLLHFYVTV----KDIFSAHQIFNSVVF--PDVVTWT  136 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~------~~~~~~ll~~~~~~----g~~~~a~~~~~~~~~--~~~~~~~  136 (209)
                      +..+++..+=.|+-+.+.+.+..-.+.+--..      ...|...+..++..    ...+.|+++++.+.+  |+...|.
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~yP~s~lfl  270 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRYPNSALFL  270 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhCCCcHHHH
Confidence            45556666777888888888877655431122      23466666655554    577899999999954  8877776


Q ss_pred             HHH-HHHHhCCChHHHHHHHhhC-CCCC-----CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          137 TII-SGLSKCGFHKEAIDMFCGI-DVKP-----NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       137 ~li-~~~~~~g~~~~a~~~~~~m-~~~p-----~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ..- +.+...|++++|.+.|++. ..+.     ....+--+.-.+.-..++++|.+.|..+.+.
T Consensus       271 ~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~  334 (468)
T PF10300_consen  271 FFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKE  334 (468)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhc
Confidence            554 5556689999999999976 1111     1122223333455678999999999988765

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.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=87.38  E-value=19  Score=32.01  Aligned_cols=123  Identities=13%  Similarity=0.042  Sum_probs=88.7

Q ss_pred             HHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCC-cHhHHHHHHHHHHhCC
Q 045511           70 TQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFP-DVVTWTTIISGLSKCG  146 (209)
Q Consensus        70 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~-~~~~~~~li~~~~~~g  146 (209)
                      ...-..+.+.+..+++...+.+..+.- +.....|.-.-..+...|..++|.+.|...  ..| ++...+++-..+.+.|
T Consensus       654 llaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~hv~s~~Ala~~lle~G  732 (799)
T KOG4162|consen  654 LLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPDHVPSMTALAELLLELG  732 (799)
T ss_pred             HHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC
Confidence            344455566666666665555544332 344556666667777888999999998876  345 4667888899999999


Q ss_pred             ChHHHHH--HHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          147 FHKEAID--MFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       147 ~~~~a~~--~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +...|..  ++.++ .+.|+- ..|-.+-......|+.+.|.+-|+-..+-
T Consensus       733 ~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  733 SPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             CcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhh
Confidence            8877777  88888 777754 67888888899999999999988865443

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=87.17  E-value=9.3  Score=31.12  Aligned_cols=91  Identities=9%  Similarity=0.023  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHhHH-HHHHHHHH
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVVTW-TTIISGLS  143 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~~~-~~li~~~~  143 (209)
                      .++..+.-.+.+.+++..|.+.=+..++.. ++|....=.=-.+|...|+++.|+..|..+  .+|+...- +-++..--
T Consensus       258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~  336 (397)
T KOG0543|consen  258 ACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQ  336 (397)
T ss_pred             HHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            345555666667777777777766666654 455555545556677777777777777776  23443333 33333333


Q ss_pred             hCCChH-HHHHHHhhC
Q 045511          144 KCGFHK-EAIDMFCGI  158 (209)
Q Consensus       144 ~~g~~~-~a~~~~~~m  158 (209)
                      +..... ...++|+.|
T Consensus       337 k~~~~~~kekk~y~~m  352 (397)
T KOG0543|consen  337 KIREYEEKEKKMYANM  352 (397)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            333322 335666666

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=86.99  E-value=8.4  Score=26.93  Aligned_cols=18  Identities=11%  Similarity=0.205  Sum_probs=9.1

Q ss_pred             HHhCCChhhHHHHHHhcC
Q 045511          111 YVTVKDIFSAHQIFNSVV  128 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~  128 (209)
                      +..+|++++|.++|++..
T Consensus        54 ~i~rg~w~eA~rvlr~l~   71 (153)
T TIGR02561        54 LIARGNYDEAARILRELL   71 (153)
T ss_pred             HHHcCCHHHHHHHHHhhh
Confidence            344555555555555553

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>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=86.72  E-value=2.7  Score=34.97  Aligned_cols=113  Identities=12%  Similarity=0.021  Sum_probs=80.1

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      -.....+.|+++.|.++-++.      .+...|..|-....+.|+++.|++.|....         -+..|+-.|.-.|+
T Consensus       324 rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~---------d~~~L~lLy~~~g~  388 (443)
T PF04053_consen  324 RFELALQLGNLDIALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAK---------DFSGLLLLYSSTGD  388 (443)
T ss_dssp             HHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-
T ss_pred             HhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhc---------CccccHHHHHHhCC
Confidence            344566788888888775443      377899999999999999999999987654         36678888888999


Q ss_pred             hhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHh
Q 045511          117 IFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANT  166 (209)
Q Consensus       117 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t  166 (209)
                      .+.-.++-+.....  .-+|..+.++...|+.++..+++.+-|..|-+..
T Consensus       389 ~~~L~kl~~~a~~~--~~~n~af~~~~~lgd~~~cv~lL~~~~~~~~A~~  436 (443)
T PF04053_consen  389 REKLSKLAKIAEER--GDINIAFQAALLLGDVEECVDLLIETGRLPEAAL  436 (443)
T ss_dssp             HHHHHHHHHHHHHT--T-HHHHHHHHHHHT-HHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHHHHHHHHHHc--cCHHHHHHHHHHcCCHHHHHHHHHHcCCchHHHH
Confidence            88877777654322  2266666777778999999988888655554443

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.

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=86.57  E-value=13  Score=28.77  Aligned_cols=157  Identities=12%  Similarity=0.035  Sum_probs=81.7

Q ss_pred             HcCCCccchHHHHHHhhhCC--CCCCH------HHHHHHHHHHhccccHHHHHHHHHHHHHh--------ccCcc-----
Q 045511           42 TQSSTPQNAIPLYNKMLNCP--SSYNH------YTFTQALKACSLAHAHQKGLEIHAHVIKY--------GHLHD-----  100 (209)
Q Consensus        42 ~~~g~~~~a~~l~~~m~~~g--~~p~~------~t~~~ll~~~~~~~~~~~a~~~~~~m~~~--------g~~~~-----  100 (209)
                      .+.|+.+.|..++.+....-  ..|+.      ..|+.-...+.+..+++.|..+++.-.+-        ...|+     
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            35677777887777776543  22222      12333334433333666666655443322        12232     


Q ss_pred             HhHHHHHHHHHHhCCChhhHHH---HHHhcC--CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHH
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQ---IFNSVV--FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLS  172 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~---~~~~~~--~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~  172 (209)
                      ..++..++.+|...+..+...+   +++.+.  -|+ ..++-.-|+.+.+.++.+.+.+++.+|  .+.-....+..++.
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~  163 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILH  163 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHH
Confidence            2366777777777776554444   444441  133 344444555565677888888888888  33323334444444


Q ss_pred             Hh---ccccchhHHHHHHHHHHHhccCCCc
Q 045511          173 AC---SSLGSRKLGKAIHAHSLRNLNENNI  199 (209)
Q Consensus       173 ~~---~~~g~~~~a~~~~~~~~~~~~~p~~  199 (209)
                      .+   ... ....+...+..+....+.|..
T Consensus       164 ~i~~l~~~-~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  164 HIKQLAEK-SPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHHhh-CcHHHHHHHHHHHHHHhCCCh
Confidence            43   332 233455555555555555544

It is also involved in sporulation [].

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=86.12  E-value=18  Score=29.78  Aligned_cols=161  Identities=14%  Similarity=0.041  Sum_probs=81.6

Q ss_pred             CCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHHH--HHHHH-------------------------------
Q 045511           29 PQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHYT--FTQAL-------------------------------   73 (209)
Q Consensus        29 p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~t--~~~ll-------------------------------   73 (209)
                      |.. =.+.+.+...|..|+++.|+++++.-+... +.+|+.-  =..|+                               
T Consensus       185 p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pdlvP  264 (531)
T COG3898         185 PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVP  264 (531)
T ss_pred             cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCccch
Confidence            444 567889999999999999999998876643 3344322  12222                               


Q ss_pred             ------HHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhH--H--HHHHhcCCCcHhHHHHHHHHHH
Q 045511           74 ------KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSA--H--QIFNSVVFPDVVTWTTIISGLS  143 (209)
Q Consensus        74 ------~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a--~--~~~~~~~~~~~~~~~~li~~~~  143 (209)
                            .++.+.|++.++-.+++.+-+....|++.    .+..+.+.|+....  .  +-+..|...+..+--.+..+-.
T Consensus       265 aav~AAralf~d~~~rKg~~ilE~aWK~ePHP~ia----~lY~~ar~gdta~dRlkRa~~L~slk~nnaes~~~va~aAl  340 (531)
T COG3898         265 AAVVAARALFRDGNLRKGSKILETAWKAEPHPDIA----LLYVRARSGDTALDRLKRAKKLESLKPNNAESSLAVAEAAL  340 (531)
T ss_pred             HHHHHHHHHHhccchhhhhhHHHHHHhcCCChHHH----HHHHHhcCCCcHHHHHHHHHHHHhcCccchHHHHHHHHHHH
Confidence                  22333344444444444444433222221    12223333332211  1  1123333334444444555555


Q ss_pred             hCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhc-cccchhHHHHHHHHHHHh
Q 045511          144 KCGFHKEAIDMFCGI-DVKPNANTLVSVLSACS-SLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~-~~g~~~~a~~~~~~~~~~  193 (209)
                      ..|++..|..--... ...|....|-.|-..-. .-||-.++.+.+.+..+.
T Consensus       341 da~e~~~ARa~Aeaa~r~~pres~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         341 DAGEFSAARAKAEAAAREAPRESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             hccchHHHHHHHHHHhhhCchhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            556655544333333 44666666655555443 336666666666555444

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.98  E-value=11  Score=27.29  Aligned_cols=125  Identities=10%  Similarity=0.039  Sum_probs=82.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHH--HHHHhccccHHHHHHHHHHHHHhccCccHh-HHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQA--LKACSLAHAHQKGLEIHAHVIKYGHLHDIF-IQNSLL  108 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~l--l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~ll  108 (209)
                      ..|-.-+. +++.+..++|+.-|..+.+.|.. +-..+..+  -......|+...|...|+++-...-.|-+. -...|=
T Consensus        60 d~flaAL~-lA~~~k~d~Alaaf~~lektg~g-~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlr  137 (221)
T COG4649          60 DAFLAALK-LAQENKTDDALAAFTDLEKTGYG-SYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLR  137 (221)
T ss_pred             HHHHHHHH-HHHcCCchHHHHHHHHHHhcCCC-cchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHH
Confidence            44544444 56778889999999999988753 22223332  233466788889999999998776555444 223333


Q ss_pred             H--HHHhCCChhhHHHHHHhcCCC-c---HhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          109 H--FYVTVKDIFSAHQIFNSVVFP-D---VVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       109 ~--~~~~~g~~~~a~~~~~~~~~~-~---~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .  .+..+|.+++...-.+-+..+ +   ...-..|--+-.+.|++.+|.+.|..+
T Consensus       138 aa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qi  193 (221)
T COG4649         138 AAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQI  193 (221)
T ss_pred             HHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHH
Confidence            3  345678888888888777432 1   233445555666889999999999888

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

Probab=85.61  E-value=13  Score=31.44  Aligned_cols=67  Identities=6%  Similarity=0.109  Sum_probs=44.5

Q ss_pred             HHhccccHHHHHHHHHHHHHhccC-ccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-----CcHhHHHHHHHH
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHL-HDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----PDVVTWTTIISG  141 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~~~~~~~~li~~  141 (209)
                      .+-+.|+.++|.+.+.+|.+.... -+..+...|+.++...++++++..++.+-.+     .-...|+..+-.
T Consensus       268 CarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLk  340 (539)
T PF04184_consen  268 CARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLK  340 (539)
T ss_pred             HHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHH
Confidence            345668888888888887654322 2345777888888888888888888766532     234567766543

The molecular function of this protein is uncertain.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=85.57  E-value=26  Score=31.19  Aligned_cols=125  Identities=10%  Similarity=0.044  Sum_probs=95.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|...-..+.+.++.++|..-+.+..+.. +-.+..|...=..+...|..++|.+.|..-..-. +-++.+.+++-.++
T Consensus       651 ~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ld-P~hv~s~~Ala~~l  728 (799)
T KOG4162|consen  651 KLWLLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLLLEVKGQLEEAKEAFLVALALD-PDHVPSMTALAELL  728 (799)
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcC-CCCcHHHHHHHHHH
Confidence            345566677778888888887777776643 3455666666666777888899999888776543 23456888999999


Q ss_pred             HhCCChhhHHH--HHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          112 VTVKDIFSAHQ--IFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       112 ~~~g~~~~a~~--~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .+.|+...|..  ++.++.+   .+...|--+=..+-+.|+.++|-+.|+.-
T Consensus       729 le~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa  780 (799)
T KOG4162|consen  729 LELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAA  780 (799)
T ss_pred             HHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHH
Confidence            99998888887  8877743   46788989999999999999999999876

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=85.48  E-value=1.9  Score=21.61  Aligned_cols=22  Identities=23%  Similarity=0.209  Sum_probs=12.7

Q ss_pred             cHhHHHHHHHHHHhCCChhhHH
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAH  121 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~  121 (209)
                      |...|+.+-..|...|+.++|+
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            4455666666666666665554

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=85.42  E-value=19  Score=29.66  Aligned_cols=125  Identities=10%  Similarity=0.005  Sum_probs=71.8

Q ss_pred             ccHHHHHHHHHc--CCCccchHHHHHHhhhCCCCCCHHHHHHHHH---HH----------hccccHHHHHHHHHHHHHh-
Q 045511           32 HILNTLLKLLTQ--SSTPQNAIPLYNKMLNCPSSYNHYTFTQALK---AC----------SLAHAHQKGLEIHAHVIKY-   95 (209)
Q Consensus        32 ~~~~~li~~~~~--~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~---~~----------~~~~~~~~a~~~~~~m~~~-   95 (209)
                      ..+..++++.+-  +++.+.+...|++-.+.+  |+...-..+-.   .|          .+.|.+..|.+.+.+-+.. 
T Consensus       202 n~~al~vrg~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~id  279 (486)
T KOG0550|consen  202 NAEALYVRGLCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNID  279 (486)
T ss_pred             hhHHHHhcccccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCC
Confidence            344444444442  355556666665555533  55444333222   21          4567788888888777644 


Q ss_pred             --ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhH-HHHH--HHHHHhCCChHHHHHHHhhC
Q 045511           96 --GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVT-WTTI--ISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        96 --g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~l--i~~~~~~g~~~~a~~~~~~m  158 (209)
                        .+.|+...|...-....+.|+.++|..--++....|..- .--+  -.++...++|++|.+-|...
T Consensus       280 P~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~syikall~ra~c~l~le~~e~AV~d~~~a  347 (486)
T KOG0550|consen  280 PSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKA  347 (486)
T ss_pred             ccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              355667777777778888888888887777665544322 2222  23344456677776666554

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

Probab=85.39  E-value=1.3  Score=21.73  Aligned_cols=17  Identities=18%  Similarity=0.270  Sum_probs=6.1

Q ss_pred             HHHHhCCChHHHHHHHh
Q 045511          140 SGLSKCGFHKEAIDMFC  156 (209)
Q Consensus       140 ~~~~~~g~~~~a~~~~~  156 (209)
                      ..|...|++++|+..|+
T Consensus         9 ~~~~~~~~~~~A~~~~~   25 (34)
T PF00515_consen    9 NAYFQLGDYEEALEYYQ   25 (34)
T ss_dssp             HHHHHTT-HHHHHHHHH
T ss_pred             HHHHHhCCchHHHHHHH
Confidence            33333333333333333

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 ....

>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=84.88  E-value=1.5  Score=29.92  Aligned_cols=30  Identities=20%  Similarity=0.330  Sum_probs=16.9

Q ss_pred             CCCccchHHHHHHhhhCCCCCCHHHHHHHHHH
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKA   75 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~   75 (209)
                      .|.-.+|..+|++|.+.|-+||.  |+.|+..
T Consensus       108 ygsk~DaY~VF~kML~~G~pPdd--W~~Ll~~  137 (140)
T PF11663_consen  108 YGSKTDAYAVFRKMLERGNPPDD--WDALLKE  137 (140)
T ss_pred             hccCCcHHHHHHHHHhCCCCCcc--HHHHHHH
Confidence            35555666666666666665552  4444443

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 [].

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

Probab=84.71  E-value=13  Score=31.40  Aligned_cols=136  Identities=12%  Similarity=0.088  Sum_probs=87.7

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHH-------------------------HHHHHhccccHHHHHHHHHHHHH
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQ-------------------------ALKACSLAHAHQKGLEIHAHVIK   94 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~-------------------------ll~~~~~~~~~~~a~~~~~~m~~   94 (209)
                      ++.+.++.+.+...|.+-...--.||..+=..                         =-+.+-+.|++..|..-|.++.+
T Consensus       307 a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIk  386 (539)
T KOG0548|consen  307 AYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIK  386 (539)
T ss_pred             hhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHh
Confidence            45555677777777766554433333322000                         02334566888888888888887


Q ss_pred             hccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHh---HHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHH
Q 045511           95 YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVV---TWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSV  170 (209)
Q Consensus        95 ~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~l  170 (209)
                      .. +-|...|...--+|.+.|.+..|.+--+...+.|..   .|.-=-.++..-.++++|.+.|.+- ...|+..-+..-
T Consensus       387 r~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale~dp~~~e~~~~  465 (539)
T KOG0548|consen  387 RD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALELDPSNAEAIDG  465 (539)
T ss_pred             cC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhHHHHHH
Confidence            76 667788999999999999998888876666543333   2333334444456788888888886 666666666655


Q ss_pred             HHHhcc
Q 045511          171 LSACSS  176 (209)
Q Consensus       171 i~~~~~  176 (209)
                      +.-|..
T Consensus       466 ~~rc~~  471 (539)
T KOG0548|consen  466 YRRCVE  471 (539)
T ss_pred             HHHHHH
Confidence            666655

>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=84.37  E-value=2.2  Score=19.78  Aligned_cols=17  Identities=12%  Similarity=0.077  Sum_probs=7.7

Q ss_pred             HHHHHhCCChhhHHHHH
Q 045511          108 LHFYVTVKDIFSAHQIF  124 (209)
Q Consensus       108 l~~~~~~g~~~~a~~~~  124 (209)
                      -..+...|++++|+.++
T Consensus         8 a~~~~~~G~~~eA~~~l   24 (26)
T PF07721_consen    8 ARALLAQGDPDEAERLL   24 (26)
T ss_pred             HHHHHHcCCHHHHHHHH
Confidence            33444444444444443

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

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

Probab=84.34  E-value=3.9  Score=22.41  Aligned_cols=32  Identities=6%  Similarity=-0.056  Sum_probs=18.6

Q ss_pred             ccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +.|-.+++..+++.|.+.|+..+...+..++.
T Consensus        14 ~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen   14 RRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            44555556666666666666666665555543

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=84.33  E-value=2.2  Score=21.79  Aligned_cols=27  Identities=15%  Similarity=0.183  Sum_probs=18.3

Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      .+++.+-..|...|++++|..++.+..
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            466677777777777777777777653

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.99  E-value=24  Score=31.78  Aligned_cols=138  Identities=14%  Similarity=0.055  Sum_probs=88.7

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhh
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFS  119 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~  119 (209)
                      .+.+.|++++|...|-+-... +.|.     -+|+-|....+...-...++.+.+.|+ .+...-+.|+.+|.+.++.+.
T Consensus       377 ~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kfLdaq~IknLt~YLe~L~~~gl-a~~dhttlLLncYiKlkd~~k  449 (933)
T KOG2114|consen  377 YLYGKGDFDEATDQYIETIGF-LEPS-----EVIKKFLDAQRIKNLTSYLEALHKKGL-ANSDHTTLLLNCYIKLKDVEK  449 (933)
T ss_pred             HHHhcCCHHHHHHHHHHHccc-CChH-----HHHHHhcCHHHHHHHHHHHHHHHHccc-ccchhHHHHHHHHHHhcchHH
Confidence            344678888887776544322 2232     245555666666667777888888885 345556789999999999999


Q ss_pred             HHHHHHhcCCCcHh--HHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHH
Q 045511          120 AHQIFNSVVFPDVV--TWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       120 a~~~~~~~~~~~~~--~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      -.+..+... ....  -....+..+-+.+-.++|..+-...+.  +......++.   ..+++++|.+.++-+
T Consensus       450 L~efI~~~~-~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~--he~vl~ille---~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  450 LTEFISKCD-KGEWFFDVETALEILRKSNYLDEAELLATKFKK--HEWVLDILLE---DLHNYEEALRYISSL  516 (933)
T ss_pred             HHHHHhcCC-CcceeeeHHHHHHHHHHhChHHHHHHHHHHhcc--CHHHHHHHHH---HhcCHHHHHHHHhcC
Confidence            999888766 2222  245667777777777777666555422  3334444433   456788887776643

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

Probab=83.61  E-value=10  Score=25.78  Aligned_cols=40  Identities=15%  Similarity=0.243  Sum_probs=20.1

Q ss_pred             HHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHH
Q 045511           54 YNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVI   93 (209)
Q Consensus        54 ~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~   93 (209)
                      ++.+...++.|+.......+.+|.+.+++..|..+|+.++
T Consensus        72 lN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK  111 (149)
T KOG4077|consen   72 LNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIK  111 (149)
T ss_pred             HHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            3333344445555555555555555555555555555444

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=83.33  E-value=1.5  Score=23.67  Aligned_cols=28  Identities=11%  Similarity=0.168  Sum_probs=19.9

Q ss_pred             HHHHhccccchhHHHHHHHHHHHhccCC
Q 045511          170 VLSACSSLGSRKLGKAIHAHSLRNLNEN  197 (209)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~~~~~~~~p  197 (209)
                      +-++|...|+.+.|.++++++.+.|-.|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~~~~   32 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEGDEA   32 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcCCHH
Confidence            4567778888888888888777655433

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.

>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9

Probab=82.99  E-value=7.2  Score=24.29  Aligned_cols=61  Identities=13%  Similarity=0.146  Sum_probs=36.7

Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHH
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEA  151 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  151 (209)
                      .+++.+.+.|+-    |-.-.=..-+...+.+.|+++++.++..+..+|.+..+++-..|..+.|
T Consensus        20 ~v~~~L~~~~Vl----t~~~~e~I~~~~tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~~~~~LA   80 (84)
T cd08326          20 YLWDHLLSRGVF----TPDMIEEIQAAGSRRDQARQLLIDLETRGKQAFPAFLSALRETGQTDLA   80 (84)
T ss_pred             HHHHHHHhcCCC----CHHHHHHHHcCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCchHHH
Confidence            455666666521    1122222223445677777777777777777777777777777665544

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

>KOG4567 consensus GTPase-activating protein [General function prediction only]

Probab=82.28  E-value=21  Score=28.30  Aligned_cols=79  Identities=10%  Similarity=0.073  Sum_probs=49.7

Q ss_pred             HHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh----------CCChhhH
Q 045511           51 IPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT----------VKDIFSA  120 (209)
Q Consensus        51 ~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----------~g~~~~a  120 (209)
                      .++|+.|+..++.|.-..+.-+.-.+.+.=.+..+..+++.+....-.     |..|+..||.          .|++..-
T Consensus       263 ~EL~~~L~~~~i~PqfyaFRWitLLLsQEF~lpDvi~lWDsl~sD~~r-----fd~Ll~iCcsmlil~Re~il~~DF~~n  337 (370)
T KOG4567|consen  263 EELWRHLEEKEIHPQFYAFRWITLLLSQEFPLPDVIRLWDSLLSDPQR-----FDFLLYICCSMLILVRERILEGDFTVN  337 (370)
T ss_pred             HHHHHHHHhcCCCccchhHHHHHHHHhccCCchhHHHHHHHHhcChhh-----hHHHHHHHHHHHHHHHHHHHhcchHHH
Confidence            456777777777777777777777676666777777777777653322     5556665554          3666666


Q ss_pred             HHHHHhcCCCcHhH
Q 045511          121 HQIFNSVVFPDVVT  134 (209)
Q Consensus       121 ~~~~~~~~~~~~~~  134 (209)
                      .+++..-+..|...
T Consensus       338 mkLLQ~yp~tdi~~  351 (370)
T KOG4567|consen  338 MKLLQNYPTTDISK  351 (370)
T ss_pred             HHHHhcCCCCCHHH
Confidence            66666554444433

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

Probab=82.24  E-value=4.8  Score=22.05  Aligned_cols=38  Identities=13%  Similarity=0.174  Sum_probs=31.3

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHH
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKA   75 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~   75 (209)
                      +....+.|-.+++..++++|.+.|+-.+...|..++..
T Consensus         9 L~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen    9 LLLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            44456778888999999999999998888888887764

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

>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=81.61  E-value=14  Score=27.21  Aligned_cols=67  Identities=13%  Similarity=-0.021  Sum_probs=42.1

Q ss_pred             hhhHHHHHHhcCC----CcHhHHHHHHHHHHhCCChHHHHHHHhhC------CCCCCHHhHHHHHHHhccccchhHHH
Q 045511          117 IFSAHQIFNSVVF----PDVVTWTTIISGLSKCGFHKEAIDMFCGI------DVKPNANTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       117 ~~~a~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~a~~~~~~m------~~~p~~~t~~~li~~~~~~g~~~~a~  184 (209)
                      -++|.+.|-.+..    -+...--.+..-|. ..+.+++..++.+.      +-.+|...+.+|...+.+.|+++.|.
T Consensus       122 d~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  122 DQEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            3455666655521    23344444444443 66777777777666      44677788888888888888887764

>PHA02875 ankyrin repeat protein; Provisional

Probab=81.57  E-value=7.5  Score=31.80  Aligned_cols=151  Identities=11%  Similarity=0.002  Sum_probs=81.1

Q ss_pred             HHHHHHHHcCCCccchHHHHHHhhhCCCCCCHH--HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHh---HHHHHHH
Q 045511           35 NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHY--TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIF---IQNSLLH  109 (209)
Q Consensus        35 ~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~---~~~~ll~  109 (209)
                      .+.+...++.|+.+    +.+.+.+.|..|+..  .....+...+..|+.+.+..++    +.|...+..   .-.+.+.
T Consensus        36 ~tpL~~A~~~~~~~----~v~~Ll~~ga~~~~~~~~~~t~L~~A~~~g~~~~v~~Ll----~~~~~~~~~~~~~g~tpL~  107 (413)
T PHA02875         36 ISPIKLAMKFRDSE----AIKLLMKHGAIPDVKYPDIESELHDAVEEGDVKAVEELL----DLGKFADDVFYKDGMTPLH  107 (413)
T ss_pred             CCHHHHHHHcCCHH----HHHHHHhCCCCccccCCCcccHHHHHHHCCCHHHHHHHH----HcCCcccccccCCCCCHHH
Confidence            34445556666654    445556667655532  1233455556778876654444    444222111   1235566


Q ss_pred             HHHhCCChhhHHHHHHhcCCCcHh--HHHHHHHHHHhCCChHHHHHHHhhCCCCCC---HHhHHHHHHHhccccchhHHH
Q 045511          110 FYVTVKDIFSAHQIFNSVVFPDVV--TWTTIISGLSKCGFHKEAIDMFCGIDVKPN---ANTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~~~~~~--~~~~li~~~~~~g~~~~a~~~~~~m~~~p~---~~t~~~li~~~~~~g~~~~a~  184 (209)
                      ..+..|+.+-+..+++.-..++..  .-.+.+...+..|+.+.+..+++. |..++   ..-.+.+.-++ ..|+.+   
T Consensus       108 ~A~~~~~~~iv~~Ll~~gad~~~~~~~g~tpLh~A~~~~~~~~v~~Ll~~-g~~~~~~d~~g~TpL~~A~-~~g~~e---  182 (413)
T PHA02875        108 LATILKKLDIMKLLIARGADPDIPNTDKFSPLHLAVMMGDIKGIELLIDH-KACLDIEDCCGCTPLIIAM-AKGDIA---  182 (413)
T ss_pred             HHHHhCCHHHHHHHHhCCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHhc-CCCCCCCCCCCCCHHHHHH-HcCCHH---
Confidence            677788888777777765433321  112344555577887776666554 44333   33344444444 456655   


Q ss_pred             HHHHHHHHhccCCCc
Q 045511          185 AIHAHSLRNLNENNI  199 (209)
Q Consensus       185 ~~~~~~~~~~~~p~~  199 (209)
                       +.+.+.+.|..|+.
T Consensus       183 -iv~~Ll~~ga~~n~  196 (413)
T PHA02875        183 -ICKMLLDSGANIDY  196 (413)
T ss_pred             -HHHHHHhCCCCCCc
Confidence             44556677776654

>PF01347 Vitellogenin_N: Lipoprotein amino terminal region; InterPro: IPR001747 This entry represents a conserved region found in several lipid transport proteins, including vitellogenin, microsomal triglyceride transfer protein and apolipoprotein B-100 []

Probab=81.40  E-value=23  Score=30.82  Aligned_cols=159  Identities=11%  Similarity=-0.021  Sum_probs=76.6

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc--ccHHHHHHHHHHHHHhccCcc-------H
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA--HAHQKGLEIHAHVIKYGHLHD-------I  101 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~--~~~~~a~~~~~~m~~~g~~~~-------~  101 (209)
                      ...++.+++++..+|....+.-+.+.+.. +-.++...-..+.......  -..+....+++.+.......+       .
T Consensus       378 ~~~r~~~lDal~~aGT~~av~~i~~~I~~-~~~~~~ea~~~l~~l~~~~~~Pt~e~l~~l~~L~~~~~~~~~~~l~~ta~  456 (618)
T PF01347_consen  378 EQARKIFLDALPQAGTNPAVKFIKDLIKS-KKLTDDEAAQLLASLPFHVRRPTEELLKELFELAKSPKVKNSPYLRETAL  456 (618)
T ss_dssp             HHHHHHHHHHHHHH-SHHHHHHHHHHHHT-T-S-HHHHHHHHHHHHHT-----HHHHHHHHHHHT-HHHHT-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhCccccCChhHHHHHH
Confidence            46889999999999986655555555555 4334444444444443333  222333333333333333332       3


Q ss_pred             hHHHHHHHHHHhCC---------C---hhhHHHHHHh-c----CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC-CC
Q 045511          102 FIQNSLLHFYVTVK---------D---IFSAHQIFNS-V----VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV-KP  162 (209)
Q Consensus       102 ~~~~~ll~~~~~~g---------~---~~~a~~~~~~-~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~-~p  162 (209)
                      .++.++++-+|...         .   .++..+.+.. .    ...|...--..|+++++.|....+..+..-+ +. ..
T Consensus       457 L~~~~lv~~~c~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~LkaLgN~g~~~~i~~l~~~i~~~~~~  536 (618)
T PF01347_consen  457 LSLGSLVHKYCVNSDSAEFCDPCSRCIIEKYVPYLEQELKEAVSRGDEEEKIVYLKALGNLGHPESIPVLLPYIEGKEEV  536 (618)
T ss_dssp             HHHHHHHHHHHTT-----------SS--GGGTHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-GGGHHHHHTTSTTSS-S
T ss_pred             HHHHHHhCceeecccccccccccchhhHHHHHHHHHHHHHHHhhccCHHHHHHHHHHhhccCCchhhHHHHhHhhhcccc
Confidence            46778888888774         1   1111111111 1    2334455567789999999876443333333 33 33


Q ss_pred             CHHhHHHHHHHhc--cccchhHHHHHHHHH
Q 045511          163 NANTLVSVLSACS--SLGSRKLGKAIHAHS  190 (209)
Q Consensus       163 ~~~t~~~li~~~~--~~g~~~~a~~~~~~~  190 (209)
                      +...=...|.++.  ..-..+++.+++-.+
T Consensus       537 ~~~~R~~Ai~Alr~~~~~~~~~v~~~l~~I  566 (618)
T PF01347_consen  537 PHFIRVAAIQALRRLAKHCPEKVREILLPI  566 (618)
T ss_dssp             -HHHHHHHHHTTTTGGGT-HHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhhcCcHHHHHHHHHH
Confidence            4444445566665  333445555555544

Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved. In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40) [, ]. Microsomal triglyceride transfer protein (MTTP) is an endoplasmic reticulum lipid transfer protein involved in the biosynthesis and lipid loading of apolipoprotein B. MTTP is also involved in the late stage of CD1d trafficking in the lysosomal compartment, CD1d being the MHC I-like lipid antigen presenting molecule []. Apolipoprotein B can exist in two forms: B-100 and B-48. Apoliporotein B-100 is present on several lipoproteins, including very low-density lipoproteins (VLDL), intermediate density lipoproteins (IDL) and low density lipoproteins (LDL), and can assemble VLDL particles in the liver []. Apolipoprotein B-100 has been linked to the development of atherosclerosis.; GO: 0005319 lipid transporter activity, 0006869 lipid transport; PDB: 1LSH_A.

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=81.03  E-value=8.8  Score=28.82  Aligned_cols=119  Identities=13%  Similarity=0.108  Sum_probs=73.2

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHH---hcCC---CcHhHHHHHHHH
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFN---SVVF---PDVVTWTTIISG  141 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~---~~~~---~~~~~~~~li~~  141 (209)
                      |.+..++.+.+.+.+.++.....+-.+.. +.|..+-..+++.||-.|++++|..=++   .|..   +....|..+|.+
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            55667778888889999888877776664 5677788889999999999999965554   4422   446678877775


Q ss_pred             HHhCCChHHHHHHHhhC---CCC--CCHHhHHHHHHHh-ccccchhHHHHHHHH-HHHh
Q 045511          142 LSKCGFHKEAIDMFCGI---DVK--PNANTLVSVLSAC-SSLGSRKLGKAIHAH-SLRN  193 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m---~~~--p~~~t~~~li~~~-~~~g~~~~a~~~~~~-~~~~  193 (209)
                      -...      -++|..=   |+.  |...=...++.+. ++.+...++.+-+.+ ..+.
T Consensus        82 ea~R------~evfag~~~Pgflg~p~p~wva~L~aala~h~dg~gea~~alreqal~a  134 (273)
T COG4455          82 EAAR------NEVFAGGAVPGFLGGPSPEWVAALLAALALHSDGAGEARTALREQALKA  134 (273)
T ss_pred             HHHH------HHHhccCCCCCCcCCCCHHHHHHHHHHHhcccCCcchHHHHHHHHHHhh
Confidence            4332      1344332   221  2333334444444 344445555555443 3444

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=80.78  E-value=23  Score=27.11  Aligned_cols=158  Identities=12%  Similarity=0.096  Sum_probs=103.2

Q ss_pred             hhccCCCcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHHHHHHHHHHHhcc----
Q 045511            6 LKSLKPTLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHYTFTQALKACSLA----   79 (209)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~----   79 (209)
                      ++.|+.++|.+.+..+...++..|=. .+-=.++-++-+.++.++|...+++..+.- -.|| .-|..-|.+.+.-    
T Consensus        45 L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n-~dY~~YlkgLs~~~~i~  123 (254)
T COG4105          45 LQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPN-ADYAYYLKGLSYFFQID  123 (254)
T ss_pred             HhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCC-hhHHHHHHHHHHhccCC
Confidence            46788888888888888776554433 555667777889999999999999987643 3444 3355555555432    


Q ss_pred             ---ccHHHHHH---HHHHHHHh----ccCccHhHH------------HHHHHHHHhCCChhhHHHHHHhcCC--C----c
Q 045511           80 ---HAHQKGLE---IHAHVIKY----GHLHDIFIQ------------NSLLHFYVTVKDIFSAHQIFNSVVF--P----D  131 (209)
Q Consensus        80 ---~~~~~a~~---~~~~m~~~----g~~~~~~~~------------~~ll~~~~~~g~~~~a~~~~~~~~~--~----~  131 (209)
                         ++...+.+   -|+.+.++    ...||+..-            ..+-+.|.++|.+..|..-+++|.+  +    .
T Consensus       124 ~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~  203 (254)
T COG4105         124 DVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVLENYPDTSAV  203 (254)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHhccccccch
Confidence               23333333   34444443    233443321            3556788999999999888888842  2    2


Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH
Q 045511          132 VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       132 ~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      ....-.|..+|-.-|..++|...-+-+ -=.||.
T Consensus       204 ~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N~p~s  237 (254)
T COG4105         204 REALARLEEAYYALGLTDEAKKTAKVLGANYPDS  237 (254)
T ss_pred             HHHHHHHHHHHHHhCChHHHHHHHHHHHhcCCCC
Confidence            345666778888899888887776666 234444

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=80.74  E-value=13  Score=24.19  Aligned_cols=75  Identities=20%  Similarity=0.228  Sum_probs=48.7

Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..++|.-|-+.+...+-. ...+--.-+.++..+|++++|..+.+....||...|-++-.+  +.|..+....-+.+|
T Consensus        20 cHqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce~--rlGl~s~l~~rl~rl   94 (115)
T TIGR02508        20 CHQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCEW--RLGLGSALESRLNRL   94 (115)
T ss_pred             HHHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHHH--hhccHHHHHHHHHHH
Confidence            456777776666655422 233333344567788888888888888888888888776543  466666666666566

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.

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=80.72  E-value=3.4  Score=32.28  Aligned_cols=48  Identities=4%  Similarity=-0.053  Sum_probs=36.5

Q ss_pred             CCCCCHHh-HHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          159 DVKPNANT-LVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       159 ~~~p~~~t-~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                      .+.||..+ |+..|+...+.||+++|..++++.++.|+.--..+|-.-|
T Consensus       251 ~v~~dTe~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V  299 (303)
T PRK10564        251 PMLNDTESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSV  299 (303)
T ss_pred             ccCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHh
Confidence            45577765 6788888889999999999999988888776655554443

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

Probab=80.68  E-value=11  Score=27.43  Aligned_cols=50  Identities=10%  Similarity=-0.087  Sum_probs=27.9

Q ss_pred             ccccHHHHHHHHHHHHHh-ccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           78 LAHAHQKGLEIHAHVIKY-GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ..++.+......+...+. ...|++.+|..++..+...|+.++|.++..++
T Consensus       120 ~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~  170 (193)
T PF11846_consen  120 LPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARA  170 (193)
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444444444443333322 24566666666666677777777776666655

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

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

Probab=80.60  E-value=2.7  Score=20.41  Aligned_cols=11  Identities=36%  Similarity=0.456  Sum_probs=3.6

Q ss_pred             hCCChHHHHHH
Q 045511          144 KCGFHKEAIDM  154 (209)
Q Consensus       144 ~~g~~~~a~~~  154 (209)
                      ..|++++|++.
T Consensus        13 ~~~~~~~A~~~   23 (34)
T PF07719_consen   13 QLGNYEEAIEY   23 (34)
T ss_dssp             HTT-HHHHHHH
T ss_pred             HhCCHHHHHHH
Confidence            33333333333

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

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=80.11  E-value=27  Score=27.44  Aligned_cols=171  Identities=13%  Similarity=0.145  Sum_probs=97.9

Q ss_pred             chhccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHH
Q 045511            5 GLKSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         5 ~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~   84 (209)
                      ++....|++..   .++...+...+....+.. -......|+..+|..+|+......- -+...--.+...+...|+.+.
T Consensus       112 gF~G~qPesql---r~~ld~~~~~~~e~~~~~-~~~~~~~e~~~~a~~~~~~al~~~~-~~~~~~~~la~~~l~~g~~e~  186 (304)
T COG3118         112 GFQGAQPESQL---RQFLDKVLPAEEEEALAE-AKELIEAEDFGEAAPLLKQALQAAP-ENSEAKLLLAECLLAAGDVEA  186 (304)
T ss_pred             ccCCCCcHHHH---HHHHHHhcChHHHHHHHH-hhhhhhccchhhHHHHHHHHHHhCc-ccchHHHHHHHHHHHcCChHH
Confidence            33344444444   333344333333344433 2346678888899998888877532 234556677788888899999


Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc-CCC-cHhHHHHHHHHHHhCCChHHHHHHHhhC----
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV-VFP-DVVTWTTIISGLSKCGFHKEAIDMFCGI----  158 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~-~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m----  158 (209)
                      +..+++.+...--....+....=|..+.+.....+...+-.+. ..| |...=-.+-..+...|+.+.|.+.+-.+    
T Consensus       187 A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d  266 (304)
T COG3118         187 AQAILAALPLQAQDKAAHGLQAQIELLEQAAATPEIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRRD  266 (304)
T ss_pred             HHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            9999988765443333333333344444444444333333333 234 4555556677788888888887766665    


Q ss_pred             -CCCCCHHhHHHHHHHhccccchh
Q 045511          159 -DVKPNANTLVSVLSACSSLGSRK  181 (209)
Q Consensus       159 -~~~p~~~t~~~li~~~~~~g~~~  181 (209)
                       |.. |...=..++..+.-.|..+
T Consensus       267 ~~~~-d~~~Rk~lle~f~~~g~~D  289 (304)
T COG3118         267 RGFE-DGEARKTLLELFEAFGPAD  289 (304)
T ss_pred             cccc-CcHHHHHHHHHHHhcCCCC
Confidence             333 3444455555555555333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	209
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	99.89
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.88
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.82
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.81
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.55
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.55
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.55
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.52
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.49
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.48
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.47
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.46
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.45
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.43
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.42
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.42
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.41
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.4
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.39
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.39
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.38
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.37
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.36
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.35
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.35
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.34
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.34
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.32
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.32
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.29
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.28
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.27
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.27
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.27
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.27
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.25
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.21
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.19
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.19
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.18
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.16
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.16
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.15
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.15
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.15
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.15
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.14
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.14
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.13
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.12
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.09
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.09
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.08
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.06
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.06
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.05
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.03
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.99
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.93
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.91
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.87
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.85
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.84
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.84
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.84
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.83
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.82
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.81
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.8
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.8
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.78
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.77
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.76
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.76
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.76
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.75
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.75
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.75
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.74
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.74
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.73
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.73
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.72
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.68
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.67
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.67
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.66
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.65
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.65
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.64
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.64
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.64
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.6
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.59
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.59
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.57
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.57
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.55
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.54
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.53
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.53
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.52
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.52
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.51
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.51
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.5
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.49
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.46
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.45
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.43
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.43
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.42
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.39
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.37
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.36
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.36
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.36
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.36
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.35
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.34
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.34
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.32
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.31
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.3
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.3
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.3
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.3
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.3
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.29
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.26
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.26
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.24
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.24
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.24
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.23
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.22
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.21
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.2
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.2
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.18
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.18
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.14
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.14
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.13
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.13
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.12
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.11
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.1
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.09
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.08
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.07
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.07
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.04
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.04
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.03
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.02
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.01
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.01
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.99
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.97
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.97
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.96
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.96
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.96
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.95
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.89
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.89
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.87
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.86
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.85
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.85
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.81
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.8
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.79
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.76
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.76
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.76
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.75
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.69
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.64
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.6
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.55
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.52
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.47
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.32
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.29
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.23
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.2
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.19
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.19
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.17
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.15
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.13
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.1
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.01
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.97
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.95
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.91
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.9
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.89
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.79
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	96.77
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.72
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.65
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.58
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.39
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.39
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.22
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.2
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.14
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.12
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	95.75
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	95.58
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.49
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	95.48
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.25
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.2
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.91
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	94.72
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.28
1pc2_A	152	Mitochondria fission protein; unknown function; NM	94.26
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.22
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.14
1pc2_A	152	Mitochondria fission protein; unknown function; NM	94.1
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	94.0
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	93.87
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.66
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	93.38
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	93.28
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.41
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	91.98
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	91.46
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	91.35
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	91.15
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	91.11
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	90.2
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.79
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.73
1wgl_A	59	TOLL-interacting protein; CUE domain, structural g	89.29
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	88.84
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	88.12
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	87.86
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	87.21
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	86.69
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	86.17
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	85.36
2p58_C	116	Putative type III secretion protein YSCG; type III	85.18
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	81.32
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	81.03
2zu6_B	307	Programmed cell death protein 4; protein-protein c	81.03
3hra_A	201	Ankyrin repeat family protein; structural protein;	80.87
2p58_C	116	Putative type III secretion protein YSCG; type III	80.24

>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=8.5e-40  Score=269.45  Aligned_cols=179  Identities=15%  Similarity=0.201  Sum_probs=171.5

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc---------HHHHHHHHHHHHHhccCccH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA---------HQKGLEIHAHVIKYGHLHDI  101 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~---------~~~a~~~~~~m~~~g~~~~~  101 (209)
                      ...++.+|++|++.|++++|.++|++|.+.|+.||..||+++|.+|++.+.         ++.|.++|++|.+.|+.||.
T Consensus        26 e~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~  105 (501)
T 4g26_A           26 EALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNE  105 (501)
T ss_dssp             HHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCH
Confidence            356899999999999999999999999999999999999999999987654         78899999999999999999


Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhc----CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC---CCCCCHHhHHHHHHHh
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI---DVKPNANTLVSVLSAC  174 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m---~~~p~~~t~~~li~~~  174 (209)
                      .|||+||++|++.|++++|.++|++|    ..||..+||++|.+|++.|++++|.++|++|   |+.||..||++||++|
T Consensus       106 ~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~  185 (501)
T 4g26_A          106 ATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVS  185 (501)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999    3699999999999999999999999999999   9999999999999999


Q ss_pred             ccccchhHHHHHHHHHHHhccCCCchhHhHhhhcC
Q 045511          175 SSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDFM  209 (209)
Q Consensus       175 ~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~y  209 (209)
                      ++.|++++|.+++++|++.|..|+..||+.|++.|
T Consensus       186 ~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F  220 (501)
T 4g26_A          186 MDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWF  220 (501)
T ss_dssp             HHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHH
T ss_pred             hhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHH
Confidence            99999999999999999999999999999998753

>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=8.4e-35  Score=239.73  Aligned_cols=176  Identities=10%  Similarity=0.035  Sum_probs=166.5

Q ss_pred             hhcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCC---------ccchHHHHHHhhhCCCCCCHHHHHH
Q 045511            2 FVNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSST---------PQNAIPLYNKMLNCPSSYNHYTFTQ   71 (209)
Q Consensus         2 li~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~---------~~~a~~l~~~m~~~g~~p~~~t~~~   71 (209)
                      +|+++ +.|+.++|.+.+.++.+.. ..||..+||+||.+|++.+.         +++|.++|++|.+.|+.||..||++
T Consensus        32 ~id~c~k~G~~~~A~~lf~~M~~~G-v~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~  110 (501)
T 4g26_A           32 KLDMCSKKGDVLEALRLYDEARRNG-VQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTN  110 (501)
T ss_dssp             HHHHTTTSCCHHHHHHHHHHHHHHT-CCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcC-CCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            46778 9999999999999998864 67999999999999998776         4679999999999999999999999


Q ss_pred             HHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc----CCCcHhHHHHHHHHHHhCCC
Q 045511           72 ALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDVVTWTTIISGLSKCGF  147 (209)
Q Consensus        72 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----~~~~~~~~~~li~~~~~~g~  147 (209)
                      +|.+|++.|++++|.++|++|.+.|+.||..|||+||.+|++.|++++|.++|++|    ..||..+|++||++|++.|+
T Consensus       111 lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~  190 (501)
T 4g26_A          111 GARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKN  190 (501)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCC
Confidence            99999999999999999999999999999999999999999999999999999999    46999999999999999999


Q ss_pred             hHHHHHHHhhC---CCCCCHHhHHHHHHHhcccc
Q 045511          148 HKEAIDMFCGI---DVKPNANTLVSVLSACSSLG  178 (209)
Q Consensus       148 ~~~a~~~~~~m---~~~p~~~t~~~li~~~~~~g  178 (209)
                      +++|.++|++|   |+.|+..||+.++..++..+
T Consensus       191 ~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          191 ADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHH
T ss_pred             HHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCc
Confidence            99999999999   99999999999999988754

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

Probab=99.89  E-value=8.6e-24  Score=181.64  Aligned_cols=145  Identities=10%  Similarity=-0.029  Sum_probs=125.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhh---CCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLN---CPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~---~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      .+||++|++||++|++++|.++|++|.+   .|+.||+.|||+||.+||+.|++++|.++|++|.+.|+.||.+|||+||
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI  207 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAAL  207 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            6899999999999999999999988764   5899999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCh-hhHHHHHHhc----CCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCC------HHhHHHHHHHhccc
Q 045511          109 HFYVTVKDI-FSAHQIFNSV----VFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPN------ANTLVSVLSACSSL  177 (209)
Q Consensus       109 ~~~~~~g~~-~~a~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~------~~t~~~li~~~~~~  177 (209)
                      +++++.|+. ++|.++|++|    ..||..+|++++++..+.+-++.+.++..  +++|+      ..|...|.+.|.+.
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P--~f~p~~~~~~~~~t~~LL~dl~s~d  285 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKP--TFSLPPQLPPPVNTSKLLRDVYAKD  285 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCC--CCCCCCCCCCCCCCCTTTHHHHCCC
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCc--ccCCCCCCcccccchHHHHHHHccC
Confidence            999999985 7899999999    46999999999987777655444444433  44544      56777778888865


Q ss_pred             c
Q 045511          178 G  178 (209)
Q Consensus       178 g  178 (209)
                      +
T Consensus       286 ~  286 (1134)
T 3spa_A          286 G  286 (1134)
T ss_dssp             S
T ss_pred             C
Confidence            5

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

Probab=99.88  E-value=3.4e-23  Score=177.98  Aligned_cols=112  Identities=11%  Similarity=0.088  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHH---HhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc----CCCcHhHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVI---KYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDVVTWTTI  138 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~---~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----~~~~~~~~~~l  138 (209)
                      ..||+++|.+||+.|++++|.++|+.|.   +.|+.||++|||+||++||+.|++++|.++|++|    ..||..|||++
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            3467777777777777777777766654   3466677777777777777777777777777666    34667777777


Q ss_pred             HHHHHhCCCh-HHHHHHHhhC---CCCCCHHhHHHHHHHhccc
Q 045511          139 ISGLSKCGFH-KEAIDMFCGI---DVKPNANTLVSVLSACSSL  177 (209)
Q Consensus       139 i~~~~~~g~~-~~a~~~~~~m---~~~p~~~t~~~li~~~~~~  177 (209)
                      |.++|+.|+. ++|.++|++|   |+.||..||+.++.++.+.
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            7777776653 5666677777   6777777776666555433

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

Probab=99.82  E-value=3.9e-19  Score=148.46  Aligned_cols=202  Identities=6%  Similarity=-0.106  Sum_probs=147.0

Q ss_pred             hcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc
Q 045511            3 VNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA   81 (209)
Q Consensus         3 i~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~   81 (209)
                      +.++ +.|+.++|.+.+.++.+..  +.+..+|+.++..+.+.|+.++|..+++++.+.. +.+..+|..+...|.+.|+
T Consensus       312 ~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~  388 (597)
T 2xpi_A          312 ADTLFVRSRFIDVLAITTKILEID--PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNK  388 (597)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC--TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHcC--cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhcc
Confidence            3444 5666666666666665542  2355667777777777777777777777776432 3467778888888888888


Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +++|.++|+.+.+.. +.+..+|+.+..+|.+.|++++|.++|+++.   ..+..+|+.+..+|.+.|++++|.++|+++
T Consensus       389 ~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  467 (597)
T 2xpi_A          389 ISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSS  467 (597)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            888888888887653 3456788888888888888888888888762   346778888888888888888888888888


Q ss_pred             -CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh----ccCCC--chhHhHhhhc
Q 045511          159 -DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN----LNENN--IILDNAVLDF  208 (209)
Q Consensus       159 -~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~p~--~~~~~~li~~  208 (209)
                       ...| +..+|+.+...|.+.|++++|.++|+.+.+.    +..|+  ..+|..+..+
T Consensus       468 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~  525 (597)
T 2xpi_A          468 YALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHA  525 (597)
T ss_dssp             HHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHH
T ss_pred             HHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHH
Confidence             3333 5678888888888888888888888887766    66776  5677776654

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

Probab=99.81  E-value=1.2e-18  Score=145.56  Aligned_cols=196  Identities=10%  Similarity=-0.031  Sum_probs=110.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.+++.+.+.++.+.  .+.+..+|+.+...|.+.|++++|.++|+++.+.+ +.+..+|..+...+.+.|++++|.
T Consensus       351 ~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~  427 (597)
T 2xpi_A          351 ESGEKNKLYLISNDLVDR--HPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAI  427 (597)
T ss_dssp             HHTCHHHHHHHHHHHHHH--CTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HhCCHHHHHHHHHHHHhh--CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHH
Confidence            455555555555555432  12344566666666666666666666666665532 123456666666666666666666


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-----
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-----  158 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-----  158 (209)
                      ++|+.+.+.+ +.+..+|+.+..+|.+.|++++|.++|+++.   ..+..+|+.+...|.+.|++++|.++|+++     
T Consensus       428 ~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  506 (597)
T 2xpi_A          428 SAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVK  506 (597)
T ss_dssp             HHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhh
Confidence            6666665543 3355566666666666666666666666552   234555666666666666666666666665     


Q ss_pred             --CCCCC--HHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhh
Q 045511          159 --DVKPN--ANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLD  207 (209)
Q Consensus       159 --~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~  207 (209)
                        +..|+  ..+|..+..+|.+.|++++|.++++.+.+.+ ..+..+|..|..
T Consensus       507 ~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~  558 (597)
T 2xpi_A          507 KTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIAL  558 (597)
T ss_dssp             HSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHH
T ss_pred             ccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence              23555  4556666666666666666666666655543 224444544433

>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=99.55  E-value=1.1e-12  Score=104.02  Aligned_cols=158  Identities=12%  Similarity=0.049  Sum_probs=66.5

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      +..+-..+.+.|++++|.+.|+++.+.. +-+..+|..+...+.+.|++++|.+.|+.+.+.. +.+...|..+-..+..
T Consensus       138 ~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~  215 (388)
T 1w3b_A          138 RSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKE  215 (388)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHH
Confidence            3333334444444444444444444321 1123444444444455555555555444444332 1122233333333333


Q ss_pred             CCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHH
Q 045511          114 VKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       114 ~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      .|++++|...|++.   ...+..++..+...|.+.|++++|.+.|+++ ...|+ ..++..+...+.+.|++++|.+.++
T Consensus       216 ~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  295 (388)
T 1w3b_A          216 ARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYN  295 (388)
T ss_dssp             TTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            33333333333322   1112344444555555555555555555554 33332 2344444555555555555555555


Q ss_pred             HHHHh
Q 045511          189 HSLRN  193 (209)
Q Consensus       189 ~~~~~  193 (209)
                      .+.+.
T Consensus       296 ~al~~  300 (388)
T 1w3b_A          296 TALRL  300 (388)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            44433

>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=99.55  E-value=8.3e-13  Score=104.73  Aligned_cols=160  Identities=12%  Similarity=0.064  Sum_probs=118.9

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|..+-..+.+.|++++|...|++..+.. +-+..++..+...+.+.|++++|.+.|+.+.+.. +.+..+|..+...|
T Consensus       204 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  281 (388)
T 1w3b_A          204 DAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANAL  281 (388)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            444445555555555555555555554422 1245777788888888888888888888887754 33566788888888


Q ss_pred             HhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHH
Q 045511          112 VTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~  186 (209)
                      .+.|++++|.+.|+++.   ..+..+|+.+...+...|++++|...|+++ ...|+ ..++..+...+.+.|++++|.+.
T Consensus       282 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  361 (388)
T 1w3b_A          282 KEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMH  361 (388)
T ss_dssp             HHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            88888888888888773   356778888888899999999999999888 55564 56788888888899999999999


Q ss_pred             HHHHHHh
Q 045511          187 HAHSLRN  193 (209)
Q Consensus       187 ~~~~~~~  193 (209)
                      ++.+.+.
T Consensus       362 ~~~a~~~  368 (388)
T 1w3b_A          362 YKEAIRI  368 (388)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHhh
Confidence            8888764

>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=99.55  E-value=2.3e-12  Score=95.94  Aligned_cols=198  Identities=11%  Similarity=-0.044  Sum_probs=163.1

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ..+ ..++.++|.+.+.++.+..  +.+...|..+...+.+.|++++|...|++..+.. +.+...+..+...+...|++
T Consensus        45 ~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~  121 (252)
T 2ho1_A           45 LGYLQRGNTEQAKVPLRKALEID--PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYEQKRY  121 (252)
T ss_dssp             HHHHHTTCTGGGHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcCChHHHHHHHHHHHhcC--CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHHhHH
Confidence            344 7889999999998887763  2356888999999999999999999999998764 23678889999999999999


Q ss_pred             HHHHHHHHHHHHhccCc-cHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           83 QKGLEIHAHVIKYGHLH-DIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ++|.+.++...+.+..| +...+..+...|...|++++|.+.+++..   ..+...+..+...+...|++++|...|.+.
T Consensus       122 ~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  201 (252)
T 2ho1_A          122 EEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLF  201 (252)
T ss_dssp             HHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99999999998843344 56788999999999999999999999873   345788999999999999999999999998


Q ss_pred             -CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          159 -DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       159 -~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                       ...| +...+..+...+...|+.++|.+.++.+.+.  .|+......++
T Consensus       202 ~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l  249 (252)
T 2ho1_A          202 AQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL--YPGSLEYQEFQ  249 (252)
T ss_dssp             HTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTSHHHHHHH
T ss_pred             HHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--CCCCHHHHHHH
Confidence             5454 5567888888899999999999999998776  45544444443

>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=99.52  E-value=5e-13  Score=107.65  Aligned_cols=182  Identities=8%  Similarity=0.020  Sum_probs=108.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH----HHHHHHHH--------
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH----YTFTQALK--------   74 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~----~t~~~ll~--------   74 (209)
                      +.++.++|...+.++.+..  +.+..+|..+...+.+.|++++|...|+++.+.+  |+.    ..+..+..        
T Consensus        72 ~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~  147 (450)
T 2y4t_A           72 AMGKSKAALPDLTKVIQLK--MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN--PSENEEKEAQSQLIKSDEMQRLR  147 (450)
T ss_dssp             HTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHHHHHHHHH
Confidence            4455555555555554432  1233556666666666666666666666665532  332    33333322        


Q ss_pred             ----HHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCC
Q 045511           75 ----ACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGF  147 (209)
Q Consensus        75 ----~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~  147 (209)
                          .+.+.|++++|.+.|+.+.+.. +.+..++..+..+|.+.|++++|.++|+++.   ..+..+|..+...|...|+
T Consensus       148 ~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  226 (450)
T 2y4t_A          148 SQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGD  226 (450)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence                2555666666666666665543 3455666777777777777777777777662   2456677777777777777


Q ss_pred             hHHHHHHHhhC-CCCCCHHh-HHHH------------HHHhccccchhHHHHHHHHHHHh
Q 045511          148 HKEAIDMFCGI-DVKPNANT-LVSV------------LSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       148 ~~~a~~~~~~m-~~~p~~~t-~~~l------------i~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +++|...|.++ ...|+... +..+            ...|.+.|++++|...++.+.+.
T Consensus       227 ~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~  286 (450)
T 2y4t_A          227 HELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT  286 (450)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            77777777777 55555433 2222            56666777777777777766653

>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=99.49  E-value=1.2e-12  Score=105.41  Aligned_cols=186  Identities=12%  Similarity=0.035  Sum_probs=152.2

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ..+ +.++.++|...+.++.+.  .+.+..+|..+...+.+.|++++|...|+++.+.+ +.+...+..+...+.+.|++
T Consensus        34 ~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~  110 (450)
T 2y4t_A           34 KKLLAAGQLADALSQFHAAVDG--DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKL  110 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCH
Confidence            345 778888888888888765  22456889999999999999999999999998865 24578889999999999999


Q ss_pred             HHHHHHHHHHHHhccCccH---hHHHHHHH------------HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh
Q 045511           83 QKGLEIHAHVIKYGHLHDI---FIQNSLLH------------FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK  144 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~---~~~~~ll~------------~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~  144 (209)
                      ++|.+.|+.+.+.. +.+.   ..+..+..            .+.+.|++++|.+.|+++.   ..+...+..+...|.+
T Consensus       111 ~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (450)
T 2y4t_A          111 DEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIK  189 (450)
T ss_dssp             HHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH
Confidence            99999999998754 2334   56665544            4888999999999999873   3467889999999999


Q ss_pred             CCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          145 CGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       145 ~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .|++++|.+.|.++ ...| +..++..+...+...|++++|...++.+.+.
T Consensus       190 ~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  240 (450)
T 2y4t_A          190 EGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  240 (450)
T ss_dssp             TTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            99999999999998 4344 5678999999999999999999999988755

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

Probab=99.48  E-value=6.7e-12  Score=91.40  Aligned_cols=198  Identities=7%  Similarity=-0.100  Sum_probs=160.7

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc-cc
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA-HA   81 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~-~~   81 (209)
                      ..+ +.++.++|.+.+.++.+..  +.+...|..+...+...|++++|...+++..+.. +.+..++..+...+... |+
T Consensus        16 ~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~   92 (225)
T 2vq2_A           16 MEYMRGQDYRQATASIEDALKSD--PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNR   92 (225)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCc
Confidence            344 7788888888888887753  2346788999999999999999999999998754 34678889999999999 99


Q ss_pred             HHHHHHHHHHHHHhccCc-cHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511           82 HQKGLEIHAHVIKYGHLH-DIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      +++|...++...+.+..| +...+..+...+...|++++|.+.+++..   ..+...+..+...+...|++++|...|++
T Consensus        93 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  172 (225)
T 2vq2_A           93 PAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKK  172 (225)
T ss_dssp             HHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999999998843333 36788999999999999999999998873   34578889999999999999999999999


Q ss_pred             C-CCCC--CHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhh
Q 045511          158 I-DVKP--NANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVL  206 (209)
Q Consensus       158 m-~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li  206 (209)
                      . ...|  +...+..+...+...|+.+.+..++..+.+.  .|+......++
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~~~l  222 (225)
T 2vq2_A          173 YQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--FPYSEELQTVL  222 (225)
T ss_dssp             HHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHHHHh
Confidence            8 4444  5667777888888999999999999888665  46555554443

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

Probab=99.47  E-value=4.9e-13  Score=102.84  Aligned_cols=156  Identities=9%  Similarity=0.055  Sum_probs=70.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      .++..+...+.+.++.++|.+.++++...+..|+. ..+..+-..+...|++++|.+.++.      +.+...+..+...
T Consensus        66 ~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~  139 (291)
T 3mkr_A           66 QAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQI  139 (291)
T ss_dssp             HHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHH
Confidence            44455555555555555555555555444433332 2223333444555555555555443      2344455555555


Q ss_pred             HHhCCChhhHHHHHHhcC--CCcHhH---HHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHH
Q 045511          111 YVTVKDIFSAHQIFNSVV--FPDVVT---WTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLG  183 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~--~~~~~~---~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a  183 (209)
                      |.+.|++++|.+.|+++.  .|+...   ....+..+...|++++|..+|+++  ....+...++.+-.++.+.|++++|
T Consensus       140 ~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA  219 (291)
T 3mkr_A          140 LLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAA  219 (291)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHH
Confidence            555555555555555442  122110   011222222334555555555555  2222334444444555555555555


Q ss_pred             HHHHHHHHHh
Q 045511          184 KAIHAHSLRN  193 (209)
Q Consensus       184 ~~~~~~~~~~  193 (209)
                      ++.++...+.
T Consensus       220 ~~~l~~al~~  229 (291)
T 3mkr_A          220 EGVLQEALDK  229 (291)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            5555544433

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

Probab=99.46  E-value=7.8e-12  Score=92.32  Aligned_cols=184  Identities=12%  Similarity=0.100  Sum_probs=152.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|...+.++.+..  +.+...+..+...+.+.|++++|...|++..+.. +.+...+..+...+...|++++|.
T Consensus        35 ~~~~~~~A~~~~~~~l~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~  111 (243)
T 2q7f_A           35 EFGDYEKAAEAFTKAIEEN--KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVVKEMYKEAK  111 (243)
T ss_dssp             -------CCTTHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HhhCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHhccHHHHH
Confidence            7788889998888887642  2356888889999999999999999999998754 246788899999999999999999


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP  162 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p  162 (209)
                      +.++...+.. +.+...+..+...+.+.|++++|.+.+++..   ..+...+..+...+...|++++|...|.+. ...|
T Consensus       112 ~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  190 (243)
T 2q7f_A          112 DMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDP  190 (243)
T ss_dssp             HHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc
Confidence            9999998875 4567889999999999999999999999873   346778899999999999999999999998 4444


Q ss_pred             -CHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          163 -NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       163 -~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                       +..++..+...+...|++++|.+.++...+..
T Consensus       191 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          191 GHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             TCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence             46788899999999999999999999887763

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

Probab=99.45  E-value=3e-12  Score=100.64  Aligned_cols=184  Identities=15%  Similarity=0.127  Sum_probs=131.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|.+.+.++.+..  +.+..+|..+...+.+.|++++|...|++..+.. +.+..+|..+...+...|++++|.
T Consensus        77 ~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~  153 (365)
T 4eqf_A           77 KEGDLPVTILFMEAAILQD--PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYTNTSHQQDAC  153 (365)
T ss_dssp             HHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHccccHHHHH
Confidence            5556666666666665542  1244666777777777777777777777766543 224566666666666666666666


Q ss_pred             HHHHHHHHhcc------------------------------------------Cc---cHhHHHHHHHHHHhCCChhhHH
Q 045511           87 EIHAHVIKYGH------------------------------------------LH---DIFIQNSLLHFYVTVKDIFSAH  121 (209)
Q Consensus        87 ~~~~~m~~~g~------------------------------------------~~---~~~~~~~ll~~~~~~g~~~~a~  121 (209)
                      +.++...+...                                          .|   +..++..+...|.+.|++++|.
T Consensus       154 ~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~  233 (365)
T 4eqf_A          154 EALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAI  233 (365)
T ss_dssp             HHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHH
Confidence            66665544320                                          12   5778888888899999999999


Q ss_pred             HHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          122 QIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       122 ~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +.|++..   ..+..+|+.+...|...|++++|...|.+. ...|+ ..++..+...|.+.|++++|...+....+.
T Consensus       234 ~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  310 (365)
T 4eqf_A          234 DAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYREAVSNFLTALSL  310 (365)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            9988872   346778888999999999999999999888 55565 567888888888999999999999877665

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

Probab=99.43  E-value=5.2e-12  Score=93.88  Aligned_cols=185  Identities=13%  Similarity=0.020  Sum_probs=154.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCC--CCCC----HHHHHHHHHHHhccc
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCP--SSYN----HYTFTQALKACSLAH   80 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g--~~p~----~~t~~~ll~~~~~~~   80 (209)
                      +.++.++|...+.++.+..   ++...|..+...+.+.|++++|...+++..+..  ..|+    ..+|..+-..+...|
T Consensus        17 ~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   93 (258)
T 3uq3_A           17 KARQFDEAIEHYNKAWELH---KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLG   93 (258)
T ss_dssp             HTTCHHHHHHHHHHHHHHS---CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HhccHHHHHHHHHHHHHhh---ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcc
Confidence            6788888888888888775   778899999999999999999999999987643  1122    578888999999999


Q ss_pred             cHHHHHHHHHHHHHhc------------------------cC-ccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcH
Q 045511           81 AHQKGLEIHAHVIKYG------------------------HL-HDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDV  132 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g------------------------~~-~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~  132 (209)
                      ++++|.+.|+...+..                        .. .+...+..+...+...|++++|.+.+++..   ..+.
T Consensus        94 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~  173 (258)
T 3uq3_A           94 DLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDA  173 (258)
T ss_dssp             CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             cHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccH
Confidence            9999999999888742                        22 245678889999999999999999999873   3467


Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ..|..+...|...|++++|...|.+. ...|+ ..++..+-..+...|++++|.+.+....+..
T Consensus       174 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          174 RGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALETLDAARTKD  237 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            88999999999999999999999998 55555 6788889999999999999999999876653

>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=99.42  E-value=5.8e-12  Score=98.73  Aligned_cols=184  Identities=12%  Similarity=0.109  Sum_probs=122.5

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|...+.++.+..  +.+..+|..+...+.+.|++++|...|++..+.+ +.+..++..+...+...|++++|.
T Consensus        76 ~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~  152 (368)
T 1fch_A           76 QEGDLPNAVLLFEAAVQQD--PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQAC  152 (368)
T ss_dssp             HTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHH
Confidence            4445555555555544331  1233455555555555555555555555554432 123444555555555555555544


Q ss_pred             -------------------------------------------------HHHHHHHHhccCc-cHhHHHHHHHHHHhCCC
Q 045511           87 -------------------------------------------------EIHAHVIKYGHLH-DIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        87 -------------------------------------------------~~~~~m~~~g~~~-~~~~~~~ll~~~~~~g~  116 (209)
                                                                       +.++.+.+..... +..++..+...|.+.|+
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~  232 (368)
T 1fch_A          153 EILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGE  232 (368)
T ss_dssp             HHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCC
Confidence                                                             4444444433111 47788999999999999


Q ss_pred             hhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          117 IFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       117 ~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      +++|.+.|++..   ..+...|..+...+...|++++|...|.+. ...|+ ..++..+...+.+.|++++|...+....
T Consensus       233 ~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  312 (368)
T 1fch_A          233 YDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEAL  312 (368)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999999998873   345778999999999999999999999998 55554 5688889999999999999999999876


Q ss_pred             Hh
Q 045511          192 RN  193 (209)
Q Consensus       192 ~~  193 (209)
                      +.
T Consensus       313 ~~  314 (368)
T 1fch_A          313 NM  314 (368)
T ss_dssp             HH
T ss_pred             Hh
Confidence            65

>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=99.42  E-value=2.2e-11  Score=93.67  Aligned_cols=183  Identities=10%  Similarity=-0.029  Sum_probs=115.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCC-CccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSS-TPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +.++.+++...+.++.+..  +.+...|..+...+...| ++++|...|++..+.. +.+...|..+...+...|++++|
T Consensus        68 ~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A  144 (330)
T 3hym_B           68 ELNKANELFYLSHKLVDLY--PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQA  144 (330)
T ss_dssp             HHTCHHHHHHHHHHHHHHC--TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHH
T ss_pred             HhhhHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHH
Confidence            4555555555555555432  123456666666667777 6777777777766543 22445666667777777777777


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC-
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV-  160 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~-  160 (209)
                      .+.++...+.. +.+...+..+...|...|++++|.+.+++..   ..+...+..+...+...|++++|...|.+. .. 
T Consensus       145 ~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~  223 (330)
T 3hym_B          145 MAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKI  223 (330)
T ss_dssp             HHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHh
Confidence            77777766654 2234555556667777777777777776652   234566677777777777777777777666 11 


Q ss_pred             ---------CCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          161 ---------KPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       161 ---------~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                               ..+..++..+...+...|++++|...++...+.
T Consensus       224 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  265 (330)
T 3hym_B          224 KAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVL  265 (330)
T ss_dssp             TTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhh
Confidence                     223456666777777777777777777766655

>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=99.41  E-value=7.9e-12  Score=96.11  Aligned_cols=118  Identities=14%  Similarity=0.177  Sum_probs=92.6

Q ss_pred             HhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHH
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAI  152 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~  152 (209)
                      +...|++++|.+.++...+.. +.+..++..+...|.+.|++++|.+.+++..   ..+...|..+...+...|++++|.
T Consensus       148 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  226 (327)
T 3cv0_A          148 FAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEAL  226 (327)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHH
Confidence            444455555555555555443 3357788889999999999999999998873   345778999999999999999999


Q ss_pred             HHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          153 DMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       153 ~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ..|.+. ...| +..++..+...+...|++++|.+.++...+..
T Consensus       227 ~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  270 (327)
T 3cv0_A          227 DAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQ  270 (327)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            999998 4445 46788888999999999999999999887664

>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=99.40  E-value=2.4e-13  Score=109.08  Aligned_cols=140  Identities=14%  Similarity=0.050  Sum_probs=48.5

Q ss_pred             CCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHH
Q 045511           28 IPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSL  107 (209)
Q Consensus        28 ~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  107 (209)
                      .+|...|..++..+.+.|++++|...++..++.  .++..+.+.++.+|.+.|++++++++++       .|+..+|+.+
T Consensus        58 a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~I  128 (449)
T 1b89_A           58 ADDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQV  128 (449)
T ss_dssp             -----------------------------------------------------CHHHHTTTTT-------CC--------
T ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHH
Confidence            356667777777777777777777755544442  3445666667777777777766666663       3555677777


Q ss_pred             HHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHH
Q 045511          108 LHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       108 l~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~  184 (209)
                      ...|...|++++|..+|..+     ..|..+..++.+.|++++|.+.+.++   .+..||..++.+|...|+++.|.
T Consensus       129 Gd~~~~~g~yeeA~~~Y~~a-----~n~~~LA~~L~~Lg~yq~AVea~~KA---~~~~~Wk~v~~aCv~~~ef~lA~  197 (449)
T 1b89_A          129 GDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKA---NSTRTWKEVCFACVDGKEFRLAQ  197 (449)
T ss_dssp             --------CTTTHHHHHHHT-----TCHHHHHHHHHTTTCHHHHHHHHHHH---TCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHh-----hhHHHHHHHHHHhccHHHHHHHHHHc---CCchhHHHHHHHHHHcCcHHHHH
Confidence            77777777777777777765     35667777777777777777777664   25667777777777666666653

>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=99.39  E-value=9.4e-14  Score=111.41  Aligned_cols=171  Identities=11%  Similarity=0.097  Sum_probs=53.2

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLE   87 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~   87 (209)
                      -++.++|.+.+++.       +++.+|..+..++.+.|++++|.+.|.+.      +|..+|..++.++...|+++++..
T Consensus        16 ~~~ld~A~~fae~~-------~~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           16 IGNLDRAYEFAERC-------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCHHHHHHHHHhC-------CChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHH
Confidence            34455666555555       55579999999999999999999999763      678899999999999999999999


Q ss_pred             HHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhH
Q 045511           88 IHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTL  167 (209)
Q Consensus        88 ~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~  167 (209)
                      .++..++.  .+++.+.+.|+.+|.+.|++++++++++.   |+..+|+.+-..|...|++++|...|..+      ..|
T Consensus        83 yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a------~n~  151 (449)
T 1b89_A           83 YLQMARKK--ARESYVETELIFALAKTNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNV------SNF  151 (449)
T ss_dssp             ----------------------------CHHHHTTTTTC---C----------------CTTTHHHHHHHT------TCH
T ss_pred             HHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHh------hhH
Confidence            88777764  56688999999999999999999988864   78889999999999999999999999986      489


Q ss_pred             HHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHhhhc
Q 045511          168 VSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAVLDF  208 (209)
Q Consensus       168 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~~  208 (209)
                      ..+..++.+.|+++.|.+.+...      .++.+|..++.+
T Consensus       152 ~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~a  186 (449)
T 1b89_A          152 GRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFA  186 (449)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHH
Confidence            99999999999999999999877      256677776654

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

Probab=99.39  E-value=1.8e-11  Score=94.10  Aligned_cols=178  Identities=9%  Similarity=0.057  Sum_probs=140.2

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC-cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      ..++.+++.+.+.++..... .|+ ...+..+-..+.+.|++++|.+.+++      +.+...+..+...+.+.|++++|
T Consensus        77 ~~~~~~~A~~~l~~ll~~~~-~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A  149 (291)
T 3mkr_A           77 SHSRRDAIVAELDREMSRSV-DVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLA  149 (291)
T ss_dssp             CSTTHHHHHHHHHHHHHSCC-CCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHhccc-CCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHH
Confidence            44555666666666654321 244 45666667889999999999999987      46888999999999999999999


Q ss_pred             HHHHHHHHHhccCccHh---HHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           86 LEIHAHVIKYGHLHDIF---IQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~---~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      .+.|+.+.+..  |+..   ....++..+...|++++|..+|+++.   ..+...|+.+..++.+.|++++|...|.+. 
T Consensus       150 ~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al  227 (291)
T 3mkr_A          150 RKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEAL  227 (291)
T ss_dssp             HHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999875  4432   12334455566799999999999983   357889999999999999999999999998 


Q ss_pred             CCCC-CHHhHHHHHHHhccccchhH-HHHHHHHHHHh
Q 045511          159 DVKP-NANTLVSVLSACSSLGSRKL-GKAIHAHSLRN  193 (209)
Q Consensus       159 ~~~p-~~~t~~~li~~~~~~g~~~~-a~~~~~~~~~~  193 (209)
                      ...| +..++..++..+...|+.++ +.++++.+.+.
T Consensus       228 ~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          228 DKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            6666 45688889999999999865 67888887665

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

Probab=99.38  E-value=3.3e-11  Score=87.68  Aligned_cols=163  Identities=10%  Similarity=0.024  Sum_probs=141.3

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +...|..+...+.+.|++++|...|++..+.. +.+...+..+...+...|++++|.+.++...+.. +.+..++..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            34678889999999999999999999998754 3457889999999999999999999999998875 456789999999


Q ss_pred             HHHhC-CChhhHHHHHHhcCC----C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchh
Q 045511          110 FYVTV-KDIFSAHQIFNSVVF----P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRK  181 (209)
Q Consensus       110 ~~~~~-g~~~~a~~~~~~~~~----~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~  181 (209)
                      .|... |++++|.+.++++.+    | +...+..+...+...|++++|...|.+. ...|+ ...+..+...+...|+++
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~  164 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLG  164 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHH
Confidence            99999 999999999998743    2 2578889999999999999999999998 55554 678888999999999999


Q ss_pred             HHHHHHHHHHHhc
Q 045511          182 LGKAIHAHSLRNL  194 (209)
Q Consensus       182 ~a~~~~~~~~~~~  194 (209)
                      +|...++...+..
T Consensus       165 ~A~~~~~~~~~~~  177 (225)
T 2vq2_A          165 DADYYFKKYQSRV  177 (225)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999887764

>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=99.37  E-value=5.5e-11  Score=91.46  Aligned_cols=183  Identities=9%  Similarity=-0.025  Sum_probs=153.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc-cHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH-AHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~-~~~~a   85 (209)
                      ..++.++|.+.+.++.+..  +.+...+..+...+.+.|++++|..+++++.+.. +.+...|..+-..+...| ++++|
T Consensus        34 ~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~A  110 (330)
T 3hym_B           34 YNCDFKMCYKLTSVVMEKD--PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYYLMVGHKNEHA  110 (330)
T ss_dssp             HTTCHHHHHHHHHHHHHHC--TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHHHHSCSCHHHH
T ss_pred             HcCCHHHHHHHHHHHHHcC--CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhhhhHHHH
Confidence            6678888888888877653  2345677778888999999999999999998854 235678888889999999 99999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK  161 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~  161 (209)
                      .+.|+...+.. +.+...|..+...+...|++++|.+.+++..   ..+...+..+...|...|++++|...|.+. ...
T Consensus       111 ~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~  189 (330)
T 3hym_B          111 RRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA  189 (330)
T ss_dssp             HHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            99999998765 4457789999999999999999999999873   234567777899999999999999999998 555


Q ss_pred             CC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |+ ..++..+...+...|++++|...+....+.
T Consensus       190 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  222 (330)
T 3hym_B          190 PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEK  222 (330)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            54 578889999999999999999999988765

>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=99.36  E-value=1.1e-10  Score=86.68  Aligned_cols=161  Identities=9%  Similarity=-0.081  Sum_probs=140.5

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      ...|..+...+...|++++|...|++..+.. +.+...+..+...+...|++++|.+.++...+.. +.+..++..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH
Confidence            4678888899999999999999999998764 3467889999999999999999999999998875 4467899999999


Q ss_pred             HHhCCChhhHHHHHHhcCC----C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHH
Q 045511          111 YVTVKDIFSAHQIFNSVVF----P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLG  183 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~~----~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a  183 (209)
                      |...|++++|.+++++..+    | +...+..+...+...|++++|...|.+. ...| +...+..+...+...|++++|
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999998744    3 4668888999999999999999999998 4445 467888999999999999999


Q ss_pred             HHHHHHHHHh
Q 045511          184 KAIHAHSLRN  193 (209)
Q Consensus       184 ~~~~~~~~~~  193 (209)
                      ...+....+.
T Consensus       195 ~~~~~~~~~~  204 (252)
T 2ho1_A          195 RQYYDLFAQG  204 (252)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHHh
Confidence            9999988765

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

Probab=99.35  E-value=3.1e-11  Score=88.61  Aligned_cols=181  Identities=9%  Similarity=-0.019  Sum_probs=125.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc-------
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA-------   79 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~-------   79 (209)
                      +.++.++|...+.++.+..  +.+...|..+-..+.+.|++++|...|++..+.. +-+...+..+-..+.+.       
T Consensus        17 ~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~   93 (217)
T 2pl2_A           17 ALGRYDAALTLFERALKEN--PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLSEAYVALYRQAEDR   93 (217)
T ss_dssp             HTTCHHHHHHHHHHHHTTS--SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHTCSSH
T ss_pred             HcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhhhhhhhh
Confidence            6677777777776665542  2345778888888888888888888888887754 23456777777888888       


Q ss_pred             ----ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--CcHhHHHHHHHHHHhCCChHHHHH
Q 045511           80 ----HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--PDVVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        80 ----~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~  153 (209)
                          |++++|...++...+.. +-+...+..+-..|...|++++|...|++..+  .+...+..+-..|...|++++|..
T Consensus        94 ~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~~~~~g~~~~A~~  172 (217)
T 2pl2_A           94 ERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALAELYLSMGRLDEALA  172 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             cccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHHHHHHHcCCHHHHHH
Confidence                88888888888887764 34567788888888888888888888877621  567778888888888888888888


Q ss_pred             HHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          154 MFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       154 ~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      .|++. ...|+ ...+..+...+...|++++|.+.++...
T Consensus       173 ~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          173 QYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHSTTCHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            88888 55564 4567777888888888888888877653

>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=99.35  E-value=8.8e-11  Score=82.65  Aligned_cols=161  Identities=13%  Similarity=0.070  Sum_probs=139.2

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|..+...+.+.|++++|...+++..+.. +.+...+..+...+...|++++|.+.++...+.. +.+..++..+...+
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            567778888999999999999999988753 3467889999999999999999999999998774 45678899999999


Q ss_pred             HhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHH
Q 045511          112 VTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~  186 (209)
                      ...|++++|.+.+++..   ..+...+..+...+...|++++|.+.|.+. ...| +..++..+...+...|++++|...
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~  166 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPH  166 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHH
Confidence            99999999999999873   356788889999999999999999999998 4444 457888899999999999999999


Q ss_pred             HHHHHHhc
Q 045511          187 HAHSLRNL  194 (209)
Q Consensus       187 ~~~~~~~~  194 (209)
                      +....+..
T Consensus       167 ~~~~~~~~  174 (186)
T 3as5_A          167 FKKANELD  174 (186)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHcC
Confidence            99887664

>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=99.34  E-value=1.4e-11  Score=96.58  Aligned_cols=183  Identities=10%  Similarity=-0.049  Sum_probs=142.1

Q ss_pred             cCCCcchH-hHHHHHHHHhhCC--CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            9 LKPTLSFK-QLNQIHAQIIKIP--QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         9 ~~~~~a~~-~~~~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      ++.+.+.+ .+.+.....+..|  +...+..+-..+.+.|++++|...|+++.+.. +.+..+|..+...+.+.|++++|
T Consensus        39 ~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A  117 (368)
T 1fch_A           39 SDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLA  117 (368)
T ss_dssp             -------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHH
Confidence            44445555 4554443333333  45788899999999999999999999999864 34678899999999999999999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC-------------------------------------
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV-------------------------------------  128 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------------------------------------  128 (209)
                      .+.|+...+.. +.+..++..+...|...|++++|.+.++++.                                     
T Consensus       118 ~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (368)
T 1fch_A          118 ISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSL  196 (368)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHH
T ss_pred             HHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhccc
Confidence            99999999876 4578899999999999999999999887651                                     


Q ss_pred             --------------CC---cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHH
Q 045511          129 --------------FP---DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       129 --------------~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                                    .|   +..++..+...|...|++++|...|.+. ...|+ ..++..+...+...|++++|...++.
T Consensus       197 ~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  276 (368)
T 1fch_A          197 FLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRR  276 (368)
T ss_dssp             HHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence                          01   4567788888888889999998888887 44554 56788888888888999999888888


Q ss_pred             HHHh
Q 045511          190 SLRN  193 (209)
Q Consensus       190 ~~~~  193 (209)
                      ..+.
T Consensus       277 al~~  280 (368)
T 1fch_A          277 ALEL  280 (368)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            7765

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

Probab=99.34  E-value=1.5e-10  Score=84.97  Aligned_cols=163  Identities=12%  Similarity=-0.031  Sum_probs=141.9

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      ++...+..+-..+.+.|++++|...|++..+.. +.+...+..+-..+.+.|++++|...++...+.. +.+...+..+-
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            566788889999999999999999999998864 2466888889999999999999999999999875 45678899999


Q ss_pred             HHHHhC-----------CChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHH
Q 045511          109 HFYVTV-----------KDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSA  173 (209)
Q Consensus       109 ~~~~~~-----------g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~  173 (209)
                      ..|.+.           |++++|...|++..  .| +...|..+-..|...|++++|+..|++. .+..+...+..+-..
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~  160 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALAEL  160 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHHHH
Confidence            999999           99999999999873  34 5778888999999999999999999998 222778889999999


Q ss_pred             hccccchhHHHHHHHHHHHh
Q 045511          174 CSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       174 ~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +...|++++|...++...+.
T Consensus       161 ~~~~g~~~~A~~~~~~al~~  180 (217)
T 2pl2_A          161 YLSMGRLDEALAQYAKALEQ  180 (217)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            99999999999999998776

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

Probab=99.32  E-value=8.7e-11  Score=86.61  Aligned_cols=174  Identities=8%  Similarity=-0.027  Sum_probs=128.4

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      .....|..+-..+.+.|++++|...|++..+.. +.+...+..+...+.+.|++++|.+.++...+.. +.+..++..+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la   98 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAG   98 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHH
Confidence            344788888889999999999999999998854 3467889999999999999999999999998875 45678999999


Q ss_pred             HHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHH
Q 045511          109 HFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLG  183 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a  183 (209)
                      ..|...|++++|.+.+++.   ...+...+..+...+...|++++|...+.+. ...| +...+..+...+...|++++|
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  178 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEA  178 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999999987   3356778999999999999999999999998 4444 567888899999999999999


Q ss_pred             HHHHHHHHHhccCCCchhHhHh
Q 045511          184 KAIHAHSLRNLNENNIILDNAV  205 (209)
Q Consensus       184 ~~~~~~~~~~~~~p~~~~~~~l  205 (209)
                      ...+....+.. ..+...+..+
T Consensus       179 ~~~~~~~~~~~-~~~~~~~~~l  199 (243)
T 2q7f_A          179 LSQFAAVTEQD-PGHADAFYNA  199 (243)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHhC-cccHHHHHHH
Confidence            99999887763 2233444443

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

Probab=99.32  E-value=3.7e-11  Score=98.00  Aligned_cols=183  Identities=7%  Similarity=-0.015  Sum_probs=102.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|.+.+.++.+..  +.+..+|..+...+.+.|++++|...|++..+... .+...+..+...+...|++++|.
T Consensus       282 ~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~  358 (514)
T 2gw1_A          282 DRNDSTEYYNYFDKALKLD--SNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDP-ENIFPYIQLACLAYRENKFDDCE  358 (514)
T ss_dssp             TSSCCTTGGGHHHHHHTTC--TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCS-SCSHHHHHHHHHTTTTTCHHHHH
T ss_pred             HCCCHHHHHHHHHHHhhcC--cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCh-hhHHHHHHHHHHHHHcCCHHHHH
Confidence            4555555555555554432  12335555566666666666666666666555431 23455555566666666666666


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-----Cc----HhHHHHHHHHHHh---CCChHHHHHH
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----PD----VVTWTTIISGLSK---CGFHKEAIDM  154 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~---~g~~~~a~~~  154 (209)
                      ..++...+.. +.+..++..+...|.+.|++++|.+.++++.+     ++    ...|..+...+..   .|++++|...
T Consensus       359 ~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~  437 (514)
T 2gw1_A          359 TLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNL  437 (514)
T ss_dssp             HHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHH
T ss_pred             HHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHH
Confidence            6666655543 23445566666666666666666666655521     11    2255666666666   6666666666


Q ss_pred             HhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          155 FCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       155 ~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |+.. ...| +..++..+...+.+.|++++|.+.++...+.
T Consensus       438 ~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  478 (514)
T 2gw1_A          438 LEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEESADL  478 (514)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            6665 3333 3345555666666666666666666655554

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

Probab=99.29  E-value=1.7e-11  Score=96.29  Aligned_cols=185  Identities=12%  Similarity=0.020  Sum_probs=144.6

Q ss_pred             hcch-hccCCCcchHhHHHHHHHHhhCCCc--------ccHHHHHHHHHcCCCccchHHHHHHhhhCCCC-CCHHHHHHH
Q 045511            3 VNGL-KSLKPTLSFKQLNQIHAQIIKIPQP--------HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSS-YNHYTFTQA   72 (209)
Q Consensus         3 i~~~-~~~~~~~a~~~~~~~~~~~~~~p~~--------~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-p~~~t~~~l   72 (209)
                      ..++ +.++.++|.+.+.++.+..+..++.        ..+..+...+.+.|++++|...|+++.+.+.. ++..++..+
T Consensus       140 ~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  219 (365)
T 4eqf_A          140 AVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGL  219 (365)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHH
T ss_pred             HHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHH
Confidence            3455 7788888888888887765332222        23345578899999999999999999886422 267899999


Q ss_pred             HHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChH
Q 045511           73 LKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHK  149 (209)
Q Consensus        73 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~  149 (209)
                      ...+.+.|++++|.+.|+...+.. +.+..+|+.+...|.+.|++++|.+.|++..   ..+..+|..+...|...|+++
T Consensus       220 ~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~  298 (365)
T 4eqf_A          220 GVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYR  298 (365)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHH
Confidence            999999999999999999998875 4568899999999999999999999999873   345788999999999999999


Q ss_pred             HHHHHHhhC-CCCCC-------------HHhHHHHHHHhccccchhHHHHHHH
Q 045511          150 EAIDMFCGI-DVKPN-------------ANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       150 ~a~~~~~~m-~~~p~-------------~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      +|...|++. ...|+             ...+..+-.++...|+.+.+..+..
T Consensus       299 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  351 (365)
T 4eqf_A          299 EAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANL  351 (365)
T ss_dssp             HHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            999999998 33332             6788999999999999998887754

>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=99.28  E-value=5.7e-11  Score=91.25  Aligned_cols=194  Identities=7%  Similarity=-0.047  Sum_probs=149.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|...+.++.+..  +.+...|..+...+.+.|++++|...|++..+.. +.+..++..+...+...|++++|.
T Consensus        33 ~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~  109 (327)
T 3cv0_A           33 KLANLAEAALAFEAVCQAA--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAAL  109 (327)
T ss_dssp             HTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHHHcCCHHHHH
Confidence            6777788888888777653  2355788889999999999999999999998763 346788889999999999999999


Q ss_pred             HHHHHHHHhccCccHhHHHHH--------------HH-HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCCh
Q 045511           87 EIHAHVIKYGHLHDIFIQNSL--------------LH-FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFH  148 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~l--------------l~-~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~  148 (209)
                      +.++...+.. +.+...+..+              .. .+...|++++|.+.+++..   ..+...+..+...+...|++
T Consensus       110 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~  188 (327)
T 3cv0_A          110 ASLRAWLLSQ-PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNY  188 (327)
T ss_dssp             HHHHHHHHTS-TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHhC-CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccH
Confidence            9999988764 2222333333              22 3778889999999998873   34678899999999999999


Q ss_pred             HHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHh
Q 045511          149 KEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAV  205 (209)
Q Consensus       149 ~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  205 (209)
                      ++|...|.+. ...| +..++..+...+...|++++|.+.+....+.. ..+...+..+
T Consensus       189 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l  246 (327)
T 3cv0_A          189 DSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNM  246 (327)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHH
Confidence            9999999998 4455 46788999999999999999999999887764 2233444443

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

Probab=99.27  E-value=3.3e-10  Score=87.87  Aligned_cols=187  Identities=12%  Similarity=0.012  Sum_probs=155.6

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ..+ +.++.++|...+.++.+..  +.+...|..+...+.+.|++++|...|++..+.. +-+...|..+...+...|++
T Consensus        11 ~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~   87 (359)
T 3ieg_A           11 KKLLAAGQLADALSQFHAAVDGD--PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKL   87 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCCh
Confidence            344 7888889998888888753  2356889999999999999999999999998754 23668899999999999999


Q ss_pred             HHHHHHHHHHHHhccC--ccHhHHHHH------------HHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           83 QKGLEIHAHVIKYGHL--HDIFIQNSL------------LHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~--~~~~~~~~l------------l~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      ++|.+.++...+....  .+...+..+            ...+...|++++|.+++++..   ..+...+..+...+...
T Consensus        88 ~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (359)
T 3ieg_A           88 DEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKE  167 (359)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHC
Confidence            9999999999876420  244555555            578999999999999999873   35678899999999999


Q ss_pred             CChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          146 GFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       146 g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |++++|...|.+. ...| +..++..+...+...|++++|...+....+.
T Consensus       168 ~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  217 (359)
T 3ieg_A          168 GEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  217 (359)
T ss_dssp             TCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            9999999999998 5555 5678889999999999999999999988765

>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=7e-10  Score=78.69  Aligned_cols=162  Identities=14%  Similarity=0.073  Sum_probs=139.6

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ++.+|..+=..+.+.|++++|.+.|++..+.. +-+...+..+-..+.+.|+++.+.+.+....+.. +.+...+..+-.
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHH
Confidence            45788899999999999999999999998854 2366788999999999999999999999988765 456778888888


Q ss_pred             HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHH
Q 045511          110 FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~  184 (209)
                      .+...++++.|.+.+.+..   ..+...+..+-..|.+.|++++|++.|++. .+.|+ ..++..+-..+.+.|++++|.
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~  161 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAV  161 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHH
Confidence            9999999999999998873   346778889999999999999999999998 66664 467888999999999999999


Q ss_pred             HHHHHHHHh
Q 045511          185 AIHAHSLRN  193 (209)
Q Consensus       185 ~~~~~~~~~  193 (209)
                      +.|+...+.
T Consensus       162 ~~~~~al~~  170 (184)
T 3vtx_A          162 KYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHhC
Confidence            999988765

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

Probab=99.27  E-value=4.3e-10  Score=91.71  Aligned_cols=186  Identities=8%  Similarity=0.000  Sum_probs=158.1

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      .++ +.++.++|.+.+.++.+..   |+...|..+...+.+.|++++|...+++..+.. +.+...+..+...+...|++
T Consensus       245 ~~~~~~~~~~~A~~~~~~~l~~~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~  320 (514)
T 2gw1_A          245 IFKFLKNDPLGAHEDIKKAIELF---PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNY  320 (514)
T ss_dssp             HHHHHSSCHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCT
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC---ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCH
Confidence            445 7788888888888887764   448888999999999999999999999998864 34667899999999999999


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      +.|...++...+.. +.+..++..+...|...|++++|.++++...   ..+...|..+...+...|++++|...|.++ 
T Consensus       321 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  399 (514)
T 2gw1_A          321 DQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFDKALKQYDLAI  399 (514)
T ss_dssp             THHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            99999999998865 4467799999999999999999999999873   345678899999999999999999999998 


Q ss_pred             CCCCC-------HHhHHHHHHHhcc---ccchhHHHHHHHHHHHhc
Q 045511          159 DVKPN-------ANTLVSVLSACSS---LGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       159 ~~~p~-------~~t~~~li~~~~~---~g~~~~a~~~~~~~~~~~  194 (209)
                      ...|+       ..++..+...+..   .|++++|...++...+..
T Consensus       400 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~  445 (514)
T 2gw1_A          400 ELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD  445 (514)
T ss_dssp             HHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC
T ss_pred             HhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC
Confidence            33333       3388888999999   999999999999887763

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

Probab=99.27  E-value=1.8e-10  Score=85.42  Aligned_cols=161  Identities=11%  Similarity=-0.007  Sum_probs=138.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC--cc----HhHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL--HD----IFIQN  105 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~--~~----~~~~~  105 (209)
                      ..|..+-..+.+.|++++|...|++..+..  .+...|..+-..+...|++++|.+.++...+....  ++    ..++.
T Consensus         6 ~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   83 (258)
T 3uq3_A            6 DKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFA   83 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHH
Confidence            567888889999999999999999999887  78899999999999999999999999998876422  12    57899


Q ss_pred             HHHHHHHhCCChhhHHHHHHhcCC-----------------------------CcHhHHHHHHHHHHhCCChHHHHHHHh
Q 045511          106 SLLHFYVTVKDIFSAHQIFNSVVF-----------------------------PDVVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus       106 ~ll~~~~~~g~~~~a~~~~~~~~~-----------------------------~~~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      .+...|.+.|++++|.+.|++..+                             .+...|..+...+...|++++|...|.
T Consensus        84 ~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~  163 (258)
T 3uq3_A           84 RIGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYT  163 (258)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            999999999999999999987632                             134578888899999999999999999


Q ss_pred             hC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          157 GI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       157 ~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      +. ...| +..++..+...+...|++++|...+....+..
T Consensus       164 ~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~  203 (258)
T 3uq3_A          164 EMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD  203 (258)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            98 4444 46788999999999999999999999987764

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

Probab=99.25  E-value=1.1e-09  Score=84.93  Aligned_cols=186  Identities=15%  Similarity=0.044  Sum_probs=150.8

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ..+ ..++.++|.+.+.++.+..+  .+...+..+...+.+.|++++|...+++..+.. +.+..++..+...+...|++
T Consensus       128 ~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~  204 (359)
T 3ieg_A          128 LDAFDGADYTAAITFLDKILEVCV--WDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDH  204 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence            344 67788888888888876642  355889999999999999999999999998864 45778899999999999999


Q ss_pred             HHHHHHHHHHHHhccCccHhHHH------------HHHHHHHhCCChhhHHHHHHhcC--CCc-H----hHHHHHHHHHH
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQN------------SLLHFYVTVKDIFSAHQIFNSVV--FPD-V----VTWTTIISGLS  143 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~------------~ll~~~~~~g~~~~a~~~~~~~~--~~~-~----~~~~~li~~~~  143 (209)
                      ++|.+.++...+.. +.+...+.            .+...+.+.|++++|.+.+++..  .|+ .    ..+..+-..+.
T Consensus       205 ~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~  283 (359)
T 3ieg_A          205 ELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFS  283 (359)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC-ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHH
Confidence            99999999998765 23333333            23667899999999999999873  233 2    23556778999


Q ss_pred             hCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          144 KCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ..|++++|...|.+. ...| +..++..+-..+...|++++|.+.+....+.
T Consensus       284 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~  335 (359)
T 3ieg_A          284 KDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH  335 (359)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            999999999999998 5556 6678999999999999999999999988776

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

Probab=99.21  E-value=1.3e-09  Score=81.78  Aligned_cols=184  Identities=11%  Similarity=0.020  Sum_probs=147.2

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC--HHHHHHHHHHHhccccHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN--HYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~   84 (209)
                      +.++.++|.+.+.++.+..+  .+...|..+...+.+.|++++|...+++..+.+-.|+  ...|..+-..+...|++++
T Consensus        15 ~~~~~~~A~~~~~~~l~~~p--~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~   92 (272)
T 3u4t_A           15 KNNNYAEAIEVFNKLEAKKY--NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSL   92 (272)
T ss_dssp             TTTCHHHHHHHHHHHHHTTC--CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HhcCHHHHHHHHHHHHHhCC--CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHH
Confidence            77888888888888876532  2446899999999999999999999999988442222  2348889999999999999


Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV  160 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~  160 (209)
                      |.+.|+...+.. +.+..++..+-..|...|++++|.+.|++..+   .+...|..+-..+...+++++|.+.|.+. ..
T Consensus        93 A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  171 (272)
T 3u4t_A           93 AIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKADSSFVKVLEL  171 (272)
T ss_dssp             HHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999998875 44668999999999999999999999999843   35666777663444556999999999999 66


Q ss_pred             CCC-HHhHHHHHHHhccccc---hhHHHHHHHHHHHh
Q 045511          161 KPN-ANTLVSVLSACSSLGS---RKLGKAIHAHSLRN  193 (209)
Q Consensus       161 ~p~-~~t~~~li~~~~~~g~---~~~a~~~~~~~~~~  193 (209)
                      .|+ ...+..+...+...|+   .++|...+....+.
T Consensus       172 ~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  208 (272)
T 3u4t_A          172 KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEV  208 (272)
T ss_dssp             STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHH
T ss_pred             CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHH
Confidence            666 4667777777777787   88899888877655

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.19  E-value=1.1e-09  Score=89.97  Aligned_cols=183  Identities=10%  Similarity=-0.002  Sum_probs=145.2

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      ..++.++|.+.+.++.+.   .|+...|..+...+.+.|++++|...|++..+.. +.+..+|..+...+...|++++|.
T Consensus       255 ~~~~~~~A~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~  330 (537)
T 3fp2_A          255 LKNNLLDAQVLLQESINL---HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAK  330 (537)
T ss_dssp             HTTCHHHHHHHHHHHHHH---CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hcccHHHHHHHHHHHHhc---CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHH
Confidence            456666777777776664   3667888889999999999999999999998754 245788999999999999999999


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP  162 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p  162 (209)
                      +.++...+.. +.+..++..+...|...|++++|.+.+++..   ..+...+..+...+...|++++|...|.+. ...|
T Consensus       331 ~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~  409 (537)
T 3fp2_A          331 EDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEE  409 (537)
T ss_dssp             HHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCC
Confidence            9999998875 3456789999999999999999999998873   345678889999999999999999999987 2222


Q ss_pred             -------CHHhHHHHHHHhccc----------cchhHHHHHHHHHHHhc
Q 045511          163 -------NANTLVSVLSACSSL----------GSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       163 -------~~~t~~~li~~~~~~----------g~~~~a~~~~~~~~~~~  194 (209)
                             ....+......+...          |++++|...++...+..
T Consensus       410 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~  458 (537)
T 3fp2_A          410 VQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD  458 (537)
T ss_dssp             HCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC
T ss_pred             cchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC
Confidence                   222233444556666          99999999999887763

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

Probab=99.19  E-value=1.7e-09  Score=83.46  Aligned_cols=178  Identities=12%  Similarity=0.047  Sum_probs=141.4

Q ss_pred             CcchHhHHHHHHHHhhCCCc-ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-H-HHHHHHHHHhccccHHHHHHH
Q 045511           12 TLSFKQLNQIHAQIIKIPQP-HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-Y-TFTQALKACSLAHAHQKGLEI   88 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~-t~~~ll~~~~~~~~~~~a~~~   88 (209)
                      ++|...+.++.+.  ..|+. ..|..+...+.+.|++++|..+|++..+  +.|+. . .|..+...+.+.|++++|..+
T Consensus        81 ~~A~~~~~rAl~~--~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~  156 (308)
T 2ond_A           81 DEAANIYERAIST--LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMI  156 (308)
T ss_dssp             HHHHHHHHHHHTT--TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             HHHHHHHHHHHHH--hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHH
Confidence            5566555555542  13544 6899999999999999999999999998  44543 3 799999999999999999999


Q ss_pred             HHHHHHhccCccHhHHHHHHHHHH-hCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-C---C
Q 045511           89 HAHVIKYGHLHDIFIQNSLLHFYV-TVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-D---V  160 (209)
Q Consensus        89 ~~~m~~~g~~~~~~~~~~ll~~~~-~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~---~  160 (209)
                      |+...+.. +++...|........ ..|++++|.++|+...   ..+...|..++..+.+.|++++|..+|.+. .   +
T Consensus       157 ~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l  235 (308)
T 2ond_A          157 FKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  235 (308)
T ss_dssp             HHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSS
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCC
Confidence            99998765 344555654444322 3799999999999873   236788999999999999999999999998 3   3


Q ss_pred             CCC--HHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          161 KPN--ANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       161 ~p~--~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .|+  ...|..++....+.|+.+.|..++..+.+..
T Consensus       236 ~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~~  271 (308)
T 2ond_A          236 PPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF  271 (308)
T ss_dssp             CGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc
Confidence            653  4678888999999999999999999887763

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

Probab=99.18  E-value=8e-10  Score=82.88  Aligned_cols=186  Identities=11%  Similarity=-0.052  Sum_probs=113.8

Q ss_pred             hccCCCcchHhHHHHHHHHhh--CCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIK--IPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~   84 (209)
                      +.++.++|.+.+.++.+....  ..+..+|..+...+...|++++|...|++..+.+ +.+..+|..+-..+...|++++
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHH
Confidence            455666666666666654211  1133666666677777777777777777766543 2345666666677777777777


Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHH-------------------------
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTT-------------------------  137 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~-------------------------  137 (209)
                      |.+.|+...+.. +.+..++..+...|.+.|++++|.+.|++..  .|+......                         
T Consensus        96 A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  174 (275)
T 1xnf_A           96 AYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS  174 (275)
T ss_dssp             HHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            777777666653 3345666677777777777777777776652  232222222                         


Q ss_pred             --------HHHHHHhCCChHHHHHHHhhC-CCCCC-----HHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          138 --------IISGLSKCGFHKEAIDMFCGI-DVKPN-----ANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       138 --------li~~~~~~g~~~~a~~~~~~m-~~~p~-----~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                              +...+...++.++|...+.+. ...|+     ..++..+...+.+.|++++|...++...+..
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  245 (275)
T 1xnf_A          175 DKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN  245 (275)
T ss_dssp             CCCSTHHHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             CcchHHHHHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC
Confidence                    333333444444444444444 33332     4677788888889999999999998887653

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

Probab=99.16  E-value=1.6e-10  Score=88.09  Aligned_cols=190  Identities=13%  Similarity=0.076  Sum_probs=149.9

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhC------CCcccHHHHHHHHHcCCCccchHHHHHHhhhC------C-CCCCHHHH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKI------PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNC------P-SSYNHYTF   69 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~------p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~------g-~~p~~~t~   69 (209)
                      ..+ ..++.++|...+.++.+.....      ....++..+...+...|++++|...+++....      + .+....++
T Consensus        35 ~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  114 (311)
T 3nf1_A           35 IQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATL  114 (311)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHH
Confidence            445 7788888998888888764321      12377888999999999999999999998764      2 22345778


Q ss_pred             HHHHHHHhccccHHHHHHHHHHHHHhc------c-CccHhHHHHHHHHHHhCCChhhHHHHHHhcC----------CC-c
Q 045511           70 TQALKACSLAHAHQKGLEIHAHVIKYG------H-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV----------FP-D  131 (209)
Q Consensus        70 ~~ll~~~~~~~~~~~a~~~~~~m~~~g------~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~----------~~-~  131 (209)
                      ..+...+...|++++|.+.++...+..      - +....++..+-..|...|++++|.+++++..          .| .
T Consensus       115 ~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  194 (311)
T 3nf1_A          115 NNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNV  194 (311)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHH
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHH
Confidence            889999999999999999999887652      2 2245678899999999999999999998762          12 2


Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHhhC-C-------------------------------------------------CC
Q 045511          132 VVTWTTIISGLSKCGFHKEAIDMFCGI-D-------------------------------------------------VK  161 (209)
Q Consensus       132 ~~~~~~li~~~~~~g~~~~a~~~~~~m-~-------------------------------------------------~~  161 (209)
                      ..++..+...|...|++++|...|.+. .                                                 ..
T Consensus       195 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  274 (311)
T 3nf1_A          195 AKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDS  274 (311)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---------C
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCC
Confidence            457888999999999999999999887 2                                                 12


Q ss_pred             CC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |+ ..++..+...|.+.|++++|.+.++...+.
T Consensus       275 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  307 (311)
T 3nf1_A          275 PTVTTTLKNLGALYRRQGKFEAAETLEEAAMRS  307 (311)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            32 356888899999999999999999877654

>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=99.16  E-value=1.4e-09  Score=72.24  Aligned_cols=122  Identities=15%  Similarity=0.103  Sum_probs=55.9

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      |..+...+.+.|++++|..+++++.+.+ +.+...+..+...+...|+++.|...++.+.+.+ +.+...+..+...+..
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            3444445555555555555555554432 1233444444445555555555555555544433 2233444444444444


Q ss_pred             CCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          114 VKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       114 ~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      .|++++|.++++++.   ..+...+..+...+...|++++|...|.+
T Consensus        82 ~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  128 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQK  128 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHH
Confidence            455555544444431   12233444444444444444444444443

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

Probab=99.15  E-value=2.9e-10  Score=85.30  Aligned_cols=152  Identities=12%  Similarity=-0.019  Sum_probs=128.7

Q ss_pred             HHcCCCccchHHHHHHhhhCCCC---CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSS---YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~---p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~  117 (209)
                      ....|++++|...|+++.+....   .+..+|..+...+...|++++|.+.|+...+.. +.+..+|..+...|...|++
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~   93 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNF   93 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCH
Confidence            34568899999999999886421   246788899999999999999999999999875 45688999999999999999


Q ss_pred             hhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          118 FSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       118 ~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ++|.+.|++..   ..+...+..+...|...|++++|...|+++ ...|+.......+..+...|++++|...+....+.
T Consensus        94 ~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  173 (275)
T 1xnf_A           94 DAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  173 (275)
T ss_dssp             HHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            99999999883   346788999999999999999999999999 77777776666666777889999999999877665

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.15  E-value=2.1e-10  Score=86.07  Aligned_cols=186  Identities=15%  Similarity=0.086  Sum_probs=148.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhC-----C-CcccHHHHHHHHHcCCCccchHHHHHHhhhC------CC-CCCHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKI-----P-QPHILNTLLKLLTQSSTPQNAIPLYNKMLNC------PS-SYNHYTFTQAL   73 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~-----p-~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~------g~-~p~~~t~~~ll   73 (209)
                      ..+.++.|.+.+.+..+.....     | ...++..+-..+...|++++|...+++..+.      +- +....++..+-
T Consensus        13 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~   92 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLA   92 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHH
Confidence            5678889999999888876322     1 2378899999999999999999999998764      22 23457889999


Q ss_pred             HHHhccccHHHHHHHHHHHHHhc-------cCccHhHHHHHHHHHHhCCChhhHHHHHHhcC----------CC-cHhHH
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYG-------HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV----------FP-DVVTW  135 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g-------~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~----------~~-~~~~~  135 (209)
                      ..+...|++++|.+.++...+..       -+....++..+-..|...|++++|.+.+++..          .| ...++
T Consensus        93 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  172 (283)
T 3edt_B           93 VLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTK  172 (283)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            99999999999999999887652       12345688999999999999999999998762          22 35678


Q ss_pred             HHHHHHHHhCCChHHHHHHHhhC-CC-------------------------------------------------CCC-H
Q 045511          136 TTIISGLSKCGFHKEAIDMFCGI-DV-------------------------------------------------KPN-A  164 (209)
Q Consensus       136 ~~li~~~~~~g~~~~a~~~~~~m-~~-------------------------------------------------~p~-~  164 (209)
                      ..+...|...|++++|...|.+. ..                                                 .|+ .
T Consensus       173 ~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (283)
T 3edt_B          173 NNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVN  252 (283)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHHH
Confidence            88999999999999999999877 11                                                 122 2


Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      .++..+...+...|++++|...++...+
T Consensus       253 ~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          253 TTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4678888899999999999999987754

>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=99.15  E-value=1.2e-09  Score=93.64  Aligned_cols=159  Identities=13%  Similarity=0.066  Sum_probs=140.1

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..+|+.+-..+.+.|++++|.+.|++..+..  | +...|..+-.++.+.|++++|.+.|+...+.. +-+...|+.+-.
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~--P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~   85 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVF--PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            3789999999999999999999999998853  4 46889999999999999999999999998865 345789999999


Q ss_pred             HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHH
Q 045511          110 FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~  184 (209)
                      .|.+.|++++|.+.|++..   ..+...|+.+-..|.+.|++++|++.|++. .+.|+. ..+..+...+...|++++|.
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~  165 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYD  165 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHH
Confidence            9999999999999999873   346789999999999999999999999998 777865 67889999999999999999


Q ss_pred             HHHHHHHH
Q 045511          185 AIHAHSLR  192 (209)
Q Consensus       185 ~~~~~~~~  192 (209)
                      +.++...+
T Consensus       166 ~~~~kal~  173 (723)
T 4gyw_A          166 ERMKKLVS  173 (723)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88886644

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.15  E-value=6.6e-10  Score=91.25  Aligned_cols=159  Identities=11%  Similarity=-0.013  Sum_probs=139.0

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      +|..+-..+...|++++|...|++..+.  .|+...+..+-..+...|+++.|.+.++...+.. +.+..++..+...|.
T Consensus       245 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~  321 (537)
T 3fp2_A          245 ALCYTGIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYF  321 (537)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHH
Confidence            5677778888999999999999999985  4668889999999999999999999999998875 456789999999999


Q ss_pred             hCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHH
Q 045511          113 TVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIH  187 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~  187 (209)
                      ..|++++|.+.|++..   ..+...|..+...+...|++++|...|.+. ...|+ ...+..+...+...|++++|.+.+
T Consensus       322 ~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  401 (537)
T 3fp2_A          322 ILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQY  401 (537)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHH
Confidence            9999999999999873   335678999999999999999999999998 44554 568888999999999999999999


Q ss_pred             HHHHHhc
Q 045511          188 AHSLRNL  194 (209)
Q Consensus       188 ~~~~~~~  194 (209)
                      ....+..
T Consensus       402 ~~a~~~~  408 (537)
T 3fp2_A          402 DIAKRLE  408 (537)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHcC
Confidence            9887654

>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=99.14  E-value=5.1e-09  Score=69.41  Aligned_cols=125  Identities=14%  Similarity=0.105  Sum_probs=108.0

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK  144 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~  144 (209)
                      .|..+...+...|++++|..+++.+.+.. +.+..++..+...+...|++++|.++++++.   ..+...+..+...+..
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHH
Confidence            56777888899999999999999998775 4567888999999999999999999999873   3467788899999999


Q ss_pred             CCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          145 CGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       145 ~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .|++++|...|.++ ...| +..++..+...+...|++++|...+..+.+.
T Consensus        82 ~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            99999999999998 4444 5678888999999999999999999988765

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.14  E-value=9.3e-09  Score=75.39  Aligned_cols=164  Identities=12%  Similarity=0.046  Sum_probs=128.8

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      .|+..|...-..+.+.|++++|...|++..+..-+++...+..+-..+...|++++|.+.++...+.. +.+..+|..+-
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHH
Confidence            34567777778888899999999999988886544677777778888889999999999999888754 33567888888


Q ss_pred             HHHHhCCChhhHHHHHHhcC--CC-cH-------hHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC---HHhHHHHHHHh
Q 045511          109 HFYVTVKDIFSAHQIFNSVV--FP-DV-------VTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN---ANTLVSVLSAC  174 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~--~~-~~-------~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~---~~t~~~li~~~  174 (209)
                      ..|...|++++|.+.+++..  .| +.       ..|..+-..+...|++++|.+.|.+. ...|+   ...+..+-..+
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~  163 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLF  163 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHH
Confidence            99999999999999998873  23 33       45777778888899999999999888 77777   35667777777


Q ss_pred             ccccch---------------------------hHHHHHHHHHHHh
Q 045511          175 SSLGSR---------------------------KLGKAIHAHSLRN  193 (209)
Q Consensus       175 ~~~g~~---------------------------~~a~~~~~~~~~~  193 (209)
                      ...|+.                           ++|...++...+.
T Consensus       164 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l  209 (228)
T 4i17_A          164 YNNGADVLRKATPLASSNKEKYASEKAKADAAFKKAVDYLGEAVTL  209 (228)
T ss_dssp             HHHHHHHHHHHGGGTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            777776                           7888888777665

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

Probab=99.13  E-value=6.4e-09  Score=80.13  Aligned_cols=189  Identities=11%  Similarity=-0.003  Sum_probs=140.6

Q ss_pred             chHhHHHHHHHHhhCCCcccHHHHHHHHH-------cCCCc-------cchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc
Q 045511           14 SFKQLNQIHAQIIKIPQPHILNTLLKLLT-------QSSTP-------QNAIPLYNKMLNCPSSYNHYTFTQALKACSLA   79 (209)
Q Consensus        14 a~~~~~~~~~~~~~~p~~~~~~~li~~~~-------~~g~~-------~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~   79 (209)
                      +...+.++.+..  +.++..|..+...+.       +.|++       ++|..+|++..+.--+-+...|..+...+.+.
T Consensus        35 a~~~~~~al~~~--p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~  112 (308)
T 2ond_A           35 VMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR  112 (308)
T ss_dssp             HHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHc--CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhc
Confidence            344555555543  234578888777775       45887       89999999998841223556899999999999


Q ss_pred             ccHHHHHHHHHHHHHhccCcc-Hh-HHHHHHHHHHhCCChhhHHHHHHhcCC---CcHhHHHHHHHH-HHhCCChHHHHH
Q 045511           80 HAHQKGLEIHAHVIKYGHLHD-IF-IQNSLLHFYVTVKDIFSAHQIFNSVVF---PDVVTWTTIISG-LSKCGFHKEAID  153 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~-~~-~~~~ll~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~-~~~~g~~~~a~~  153 (209)
                      |++++|.++|+...+.  .|+ .. +|..+...+.+.|++++|.++|++..+   .+...|...... +...|++++|..
T Consensus       113 ~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~~A~~  190 (308)
T 2ond_A          113 MKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFK  190 (308)
T ss_dssp             TCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHHHHHH
Confidence            9999999999999984  454 33 899999999999999999999998743   233444433322 223799999999


Q ss_pred             HHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHhc-cCCC--chhHhHhh
Q 045511          154 MFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL-NENN--IILDNAVL  206 (209)
Q Consensus       154 ~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~p~--~~~~~~li  206 (209)
                      +|.+. ...| +...+..++..+.+.|++++|..+|+...+.. +.|+  ...|..++
T Consensus       191 ~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~  248 (308)
T 2ond_A          191 IFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFL  248 (308)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHH
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence            99988 4445 45678888999999999999999999998873 4553  34555544

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

Probab=99.12  E-value=2.6e-09  Score=75.69  Aligned_cols=161  Identities=11%  Similarity=0.034  Sum_probs=134.1

Q ss_pred             hcch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc
Q 045511            3 VNGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA   81 (209)
Q Consensus         3 i~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~   81 (209)
                      ..++ +.|+.++|.+.+.++.+..+  -+..+|..+-..+.+.|++++|...++....... -+...+..+-..+...++
T Consensus        12 G~~~~~~g~~~~A~~~~~~al~~~p--~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   88 (184)
T 3vtx_A           12 GDKKRTKGDFDGAIRAYKKVLKADP--NNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDT-TSAEAYYILGSANFMIDE   88 (184)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-hhHHHHHHHHHHHHHcCC
Confidence            3455 78889999999998887642  3558899999999999999999999999887543 355677777888899999


Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ++.+.+.+....+.. +.+...+..+-..|.+.|++++|.+.|++..   ..+..+|..+-..|.+.|++++|.+.|++.
T Consensus        89 ~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a  167 (184)
T 3vtx_A           89 KQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKYFKKA  167 (184)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            999999999888765 4567889999999999999999999999873   346788999999999999999999999987


Q ss_pred             -CCCCCHHhH
Q 045511          159 -DVKPNANTL  167 (209)
Q Consensus       159 -~~~p~~~t~  167 (209)
                       .+.|+..-|
T Consensus       168 l~~~p~~a~~  177 (184)
T 3vtx_A          168 LEKEEKKAKY  177 (184)
T ss_dssp             HHTTHHHHHH
T ss_pred             HhCCccCHHH
Confidence             666665433

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

Probab=99.09  E-value=1e-09  Score=89.77  Aligned_cols=176  Identities=9%  Similarity=-0.094  Sum_probs=113.2

Q ss_pred             hccCC-CcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc------
Q 045511            7 KSLKP-TLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA------   79 (209)
Q Consensus         7 ~~~~~-~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~------   79 (209)
                      ..++. ++|.+.+.++.+..  +.+...|..+-..+.+.|++++|...|++..+..  |+...+..+-..+...      
T Consensus       114 ~~g~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg~~~~~~~~~~~~  189 (474)
T 4abn_A          114 VTPDYSPEAEVLLSKAVKLE--PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLSMVLRQLQTDSGD  189 (474)
T ss_dssp             SSSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHHHHHTTCCCSCHH
T ss_pred             hccccHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHHHHHHHhccCChh
Confidence            45555 66666666665542  1234667777777777777777777777776643  5566666677777776      


Q ss_pred             ---ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC--------CChhhHHHHHHhcC--CC----cHhHHHHHHHHH
Q 045511           80 ---HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV--------KDIFSAHQIFNSVV--FP----DVVTWTTIISGL  142 (209)
Q Consensus        80 ---~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~--------g~~~~a~~~~~~~~--~~----~~~~~~~li~~~  142 (209)
                         |++++|.+.|+...+.. +.+...|..+-..|...        |++++|.+.|++..  .|    +...|..+-..|
T Consensus       190 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~  268 (474)
T 4abn_A          190 EHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLH  268 (474)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHH
Confidence               77777777777766654 33456667777777666        67777777776652  23    556677777777


Q ss_pred             HhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHH
Q 045511          143 SKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIH  187 (209)
Q Consensus       143 ~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~  187 (209)
                      ...|++++|.+.|++. ...|+. ..+..+-..+...|++++|.+.+
T Consensus       269 ~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          269 KYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7777777777777766 444543 34556666666666666666543

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

Probab=99.09  E-value=1.2e-08  Score=76.36  Aligned_cols=162  Identities=10%  Similarity=-0.050  Sum_probs=130.4

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--HhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--IFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~  109 (209)
                      ..+-..-..+.+.|++++|...|++..+... -+...+..+...+...|++++|.+.++...+.+..++  ..+|..+-.
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGK   82 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHH
Confidence            3455667788899999999999999988642 3445888888899999999999999999988442222  335899999


Q ss_pred             HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHH
Q 045511          110 FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~  184 (209)
                      .|...|++++|.+.|++..   ..+...|..+-..|...|++++|...|.+. ...|+. ..+..+-..+...+++++|.
T Consensus        83 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~  162 (272)
T 3u4t_A           83 ILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKAD  162 (272)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999873   345678999999999999999999999998 666755 45555552455566999999


Q ss_pred             HHHHHHHHhc
Q 045511          185 AIHAHSLRNL  194 (209)
Q Consensus       185 ~~~~~~~~~~  194 (209)
                      +.+....+..
T Consensus       163 ~~~~~a~~~~  172 (272)
T 3u4t_A          163 SSFVKVLELK  172 (272)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHHHHHHhC
Confidence            9999887763

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.08  E-value=5.2e-09  Score=83.38  Aligned_cols=180  Identities=9%  Similarity=0.046  Sum_probs=148.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCC-ccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSST-PQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~-~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +.++.++|.+.+.++.+..  +.+..+|+.+-..+.+.|+ +++|...|++..+.+- -+...|..+-.++.+.|++++|
T Consensus       109 ~~g~~~~Al~~~~~al~l~--P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P-~~~~a~~~~g~~~~~~g~~~eA  185 (382)
T 2h6f_A          109 RDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRVLVEWLRDPSQE  185 (382)
T ss_dssp             HTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTH
T ss_pred             HCCChHHHHHHHHHHHHhC--ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHccCHHHH
Confidence            5677888888888887764  2245889999999999997 9999999999998542 3668899999999999999999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh-CCChHHH-----HHHHh
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK-CGFHKEA-----IDMFC  156 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~-~g~~~~a-----~~~~~  156 (209)
                      ...|+..++.. +-+...|..+-..+.+.|++++|...|++..   ..+...|+.+-..+.. .|..++|     +..|+
T Consensus       186 l~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~  264 (382)
T 2h6f_A          186 LEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTL  264 (382)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHH
Confidence            99999999875 5578899999999999999999999999983   3467889999999999 6665777     47777


Q ss_pred             hC-CCCCCH-HhHHHHHHHhcccc--chhHHHHHHHHH
Q 045511          157 GI-DVKPNA-NTLVSVLSACSSLG--SRKLGKAIHAHS  190 (209)
Q Consensus       157 ~m-~~~p~~-~t~~~li~~~~~~g--~~~~a~~~~~~~  190 (209)
                      +. .+.|+. ..|..+-..+...|  ++++|.+.+..+
T Consensus       265 ~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          265 EMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh
Confidence            77 667754 56777777788877  688998888776

>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=99.06  E-value=1e-09  Score=77.15  Aligned_cols=148  Identities=12%  Similarity=-0.004  Sum_probs=122.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      ..++.+++.+.+.++.+..  +.+...+..+...+.+.|++++|...+++..+.. +.+...+..+...+...|++++|.
T Consensus        20 ~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~   96 (186)
T 3as5_A           20 KAGRYSQAVMLLEQVYDAD--AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQVQKYDLAV   96 (186)
T ss_dssp             HHTCHHHHHHHHTTTCCTT--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC--ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHH
Confidence            4556666665555554332  2345788899999999999999999999998763 346788888999999999999999


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +.++...+.. +.+...+..+...+...|++++|.+.+++..   ..+...+..+...+...|++++|...+++.
T Consensus        97 ~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  170 (186)
T 3as5_A           97 PLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKA  170 (186)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999998875 4577889999999999999999999999873   346788999999999999999999999887

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.06  E-value=1.8e-08  Score=75.91  Aligned_cols=176  Identities=14%  Similarity=-0.021  Sum_probs=89.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHc----CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc----
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQ----SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL----   78 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~----   78 (209)
                      +.++.++|.+.+.+..+    ..+..++..+-..+.+    .+++++|...|++..+.+   +...+..+-..+..    
T Consensus        18 ~~~~~~~A~~~~~~a~~----~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~   90 (273)
T 1ouv_A           18 KEKDFTQAKKYFEKACD----LKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLGNLYYSGQGV   90 (273)
T ss_dssp             HTTCHHHHHHHHHHHHH----TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSS
T ss_pred             hCCCHHHHHHHHHHHHH----CCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhCCCCc
Confidence            34455555555555544    1233455555555555    566666666666655544   44555555555555    


Q ss_pred             cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh----CCChhhHHHHHHhcCC-CcHhHHHHHHHHHHh----CCChH
Q 045511           79 AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT----VKDIFSAHQIFNSVVF-PDVVTWTTIISGLSK----CGFHK  149 (209)
Q Consensus        79 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~g~~~  149 (209)
                      .+++++|.+.|+...+.+   +...+..+-..|..    .+++++|.+.|++..+ .+...+..+-..|..    .++++
T Consensus        91 ~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~  167 (273)
T 1ouv_A           91 SQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRGTPKDLK  167 (273)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             ccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCCCCCCCHH
Confidence            566666666665555543   44555555555555    5566666655555421 233344444444444    55555


Q ss_pred             HHHHHHhhC-CCCCCHHhHHHHHHHhcc----ccchhHHHHHHHHHHHh
Q 045511          150 EAIDMFCGI-DVKPNANTLVSVLSACSS----LGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       150 ~a~~~~~~m-~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~~~~~  193 (209)
                      +|...|++. .. -+...+..+-..+..    .+++++|.+.++...+.
T Consensus       168 ~A~~~~~~a~~~-~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~  215 (273)
T 1ouv_A          168 KALASYDKACDL-KDSPGCFNAGNMYHHGEGATKNFKEALARYSKACEL  215 (273)
T ss_dssp             HHHHHHHHHHHT-TCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHC-CCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhC
Confidence            555555554 11 122334444444444    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=99.05  E-value=2.8e-08  Score=74.80  Aligned_cols=176  Identities=11%  Similarity=-0.025  Sum_probs=146.1

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHc----CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc----c
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQ----SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL----A   79 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~   79 (209)
                      .++.++|.+.+.+..+.    .+..++..+-..+.+    .+++++|...|++..+.+   +...+..+-..+..    .
T Consensus        55 ~~~~~~A~~~~~~a~~~----~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~  127 (273)
T 1ouv_A           55 EKNLKKAASFYAKACDL----NYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVT  127 (273)
T ss_dssp             CCCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSC
T ss_pred             CCCHHHHHHHHHHHHHC----CCHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcc
Confidence            56666677667666554    367888889899999    999999999999999876   67788888888888    9


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh----CCChhhHHHHHHhcCC-CcHhHHHHHHHHHHh----CCChHH
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT----VKDIFSAHQIFNSVVF-PDVVTWTTIISGLSK----CGFHKE  150 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~g~~~~  150 (209)
                      +++++|.+.|+...+.+   +...+..+-..|..    .+++++|.+.|++..+ .+...+..+-..|..    .+++++
T Consensus       128 ~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~  204 (273)
T 1ouv_A          128 RDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKE  204 (273)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHH
T ss_pred             cCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHH
Confidence            99999999999998876   56778888888888    8999999999988733 456778888888888    999999


Q ss_pred             HHHHHhhC-CCCCCHHhHHHHHHHhcc----ccchhHHHHHHHHHHHhc
Q 045511          151 AIDMFCGI-DVKPNANTLVSVLSACSS----LGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       151 a~~~~~~m-~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~~~~~~  194 (209)
                      |...|++. ...| ...+..+-..+.+    .+++++|.+.++...+.|
T Consensus       205 A~~~~~~a~~~~~-~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          205 ALARYSKACELEN-GGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHHHHHTTC-HHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCC-HHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            99999987 4444 5667777778888    999999999999988886

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

Probab=99.03  E-value=9.8e-09  Score=84.00  Aligned_cols=162  Identities=9%  Similarity=-0.008  Sum_probs=142.0

Q ss_pred             CcccHHHHHHHHHcCCCc-cchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTP-QNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~-~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      +...|..+-..+...|++ ++|...|++..+.. +-+...|..+-..+.+.|++++|.+.|+...+..  |+...+..+-
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg  177 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLS  177 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHH
Confidence            447888888999999999 99999999998754 2357889999999999999999999999998864  6678999999


Q ss_pred             HHHHhC---------CChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC--------CChHHHHHHHhhC-CCCC----C
Q 045511          109 HFYVTV---------KDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC--------GFHKEAIDMFCGI-DVKP----N  163 (209)
Q Consensus       109 ~~~~~~---------g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~--------g~~~~a~~~~~~m-~~~p----~  163 (209)
                      ..|...         |++++|.+.|++..   ..+...|..+-..|...        |++++|...|++. .+.|    +
T Consensus       178 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  257 (474)
T 4abn_A          178 MVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSN  257 (474)
T ss_dssp             HHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGC
T ss_pred             HHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccC
Confidence            999999         99999999999873   34678899999999888        9999999999998 6666    6


Q ss_pred             HHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          164 ANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       164 ~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ...+..+-..+...|++++|.+.|+...+..
T Consensus       258 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~  288 (474)
T 4abn_A          258 PDLHLNRATLHKYEESYGEALEGFSQAAALD  288 (474)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            6789999999999999999999999887763

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

Probab=98.99  E-value=3.2e-09  Score=80.83  Aligned_cols=162  Identities=13%  Similarity=0.074  Sum_probs=133.5

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhC-------CCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhc------c-
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNC-------PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYG------H-   97 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~-------g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g------~-   97 (209)
                      .++..+...+...|++++|..+|++..+.       ..+.....+..+-..+...|++++|.+.++...+..      - 
T Consensus        28 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  107 (311)
T 3nf1_A           28 RTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDH  107 (311)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            77888999999999999999999999873       233455778889999999999999999999887652      1 


Q ss_pred             CccHhHHHHHHHHHHhCCChhhHHHHHHhcCC----------C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CC-----
Q 045511           98 LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF----------P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DV-----  160 (209)
Q Consensus        98 ~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~----------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~-----  160 (209)
                      +....++..+...|...|++++|.+.+++..+          | ....+..+...+...|++++|.+.|.+. ..     
T Consensus       108 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~  187 (311)
T 3nf1_A          108 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKL  187 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence            23456899999999999999999999987621          2 3557888899999999999999999888 22     


Q ss_pred             ---CCC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          161 ---KPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       161 ---~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                         .|+ ..++..+...+...|++++|.+.+....+.
T Consensus       188 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  224 (311)
T 3nf1_A          188 GPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTR  224 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence               333 357888889999999999999999988764

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.93  E-value=1.5e-08  Score=80.17  Aligned_cols=187  Identities=7%  Similarity=-0.089  Sum_probs=147.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC-----cccHHHHHHHHHcCCCccchHHHHHHhhhC----CCCC-CHHHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ-----PHILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSSY-NHYTFTQALKAC   76 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-~~~t~~~ll~~~   76 (209)
                      ..++.+.|...+.++.+.....++     ..+++.+-..+...|++++|...|++..+.    +-.+ ...++..+-..+
T Consensus       155 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y  234 (383)
T 3ulq_A          155 YMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCK  234 (383)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHH
Confidence            678888889899998888766655     267888889999999999999999888653    2111 124788888899


Q ss_pred             hccccHHHHHHHHHHHHHh----cc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcC-------CCc-HhHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKY----GH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV-------FPD-VVTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~----g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~~~-~~~~~~li~~~~  143 (209)
                      ...|++++|.+.++...+.    +. +....++..+-..|.+.|++++|.+.+++..       .+. ...++.+-..+.
T Consensus       235 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~  314 (383)
T 3ulq_A          235 NSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYL  314 (383)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            9999999999999988763    22 3346789999999999999999999998762       222 234567778888


Q ss_pred             hCCC---hHHHHHHHhhCCCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          144 KCGF---HKEAIDMFCGIDVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       144 ~~g~---~~~a~~~~~~m~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ..|+   +++|+.++.+.+..|+. ..+..+-..|...|++++|.+.+....+.
T Consensus       315 ~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          315 SGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            8888   88999999988444444 46778888999999999999999977554

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

Probab=98.91  E-value=6e-08  Score=80.14  Aligned_cols=176  Identities=13%  Similarity=0.049  Sum_probs=134.9

Q ss_pred             cchHhHHHHHHHHhhCC-CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH--HHHHHHHHHHhccccHHHHHHHH
Q 045511           13 LSFKQLNQIHAQIIKIP-QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH--YTFTQALKACSLAHAHQKGLEIH   89 (209)
Q Consensus        13 ~a~~~~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~   89 (209)
                      ++...+....+.  ..| +...|..+...+.+.|++++|..+|++..+.  .|+.  ..|......+.+.|+++.|.++|
T Consensus       304 ~A~~~~~~Al~~--~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  379 (530)
T 2ooe_A          304 EAANIYERAIST--LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIF  379 (530)
T ss_dssp             HHHHHHHHHTTT--TCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHH
Confidence            455555554431  234 4588999999999999999999999999984  4543  47888899899999999999999


Q ss_pred             HHHHHhccCccHhHHHHHH-HHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC---C
Q 045511           90 AHVIKYGHLHDIFIQNSLL-HFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV---K  161 (209)
Q Consensus        90 ~~m~~~g~~~~~~~~~~ll-~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~---~  161 (209)
                      +...+.. +.+...|-... -.+...|+.++|.++|+...   ..+...|..++..+.+.|+.++|..+|.+. ..   .
T Consensus       380 ~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~  458 (530)
T 2ooe_A          380 KKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  458 (530)
T ss_dssp             HHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSC
T ss_pred             HHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCC
Confidence            9988753 22233332222 22346899999999999773   235788999999999999999999999998 22   3


Q ss_pred             CC--HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PN--ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~--~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |+  ...|...+......|+.+.+..+..++.+.
T Consensus       459 ~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          459 PEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             GGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            32  347888888888899999999999887665

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

Probab=98.87  E-value=1.1e-07  Score=72.65  Aligned_cols=183  Identities=8%  Similarity=-0.093  Sum_probs=129.3

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCCccchHHHHHHhhhC----CCCC-CHHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSSY-NHYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-~~~t~~~ll~~~~   77 (209)
                      ..++.++|...+.+..+......+    ..+|+.+-..+.+.|++++|...|++..+.    |-.+ -..+|..+-..+.
T Consensus        49 ~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~  128 (292)
T 1qqe_A           49 LRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILE  128 (292)
T ss_dssp             HTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            567788888888888777544333    368889999999999999999998887652    2111 1357888888888


Q ss_pred             cc-ccHHHHHHHHHHHHHhccCc-c----HhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc---H-----hHHHHHHHH
Q 045511           78 LA-HAHQKGLEIHAHVIKYGHLH-D----IFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD---V-----VTWTTIISG  141 (209)
Q Consensus        78 ~~-~~~~~a~~~~~~m~~~g~~~-~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~---~-----~~~~~li~~  141 (209)
                      .. |++++|...|+...+..... +    ..+++.+-..|.+.|++++|...|++..  .|+   .     ..|..+..+
T Consensus       129 ~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~  208 (292)
T 1qqe_A          129 NDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLC  208 (292)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHH
T ss_pred             HhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHH
Confidence            86 99999999998887643211 1    3578889999999999999999998872  121   1     156777788


Q ss_pred             HHhCCChHHHHHHHhhC-CCCCCHH------hHHHHHHHhc--cccchhHHHHHHHH
Q 045511          142 LSKCGFHKEAIDMFCGI-DVKPNAN------TLVSVLSACS--SLGSRKLGKAIHAH  189 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m-~~~p~~~------t~~~li~~~~--~~g~~~~a~~~~~~  189 (209)
                      +...|++++|...|++. .+.|+..      .+..++.++.  ..+++++|...|+.
T Consensus       209 ~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~  265 (292)
T 1qqe_A          209 QLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDN  265 (292)
T ss_dssp             HHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTT
T ss_pred             HHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhcc
Confidence            88999999999999988 6666543      3445566664  34556666666543

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

Probab=98.85  E-value=3e-07  Score=75.92  Aligned_cols=163  Identities=12%  Similarity=0.051  Sum_probs=128.9

Q ss_pred             CcccHHHHHHHHHc-------CCCcc-------chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           30 QPHILNTLLKLLTQ-------SSTPQ-------NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        30 ~~~~~~~li~~~~~-------~g~~~-------~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      +...|..+...+.+       .|+++       +|..+|++..+.-.+-+...|..+...+.+.|++++|.++|+...+.
T Consensus       271 ~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~  350 (530)
T 2ooe_A          271 HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI  350 (530)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc
Confidence            45788888887775       79987       89999999886323345788999999999999999999999999985


Q ss_pred             ccCcc--HhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHH-HHHHhCCChHHHHHHHhhC-CCCC-CHHhH
Q 045511           96 GHLHD--IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTII-SGLSKCGFHKEAIDMFCGI-DVKP-NANTL  167 (209)
Q Consensus        96 g~~~~--~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li-~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~  167 (209)
                        .|+  ...|..+...+.+.|++++|.++|++..+  | +...|-... ..+...|++++|..+|.+. ...| +...+
T Consensus       351 --~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~  428 (530)
T 2ooe_A          351 --EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYV  428 (530)
T ss_dssp             --SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             --cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHH
Confidence              454  35899999999999999999999998733  2 222222211 2234689999999999987 5556 46788


Q ss_pred             HHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          168 VSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       168 ~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ..++....+.|+.++|..+|+...+.+
T Consensus       429 ~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          429 LAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             HHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            999999999999999999999988764

>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=98.84  E-value=1.4e-07  Score=75.20  Aligned_cols=180  Identities=8%  Similarity=0.021  Sum_probs=144.7

Q ss_pred             hccC-CCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLK-PTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~-~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +.++ .++|...+.++.+..+  .+...|+.+-..+.+.|++++|...|++..+..- -+...|..+-.++.+.|++++|
T Consensus       143 ~~g~d~~eAl~~~~~al~l~P--~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP-~~~~a~~~lg~~~~~~g~~~eA  219 (382)
T 2h6f_A          143 SLQKDLHEEMNYITAIIEEQP--KNYQVWHHRRVLVEWLRDPSQELEFIADILNQDA-KNYHAWQHRQWVIQEFKLWDNE  219 (382)
T ss_dssp             HTTCCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTH
T ss_pred             HcccCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCc-cCHHHHHHHHHHHHHcCChHHH
Confidence            5565 7788888877777532  2558999999999999999999999999998642 3678899999999999999999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHh-CCChhhH-----HHHHHhcC---CCcHhHHHHHHHHHHhCC--ChHHHHHH
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVT-VKDIFSA-----HQIFNSVV---FPDVVTWTTIISGLSKCG--FHKEAIDM  154 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~-~g~~~~a-----~~~~~~~~---~~~~~~~~~li~~~~~~g--~~~~a~~~  154 (209)
                      .+.++..++.. +-+...|+.+-..+.+ .|..++|     .+.|++..   ..+...|+.+-..+...|  ++++|++.
T Consensus       220 l~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~  298 (382)
T 2h6f_A          220 LQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQ  298 (382)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHH
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHH
Confidence            99999999876 4578899999999999 6766887     46776652   345778999888898888  68999998


Q ss_pred             HhhCCCCC-CHHhHHHHHHHhcccc--------c-hhHHHHHHHHH
Q 045511          155 FCGIDVKP-NANTLVSVLSACSSLG--------S-RKLGKAIHAHS  190 (209)
Q Consensus       155 ~~~m~~~p-~~~t~~~li~~~~~~g--------~-~~~a~~~~~~~  190 (209)
                      +.++...| +...+..+...+.+.|        + .++|.++++.+
T Consensus       299 ~~~~~~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l  344 (382)
T 2h6f_A          299 LLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEIL  344 (382)
T ss_dssp             HHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred             HHHhccCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHH
Confidence            88873344 4567888888888764        3 58899999887

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.84  E-value=8.4e-08  Score=75.80  Aligned_cols=188  Identities=10%  Similarity=-0.034  Sum_probs=144.7

Q ss_pred             ch-hccCCCcchHhHHHHHHHHhhCCC-----cccHHHHHHHHHcCCCccchHHHHHHhhhC----CCCC-CHHHHHHHH
Q 045511            5 GL-KSLKPTLSFKQLNQIHAQIIKIPQ-----PHILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSSY-NHYTFTQAL   73 (209)
Q Consensus         5 ~~-~~~~~~~a~~~~~~~~~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-~~~t~~~ll   73 (209)
                      ++ ..++.+.|...+.++.+.+...++     ..+++.+-..+...|++++|...|++..+.    |-.+ ...++..+-
T Consensus       150 ~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg  229 (378)
T 3q15_A          150 AYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIA  229 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44 678888889899998888766554     267888889999999999999999887652    2111 235677788


Q ss_pred             HHHhccccHHHHHHHHHHHHHh----ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC-------CCc-HhHHHHHHHH
Q 045511           74 KACSLAHAHQKGLEIHAHVIKY----GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV-------FPD-VVTWTTIISG  141 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~----g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~~~-~~~~~~li~~  141 (209)
                      ..+...|++++|.+.++...+.    +.+....++..+-..|.+.|++++|...+++..       .+. ...++.+-..
T Consensus       230 ~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~l  309 (378)
T 3q15_A          230 NSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAV  309 (378)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            8889999999999999888762    223347788999999999999999999998761       222 3456666677


Q ss_pred             HHhCCC---hHHHHHHHhhCCCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          142 LSKCGF---HKEAIDMFCGIDVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       142 ~~~~g~---~~~a~~~~~~m~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      +...++   +++|+..+.+.+..|+. ..+..+-..|...|++++|...+....+
T Consensus       310 y~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          310 YKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            777788   88899999887444444 4667788889999999999999987644

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.84  E-value=1.1e-08  Score=81.36  Aligned_cols=187  Identities=10%  Similarity=-0.049  Sum_probs=120.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCCccchHHHHHHhhhC----C-CCCCHHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSSTPQNAIPLYNKMLNC----P-SSYNHYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g-~~p~~~t~~~ll~~~~   77 (209)
                      ..++.++|...+.++.+......+    ...+..+-..+...|++++|...+++..+.    + .+....++..+-..+.
T Consensus        98 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~  177 (411)
T 4a1s_A           98 YLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYH  177 (411)
T ss_dssp             HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHH
Confidence            556666677666666665433222    256667777777777877777777766542    1 1112346666677777


Q ss_pred             cccc-----------------HHHHHHHHHHHHHhc----c-CccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-----C
Q 045511           78 LAHA-----------------HQKGLEIHAHVIKYG----H-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----P  130 (209)
Q Consensus        78 ~~~~-----------------~~~a~~~~~~m~~~g----~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~  130 (209)
                      ..|+                 ++.|.+.++...+..    - .....++..+-..|...|++++|.+.+++..+     .
T Consensus       178 ~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  257 (411)
T 4a1s_A          178 AKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFG  257 (411)
T ss_dssp             HHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             HcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcC
Confidence            7777                 777777776654321    1 11234677777778888888888888776621     1


Q ss_pred             c----HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-------CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          131 D----VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-------NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       131 ~----~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-------~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +    ...+..+...|...|++++|...|++. ...|       ...++..+-..+...|++++|.+.++...+.
T Consensus       258 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  332 (411)
T 4a1s_A          258 DRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAI  332 (411)
T ss_dssp             CHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            1    236777778888888888888888776 2111       1356677777777888888888888766443

>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=98.83  E-value=7.4e-08  Score=82.66  Aligned_cols=150  Identities=11%  Similarity=0.030  Sum_probs=130.3

Q ss_pred             hcch-hccCCCcchHhHHHHHHHHhhCCC-cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC-CHHHHHHHHHHHhcc
Q 045511            3 VNGL-KSLKPTLSFKQLNQIHAQIIKIPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY-NHYTFTQALKACSLA   79 (209)
Q Consensus         3 i~~~-~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p-~~~t~~~ll~~~~~~   79 (209)
                      ..++ +.|+.++|.+.+.++.+..   |+ ..+|+.+-..+.+.|++++|...|++..+.+  | +...|..+-.++.+.
T Consensus        16 G~~~~~~G~~~eAi~~~~kAl~l~---P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~--P~~~~a~~nLg~~l~~~   90 (723)
T 4gyw_A           16 ANIKREQGNIEEAVRLYRKALEVF---PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS--PTFADAYSNMGNTLKEM   90 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC---SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHc
Confidence            3456 7889999999998888763   44 5899999999999999999999999998853  4 468899999999999


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHh
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      |++++|.+.|+...+.. +-+...|+.+-..|.+.|++++|.+.|++..  .| +...|..+...|...|++++|.+.|+
T Consensus        91 g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~~  169 (723)
T 4gyw_A           91 QDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMK  169 (723)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHHH
Confidence            99999999999998865 4457899999999999999999999999873  34 57889999999999999999999888


Q ss_pred             hC
Q 045511          157 GI  158 (209)
Q Consensus       157 ~m  158 (209)
                      +.
T Consensus       170 ka  171 (723)
T 4gyw_A          170 KL  171 (723)
T ss_dssp             HH
T ss_pred             HH
Confidence            77

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

Probab=98.82  E-value=1.7e-07  Score=72.14  Aligned_cols=143  Identities=12%  Similarity=0.054  Sum_probs=113.0

Q ss_pred             hHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc-CccHhHHHHHHHHHHhCCChhhHHHHHHhcC
Q 045511           50 AIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH-LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV  128 (209)
Q Consensus        50 a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~  128 (209)
                      +...|++....+ .++..++-.+-.++...|++++|.+++......+. .-+...+-.++..+.+.|+++.|.+.+++|.
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            778888887765 56667777888999999999999999998876653 2366788999999999999999999999984


Q ss_pred             --CC-----cHhHHHHHHHH--HHh--CCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          129 --FP-----DVVTWTTIISG--LSK--CGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       129 --~~-----~~~~~~~li~~--~~~--~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                        .|     +..+..-+..+  ...  .+++.+|+.+|+++ ...|+..+-..+++++.+.|++++|++.++.+.+.
T Consensus       164 ~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~  240 (310)
T 3mv2_B          164 NAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSD  240 (310)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSH
T ss_pred             hcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence              35     24555555555  222  33899999999999 76777555566667889999999999999976654

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.81  E-value=1.5e-08  Score=77.55  Aligned_cols=187  Identities=9%  Similarity=-0.016  Sum_probs=119.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCCccchHHHHHHhhhCCC-CCC----HHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SYN----HYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p~----~~t~~~ll~~~~   77 (209)
                      ..++.+++.+.+.+..+.....++    ..++..+-..+...|++++|...+++..+..- .++    ..++..+-..+.
T Consensus        55 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~  134 (338)
T 3ro2_A           55 YLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYH  134 (338)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHH
Confidence            556666666666666555433222    25666677777777777777777776644210 011    336666777777


Q ss_pred             cccc--------------------HHHHHHHHHHHHHh----ccC-ccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---
Q 045511           78 LAHA--------------------HQKGLEIHAHVIKY----GHL-HDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---  129 (209)
Q Consensus        78 ~~~~--------------------~~~a~~~~~~m~~~----g~~-~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---  129 (209)
                      ..|+                    ++.|.+.++...+.    +.. ....++..+-..|...|++++|.+.+++..+   
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~  214 (338)
T 3ro2_A          135 AKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAK  214 (338)
T ss_dssp             HHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence            7777                    77777777665432    111 1234677777778888888888888776521   


Q ss_pred             --C----cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC---C----HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          130 --P----DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP---N----ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       130 --~----~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p---~----~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                        +    ...++..+...+...|++++|...+.+. .+.|   +    ..++..+-..+...|++++|...++...+.
T Consensus       215 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  292 (338)
T 3ro2_A          215 EFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAI  292 (338)
T ss_dssp             HHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence              1    1236777777888888888888888776 1111   1    346677777788888888888888766443

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.80  E-value=2.4e-08  Score=76.36  Aligned_cols=190  Identities=13%  Similarity=0.077  Sum_probs=146.7

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCC--------------------ccchHHHHHHhh
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSST--------------------PQNAIPLYNKML   58 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~--------------------~~~a~~l~~~m~   58 (209)
                      .++ ..++.++|...+.+..+.....++.    .++..+-..+...|+                    +++|...+++..
T Consensus        91 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~  170 (338)
T 3ro2_A           91 NTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENL  170 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence            344 6788889999999988887665553    588888889999999                    899998888764


Q ss_pred             hC----CCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC-c----cHhHHHHHHHHHHhCCChhhHHHHHHhcC
Q 045511           59 NC----PSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL-H----DIFIQNSLLHFYVTVKDIFSAHQIFNSVV  128 (209)
Q Consensus        59 ~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~----~~~~~~~ll~~~~~~g~~~~a~~~~~~~~  128 (209)
                      ..    +..| ...++..+-..+...|++++|.+.++...+.... +    ...++..+...|...|++++|.+.+++..
T Consensus       171 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  250 (338)
T 3ro2_A          171 SLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTL  250 (338)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            32    2111 2356788888899999999999999887754211 1    13488899999999999999999998762


Q ss_pred             C-----Cc----HhHHHHHHHHHHhCCChHHHHHHHhhC-CC------CC-CHHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          129 F-----PD----VVTWTTIISGLSKCGFHKEAIDMFCGI-DV------KP-NANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       129 ~-----~~----~~~~~~li~~~~~~g~~~~a~~~~~~m-~~------~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      +     .+    ..++..+-..|...|++++|...+++. ..      .+ ...++..+-..+.+.|++++|...++...
T Consensus       251 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  330 (338)
T 3ro2_A          251 LLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  330 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            1     11    567888889999999999999999887 11      11 13477888899999999999999999876


Q ss_pred             Hh
Q 045511          192 RN  193 (209)
Q Consensus       192 ~~  193 (209)
                      +.
T Consensus       331 ~~  332 (338)
T 3ro2_A          331 EI  332 (338)
T ss_dssp             HC
T ss_pred             HH
Confidence            54

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.80  E-value=2.4e-08  Score=78.77  Aligned_cols=186  Identities=12%  Similarity=0.081  Sum_probs=121.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCC--------------------ccchHHHHHHhhh---
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSST--------------------PQNAIPLYNKMLN---   59 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~--------------------~~~a~~l~~~m~~---   59 (209)
                      ..|+.++|...+.++.+.....++    ..++..+-..+...|+                    +++|...+++..+   
T Consensus        99 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~  178 (406)
T 3sf4_A           99 VLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVT  178 (406)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            566777777777777666554444    2466777777777777                    7777777766543   


Q ss_pred             -CCCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc-Ccc----HhHHHHHHHHHHhCCChhhHHHHHHhcCC---
Q 045511           60 -CPSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH-LHD----IFIQNSLLHFYVTVKDIFSAHQIFNSVVF---  129 (209)
Q Consensus        60 -~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---  129 (209)
                       .+..| ...++..+-..+...|++++|.+.++...+... .++    ..++..+-..|...|++++|.+.+++..+   
T Consensus       179 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  258 (406)
T 3sf4_A          179 ALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLAR  258 (406)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             hccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence             11111 234566777777777888888888777664421 111    23677777788888888888888776521   


Q ss_pred             --Cc----HhHHHHHHHHHHhCCChHHHHHHHhhC-CC------CCC-HHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          130 --PD----VVTWTTIISGLSKCGFHKEAIDMFCGI-DV------KPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       130 --~~----~~~~~~li~~~~~~g~~~~a~~~~~~m-~~------~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                        .+    ..++..+-..|...|++++|...|.+. .+      .+. ..++..+-..+...|++++|.+.+....+
T Consensus       259 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          259 QLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              11    456777778888888888888887776 11      111 34666777777788888888888776543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.78  E-value=2.3e-08  Score=79.44  Aligned_cols=190  Identities=12%  Similarity=0.039  Sum_probs=145.9

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCC-----------------ccchHHHHHHhhhC-
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSST-----------------PQNAIPLYNKMLNC-   60 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~-----------------~~~a~~l~~~m~~~-   60 (209)
                      .++ ..++.++|...+.++.+......+    ..++..+-..+...|+                 +++|...+++..+. 
T Consensus       134 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~  213 (411)
T 4a1s_A          134 NTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLM  213 (411)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            344 678888888888888877644333    3688888889999999                 99999988876542 


Q ss_pred             ---CCC-CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC-cc----HhHHHHHHHHHHhCCChhhHHHHHHhcCC--
Q 045511           61 ---PSS-YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL-HD----IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--  129 (209)
Q Consensus        61 ---g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--  129 (209)
                         +-. ....++..+-..+...|++++|.+.++...+.... ++    ..++..+...|...|++++|.+.+++..+  
T Consensus       214 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  293 (411)
T 4a1s_A          214 RDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALA  293 (411)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence               111 12357888888899999999999999888764311 11    23888999999999999999999987622  


Q ss_pred             -------CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC------CC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          130 -------PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV------KP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       130 -------~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~------~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                             ....++..+-..|...|++++|...|++. .+      .+ ...++..+-..+...|++++|.+.+....+.
T Consensus       294 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          294 VELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence                   12567888999999999999999999987 21      11 1347888888999999999999999876544

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.77  E-value=3.2e-08  Score=78.08  Aligned_cols=187  Identities=9%  Similarity=-0.034  Sum_probs=119.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCCccchHHHHHHhhhCCC-CCC----HHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SYN----HYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p~----~~t~~~ll~~~~   77 (209)
                      ..++.++|...+.++........+    ..++..+-..+...|++++|...+++..+..- .++    ..++..+-..+.
T Consensus        59 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~  138 (406)
T 3sf4_A           59 YLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYH  138 (406)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHH
Confidence            556666666666666555433222    25666677777777777777777776654210 011    346666677777


Q ss_pred             cccc--------------------HHHHHHHHHHHHHhc----cCc-cHhHHHHHHHHHHhCCChhhHHHHHHhcCC---
Q 045511           78 LAHA--------------------HQKGLEIHAHVIKYG----HLH-DIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---  129 (209)
Q Consensus        78 ~~~~--------------------~~~a~~~~~~m~~~g----~~~-~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---  129 (209)
                      ..|+                    ++.|.+.++...+..    -.| ...++..+-..|...|++++|.+.+++..+   
T Consensus       139 ~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  218 (406)
T 3sf4_A          139 AKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAK  218 (406)
T ss_dssp             HHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHH
T ss_pred             HcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHH
Confidence            7777                    777777776654331    111 234677777778888888888887776521   


Q ss_pred             --Cc----HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC---C----HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          130 --PD----VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP---N----ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       130 --~~----~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p---~----~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                        ++    ..++..+-..|...|++++|...+.+. .+.|   +    ..++..+-..+...|++++|.+.+....+.
T Consensus       219 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  296 (406)
T 3sf4_A          219 EFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAI  296 (406)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence              11    336777778888888888888888776 1111   1    356777777788888888888888766543

>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=98.76  E-value=5.3e-08  Score=72.77  Aligned_cols=153  Identities=12%  Similarity=0.061  Sum_probs=121.3

Q ss_pred             HHcCCCccchHHHHHHhhhC-------CCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh------cc-CccHhHHHH
Q 045511           41 LTQSSTPQNAIPLYNKMLNC-------PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY------GH-LHDIFIQNS  106 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~-------g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~-~~~~~~~~~  106 (209)
                      ....|+++.|..+|++..+.       +.+....++..+-..+...|++++|.+.++...+.      +- +....++..
T Consensus        11 ~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~   90 (283)
T 3edt_B           11 SSGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNN   90 (283)
T ss_dssp             --CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHH
Confidence            34567888888888777652       22334678889999999999999999999988765      22 234568999


Q ss_pred             HHHHHHhCCChhhHHHHHHhcC----------CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CC--------CCC-HH
Q 045511          107 LLHFYVTVKDIFSAHQIFNSVV----------FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DV--------KPN-AN  165 (209)
Q Consensus       107 ll~~~~~~g~~~~a~~~~~~~~----------~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~--------~p~-~~  165 (209)
                      +-..|...|++++|.+.+.+..          .| ...++..+-..|...|++++|...|.+. ..        .|+ ..
T Consensus        91 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  170 (283)
T 3edt_B           91 LAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAK  170 (283)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHH
Confidence            9999999999999999998762          12 3567888999999999999999999988 22        343 45


Q ss_pred             hHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          166 TLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       166 t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ++..+-..+...|++++|.+.+....+.
T Consensus       171 ~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          171 TKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7888899999999999999999987654

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

Probab=98.76  E-value=4.9e-07  Score=67.59  Aligned_cols=162  Identities=10%  Similarity=0.037  Sum_probs=126.9

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC----HHHHHHHHHHHhccccHHHHHHHHHHHHHhcc-C-ccHhH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN----HYTFTQALKACSLAHAHQKGLEIHAHVIKYGH-L-HDIFI  103 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~-~~~~~  103 (209)
                      +...+-.+-..+.+.|++++|...|++..+..  |+    ...+..+-.++.+.|++++|...|+...+... . .....
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            44666667778889999999999999998854  33    56778888889999999999999999998742 2 22456


Q ss_pred             HHHHHHHHHh--------CCChhhHHHHHHhcC--CCc-HhHH-----------------HHHHHHHHhCCChHHHHHHH
Q 045511          104 QNSLLHFYVT--------VKDIFSAHQIFNSVV--FPD-VVTW-----------------TTIISGLSKCGFHKEAIDMF  155 (209)
Q Consensus       104 ~~~ll~~~~~--------~g~~~~a~~~~~~~~--~~~-~~~~-----------------~~li~~~~~~g~~~~a~~~~  155 (209)
                      +..+-.++.+        .|++++|.+.|++..  .|+ ....                 -.+-..|.+.|++++|...|
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  171 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTY  171 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHH
Confidence            7778888888        999999999999873  232 2333                 44567889999999999999


Q ss_pred             hhC-CCCCC----HHhHHHHHHHhccc----------cchhHHHHHHHHHHHh
Q 045511          156 CGI-DVKPN----ANTLVSVLSACSSL----------GSRKLGKAIHAHSLRN  193 (209)
Q Consensus       156 ~~m-~~~p~----~~t~~~li~~~~~~----------g~~~~a~~~~~~~~~~  193 (209)
                      ++. ...|+    ...+..+..++...          |++++|...+..+.+.
T Consensus       172 ~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          172 EAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            998 55555    34566677777765          8889999999988776

>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=98.76  E-value=7.9e-07  Score=64.08  Aligned_cols=127  Identities=9%  Similarity=-0.050  Sum_probs=107.8

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      .+..+-..+.+.|++++|...|++..    .|+...|..+-..+.+.|++++|.+.|+...+.. +.+...|..+-..|.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHH
Confidence            34556667788999999999998874    5788999999999999999999999999998875 456789999999999


Q ss_pred             hCCChhhHHHHHHhcCC--C-----------------cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH
Q 045511          113 TVKDIFSAHQIFNSVVF--P-----------------DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~~--~-----------------~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      ..|++++|.+.|++..+  |                 ....+..+-..|...|++++|...|... ...|+.
T Consensus        83 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  154 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  154 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             HcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCccc
Confidence            99999999999988722  1                 2367888899999999999999999998 777765

>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=98.75  E-value=4.3e-07  Score=75.68  Aligned_cols=153  Identities=7%  Similarity=-0.138  Sum_probs=108.6

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLE   87 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~   87 (209)
                      .++.++|.+.+.++.+..  +.+...|..+-..+.+.|++++|.+.|++..+.. +-+...+..+-..+...|++++|.+
T Consensus         2 ~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR--PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            356677777777776653  1245788888888999999999999999988754 2356788888888899999999999


Q ss_pred             HHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC---CChHHHHHHHhhC-CC
Q 045511           88 IHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC---GFHKEAIDMFCGI-DV  160 (209)
Q Consensus        88 ~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~---g~~~~a~~~~~~m-~~  160 (209)
                      .++...+.. +.+...+..+-..|.+.|++++|.+.+++..   ..+...+..+...+...   |+.++|.+.|++. ..
T Consensus        79 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           79 LLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            999888765 4457788889999999999999999998872   24567888888888888   8999999999888 44


Q ss_pred             CCCH
Q 045511          161 KPNA  164 (209)
Q Consensus       161 ~p~~  164 (209)
                      .|+.
T Consensus       158 ~p~~  161 (568)
T 2vsy_A          158 GVGA  161 (568)
T ss_dssp             TCCC
T ss_pred             CCcc
Confidence            4443

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

Probab=98.75  E-value=3.2e-07  Score=70.61  Aligned_cols=162  Identities=10%  Similarity=-0.007  Sum_probs=122.0

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCC-CCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCc-----cHh
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLH-----DIF  102 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-----~~~  102 (209)
                      ++..++..+-..+...|++++|++++++-...|- .-+...+..++..+.+.|+.+.|.+.++.|.+.  .|     +..
T Consensus        98 ~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~  175 (310)
T 3mv2_B           98 NSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDNE  175 (310)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CccccccchH
Confidence            4445556777888889999999999999866553 236688999999999999999999999999775  45     345


Q ss_pred             HHHHHHHHH--H--hCCChhhHHHHHHhcCC--CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CC----------CC-CH
Q 045511          103 IQNSLLHFY--V--TVKDIFSAHQIFNSVVF--PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DV----------KP-NA  164 (209)
Q Consensus       103 ~~~~ll~~~--~--~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~----------~p-~~  164 (209)
                      +...|..++  .  ..++.++|..+|+++.+  |+..+-..++.++.+.|++++|.+.++.+ ..          .| |.
T Consensus       176 ~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~  255 (310)
T 3mv2_B          176 MILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKP  255 (310)
T ss_dssp             HHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHH
T ss_pred             HHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCH
Confidence            555555552  2  23499999999999943  55444455666899999999999999876 32          24 45


Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .+..-+|......|+  .|.++++++.+..
T Consensus       256 ~~LaN~i~l~~~lgk--~a~~l~~qL~~~~  283 (310)
T 3mv2_B          256 TFLANQITLALMQGL--DTEDLTNQLVKLD  283 (310)
T ss_dssp             HHHHHHHHHHHHTTC--TTHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCh--HHHHHHHHHHHhC
Confidence            667566666666776  7889998887763

>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=98.75  E-value=1e-06  Score=67.21  Aligned_cols=187  Identities=9%  Similarity=-0.055  Sum_probs=137.2

Q ss_pred             hhccCCCcchHhHHHHHHHHhhCCCc----------c---cHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHH----
Q 045511            6 LKSLKPTLSFKQLNQIHAQIIKIPQP----------H---ILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHY----   67 (209)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~~~~~p~~----------~---~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~----   67 (209)
                      +.+|+..-....+..+.+.++..++.          .   .+...+..+.+.|++++|..++++..+.. ..|+..    
T Consensus        37 ~e~g~~~~~~~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~  116 (293)
T 3u3w_A           37 IESGAVYPSMDILQGIAAKLQIPIIHFYEVLIYSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQ  116 (293)
T ss_dssp             HHTTSCCCCHHHHHHHHHHHTCCTHHHHHTTTSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHCCCCCCCHHHHHHHHHHhCcCHHHHhCCCCCCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHH
Confidence            45666666777777777776554321          1   22334677889999999999999988743 233322    


Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccC-cc----HhHHHHHHHHHHhCCChhhHHHHHHhcC-------C--C-cH
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHL-HD----IFIQNSLLHFYVTVKDIFSAHQIFNSVV-------F--P-DV  132 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~--~-~~  132 (209)
                      .|..+...+...++++.|.+.++...+.... ++    ..+++.+-..|...|++++|...|++..       .  + ..
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            3334666677778999999999999874322 22    3379999999999999999999998763       2  1 23


Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC-------CCCCC-HHhHHHHHHHhccccc-hhHHHHHHHHHHH
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI-------DVKPN-ANTLVSVLSACSSLGS-RKLGKAIHAHSLR  192 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m-------~~~p~-~~t~~~li~~~~~~g~-~~~a~~~~~~~~~  192 (209)
                      .+|..+-..|.+.|++++|...+++.       +..+. ..+|..+-.++.+.|+ .++|.+.+....+
T Consensus       197 ~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          197 KVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            47888999999999999999999877       22333 4678888888889995 5999998886643

>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=98.74  E-value=2.6e-07  Score=78.94  Aligned_cols=171  Identities=9%  Similarity=-0.029  Sum_probs=133.6

Q ss_pred             hhccCCCcchHhHHHHHH-----HHhhCC-CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc
Q 045511            6 LKSLKPTLSFKQLNQIHA-----QIIKIP-QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA   79 (209)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~-----~~~~~p-~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~   79 (209)
                      +..+++++|.+.+.++.+     .....| +...|..+-..+.+.|++++|...|++..+.+ +-+...|..+-.++...
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            345566666666666651     112223 45788888899999999999999999998854 23567888888899999


Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHh
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFC  156 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~  156 (209)
                      |++++|.+.|+...+.. +-+...|..+-..|.+.|++++ .+.|++..   ..+...|..+-..+.+.|++++|.+.|+
T Consensus       481 g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~  558 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLD  558 (681)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            99999999999998875 4467889999999999999999 99998873   3467789999999999999999999999


Q ss_pred             hC-CCCCCH-HhHHHHHHHhccccc
Q 045511          157 GI-DVKPNA-NTLVSVLSACSSLGS  179 (209)
Q Consensus       157 ~m-~~~p~~-~t~~~li~~~~~~g~  179 (209)
                      +. ...|+. ..+..+..++...|+
T Consensus       559 ~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          559 EVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             TSCTTSTTHHHHHHHHHHHTC----
T ss_pred             hhcccCcccHHHHHHHHHHHHccCC
Confidence            99 888875 567777777766554

>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=98.74  E-value=2.6e-07  Score=83.14  Aligned_cols=162  Identities=13%  Similarity=0.047  Sum_probs=95.2

Q ss_pred             HhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           16 KQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        16 ~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      ..+.++...+....|...|..++..+.+.|++++|.+.|..-++..  ++....+.+..+|++.+++++...+.    + 
T Consensus      1119 G~~kEAIdsYiKAdD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~- 1191 (1630)
T 1xi4_A         1119 GMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N- 1191 (1630)
T ss_pred             CCHHHHHHHHHhcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h-
Confidence            3344444444444455555556666666666666666665544433  22112223555555555555333221    1 


Q ss_pred             ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC-------------
Q 045511           96 GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK-------------  161 (209)
Q Consensus        96 g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~-------------  161 (209)
                        .++...|..+-..|...|++++|..+|...     ..|..+...|++.|+++.|.+.+++- ..+             
T Consensus      1192 --~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA-----~ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~ 1264 (1630)
T 1xi4_A         1192 --GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGK 1264 (1630)
T ss_pred             --CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh-----hHHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhh
Confidence              234455556666777777777777777763     47888888888888888888888764 111             


Q ss_pred             -------------CCHHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          162 -------------PNANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       162 -------------p~~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                                   .+...+..+++.|.+.|.+++|..+++...
T Consensus      1265 Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL 1307 (1630)
T 1xi4_A         1265 EFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAAL 1307 (1630)
T ss_pred             HHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence                         133455567777777788887777775443

>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=98.73  E-value=2.4e-07  Score=67.80  Aligned_cols=157  Identities=9%  Similarity=0.000  Sum_probs=124.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|.+.+.++.+..+. ++...+..+-..+.+.|++++|...|++..+... -+...|..+-..+...|++++|.
T Consensus        19 ~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~~~A~   96 (228)
T 4i17_A           19 NAKNYAVAFEKYSEYLKLTNN-QDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNY-NLANAYIGKSAAYRDMKNNQEYI   96 (228)
T ss_dssp             HTTCHHHHHHHHHHHHHHTTT-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC-SHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HccCHHHHHHHHHHHHhccCC-CCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCc-chHHHHHHHHHHHHHcccHHHHH
Confidence            778888899888888877532 5667777788899999999999999999988542 25578888999999999999999


Q ss_pred             HHHHHHHHhccCccH-------hHHHHHHHHHHhCCChhhHHHHHHhcCC--Cc---HhHHHHHHHHHHhCCCh------
Q 045511           87 EIHAHVIKYGHLHDI-------FIQNSLLHFYVTVKDIFSAHQIFNSVVF--PD---VVTWTTIISGLSKCGFH------  148 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~-------~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~---~~~~~~li~~~~~~g~~------  148 (209)
                      +.++...+.. +.+.       .+|..+-..+...|++++|.+.|++..+  |+   ...|..+-..|...|+.      
T Consensus        97 ~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~~~a~  175 (228)
T 4i17_A           97 ATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLFYNNGADVLRKAT  175 (228)
T ss_dssp             HHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHG
T ss_pred             HHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999998765 2334       4578888889999999999999999843  44   46777777888777776      


Q ss_pred             ---------------------HHHHHHHhhC-CCCCCHHh
Q 045511          149 ---------------------KEAIDMFCGI-DVKPNANT  166 (209)
Q Consensus       149 ---------------------~~a~~~~~~m-~~~p~~~t  166 (209)
                                           ++|...|.+. .+.|+...
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l~p~~~~  215 (228)
T 4i17_A          176 PLASSNKEKYASEKAKADAAFKKAVDYLGEAVTLSPNRTE  215 (228)
T ss_dssp             GGTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCHH
T ss_pred             hcccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCHH
Confidence                                 6677777766 55665543

>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=2e-07  Score=65.70  Aligned_cols=159  Identities=11%  Similarity=0.042  Sum_probs=117.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH-
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF-  110 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~-  110 (209)
                      ..+...-..+.+.|++++|...|++..+.. +-+...+..+-..+.+.|++++|...++...+...  +...+..+... 
T Consensus         7 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~~~~~~~~   83 (176)
T 2r5s_A            7 EQLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYKSLIAKLE   83 (176)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHHHHHHHHH
Confidence            445566677888999999999999887643 23567788888889999999999999988876542  44333322211 


Q ss_pred             HHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC---HHhHHHHHHHhccccchhHH
Q 045511          111 YVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN---ANTLVSVLSACSSLGSRKLG  183 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~---~~t~~~li~~~~~~g~~~~a  183 (209)
                      +...+...+|.+.+++..  .| +...+..+-..+...|++++|...|.+. ...|+   ...+..+...+...|+.++|
T Consensus        84 ~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A  163 (176)
T 2r5s_A           84 LHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAI  163 (176)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHH
T ss_pred             HHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcH
Confidence            223233445677777662  34 5788888999999999999999999998 66765   45788888999999999999


Q ss_pred             HHHHHHHHHh
Q 045511          184 KAIHAHSLRN  193 (209)
Q Consensus       184 ~~~~~~~~~~  193 (209)
                      ...++....+
T Consensus       164 ~~~y~~al~~  173 (176)
T 2r5s_A          164 ASKYRRQLYS  173 (176)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998876543

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.72  E-value=1.9e-06  Score=62.70  Aligned_cols=175  Identities=10%  Similarity=-0.075  Sum_probs=138.2

Q ss_pred             CcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc----cHHHHHH
Q 045511           12 TLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH----AHQKGLE   87 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~----~~~~a~~   87 (209)
                      .+|.+.+.+..+.    -++.++..+-..+...+++++|..+|++..+.|   +...+..+-..|.. +    +.++|.+
T Consensus         3 ~eA~~~~~~aa~~----g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~   74 (212)
T 3rjv_A            3 TEPGSQYQQQAEA----GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQ   74 (212)
T ss_dssp             -CTTHHHHHHHHT----TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHH
T ss_pred             chHHHHHHHHHHC----CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHH
Confidence            3556666666543    577888888889999999999999999999876   45666666666766 6    8999999


Q ss_pred             HHHHHHHhccCccHhHHHHHHHHHHh----CCChhhHHHHHHhcCCCc-----HhHHHHHHHHHHh----CCChHHHHHH
Q 045511           88 IHAHVIKYGHLHDIFIQNSLLHFYVT----VKDIFSAHQIFNSVVFPD-----VVTWTTIISGLSK----CGFHKEAIDM  154 (209)
Q Consensus        88 ~~~~m~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~~~~~~~~~-----~~~~~~li~~~~~----~g~~~~a~~~  154 (209)
                      +|+...+.|   ++..+..|-..|..    .+++++|.++|.+..+.+     ...+..|-..|..    .+++++|+..
T Consensus        75 ~~~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~  151 (212)
T 3rjv_A           75 LAEKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEY  151 (212)
T ss_dssp             HHHHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            999998776   67778888888887    889999999999985432     6788888888888    8899999999


Q ss_pred             HhhC-CCCCCHHhHHHHHHHhccc-c-----chhHHHHHHHHHHHhccCC
Q 045511          155 FCGI-DVKPNANTLVSVLSACSSL-G-----SRKLGKAIHAHSLRNLNEN  197 (209)
Q Consensus       155 ~~~m-~~~p~~~t~~~li~~~~~~-g-----~~~~a~~~~~~~~~~~~~p  197 (209)
                      |.+. ...++...+..+-..|... |     +.++|...++...+.|...
T Consensus       152 ~~~A~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~~~  201 (212)
T 3rjv_A          152 FKGSSSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGFDT  201 (212)
T ss_dssp             HHHHHHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCCHH
Confidence            9998 4444556666666666543 3     8999999999998888544

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.68  E-value=1.7e-06  Score=67.88  Aligned_cols=186  Identities=9%  Similarity=-0.004  Sum_probs=132.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC------cccHHHHHHHHHcCCCccchHHHHHHhhhCCCC--C--CHHHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ------PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSS--Y--NHYTFTQALKAC   76 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~------~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~--p--~~~t~~~ll~~~   76 (209)
                      ..|+.++|...+.+..+.....++      ...+..+-..+...|++++|...+++.....-.  +  ...+|..+-..+
T Consensus       105 ~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~  184 (373)
T 1hz4_A          105 AQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCS  184 (373)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHH
Confidence            677888888888888777644322      245666777888999999999999887653211  1  235677778888


Q ss_pred             hccccHHHHHHHHHHHHHhccCccH-hHHH-----HHHHHHHhCCChhhHHHHHHhcCCCc-------HhHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHLHDI-FIQN-----SLLHFYVTVKDIFSAHQIFNSVVFPD-------VVTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~~~~-~~~~-----~ll~~~~~~g~~~~a~~~~~~~~~~~-------~~~~~~li~~~~  143 (209)
                      ...|++++|...++...+....++. ..+.     .....+...|++++|...+++...++       ...+..+...+.
T Consensus       185 ~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~  264 (373)
T 1hz4_A          185 LARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQI  264 (373)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHH
Confidence            8999999999999988765322221 1121     23344779999999999998884321       224667778899


Q ss_pred             hCCChHHHHHHHhhC-------CCCCCHH-hHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          144 KCGFHKEAIDMFCGI-------DVKPNAN-TLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-------~~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ..|++++|...+++.       |..++.. ++..+-.++...|+.++|...+....+
T Consensus       265 ~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          265 LLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            999999999999887       2222332 566667778889999999998886644

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

Probab=98.67  E-value=6e-07  Score=68.47  Aligned_cols=160  Identities=13%  Similarity=0.040  Sum_probs=124.9

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhH-HHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFI-QNSLL  108 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~-~~~ll  108 (209)
                      +...+-.+-..+.+.|++++|...|++..... +-+...+..+-..+.+.|++++|...++...+..  |+... .....
T Consensus       116 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~  192 (287)
T 3qou_A          116 EEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQ  192 (287)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHH
T ss_pred             chhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHH
Confidence            33666777778889999999999999988754 2355778888889999999999999999887654  44432 23333


Q ss_pred             HHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC---HHhHHHHHHHhccccchh
Q 045511          109 HFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN---ANTLVSVLSACSSLGSRK  181 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~---~~t~~~li~~~~~~g~~~  181 (209)
                      ..+...++.++|.+.+++..   ..+...+..+-..|...|++++|...|.+. ...|+   ...+..+...+...|+.+
T Consensus       193 ~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          193 IELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             HHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCC
Confidence            34667788888888887762   346778889999999999999999999998 55565   567888999999999999


Q ss_pred             HHHHHHHHHHH
Q 045511          182 LGKAIHAHSLR  192 (209)
Q Consensus       182 ~a~~~~~~~~~  192 (209)
                      .|...+++...
T Consensus       273 ~a~~~~r~al~  283 (287)
T 3qou_A          273 ALASXYRRQLY  283 (287)
T ss_dssp             HHHHHHHHHHH
T ss_pred             cHHHHHHHHHH
Confidence            99888876543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.67  E-value=9.1e-07  Score=64.84  Aligned_cols=162  Identities=11%  Similarity=0.028  Sum_probs=110.7

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCC-CC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccH--hHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI--FIQNSLL  108 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~--~~~~~ll  108 (209)
                      .+-.+...+.+.|++++|...|+++.+... .| ....+..+..++.+.|++++|...|+...+.......  ..+-.+-
T Consensus         6 ~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g   85 (225)
T 2yhc_A            6 EIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRG   85 (225)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHH
Confidence            344455567778888888888888876431 11 1245666777788888888888888888765422111  1233333


Q ss_pred             HHHH------------------hCCChhhHHHHHHhcCC--CcH-hHH-----------------HHHHHHHHhCCChHH
Q 045511          109 HFYV------------------TVKDIFSAHQIFNSVVF--PDV-VTW-----------------TTIISGLSKCGFHKE  150 (209)
Q Consensus       109 ~~~~------------------~~g~~~~a~~~~~~~~~--~~~-~~~-----------------~~li~~~~~~g~~~~  150 (209)
                      .++.                  ..|+.++|...|+++.+  |+. ..+                 -.+-..|.+.|++++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~  165 (225)
T 2yhc_A           86 LTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVA  165 (225)
T ss_dssp             HHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHH
Confidence            3333                  25678888888888732  332 222                 234456788999999


Q ss_pred             HHHHHhhC-CCCCCH----HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          151 AIDMFCGI-DVKPNA----NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       151 a~~~~~~m-~~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      |...|+++ ...|+.    ..+..+..++.+.|+.++|.+.++.+...+
T Consensus       166 A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          166 VVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            99999998 555654    467788899999999999999999887764

>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=98.66  E-value=1.9e-07  Score=71.85  Aligned_cols=158  Identities=8%  Similarity=-0.042  Sum_probs=85.1

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhC----CCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc---Cc--cHh
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH---LH--DIF  102 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~---~~--~~~  102 (209)
                      .|+.....|...|++++|...|.+..+.    |-.+ -..+|..+-..|.+.|++++|.+.|+...+.-.   .+  -..
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            4555555566666666666666655432    1101 123556666666666666666666665443311   11  134


Q ss_pred             HHHHHHHHHHhCCChhhHHHHHHhcCC-------C--cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC------CCH-H
Q 045511          103 IQNSLLHFYVTVKDIFSAHQIFNSVVF-------P--DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK------PNA-N  165 (209)
Q Consensus       103 ~~~~ll~~~~~~g~~~~a~~~~~~~~~-------~--~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~------p~~-~  165 (209)
                      +++.+-..|.. |++++|.+.|++..+       +  ...+++.+-..|.+.|++++|+..|.+. .+.      ++. .
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            55666666666 666666666655411       0  1345566666666666666666666665 111      111 1


Q ss_pred             hHHHHHHHhccccchhHHHHHHHHHH
Q 045511          166 TLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       166 t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      ++..+...+...|++++|...++...
T Consensus       197 ~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          197 KCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            34444445555566666666666554

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

Probab=98.65  E-value=4.7e-07  Score=65.66  Aligned_cols=120  Identities=4%  Similarity=-0.113  Sum_probs=55.0

Q ss_pred             HHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--C-CcHhHHHHHHHHHHhCCC-
Q 045511           72 ALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--F-PDVVTWTTIISGLSKCGF-  147 (209)
Q Consensus        72 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~g~-  147 (209)
                      +-..+.+.|++++|...|+...+.. +-+...+..+-..|...|++++|.+.|++..  . .+..+|..+-..|...|+ 
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~  138 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQ  138 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHH
Confidence            4445555556666665555555543 2344555555555555666666665555542  1 234445555444443332 


Q ss_pred             -hHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          148 -HKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       148 -~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                       .+.+...++.. ...|....+...-.++...|++++|...|+...+
T Consensus       139 ~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~  185 (208)
T 3urz_A          139 EKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL  185 (208)
T ss_dssp             HHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence             23334444443 2222221222222223344555555555555443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.65  E-value=9.2e-07  Score=67.42  Aligned_cols=159  Identities=7%  Similarity=-0.034  Sum_probs=119.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC-H----HHHHHHHHHHhccccHHHHHHHHHHHHHhcc---Ccc--H
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN-H----YTFTQALKACSLAHAHQKGLEIHAHVIKYGH---LHD--I  101 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~-~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~---~~~--~  101 (209)
                      ..+...+..+...|++++|.+.+++..+..-..+ .    ..+..+...+...|++++|.+.++...+...   .+.  .
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            4455667788899999999999988776532211 1    2233455566788899999999998875431   111  4


Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcC-----CCc-----HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-------
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVV-----FPD-----VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-------  163 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~-----~~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-------  163 (209)
                      .+|+.+-..|...|++++|...|++..     .++     ..+|+.+-..|...|++++|...|++. .+.++       
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            589999999999999999999998762     122     258889999999999999999999887 22222       


Q ss_pred             HHhHHHHHHHhccccchhHH-HHHHHHH
Q 045511          164 ANTLVSVLSACSSLGSRKLG-KAIHAHS  190 (209)
Q Consensus       164 ~~t~~~li~~~~~~g~~~~a-~~~~~~~  190 (209)
                      ..+|..+-..+.+.|+.++| ...+...
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            56788888899999999999 7767654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.64  E-value=6.1e-07  Score=70.87  Aligned_cols=182  Identities=6%  Similarity=-0.123  Sum_probs=126.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhCC--C---C-CCHHHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNCP--S---S-YNHYTFTQALKAC   76 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~g--~---~-p~~~t~~~ll~~~   76 (209)
                      ..++.++|...+.++.+.....|+.    .+|..+-..+...|+++.|...+++..+.-  .   . ....++..+-..+
T Consensus       115 ~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~  194 (383)
T 3ulq_A          115 DQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNF  194 (383)
T ss_dssp             HTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHH
Confidence            5677778888888777765554543    677888888888899988888888776521  1   1 1235677777888


Q ss_pred             hccccHHHHHHHHHHHHHhccC-c----cHhHHHHHHHHHHhCCChhhHHHHHHhcC-------C-C-cHhHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHL-H----DIFIQNSLLHFYVTVKDIFSAHQIFNSVV-------F-P-DVVTWTTIISGL  142 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~-~----~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~-~-~~~~~~~li~~~  142 (209)
                      ...|++++|.+.++...+.... +    ...++..+-..|...|++++|.+.+++..       . | ...++..+-..|
T Consensus       195 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~  274 (383)
T 3ulq_A          195 LDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIH  274 (383)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHH
Confidence            8888999888888877654211 1    12478888888888999988888887652       1 2 245677888888


Q ss_pred             HhCCChHHHHHHHhhC-------CCCCCHHhHHHHHHHhccccc---hhHHHHHHH
Q 045511          143 SKCGFHKEAIDMFCGI-------DVKPNANTLVSVLSACSSLGS---RKLGKAIHA  188 (209)
Q Consensus       143 ~~~g~~~~a~~~~~~m-------~~~p~~~t~~~li~~~~~~g~---~~~a~~~~~  188 (209)
                      .+.|++++|...+.+.       +-......+..+-..+...|+   +++|..++.
T Consensus       275 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~  330 (383)
T 3ulq_A          275 YKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLE  330 (383)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            8889999888888876       111122345667777777887   555555544

>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=98.64  E-value=6.4e-07  Score=74.65  Aligned_cols=149  Identities=8%  Similarity=-0.069  Sum_probs=111.8

Q ss_pred             CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHH
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQI  123 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~  123 (209)
                      .|++++|.+.|++..+.. +-+...|..+-..+.+.|++++|.+.++...+.. +.+...+..+-..|...|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            478899999999887653 2356888889999999999999999999998765 44678899999999999999999999


Q ss_pred             HHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccc---cchhHHHHHHHHHHHhc
Q 045511          124 FNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSL---GSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       124 ~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~---g~~~~a~~~~~~~~~~~  194 (209)
                      +++..   ..+...+..+-..|.+.|++++|.+.|++. ...|+ ...+..+...+...   |+.++|.+.++...+.+
T Consensus        80 ~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~~  158 (568)
T 2vsy_A           80 LQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQG  158 (568)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhcC
Confidence            99873   345778999999999999999999999998 55564 56788888888888   99999999999887764

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.64  E-value=2.2e-06  Score=67.21  Aligned_cols=187  Identities=11%  Similarity=-0.043  Sum_probs=134.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhC----CCC--CC-HHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSS--YN-HYTFTQALKA   75 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~--p~-~~t~~~ll~~   75 (209)
                      ..|+.+++.+.+.+..+.....++.    .+++.+-..+...|++++|...+++....    +..  |. ...+..+-..
T Consensus        65 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~  144 (373)
T 1hz4_A           65 CKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQL  144 (373)
T ss_dssp             HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHH
T ss_pred             hcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHH
Confidence            5678888888888888776554544    33566777788899999999999887642    222  32 3456667778


Q ss_pred             HhccccHHHHHHHHHHHHHhccC----ccHhHHHHHHHHHHhCCChhhHHHHHHhc----CCCcH-hHHH-----HHHHH
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHL----HDIFIQNSLLHFYVTVKDIFSAHQIFNSV----VFPDV-VTWT-----TIISG  141 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~----~~~~~~~~ll~~~~~~g~~~~a~~~~~~~----~~~~~-~~~~-----~li~~  141 (209)
                      +...|++++|...++...+....    ....++..+-..+...|++++|...+++.    ..++. ..+.     .....
T Consensus       145 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~  224 (373)
T 1hz4_A          145 LWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIY  224 (373)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHH
Confidence            88999999999999988765422    12357888888999999999999999876    22221 1222     23344


Q ss_pred             HHhCCChHHHHHHHhhC-CCCCC-----HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          142 LSKCGFHKEAIDMFCGI-DVKPN-----ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m-~~~p~-----~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      +...|++++|...+.+. ...|.     ...+..+...+...|++++|...++...+.
T Consensus       225 ~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~  282 (373)
T 1hz4_A          225 WQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNEN  282 (373)
T ss_dssp             HHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            77899999999999988 33222     234566778888999999999999876544

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

Probab=98.60  E-value=1.6e-06  Score=66.12  Aligned_cols=164  Identities=12%  Similarity=0.021  Sum_probs=122.5

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcC-CCccchHHHHHHhhhCC----CCCC-HHHHHHH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQS-STPQNAIPLYNKMLNCP----SSYN-HYTFTQA   72 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~-g~~~~a~~l~~~m~~~g----~~p~-~~t~~~l   72 (209)
                      .++ +.|+.++|...+.+..+......+.    .+|+.+-..+.+. |++++|...|++..+..    -.+. ..+|..+
T Consensus        85 ~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~l  164 (292)
T 1qqe_A           85 KCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKC  164 (292)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHH
Confidence            345 6778888998888888887654443    5788888999996 99999999999887632    1111 3568888


Q ss_pred             HHHHhccccHHHHHHHHHHHHHhccCccH------hHHHHHHHHHHhCCChhhHHHHHHhcCC--CcH------hHHHHH
Q 045511           73 LKACSLAHAHQKGLEIHAHVIKYGHLHDI------FIQNSLLHFYVTVKDIFSAHQIFNSVVF--PDV------VTWTTI  138 (209)
Q Consensus        73 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~------~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~~~------~~~~~l  138 (209)
                      -..+.+.|++++|.+.|+...+.......      ..|..+..++...|++++|...|++..+  |+.      ..+..+
T Consensus       165 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l  244 (292)
T 1qqe_A          165 ADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSL  244 (292)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHH
Confidence            99999999999999999999876533222      2678888899999999999999999843  321      134455


Q ss_pred             HHHHH--hCCChHHHHHHHhhC-CCCCCHHhH
Q 045511          139 ISGLS--KCGFHKEAIDMFCGI-DVKPNANTL  167 (209)
Q Consensus       139 i~~~~--~~g~~~~a~~~~~~m-~~~p~~~t~  167 (209)
                      +.++.  ..+++++|+..|+.+ .+.|+....
T Consensus       245 ~~~~~~~~~~~~~~A~~~~~~~~~l~~~~~~~  276 (292)
T 1qqe_A          245 IDAVNEGDSEQLSEHCKEFDNFMRLDKWKITI  276 (292)
T ss_dssp             HHHHHTTCTTTHHHHHHHHTTSSCCCHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHhccCCccHHHHHHH
Confidence            66664  456799999999888 777765443

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

Probab=98.59  E-value=1.3e-07  Score=70.75  Aligned_cols=157  Identities=10%  Similarity=0.054  Sum_probs=117.4

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC-cccHHHHHHHHHcCCCccchHHHHHHhhhCCC-CCC-HHHHHHHHHHHhc-----
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SYN-HYTFTQALKACSL-----   78 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p~-~~t~~~ll~~~~~-----   78 (209)
                      +.++.++|...+.++.+..+..|. ...+..+-..+.+.|++++|...|++..+... .|. ...+..+-.++..     
T Consensus        27 ~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~  106 (261)
T 3qky_A           27 NQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPY  106 (261)
T ss_dssp             HTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCT
T ss_pred             HhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccc
Confidence            678888888888887765433222 36778888889999999999999999988531 122 3456666667777     


Q ss_pred             ---cccHHHHHHHHHHHHHhccCccHhHH-----------------HHHHHHHHhCCChhhHHHHHHhcC--CCc----H
Q 045511           79 ---AHAHQKGLEIHAHVIKYGHLHDIFIQ-----------------NSLLHFYVTVKDIFSAHQIFNSVV--FPD----V  132 (209)
Q Consensus        79 ---~~~~~~a~~~~~~m~~~g~~~~~~~~-----------------~~ll~~~~~~g~~~~a~~~~~~~~--~~~----~  132 (209)
                         .|++++|...|+...+.. +.+....                 -.+-..|.+.|++++|...|++..  .|+    .
T Consensus       107 ~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~  185 (261)
T 3qky_A          107 ELDQTDTRKAIEAFQLFIDRY-PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWAD  185 (261)
T ss_dssp             TSCCHHHHHHHHHHHHHHHHC-TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHH
T ss_pred             cccchhHHHHHHHHHHHHHHC-cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHH
Confidence               999999999999998865 2223333                 455778999999999999999873  233    3


Q ss_pred             hHHHHHHHHHHhC----------CChHHHHHHHhhC-CCCCCH
Q 045511          133 VTWTTIISGLSKC----------GFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       133 ~~~~~li~~~~~~----------g~~~~a~~~~~~m-~~~p~~  164 (209)
                      ..+..+..+|...          |++++|...|++. ...|+.
T Consensus       186 ~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~  228 (261)
T 3qky_A          186 DALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDS  228 (261)
T ss_dssp             HHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCC
Confidence            4677777777765          8899999999998 556665

>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=98.59  E-value=8.7e-07  Score=62.15  Aligned_cols=128  Identities=7%  Similarity=0.088  Sum_probs=93.4

Q ss_pred             HHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH-HHhCCCh--
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF-YVTVKDI--  117 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~-~~~~g~~--  117 (209)
                      +...|++++|...+++..+.. +.+...|..+-..+...|+++.|...|+...+.. +.+...+..+-.. +...|++  
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~   97 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMT   97 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             hhhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcch
Confidence            345788888888888877653 2456778888888888999999999998888765 3466777777777 7788888  


Q ss_pred             hhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHH
Q 045511          118 FSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSV  170 (209)
Q Consensus       118 ~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~l  170 (209)
                      ++|.+.++...   ..+...+..+-..|...|++++|...|.+. ...|+......+
T Consensus        98 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~  154 (177)
T 2e2e_A           98 AQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPRINRTQL  154 (177)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTSCHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCccHHHH
Confidence            99999988773   235677888888899999999999999887 556654433333

>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=98.57  E-value=3.4e-06  Score=60.66  Aligned_cols=122  Identities=11%  Similarity=-0.056  Sum_probs=102.0

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      +..+-..+...|++++|.+.|+..    +.|+..+|..+-..|.+.|++++|.+.|++..   ..+...|..+-..|...
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~   84 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQT   84 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHc
Confidence            444556677889999999999876    46788999999999999999999999999873   34677899999999999


Q ss_pred             CChHHHHHHHhhC-CCCC----------------CH-HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          146 GFHKEAIDMFCGI-DVKP----------------NA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       146 g~~~~a~~~~~~m-~~~p----------------~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      |++++|...|++. ...|                +. ..+..+-..+...|++++|.+.+....+..
T Consensus        85 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           85 EKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             TCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             ccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            9999999999988 3222                22 577888888999999999999999887664

>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=98.57  E-value=3.7e-06  Score=57.74  Aligned_cols=123  Identities=9%  Similarity=0.007  Sum_probs=74.9

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK  144 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~  144 (209)
                      .+..+-..+...|+++.|...|+...+.. +.+..++..+...+...|++++|.+.+++..   ..+...|..+-..+..
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~   93 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA   93 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            34445555566666777776666666543 3345666666667777777777777776652   2345566666777777


Q ss_pred             CCChHHHHHHHhhC-CCCCCH-HhH--HHHHHHhccccchhHHHHHHHHHH
Q 045511          145 CGFHKEAIDMFCGI-DVKPNA-NTL--VSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       145 ~g~~~~a~~~~~~m-~~~p~~-~t~--~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      .|++++|...|.+. ...|+. ..+  -.....+...|++++|.+.+....
T Consensus        94 ~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           94 LGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             TTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            77777777777776 434432 233  222333556677777777776543

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

Probab=98.55  E-value=2.7e-06  Score=55.19  Aligned_cols=90  Identities=13%  Similarity=0.105  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK  144 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~  144 (209)
                      .+..+...+...|+++.|.+.++...+.. +.+..++..+...+.+.|++++|..+++++.   ..+...+..+...+..
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~   89 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYK   89 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH
Confidence            34444444444444444444444444332 2233444444444444455555544444431   1233444444444555


Q ss_pred             CCChHHHHHHHhhC
Q 045511          145 CGFHKEAIDMFCGI  158 (209)
Q Consensus       145 ~g~~~~a~~~~~~m  158 (209)
                      .|++++|...|.+.
T Consensus        90 ~~~~~~A~~~~~~~  103 (125)
T 1na0_A           90 QGDYDEAIEYYQKA  103 (125)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHH
Confidence            55555555555444

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

Probab=98.54  E-value=1.2e-06  Score=63.44  Aligned_cols=159  Identities=9%  Similarity=0.026  Sum_probs=120.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHH----------------HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNT----------------LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFT   70 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~----------------li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~   70 (209)
                      +.++.++|...+.++.+..+.  +...|..                +-..+.+.|++++|...|++..+.. +-+...+.
T Consensus        16 ~~g~~~~A~~~~~~al~~~p~--~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~   92 (208)
T 3urz_A           16 EAGQNGQAVSYFRQTIALNID--RTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLE   92 (208)
T ss_dssp             HTTCHHHHHHHHHHHHHHCHH--HHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhCCC--ChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHH
Confidence            678888888888888776433  2345555                8888999999999999999998854 23678899


Q ss_pred             HHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC--hhhHHHHHHhcCCCcHhH--HHHHHHHHHhCC
Q 045511           71 QALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD--IFSAHQIFNSVVFPDVVT--WTTIISGLSKCG  146 (209)
Q Consensus        71 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~--~~~a~~~~~~~~~~~~~~--~~~li~~~~~~g  146 (209)
                      .+-..+...|++++|.+.|+...+.. +.+..+|..+-..|...|+  .+.+...+.....|+...  +...-.++...|
T Consensus        93 ~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~  171 (208)
T 3urz_A           93 ACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTT  171 (208)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHcc
Confidence            99999999999999999999999875 4467788888888766654  456677777776665433  333344556689


Q ss_pred             ChHHHHHHHhhC-CCCCCHHhHHH
Q 045511          147 FHKEAIDMFCGI-DVKPNANTLVS  169 (209)
Q Consensus       147 ~~~~a~~~~~~m-~~~p~~~t~~~  169 (209)
                      ++++|...|++. .+.|+......
T Consensus       172 ~~~~A~~~~~~al~l~P~~~~~~~  195 (208)
T 3urz_A          172 RYEKARNSLQKVILRFPSTEAQKT  195 (208)
T ss_dssp             THHHHHHHHHHHTTTSCCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCHHHHHH
Confidence            999999999998 88998754443

>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=98.53  E-value=2.9e-06  Score=65.15  Aligned_cols=180  Identities=8%  Similarity=-0.090  Sum_probs=129.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhC----CCCC-CHHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSSY-NHYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-~~~t~~~ll~~~~   77 (209)
                      ..++.++|...+.+..+......+.    .+|+.+-..|.+.|++++|...|++..+.    |-.. -..++..+-..|.
T Consensus        48 ~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~  127 (307)
T 2ifu_A           48 NAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLME  127 (307)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHT
T ss_pred             HcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            4567777777777777776544443    68889999999999999999999886542    2111 2367778888888


Q ss_pred             ccccHHHHHHHHHHHHHhccCc-----cHhHHHHHHHHHHhCCChhhHHHHHHhcCC-----Cc----HhHHHHHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYGHLH-----DIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----PD----VVTWTTIISGLS  143 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g~~~-----~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~  143 (209)
                      . |++++|.+.|+...+.....     ...+++.+-..|.+.|++++|.+.|++..+     ++    ...+..+...+.
T Consensus       128 ~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~  206 (307)
T 2ifu_A          128 P-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQL  206 (307)
T ss_dssp             T-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             c-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHH
Confidence            8 99999999998877543111     146889999999999999999999988732     11    236677778888


Q ss_pred             hCCChHHHHHHHhhCCCCCC------HHhHHHHHHHhccccchhHHHHHHH
Q 045511          144 KCGFHKEAIDMFCGIDVKPN------ANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m~~~p~------~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      ..|++++|...|++.-..|+      ......++.++ ..|+.+...++.+
T Consensus       207 ~~g~~~~A~~~~~~al~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~~~~  256 (307)
T 2ifu_A          207 HRADYVAAQKCVRESYSIPGFSGSEDCAALEDLLQAY-DEQDEEQLLRVCR  256 (307)
T ss_dssp             HTTCHHHHHHHHHHHTTSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHHHTT
T ss_pred             HcCCHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHHHHh
Confidence            88999999999987522232      12455666666 5677776666443

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

Probab=98.53  E-value=3.6e-06  Score=54.60  Aligned_cols=110  Identities=13%  Similarity=0.064  Sum_probs=89.9

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      ...|..+...+.+.|++++|.+.|+++.+.. +.+..++..+...+.+.|++++|...++.+.+.. +.+..++..+...
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            4678888899999999999999999998754 3467888899999999999999999999998875 4567889999999


Q ss_pred             HHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHH
Q 045511          111 YVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGL  142 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~  142 (209)
                      |...|++++|.+.|++..  .| +...+..+-..+
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  121 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAK  121 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            999999999999999873  23 344444444443

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.52  E-value=2.5e-06  Score=67.27  Aligned_cols=182  Identities=8%  Similarity=-0.071  Sum_probs=120.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhC----C-CCC-CHHHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNC----P-SSY-NHYTFTQALKAC   76 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g-~~p-~~~t~~~ll~~~   76 (209)
                      ..++.++|...+.++.+.....++.    .++..+-..+...|+++.|...+++..+.    + ..+ ...++..+-..+
T Consensus       113 ~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y  192 (378)
T 3q15_A          113 DQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNY  192 (378)
T ss_dssp             HTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHH
T ss_pred             HHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHH
Confidence            5667777777777777665554543    56777777888888888888888776542    1 111 245677777788


Q ss_pred             hccccHHHHHHHHHHHHHhcc----C-ccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-------C-cHhHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGH----L-HDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-------P-DVVTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~----~-~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-------~-~~~~~~~li~~~~  143 (209)
                      ...|+++.|.+.|+...+...    . ....+++.+-..|...|++++|.+.|++..+       | ...++..+-..|.
T Consensus       193 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~  272 (378)
T 3q15_A          193 DDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLC  272 (378)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHH
Confidence            888888888888877665321    1 1234677788888888888888888876521       2 2456777778888


Q ss_pred             hCCChHHHHHHHhhC-------CCCCCHHhHHHHHHHhccccc---hhHHHHHHH
Q 045511          144 KCGFHKEAIDMFCGI-------DVKPNANTLVSVLSACSSLGS---RKLGKAIHA  188 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-------~~~p~~~t~~~li~~~~~~g~---~~~a~~~~~  188 (209)
                      +.|++++|...+++.       +-+.....+..+-..+...|+   +++|...+.
T Consensus       273 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~  327 (378)
T 3q15_A          273 KAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFE  327 (378)
T ss_dssp             HTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            888888888888776       111122345555556666676   455544443

>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=98.52  E-value=6.2e-07  Score=63.12  Aligned_cols=146  Identities=10%  Similarity=-0.016  Sum_probs=108.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHH-HhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKA-CSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~-~~~~~~~~~a   85 (209)
                      +.++.++|...+.++.+..+  .+...+..+-..+.+.|++++|...|++.....  |+...+...... +...+....+
T Consensus        18 ~~g~~~~A~~~~~~al~~~P--~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~~~~a   93 (176)
T 2r5s_A           18 QQGEHAQALNVIQTLSDELQ--SRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELHQQAAESPE   93 (176)
T ss_dssp             HTTCHHHHHHHHHTSCHHHH--TSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHHHHHTSCHH
T ss_pred             HcCCHHHHHHHHHHHHHHCC--CcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHHhhcccchH
Confidence            67777788877777766542  355888999999999999999999999987643  444333222111 1222333446


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc---HhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD---VVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~---~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      ...++...+.. +.+...+..+-..+...|++++|...|++..  .|+   ...+..+...+...|+.++|...|++
T Consensus        94 ~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~  169 (176)
T 2r5s_A           94 LKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRR  169 (176)
T ss_dssp             HHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHH
Confidence            77888877654 3457899999999999999999999999873  343   55888999999999999999988875

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

Probab=98.51  E-value=2.6e-06  Score=58.75  Aligned_cols=99  Identities=7%  Similarity=-0.054  Sum_probs=76.2

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGL  142 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~  142 (209)
                      ...+..+-..+.+.|++++|...|+...+.. +.+...|..+-.+|...|++++|.+.|++..   ..+...|..+-.+|
T Consensus        36 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~  114 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQ  114 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHH
Confidence            3456666677788888888888888888765 4567788888888888888888888888772   23466777888888


Q ss_pred             HhCCChHHHHHHHhhC-CCCCCHH
Q 045511          143 SKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       143 ~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      ...|++++|...|++. ...||..
T Consensus       115 ~~lg~~~eA~~~~~~al~l~~~~~  138 (151)
T 3gyz_A          115 LRLKAPLKAKECFELVIQHSNDEK  138 (151)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCCCHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCHH
Confidence            8888888888888887 5566654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.51  E-value=1.4e-06  Score=62.09  Aligned_cols=147  Identities=6%  Similarity=-0.100  Sum_probs=64.7

Q ss_pred             cCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhc----c-CccHhHHHHHHHHHHhCCCh
Q 045511           43 QSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYG----H-LHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        43 ~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~-~~~~~~~~~ll~~~~~~g~~  117 (209)
                      ..|++++|.+.++.... ........+..+-..+...|++++|...++...+..    . .....++..+-..|...|++
T Consensus         4 ~~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~   82 (203)
T 3gw4_A            4 EAHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNW   82 (203)
T ss_dssp             ---CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             ccccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCH
Confidence            34555555553332222 111233445555555555555555555555444311    1 11223455555555555555


Q ss_pred             hhHHHHHHhcC-----CC-c----HhHHHHHHHHHHhCCChHHHHHHHhhC----CCCCC----HHhHHHHHHHhccccc
Q 045511          118 FSAHQIFNSVV-----FP-D----VVTWTTIISGLSKCGFHKEAIDMFCGI----DVKPN----ANTLVSVLSACSSLGS  179 (209)
Q Consensus       118 ~~a~~~~~~~~-----~~-~----~~~~~~li~~~~~~g~~~~a~~~~~~m----~~~p~----~~t~~~li~~~~~~g~  179 (209)
                      ++|.+.+++..     .+ +    ...+..+-..+...|++++|...+.+.    .-.++    ..++..+-..+...|+
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            55555554431     01 1    223444455555555555555555444    00011    1223444445555555


Q ss_pred             hhHHHHHHHHH
Q 045511          180 RKLGKAIHAHS  190 (209)
Q Consensus       180 ~~~a~~~~~~~  190 (209)
                      +++|.+.+...
T Consensus       163 ~~~A~~~~~~a  173 (203)
T 3gw4_A          163 LLEAQQHWLRA  173 (203)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555555544

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

Probab=98.50  E-value=3.1e-06  Score=55.37  Aligned_cols=94  Identities=12%  Similarity=-0.003  Sum_probs=43.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+..+...+...|++++|...|++..... +.+...+..+...+...|++++|.+.++...+.. +.+...+..+-..|
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            344444445555555555555555544432 1233444444444455555555555555444432 22334444444444


Q ss_pred             HhCCChhhHHHHHHhc
Q 045511          112 VTVKDIFSAHQIFNSV  127 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~  127 (209)
                      .+.|++++|.+.|++.
T Consensus        91 ~~~~~~~~A~~~~~~~  106 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKA  106 (131)
T ss_dssp             HHTTCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHH
Confidence            5555555555444443

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.49  E-value=1e-06  Score=75.23  Aligned_cols=149  Identities=12%  Similarity=-0.035  Sum_probs=126.6

Q ss_pred             HcCCCccchHHHHHHhh--------hCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           42 TQSSTPQNAIPLYNKML--------NCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        42 ~~~g~~~~a~~l~~~m~--------~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      ...|++++|.+.+++..        +. -+.+...+..+-.++.+.|++++|.+.|+...+.. +.+...|..+-..|..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHH
Confidence            78899999999999987        32 23456778888899999999999999999998875 4567899999999999


Q ss_pred             CCChhhHHHHHHhcC--C-CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHH
Q 045511          114 VKDIFSAHQIFNSVV--F-PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHA  188 (209)
Q Consensus       114 ~g~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~  188 (209)
                      .|++++|.+.|++..  . .+...|..+-..|.+.|++++ .+.|++. ...|+ ...+..+-.++.+.|++++|.+.++
T Consensus       480 ~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~  558 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLD  558 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999999999999873  2 356788899999999999999 9999988 66665 4678888999999999999999998


Q ss_pred             HHHHh
Q 045511          189 HSLRN  193 (209)
Q Consensus       189 ~~~~~  193 (209)
                      ...+.
T Consensus       559 ~al~l  563 (681)
T 2pzi_A          559 EVPPT  563 (681)
T ss_dssp             TSCTT
T ss_pred             hhccc
Confidence            76543

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

Probab=98.46  E-value=1.5e-06  Score=66.29  Aligned_cols=146  Identities=10%  Similarity=-0.079  Sum_probs=116.7

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHH-HHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQAL-KACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll-~~~~~~~~~~~a   85 (209)
                      +.|+.++|...+.++.+..+  .+...+..+-..+.+.|++++|...+++.....  |+........ ..+.+.++.+.+
T Consensus       129 ~~g~~~~A~~~~~~al~~~P--~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~~~l~~~~~~~~a  204 (287)
T 3qou_A          129 QESNYTDALPLLXDAWQLSN--QNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQIELLXQAADTPE  204 (287)
T ss_dssp             HTTCHHHHHHHHHHHHHHTT--SCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHHHHHHHHHTSCHH
T ss_pred             hCCCHHHHHHHHHHHHHhCC--cchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHHHHHHhhcccCcc
Confidence            67888888888888877642  245788999999999999999999999987753  5544332222 235677788888


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc---HhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD---VVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~---~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      ...++...+.. +.+...+..+-..|...|++++|...|.+..  .|+   ...+..+...|...|+.++|...|++
T Consensus       205 ~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~  280 (287)
T 3qou_A          205 IQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXYRR  280 (287)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            88898888775 5578899999999999999999999999983  243   66899999999999999999888765

>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=98.45  E-value=5.9e-06  Score=56.69  Aligned_cols=125  Identities=14%  Similarity=-0.014  Sum_probs=101.2

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|..+-..+.+.|++++|...|++..+.. +.+...+..+-..+...|++++|.+.++...+.. +.+...+..+-..+
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            567778888899999999999999988753 2367888888999999999999999999998875 45678899999999


Q ss_pred             HhCCChhhHHHHHHhcC---CCcHhHHHH--HHHHHHhCCChHHHHHHHhhC
Q 045511          112 VTVKDIFSAHQIFNSVV---FPDVVTWTT--IISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~---~~~~~~~~~--li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ...|++++|.+.|++..   ..+...+..  ....+...|++++|...+...
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            99999999999998873   224444433  344477789999998888764

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

Probab=98.43  E-value=9.3e-06  Score=53.98  Aligned_cols=95  Identities=6%  Similarity=-0.020  Sum_probs=49.8

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      +...=..+.+.|++++|.+.|+...+.. +.+..+|..+-.+|.+.|++++|.+.|++..   ..+...|..+-.+|...
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~   94 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLVAM   94 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC
Confidence            3334444555555555555555555443 3344555555555555555555555555541   22344555555555555


Q ss_pred             CChHHHHHHHhhC-CCCCCH
Q 045511          146 GFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       146 g~~~~a~~~~~~m-~~~p~~  164 (209)
                      |++++|.+.|++. .+.|+.
T Consensus        95 ~~~~~A~~~~~~al~l~P~~  114 (126)
T 4gco_A           95 REWSKAQRAYEDALQVDPSN  114 (126)
T ss_dssp             TCHHHHHHHHHHHHHHCTTC
T ss_pred             CCHHHHHHHHHHHHHHCcCC
Confidence            5555555555555 444443

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

Probab=98.43  E-value=7.2e-06  Score=53.96  Aligned_cols=112  Identities=9%  Similarity=-0.039  Sum_probs=75.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..|..+-..+.+.|++++|...|++..+.. +.+...+..+-..+...|++++|.+.++...+.. +.+...+..+-..|
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~   94 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAAL   94 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHH
Confidence            667777777778888888888888777643 2356677777777777788888888887777654 33566777777777


Q ss_pred             HhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhC
Q 045511          112 VTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKC  145 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~  145 (209)
                      .+.|++++|.+.|++..  .| +...+..+-..+...
T Consensus        95 ~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  131 (133)
T 2lni_A           95 EAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQ  131 (133)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHh
Confidence            77777777777777652  22 234444444444433

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.42  E-value=4.4e-06  Score=61.11  Aligned_cols=149  Identities=8%  Similarity=0.044  Sum_probs=111.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCC-cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHH----HHHHHHHHHh----
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHY----TFTQALKACS----   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~----t~~~ll~~~~----   77 (209)
                      +.++.++|...+.++.+..+..|. ...+..+...+.+.|++++|...|++..+..  |+..    .+-.+-.++.    
T Consensus        16 ~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~--P~~~~~~~a~~~~g~~~~~~~~   93 (225)
T 2yhc_A           16 QDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN--PTHPNIDYVMYMRGLTNMALDD   93 (225)
T ss_dssp             HHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHC
T ss_pred             HcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCcHHHHHHHHHHHHHhhhh
Confidence            788889999999998887544333 2577888899999999999999999998754  3321    2322223332    


Q ss_pred             --------------ccccHHHHHHHHHHHHHhccCccHhHH-----------------HHHHHHHHhCCChhhHHHHHHh
Q 045511           78 --------------LAHAHQKGLEIHAHVIKYGHLHDIFIQ-----------------NSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        78 --------------~~~~~~~a~~~~~~m~~~g~~~~~~~~-----------------~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                                    ..|+.++|...|+.+.+.. +-+...+                 -.+-..|.+.|++++|...|++
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~  172 (225)
T 2yhc_A           94 SALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-PNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEG  172 (225)
T ss_dssp             --------------CCHHHHHHHHHHHHHHTTC-TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence                          3678999999999998764 2222222                 2345578899999999999998


Q ss_pred             cC--CCc----HhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          127 VV--FPD----VVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       127 ~~--~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +.  .|+    ...+..+..+|.+.|++++|.+.++.+
T Consensus       173 ~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l  210 (225)
T 2yhc_A          173 MLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKII  210 (225)
T ss_dssp             HHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            83  233    256888899999999999999999987

>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=1.7e-05  Score=71.72  Aligned_cols=147  Identities=11%  Similarity=0.125  Sum_probs=122.0

Q ss_pred             hCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHH
Q 045511           27 KIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNS  106 (209)
Q Consensus        27 ~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  106 (209)
                      ..-+..+|..+-.++.+.|++++|.+-|.+-      -|...|.-+..+|.+.|+++++.+.+...++..  +++...+.
T Consensus      1101 rvn~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~ 1172 (1630)
T 1xi4_A         1101 RCNEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETE 1172 (1630)
T ss_pred             hcCCHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHH
Confidence            3345689999999999999999999999664      467888999999999999999999998776654  44445556


Q ss_pred             HHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHH
Q 045511          107 LLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAI  186 (209)
Q Consensus       107 ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~  186 (209)
                      +..+|++.+++++.....   ..++...|..+-..|...|++++|..+|...      ..|..+...+.+.|+++.|.+.
T Consensus      1173 LafaYAKl~rleele~fI---~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA------~ny~rLA~tLvkLge~q~AIEa 1243 (1630)
T 1xi4_A         1173 LIFALAKTNRLAELEEFI---NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV------SNFGRLASTLVHLGEYQAAVDG 1243 (1630)
T ss_pred             HHHHHHhhcCHHHHHHHH---hCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh------hHHHHHHHHHHHhCCHHHHHHH
Confidence            999999999998755554   4567777888889999999999999999984      4888899999999999999888


Q ss_pred             HHHH
Q 045511          187 HAHS  190 (209)
Q Consensus       187 ~~~~  190 (209)
                      ++..
T Consensus      1244 arKA 1247 (1630)
T 1xi4_A         1244 ARKA 1247 (1630)
T ss_pred             HHHh
Confidence            7654

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

Probab=98.37  E-value=9.4e-06  Score=53.39  Aligned_cols=100  Identities=11%  Similarity=0.069  Sum_probs=71.4

Q ss_pred             CCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHH
Q 045511           63 SYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTII  139 (209)
Q Consensus        63 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li  139 (209)
                      +.+...+..+-..+.+.|++++|...|+...+.. +.+..++..+-..|...|++++|.+.+++..   ..+...+..+-
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la   91 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKA   91 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHH
Confidence            3455667777777778888888888888777653 3356677777778888888888888877762   23566777777


Q ss_pred             HHHHhCCChHHHHHHHhhC-CCCCC
Q 045511          140 SGLSKCGFHKEAIDMFCGI-DVKPN  163 (209)
Q Consensus       140 ~~~~~~g~~~~a~~~~~~m-~~~p~  163 (209)
                      ..+.+.|++++|.+.|.+. ...|+
T Consensus        92 ~~~~~~~~~~~A~~~~~~~~~~~p~  116 (133)
T 2lni_A           92 AALEAMKDYTKAMDVYQKALDLDSS  116 (133)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCGG
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhCCC
Confidence            7778888888888887776 44443

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

Probab=98.36  E-value=1.3e-05  Score=52.30  Aligned_cols=116  Identities=11%  Similarity=0.035  Sum_probs=95.4

Q ss_pred             CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHH
Q 045511           64 YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIIS  140 (209)
Q Consensus        64 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~  140 (209)
                      .+...+..+-..+...|+++.|.+.++...+.. +.+...+..+...+...|++++|.+.++...   ..+...+..+..
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~   88 (131)
T 2vyi_A           10 AEAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHH
Confidence            345677888888999999999999999998764 4567889999999999999999999998873   345778888999


Q ss_pred             HHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccch
Q 045511          141 GLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSR  180 (209)
Q Consensus       141 ~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~  180 (209)
                      .+...|++++|...|.+. ...| +...+..+...+...|++
T Consensus        89 ~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           89 ALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcC
Confidence            999999999999999998 5556 455677777777666654

>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=98.36  E-value=1.1e-06  Score=60.38  Aligned_cols=77  Identities=16%  Similarity=-0.009  Sum_probs=31.7

Q ss_pred             HHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChH
Q 045511           73 LKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHK  149 (209)
Q Consensus        73 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~  149 (209)
                      -..|.+.|++++|.+.|+...+.. +-+..+|..+-..|.+.|++++|...|++..  .| +...|..+-..|.+.|+++
T Consensus        38 a~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~  116 (150)
T 4ga2_A           38 AKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTD  116 (150)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChH
Confidence            333444444444444444444332 2233344444444444444444444444431  11 2334444444444444443


Q ss_pred             H
Q 045511          150 E  150 (209)
Q Consensus       150 ~  150 (209)
                      +
T Consensus       117 ~  117 (150)
T 4ga2_A          117 G  117 (150)
T ss_dssp             S
T ss_pred             H
Confidence            3

>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=98.36  E-value=2.8e-06  Score=58.20  Aligned_cols=97  Identities=8%  Similarity=-0.139  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHH
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGL  142 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~  142 (209)
                      ...+..+-..+.+.|++++|...|+...+.. +.+...|..+-.+|...|++++|.+.|++..   ..+...|..+-.+|
T Consensus        21 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~   99 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            3455556666777778888888877777654 4466677777777778888888888877762   23456667777777


Q ss_pred             HhCCChHHHHHHHhhC-CCCCC
Q 045511          143 SKCGFHKEAIDMFCGI-DVKPN  163 (209)
Q Consensus       143 ~~~g~~~~a~~~~~~m-~~~p~  163 (209)
                      ...|++++|...|... .+.|+
T Consensus       100 ~~~g~~~~A~~~~~~al~~~p~  121 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQELIAN  121 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHTT
T ss_pred             HHcCCHHHHHHHHHHHHHHCcC
Confidence            7888888888777776 44444

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.36  E-value=2.5e-05  Score=66.55  Aligned_cols=185  Identities=10%  Similarity=-0.001  Sum_probs=133.5

Q ss_pred             hccCCCcch-HhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCC---------CCCC-----------
Q 045511            7 KSLKPTLSF-KQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCP---------SSYN-----------   65 (209)
Q Consensus         7 ~~~~~~~a~-~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g---------~~p~-----------   65 (209)
                      +.++.+++. +.+.......  +.+...|-.++...-+.|++++|.++|+++.+..         -.|+           
T Consensus       355 ~~~~~~~a~r~il~rAi~~~--P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~  432 (679)
T 4e6h_A          355 EKNTDSTVITKYLKLGQQCI--PNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSK  432 (679)
T ss_dssp             HHSCCTTHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             hcCcHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccc
Confidence            456667775 7777776532  1344556778888888999999999999987631         0132           


Q ss_pred             -HHHHHHHHHHHhccccHHHHHHHHHHHHHh-ccCccHhHHHHHHHHHHhC-CChhhHHHHHHhcCC---CcHhHHHHHH
Q 045511           66 -HYTFTQALKACSLAHAHQKGLEIHAHVIKY-GHLHDIFIQNSLLHFYVTV-KDIFSAHQIFNSVVF---PDVVTWTTII  139 (209)
Q Consensus        66 -~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~ll~~~~~~-g~~~~a~~~~~~~~~---~~~~~~~~li  139 (209)
                       ...|...+....+.|.++.|..+|+...+. + .....+|-.....-.+. ++.+.|.++|+...+   .+...|...+
T Consensus       433 ~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~-~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~  511 (679)
T 4e6h_A          433 LTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKK-LVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYL  511 (679)
T ss_dssp             HHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGG-GSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHH
Confidence             236788888888889999999999998876 3 12233333322222333 458999999988732   3556678888


Q ss_pred             HHHHhCCChHHHHHHHhhC-CCCC----CHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          140 SGLSKCGFHKEAIDMFCGI-DVKP----NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       140 ~~~~~~g~~~~a~~~~~~m-~~~p----~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ......|+.+.|..+|.+. ...|    ....|...++.-.+.|+.+.+..+..++.+.-
T Consensus       512 ~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~  571 (679)
T 4e6h_A          512 DFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKF  571 (679)
T ss_dssp             HHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHS
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            8888899999999999987 4444    23578888888889999999999999988773

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.35  E-value=1e-05  Score=65.27  Aligned_cols=168  Identities=13%  Similarity=-0.014  Sum_probs=78.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC-HHHHHHHHHHHhcc-------------------ccHHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN-HYTFTQALKACSLA-------------------HAHQKGLEIHAH   91 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~-------------------~~~~~a~~~~~~   91 (209)
                      .++..+-..+.+.|++++|...+++..+..  |+ ..++..+-..+...                   +..+.|...++.
T Consensus       248 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  325 (472)
T 4g1t_A          248 DVLRSAAKFYRRKDEPDKAIELLKKALEYI--PNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKK  325 (472)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCchHHHHHHHHHHHHhC--CChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            455555566666666666666666655432  22 23333332222111                   123344444444


Q ss_pred             HHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHh----HHHHHH-HHHHhCCChHHHHHHHhhC-CCC--
Q 045511           92 VIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVV----TWTTII-SGLSKCGFHKEAIDMFCGI-DVK--  161 (209)
Q Consensus        92 m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~----~~~~li-~~~~~~g~~~~a~~~~~~m-~~~--  161 (209)
                      ..+.. +.+..++..+-..|...|++++|.+.|++.  ..++..    .+..+- -.+...|++++|+..|.+. .+.  
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            44432 233445666777777788888888888765  222221    122222 1234567777777777654 222  


Q ss_pred             ----------------------C-CHHhHHHHHHHhccccchhHHHHHHHHHHHhc-cCCCchhH
Q 045511          162 ----------------------P-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL-NENNIILD  202 (209)
Q Consensus       162 ----------------------p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~p~~~~~  202 (209)
                                            | +..+|..+-..+...|++++|.+.|+...+.+ ..|+..+|
T Consensus       405 ~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          405 SREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC----------------------
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence                                  2 34567777777777788888888887776654 34554433

>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=98.34  E-value=3.6e-06  Score=57.75  Aligned_cols=136  Identities=7%  Similarity=-0.095  Sum_probs=99.9

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLE   87 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~   87 (209)
                      .+..+++.+.+.+.....+.  +...+-.+-..|.+.|++++|.+.|++..+.. +-+...|..+-..+.+.|++++|..
T Consensus        10 ~~~~e~ai~~~~~a~~~~p~--~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~   86 (150)
T 4ga2_A           10 KADVERYIASVQGSTPSPRQ--KSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVE   86 (150)
T ss_dssp             HHHHHHHHHHHHHHSCSHHH--HHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cChHHHHHHHHHHhcccCcc--cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHH
Confidence            44444444444444332211  23566678888999999999999999998854 2366889999999999999999999


Q ss_pred             HHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHH-HHhc---CCCcHhHHHHHHHHHHhCCC
Q 045511           88 IHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQI-FNSV---VFPDVVTWTTIISGLSKCGF  147 (209)
Q Consensus        88 ~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~-~~~~---~~~~~~~~~~li~~~~~~g~  147 (209)
                      .|+...+.. +-+..+|..+-..|.+.|+.++|.+. +++.   ...+..+|+..-..+...|+
T Consensus        87 ~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           87 CYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            999998865 44678999999999999999876665 4654   23356677777666666654

>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=98.34  E-value=4e-06  Score=63.81  Aligned_cols=152  Identities=10%  Similarity=0.004  Sum_probs=109.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhCCCC-CC----HHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSS-YN----HYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-p~----~~t~~~ll~~~~   77 (209)
                      +.++.+++.+.+.+........|+.    ..|..+...+...|++++|...|++..+.... ++    ..+|+.+-..|.
T Consensus        87 ~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~  166 (293)
T 3u3w_A           87 KQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYA  166 (293)
T ss_dssp             HTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHH
Confidence            5566666666666665533222222    23345666677788999999999999874322 22    236889999999


Q ss_pred             ccccHHHHHHHHHHHHHh-----ccCcc-HhHHHHHHHHHHhCCChhhHHHHHHhcCC--------C-cHhHHHHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKY-----GHLHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--------P-DVVTWTTIISGL  142 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~-----g~~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--------~-~~~~~~~li~~~  142 (209)
                      ..|+++.|.+.|+...+.     +..+. ..++..+-..|.+.|++++|.+.+++..+        + -..+|..+-..|
T Consensus       167 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~  246 (293)
T 3u3w_A          167 ENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECL  246 (293)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHH
Confidence            999999999999988842     11222 34889999999999999999999987621        1 156788888999


Q ss_pred             HhCCC-hHHHHHHHhhC
Q 045511          143 SKCGF-HKEAIDMFCGI  158 (209)
Q Consensus       143 ~~~g~-~~~a~~~~~~m  158 (209)
                      .+.|+ +++|.+.|++.
T Consensus       247 ~~~g~~~~~A~~~~~~A  263 (293)
T 3u3w_A          247 RKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHTTCCHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHH
Confidence            99995 68888888774

>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=98.32  E-value=2e-05  Score=61.41  Aligned_cols=145  Identities=8%  Similarity=-0.020  Sum_probs=108.6

Q ss_pred             CCccchHHHHHHhhhCCCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--------------HhHHHHHHH
Q 045511           45 STPQNAIPLYNKMLNCPSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--------------IFIQNSLLH  109 (209)
Q Consensus        45 g~~~~a~~l~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--------------~~~~~~ll~  109 (209)
                      +++++|...|+.....  .| +...|..+-..+.+.|++++|...|+...+......              ..+|..+-.
T Consensus       127 ~~~~~A~~~~~~a~~~--~p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~  204 (336)
T 1p5q_A          127 KSFEKAKESWEMNSEE--KLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAM  204 (336)
T ss_dssp             EEEECCCCGGGCCHHH--HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHH
T ss_pred             eecccccchhcCCHHH--HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHH
Confidence            3445555554433321  13 356777788888889999999999998887653221              578999999


Q ss_pred             HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHH-
Q 045511          110 FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLG-  183 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a-  183 (209)
                      +|.+.|++++|...+++..   ..+...|..+-.+|...|++++|...|++. .+.|+ ...+..+-..+.+.|+.+++ 
T Consensus       205 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~  284 (336)
T 1p5q_A          205 CHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLARE  284 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998873   346778889999999999999999999988 66665 45677788888888998888 


Q ss_pred             HHHHHHHH
Q 045511          184 KAIHAHSL  191 (209)
Q Consensus       184 ~~~~~~~~  191 (209)
                      ..++..|.
T Consensus       285 ~~~~~~~~  292 (336)
T 1p5q_A          285 KKLYANMF  292 (336)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            44555543

>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=2.8e-05  Score=49.70  Aligned_cols=89  Identities=12%  Similarity=-0.029  Sum_probs=41.6

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC  145 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~  145 (209)
                      +..+...+...|+++.|...++...+.. +.+...+..+...+...|++++|...+++..   ..+...+..+...+...
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~   85 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFL   85 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            3344444444455555555554444432 2234444444445555555555555554431   12334444444555555


Q ss_pred             CChHHHHHHHhhC
Q 045511          146 GFHKEAIDMFCGI  158 (209)
Q Consensus       146 g~~~~a~~~~~~m  158 (209)
                      |++++|.+.|.+.
T Consensus        86 ~~~~~A~~~~~~~   98 (118)
T 1elw_A           86 NRFEEAKRTYEEG   98 (118)
T ss_dssp             TCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHH
Confidence            5555555555544

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

Probab=98.30  E-value=7.1e-06  Score=52.18  Aligned_cols=59  Identities=14%  Similarity=0.024  Sum_probs=22.4

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHH
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVI   93 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~   93 (209)
                      |..+-..+.+.|++++|...|++..+.. +.+...+..+-..+...|++++|.+.++...
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~   67 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVI   67 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            3333333444444444444444433321 1122333333333334444444444443333

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.30  E-value=5.9e-05  Score=54.63  Aligned_cols=139  Identities=11%  Similarity=-0.056  Sum_probs=113.4

Q ss_pred             cchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCC----ChhhHHHH
Q 045511           48 QNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVK----DIFSAHQI  123 (209)
Q Consensus        48 ~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g----~~~~a~~~  123 (209)
                      .+|.+.|++..+.|   +...+..+-..+...+++++|.++|+...+.|   ++..+..|-..|.. +    +.++|.++
T Consensus         3 ~eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~   75 (212)
T 3rjv_A            3 TEPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQL   75 (212)
T ss_dssp             -CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHH
T ss_pred             chHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHH
Confidence            46888898888875   56777778888888999999999999998876   56777778888887 6    89999999


Q ss_pred             HHhcCC-CcHhHHHHHHHHHHh----CCChHHHHHHHhhC-CCCCC---HHhHHHHHHHhcc----ccchhHHHHHHHHH
Q 045511          124 FNSVVF-PDVVTWTTIISGLSK----CGFHKEAIDMFCGI-DVKPN---ANTLVSVLSACSS----LGSRKLGKAIHAHS  190 (209)
Q Consensus       124 ~~~~~~-~~~~~~~~li~~~~~----~g~~~~a~~~~~~m-~~~p~---~~t~~~li~~~~~----~g~~~~a~~~~~~~  190 (209)
                      |.+..+ .+...+..|-..|..    .+++++|+..|.+. ...|+   ...+..+-..|..    .++.++|...|...
T Consensus        76 ~~~A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A  155 (212)
T 3rjv_A           76 AEKAVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGS  155 (212)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            998744 466777778778877    88999999999998 55553   6677777777776    77899999999988


Q ss_pred             HHh
Q 045511          191 LRN  193 (209)
Q Consensus       191 ~~~  193 (209)
                      .+.
T Consensus       156 ~~~  158 (212)
T 3rjv_A          156 SSL  158 (212)
T ss_dssp             HHT
T ss_pred             HHc
Confidence            776

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

Probab=98.30  E-value=8.8e-06  Score=51.74  Aligned_cols=90  Identities=11%  Similarity=0.074  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC---HHhHHHHHHHhcc
Q 045511          104 QNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN---ANTLVSVLSACSS  176 (209)
Q Consensus       104 ~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~---~~t~~~li~~~~~  176 (209)
                      +..+-..+...|++++|...|++..   ..+...|..+-..+...|++++|...|.+. ...|+   ...+..+...+..
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~~   88 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALRY   88 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHHH
Confidence            3334444444444444444444331   123334444444444555555555555444 22332   3444444445555


Q ss_pred             c-cchhHHHHHHHHHHHh
Q 045511          177 L-GSRKLGKAIHAHSLRN  193 (209)
Q Consensus       177 ~-g~~~~a~~~~~~~~~~  193 (209)
                      . |++++|.+.+....+.
T Consensus        89 ~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           89 IEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             CSSCSHHHHHHHHHHGGG
T ss_pred             HhCCHHHHHHHHHHHhhc
Confidence            5 5555555555544433

>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=98.30  E-value=7.9e-06  Score=53.47  Aligned_cols=96  Identities=9%  Similarity=0.044  Sum_probs=47.3

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC------Cc----HhHHHHH
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF------PD----VVTWTTI  138 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~------~~----~~~~~~l  138 (209)
                      |..+-..+...|+++.|...|+...+.. +.+...+..+...|...|++++|...+++...      ++    ...|..+
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l   85 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHH
Confidence            3444444445555555555555554433 23344455555555555555555555554411      11    3445555


Q ss_pred             HHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511          139 ISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      ...+...|++++|.+.|.+. ...|+..
T Consensus        86 a~~~~~~~~~~~A~~~~~~~~~~~~~~~  113 (131)
T 1elr_A           86 GNSYFKEEKYKDAIHFYNKSLAEHRTPD  113 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCCCHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhCCCHH
Confidence            55555566666666665555 3334433

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.30  E-value=4.7e-05  Score=61.37  Aligned_cols=186  Identities=6%  Similarity=-0.083  Sum_probs=129.1

Q ss_pred             hccCCCcchHhHHHHHHHHhh------CCC-cccHHHHHHHHHcCCCccchHHHHHHhhhC-----C-CCC-CHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIK------IPQ-PHILNTLLKLLTQSSTPQNAIPLYNKMLNC-----P-SSY-NHYTFTQA   72 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~------~p~-~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----g-~~p-~~~t~~~l   72 (209)
                      ..|+.++|.+.+.+..+....      .|+ ..+|+.+-..|...|++++|...+++..+.     + ..+ ...+|...
T Consensus        63 ~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~  142 (472)
T 4g1t_A           63 LKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEE  142 (472)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHH
Confidence            678899999999888776422      132 278999999999999999999999887541     1 112 23455554


Q ss_pred             HHHHhc--cccHHHHHHHHHHHHHhccCccHhHHHHHHHH---HHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHh
Q 045511           73 LKACSL--AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF---YVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSK  144 (209)
Q Consensus        73 l~~~~~--~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~---~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~  144 (209)
                      -.++.+  .+++++|.+.|+...+.. +-++..+..+...   +...++.++|.+.+++.   ...+...+..+-..+..
T Consensus       143 g~~~~~~~~~~y~~A~~~~~kal~~~-p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~~~~l~~~~~~  221 (472)
T 4g1t_A          143 GWTRLKCGGNQNERAKVCFEKALEKK-PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYLKVLLALKLHK  221 (472)
T ss_dssp             HHHHHHHCTTHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHccccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHH
Confidence            444443  457899999999988764 2234444444443   45668888888888765   23455566555555544


Q ss_pred             ----CCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          145 ----CGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       145 ----~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                          .|++++|.+.+.+. ...|+ ..++..+-..+...|++++|.+.+....+.
T Consensus       222 ~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  276 (472)
T 4g1t_A          222 MREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEY  276 (472)
T ss_dssp             CC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHh
Confidence                46778899999887 44554 467888899999999999999999988765

>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=98.29  E-value=2e-05  Score=51.87  Aligned_cols=90  Identities=9%  Similarity=-0.084  Sum_probs=52.3

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHh
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSK  144 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~  144 (209)
                      .|...-..+.+.|++++|.+.|+...+.. +.+...|..+-.+|.+.|++++|.+.+++..   ..+...|..+-.++..
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~   84 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIA   84 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            34444455556666666666666655543 3345566666666666666666666666552   2234555566666666


Q ss_pred             CCChHHHHHHHhhC
Q 045511          145 CGFHKEAIDMFCGI  158 (209)
Q Consensus       145 ~g~~~~a~~~~~~m  158 (209)
                      .|++++|...|.+.
T Consensus        85 ~~~~~~A~~~~~~a   98 (126)
T 3upv_A           85 VKEYASALETLDAA   98 (126)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             HhCHHHHHHHHHHH
Confidence            66666666666655

>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=1.4e-05  Score=62.31  Aligned_cols=128  Identities=10%  Similarity=0.028  Sum_probs=108.0

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC--------------HHHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN--------------HYTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~--------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      +...|..+-..+.+.|++++|...|++..+..-...              ...|..+-.++.+.|++++|...++..++.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            346788888999999999999999999987542211              488999999999999999999999999987


Q ss_pred             ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHH-HHHHhhC
Q 045511           96 GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEA-IDMFCGI  158 (209)
Q Consensus        96 g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a-~~~~~~m  158 (209)
                      . +.+...|..+-.+|...|++++|...|++..   ..+...+..+-..+.+.|+.+++ ...|+.|
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  291 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANM  291 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5 4578899999999999999999999999873   34577888899999999999988 4566666

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

Probab=98.26  E-value=2.2e-05  Score=54.09  Aligned_cols=95  Identities=12%  Similarity=-0.015  Sum_probs=82.7

Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHh
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSAC  174 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~  174 (209)
                      +...+..+-..+.+.|++++|.+.|+...   ..+...|..+-.+|...|++++|...|++. .+.|+ ...+..+-.++
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~  114 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQ  114 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHH
Confidence            34577888889999999999999999983   346788999999999999999999999999 66775 46788889999


Q ss_pred             ccccchhHHHHHHHHHHHhc
Q 045511          175 SSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       175 ~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ...|++++|...|+...+..
T Consensus       115 ~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          115 LRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC
T ss_pred             HHcCCHHHHHHHHHHHHHhC
Confidence            99999999999999988764

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.24  E-value=0.00037  Score=56.79  Aligned_cols=109  Identities=14%  Similarity=0.048  Sum_probs=45.1

Q ss_pred             CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc----cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh----CC
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL----AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT----VK  115 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~g  115 (209)
                      .++.++|.+.|++..+.|   +...+..+-..+..    .++.++|.++|+...+.|   +...+..+-..|..    .+
T Consensus       164 ~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~  237 (490)
T 2xm6_A          164 TRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQ  237 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCC
T ss_pred             CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCC
Confidence            344444444444444432   23333333333333    344444444444444333   23333344444433    44


Q ss_pred             ChhhHHHHHHhcC-CCcHhHHHHHHHHHHh----CCChHHHHHHHhhC
Q 045511          116 DIFSAHQIFNSVV-FPDVVTWTTIISGLSK----CGFHKEAIDMFCGI  158 (209)
Q Consensus       116 ~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m  158 (209)
                      +.++|.++|++.. ..+...+..+-..|..    .+++++|...|++.
T Consensus       238 ~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a  285 (490)
T 2xm6_A          238 DYTQSRVLFSQSAEQGNSIAQFRLGYILEQGLAGAKEPLKALEWYRKS  285 (490)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Confidence            4444444444432 1223333333333333    44555555555444

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.24  E-value=1e-05  Score=54.79  Aligned_cols=125  Identities=12%  Similarity=0.112  Sum_probs=70.2

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccC-cc----HhHHHHHHHHHHhCCChhhHHHHHHhcCC-----C----cHh
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHL-HD----IFIQNSLLHFYVTVKDIFSAHQIFNSVVF-----P----DVV  133 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~----~~~  133 (209)
                      ++..+-..+...|++++|...++...+.... ++    ..++..+-..|...|++++|.+.+++..+     .    ...
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            3444455555556666666665554433211 11    13556666666666666666666655411     1    133


Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC-------CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI-------DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m-------~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      .+..+-..+...|++++|...+.+.       +..+ ...++..+-..+...|++++|.+.+....+
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            5556666666777777777666665       1111 123566666667777777777777776544

>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=98.24  E-value=2.3e-05  Score=54.76  Aligned_cols=117  Identities=11%  Similarity=0.058  Sum_probs=93.5

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHH-HhccccH--H
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKA-CSLAHAH--Q   83 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~-~~~~~~~--~   83 (209)
                      ..++.++|...+.+..+..  +.+...|..+-..+...|++++|...|++..+..- .+...+..+-.. +...|++  +
T Consensus        22 ~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRG-ENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             -----CCCCHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hccCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCCcchH
Confidence            6788889998888887763  23558899999999999999999999999987542 355667777777 7788998  9


Q ss_pred             HHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           84 KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        84 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +|...++...+.. +.+...+..+-..|...|++++|...|++.
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a  141 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKV  141 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            9999999998875 445778889999999999999999999887

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

Probab=98.23  E-value=1.5e-05  Score=53.82  Aligned_cols=97  Identities=9%  Similarity=-0.159  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHH
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLS  143 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~  143 (209)
                      ..+..+-..+.+.|++++|...|+...+.. +.+...|..+-.+|.+.|++++|...|+...   ..+...|..+-.+|.
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   97 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHH
Confidence            344455566677788888888888777654 3466677777778888888888888887762   234556677777788


Q ss_pred             hCCChHHHHHHHhhC-CCCCCH
Q 045511          144 KCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      ..|++++|...|+.. .+.|+.
T Consensus        98 ~~g~~~~A~~~~~~al~~~p~~  119 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARALAAAQ  119 (142)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHTC
T ss_pred             HcCCHHHHHHHHHHHHHhCCCC
Confidence            888888888888776 444443

>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=98.22  E-value=7.9e-05  Score=49.38  Aligned_cols=93  Identities=8%  Similarity=-0.104  Sum_probs=54.8

Q ss_pred             CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHH
Q 045511           65 NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISG  141 (209)
Q Consensus        65 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~  141 (209)
                      +...|..+-..+...|+++.|...|+...+.. +.+...|..+-.+|...|++++|...++...   ..+...|..+-..
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~   86 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQC   86 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHH
Confidence            44555555556666666666666666655543 2345566666666666666666666665552   2244556666666


Q ss_pred             HHhCCChHHHHHHHhhC
Q 045511          142 LSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m  158 (209)
                      |...|++++|...|.+.
T Consensus        87 ~~~~~~~~~A~~~~~~a  103 (137)
T 3q49_B           87 QLEMESYDEAIANLQRA  103 (137)
T ss_dssp             HHHTTCHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHH
Confidence            66666666666666655

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.21  E-value=1.5e-05  Score=60.47  Aligned_cols=181  Identities=3%  Similarity=-0.106  Sum_probs=89.9

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|...+.++.+..  +.+...|..+-..+.+.|++++|...+++..+.. +-+...+..+-.++...|++++|.
T Consensus        16 ~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~   92 (281)
T 2c2l_A           16 VGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAI   92 (281)
T ss_dssp             HTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHH
Confidence            4555555555555555442  1134555666666666666666666666655532 123455555556666666666666


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      ..|+...+.... +...+...+....+..........-......+... ...+..+ ..|++++|.+.+.+. ...|+..
T Consensus        93 ~~~~~al~l~p~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~~~l~~l-~~~~~~~A~~~~~~al~~~p~~~  169 (281)
T 2c2l_A           93 ANLQRAYSLAKE-QRLNFGDDIPSALRIAKKKRWNSIEERRIHQESEL-HSYLTRL-IAAERERELEECQRNHEGHEDDG  169 (281)
T ss_dssp             HHHHHHHHHHHH-TTCCCCSHHHHHHHHHHHHHHHHHHHTCCCCCCHH-HHHHHHH-HHHHHHHHHTTTSGGGTTTSCHH
T ss_pred             HHHHHHHHhCcc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH-HHHHHHH-HHHHHHHHHHHHHhhhccccchh
Confidence            666655543310 00111111111111111111111111111122222 2222222 368888999888887 7788765


Q ss_pred             hHHHHHHH-hccc-cchhHHHHHHHHHHHh
Q 045511          166 TLVSVLSA-CSSL-GSRKLGKAIHAHSLRN  193 (209)
Q Consensus       166 t~~~li~~-~~~~-g~~~~a~~~~~~~~~~  193 (209)
                      ....-+.. +.+. +.++++.++|....+.
T Consensus       170 ~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          170 HIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             HHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            54444433 3333 6678899998877553

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.20  E-value=1.6e-05  Score=56.48  Aligned_cols=129  Identities=8%  Similarity=-0.090  Sum_probs=100.5

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhh----CCCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhc--c--Cc-
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLN----CPSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYG--H--LH-   99 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~----~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~--~~-   99 (209)
                      ...++..+-..+...|++++|...+++...    .|..| ...++..+-..+...|++++|.+.++...+..  .  .| 
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            347888899999999999999999988865    22222 34677888888999999999999998876541  1  11 


Q ss_pred             -cHhHHHHHHHHHHhCCChhhHHHHHHhcC-------CCc--HhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          100 -DIFIQNSLLHFYVTVKDIFSAHQIFNSVV-------FPD--VVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       100 -~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                       ...++..+-..+...|++++|.+.+++..       .+.  ..++..+-..+...|++++|.+.+.+.
T Consensus       105 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  173 (203)
T 3gw4_A          105 AASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRA  173 (203)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence             24568888999999999999999998762       111  335678888999999999999988875

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.20  E-value=0.00029  Score=57.40  Aligned_cols=89  Identities=11%  Similarity=-0.036  Sum_probs=37.1

Q ss_pred             ccHHHHHHHHHc----CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc----cccHHHHHHHHHHHHHhccCccHhH
Q 045511           32 HILNTLLKLLTQ----SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL----AHAHQKGLEIHAHVIKYGHLHDIFI  103 (209)
Q Consensus        32 ~~~~~li~~~~~----~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~  103 (209)
                      ..+..|-..+..    .++.++|...|++..+.|   +...+..+-..|..    .+++++|.++|+...+.|   ++..
T Consensus        76 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a  149 (490)
T 2xm6_A           76 PAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSG  149 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHH
Confidence            344444444444    444445555554444433   22233333333333    344444444444444433   2333


Q ss_pred             HHHHHHHHHh----CCChhhHHHHHHh
Q 045511          104 QNSLLHFYVT----VKDIFSAHQIFNS  126 (209)
Q Consensus       104 ~~~ll~~~~~----~g~~~~a~~~~~~  126 (209)
                      +..|-..|..    .++.++|.+.|++
T Consensus       150 ~~~Lg~~y~~g~g~~~d~~~A~~~~~~  176 (490)
T 2xm6_A          150 QQSMGDAYFEGDGVTRDYVMAREWYSK  176 (490)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            3333333433    3444444444443

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

Probab=98.18  E-value=6.9e-05  Score=51.67  Aligned_cols=99  Identities=8%  Similarity=-0.013  Sum_probs=63.5

Q ss_pred             CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHH
Q 045511           65 NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISG  141 (209)
Q Consensus        65 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~  141 (209)
                      +...|..+-..+.+.|++++|.+.|+...+.. +.+...|..+-.+|.+.|++++|...|++..   ..+...|..+-..
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~   88 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            34455556666666777777777777666654 3355667777777777777777777776652   2345666677777


Q ss_pred             HHhCCChHHHHHHHhhC-CCCCCH
Q 045511          142 LSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      |...|++++|...|.+. .+.|+.
T Consensus        89 ~~~~g~~~~A~~~~~~al~~~p~~  112 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIEAEGNG  112 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHSSS
T ss_pred             HHHccCHHHHHHHHHHHHHhCCCc
Confidence            77777777777777766 334433

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.18  E-value=3.7e-05  Score=61.29  Aligned_cols=186  Identities=8%  Similarity=-0.084  Sum_probs=134.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc---------------ccHHHHHHHHHcCCCccchHHHHHHhhhCC-CCCCHHH--
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP---------------HILNTLLKLLTQSSTPQNAIPLYNKMLNCP-SSYNHYT--   68 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~---------------~~~~~li~~~~~~g~~~~a~~l~~~m~~~g-~~p~~~t--   68 (209)
                      +.++.++|.+.+.++.+......+.               .++..+...|.+.|++++|.+.+......- -.++..+  
T Consensus        16 ~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   95 (434)
T 4b4t_Q           16 NEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVK   95 (434)
T ss_dssp             HHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHH
Confidence            6788888888888887765333332               237788999999999999999998886521 1122222  


Q ss_pred             --HHHHHHHHhccccHHHHHHHHHHHHHh----ccCcc-HhHHHHHHHHHHhCCChhhHHHHHHhcC--------CC-cH
Q 045511           69 --FTQALKACSLAHAHQKGLEIHAHVIKY----GHLHD-IFIQNSLLHFYVTVKDIFSAHQIFNSVV--------FP-DV  132 (209)
Q Consensus        69 --~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~--------~~-~~  132 (209)
                        .+.+-..+...|+.+.+.+++....+.    +..+. ..++..|...|...|++++|..++.+..        .+ ..
T Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~  175 (434)
T 4b4t_Q           96 VLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLV  175 (434)
T ss_dssp             HHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHH
Confidence              222333345568899999888776643    22222 4578899999999999999999998761        12 25


Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC-------CCCCC--HHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI-------DVKPN--ANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m-------~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ..|..+...|...|++++|...++..       +..|.  ...+..+...+...|++++|...+....+
T Consensus       176 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          176 DVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            68899999999999999999999876       22222  24567777888899999999888876644

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

Probab=98.14  E-value=7.1e-05  Score=49.60  Aligned_cols=94  Identities=11%  Similarity=0.040  Sum_probs=82.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+...=..+.+.|++++|.+.|++..+.. +.+...|..+-.++.+.|++++|.+.++...+.. +.+...|..+-.+|
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~   91 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHH
Confidence            566777788999999999999999988754 3467889999999999999999999999998875 45678999999999


Q ss_pred             HhCCChhhHHHHHHhc
Q 045511          112 VTVKDIFSAHQIFNSV  127 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~  127 (209)
                      ...|++++|.+.|++.
T Consensus        92 ~~~~~~~~A~~~~~~a  107 (126)
T 4gco_A           92 VAMREWSKAQRAYEDA  107 (126)
T ss_dssp             HHTTCHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHH
Confidence            9999999999999987

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.14  E-value=1.7e-05  Score=52.68  Aligned_cols=58  Identities=14%  Similarity=0.040  Sum_probs=28.1

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +.-+=..+.+.|++++|.+.|+...+.. +.+...|+.+-.+|.+.|++++|.+.++..
T Consensus        11 ~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~a   68 (127)
T 4gcn_A           11 EKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKA   68 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHH
Confidence            3334444455555555555555554432 223444555555555555555555555443

>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=98.13  E-value=9.2e-06  Score=55.58  Aligned_cols=94  Identities=11%  Similarity=-0.064  Sum_probs=80.7

Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHh
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSAC  174 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~  174 (209)
                      +...+..+-..+.+.|++++|...|+...   ..+...|..+-.+|...|++++|...|++. .+.|+ ...+..+-.++
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~   99 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            45577788889999999999999999873   346788888999999999999999999998 66664 46788888899


Q ss_pred             ccccchhHHHHHHHHHHHh
Q 045511          175 SSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       175 ~~~g~~~~a~~~~~~~~~~  193 (209)
                      ...|++++|...|....+.
T Consensus       100 ~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHH
Confidence            9999999999999988765

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

Probab=98.13  E-value=0.00011  Score=49.02  Aligned_cols=93  Identities=10%  Similarity=-0.059  Sum_probs=53.6

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC----HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN----HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSL  107 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  107 (209)
                      ..+..+-..+.+.|++++|...|++..+.  .|+    ...|..+-..+...|++++|.+.++...+.. +.+...+..+
T Consensus        29 ~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~  105 (148)
T 2dba_A           29 EQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRR  105 (148)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHH
Confidence            45555566666666666666666666553  244    4555555555666666666666666555542 2234555555


Q ss_pred             HHHHHhCCChhhHHHHHHhc
Q 045511          108 LHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       108 l~~~~~~g~~~~a~~~~~~~  127 (209)
                      -.+|...|++++|.+.|++.
T Consensus       106 a~~~~~~~~~~~A~~~~~~a  125 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRC  125 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHH
Confidence            55666666666666665554

>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=98.12  E-value=9e-05  Score=47.25  Aligned_cols=96  Identities=10%  Similarity=-0.005  Sum_probs=82.3

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      ...+..+...+.+.|++++|...|++..... +.+...+..+-..+...|++++|...++...+.. +.+...+..+...
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   81 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            4567778888999999999999999998753 2367788888889999999999999999998875 4467889999999


Q ss_pred             HHhCCChhhHHHHHHhcC
Q 045511          111 YVTVKDIFSAHQIFNSVV  128 (209)
Q Consensus       111 ~~~~g~~~~a~~~~~~~~  128 (209)
                      +...|++++|.+.++...
T Consensus        82 ~~~~~~~~~A~~~~~~~~   99 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGL   99 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            999999999999998873

>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=98.11  E-value=7e-06  Score=58.65  Aligned_cols=153  Identities=11%  Similarity=0.023  Sum_probs=86.8

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC-c--------------cHhHH
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL-H--------------DIFIQ  104 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~--------------~~~~~  104 (209)
                      .....|+++.+.+.|+.-... .......+..+-..+.+.|++++|...|+...+.... |              ...+|
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (198)
T 2fbn_A           13 GRENLYFQGAKKSIYDYTDEE-KVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCN   91 (198)
T ss_dssp             ---------CCCSGGGCCHHH-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhccccCchhhCCHHH-HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHH
Confidence            333445555555555322211 1112344555566666777777777777777654211 1              02677


Q ss_pred             HHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccc
Q 045511          105 NSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGS  179 (209)
Q Consensus       105 ~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~  179 (209)
                      ..+-.+|.+.|++++|...++...   ..+...|..+-.+|...|++++|...|++. .+.|+. ..+..+-..+...++
T Consensus        92 ~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~  171 (198)
T 2fbn_A           92 LNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKE  171 (198)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHH
Confidence            788888888888888888888762   345677888888888888888888888887 555644 456666666666666


Q ss_pred             hhHHH-HHHHHHHHh
Q 045511          180 RKLGK-AIHAHSLRN  193 (209)
Q Consensus       180 ~~~a~-~~~~~~~~~  193 (209)
                      .+++. ..+..+...
T Consensus       172 ~~~~~~~~~~~~f~~  186 (198)
T 2fbn_A          172 ARKKDKLTFGGMFDK  186 (198)
T ss_dssp             HHC------------
T ss_pred             HHHHHHHHHHHHhcc
Confidence            66665 444444333

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.10  E-value=2.5e-05  Score=59.37  Aligned_cols=152  Identities=11%  Similarity=0.016  Sum_probs=107.0

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhhCCC---CCC--HHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLNCPS---SYN--HYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~---~p~--~~t~~~ll~~~~   77 (209)
                      ..++.+++.+.+.+..+.....++.    ..+..+...+...|++++|...+++..+...   .+.  ..+|+.+-..|.
T Consensus        87 ~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~  166 (293)
T 2qfc_A           87 KQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYA  166 (293)
T ss_dssp             HTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHH
Confidence            4455555555555544432111111    2234455666788999999999998875321   122  458889999999


Q ss_pred             ccccHHHHHHHHHHHHHhc-cCcc-----HhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-------cHhHHHHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYG-HLHD-----IFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-------DVVTWTTIISGL  142 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g-~~~~-----~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-------~~~~~~~li~~~  142 (209)
                      ..|++++|.+.|+...+.. ..|+     ..+++.+-..|.+.|++++|.+.+++..+  +       -..+|..+-..|
T Consensus       167 ~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y  246 (293)
T 2qfc_A          167 ENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECL  246 (293)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHH
Confidence            9999999999999887331 1122     26899999999999999999999987621  1       156788888999


Q ss_pred             HhCCChHHH-HHHHhhC
Q 045511          143 SKCGFHKEA-IDMFCGI  158 (209)
Q Consensus       143 ~~~g~~~~a-~~~~~~m  158 (209)
                      .+.|++++| ...|++.
T Consensus       247 ~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          247 RKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHTTCCHHHHHHHHHHH
T ss_pred             HHcCCcHHHHHHHHHHH
Confidence            999999999 6667663

>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=98.09  E-value=3.1e-05  Score=50.55  Aligned_cols=107  Identities=13%  Similarity=0.016  Sum_probs=85.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc--Ccc----HhHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH--LHD----IFIQN  105 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~----~~~~~  105 (209)
                      ..|..+-..+.+.|++++|...|++..+.. +.+...+..+-..+...|+++.|...++...+...  .++    ..++.
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            467778888999999999999999988754 34677888889999999999999999999887652  122    67888


Q ss_pred             HHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHH
Q 045511          106 SLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTII  139 (209)
Q Consensus       106 ~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li  139 (209)
                      .+-..|.+.|++++|.+.|+...  .|+...+..+-
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~  119 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQ  119 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            99999999999999999998872  34554444443

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

Probab=98.08  E-value=0.00011  Score=49.10  Aligned_cols=100  Identities=10%  Similarity=0.010  Sum_probs=76.9

Q ss_pred             CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc----HhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHH
Q 045511           64 YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD----IFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWT  136 (209)
Q Consensus        64 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~  136 (209)
                      .+...+..+-..+...|+++.|.+.|+...+..  |+    ...|..+-..|...|++++|.+.++...   ..+...|.
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  103 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALY  103 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHH
Confidence            356777778888888899999999988887653  44    5778888888888888888888887762   23566777


Q ss_pred             HHHHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511          137 TIISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       137 ~li~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      .+-..+...|++++|...|.+. ...|+..
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~~~p~~~  133 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVSLEPKNK  133 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHCSSCH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCCcH
Confidence            7888888888888888888887 5555543

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.07  E-value=1.5e-05  Score=53.90  Aligned_cols=127  Identities=10%  Similarity=0.006  Sum_probs=96.9

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCC-CC----HHHHHHHHHHHhccccHHHHHHHHHHHHHhccC-c----cH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSS-YN----HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL-H----DI  101 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~-p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~----~~  101 (209)
                      .++..+-..+...|++++|...+++..+..-. ++    ..++..+-..+...|++++|.+.++...+.... +    ..
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            56777888888999999999999887653211 11    147788888889999999999999887654311 1    14


Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcCC-----C----cHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVVF-----P----DVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .++..+-..+...|++++|.+.+++..+     .    ....+..+-..+...|++++|.+.+.+.
T Consensus        90 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  155 (164)
T 3ro3_A           90 QSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  155 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            5788888899999999999999877621     1    2456778888999999999999988764

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.07  E-value=0.00012  Score=55.66  Aligned_cols=190  Identities=9%  Similarity=-0.062  Sum_probs=131.0

Q ss_pred             ccCCCcchHhHHHHHHHHhhCCCcccHHHH-------HHHHHcCCCccchHHHHHHhhhCCCCCCH--------------
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIPQPHILNTL-------LKLLTQSSTPQNAIPLYNKMLNCPSSYNH--------------   66 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l-------i~~~~~~g~~~~a~~l~~~m~~~g~~p~~--------------   66 (209)
                      .+.+..|.+.|.++.+..+.  ....|..+       ...+.+.++..++...+++-..  +.|+.              
T Consensus        19 ~~d~~~A~~~F~~a~~~dP~--~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~~   94 (282)
T 4f3v_A           19 PMSEARSLDLFTEITNYDES--ACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGDI   94 (282)
T ss_dssp             TTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCCC
T ss_pred             CCCHHHHHHHHHHHHHhChh--hhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCccccc
Confidence            45555666666666665322  33778877       4666666666777666655544  22211              


Q ss_pred             --------HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-Cc----Hh
Q 045511           67 --------YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-PD----VV  133 (209)
Q Consensus        67 --------~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-~~----~~  133 (209)
                              ...-.....+...|++++|.+.|+.+...+  |+....-.+-..+.+.+++++|+..|+.... ++    ..
T Consensus        95 ~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~  172 (282)
T 4f3v_A           95 TYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGA  172 (282)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHH
T ss_pred             ccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHH
Confidence                    122334566778899999999999888755  4443555556689999999999999987743 22    23


Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC--CCC-CCH--HhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhHhHh
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI--DVK-PNA--NTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILDNAV  205 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m--~~~-p~~--~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  205 (209)
                      .+..+=.++.+.|++++|+..|++.  |-. |..  ......-.++.+.|+.++|..+|+.+....  |+...+.+|
T Consensus       173 a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~--P~~~~~~aL  247 (282)
T 4f3v_A          173 AGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH--PEPKVAAAL  247 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--CCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHH
Confidence            5666778899999999999999998  433 652  244445566778999999999999998874  445555544

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

Probab=98.04  E-value=2.4e-05  Score=50.93  Aligned_cols=83  Identities=8%  Similarity=0.001  Sum_probs=52.2

Q ss_pred             CCCccchHHHHHHhhhCC--CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHH
Q 045511           44 SSTPQNAIPLYNKMLNCP--SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAH  121 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g--~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~  121 (209)
                      .|++++|...|++..+.+  -+-+...+..+-..+.+.|++++|.+.|+...+.. +-+..++..+-.+|.+.|++++|.
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            467777777777777653  12234556666666777777777777777776654 334566666777777777777777


Q ss_pred             HHHHhc
Q 045511          122 QIFNSV  127 (209)
Q Consensus       122 ~~~~~~  127 (209)
                      +.+++.
T Consensus        82 ~~~~~a   87 (117)
T 3k9i_A           82 ELLLKI   87 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777655

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.04  E-value=7.1e-05  Score=49.63  Aligned_cols=90  Identities=12%  Similarity=0.082  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH--------HhHHHH
Q 045511          103 IQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA--------NTLVSV  170 (209)
Q Consensus       103 ~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~--------~t~~~l  170 (209)
                      .+..+-..+.+.|++++|.+.|++..   ..+...|+.+-.+|...|++++|++.|.+. .+.|+.        .+|..+
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~l   89 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRA   89 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHH
Confidence            34444455555555555555555441   123444555555555555555555555544 222211        233344


Q ss_pred             HHHhccccchhHHHHHHHHHHH
Q 045511          171 LSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       171 i~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      -.++...|++++|.+.|....+
T Consensus        90 g~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           90 GNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHh
Confidence            4444455555555555554443

>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=98.03  E-value=6.1e-05  Score=49.42  Aligned_cols=95  Identities=14%  Similarity=0.025  Sum_probs=81.1

Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHh
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSAC  174 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~  174 (209)
                      +...|..+-..+.+.|++++|.+.|++..   ..+...|..+-.+|.+.|++++|+..|.+. .+.|+ ...+..+-.++
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   82 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            34567778888999999999999999873   346788999999999999999999999998 66665 56788888999


Q ss_pred             ccccchhHHHHHHHHHHHhc
Q 045511          175 SSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       175 ~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ...|++++|.+.+....+..
T Consensus        83 ~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhC
Confidence            99999999999999876653

>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=98.02  E-value=0.00011  Score=48.65  Aligned_cols=96  Identities=7%  Similarity=-0.121  Sum_probs=82.7

Q ss_pred             CccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHH
Q 045511           98 LHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLS  172 (209)
Q Consensus        98 ~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~  172 (209)
                      +.+...+..+-..+...|++++|...|....   ..+...|..+-..+...|++++|...|.+. ...|+ ...+..+-.
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   85 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQ   85 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHH
Confidence            3467788999999999999999999999872   345788999999999999999999999998 55554 567888889


Q ss_pred             HhccccchhHHHHHHHHHHHh
Q 045511          173 ACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       173 ~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .+...|++++|...+....+.
T Consensus        86 ~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHH
Confidence            999999999999999987665

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

Probab=98.01  E-value=6e-05  Score=51.99  Aligned_cols=96  Identities=13%  Similarity=0.027  Sum_probs=83.1

Q ss_pred             ccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHH
Q 045511           99 HDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSA  173 (209)
Q Consensus        99 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~  173 (209)
                      .+...+..+-..+.+.|++++|.+.|++..   ..+...|..+-.+|.+.|++++|+..|++. .+.|+ ...+..+-.+
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~   88 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            346678888899999999999999999873   346788999999999999999999999998 66665 5678888999


Q ss_pred             hccccchhHHHHHHHHHHHhc
Q 045511          174 CSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       174 ~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      +...|++++|.+.|....+..
T Consensus        89 ~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHhC
Confidence            999999999999999887763

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.01  E-value=0.00011  Score=52.31  Aligned_cols=126  Identities=10%  Similarity=-0.023  Sum_probs=96.2

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCC-CC---C-----------HHHHHHHHHHHhccccHHHHHHHHHHHHHhc
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPS-SY---N-----------HYTFTQALKACSLAHAHQKGLEIHAHVIKYG   96 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~-~p---~-----------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g   96 (209)
                      ..+..+-..+.+.|++++|...|++..+..- .|   .           ...|..+-.++.+.|++++|...++...+..
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            5677778888899999999999999987431 11   1           2678888889999999999999999998874


Q ss_pred             cCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHH-HHHhhC
Q 045511           97 HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAI-DMFCGI  158 (209)
Q Consensus        97 ~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~-~~~~~m  158 (209)
                       +.+...+..+-.+|...|++++|.+.|++..   ..+...+..+-..+...++.+++. ..|..|
T Consensus       119 -p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  183 (198)
T 2fbn_A          119 -KNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEARKKDKLTFGGM  183 (198)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHC---------
T ss_pred             -cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             4567889999999999999999999998872   335667777878777777777665 555555

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

Probab=97.99  E-value=6.3e-05  Score=61.71  Aligned_cols=118  Identities=6%  Similarity=-0.052  Sum_probs=92.6

Q ss_pred             HhccccHHHHHHHHHHHHHhc---cC---cc-HhHHHHHHHHHHhCCChhhHHHHHHhcC----------CCc-HhHHHH
Q 045511           76 CSLAHAHQKGLEIHAHVIKYG---HL---HD-IFIQNSLLHFYVTVKDIFSAHQIFNSVV----------FPD-VVTWTT  137 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g---~~---~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~----------~~~-~~~~~~  137 (209)
                      +..+|++++|+.+++..++..   +.   |+ ..+++.|...|...|++++|+.++.+..          .|+ ..+++.
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            457899999999998877553   22   22 4589999999999999999999988761          233 568999


Q ss_pred             HHHHHHhCCChHHHHHHHhhC---------CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          138 IISGLSKCGFHKEAIDMFCGI---------DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       138 li~~~~~~g~~~~a~~~~~~m---------~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |-..|...|++++|+.++.+.         .-.|++ .+.+.+-.++...+.+++|+.++..+++.
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999988877         223444 34566666777899999999999988765

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.97  E-value=0.00016  Score=57.47  Aligned_cols=155  Identities=12%  Similarity=0.052  Sum_probs=113.5

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCC----------------HHHHHHHHHHHhccccHHHHHHHHHHHHHhccC-ccH
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYN----------------HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL-HDI  101 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~----------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~~  101 (209)
                      ..+.+.|++++|.+.|....+..-..+                ...+..+...|...|+++++.+.+....+.--. ++.
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            346778999999999999876432211                124778899999999999999999887654211 221


Q ss_pred             ----hHHHHHHHHHHhCCChhhHHHHHHhcC--------CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC-------CCC
Q 045511          102 ----FIQNSLLHFYVTVKDIFSAHQIFNSVV--------FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI-------DVK  161 (209)
Q Consensus       102 ----~~~~~ll~~~~~~g~~~~a~~~~~~~~--------~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-------~~~  161 (209)
                          .+.+.+-..+...|+.+.|.+++....        .+ -..++..+...|...|++++|..++++.       +-+
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                233344444556789999999887652        12 2457888999999999999999999887       222


Q ss_pred             CC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          162 PN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       162 p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      |. ..++....+.|...|++++|..+++.....
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~  204 (434)
T 4b4t_Q          172 PSLVDVHLLESKVYHKLRNLAKSKASLTAARTA  204 (434)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence            22 357888999999999999999999876543

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

Probab=97.97  E-value=1.6e-05  Score=51.85  Aligned_cols=81  Identities=11%  Similarity=0.011  Sum_probs=62.5

Q ss_pred             ccccHHHHHHHHHHHHHhc--cCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYG--HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAI  152 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g--~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~  152 (209)
                      ..|++++|...|+...+.+  -+.+...+..+-..|.+.|++++|.+.|++..   ..+...+..+-.++.+.|++++|.
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            4578888999998888764  23356788888899999999999999998873   235678888889999999999999


Q ss_pred             HHHhhC
Q 045511          153 DMFCGI  158 (209)
Q Consensus       153 ~~~~~m  158 (209)
                      ..|.+.
T Consensus        82 ~~~~~a   87 (117)
T 3k9i_A           82 ELLLKI   87 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999887

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.96  E-value=8e-05  Score=60.89  Aligned_cols=115  Identities=10%  Similarity=-0.090  Sum_probs=60.1

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.++.++|.+.+.++.+..  +.+..+|..+-..+.+.|++++|...+++..+.. +-+...|..+-.++.+.|++++|.
T Consensus        18 ~~g~~~~A~~~~~~Al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~   94 (477)
T 1wao_1           18 KAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAAL   94 (477)
T ss_dssp             TTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHH
Confidence            4555555555555555442  1134566666666666666666666666666542 123455666666666666666666


Q ss_pred             HHHHHHHHhccCccHhHHHHHHHH--HHhCCChhhHHHHHH
Q 045511           87 EIHAHVIKYGHLHDIFIQNSLLHF--YVTVKDIFSAHQIFN  125 (209)
Q Consensus        87 ~~~~~m~~~g~~~~~~~~~~ll~~--~~~~g~~~~a~~~~~  125 (209)
                      +.|+...+.. +.+...+..+-.+  +.+.|++++|.+.++
T Consensus        95 ~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           95 RDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            6666665543 1223334333333  555666666666665

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

Probab=97.96  E-value=8.4e-05  Score=50.06  Aligned_cols=94  Identities=12%  Similarity=-0.008  Sum_probs=81.0

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+..+-..+.+.|++++|...|++....+ +.+...|..+-.++.+.|++++|...|+...+.. +.+...+..+-.+|
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   96 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHH
Confidence            556667778889999999999999998754 2466778888889999999999999999998875 45677888999999


Q ss_pred             HhCCChhhHHHHHHhc
Q 045511          112 VTVKDIFSAHQIFNSV  127 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~  127 (209)
                      ...|++++|.+.|+..
T Consensus        97 ~~~g~~~~A~~~~~~a  112 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSA  112 (142)
T ss_dssp             HHTTCHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHH
Confidence            9999999999999886

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

Probab=97.96  E-value=8.9e-05  Score=48.71  Aligned_cols=83  Identities=10%  Similarity=-0.118  Sum_probs=36.1

Q ss_pred             HHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHH
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEA  151 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a  151 (209)
                      .+.+.|++++|...|+...+.. +.+...|..+-.++...|++++|...|++..  .| +...+..+-..|...|++++|
T Consensus        26 ~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~g~~~~A  104 (121)
T 1hxi_A           26 SMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAA  104 (121)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            3344444444444444444432 2233444444444444444444444444431  11 233444444444444444444


Q ss_pred             HHHHhhC
Q 045511          152 IDMFCGI  158 (209)
Q Consensus       152 ~~~~~~m  158 (209)
                      ...|++.
T Consensus       105 ~~~~~~a  111 (121)
T 1hxi_A          105 LASLRAW  111 (121)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.95  E-value=0.002  Score=52.13  Aligned_cols=159  Identities=8%  Similarity=-0.085  Sum_probs=98.4

Q ss_pred             CCcccHHHHHHHHHcCC---CccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc----ccHHHHHHHHHHHHHhccCccH
Q 045511           29 PQPHILNTLLKLLTQSS---TPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA----HAHQKGLEIHAHVIKYGHLHDI  101 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g---~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~----~~~~~a~~~~~~m~~~g~~~~~  101 (209)
                      .++..+..|-..+.+.|   +.++|...|++..+.|. ++...+..+-..|...    ++.++|.++|+... .|   ++
T Consensus       174 ~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~  248 (452)
T 3e4b_A          174 TTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YP  248 (452)
T ss_dssp             TCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---ST
T ss_pred             CCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CH
Confidence            34457777777777788   88888888888887774 3444434444444443    57778888877766 33   44


Q ss_pred             hHHHHHHHH-H--HhCCChhhHHHHHHhcCC-CcHhHHHHHHHHHHhCC-----ChHHHHHHHhhCCCCCCHHhHHHHHH
Q 045511          102 FIQNSLLHF-Y--VTVKDIFSAHQIFNSVVF-PDVVTWTTIISGLSKCG-----FHKEAIDMFCGIDVKPNANTLVSVLS  172 (209)
Q Consensus       102 ~~~~~ll~~-~--~~~g~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~g-----~~~~a~~~~~~m~~~p~~~t~~~li~  172 (209)
                      ..+..|-.. |  ...++.++|.++|.+..+ .+...+..+-..|. .|     ++++|...|.+.- .-+...+..+-.
T Consensus       249 ~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g~~~A~~~Lg~  326 (452)
T 3e4b_A          249 ASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GREVAADYYLGQ  326 (452)
T ss_dssp             HHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CCCHHHHHHHHH
Confidence            455555544 3  457788888888877632 34555555555555 34     7777887777753 333444444444


Q ss_pred             Hhcc----ccchhHHHHHHHHHHHhc
Q 045511          173 ACSS----LGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       173 ~~~~----~g~~~~a~~~~~~~~~~~  194 (209)
                      .|..    ..+.++|...|....+.|
T Consensus       327 ~y~~G~g~~~d~~~A~~~~~~Aa~~g  352 (452)
T 3e4b_A          327 IYRRGYLGKVYPQKALDHLLTAARNG  352 (452)
T ss_dssp             HHHTTTTSSCCHHHHHHHHHHHHTTT
T ss_pred             HHHCCCCCCcCHHHHHHHHHHHHhhC
Confidence            4443    236777777777666655

>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=97.89  E-value=0.00013  Score=62.25  Aligned_cols=167  Identities=13%  Similarity=0.080  Sum_probs=126.8

Q ss_pred             hccCCCcchHhHHHHHHHHh--------hCCC------------cccHHHHHHHHHcCCCccchHHHHHHhhhC-C-CCC
Q 045511            7 KSLKPTLSFKQLNQIHAQII--------KIPQ------------PHILNTLLKLLTQSSTPQNAIPLYNKMLNC-P-SSY   64 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~--------~~p~------------~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-g-~~p   64 (209)
                      +.++.+.+.+.+..+.....        ..|+            ...|...+....+.|..+.|.++|.+..+. + ..+
T Consensus       390 ~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~  469 (679)
T 4e6h_A          390 LNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTP  469 (679)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCT
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCCh
Confidence            55666777777777766531        1242            247888898888999999999999999876 3 223


Q ss_pred             CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C----cHhHHHHH
Q 045511           65 NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P----DVVTWTTI  138 (209)
Q Consensus        65 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~----~~~~~~~l  138 (209)
                      ......+.+...+ .++.+.|..+|+...+. .+.+...|...++.....|+.+.|+.+|+....  |    ....|...
T Consensus       470 ~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~  547 (679)
T 4e6h_A          470 DIYLENAYIEYHI-SKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKV  547 (679)
T ss_dssp             HHHHHHHHHHHTT-TSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh-CCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            3333333333322 35689999999999887 456777888999999999999999999998743  3    34689999


Q ss_pred             HHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhc
Q 045511          139 ISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACS  175 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~  175 (209)
                      +.--.+.|+.+.+..+.+++ ...|+......+++-|.
T Consensus       548 ~~fE~~~G~~~~~~~v~~R~~~~~P~~~~~~~f~~ry~  585 (679)
T 4e6h_A          548 IFFESKVGSLNSVRTLEKRFFEKFPEVNKLEEFTNKYK  585 (679)
T ss_dssp             HHHHHHTCCSHHHHHHHHHHHHHSTTCCHHHHHHHHTC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHhc
Confidence            99999999999999999999 66777777777777774

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

Probab=97.89  E-value=7.3e-05  Score=58.28  Aligned_cols=143  Identities=12%  Similarity=-0.007  Sum_probs=75.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+..+-..+.+.|++++|...|++....  .|+...       +...++.+++...+          ...+|..+-.+|
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l----------~~~~~~nla~~~  240 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAV----------KNPCHLNIAACL  240 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHH----------HTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHH----------HHHHHHHHHHHH
Confidence            45677778888999999999999987763  344331       22333333332221          123677777888


Q ss_pred             HhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHh--ccccchhHHHH
Q 045511          112 VTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSAC--SSLGSRKLGKA  185 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~--~~~g~~~~a~~  185 (209)
                      .+.|++++|...++...   ..+...|..+-.+|...|++++|...|++. .+.|+.......+..+  ...+..+++..
T Consensus       241 ~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~  320 (338)
T 2if4_A          241 IKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKE  320 (338)
T ss_dssp             HTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC----------------------------
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888887762   235677778888888888888888888887 6666554332223322  23455667777


Q ss_pred             HHHHHHHh
Q 045511          186 IHAHSLRN  193 (209)
Q Consensus       186 ~~~~~~~~  193 (209)
                      ++..+.+.
T Consensus       321 ~~~~~l~~  328 (338)
T 2if4_A          321 MYKGIFKG  328 (338)
T ss_dssp             --------
T ss_pred             HHHHhhCC
Confidence            77766544

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.87  E-value=7.5e-05  Score=61.06  Aligned_cols=119  Identities=14%  Similarity=0.001  Sum_probs=72.1

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~  117 (209)
                      -..+.+.|++++|.+.|++..+.. +-+...|..+-.++.+.|++++|.+.++...+.. +.+..+|..+-..|.+.|++
T Consensus        13 g~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~   90 (477)
T 1wao_1           13 ANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKF   90 (477)
T ss_dssp             SSSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence            334556677777777777776642 1245667777777777777777777777776653 33456777777777777777


Q ss_pred             hhHHHHHHhcC--CC-cHhHHHHHHHH--HHhCCChHHHHHHHhhC
Q 045511          118 FSAHQIFNSVV--FP-DVVTWTTIISG--LSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       118 ~~a~~~~~~~~--~~-~~~~~~~li~~--~~~~g~~~~a~~~~~~m  158 (209)
                      ++|.+.|++..  .| +...+..+-.+  +.+.|++++|.+.+.+-
T Consensus        91 ~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~~  136 (477)
T 1wao_1           91 RAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  136 (477)
T ss_dssp             HHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC------C
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence            77777777652  12 23344444333  66667777777776643

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

Probab=97.86  E-value=0.00043  Score=45.18  Aligned_cols=82  Identities=11%  Similarity=0.058  Sum_probs=39.0

Q ss_pred             HhccccHHHHHHHHHHHHHhccCccH---hHHHHHHHHHHhCCChhhHHHHHHhcC--CCc----HhHHHHHHHHHHhCC
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHLHDI---FIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD----VVTWTTIISGLSKCG  146 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~~~~---~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~----~~~~~~li~~~~~~g  146 (209)
                      +...|++++|...|+...+... .+.   ..+..+-.++.+.|++++|...|+...  .|+    ...+..+-.++...|
T Consensus        12 ~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~~~~g   90 (129)
T 2xev_A           12 ALKNGKYDDASQLFLSFLELYP-NGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQYGEG   90 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCS-SSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHHHCC-CCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHcC
Confidence            3444555555555555544321 111   244444455555555555555555441  121    333444455555555


Q ss_pred             ChHHHHHHHhhC
Q 045511          147 FHKEAIDMFCGI  158 (209)
Q Consensus       147 ~~~~a~~~~~~m  158 (209)
                      ++++|...|++.
T Consensus        91 ~~~~A~~~~~~~  102 (129)
T 2xev_A           91 KNTEAQQTLQQV  102 (129)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            555555555554

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

Probab=97.85  E-value=0.00029  Score=48.33  Aligned_cols=96  Identities=10%  Similarity=0.046  Sum_probs=63.7

Q ss_pred             HHHHHHHhccccHHHHHHHHHHHHHhc-----------------cCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---C
Q 045511           70 TQALKACSLAHAHQKGLEIHAHVIKYG-----------------HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---F  129 (209)
Q Consensus        70 ~~ll~~~~~~~~~~~a~~~~~~m~~~g-----------------~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~  129 (209)
                      ...-..+.+.|+++.|...|....+.-                 -+.+..+|..+-.+|.+.|++++|...++...   .
T Consensus        15 ~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p   94 (162)
T 3rkv_A           15 RQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKREE   94 (162)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCC
Confidence            333344455555555555555544430                 12234577788888888888888888887762   3


Q ss_pred             CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511          130 PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       130 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      .+...|..+-.+|...|++++|...|... .+.|+..
T Consensus        95 ~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~  131 (162)
T 3rkv_A           95 TNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAA  131 (162)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGH
T ss_pred             cchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCH
Confidence            45677788888888888888888888877 6666654

>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=97.85  E-value=0.00033  Score=56.91  Aligned_cols=119  Identities=6%  Similarity=-0.019  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--------------HhHHHHHHHHHHhCCChhhHHHHHHhcC---
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--------------IFIQNSLLHFYVTVKDIFSAHQIFNSVV---  128 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--------------~~~~~~ll~~~~~~g~~~~a~~~~~~~~---  128 (209)
                      ...|...-..+.+.|+++.|...|+...+......              ..+|..+-.+|.+.|++++|...+++..   
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            34566666777778888888888887776542211              5778888888888888888888888762   


Q ss_pred             CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHH
Q 045511          129 FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       129 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~  184 (209)
                      ..+...|..+-.+|...|++++|...|++. .+.|+. ..+..+-..+.+.|+.+++.
T Consensus       348 p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          348 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            345677888888888888888888888887 666654 45666666677777776655

>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=0.00022  Score=57.90  Aligned_cols=125  Identities=13%  Similarity=0.043  Sum_probs=104.0

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC----------------HHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN----------------HYTFTQALKACSLAHAHQKGLEIHAHVIK   94 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~----------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~   94 (209)
                      ...|..+-..+.+.|++++|...|++..+..  |+                ...|..+-.++.+.|++++|...++..++
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  345 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG  345 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            3578888889999999999999999988743  33                57888999999999999999999999998


Q ss_pred             hccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHH-HHHhhC
Q 045511           95 YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAI-DMFCGI  158 (209)
Q Consensus        95 ~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~-~~~~~m  158 (209)
                      .. +.+...|..+-.+|...|++++|...|++..+  | +...+..+-..+.+.++.+++. ..++.|
T Consensus       346 ~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          346 LD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERDRRIYANM  412 (457)
T ss_dssp             HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            75 45688999999999999999999999998732  3 5668888888898889888765 566666

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.80  E-value=0.0014  Score=52.99  Aligned_cols=159  Identities=8%  Similarity=0.046  Sum_probs=95.8

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc---cHHHHHHHHHHHHHhccCccHhHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH---AHQKGLEIHAHVIKYGHLHDIFIQNS  106 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~g~~~~~~~~~~  106 (209)
                      +...+..+-..+...+.++.+........+.-...+...+..+-..+.+.|   +.++|.++|+...+.| .++...+..
T Consensus       140 ~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~  218 (452)
T 3e4b_A          140 YPEAGLAQVLLYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDS  218 (452)
T ss_dssp             CTTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHH
Confidence            344555555555555555554444333322212223336666666777777   8888888888888877 445555556


Q ss_pred             HHHHHHhC----CChhhHHHHHHhcCCCcHhHHHHHHHH-H--HhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhcccc
Q 045511          107 LLHFYVTV----KDIFSAHQIFNSVVFPDVVTWTTIISG-L--SKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLG  178 (209)
Q Consensus       107 ll~~~~~~----g~~~~a~~~~~~~~~~~~~~~~~li~~-~--~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g  178 (209)
                      |-..|...    +++++|.++|+....-+...+..+-.. |  ...+++++|+..|.+. ... +...+..+-..|. .|
T Consensus       219 Lg~~y~~g~~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g-~~~A~~~Lg~~y~-~G  296 (452)
T 3e4b_A          219 VARVLGDATLGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD-QPRAELLLGKLYY-EG  296 (452)
T ss_dssp             HHHHHTCGGGSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHH-HC
T ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHH-cC
Confidence            66666544    688888888888762244555555554 3  4578888888888876 111 4444554544554 34


Q ss_pred             -----chhHHHHHHHHHH
Q 045511          179 -----SRKLGKAIHAHSL  191 (209)
Q Consensus       179 -----~~~~a~~~~~~~~  191 (209)
                           ++++|...|....
T Consensus       297 ~g~~~d~~~A~~~~~~Aa  314 (452)
T 3e4b_A          297 KWVPADAKAAEAHFEKAV  314 (452)
T ss_dssp             SSSCCCHHHHHHHHHTTT
T ss_pred             CCCCCCHHHHHHHHHHHh
Confidence                 7778877776554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.79  E-value=0.00023  Score=54.01  Aligned_cols=125  Identities=6%  Similarity=-0.113  Sum_probs=95.9

Q ss_pred             HHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc--HhHHHHHHHHHHh
Q 045511           36 TLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD--IFIQNSLLHFYVT  113 (209)
Q Consensus        36 ~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~  113 (209)
                      .+...+...|++++|.++|+.+...+  |+....-.+-..+.+.++++.|+..|+...+.. .|.  ...+..+=.++..
T Consensus       107 ayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~  183 (282)
T 4f3v_A          107 GFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAAN  183 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHH
Confidence            46677888999999999999998755  554444444557889999999999997443321 111  2367778889999


Q ss_pred             CCChhhHHHHHHhcC-C---C--cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC
Q 045511          114 VKDIFSAHQIFNSVV-F---P--DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN  163 (209)
Q Consensus       114 ~g~~~~a~~~~~~~~-~---~--~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~  163 (209)
                      .|++++|++.|++.. .   |  ........-.++.+.|+.++|...|+++ ...|+
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            999999999999883 2   3  2335666778888999999999999999 77787

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

Probab=97.76  E-value=0.00033  Score=45.70  Aligned_cols=91  Identities=10%  Similarity=-0.126  Sum_probs=72.8

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH----HHHHHHHHHHhccccHHHHHHHHHHHHHhccCcc---HhHHHH
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH----YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHD---IFIQNS  106 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~  106 (209)
                      +-.+-..+.+.|++++|...|++..+..  |+.    ..+..+-..+.+.|++++|...|+...+... .+   ...+..
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~~~~   81 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYP-THDKAAGGLLK   81 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TSTTHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCC-CCcccHHHHHH
Confidence            3345566778999999999999988753  332    4677778888999999999999999987652 22   567888


Q ss_pred             HHHHHHhCCChhhHHHHHHhc
Q 045511          107 LLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       107 ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +-.+|.+.|++++|.+.|+..
T Consensus        82 la~~~~~~g~~~~A~~~~~~~  102 (129)
T 2xev_A           82 LGLSQYGEGKNTEAQQTLQQV  102 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHH
Confidence            888999999999999999887

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.76  E-value=0.0035  Score=48.19  Aligned_cols=179  Identities=11%  Similarity=0.065  Sum_probs=118.5

Q ss_pred             CCCcchHhHHHHHHHHhhCCCcccHHHHHHHH----HcC---CCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511           10 KPTLSFKQLNQIHAQIIKIPQPHILNTLLKLL----TQS---STPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus        10 ~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~----~~~---g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      ..+++++.+..+....+  .+..+|+.--..+    .+.   +++++++.+++++.+.. +-|...|+.---.+.+.|.+
T Consensus        84 ~~~eeL~~~~~~L~~nP--k~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~  160 (306)
T 3dra_A           84 NLYDELDWCEEIALDNE--KNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLH  160 (306)
T ss_dssp             CHHHHHHHHHHHHHHCT--TCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCT
T ss_pred             cHHHHHHHHHHHHHHCc--ccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccc
Confidence            34444555555544321  2345555544444    344   67777777777777654 23556666665666666666


Q ss_pred             H--HHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC------hhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHH-
Q 045511           83 Q--KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD------IFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKE-  150 (209)
Q Consensus        83 ~--~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~------~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~-  150 (209)
                      +  ++.+.++.+.+.. +-|-..|+.--..+.+.|.      ++++.+.+++..   ..|...|+-.-..+.+.|+... 
T Consensus       161 ~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~  239 (306)
T 3dra_A          161 NDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQ  239 (306)
T ss_dssp             TCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGG
T ss_pred             ChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHH
Confidence            6  7778888887765 4566677766666666665      777777777662   3467788877777777777444 


Q ss_pred             HHHHHhhC-CC----CCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          151 AIDMFCGI-DV----KPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       151 a~~~~~~m-~~----~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      +.++..+. ..    ..+...+..+...+.+.|+.++|.++++.+.+
T Consensus       240 ~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          240 LEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             GHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            55677766 32    34667888889999999999999999999865

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.76  E-value=0.00034  Score=55.23  Aligned_cols=117  Identities=8%  Similarity=0.017  Sum_probs=87.5

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHh---------------ccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC---
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKY---------------GHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF---  129 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~---------------g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~---  129 (209)
                      .+..+-..+.+.|++++|.+.|+..++.               --+.+..+|..+-.+|.+.|++++|.+.+++..+   
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p  304 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDP  304 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCc
Confidence            4666667777888888888888877651               1123457888999999999999999999988732   


Q ss_pred             CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHH
Q 045511          130 PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGK  184 (209)
Q Consensus       130 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~  184 (209)
                      .+...|..+-.+|...|++++|...|++. .+.|+. ..+..+-..+...++.+++.
T Consensus       305 ~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~~~~a~  361 (370)
T 1ihg_A          305 SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKE  361 (370)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            35778888889999999999999999988 666654 45555555556666665554

>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=97.75  E-value=0.00072  Score=51.11  Aligned_cols=96  Identities=8%  Similarity=-0.013  Sum_probs=76.9

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +...+..+-..+.+.|++++|...|++..+.. +-+...|..+-..+.+.|++++|.+.++...+.. +.+...+..+-.
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            34567777788888999999999998887753 2266778888888888999999999988887654 345678888888


Q ss_pred             HHHhCCChhhHHHHHHhc
Q 045511          110 FYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~  127 (209)
                      +|...|++++|.+.|...
T Consensus        81 ~~~~~g~~~~A~~~~~~a   98 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRA   98 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHH
Confidence            899999999999988876

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

Probab=97.69  E-value=0.00032  Score=45.96  Aligned_cols=95  Identities=6%  Similarity=-0.086  Sum_probs=80.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+-.+-..+.+.|++++|...|++..+.. +-+...|..+-.++...|++++|...|+...+.. +.+...+..+-..|
T Consensus        18 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~   95 (121)
T 1hxi_A           18 ENPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSH   95 (121)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            345556677889999999999999998854 2367788888889999999999999999998875 34677889999999


Q ss_pred             HhCCChhhHHHHHHhcC
Q 045511          112 VTVKDIFSAHQIFNSVV  128 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~~  128 (209)
                      ...|++++|...+++..
T Consensus        96 ~~~g~~~~A~~~~~~al  112 (121)
T 1hxi_A           96 TNEHNANAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            99999999999998864

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

Probab=97.64  E-value=0.00055  Score=53.27  Aligned_cols=60  Identities=18%  Similarity=0.075  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .|+.+-.+|.+.|++++|+..|.+. .+.| +...+..+-.++...|++++|...|....+.
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l  293 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKY  293 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7888999999999999999999998 5566 5578888999999999999999999876543

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

Probab=97.60  E-value=0.00015  Score=45.95  Aligned_cols=60  Identities=5%  Similarity=-0.099  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ..+..+-..+.+.|++++|.+.|+...+.. +.+...+..+-.+|.+.|++++|.+.+++.
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a   64 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQG   64 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            344444445555555555555555554442 223445555555555555555555555544

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

Probab=97.55  E-value=0.00024  Score=58.33  Aligned_cols=119  Identities=8%  Similarity=-0.085  Sum_probs=92.5

Q ss_pred             HHHcCCCccchHHHHHHhhhC---CCCCC----HHHHHHHHHHHhccccHHHHHHHHHHHHHhc---cC---cc-HhHHH
Q 045511           40 LLTQSSTPQNAIPLYNKMLNC---PSSYN----HYTFTQALKACSLAHAHQKGLEIHAHVIKYG---HL---HD-IFIQN  105 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~---g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g---~~---~~-~~~~~  105 (209)
                      .+-..|++++|..++++..+.   -+.|+    ..+++.+...|...|++++|+.+++..++.-   +.   |+ ..+++
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            355789999999999887642   13332    3679999999999999999999998776441   22   33 45899


Q ss_pred             HHHHHHHhCCChhhHHHHHHhcC----------CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          106 SLLHFYVTVKDIFSAHQIFNSVV----------FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       106 ~ll~~~~~~g~~~~a~~~~~~~~----------~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .|-..|...|++++|+.++.+..          .|+ ..+.+.+-.++...+.+++|+.+|.++
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~  461 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKM  461 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998761          133 345667778888889999999999887

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

Probab=97.52  E-value=0.00046  Score=43.65  Aligned_cols=86  Identities=15%  Similarity=0.046  Sum_probs=65.2

Q ss_pred             ccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-------HhH
Q 045511           99 HDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-------NTL  167 (209)
Q Consensus        99 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-------~t~  167 (209)
                      ++...+..+-..+.+.|++++|.+.|++..   ..+...|..+-.++.+.|++++|...|.+. ...|+.       ..+
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~   81 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSKLQ   81 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHHHH
Confidence            356678888899999999999999998872   346788889999999999999999999998 777774       334


Q ss_pred             HHHHHHhccccchhHHH
Q 045511          168 VSVLSACSSLGSRKLGK  184 (209)
Q Consensus       168 ~~li~~~~~~g~~~~a~  184 (209)
                      ..+-.++...|+.+.+.
T Consensus        82 ~~~~~~~~~~~~~~~a~   98 (111)
T 2l6j_A           82 YRLELAQGAVGSVQIPV   98 (111)
T ss_dssp             HHHHHHHHHHHCCCCCS
T ss_pred             HHHHHHHHHHHhHhhhH
Confidence            44444444445444443

>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=97.47  E-value=0.00068  Score=53.54  Aligned_cols=121  Identities=12%  Similarity=0.000  Sum_probs=96.8

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhC---------------CCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhc
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNC---------------PSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYG   96 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~---------------g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g   96 (209)
                      ..|..+-..+.+.|++++|...|++..+.               --+-+...|..+-.++.+.|++++|.+.++..++..
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            45777888899999999999999988761               112245778888889999999999999999998864


Q ss_pred             cCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHH
Q 045511           97 HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        97 ~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~  153 (209)
                       +.+...|..+-.+|...|++++|.+.|++..  .| +...+..+-..+...++.+++.+
T Consensus       304 -p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 -PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence             3467889999999999999999999999873  23 56677777777777777776643

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

Probab=97.32  E-value=0.0024  Score=43.64  Aligned_cols=95  Identities=12%  Similarity=-0.016  Sum_probs=77.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhC--------C---------CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNC--------P---------SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIK   94 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~--------g---------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~   94 (209)
                      ..+...-..+.+.|++++|...|++....        .         -+-+...|..+-.++.+.|+++.|...++..++
T Consensus        12 ~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~   91 (162)
T 3rkv_A           12 EALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLK   91 (162)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHh
Confidence            45666677788899999999999887764        1         012336788888889999999999999999988


Q ss_pred             hccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           95 YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        95 ~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .. +.+...|..+-.+|...|++++|...|...
T Consensus        92 ~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~a  123 (162)
T 3rkv_A           92 RE-ETNEKALFRRAKARIAAWKLDEAEEDLKLL  123 (162)
T ss_dssp             HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHH
Confidence            75 456788999999999999999999999887

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

Probab=97.29  E-value=0.002  Score=41.20  Aligned_cols=76  Identities=13%  Similarity=-0.045  Sum_probs=35.9

Q ss_pred             chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           49 NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        49 ~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      .+...|++..+.. +.+...+..+-..+...|++++|...|+...+.. +.+...|..+-..|...|++++|...|++
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~   78 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWES   78 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            3444555444432 1233444455555555555555555555554433 22334444444455555555555554444

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

Probab=97.23  E-value=0.0053  Score=39.18  Aligned_cols=73  Identities=14%  Similarity=0.096  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           85 GLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        85 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      +.+.|+...+.. +.+...+..+-..|...|++++|.+.|++..   ..+...|..+-..|...|++++|...|.+.
T Consensus         4 a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            4 ITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             HHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            334444444432 2345566666666666666666666666552   223455566666666666666666666655

>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=97.20  E-value=0.0035  Score=43.30  Aligned_cols=26  Identities=4%  Similarity=-0.106  Sum_probs=16.3

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhh
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLN   59 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~   59 (209)
                      +...-..+.+.|++++|...|++..+
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~   39 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAME   39 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            33444555666777777777776665

>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=97.19  E-value=0.023  Score=39.18  Aligned_cols=90  Identities=14%  Similarity=0.115  Sum_probs=62.7

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCc------c-----HhHHHHHHHHHHhCCChhhHHHHHHhcC---------
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLH------D-----IFIQNSLLHFYVTVKDIFSAHQIFNSVV---------  128 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~------~-----~~~~~~ll~~~~~~g~~~~a~~~~~~~~---------  128 (209)
                      +...-..+.+.|++++|.+.|+..++.....      +     ...|+.+-.++.+.|++++|...+++..         
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~   93 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL   93 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccC
Confidence            3444455677899999999999888765321      2     2378888888888888888888777652         


Q ss_pred             CCc-HhHH----HHHHHHHHhCCChHHHHHHHhhC
Q 045511          129 FPD-VVTW----TTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       129 ~~~-~~~~----~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .|+ ...|    ...-.++...|++++|+..|++.
T Consensus        94 ~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kA  128 (159)
T 2hr2_A           94 NQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKV  128 (159)
T ss_dssp             TSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHH
Confidence            343 4456    66667777777777777777766

>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=97.19  E-value=0.038  Score=43.17  Aligned_cols=178  Identities=10%  Similarity=0.011  Sum_probs=112.2

Q ss_pred             CcchHhHHHHHHHHhhCCCcccHHHHHHHHHcC-C-CccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHH------
Q 045511           12 TLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQS-S-TPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQ------   83 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~-g-~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~------   83 (209)
                      +++++.+..+....  +.+..+|+.--..+.+. + ++++++++++++.+... -|...|+----...+.+..+      
T Consensus       106 ~eEL~~~~~~L~~n--PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~dp-kNy~AW~~R~wvl~~l~~~~~~~~~~  182 (349)
T 3q7a_A          106 EDELRLMNEFAVQN--LKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPDP-KNYHTWAYLHWLYSHFSTLGRISEAQ  182 (349)
T ss_dssp             HHHHHHHHHHHHTT--CCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSCT-TCHHHHHHHHHHHHHHHHTTCCCHHH
T ss_pred             HHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhccccccchhh
Confidence            34444444444322  22446666666666555 5 67777788877776542 35566665555555555555      


Q ss_pred             --HHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC-------hhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCCh---
Q 045511           84 --KGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD-------IFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFH---  148 (209)
Q Consensus        84 --~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~-------~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~---  148 (209)
                        ++.+.++.+.+.. +-|-..|+..-..+.+.++       ++++.+.+++..   ..|...|+-+-..+.+.|+.   
T Consensus       183 ~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~  261 (349)
T 3q7a_A          183 WGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVP  261 (349)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGG
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCccc
Confidence              7777888887765 4577788888777777776       577777776652   34667777666666665543   


Q ss_pred             -----------------HHHHHHHhhC-CC-------CCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          149 -----------------KEAIDMFCGI-DV-------KPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       149 -----------------~~a~~~~~~m-~~-------~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                                       ....++..++ +.       .++.....-+...|...|+.++|.++++.+.+.
T Consensus       262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          262 ILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             GHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             ccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence                             3444555555 22       367778888899999999999999999988544

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.17  E-value=0.007  Score=40.45  Aligned_cols=73  Identities=18%  Similarity=0.072  Sum_probs=31.4

Q ss_pred             ccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh----CCChhhHHH
Q 045511           47 PQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT----VKDIFSAHQ  122 (209)
Q Consensus        47 ~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~  122 (209)
                      .++|..+|++..+.|. |+..    +=..|...+.++.|.++|+...+.|   ++..+..|-..|..    .+++++|.+
T Consensus        11 ~~~A~~~~~~aa~~g~-~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A           11 LKKAIQYYVKACELNE-MFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHTTC-TTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCC-Hhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            3444555555544441 2222    2233333334444555554444443   33444444444444    444555555


Q ss_pred             HHHhc
Q 045511          123 IFNSV  127 (209)
Q Consensus       123 ~~~~~  127 (209)
                      +|++.
T Consensus        83 ~~~~A   87 (138)
T 1klx_A           83 YYSKA   87 (138)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

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

Probab=97.15  E-value=0.0072  Score=36.36  Aligned_cols=57  Identities=11%  Similarity=0.026  Sum_probs=24.5

Q ss_pred             HHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           69 FTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        69 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      +..+-..+...|++++|...++...+.. +.+..++..+-..|.+.|++++|.+.|++
T Consensus        12 ~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~   68 (91)
T 1na3_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQK   68 (91)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            3333344444444444444444444332 22333444444444444444444444444

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.13  E-value=0.047  Score=41.85  Aligned_cols=154  Identities=10%  Similarity=0.055  Sum_probs=118.5

Q ss_pred             cCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCcc--chHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc-----
Q 045511            9 LKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQ--NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA-----   81 (209)
Q Consensus         9 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~--~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~-----   81 (209)
                      +..+++++.+..+.+..  +.|..+|+.---.+.+.|.++  ++++.++++.+.+. -|...|+---....+.++     
T Consensus       124 ~~~~~EL~~~~~~l~~~--pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~  200 (306)
T 3dra_A          124 FDPYREFDILEAMLSSD--PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDN  200 (306)
T ss_dssp             CCTHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHH
T ss_pred             CCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhh
Confidence            45566676666666543  346689988888888889888  99999999998764 466777766666666666     


Q ss_pred             -HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhh-HHHHHHhcC------CCcHhHHHHHHHHHHhCCChHHHHH
Q 045511           82 -HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFS-AHQIFNSVV------FPDVVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        82 -~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~-a~~~~~~~~------~~~~~~~~~li~~~~~~g~~~~a~~  153 (209)
                       ++++.+.++...+.. +-|...|+-+-..+.+.|+..+ +..+..++.      ..+...+..+...|.+.|+.++|.+
T Consensus       201 ~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~  279 (306)
T 3dra_A          201 TIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRT  279 (306)
T ss_dssp             HHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHH
Confidence             888888888888775 5678899999888988888544 556666653      2467889999999999999999999


Q ss_pred             HHhhC--CCCCCHHh
Q 045511          154 MFCGI--DVKPNANT  166 (209)
Q Consensus       154 ~~~~m--~~~p~~~t  166 (209)
                      +++.+  ...|--.-
T Consensus       280 ~~~~l~~~~Dpir~~  294 (306)
T 3dra_A          280 VYDLLKSKYNPIRSN  294 (306)
T ss_dssp             HHHHHHHTTCGGGHH
T ss_pred             HHHHHHhccChHHHH
Confidence            99998  36665543

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

Probab=97.10  E-value=0.0024  Score=40.04  Aligned_cols=57  Identities=18%  Similarity=0.152  Sum_probs=29.4

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhh
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCG  157 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~  157 (209)
                      ...+..+-..|.+.|++++|.+.|++..   ..+...|..+-.+|...|++++|.+.|++
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~   66 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQ   66 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            3445555555555555555555555541   12334455555555555555555555554

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.01  E-value=0.0015  Score=52.68  Aligned_cols=88  Identities=8%  Similarity=-0.095  Sum_probs=67.5

Q ss_pred             hCCChhhHHHHHHhcC----------CCc-HhHHHHHHHHHHhCCChHHHHHHHhhC---------CCCCCH-HhHHHHH
Q 045511          113 TVKDIFSAHQIFNSVV----------FPD-VVTWTTIISGLSKCGFHKEAIDMFCGI---------DVKPNA-NTLVSVL  171 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~----------~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m---------~~~p~~-~t~~~li  171 (209)
                      ..|++++|+.++++.-          .|+ ..+++.+...|...|++++|+.++.+.         .-.|+. .+++.+-
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            3578899998887651          132 468999999999999999999998887         344665 5799999


Q ss_pred             HHhccccchhHHHHHHHHHH---HhccCCCch
Q 045511          172 SACSSLGSRKLGKAIHAHSL---RNLNENNII  200 (209)
Q Consensus       172 ~~~~~~g~~~~a~~~~~~~~---~~~~~p~~~  200 (209)
                      ..|...|++++|+.++.+..   +.-+.|+-.
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~Hp  421 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAIMEVAHGKDHP  421 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCH
T ss_pred             HHHHhccCHHHHHHHHHHHHHHHHHHcCCCCh
Confidence            99999999999999998653   334455443

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

Probab=96.97  E-value=0.0064  Score=38.02  Aligned_cols=61  Identities=8%  Similarity=0.029  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           66 HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        66 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      ...+..+-..+.+.|++++|...|+...+.. +.+...|..+-.+|...|++++|.+.|++.
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~a   67 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQG   67 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3445555555555566666666665555543 223445555556666666666666655543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.95  E-value=0.072  Score=43.60  Aligned_cols=155  Identities=11%  Similarity=0.084  Sum_probs=90.5

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHH----------------------------------------HHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHY----------------------------------------TFT   70 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~----------------------------------------t~~   70 (209)
                      ...|-..+..+.+.|+++.|..+|++....  +.+..                                        .|.
T Consensus       213 ~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~  290 (493)
T 2uy1_A          213 EEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRI  290 (493)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHH
Confidence            467777777777888888888888877765  22221                                        122


Q ss_pred             HHHHHHhccccHHHHHHHHHHHHHhccCccHhHHH--HHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhC
Q 045511           71 QALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQN--SLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKC  145 (209)
Q Consensus        71 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~--~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~  145 (209)
                      ..+....+.+.++.|..+|+.. +.. ..+..+|-  +.+.... .++++.|.++|+...+  | +...|...+.-....
T Consensus       291 ~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~  367 (493)
T 2uy1_A          291 NHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRI  367 (493)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHc
Confidence            2222223345566677777666 221 12233332  2222222 2257777777766521  2 233455566666677


Q ss_pred             CChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          146 GFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       146 g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      |+.+.|..+|.+.  ..+...|...+.--...|+.+.+..+++...+
T Consensus       368 ~~~~~aR~l~er~--~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          368 GDEENARALFKRL--EKTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             TCHHHHHHHHHHS--CCBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7777777777775  22455666666666677888888887776654

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

Probab=96.91  E-value=0.011  Score=35.54  Aligned_cols=82  Identities=12%  Similarity=0.044  Sum_probs=64.9

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHH
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHF  110 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  110 (209)
                      ...|..+-..+.+.|++++|...|++..+.. +.+...+..+-..+.+.|++++|.+.++...+.. +.+...+..+-..
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~   86 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNA   86 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            3677778888999999999999999988754 2356788888899999999999999999998764 3455666666665


Q ss_pred             HHhC
Q 045511          111 YVTV  114 (209)
Q Consensus       111 ~~~~  114 (209)
                      +.+.
T Consensus        87 ~~~~   90 (91)
T 1na3_A           87 KQKQ   90 (91)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            5543

>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=96.90  E-value=0.0031  Score=50.86  Aligned_cols=94  Identities=7%  Similarity=-0.049  Sum_probs=72.5

Q ss_pred             HHHHHHHhCCChhhHHHHHHhcC-------CC----cHhHHHHHHHHHHhCCChHHHHHHHhhC---------CCCCCH-
Q 045511          106 SLLHFYVTVKDIFSAHQIFNSVV-------FP----DVVTWTTIISGLSKCGFHKEAIDMFCGI---------DVKPNA-  164 (209)
Q Consensus       106 ~ll~~~~~~g~~~~a~~~~~~~~-------~~----~~~~~~~li~~~~~~g~~~~a~~~~~~m---------~~~p~~-  164 (209)
                      ..+.-+.+.|++++|+.++++..       .+    ...+++.+...|...|++++|+.++.+.         .-.|+. 
T Consensus       292 ~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a  371 (429)
T 3qwp_A          292 KKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRG  371 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHH
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHH
Confidence            34556778899999999987661       12    2568999999999999999999998877         444555 


Q ss_pred             HhHHHHHHHhccccchhHHHHHHHHH---HHhccCCCc
Q 045511          165 NTLVSVLSACSSLGSRKLGKAIHAHS---LRNLNENNI  199 (209)
Q Consensus       165 ~t~~~li~~~~~~g~~~~a~~~~~~~---~~~~~~p~~  199 (209)
                      .+++.+-..|...|++++|+.++.+.   .+.-+.|+-
T Consensus       372 ~~l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~H  409 (429)
T 3qwp_A          372 VQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREH  409 (429)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTS
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence            57899999999999999999999864   333445543

>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=96.89  E-value=0.0065  Score=49.00  Aligned_cols=81  Identities=7%  Similarity=-0.050  Sum_probs=64.9

Q ss_pred             ccccHHHHHHHHHHHHHhc---cCc---c-HhHHHHHHHHHHhCCChhhHHHHHHhcC----------CCc-HhHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYG---HLH---D-IFIQNSLLHFYVTVKDIFSAHQIFNSVV----------FPD-VVTWTTII  139 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g---~~~---~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~----------~~~-~~~~~~li  139 (209)
                      ..|++++|+.+++..++..   +.|   + ..+++.|...|...|++++|+.++.+..          .|+ ..+++.|-
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            4578899999988776542   223   2 3689999999999999999999998761          243 46799999


Q ss_pred             HHHHhCCChHHHHHHHhhC
Q 045511          140 SGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       140 ~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..|...|++++|+.+|.+.
T Consensus       390 ~~~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHH
Confidence            9999999999999999875

>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=96.79  E-value=0.023  Score=37.89  Aligned_cols=111  Identities=5%  Similarity=-0.096  Sum_probs=86.9

Q ss_pred             cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC-CCcHhHHHHHHHHHHh----CCChHHHHH
Q 045511           79 AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV-FPDVVTWTTIISGLSK----CGFHKEAID  153 (209)
Q Consensus        79 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~g~~~~a~~  153 (209)
                      .+++++|.++|+...+.| .|+..    |-..|...+.+++|.++|.+.. .-+...+..+-..|..    .+++++|++
T Consensus         8 ~~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             ccCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            467889999999999888 33333    6666777788899999998873 4567778888888887    899999999


Q ss_pred             HHhhC-CCCCCHHhHHHHHHHhcc----ccchhHHHHHHHHHHHhcc
Q 045511          154 MFCGI-DVKPNANTLVSVLSACSS----LGSRKLGKAIHAHSLRNLN  195 (209)
Q Consensus       154 ~~~~m-~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~~~~~~~  195 (209)
                      .|.+- .. -+...+..+-..|..    .++.++|.+.+....+.|.
T Consensus        83 ~~~~Aa~~-g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           83 YYSKACGL-NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHT-TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcC-CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            99998 21 345666666666766    7899999999999888874

>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=96.77  E-value=0.083  Score=40.94  Aligned_cols=176  Identities=10%  Similarity=0.043  Sum_probs=117.6

Q ss_pred             chHhHHHHHHHHhhCCCcccHHHHHHHHHcCCC--ccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcccc-HHHHHHHHH
Q 045511           14 SFKQLNQIHAQIIKIPQPHILNTLLKLLTQSST--PQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHA-HQKGLEIHA   90 (209)
Q Consensus        14 a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~--~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~-~~~a~~~~~   90 (209)
                      ++..+..+...  .+.+..+|+.--..+.+.++  +++++.+++++.+... -|...|+----.+...|. .+++.+.++
T Consensus        93 EL~~~~~~L~~--~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dp-rNy~AW~~R~~vl~~l~~~~~eel~~~~  169 (331)
T 3dss_A           93 ELGFLESCLRV--NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTD  169 (331)
T ss_dssp             HHHHHHHHHHH--CTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCcCHHHHHHHHH
Confidence            34444444433  22366888888777777774  7899999999998653 466777776666777777 588999999


Q ss_pred             HHHHhccCccHhHHHHHHHHHHhC--------------CChhhHHHHHHhcC---CCcHhHHHHHHHHHHhC--------
Q 045511           91 HVIKYGHLHDIFIQNSLLHFYVTV--------------KDIFSAHQIFNSVV---FPDVVTWTTIISGLSKC--------  145 (209)
Q Consensus        91 ~m~~~g~~~~~~~~~~ll~~~~~~--------------g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~--------  145 (209)
                      .+.+.. +-|...|+..-..+.+.              +.++++.+.++...   .-|..+|+-+--.+.+.        
T Consensus       170 ~~I~~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~  248 (331)
T 3dss_A          170 SLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSV  248 (331)
T ss_dssp             HHHHHC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCH
T ss_pred             HHHHHC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccch
Confidence            998876 56777787766665554              44677888887762   33566676444344343        


Q ss_pred             ---CChHHHHHHHhhC-CCCCCHH----hHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          146 ---GFHKEAIDMFCGI-DVKPNAN----TLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       146 ---g~~~~a~~~~~~m-~~~p~~~----t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                         +.++++++.++++ ...||..    +...+..+....|..+++...+..+.+-
T Consensus       249 ~~~~~l~~el~~~~elle~~pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          249 EKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhCcccchHHHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence               3577889999998 7778762    2222233333456777778888777654

>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=96.72  E-value=0.0029  Score=43.64  Aligned_cols=111  Identities=12%  Similarity=0.025  Sum_probs=74.2

Q ss_pred             hccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh----------hhHHHHHHhcC--CC-cHhHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI----------FSAHQIFNSVV--FP-DVVTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~----------~~a~~~~~~~~--~~-~~~~~~~li~~~~  143 (209)
                      .+.+.+++|.+.++...+.. +.+...|+.+-.++...+++          ++|...|++..  .| +..+|..+=.+|.
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~   91 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYT   91 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHH
Confidence            45566777777777777665 44566666666666666554          47777777762  23 4667777777777


Q ss_pred             hC-----------CChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          144 KC-----------GFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       144 ~~-----------g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      ..           |++++|.+.|++. .+.|+...|...++.+      +++-+++-.+...+
T Consensus        92 ~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~al~~~------~ka~el~~~~~~~~  148 (158)
T 1zu2_A           92 SFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT------AKAPQLHAEAYKQG  148 (158)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH------HTHHHHHHHHHHSS
T ss_pred             HhcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHHHHHH------HhCHhccCcccccc
Confidence            66           4899999999988 8889887776555543      34445554444443

>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=96.65  E-value=0.014  Score=47.05  Aligned_cols=86  Identities=8%  Similarity=-0.021  Sum_probs=67.1

Q ss_pred             HHHHhccccHHHHHHHHHHHHHhc---cCcc----HhHHHHHHHHHHhCCChhhHHHHHHhcC----------CCc-HhH
Q 045511           73 LKACSLAHAHQKGLEIHAHVIKYG---HLHD----IFIQNSLLHFYVTVKDIFSAHQIFNSVV----------FPD-VVT  134 (209)
Q Consensus        73 l~~~~~~~~~~~a~~~~~~m~~~g---~~~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~----------~~~-~~~  134 (209)
                      +..+.+.|++++|++.++..++..   +.|+    ..+++.|...|...|++++|+.++.+..          .|+ ..+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            455667789999999988887542   2222    4588999999999999999999988761          233 457


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhhC
Q 045511          135 WTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       135 ~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ++.|-..|...|++++|+.++.+.
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~A  397 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLA  397 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH
Confidence            899999999999999999988876

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.58  E-value=0.042  Score=45.01  Aligned_cols=122  Identities=9%  Similarity=0.091  Sum_probs=91.1

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHH--HHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQ--ALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~--ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..|-..+....+.+..+.|..+|++. +.. ..+...|..  .+.... .++.+.|..+|+...+.. +-++..+...++
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~-~~~~~~~~~yid  362 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH-PDSTLLKEEFFL  362 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC-CCCHHHHHHHHH
Confidence            56777777777788899999999999 321 123334432  222222 236999999999988764 334556777888


Q ss_pred             HHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          110 FYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ...+.|+.+.|..+|+... .....|...+.-=...|+.+.+..++.+.
T Consensus       363 ~e~~~~~~~~aR~l~er~~-k~~~lw~~~~~fE~~~G~~~~~r~v~~~~  410 (493)
T 2uy1_A          363 FLLRIGDEENARALFKRLE-KTSRMWDSMIEYEFMVGSMELFRELVDQK  410 (493)
T ss_dssp             HHHHHTCHHHHHHHHHHSC-CBHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            8889999999999999985 46788999998878889999999988877

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

Probab=96.39  E-value=0.0031  Score=39.01  Aligned_cols=51  Identities=10%  Similarity=-0.052  Sum_probs=26.4

Q ss_pred             HhccccHHHHHHHHHHHHHhccCccHh-HHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGHLHDIF-IQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +.+.|++++|.+.++...+.. +.+.. .+..+-.+|...|++++|.+.|++.
T Consensus        10 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a   61 (99)
T 2kc7_A           10 LINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSA   61 (99)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            344555555555555555443 22334 5555555555555555555555554

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

Probab=96.39  E-value=0.12  Score=40.57  Aligned_cols=142  Identities=13%  Similarity=0.076  Sum_probs=84.0

Q ss_pred             hCCCcccHHHHHHHHHcC-----CCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhcc---c--cHHHHH---HHHHHH
Q 045511           27 KIPQPHILNTLLKLLTQS-----STPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLA---H--AHQKGL---EIHAHV   92 (209)
Q Consensus        27 ~~p~~~~~~~li~~~~~~-----g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~---~--~~~~a~---~~~~~m   92 (209)
                      .+.+...|..++.+....     .+..+|..+|++..+.  .|+- ..|..+--++...   +  ......   +.+...
T Consensus       190 ~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~  267 (372)
T 3ly7_A          190 LPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNI  267 (372)
T ss_dssp             SCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHH
Confidence            334668888888766532     2346788888888774  3542 3344333333210   0  001111   112211


Q ss_pred             HH-hccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHH
Q 045511           93 IK-YGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLV  168 (209)
Q Consensus        93 ~~-~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~  168 (209)
                      .. ..-+.++.+|..+-..+...|++++|...+++..  .|+...|..+=..+.-.|++++|.+.|.+. .+.|...||.
T Consensus       268 ~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~t~~  347 (372)
T 3ly7_A          268 VTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGANTLY  347 (372)
T ss_dssp             HTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHHHHH
T ss_pred             HhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcChHH
Confidence            11 1224566777777777777788888888888773  366666656667777788888888888777 7777777765


Q ss_pred             HH
Q 045511          169 SV  170 (209)
Q Consensus       169 ~l  170 (209)
                      ..
T Consensus       348 ~~  349 (372)
T 3ly7_A          348 WI  349 (372)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.22  E-value=0.091  Score=45.09  Aligned_cols=103  Identities=10%  Similarity=0.011  Sum_probs=64.4

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChh
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIF  118 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~  118 (209)
                      ....+.|++++|+++.+.+      .+...|..+-..+.+.++++.|++.|..+.+.         ..+...|...|+.+
T Consensus       660 ~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d~---------~~l~~l~~~~~~~~  724 (814)
T 3mkq_A          660 ELALKVGQLTLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHDL---------ESLFLLHSSFNNKE  724 (814)
T ss_dssp             HHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCH---------HHHHHHHHHTTCHH
T ss_pred             ehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccCh---------hhhHHHHHHcCCHH
Confidence            3456789999999886554      46688999999999999999999999887543         23444444455554


Q ss_pred             hHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          119 SAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       119 ~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ...++-+.....  .-++.-..+|.+.|++++|.+++.++
T Consensus       725 ~~~~~~~~a~~~--~~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          725 GLVTLAKDAETT--GKFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             HHHHHHHHHHHT--TCHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHc--CchHHHHHHHHHcCCHHHHHHHHHHc
Confidence            444333222110  11233333444556666666666665

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=96.20  E-value=0.11  Score=43.42  Aligned_cols=146  Identities=10%  Similarity=0.041  Sum_probs=85.3

Q ss_pred             ccHHHHHHHHHcCCC----------ccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccc--cHHHHHHHHHHHHHhccCc
Q 045511           32 HILNTLLKLLTQSST----------PQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAH--AHQKGLEIHAHVIKYGHLH   99 (209)
Q Consensus        32 ~~~~~li~~~~~~g~----------~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~--~~~~a~~~~~~m~~~g~~~   99 (209)
                      .+|+.-=..+.+.|+          ++++.+.++.+.+... -+...|+.--..+.+.+  +++++.+.++.+.+.. +.
T Consensus        64 taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~p-K~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d-~~  141 (567)
T 1dce_A           64 TLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNP-KSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ER  141 (567)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhc-cc
Confidence            556554444444455          6777777777766442 35556666555666666  5577777777777665 45


Q ss_pred             cHhHHHHHHHHHHhCC-ChhhHHHHHHhcCC---CcHhHHHHHHHHHHhC--------------CChHHHHHHHhhC-CC
Q 045511          100 DIFIQNSLLHFYVTVK-DIFSAHQIFNSVVF---PDVVTWTTIISGLSKC--------------GFHKEAIDMFCGI-DV  160 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g-~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~--------------g~~~~a~~~~~~m-~~  160 (209)
                      |-.+|+.---.+.+.| ..+++.+.++++.+   .|..+|+-.-..+.+.              +.++++++.++.. ..
T Consensus       142 N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~  221 (567)
T 1dce_A          142 NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFT  221 (567)
T ss_dssp             CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhh
Confidence            6667776666666667 67777777777643   2455555554444431              3456666666655 44


Q ss_pred             CCCH-HhHHHHHHHhccccc
Q 045511          161 KPNA-NTLVSVLSACSSLGS  179 (209)
Q Consensus       161 ~p~~-~t~~~li~~~~~~g~  179 (209)
                      .|+. ..|.-.--.+.+.+.
T Consensus       222 ~P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          222 DPNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             CSSCSHHHHHHHHHHSCCCC
T ss_pred             CCCCccHHHHHHHHHhcCCC
Confidence            4533 444444334444443

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

Probab=96.14  E-value=0.12  Score=40.60  Aligned_cols=137  Identities=6%  Similarity=-0.044  Sum_probs=92.0

Q ss_pred             CCCCHHHHHHHHHHHhcc-----ccHHHHHHHHHHHHHhccCcc-HhHHHHHHHHHH----hCCC----hh---hHHHHH
Q 045511           62 SSYNHYTFTQALKACSLA-----HAHQKGLEIHAHVIKYGHLHD-IFIQNSLLHFYV----TVKD----IF---SAHQIF  124 (209)
Q Consensus        62 ~~p~~~t~~~ll~~~~~~-----~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~----~~g~----~~---~a~~~~  124 (209)
                      .+.+...|...+.+....     ....+|..+|+...+..  |+ ...|..+--+|.    ..+.    ..   .+.+..
T Consensus       190 ~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lD--P~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~  267 (372)
T 3ly7_A          190 LPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSS--PEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNI  267 (372)
T ss_dssp             SCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHH
Confidence            456778899988877543     34578888898888764  44 334443333332    1111    11   122211


Q ss_pred             Hhc--CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchh
Q 045511          125 NSV--VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIIL  201 (209)
Q Consensus       125 ~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~  201 (209)
                      ..+  ...+...|.++-..+...|++++|...+++. .+.|+...|..+-..+...|++++|.+.++.....  .|...+
T Consensus       268 ~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t  345 (372)
T 3ly7_A          268 VTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANT  345 (372)
T ss_dssp             HTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHH
T ss_pred             HhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcCh
Confidence            122  2356778888877777789999999999999 66688888888888888999999999999877666  454444


Q ss_pred             H
Q 045511          202 D  202 (209)
Q Consensus       202 ~  202 (209)
                      |
T Consensus       346 ~  346 (372)
T 3ly7_A          346 L  346 (372)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.12  E-value=0.16  Score=33.99  Aligned_cols=81  Identities=11%  Similarity=0.022  Sum_probs=64.0

Q ss_pred             CChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          115 KDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       115 g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      |++......+-.+. .+...++.-++.+...|.-++-.+++.++  +-+|+....-.+-.+|.+.|+..++.+++.+.-+
T Consensus        75 ~NlKrVi~C~~~~n-~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~  153 (172)
T 1wy6_A           75 QNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACK  153 (172)
T ss_dssp             SCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            34444444443332 34455678889999999999999999994  7888999999999999999999999999999999


Q ss_pred             hccC
Q 045511          193 NLNE  196 (209)
Q Consensus       193 ~~~~  196 (209)
                      +|++
T Consensus       154 kG~k  157 (172)
T 1wy6_A          154 KGEK  157 (172)
T ss_dssp             TTCH
T ss_pred             hhhH
Confidence            9864

>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=95.75  E-value=0.23  Score=33.00  Aligned_cols=60  Identities=13%  Similarity=0.051  Sum_probs=42.1

Q ss_pred             chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           49 NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        49 ~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +..+-++.+...++.|+.....+.+++|.+.+++..|..+|+.++.+- .+...+|..++.
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~lq  130 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ  130 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHHH
Confidence            344555666667778888888888888888888888888888777553 333556766653

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=95.58  E-value=0.22  Score=31.30  Aligned_cols=60  Identities=13%  Similarity=0.051  Sum_probs=48.3

Q ss_pred             chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           49 NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        49 ~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +..+-++.+....+.|+.....+.+++|.+.+++..|..+|+.++.+- .....+|..++.
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lq   87 (109)
T 1v54_E           28 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   87 (109)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHH
Confidence            455667778888899999999999999999999999999999888654 233557777764

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.49  E-value=0.061  Score=46.17  Aligned_cols=77  Identities=8%  Similarity=-0.009  Sum_probs=50.9

Q ss_pred             HHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC
Q 045511           35 NTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV  114 (209)
Q Consensus        35 ~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  114 (209)
                      ..++..+.+.|..++|.++.+.       |.     .-.......|+++.|.++.+.+      .+...|..|-..+.+.
T Consensus       633 ~~~~~~l~~~~~~~~a~~~~~~-------~~-----~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~  694 (814)
T 3mkq_A          633 TKIARFLEGQEYYEEALNISPD-------QD-----QKFELALKVGQLTLARDLLTDE------SAEMKWRALGDASLQR  694 (814)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCCC-------HH-----HHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCChHHheecCCC-------cc-----hheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHc
Confidence            5556666666666666655421       11     1123345567777777764332      4677899999999999


Q ss_pred             CChhhHHHHHHhcCC
Q 045511          115 KDIFSAHQIFNSVVF  129 (209)
Q Consensus       115 g~~~~a~~~~~~~~~  129 (209)
                      |+++.|+++|..+..
T Consensus       695 ~~~~~A~~~y~~~~d  709 (814)
T 3mkq_A          695 FNFKLAIEAFTNAHD  709 (814)
T ss_dssp             TCHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHccC
Confidence            999999999988754

>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=95.48  E-value=0.92  Score=37.79  Aligned_cols=147  Identities=4%  Similarity=-0.034  Sum_probs=107.2

Q ss_pred             CCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhcccc----------HHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAHA----------HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~----------~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      ....++|++.++++...+  |+. ..|+.-=..+.+.|+          ++++.+.++.+.+.. +-+..+|+.---.+.
T Consensus        42 ~~~~eeal~~~~~~l~~n--P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~  118 (567)
T 1dce_A           42 GELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLS  118 (567)
T ss_dssp             TCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            344457899999998854  443 445544444444555          899999999999876 557788888888888


Q ss_pred             hCC--ChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCC-ChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccc-------
Q 045511          113 TVK--DIFSAHQIFNSVV---FPDVVTWTTIISGLSKCG-FHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSL-------  177 (209)
Q Consensus       113 ~~g--~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~-------  177 (209)
                      +.|  +++++.+.++++.   ..|..+|+----.+.+.| .++++++.+.++ ...|+ ...|+..-..+.+.       
T Consensus       119 ~l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~  198 (567)
T 1dce_A          119 RLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSG  198 (567)
T ss_dssp             TCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             HcccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccccc
Confidence            888  6799999999983   457778887777777888 899999999999 66664 45666655554432       


Q ss_pred             -------cchhHHHHHHHHHHHh
Q 045511          178 -------GSRKLGKAIHAHSLRN  193 (209)
Q Consensus       178 -------g~~~~a~~~~~~~~~~  193 (209)
                             +.++++.+.+......
T Consensus       199 ~~~~~~~~~~~eel~~~~~ai~~  221 (567)
T 1dce_A          199 PQGRLPENVLLKELELVQNAFFT  221 (567)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHHHHhh
Confidence                   5677888877766654

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

Probab=95.25  E-value=0.08  Score=32.29  Aligned_cols=80  Identities=16%  Similarity=0.149  Sum_probs=56.4

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCCCCCCHH-HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCPSSYNHY-TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      ...+.+.|++++|...|++..+.. +.+.. .+..+-.++...|++++|.+.|+...+... .+...+..        +.
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~--------~~   76 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNP-DSPALQAR--------KM   76 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TSTHHHHH--------HH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CcHHHHHH--------HH
Confidence            445678899999999999988753 22446 788888888999999999999999987652 22333311        44


Q ss_pred             hhhHHHHHHhc
Q 045511          117 IFSAHQIFNSV  127 (209)
Q Consensus       117 ~~~a~~~~~~~  127 (209)
                      ++++...|++.
T Consensus        77 ~~~a~~~~~~~   87 (99)
T 2kc7_A           77 VMDILNFYNKD   87 (99)
T ss_dssp             HHHHHHHHCCT
T ss_pred             HHHHHHHHHHH
Confidence            55555555544

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.20  E-value=0.42  Score=33.38  Aligned_cols=128  Identities=13%  Similarity=0.098  Sum_probs=79.6

Q ss_pred             HHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhh
Q 045511           40 LLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFS  119 (209)
Q Consensus        40 ~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~  119 (209)
                      ...+.|+++.|.++.+.+      -+...|..+-......|+++.|++.|....+         +..+.-.|.-.|+.+.
T Consensus        14 LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~   78 (177)
T 3mkq_B           14 LALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNK   78 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHH
T ss_pred             HHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHH
Confidence            344567777777776654      3567777777777777777777777765543         3344444555566555


Q ss_pred             HHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHH
Q 045511          120 AHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       120 a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                      -.++-+...  ...-+|.-...+...|+++++.++|.+.|..|....+..      ..|.-+.|.++.+.+
T Consensus        79 L~kla~iA~--~~g~~n~af~~~l~lGdv~~~i~lL~~~~r~~eA~~~A~------t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           79 LSKMQNIAQ--TREDFGSMLLNTFYNNSTKERSSIFAEGGSLPLAYAVAK------ANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHHHH--HTTCHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHHHHHH------HTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHH--HCccHHHHHHHHHHcCCHHHHHHHHHHCCChHHHHHHHH------HcCcHHHHHHHHHHh
Confidence            444432211  011255666667778999999999988866665544322      245677788887654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.91  E-value=0.22  Score=30.68  Aligned_cols=64  Identities=9%  Similarity=-0.036  Sum_probs=34.0

Q ss_pred             cHhHHHHHHHHHHhCCC---hhhHHHHHHhcC--C-CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC
Q 045511          100 DIFIQNSLLHFYVTVKD---IFSAHQIFNSVV--F-PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN  163 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~---~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~  163 (209)
                      |+..+..+-.++...++   .++|..++++..  . .+......+-..+.+.|++++|+..|.++ ...|+
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            44444444444443332   466666666552  2 23445555556666666666666666666 44444

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=94.72  E-value=0.076  Score=36.47  Aligned_cols=58  Identities=14%  Similarity=0.123  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC-----------CChhhHHHHHHhcC--CCcHhHHHHHHH
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV-----------KDIFSAHQIFNSVV--FPDVVTWTTIIS  140 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-----------g~~~~a~~~~~~~~--~~~~~~~~~li~  140 (209)
                      +++|...|+..++.. +-+..+|..+-.+|.+.           |++++|.+.|++..  .|+...|..-+.
T Consensus        62 ~~eAi~~le~AL~ld-P~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~al~  132 (158)
T 1zu2_A           62 IQEAITKFEEALLID-PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            446666666666543 22445666666666655           36777777777663  455544444333

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.28  E-value=0.2  Score=33.55  Aligned_cols=66  Identities=11%  Similarity=0.099  Sum_probs=36.7

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcc
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGH   97 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~   97 (209)
                      ....+..++.+...|+-+.-.+++.++.. +-+|+....-.+-+||.+.|+..++.+++.+.-++|+
T Consensus        91 se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A           91 NEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence            34455555555555555555555555332 2345555566666666666666666666666665554

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=94.26  E-value=0.26  Score=33.57  Aligned_cols=62  Identities=11%  Similarity=-0.027  Sum_probs=26.5

Q ss_pred             CHHHHHHHHHHHhccc---cHHHHHHHHHHHHHhccCc--cHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           65 NHYTFTQALKACSLAH---AHQKGLEIHAHVIKYGHLH--DIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        65 ~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~g~~~--~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +..+--.+-.++++.+   +++++..+++...+.. .|  ....+=.|--+|.+.|++++|.+.++..
T Consensus        31 ~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~l   97 (152)
T 1pc2_A           31 SKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGL   97 (152)
T ss_dssp             CHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            3333333333344443   4445555555555443 12  1222222333345555555555555544

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.22  E-value=0.51  Score=40.69  Aligned_cols=122  Identities=11%  Similarity=0.060  Sum_probs=76.3

Q ss_pred             HHHHHHHHcCCC-ccchHHHHHHhhhCCCCCCHHH-H-HHHHHHHhccccHH-HHHHHHHHHHHh------ccCc-cH--
Q 045511           35 NTLLKLLTQSST-PQNAIPLYNKMLNCPSSYNHYT-F-TQALKACSLAHAHQ-KGLEIHAHVIKY------GHLH-DI--  101 (209)
Q Consensus        35 ~~li~~~~~~g~-~~~a~~l~~~m~~~g~~p~~~t-~-~~ll~~~~~~~~~~-~a~~~~~~m~~~------g~~~-~~--  101 (209)
                      ..++..+...++ .+.|..+|+++....  |...+ | ..++..+.+.++-+ +|.+++.+..+.      ...+ +.  
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            445555555666 477999999998864  43333 2 23334333333221 233333333221      1111 11  


Q ss_pred             --------hHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          102 --------FIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       102 --------~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                              .....=.+.|...|+++.|.++-.+.+  .| +..+|-.|..+|...|+++.|+-.++.+
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence                    122222456778999999999998873  34 5789999999999999999999999988

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.14  E-value=0.52  Score=29.37  Aligned_cols=61  Identities=7%  Similarity=-0.102  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhc------cCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYG------HLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g------~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .-+-.+-..+.+.++++.|..+|+...+.-      -.+...++..|..+|.+.|+++.|...+++.
T Consensus         6 ~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~a   72 (104)
T 2v5f_A            6 EDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKL   72 (104)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            334455555666677777777776665442      1223445666666666666666666666554

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=94.10  E-value=0.33  Score=33.01  Aligned_cols=86  Identities=14%  Similarity=0.022  Sum_probs=63.7

Q ss_pred             cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCC---ChhhHHHHHHhcC--C-C--cHhHHHHHHHHHHhCCChHH
Q 045511           79 AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVK---DIFSAHQIFNSVV--F-P--DVVTWTTIISGLSKCGFHKE  150 (209)
Q Consensus        79 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g---~~~~a~~~~~~~~--~-~--~~~~~~~li~~~~~~g~~~~  150 (209)
                      .+.+..+++-|....+.|. ++..+.-.+--++++++   +++++..++++..  . |  +...+=.+--+|.+.|++++
T Consensus        11 ~~~l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~   89 (152)
T 1pc2_A           11 VEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEK   89 (152)
T ss_dssp             HHHHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHH
Confidence            3456667777777776664 78888888888899988   6679998888773  2 3  23344445567799999999


Q ss_pred             HHHHHhhC-CCCCCHH
Q 045511          151 AIDMFCGI-DVKPNAN  165 (209)
Q Consensus       151 a~~~~~~m-~~~p~~~  165 (209)
                      |.+.++.. .+.|+-.
T Consensus        90 A~~y~~~lL~ieP~n~  105 (152)
T 1pc2_A           90 ALKYVRGLLQTEPQNN  105 (152)
T ss_dssp             HHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHhcCCCCH
Confidence            99999999 8888543

>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=94.00  E-value=1.7  Score=33.86  Aligned_cols=152  Identities=11%  Similarity=0.049  Sum_probs=98.4

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccc-cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC-C
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAH-AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV-K  115 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-g  115 (209)
                      ....+.+..++|+++++++...+  |+. ..|+.-=..+...+ .++++.++++.+++.. +-+..+|+.---.+.+. +
T Consensus        62 ~~~~~~e~se~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~  138 (349)
T 3q7a_A           62 AIAAKEEKSERALELTEIIVRMN--PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISP  138 (349)
T ss_dssp             HHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCC
T ss_pred             HHHHhCCCCHHHHHHHHHHHHhC--chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcC
Confidence            33344555568999999998754  443 44555555555566 5889999999988765 45667787776666665 6


Q ss_pred             -ChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChH--------HHHHHHhhC-CCCC-CHHhHHHHHHHhccccc--
Q 045511          116 -DIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHK--------EAIDMFCGI-DVKP-NANTLVSVLSACSSLGS--  179 (209)
Q Consensus       116 -~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~--------~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~--  179 (209)
                       +++++.++++.+.+   .|..+|+----.+.+.|.++        ++++.+.++ ...| |...|+..-....+.+.  
T Consensus       139 ~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~N~SAW~~R~~lL~~l~~~~  218 (349)
T 3q7a_A          139 QDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGRNNSAWGWRWYLRVSRPGAE  218 (349)
T ss_dssp             SCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHTTSTTCC
T ss_pred             CChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccc
Confidence             88899999988854   34555554333333334444        788888887 4444 55677777666666664  


Q ss_pred             -----hhHHHHHHHHHHHh
Q 045511          180 -----RKLGKAIHAHSLRN  193 (209)
Q Consensus       180 -----~~~a~~~~~~~~~~  193 (209)
                           ++++.+......+.
T Consensus       219 ~~~~~~~eELe~~~~aI~~  237 (349)
T 3q7a_A          219 TSSRSLQDELIYILKSIHL  237 (349)
T ss_dssp             CCHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHh
Confidence                 45666666555443

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.87  E-value=0.81  Score=36.90  Aligned_cols=53  Identities=11%  Similarity=0.117  Sum_probs=32.1

Q ss_pred             hhccCCCcchHhHHHHHHHHhhCCC----cccHHHHHHHHHcCCCccchHHHHHHhh
Q 045511            6 LKSLKPTLSFKQLNQIHAQIIKIPQ----PHILNTLLKLLTQSSTPQNAIPLYNKML   58 (209)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~l~~~m~   58 (209)
                      +..+++..|.+.+..+.+.-....|    ......++..|.+.|+++...+.+..+.
T Consensus        27 l~~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Ls   83 (445)
T 4b4t_P           27 LAQNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLS   83 (445)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            3335556666666666554322222    2557778888888888887766655543

>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=93.66  E-value=0.33  Score=38.40  Aligned_cols=64  Identities=8%  Similarity=0.123  Sum_probs=51.6

Q ss_pred             HHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC--------CCCCCHHhHH
Q 045511          105 NSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI--------DVKPNANTLV  168 (209)
Q Consensus       105 ~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--------~~~p~~~t~~  168 (209)
                      ..++..+...|+.++|...+....   ..+...|-.+|.+|.+.|+..+|++.|++.        |+.|+..+-.
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            456667778899999988877762   246778999999999999999999998887        9999887643

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=93.38  E-value=0.00012  Score=59.30  Aligned_cols=154  Identities=12%  Similarity=-0.004  Sum_probs=94.1

Q ss_pred             HhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHH
Q 045511           25 IIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQ  104 (209)
Q Consensus        25 ~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~  104 (209)
                      +....|+..|..+|....++|++++-...+.-.++..-.|  ..=+.++-+|++.+++.+.++++       -.||..-.
T Consensus        77 yIkA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~--~IDteLi~ayAk~~rL~elEefl-------~~~N~A~i  147 (624)
T 3lvg_A           77 YIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARES--YVETELIFALAKTNRLAELEEFI-------NGPNNAHI  147 (624)
T ss_dssp             SCCCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCST--TTTHHHHHHHHTSCSSSTTTSTT-------SCCSSSCT
T ss_pred             HHhCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccc--ccHHHHHHHHHhhCcHHHHHHHH-------cCCCcccH
Confidence            3444566778888888888888888777776555543223  33457777888887766554443       24666666


Q ss_pred             HHHHHHHHhCCChhhHHHHHHhcC------------------------CCcHhHHHHHHHHHHhCCChHHHHHHHhhCCC
Q 045511          105 NSLLHFYVTVKDIFSAHQIFNSVV------------------------FPDVVTWTTIISGLSKCGFHKEAIDMFCGIDV  160 (209)
Q Consensus       105 ~~ll~~~~~~g~~~~a~~~~~~~~------------------------~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  160 (209)
                      ..+-+-|...|.++.|.-+|..++                        ..+..||--+-.+|...+.+..|.-.--.+  
T Consensus       148 q~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLni--  225 (624)
T 3lvg_A          148 QQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHI--  225 (624)
T ss_dssp             HHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHH--
T ss_pred             HHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchh--
Confidence            677777777777877777776652                        135567777777777777665542211111  


Q ss_pred             CCCHHhHHHHHHHhccccchhHHHHHHHH
Q 045511          161 KPNANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       161 ~p~~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      -....-...+++.|.+.|-+++...+++-
T Consensus       226 IvhadeL~elv~~YE~~G~f~ELIsLlEa  254 (624)
T 3lvg_A          226 VVHADELEELINYYQDRGYFEELITMLEA  254 (624)
T ss_dssp             HCCSSCCSGGGSSSSTTCCCTTSTTTHHH
T ss_pred             cccHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            11111223356667777777776666543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=93.28  E-value=0.62  Score=28.99  Aligned_cols=66  Identities=9%  Similarity=-0.070  Sum_probs=50.7

Q ss_pred             cccHHHHHHHHHcCCCccchHHHHHHhhhCC------CCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhc
Q 045511           31 PHILNTLLKLLTQSSTPQNAIPLYNKMLNCP------SSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYG   96 (209)
Q Consensus        31 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g   96 (209)
                      ...+-.+-..+.+.|+++.|..+|+...+.-      -.+....+..+-.++.+.|+++.|...++...+..
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~   76 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            3455667777888899999999988876521      12456778888889999999999999998888754

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=92.41  E-value=0.52  Score=37.24  Aligned_cols=69  Identities=10%  Similarity=-0.008  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHH-----hccCCCchhH
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLR-----NLNENNIILD  202 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~~  202 (209)
                      +...++..+...|+++++...+..+ ...| +...+..++.++.+.|+..+|.+.|+...+     .|+.|.+.+-
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            3445677788899999999888888 4444 777999999999999999999999997543     4999987653

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=91.98  E-value=1.4  Score=38.07  Aligned_cols=123  Identities=8%  Similarity=0.044  Sum_probs=80.5

Q ss_pred             HHHHHHHHHhcccc-HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC-hhhHHHHHHhc-----------CCCcHh-
Q 045511           68 TFTQALKACSLAHA-HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD-IFSAHQIFNSV-----------VFPDVV-  133 (209)
Q Consensus        68 t~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~-~~~a~~~~~~~-----------~~~~~~-  133 (209)
                      --..+++.+...++ .+.+.++|+.+.+.....+......++..+.+.++ --+|.+++.+.           ...+.. 
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            34566777776766 58899999999887533333333444444444432 22344444322           222211 


Q ss_pred             ----HH-HHH----HHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHH
Q 045511          134 ----TW-TTI----ISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHS  190 (209)
Q Consensus       134 ----~~-~~l----i~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~  190 (209)
                          .+ ..|    .+-+...|+++.|+.+-++- ...|+. .||..|.++|...|+++.|.-.+.-+
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence                11 112    34566789999999999988 778875 79999999999999999999888754

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=91.46  E-value=2.6  Score=29.40  Aligned_cols=110  Identities=10%  Similarity=-0.058  Sum_probs=79.9

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      .+...|..|-....+.|+++-|.+-|.+...         +..+.-.|...|+.+....+-+.-...|      -+|...
T Consensus        32 ~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~kla~iA~~~g------~~n~af   96 (177)
T 3mkq_B           32 NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSKMQNIAQTRE------DFGSML   96 (177)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHHHHHHHHHTT------CHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHHHHHHHHHCc------cHHHHH
Confidence            5678999999999999999999999998865         5666667777788776665544444443      356777


Q ss_pred             HHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          109 HFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..+...|+++++.++|.+..+.....+.     .-..|.-+.|.++..++
T Consensus        97 ~~~l~lGdv~~~i~lL~~~~r~~eA~~~-----A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           97 LNTFYNNSTKERSSIFAEGGSLPLAYAV-----AKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHTCHHHHHHHHHHTTCHHHHHHH-----HHHTTCHHHHHHHHHHT
T ss_pred             HHHHHcCCHHHHHHHHHHCCChHHHHHH-----HHHcCcHHHHHHHHHHh
Confidence            7788899999999999887553322111     11256677788887776

>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=91.35  E-value=0.51  Score=35.84  Aligned_cols=76  Identities=11%  Similarity=0.013  Sum_probs=48.8

Q ss_pred             ccHHHHHHHHHcC-----CCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHhccC--ccHhH
Q 045511           32 HILNTLLKLLTQS-----STPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA-HAHQKGLEIHAHVIKYGHL--HDIFI  103 (209)
Q Consensus        32 ~~~~~li~~~~~~-----g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~~m~~~g~~--~~~~~  103 (209)
                      ..|..+-..|.+.     |+.++|.+.|++-.+-+-.-+..++...-..++.. |+.+++.+.++..++....  |+...
T Consensus       200 sA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~l  279 (301)
T 3u64_A          200 AVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKL  279 (301)
T ss_dssp             HHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHH
T ss_pred             HHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhH
Confidence            5677777777774     77777777777777633111356666666666664 7777777777777776655  55544


Q ss_pred             HHHH
Q 045511          104 QNSL  107 (209)
Q Consensus       104 ~~~l  107 (209)
                      .|.+
T Consensus       280 an~~  283 (301)
T 3u64_A          280 LVIL  283 (301)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>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=91.15  E-value=1.5  Score=33.36  Aligned_cols=105  Identities=11%  Similarity=0.030  Sum_probs=74.3

Q ss_pred             cHhHHHHHHH-HHHhC--CC------hhhHHHHHHhcC--CCc---HhHHHHHHHHHHh-----CCChHHHHHHHhhC-C
Q 045511          100 DIFIQNSLLH-FYVTV--KD------IFSAHQIFNSVV--FPD---VVTWTTIISGLSK-----CGFHKEAIDMFCGI-D  159 (209)
Q Consensus       100 ~~~~~~~ll~-~~~~~--g~------~~~a~~~~~~~~--~~~---~~~~~~li~~~~~-----~g~~~~a~~~~~~m-~  159 (209)
                      ....|..++. +++..  |+      ...|+..+++..  .|+   -..|+.+-..|.+     -|+.++|.+.|++- .
T Consensus       153 e~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~  232 (301)
T 3u64_A          153 GTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTR  232 (301)
T ss_dssp             HHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHH
Confidence            3456766665 44442  33      344555555542  344   4588888888988     49999999999998 7


Q ss_pred             CCCC--HHhHHHHHHHhcc-ccchhHHHHHHHHHHHhccC--CCchhHhH
Q 045511          160 VKPN--ANTLVSVLSACSS-LGSRKLGKAIHAHSLRNLNE--NNIILDNA  204 (209)
Q Consensus       160 ~~p~--~~t~~~li~~~~~-~g~~~~a~~~~~~~~~~~~~--p~~~~~~~  204 (209)
                      +.|+  ..++...-..+++ .|+.+.+.+.++...+....  |+....+.
T Consensus       233 LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan~  282 (301)
T 3u64_A          233 YCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVI  282 (301)
T ss_dssp             HCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHHH
T ss_pred             hCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHHH
Confidence            7774  5677777888887 49999999999999888766  76665554

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=91.11  E-value=1.7  Score=26.58  Aligned_cols=45  Identities=2%  Similarity=-0.148  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           82 HQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        82 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .+++..+++..++.. +-++.....+-..+.+.|++++|...|..+
T Consensus        25 ~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~   69 (93)
T 3bee_A           25 TDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLL   69 (93)
T ss_dssp             CHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            344444444444432 223334444444445555555555555444

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=90.20  E-value=2.3  Score=26.73  Aligned_cols=75  Identities=13%  Similarity=0.044  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHhccc-cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHH
Q 045511           67 YTFTQALKACSLAH-AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISG  141 (209)
Q Consensus        67 ~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~  141 (209)
                      ..-......+-+.. +.-++..-++.+....+.|++.+..+.+++|-|.+++.-|.++|+.+.   ......|.-++.-
T Consensus        10 eF~aRy~~~F~~~~iD~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~lqE   88 (109)
T 1v54_E           10 EFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQE   88 (109)
T ss_dssp             HHHHHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHHHH
Confidence            33344555565665 666777888888888899999999999999999999999999998873   2334457666653

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=89.79  E-value=3.4  Score=28.09  Aligned_cols=95  Identities=15%  Similarity=0.228  Sum_probs=48.4

Q ss_pred             CcccHHHHHHHHHcCCCc------cchHHHHHHhhhCCCCCCHHH----HHHHHHHH---hccccHHHHHHHHHHHHHhc
Q 045511           30 QPHILNTLLKLLTQSSTP------QNAIPLYNKMLNCPSSYNHYT----FTQALKAC---SLAHAHQKGLEIHAHVIKYG   96 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~------~~a~~l~~~m~~~g~~p~~~t----~~~ll~~~---~~~~~~~~a~~~~~~m~~~g   96 (209)
                      |+.+|=..+...-+.|++      ++..++|++... .++|+...    |.-+.--|   ...+++++|.++|+.+++.+
T Consensus        12 ~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia-~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~h   90 (161)
T 4h7y_A           12 NPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIE-ALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANC   90 (161)
T ss_dssp             SHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHH-HSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHH-cCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence            446666666666666777      666666665544 24454211    11110000   11255666666666665443


Q ss_pred             cCccHhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           97 HLHDIFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        97 ~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      -.. ..+|-..-..=.+.|++..|.+++..
T Consensus        91 KkF-AKiwi~~AqFEiRqgnl~kARkILg~  119 (161)
T 4h7y_A           91 KKF-AFVHISFAQFELSQGNVKKSKQLLQK  119 (161)
T ss_dssp             TTB-HHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHH-HHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            333 44555555555556666666666554

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=89.73  E-value=2  Score=29.26  Aligned_cols=64  Identities=8%  Similarity=0.055  Sum_probs=47.8

Q ss_pred             CCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           44 SSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        44 ~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      .+++++|.++|+.+.+.+-+. ...|-..-..=.++|+++.|.+++..-...+.+|.. ..++.|.
T Consensus        73 i~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~-~le~a~~  136 (161)
T 4h7y_A           73 IQEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLE-MLEIALR  136 (161)
T ss_dssp             HHCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHH-HHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHH-HHHHHHH
Confidence            489999999999997653223 666776677778999999999999999887755543 4444443

>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, immune system; NMR {Homo sapiens} SCOP: a.5.2.4

Probab=89.29  E-value=0.85  Score=25.52  Aligned_cols=56  Identities=21%  Similarity=0.070  Sum_probs=37.4

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCC
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYN   65 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~   65 (209)
                      +++.+....+.+.++.+.|   |+.....+--..-...|+++.|...+-+|...+..|+
T Consensus         2 ~~~~~~~~ee~l~~L~emF---P~ld~~~I~~vL~a~~gdvd~aI~~LL~m~~~~~~~~   57 (59)
T 1wgl_A            2 SSGSSGCSEEDLKAIQDMF---PNMDQEVIRSVLEAQRGNKDAAINSLLQMGEEPSGPS   57 (59)
T ss_dssp             CSCSSSSCHHHHHHHHHHC---SSSCHHHHHHHHTTTTTCHHHHHHHHHHSSCCCCSCC
T ss_pred             CCCCCCCCHHHHHHHHHHC---CCCCHHHHHHHHHHcCCCHHHHHHHHHcCcCCCCCCC
Confidence            3566666777778887777   5554432222222456889999999988888777775

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=88.84  E-value=6.7  Score=30.21  Aligned_cols=159  Identities=6%  Similarity=-0.006  Sum_probs=105.0

Q ss_pred             ccHHHHHHH---HHcCCCcc-chHHHHHHhhhCCCCCCHHH-HHHHHHHHhcccc----------HHHHHHHHHHHHHhc
Q 045511           32 HILNTLLKL---LTQSSTPQ-NAIPLYNKMLNCPSSYNHYT-FTQALKACSLAHA----------HQKGLEIHAHVIKYG   96 (209)
Q Consensus        32 ~~~~~li~~---~~~~g~~~-~a~~l~~~m~~~g~~p~~~t-~~~ll~~~~~~~~----------~~~a~~~~~~m~~~g   96 (209)
                      ..|..++..   ..+.|.++ +|+.+++.+...+  |+..| |+.-=..+...+.          ++++..+++.+.+..
T Consensus        27 ~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~n--P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~  104 (331)
T 3dss_A           27 KLYQSATQAVFQKRQAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN  104 (331)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC
Confidence            455444443   34567776 7999999998854  55433 3332222222222          678888898888765


Q ss_pred             cCccHhHHHHHHHHHHhCC--ChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCC-hHHHHHHHhhC-CCCC-CHHhHH
Q 045511           97 HLHDIFIQNSLLHFYVTVK--DIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGF-HKEAIDMFCGI-DVKP-NANTLV  168 (209)
Q Consensus        97 ~~~~~~~~~~ll~~~~~~g--~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~-~~~a~~~~~~m-~~~p-~~~t~~  168 (209)
                       +-+..+|+.---.+.+.|  +++++..+++.+.   ..|..+|+----.+...|. ++++++.+..+ ...| |...|+
T Consensus       105 -PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~  183 (331)
T 3dss_A          105 -PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWH  183 (331)
T ss_dssp             -TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHH
T ss_pred             -CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHH
Confidence             557788887777777777  4889999999883   4577777777677777787 58999999988 4455 445565


Q ss_pred             HHHHHhccc--------------cchhHHHHHHHHHHHh
Q 045511          169 SVLSACSSL--------------GSRKLGKAIHAHSLRN  193 (209)
Q Consensus       169 ~li~~~~~~--------------g~~~~a~~~~~~~~~~  193 (209)
                      ..-....+.              +.++++.+.+......
T Consensus       184 ~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~  222 (331)
T 3dss_A          184 YRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFT  222 (331)
T ss_dssp             HHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHh
Confidence            554444333              4566777776666554

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=88.12  E-value=0.92  Score=32.42  Aligned_cols=87  Identities=11%  Similarity=0.012  Sum_probs=38.8

Q ss_pred             HHHHHHhCCChhhHHHHHHhcCCCcH---hHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHH---hHHHHHHHhccccch
Q 045511          107 LLHFYVTVKDIFSAHQIFNSVVFPDV---VTWTTIISGLSKCGFHKEAIDMFCGIDVKPNAN---TLVSVLSACSSLGSR  180 (209)
Q Consensus       107 ll~~~~~~g~~~~a~~~~~~~~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~---t~~~li~~~~~~g~~  180 (209)
                      .+...++.|+.+-+..+++.-..++.   ..-.+.+...+..|+.+-+..+++. |..++..   -.+. +...+..|+.
T Consensus       119 ~L~~A~~~~~~~~~~~Ll~~g~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~-g~~~~~~~~~g~t~-L~~A~~~~~~  196 (241)
T 1k1a_A          119 ALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQH-GANVNAQMYSGSSA-LHSASGRGLL  196 (241)
T ss_dssp             HHHHHHHHTCHHHHHHHHHTTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHHT-TCCTTCBCTTSCBH-HHHHHHHTCH
T ss_pred             HHHHHHHcCCHHHHHHHHHcCCCcccccccCCCcHHHHHHHcCCHHHHHHHHHc-CCCCCCcCCCCCCH-HHHHHHcCCH
Confidence            34444455666666666554322211   1112233344455666555554444 4444332   1222 3333344554


Q ss_pred             hHHHHHHHHHHHhccCCCc
Q 045511          181 KLGKAIHAHSLRNLNENNI  199 (209)
Q Consensus       181 ~~a~~~~~~~~~~~~~p~~  199 (209)
                      +    +.+.+.+.|..|+.
T Consensus       197 ~----~v~~Ll~~ga~~~~  211 (241)
T 1k1a_A          197 P----LVRTLVRSGADSSL  211 (241)
T ss_dssp             H----HHHHHHHTTCCTTC
T ss_pred             H----HHHHHHhcCCCCCC
Confidence            4    33444556665543

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=87.86  E-value=4.1  Score=26.61  Aligned_cols=89  Identities=9%  Similarity=-0.063  Sum_probs=51.6

Q ss_pred             HHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhh---HHHHHHhcCCCc-----HhHHHHHHHHHHhCC
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFS---AHQIFNSVVFPD-----VVTWTTIISGLSKCG  146 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~---a~~~~~~~~~~~-----~~~~~~li~~~~~~g  146 (209)
                      .-.....+..+++-|......|. ++..+--.+--+++++.+..+   +..++++..+.+     ....=-+--|+.+.|
T Consensus        10 ~~~~~~~l~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg   88 (126)
T 1nzn_A           10 ELVSVEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLK   88 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             ccCCHHHHHHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhh
Confidence            33344455555555655555553 666666666667777766555   666666653222     122223346677778


Q ss_pred             ChHHHHHHHhhC-CCCCCH
Q 045511          147 FHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       147 ~~~~a~~~~~~m-~~~p~~  164 (209)
                      ++++|.+.++.+ .+.|+-
T Consensus        89 ~Y~~A~~~~~~lL~~eP~n  107 (126)
T 1nzn_A           89 EYEKALKYVRGLLQTEPQN  107 (126)
T ss_dssp             CHHHHHHHHHHHHHHCTTC
T ss_pred             hHHHHHHHHHHHHHhCCCC
Confidence            888887777777 666643

>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=87.21  E-value=4.9  Score=26.74  Aligned_cols=78  Identities=13%  Similarity=0.045  Sum_probs=57.4

Q ss_pred             CCHHHHHHHHHHHhccc-cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHH
Q 045511           64 YNHYTFTQALKACSLAH-AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTII  139 (209)
Q Consensus        64 p~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li  139 (209)
                      ++...-....+.+-+.. |.-+..+-++.+....+.|++.+..+.+++|-+.+++.-|.++|+.+.   .+....|.-++
T Consensus        50 t~EeFdaRy~~~F~~~~iD~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~l  129 (152)
T 2y69_E           50 TDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI  129 (152)
T ss_dssp             CHHHHHHHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHH
Confidence            34444444555555555 666677778888888899999999999999999999999999998873   34445576666


Q ss_pred             HH
Q 045511          140 SG  141 (209)
Q Consensus       140 ~~  141 (209)
                      .-
T Consensus       130 qE  131 (152)
T 2y69_E          130 QE  131 (152)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=86.69  E-value=2.2  Score=27.90  Aligned_cols=76  Identities=11%  Similarity=-0.045  Sum_probs=35.2

Q ss_pred             hHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH---HHHHHHHHHHHHhccCc--cHhHHHHHHHHHHhCCChhhHHHHH
Q 045511           50 AIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH---QKGLEIHAHVIKYGHLH--DIFIQNSLLHFYVTVKDIFSAHQIF  124 (209)
Q Consensus        50 a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~---~~a~~~~~~m~~~g~~~--~~~~~~~ll~~~~~~g~~~~a~~~~  124 (209)
                      +.+-|.+....|. |+..+-=.+-.++.+....   ..+..+++.+.+.+ .|  .....=.|--++.+.|++++|.+.+
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            3344444433333 3333333333334444433   33555566555543 12  2222333444666666777776666


Q ss_pred             Hhc
Q 045511          125 NSV  127 (209)
Q Consensus       125 ~~~  127 (209)
                      +.+
T Consensus        98 ~~l  100 (126)
T 1nzn_A           98 RGL  100 (126)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            665

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.17  E-value=11  Score=29.95  Aligned_cols=114  Identities=14%  Similarity=0.047  Sum_probs=75.6

Q ss_pred             CcchHhHHHHHHHHhh-----CCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCC--CHHHHHHHHHHHhccccHHH
Q 045511           12 TLSFKQLNQIHAQIIK-----IPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSY--NHYTFTQALKACSLAHAHQK   84 (209)
Q Consensus        12 ~~a~~~~~~~~~~~~~-----~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~   84 (209)
                      +.-.+.+.+.......     .--..+...+-..+.+.|+.++|.+.|.++...-..+  -...+-.++..+...+++..
T Consensus       107 ~~~l~~l~~~~~~~~~~~~~e~e~~~~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~  186 (429)
T 4b4t_R          107 ESKIKELNEKIQKLEEDDEGELEQAQAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLY  186 (429)
T ss_dssp             SCCHHHHHHHHHHHHHCCSCCCCCSSCCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHH
Confidence            3445555555443222     1122578889999999999999999999998753333  34567777888889999999


Q ss_pred             HHHHHHHHHHh---ccCccHh----HHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           85 GLEIHAHVIKY---GHLHDIF----IQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        85 a~~~~~~m~~~---g~~~~~~----~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +...+......   +-.|+..    .|..+  .+...+++.+|-+.|-+.
T Consensus       187 ~~~~~~ka~~~~~~~~d~~~~~~lk~~~gl--~~l~~r~f~~Aa~~f~e~  234 (429)
T 4b4t_R          187 VKEKLEAVNSMIEKGGDWERRNRYKTYYGI--HCLAVRNFKEAAKLLVDS  234 (429)
T ss_dssp             HHHHHHHHHHHHTTCCCTHHHHHHHHHHHH--GGGGTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhcCCCHHHHHHHHHHHHH--HHHHhChHHHHHHHHHHH
Confidence            99988877543   2222221    22222  234568888888888665

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=85.36  E-value=5  Score=25.13  Aligned_cols=74  Identities=14%  Similarity=0.183  Sum_probs=54.6

Q ss_pred             cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           81 AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        81 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..++|.-|-+.+...+-  ...+--.-+.++..+|++++|..+.+....||...|-++-.  .+.|..+++..-+.++
T Consensus        21 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~l   94 (115)
T 2uwj_G           21 CHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGL   94 (115)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHH
Confidence            56788888777776663  33333344557788899999999999888899988887755  3677777777777666

>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=85.18  E-value=5.2  Score=25.12  Aligned_cols=75  Identities=20%  Similarity=0.217  Sum_probs=55.5

Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      .+.++|.-|-+.+...|-  ...+--.-+.++..+|++++|..+.+....||...|-++-.+  +.|..+++..-+.++
T Consensus        21 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce~--rlGl~s~le~rL~~l   95 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCEY--RLGLGSALESRLNRL   95 (116)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHHH--HHTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHHH--hcccHHHHHHHHHHH
Confidence            356788888888777663  333333445578889999999999999999999998887653  567777777777666

>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=81.32  E-value=2.8  Score=27.49  Aligned_cols=95  Identities=13%  Similarity=0.171  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHhCCChhhHHHHHHhcCCCc---HhHHHHHHHHHHhCCC--hHHHHHHHhhC---CCCCCHHh---HHHHH
Q 045511          103 IQNSLLHFYVTVKDIFSAHQIFNSVVFPD---VVTWTTIISGLSKCGF--HKEAIDMFCGI---DVKPNANT---LVSVL  171 (209)
Q Consensus       103 ~~~~ll~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g~--~~~a~~~~~~m---~~~p~~~t---~~~li  171 (209)
                      ..+.++.=|...|+.++|.+.++++..|.   ..+..++..++-+.++  .+.+..++..+   |+-+....   |..++
T Consensus         9 ki~~ll~EY~~~~D~~Ea~~cl~eL~~p~f~~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~~~~~is~~q~~~Gf~~v~   88 (129)
T 2nsz_A            9 EIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGYERIY   88 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcCHHHHHHHHHHHH
Confidence            45678888888899999999999886653   3445556666666542  34566777766   43333322   33333


Q ss_pred             HHhcccc-chhHHHHHHHHHHHhccCC
Q 045511          172 SACSSLG-SRKLGKAIHAHSLRNLNEN  197 (209)
Q Consensus       172 ~~~~~~g-~~~~a~~~~~~~~~~~~~p  197 (209)
                      ..+-... |.-.|.+++..+..+.+.-
T Consensus        89 ~~l~Dl~lDiP~a~~~l~~~v~~ai~~  115 (129)
T 2nsz_A           89 NEIPDINLDVPHSYSVLERFVEECFQA  115 (129)
T ss_dssp             HHHHHHHHHSTTHHHHHHHHHHHHHHT
T ss_pred             hhChHhhcCccchHHHHHHHHHHHHHC
Confidence            3333232 3445666666665554433

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=81.03  E-value=8  Score=24.24  Aligned_cols=60  Identities=18%  Similarity=0.040  Sum_probs=44.4

Q ss_pred             HHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchhH
Q 045511          139 ISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIILD  202 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  202 (209)
                      ++.+.+.|++++|..+...+ ..||...+-.+-.  .+.|..++++.-+.++..+| .|....|
T Consensus        46 ~sSLmNrG~Yq~Al~l~~~~-c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg-~p~~q~F  105 (115)
T 2uwj_G           46 ISSLANQGRYQEALAFAHGN-PWPALEPWFALCE--WHLGLGAALDRRLAGLGGSS-DPALADF  105 (115)
T ss_dssp             HHHHHHTTCHHHHHGGGTTC-CCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHTCS-SHHHHHH
T ss_pred             HHHHHcchhHHHHHHhcCCC-CCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC-CHHHHHH
Confidence            45677899999999998886 5899988866533  47788888888777787776 4443333

>2zu6_B Programmed cell death protein 4; protein-protein complex, ATP-binding, helicase, hydrolase, initiation factor, nucleotide-binding; 2.80A {Homo sapiens} PDB: 3eij_A

Probab=81.03  E-value=16  Score=27.77  Aligned_cols=69  Identities=12%  Similarity=0.073  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhhCCCCCC---HHhHHHHHHHhcccc--chhHHHHHHHHHHHhccCCCchhHh
Q 045511          134 TWTTIISGLSKCGFHKEAIDMFCGIDVKPN---ANTLVSVLSACSSLG--SRKLGKAIHAHSLRNLNENNIILDN  203 (209)
Q Consensus       134 ~~~~li~~~~~~g~~~~a~~~~~~m~~~p~---~~t~~~li~~~~~~g--~~~~a~~~~~~~~~~~~~p~~~~~~  203 (209)
                      ..+.++.-|...|+.++|.+.+++++. |.   ......+..+.-+.+  ..+....++..+.+.|+-+......
T Consensus       168 ki~~lL~EY~~~~D~~EA~~ci~EL~~-p~f~~e~V~~ai~~alE~~~~~~re~~~~LL~~L~~~~~ls~~q~~~  241 (307)
T 2zu6_B          168 EIDMLLKEYLLSGDISEAEHCLKELEV-PHFHHELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMKR  241 (307)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHCC-GGGHHHHHHHHHHHHHTCCSSHHHHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHcCC-CcchHHHHHHHHHHHHccCChHHHHHHHHHHHHHHHCCCCCHHHHHH
Confidence            467899999999999999999999832 22   234455555665543  3566778888888888766554433

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis}

Probab=80.87  E-value=4.7  Score=27.69  Aligned_cols=153  Identities=8%  Similarity=-0.026  Sum_probs=73.7

Q ss_pred             HHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhH--HHHHHHHHHhCCChh
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFI--QNSLLHFYVTVKDIF  118 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~--~~~ll~~~~~~g~~~  118 (209)
                      .+..|+.+.+..++..-...--..|..-.+. +...++.|+.+    +++.+.+.|..++...  -.+.+...+..|+.+
T Consensus        12 A~~~g~~~~v~~ll~~~~~~~~~~~~~g~t~-L~~A~~~~~~~----~v~~Ll~~g~~~~~~~~~g~t~l~~A~~~~~~~   86 (201)
T 3hra_A           12 AANQRDTKKVKEILQDTTYQVDEVDTEGNTP-LNIAVHNNDIE----IAKALIDRGADINLQNSISDSPYLYAGAQGRTE   86 (201)
T ss_dssp             HHHTTCHHHHHHHHTCTTCCTTCCCTTSCCH-HHHHHHHTCHH----HHHHHHHTTCCTTCCCTTSCCHHHHHHHTTCHH
T ss_pred             HHHhccHHHHHHHHHcCCCCCCCCCCCCCCH-HHHHHHcCCHH----HHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCHH
Confidence            4455666666555543220001122222223 33334556543    4455555665554321  234455566778888


Q ss_pred             hHHHHHHhcC-C---CcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCC---CHHhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          119 SAHQIFNSVV-F---PDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKP---NANTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       119 ~a~~~~~~~~-~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p---~~~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      -+..+++.-. .   ++..-.+ .+...+..|+.+.+..+++.-+..+   |..-.+.+..++........-.++.+.+.
T Consensus        87 ~~~~Ll~~~~~~~~~~~~~g~t-~L~~A~~~~~~~~v~~Ll~~g~~~~~~~~~~g~t~L~~A~~~~~~~~~~~~~v~~Ll  165 (201)
T 3hra_A           87 ILAYMLKHATPDLNKHNRYGGN-ALIPAAEKGHIDNVKLLLEDGREDIDFQNDFGYTALIEAVGLREGNQLYQDIVKLLM  165 (201)
T ss_dssp             HHHHHHHHSCCCTTCCCTTSCC-SHHHHHHTTCHHHHHHHHHHCCCCTTCCCTTSCCHHHHHHHSSCCSHHHHHHHHHHH
T ss_pred             HHHHHHhccCcccccccCCCCc-HHHHHHHcCCHHHHHHHHHcCCCCcCCCCCCCCCHHHHHHHhccchhhHHHHHHHHH
Confidence            7777775432 1   2222222 2334456677777666665521222   22334444444433322333356666777


Q ss_pred             HhccCCCc
Q 045511          192 RNLNENNI  199 (209)
Q Consensus       192 ~~~~~p~~  199 (209)
                      +.|..++.
T Consensus       166 ~~ga~~~~  173 (201)
T 3hra_A          166 ENGADQSI  173 (201)
T ss_dssp             HTTCCTTC
T ss_pred             HCCCCCCc
Confidence            77777654

>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=80.24  E-value=8.6  Score=24.13  Aligned_cols=59  Identities=15%  Similarity=0.105  Sum_probs=43.1

Q ss_pred             HHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCchh
Q 045511          139 ISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNIIL  201 (209)
Q Consensus       139 i~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~  201 (209)
                      ++.+.+.|++++|..+...+ ..||...+-.+-.  .+.|..++++.-+.++..+| .|....
T Consensus        47 ~sSLmNrG~Yq~Al~l~~~~-c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg-~p~~q~  105 (116)
T 2p58_C           47 LSSLMNRGDYASALQQGNKL-AYPDLEPWLALCE--YRLGLGSALESRLNRLARSQ-DPRIQT  105 (116)
T ss_dssp             HHHHHHTTCHHHHHHHHTTS-CCGGGHHHHHHHH--HHHTCHHHHHHHHHHHTTCC-CHHHHH
T ss_pred             HHHHHcchhHHHHHHhcCCC-CCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC-CHHHHH
Confidence            45677899999999999996 5899998866533  36777777777776776666 443333

---

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	209
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.33
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.17
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.1
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.03
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.81
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.78
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.73
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.47
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.45
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.36
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.21
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.18
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.17
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.17
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.15
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.15
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.14
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.1
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.09
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.07
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.06
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.03
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.03
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.96
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.85
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.8
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.75
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.71
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.68
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.62
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.53
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.47
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.31
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.29
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.25
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.25
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.23
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.22
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.21
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.18
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.04
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.82
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.68
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.56
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.42
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.31
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.14
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.63
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.27
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	95.18
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	94.82
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	94.56
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.48
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	93.97
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.53
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	89.56
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	89.4
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	89.27
d1khda1	69	Anthranilate phosphoribosyltransferase (TrpD) {Pec	85.9
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	81.66

>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=99.33  E-value=8.2e-11  Score=90.08  Aligned_cols=192  Identities=10%  Similarity=0.027  Sum_probs=155.2

Q ss_pred             hccCCCcchHhHHHHHHHHhhCC-CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIP-QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      ..+..+.|...+.+..+.   .| +..+|..+...+...|++++|...+++....+. .+...+..+-..+.+.|++++|
T Consensus       181 ~~~~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A  256 (388)
T d1w3ba_         181 AQGEIWLAIHHFEKAVTL---DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NHAVVHGNLACVYYEQGLIDLA  256 (388)
T ss_dssp             TTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             ccCcHHHHHHHHHHHHHh---CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh-hHHHHHHHHHHHHHHCCCHHHH
Confidence            345555566666655544   24 347888899999999999999999999887653 4567788888899999999999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCC
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVK  161 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~  161 (209)
                      .+.|+...+.. +.+..++..+...+...|++++|.+.++..   ...+...+..+...+...|++++|+..|++. .+.
T Consensus       257 ~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~  335 (388)
T d1w3ba_         257 IDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVF  335 (388)
T ss_dssp             HHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            99999988764 445778999999999999999999999877   3456778889999999999999999999998 777


Q ss_pred             CCH-HhHHHHHHHhccccchhHHHHHHHHHHHhccCCC-chhHhHh
Q 045511          162 PNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENN-IILDNAV  205 (209)
Q Consensus       162 p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l  205 (209)
                      |+. .++..+-..+.+.|++++|...++...+.  .|+ +..+..|
T Consensus       336 p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l  379 (388)
T d1w3ba_         336 PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNM  379 (388)
T ss_dssp             TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            764 56888889999999999999999987654  564 3445444

>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=99.17  E-value=1.9e-09  Score=82.29  Aligned_cols=172  Identities=10%  Similarity=0.050  Sum_probs=142.0

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      .++ ..++.++|...+.+.....  ..+...+..+-..+.+.|++++|...|++..+.. +-+..++..+-..+...|++
T Consensus       211 ~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~  287 (388)
T d1w3ba_         211 NVLKEARIFDRAVAAYLRALSLS--PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSV  287 (388)
T ss_dssp             HHHHTTTCTTHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCH
T ss_pred             hhhhccccHHHHHHHHHHhHHHh--hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence            344 6778888888777776653  2345778888899999999999999999988753 23467888999999999999


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHHHHHhCCChHHHHHHHhhC-
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIISGLSKCGFHKEAIDMFCGI-  158 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m-  158 (209)
                      ++|.+.++...+.. +.+...+..+...+.+.|++++|.+.|++..+  | +..++..+-..|.+.|++++|...|++. 
T Consensus       288 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al  366 (388)
T d1w3ba_         288 AEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAI  366 (388)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999887764 66788999999999999999999999998743  4 5678888999999999999999999998 


Q ss_pred             CCCCCH-HhHHHHHHHhccccc
Q 045511          159 DVKPNA-NTLVSVLSACSSLGS  179 (209)
Q Consensus       159 ~~~p~~-~t~~~li~~~~~~g~  179 (209)
                      .+.|+. ..+..+-..+.+.||
T Consensus       367 ~l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         367 RISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             TTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HhCCCCHHHHHHHHHHHHHcCC
Confidence            888864 578888888777665

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=2.4e-09  Score=80.76  Aligned_cols=184  Identities=13%  Similarity=0.112  Sum_probs=141.8

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGL   86 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~   86 (209)
                      +.|+.++|.+.+.++.+..+  .+..+|..+-..+.+.|++++|...|++..+.. +-+...|..+...+...|+++.|.
T Consensus        31 ~~g~~~~A~~~~~~al~~~P--~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~  107 (323)
T d1fcha_          31 QEGDLPNAVLLFEAAVQQDP--KHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQAC  107 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHSCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccccccc
Confidence            77788888888888776531  245788888888999999999999998887643 124567777777888888888887


Q ss_pred             HHHHHHHHhc--------------------------------------------------cCccHhHHHHHHHHHHhCCC
Q 045511           87 EIHAHVIKYG--------------------------------------------------HLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        87 ~~~~~m~~~g--------------------------------------------------~~~~~~~~~~ll~~~~~~g~  116 (209)
                      +.++...+..                                                  -.++..++..+-..+...|+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~  187 (323)
T d1fcha_         108 EILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGE  187 (323)
T ss_dssp             HHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTC
T ss_pred             cchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHH
Confidence            7776654321                                                  01234566777788889999


Q ss_pred             hhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHH
Q 045511          117 IFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSL  191 (209)
Q Consensus       117 ~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~  191 (209)
                      +++|...|++..   ..+...|..+-..|...|++++|.+.|.+. ...|+. .++..+-.+|.+.|++++|.+.|....
T Consensus       188 ~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al  267 (323)
T d1fcha_         188 YDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEAL  267 (323)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999999998862   235778888999999999999999999988 666654 568888889999999999999998776


Q ss_pred             Hh
Q 045511          192 RN  193 (209)
Q Consensus       192 ~~  193 (209)
                      +.
T Consensus       268 ~l  269 (323)
T d1fcha_         268 NM  269 (323)
T ss_dssp             HH
T ss_pred             Hh
Confidence            53

>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=99.03  E-value=2.3e-08  Score=75.26  Aligned_cols=163  Identities=13%  Similarity=0.087  Sum_probs=130.3

Q ss_pred             CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           30 QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      +...|..+.....+.|+.+.|..+|+++.+.........|...+..+.+.|+++.|.++|+...+.+. .+...|-....
T Consensus        98 ~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~-~~~~~~~~~a~  176 (308)
T d2onda1          98 NMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTAAL  176 (308)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CcHHHHHHHHH
Confidence            33678888888999999999999999998765433345789999999999999999999999987763 33344444333


Q ss_pred             H-HHhCCChhhHHHHHHhcCC---CcHhHHHHHHHHHHhCCChHHHHHHHhhC----CCCCC--HHhHHHHHHHhccccc
Q 045511          110 F-YVTVKDIFSAHQIFNSVVF---PDVVTWTTIISGLSKCGFHKEAIDMFCGI----DVKPN--ANTLVSVLSACSSLGS  179 (209)
Q Consensus       110 ~-~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m----~~~p~--~~t~~~li~~~~~~g~  179 (209)
                      . +...|+.+.|.++|+....   .+...|...+..+.+.|+.+.|..+|.+.    +..|+  ...|...+..-...|+
T Consensus       177 ~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~  256 (308)
T d2onda1         177 MEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGD  256 (308)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSC
T ss_pred             HHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCC
Confidence            3 4456899999999998843   45778999999999999999999999987    34554  3478888888888999


Q ss_pred             hhHHHHHHHHHHHh
Q 045511          180 RKLGKAIHAHSLRN  193 (209)
Q Consensus       180 ~~~a~~~~~~~~~~  193 (209)
                      .+.+..+..++.+.
T Consensus       257 ~~~~~~~~~r~~~~  270 (308)
T d2onda1         257 LASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999987654

>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=98.81  E-value=2.6e-07  Score=69.20  Aligned_cols=155  Identities=11%  Similarity=-0.019  Sum_probs=126.6

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      .-..+.+.|++++|...|++..+.. +-+..+|..+-..+...|+++.|...|+...+.. +-+...|..+...|...|+
T Consensus        25 ~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          25 EGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-ccccccccccccccccccc
Confidence            3445779999999999999998864 2356789999999999999999999999988765 3467889999999999999


Q ss_pred             hhhHHHHHHhcC------------------------------------------------------CCcHhHHHHHHHHH
Q 045511          117 IFSAHQIFNSVV------------------------------------------------------FPDVVTWTTIISGL  142 (209)
Q Consensus       117 ~~~a~~~~~~~~------------------------------------------------------~~~~~~~~~li~~~  142 (209)
                      +++|.+.++...                                                      ..+...+..+-..+
T Consensus       103 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~  182 (323)
T d1fcha_         103 QRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLF  182 (323)
T ss_dssp             HHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHH
T ss_pred             ccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHH
Confidence            999988885430                                                      01234566677788


Q ss_pred             HhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          143 SKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       143 ~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ...|++++|...|.+. ...|+ ..++..+-..+.+.|++++|.+.++...+.
T Consensus       183 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  235 (323)
T d1fcha_         183 NLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL  235 (323)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHH
Confidence            8999999999999988 55665 467888888899999999999999988765

>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=98.78  E-value=3.5e-07  Score=68.58  Aligned_cols=161  Identities=11%  Similarity=0.013  Sum_probs=121.8

Q ss_pred             CccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHH
Q 045511           46 TPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFN  125 (209)
Q Consensus        46 ~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~  125 (209)
                      ..++|..+|++..+...+-+...|........+.|+.+.+..+|+.+.+........+|...+..+.+.|+++.|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            45778889998887655556677888888899999999999999999876544445689999999999999999999999


Q ss_pred             hcCC--C-cHhHHHHHHH-HHHhCCChHHHHHHHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHHHhc-cCCC
Q 045511          126 SVVF--P-DVVTWTTIIS-GLSKCGFHKEAIDMFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSLRNL-NENN  198 (209)
Q Consensus       126 ~~~~--~-~~~~~~~li~-~~~~~g~~~~a~~~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~p~  198 (209)
                      ....  | +...|-.... -+...|+.+.|..+|... ...| +...+...++...+.|+.++|+.+|++..+.. ..|+
T Consensus       159 ~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~  238 (308)
T d2onda1         159 KAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPE  238 (308)
T ss_dssp             HHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGG
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChH
Confidence            8732  2 2333333322 234568999999999998 4344 45788999999999999999999999987763 4443


Q ss_pred             --chhHhHhh
Q 045511          199 --IILDNAVL  206 (209)
Q Consensus       199 --~~~~~~li  206 (209)
                        ...|...+
T Consensus       239 ~~~~iw~~~~  248 (308)
T d2onda1         239 KSGEIWARFL  248 (308)
T ss_dssp             GCHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence              23454443

>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=98.73  E-value=3.1e-07  Score=69.32  Aligned_cols=183  Identities=8%  Similarity=0.008  Sum_probs=137.4

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCC-CccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSS-TPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      +..+.++|.+.+.++.+..  +-+..+|+..-..+.+.| ++++|...++...+..- -+..+|...-..+.+.|++++|
T Consensus        55 ~~e~~~~Al~~~~~ai~ln--P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p-~~~~a~~~~~~~~~~l~~~~eA  131 (315)
T d2h6fa1          55 RDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRVLVEWLRDPSQE  131 (315)
T ss_dssp             HTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTH
T ss_pred             hCCchHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHH-hhhhHHHHHhHHHHhhccHHHH
Confidence            5567788888888887763  124478888888888776 48999999999877542 3578888888999999999999


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCC------hHHHHHHHh
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGF------HKEAIDMFC  156 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~------~~~a~~~~~  156 (209)
                      .+.++...+.. +.+...|+.+...+.+.|++++|.+.++...   ..+...|+.+-..+.+.+.      +++|++.+.
T Consensus       132 l~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~  210 (315)
T d2h6fa1         132 LEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTL  210 (315)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccchhhhhHHhHHHHH
Confidence            99999998865 5578899999999999999999999999883   2456778776666666555      567888887


Q ss_pred             hC-CCCCC-HHhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          157 GI-DVKPN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       157 ~m-~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .. ...|+ ...|.-+-..+... ..+++.+.+....+..
T Consensus       211 ~al~~~P~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~l~  249 (315)
T d2h6fa1         211 EMIKLVPHNESAWNYLKGILQDR-GLSKYPNLLNQLLDLQ  249 (315)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHTTT-CGGGCHHHHHHHHHHT
T ss_pred             HHHHhCCCchHHHHHHHHHHHhc-ChHHHHHHHHHHHHhC
Confidence            76 66664 45565555555444 4577777777766553

>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=98.47  E-value=4.7e-06  Score=62.61  Aligned_cols=159  Identities=4%  Similarity=0.010  Sum_probs=125.7

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCH-HHHHHHHHHHhccc-cHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNH-YTFTQALKACSLAH-AHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ..|+.+-..+.+.+..++|+.++++..+.  .|+. ..|+..-.++...| ++++|.+.++...+.. +-+..+|+.+-.
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~  120 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhH
Confidence            56666767788889999999999999985  4555 56677666777766 5899999999998875 556889999999


Q ss_pred             HHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhcc------cc
Q 045511          110 FYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSS------LG  178 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~------~g  178 (209)
                      .+.+.|++++|.+.++++.   ..+...|+.+...+...|++++|++.|+.. .+.|+ ...|+.+-..+.+      .+
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~~  200 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRA  200 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHH
T ss_pred             HHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccchhh
Confidence            9999999999999999983   356889999999999999999999999999 77775 4556654444333      34


Q ss_pred             chhHHHHHHHHHHHh
Q 045511          179 SRKLGKAIHAHSLRN  193 (209)
Q Consensus       179 ~~~~a~~~~~~~~~~  193 (209)
                      .+++|.+.+....+.
T Consensus       201 ~~~~ai~~~~~al~~  215 (315)
T d2h6fa1         201 VLEREVQYTLEMIKL  215 (315)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             hhHHhHHHHHHHHHh
Confidence            466777777666555

>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=98.45  E-value=3.8e-06  Score=60.58  Aligned_cols=118  Identities=11%  Similarity=-0.053  Sum_probs=67.2

Q ss_pred             ccCCCcchHhHHHHHHHHhhCC--CcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHH
Q 045511            8 SLKPTLSFKQLNQIHAQIIKIP--QPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKG   85 (209)
Q Consensus         8 ~~~~~~a~~~~~~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a   85 (209)
                      ..+.+.++..+.++.......+  ...+|..+-..+.+.|++++|...|++..+.. +-+..+|..+-.++.+.|++++|
T Consensus        12 ~~~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A   90 (259)
T d1xnfa_          12 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAA   90 (259)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHh
Confidence            4444455555555554322111  11445555556666666666666666666532 12445566666666666666666


Q ss_pred             HHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           86 LEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        86 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .+.|+...+.. +-+..++..+-..|...|++++|.+.|+..
T Consensus        91 ~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~a  131 (259)
T d1xnfa_          91 YEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAF  131 (259)
T ss_dssp             HHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhhhhHHHHHH-hhhhhhHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            66666666543 223445666666666666666666666554

>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=98.36  E-value=6.1e-06  Score=52.62  Aligned_cols=92  Identities=13%  Similarity=-0.022  Sum_probs=56.9

Q ss_pred             HHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHH
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEA  151 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a  151 (209)
                      .+.+.|++++|...|+...+.. +.+...|..+-.+|.+.|++++|.+.+...   ...+...|..+-.++...|++++|
T Consensus        12 ~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~~A   90 (117)
T d1elwa_          12 KALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEA   90 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHHHH
Confidence            3455666666666666666554 445556666666666666666666666665   223555666666666666666666


Q ss_pred             HHHHhhC-CCCCCHHhH
Q 045511          152 IDMFCGI-DVKPNANTL  167 (209)
Q Consensus       152 ~~~~~~m-~~~p~~~t~  167 (209)
                      +..|+.. ...|+...+
T Consensus        91 ~~~~~~a~~~~p~~~~~  107 (117)
T d1elwa_          91 KRTYEEGLKHEANNPQL  107 (117)
T ss_dssp             HHHHHHHHTTCTTCHHH
T ss_pred             HHHHHHHHHhCCCCHHH
Confidence            6666666 555555443

>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=98.21  E-value=2.6e-05  Score=54.14  Aligned_cols=126  Identities=10%  Similarity=-0.033  Sum_probs=100.8

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      .|+- -..+...|+++.|.+.|++.    .+|+..+|..+=..+...|++++|.+.|+...+.. +.+...|..+-.+|.
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~   81 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   81 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHH
Confidence            3443 34457789999999999875    34778888899999999999999999999999876 556789999999999


Q ss_pred             hCCChhhHHHHHHhcC---CC----------------cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH
Q 045511          113 TVKDIFSAHQIFNSVV---FP----------------DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA  164 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~~---~~----------------~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~  164 (209)
                      +.|++++|.+.|++..   +.                ...++..+-.++.+.|++++|.+.|... ...|+.
T Consensus        82 ~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~  153 (192)
T d1hh8a_          82 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  153 (192)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             hhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            9999999998887641   00                1245566777899999999999999887 666653

>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=98.18  E-value=1.6e-05  Score=53.28  Aligned_cols=92  Identities=10%  Similarity=0.046  Sum_probs=72.7

Q ss_pred             HHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHH
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKE  150 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~  150 (209)
                      ..+.+.|++++|...|+...+.. +.+...|..+-.+|...|++++|.+.|+...   ..+..+|..+..+|...|++++
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~~~e   96 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRA   96 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCCHHH
Confidence            34668888888888888888775 4567788888888888899999988888773   3456788888888889999999


Q ss_pred             HHHHHhhC-CCCCCHHh
Q 045511          151 AIDMFCGI-DVKPNANT  166 (209)
Q Consensus       151 a~~~~~~m-~~~p~~~t  166 (209)
                      |...|.+. .+.|+...
T Consensus        97 A~~~~~~a~~~~p~~~~  113 (159)
T d1a17a_          97 ALRDYETVVKVKPHDKD  113 (159)
T ss_dssp             HHHHHHHHHHHSTTCHH
T ss_pred             HHHHHHHHHHcCCCCHH
Confidence            98888888 66666543

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.17  E-value=5.3e-05  Score=55.78  Aligned_cols=182  Identities=9%  Similarity=-0.071  Sum_probs=116.6

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc----ccHHHHHHHHHcCCCccchHHHHHHhhh----CC-CCCCHHHHHHHHHHHh
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP----HILNTLLKLLTQSSTPQNAIPLYNKMLN----CP-SSYNHYTFTQALKACS   77 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~l~~~m~~----~g-~~p~~~t~~~ll~~~~   77 (209)
                      ..++.++|.+-+.++.+......+.    .+|+.+-..|.+.|++++|...+++..+    .| ......++..+...+-
T Consensus        49 ~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~  128 (290)
T d1qqea_          49 LRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILE  128 (290)
T ss_dssp             HTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHh
Confidence            4566777777777777765444443    6788888888899999999988887644    22 1112344555555553


Q ss_pred             -ccccHHHHHHHHHHHHHh----ccCc-cHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-------cH-hHHHHHHHH
Q 045511           78 -LAHAHQKGLEIHAHVIKY----GHLH-DIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-------DV-VTWTTIISG  141 (209)
Q Consensus        78 -~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-------~~-~~~~~li~~  141 (209)
                       ..|+++.|.+.++...+-    +.++ -..++..+...|.+.|++++|.+.|++..  .+       +. ..+......
T Consensus       129 ~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  208 (290)
T d1qqea_         129 NDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLC  208 (290)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHH
Confidence             458899999888776532    2111 13467888889999999999999998762  11       11 123444556


Q ss_pred             HHhCCChHHHHHHHhhC-CCCCC------HHhHHHHHHHhcc--ccchhHHHHHHH
Q 045511          142 LSKCGFHKEAIDMFCGI-DVKPN------ANTLVSVLSACSS--LGSRKLGKAIHA  188 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m-~~~p~------~~t~~~li~~~~~--~g~~~~a~~~~~  188 (209)
                      +...|+++.|...|.+. .+.|+      ......++.++..  .+.+++|..-|+
T Consensus       209 ~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~  264 (290)
T d1qqea_         209 QLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFD  264 (290)
T ss_dssp             HHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHT
T ss_pred             HHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            67789999999999888 55543      2345666666643  233555555543

>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=98.17  E-value=2.5e-05  Score=53.96  Aligned_cols=97  Identities=9%  Similarity=0.013  Sum_probs=55.4

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      |+...+-..=..+.+.|++++|...|++..... +-+...|..+-.+|.+.|+++.|...|+...+.. +-+..+|..+-
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~-p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC-CCcHHHHHHHH
Confidence            344444444555666666666666666655532 2344556666666666666666666666665432 22345566666


Q ss_pred             HHHHhCCChhhHHHHHHhc
Q 045511          109 HFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~  127 (209)
                      .+|.+.|++++|...|...
T Consensus        80 ~~~~~l~~~~~A~~~~~~a   98 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRA   98 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHH
Confidence            6666666666666666654

>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=98.15  E-value=5.1e-05  Score=52.59  Aligned_cols=121  Identities=12%  Similarity=-0.006  Sum_probs=95.2

Q ss_pred             HHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHH
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEA  151 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a  151 (209)
                      .+...|+++.|.+.|..+    .+|++.+|..+-..|.+.|++++|.+.|++..   ..+...|+.+-.+|.+.|++++|
T Consensus        14 ~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A   89 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLA   89 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHH
Confidence            346789999999998764    46788899999999999999999999999873   34577899999999999999999


Q ss_pred             HHHHhhC--CCC---------------CC-HHhHHHHHHHhccccchhHHHHHHHHHHHhccCCCc
Q 045511          152 IDMFCGI--DVK---------------PN-ANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENNI  199 (209)
Q Consensus       152 ~~~~~~m--~~~---------------p~-~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~  199 (209)
                      ...|++.  -.+               ++ ..++..+-.++.+.|++++|.+.+....+....|..
T Consensus        90 ~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~  155 (192)
T d1hh8a_          90 IKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRH  155 (192)
T ss_dssp             HHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGG
T ss_pred             HHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcch
Confidence            9888774  111               11 234455666788999999999999887766555433

>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=1.9e-05  Score=54.54  Aligned_cols=99  Identities=7%  Similarity=-0.101  Sum_probs=85.8

Q ss_pred             CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C-cHhHHHHHHH
Q 045511           64 YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P-DVVTWTTIIS  140 (209)
Q Consensus        64 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~  140 (209)
                      |+...+.-.=..+.+.|+++.|...|...++.. +.+...|+.+-.+|.+.|++++|...|+...+  | +..+|..+-.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~   80 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQ   80 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHH
Confidence            677777788888999999999999999988875 56788999999999999999999999999843  4 5778999999


Q ss_pred             HHHhCCChHHHHHHHhhC-CCCCC
Q 045511          141 GLSKCGFHKEAIDMFCGI-DVKPN  163 (209)
Q Consensus       141 ~~~~~g~~~~a~~~~~~m-~~~p~  163 (209)
                      +|...|++++|+..|+.. .+.|+
T Consensus        81 ~~~~l~~~~~A~~~~~~al~l~p~  104 (201)
T d2c2la1          81 CQLEMESYDEAIANLQRAYSLAKE  104 (201)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCcc
Confidence            999999999999999987 54553

>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=98.14  E-value=2.2e-05  Score=56.39  Aligned_cols=186  Identities=12%  Similarity=-0.018  Sum_probs=125.3

Q ss_pred             cch-hccCCCcchHhHHHHHHHHhhCCCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccH
Q 045511            4 NGL-KSLKPTLSFKQLNQIHAQIIKIPQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAH   82 (209)
Q Consensus         4 ~~~-~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~   82 (209)
                      .++ +.|+.++|...+.++.+..  +.++.+|+.+-..+.+.|++++|...|++..+... -+..++..+-..+...|++
T Consensus        45 ~~y~~~g~~~~A~~~~~~al~l~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~  121 (259)
T d1xnfa_          45 VLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP-TYNYAHLNRGIALYYGGRD  121 (259)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHHHHTTCH
T ss_pred             HHHHHCCCHHHHHHHHHHhhccC--CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHh-hhhhhHHHHHHHHHHHhhH
Confidence            345 7888899999998888763  23558899999999999999999999999998542 2456788888889999999


Q ss_pred             HHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc--CCCcHhHHHHHHHHHHhCCC----hHHHHHHHh
Q 045511           83 QKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV--VFPDVVTWTTIISGLSKCGF----HKEAIDMFC  156 (209)
Q Consensus        83 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~--~~~~~~~~~~li~~~~~~g~----~~~a~~~~~  156 (209)
                      +.|.+.|+...+.. +.+......+..++.+.+..+.+..+....  ..++...++. +..+.....    .+.+...+.
T Consensus       122 ~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  199 (259)
T d1xnfa_         122 KLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNI-VEFYLGNISEQTLMERLKADAT  199 (259)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHHH-HHHHTTSSCHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhhhhhhH-HHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999998765 334444444445555666555555544443  2222223332 222222222    222222222


Q ss_pred             hC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHhc
Q 045511          157 GI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNL  194 (209)
Q Consensus       157 ~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~  194 (209)
                      .- ...|+. .++..+-..+...|++++|...|+...+..
T Consensus       200 ~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  239 (259)
T d1xnfa_         200 DNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN  239 (259)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            22 334443 466677888999999999999999887654

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.10  E-value=0.00018  Score=52.98  Aligned_cols=186  Identities=7%  Similarity=-0.036  Sum_probs=129.5

Q ss_pred             hccCCCcchHhHHHHHHHHhhCCCc------ccHHHHHHHHHcCCCccchHHHHHHhhhCC----CCCCHHHHHHHHHHH
Q 045511            7 KSLKPTLSFKQLNQIHAQIIKIPQP------HILNTLLKLLTQSSTPQNAIPLYNKMLNCP----SSYNHYTFTQALKAC   76 (209)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~~~~~p~~------~~~~~li~~~~~~g~~~~a~~l~~~m~~~g----~~p~~~t~~~ll~~~   76 (209)
                      ..++...+...+.+........+..      ..+..+-..+...|+++.+...++......    ......++......+
T Consensus       103 ~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (366)
T d1hz4a_         103 AQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCS  182 (366)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHH
Confidence            4455566666666665554333222      344555667778899999999988876532    223345566666677


Q ss_pred             hccccHHHHHHHHHHHHHhcc----Cc--cHhHHHHHHHHHHhCCChhhHHHHHHhcCC-------CcHhHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGH----LH--DIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-------PDVVTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~----~~--~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-------~~~~~~~~li~~~~  143 (209)
                      ...++...+...+........    .+  ....+..+...+...|++++|...+.....       .....+..+...+.
T Consensus       183 ~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~  262 (366)
T d1hz4a_         183 LARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQI  262 (366)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHH
Confidence            778888888877766554321    11  234567777788999999999999987732       12445667788999


Q ss_pred             hCCChHHHHHHHhhC-------CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          144 KCGFHKEAIDMFCGI-------DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       144 ~~g~~~~a~~~~~~m-------~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ..|++++|...+.+.       +..|+. .++..+-..+.+.|++++|.+.+....+
T Consensus       263 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         263 LLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999876       555554 4677778889999999999999987644

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=3.8e-05  Score=49.26  Aligned_cols=98  Identities=10%  Similarity=-0.036  Sum_probs=70.5

Q ss_pred             HHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh---hhHHHHHHhcCC--CcH---hHHHHHHHH
Q 045511           70 TQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI---FSAHQIFNSVVF--PDV---VTWTTIISG  141 (209)
Q Consensus        70 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~---~~a~~~~~~~~~--~~~---~~~~~li~~  141 (209)
                      ..+++.+...++++.|++.|+..++.+ +.++.++..+-.++.+.++.   ++|.+++++...  |+.   .+|..+-.+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            456777788888888888888888766 55677777788888776554   457888877643  222   356667788


Q ss_pred             HHhCCChHHHHHHHhhC-CCCCCHHhHH
Q 045511          142 LSKCGFHKEAIDMFCGI-DVKPNANTLV  168 (209)
Q Consensus       142 ~~~~g~~~~a~~~~~~m-~~~p~~~t~~  168 (209)
                      |.+.|++++|.+.|++. .+.|+..-..
T Consensus        82 y~~~g~~~~A~~~~~~aL~~~P~~~~A~  109 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQTEPQNNQAK  109 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHHhCcCCHHHH
Confidence            88888888888888887 6677655433

>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=98.07  E-value=2.9e-05  Score=51.97  Aligned_cols=88  Identities=13%  Similarity=0.029  Sum_probs=77.2

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~  117 (209)
                      -+.+.+.|++++|...|++..+.+ +-+...|..+-..+...|+++.|.+.|+..++.. +.+..+|..+..+|...|++
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            446779999999999999999865 3466888888899999999999999999998875 55678999999999999999


Q ss_pred             hhHHHHHHhc
Q 045511          118 FSAHQIFNSV  127 (209)
Q Consensus       118 ~~a~~~~~~~  127 (209)
                      ++|.+.+++.
T Consensus        95 ~eA~~~~~~a  104 (159)
T d1a17a_          95 RAALRDYETV  104 (159)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999887

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.06  E-value=0.00015  Score=53.52  Aligned_cols=60  Identities=8%  Similarity=-0.087  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-----CHHhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          133 VTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-----NANTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       133 ~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-----~~~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                      ..+......+...|++++|...+... ...|     ....+..+-..+...|++++|.+.++....
T Consensus       214 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  279 (366)
T d1hz4a_         214 NANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNE  279 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34566667788889999999998877 2222     224455677788899999999999987654

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.03  E-value=1.9e-05  Score=58.32  Aligned_cols=162  Identities=8%  Similarity=-0.040  Sum_probs=116.5

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhC----CCCC-CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC-----ccH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNC----PSSY-NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL-----HDI  101 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-----~~~  101 (209)
                      ..|...-..|...|++++|.+.|.+..+.    +-++ -..+|..+-..|.+.|++++|.+.++...+--..     ...
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            45777888888999999999999988652    2222 2367888999999999999999998876543211     124


Q ss_pred             hHHHHHHHHHHh-CCChhhHHHHHHhcC-------CC--cHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCC-------C
Q 045511          102 FIQNSLLHFYVT-VKDIFSAHQIFNSVV-------FP--DVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKP-------N  163 (209)
Q Consensus       102 ~~~~~ll~~~~~-~g~~~~a~~~~~~~~-------~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p-------~  163 (209)
                      .++..+...|-. .|++++|.+.+.+..       .+  ...+|..+...|...|++++|.+.|.+. ...|       +
T Consensus       118 ~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~  197 (290)
T d1qqea_         118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWS  197 (290)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGG
T ss_pred             HHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhh
Confidence            466677767754 699999999998762       11  2446888899999999999999999987 2111       2


Q ss_pred             HH-hHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          164 AN-TLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       164 ~~-t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      .. .+...+..+...|+++.|...++...+.
T Consensus       198 ~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         198 LKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            11 2233444556789999999888866444

>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=98.03  E-value=8.1e-05  Score=47.13  Aligned_cols=89  Identities=10%  Similarity=-0.003  Sum_probs=78.3

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCCh
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDI  117 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~  117 (209)
                      -..+.+.|++++|...|++..+.. +-+...|..+-.++.+.|++++|...+....+.. +.+...|..+-.++...|++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCH
Confidence            356778999999999999998764 3466789999999999999999999999999876 56788999999999999999


Q ss_pred             hhHHHHHHhcC
Q 045511          118 FSAHQIFNSVV  128 (209)
Q Consensus       118 ~~a~~~~~~~~  128 (209)
                      ++|.+.|+...
T Consensus        88 ~~A~~~~~~a~   98 (117)
T d1elwa_          88 EEAKRTYEEGL   98 (117)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999873

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.96  E-value=3.2e-05  Score=48.70  Aligned_cols=77  Identities=9%  Similarity=-0.137  Sum_probs=30.0

Q ss_pred             ccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDM  154 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~  154 (209)
                      +.|++++|...|+...+.. +-+..+|..+-.++.+.|++++|...|+...   ..+...|..+-..|...|++++|.+.
T Consensus        28 ~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~~~A~~~  106 (112)
T d1hxia_          28 KLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALAS  106 (112)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCCCHHHHHHH
Confidence            3344444444444443332 1123344444444444444444444443331   11233333444444444444444443


Q ss_pred             H
Q 045511          155 F  155 (209)
Q Consensus       155 ~  155 (209)
                      |
T Consensus       107 l  107 (112)
T d1hxia_         107 L  107 (112)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.85  E-value=3.9e-05  Score=48.28  Aligned_cols=88  Identities=7%  Similarity=-0.064  Sum_probs=76.8

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCC
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKD  116 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~  116 (209)
                      .-..+.+.|++++|...|++.....- -+...|..+-.++.+.|++++|...|+...+.. +.+..+|..+-..|...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccccc-ccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCC
Confidence            44567889999999999999988642 267889999999999999999999999998875 4568899999999999999


Q ss_pred             hhhHHHHHHh
Q 045511          117 IFSAHQIFNS  126 (209)
Q Consensus       117 ~~~a~~~~~~  126 (209)
                      .++|.+.+++
T Consensus       100 ~~~A~~~l~~  109 (112)
T d1hxia_         100 ANAALASLRA  109 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999886

>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=97.80  E-value=4e-05  Score=49.14  Aligned_cols=93  Identities=11%  Similarity=-0.007  Sum_probs=74.0

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhcc---ccHHHHHHHHHHHHHhccCcc-HhHHHHHHH
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLA---HAHQKGLEIHAHVIKYGHLHD-IFIQNSLLH  109 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~---~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~  109 (209)
                      ...+++.+...+++++|.+.|++....+. .+..++..+-.++.+.   ++.++|..+++...+....|+ ..+|..|-.
T Consensus         2 ~~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p-~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~   80 (122)
T d1nzna_           2 MEAVLNELVSVEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH
Confidence            35678888999999999999999988653 4667777777777664   455678999998887664444 347888889


Q ss_pred             HHHhCCChhhHHHHHHhc
Q 045511          110 FYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       110 ~~~~~g~~~~a~~~~~~~  127 (209)
                      +|.+.|++++|.+.|++.
T Consensus        81 ~y~~~g~~~~A~~~~~~a   98 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGL   98 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHH
Confidence            999999999999999988

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.75  E-value=0.0004  Score=47.40  Aligned_cols=114  Identities=7%  Similarity=0.024  Sum_probs=75.7

Q ss_pred             HHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChh
Q 045511           39 KLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIF  118 (209)
Q Consensus        39 ~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~  118 (209)
                      ......|++++|.+.|++-...-  ++..        +......+-+...-..+...    ....+..+...+.+.|+++
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~--rG~~--------l~~~~~~~w~~~~r~~l~~~----~~~a~~~la~~~~~~g~~~   84 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREW--RGPV--------LDDLRDFQFVEPFATALVED----KVLAHTAKAEAEIACGRAS   84 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTC--CSST--------TGGGTTSTTHHHHHHHHHHH----HHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC--cccc--------cccCcchHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCch
Confidence            45677888888888888876631  1110        00000000011111111111    2456788888999999999


Q ss_pred             hHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC--------CCCCCHHh
Q 045511          119 SAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI--------DVKPNANT  166 (209)
Q Consensus       119 ~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m--------~~~p~~~t  166 (209)
                      +|...++...   ..+...|..++.+|.+.|++++|++.|++.        |+.|+..|
T Consensus        85 ~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          85 AVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            9999998873   346788999999999999999999998886        88888765

>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=97.71  E-value=0.00021  Score=48.89  Aligned_cols=118  Identities=9%  Similarity=0.004  Sum_probs=82.0

Q ss_pred             HHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHH
Q 045511           74 KACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus        74 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  153 (209)
                      ......|++++|.+.|...++.-  ++..        +......+.+...-..+.......+..+...+...|++++|+.
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~--rG~~--------l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~   88 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREW--RGPV--------LDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIA   88 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTC--CSST--------TGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC--cccc--------cccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHH
Confidence            34567788888888887776531  1110        0001111112222222222345678889999999999999999


Q ss_pred             HHhhC-CCCC-CHHhHHHHHHHhccccchhHHHHHHHHHH-----HhccCCCchh
Q 045511          154 MFCGI-DVKP-NANTLVSVLSACSSLGSRKLGKAIHAHSL-----RNLNENNIIL  201 (209)
Q Consensus       154 ~~~~m-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~-----~~~~~p~~~~  201 (209)
                      .++.. .+.| +...|..++.++...|+.++|.+.|+...     +.|+.|...+
T Consensus        89 ~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          89 ELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            99999 6666 55789999999999999999999999763     3599998765

>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=97.68  E-value=9e-06  Score=61.13  Aligned_cols=165  Identities=9%  Similarity=-0.040  Sum_probs=116.5

Q ss_pred             CcccHHHHHHHHHcCCC--ccchHHHHHHhhhCCCCCCHHHHH-HHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHH
Q 045511           30 QPHILNTLLKLLTQSST--PQNAIPLYNKMLNCPSSYNHYTFT-QALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNS  106 (209)
Q Consensus        30 ~~~~~~~li~~~~~~g~--~~~a~~l~~~m~~~g~~p~~~t~~-~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  106 (209)
                      +...|..+-..+...++  .++|...+++..+... ++...+. ..-..+...+..+.|.+.++...+.. +-+...|+.
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~  183 (334)
T d1dcea1         106 SYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHY  183 (334)
T ss_dssp             CHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHH
T ss_pred             cHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHH
Confidence            44677777777776654  6789999999877542 3455544 44466777899999999999888775 456788888


Q ss_pred             HHHHHHhCCChhhHHHHHHhc---------------------------------CCCcHhHHHHHHHHHHhCCChHHHHH
Q 045511          107 LLHFYVTVKDIFSAHQIFNSV---------------------------------VFPDVVTWTTIISGLSKCGFHKEAID  153 (209)
Q Consensus       107 ll~~~~~~g~~~~a~~~~~~~---------------------------------~~~~~~~~~~li~~~~~~g~~~~a~~  153 (209)
                      +-..+.+.|++++|...+...                                 ..++...+..+...+...|+.++|..
T Consensus       184 l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~  263 (334)
T d1dcea1         184 RSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELESCK  263 (334)
T ss_dssp             HHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHH
Confidence            888888888876664433222                                 01122233344556666788888888


Q ss_pred             HHhhC-CCCCCH-HhHHHHHHHhccccchhHHHHHHHHHHHhccCCC
Q 045511          154 MFCGI-DVKPNA-NTLVSVLSACSSLGSRKLGKAIHAHSLRNLNENN  198 (209)
Q Consensus       154 ~~~~m-~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~  198 (209)
                      .+.+. ...|+. .++..+...+.+.|+.++|.+.++...+.  .|+
T Consensus       264 ~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~  308 (334)
T d1dcea1         264 ELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPM  308 (334)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGG
T ss_pred             HHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--Ccc
Confidence            88876 555543 57788888899999999999999988765  564

>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=97.62  E-value=0.00082  Score=45.21  Aligned_cols=71  Identities=11%  Similarity=-0.008  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhcC--C-CcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHH
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSVV--F-PDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLS  172 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~~--~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~  172 (209)
                      .+|+.+-.+|.+.|++++|...++...  . .+..+|..+-.+|...|++++|...|+.. .+.|+.......+.
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~l~  137 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLA  137 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            467788889999999999999998873  3 46788889999999999999999999998 77776544443333

>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=97.53  E-value=0.00039  Score=44.54  Aligned_cols=83  Identities=10%  Similarity=0.067  Sum_probs=45.1

Q ss_pred             HHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC--C---c-----HhHHHHHHHHHHh
Q 045511           75 ACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF--P---D-----VVTWTTIISGLSK  144 (209)
Q Consensus        75 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~--~---~-----~~~~~~li~~~~~  144 (209)
                      .+.+.|++++|.+.|...++.. +.+..++..+-.+|.+.|++++|.+.++...+  |   .     ..+|..+-..+..
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~~~   91 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFK   91 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHH
Confidence            3455556666666666555543 33455566666666666666666666655421  1   0     1244445555556


Q ss_pred             CCChHHHHHHHhhC
Q 045511          145 CGFHKEAIDMFCGI  158 (209)
Q Consensus       145 ~g~~~~a~~~~~~m  158 (209)
                      .+++++|++.|..-
T Consensus        92 ~~~~~~A~~~~~ka  105 (128)
T d1elra_          92 EEKYKDAIHFYNKS  105 (128)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHH
Confidence            66666666666543

>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=97.47  E-value=0.0018  Score=42.64  Aligned_cols=71  Identities=20%  Similarity=0.108  Sum_probs=53.4

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHH
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVL  171 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li  171 (209)
                      ..+|+.+-.+|.+.|++++|.+.+...   ...+..+|..+-.+|...|++++|+..|... .+.|+.......+
T Consensus        67 ~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~~~~l  141 (153)
T d2fbna1          67 ISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSY  141 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHHhhHHHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            346777888888888888888888876   2346778888888888888888888888887 6677655443333

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.31  E-value=0.00044  Score=50.26  Aligned_cols=115  Identities=10%  Similarity=0.051  Sum_probs=53.1

Q ss_pred             ccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CCc-HhHHHHHHHHHHhCCChHHHHHH
Q 045511           78 LAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FPD-VVTWTTIISGLSKCGFHKEAIDM  154 (209)
Q Consensus        78 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~g~~~~a~~~  154 (209)
                      +.|++++|...++..++.. +.|...+..+...|+..|++++|.+.++...  .|+ ...+..+-..+...+..+++..-
T Consensus         8 ~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~a~~~   86 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDFAQG   86 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHHHHH
Confidence            4455666666665555543 3445556666666666666666666655552  222 22333333333333333332222


Q ss_pred             HhhC---CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHh
Q 045511          155 FCGI---DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       155 ~~~m---~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ...-   +-.++..........+...|+.++|.+++..+.+.
T Consensus        87 ~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          87 AATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             CCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            1111   11112223333344455566666666666655444

>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=97.29  E-value=0.0019  Score=43.27  Aligned_cols=91  Identities=12%  Similarity=0.008  Sum_probs=69.8

Q ss_pred             HHHHHHHcCCCccchHHHHHHhhhCC-----CCC---------CHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccH
Q 045511           36 TLLKLLTQSSTPQNAIPLYNKMLNCP-----SSY---------NHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI  101 (209)
Q Consensus        36 ~li~~~~~~g~~~~a~~l~~~m~~~g-----~~p---------~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~  101 (209)
                      ..=..+.+.|++++|...|++.....     ...         -..+|+.+-.+|.+.|+++.|.+.++..++.. +.++
T Consensus        18 ~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~   96 (170)
T d1p5qa1          18 ERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNE   96 (170)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccch
Confidence            33456777788888888887765421     110         12456667777889999999999999998875 4578


Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .+|..+-.+|...|++++|...|+..
T Consensus        97 ~a~~~~g~~~~~~g~~~~A~~~~~~a  122 (170)
T d1p5qa1          97 KGLSRRGEAHLAVNDFELARADFQKV  122 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhhhHHHHHHHHHHH
Confidence            89999999999999999999999987

>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=97.25  E-value=0.005  Score=41.01  Aligned_cols=91  Identities=10%  Similarity=0.045  Sum_probs=66.1

Q ss_pred             HhHHHHHHHHHHhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHHhHHHHHHHh-c
Q 045511          101 IFIQNSLLHFYVTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNANTLVSVLSAC-S  175 (209)
Q Consensus       101 ~~~~~~ll~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~t~~~li~~~-~  175 (209)
                      ..+|+.+-.+|.+.|++++|...++..   ...+..+|..+-.+|...|++++|...|.+. .+.|+.......+..+ .
T Consensus        64 ~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~  143 (168)
T d1kt1a1          64 LAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQK  143 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHH
T ss_pred             HHHHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            346777888899999999999999887   3456788888899999999999999999998 7777766554444444 2


Q ss_pred             cccch-hHHHHHHHHHH
Q 045511          176 SLGSR-KLGKAIHAHSL  191 (209)
Q Consensus       176 ~~g~~-~~a~~~~~~~~  191 (209)
                      ..+.. +...+++..|-
T Consensus       144 ~~~~~~e~~kk~~~~~f  160 (168)
T d1kt1a1         144 KAKEHNERDRRTYANMF  160 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHH
Confidence            33333 33445555443

>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=97.25  E-value=0.00057  Score=43.72  Aligned_cols=90  Identities=12%  Similarity=-0.002  Sum_probs=72.6

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCC--------HHhHHHHH
Q 045511          104 QNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPN--------ANTLVSVL  171 (209)
Q Consensus       104 ~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~--------~~t~~~li  171 (209)
                      +-.+=..|.+.|++++|.+.|.+..   ..+...|..+-.+|.+.|++++|...+.+. .+.|+        ..+|..+-
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            4455677899999999999998873   346889999999999999999999999997 33332        24677777


Q ss_pred             HHhccccchhHHHHHHHHHHHh
Q 045511          172 SACSSLGSRKLGKAIHAHSLRN  193 (209)
Q Consensus       172 ~~~~~~g~~~~a~~~~~~~~~~  193 (209)
                      ..+...+++++|.+.+......
T Consensus        87 ~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHhc
Confidence            7888889999999999876654

>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=97.23  E-value=0.0036  Score=41.09  Aligned_cols=90  Identities=10%  Similarity=-0.030  Sum_probs=71.3

Q ss_pred             HHHHHHcCCCccchHHHHHHhhhCC----CCCC-----------HHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccH
Q 045511           37 LLKLLTQSSTPQNAIPLYNKMLNCP----SSYN-----------HYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDI  101 (209)
Q Consensus        37 li~~~~~~g~~~~a~~l~~~m~~~g----~~p~-----------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~  101 (209)
                      --..+.+.|++.+|...|.+..+.-    ..++           ..+|..+-.+|.+.|++++|.+.++..++.. +.+.
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            3356677888888888888766421    1111           2456677888899999999999999998875 5678


Q ss_pred             hHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511          102 FIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus       102 ~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .+|-.+-.+|...|++++|...|...
T Consensus       102 ka~~~~g~~~~~lg~~~~A~~~~~~a  127 (153)
T d2fbna1         102 KALYKLGVANMYFGFLEEAKENLYKA  127 (153)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             hhhHHhHHHHHHcCCHHHHHHHHHHH
Confidence            89999999999999999999999887

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.22  E-value=0.001  Score=43.58  Aligned_cols=112  Identities=12%  Similarity=0.001  Sum_probs=67.0

Q ss_pred             hccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC----------CChhhHHHHHHhcC---CCcHhHHHHHHHHHH
Q 045511           77 SLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV----------KDIFSAHQIFNSVV---FPDVVTWTTIISGLS  143 (209)
Q Consensus        77 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~----------g~~~~a~~~~~~~~---~~~~~~~~~li~~~~  143 (209)
                      -+.+.+++|.+.|+...+.. +.++.++..+-.+|...          +.+++|.+.|++..   ..+..+|..+-.+|.
T Consensus         8 ~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~   86 (145)
T d1zu2a1           8 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYT   86 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHH
Confidence            34455666666666666554 34445555555554432          33455666665552   234556655555554


Q ss_pred             hCC-----------ChHHHHHHHhhC-CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhcc
Q 045511          144 KCG-----------FHKEAIDMFCGI-DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLN  195 (209)
Q Consensus       144 ~~g-----------~~~~a~~~~~~m-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~  195 (209)
                      ..|           ++++|.+.|+.. .+.|+..+|..-+..+      .++.+++.+..+.|+
T Consensus        87 ~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1          87 SFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH------HTHHHHHHHHHHSSS
T ss_pred             HcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence            433           357788888888 8899888776655544      466777777777664

>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=97.21  E-value=0.0032  Score=41.98  Aligned_cols=66  Identities=8%  Similarity=-0.019  Sum_probs=51.9

Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCHH
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNAN  165 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~~  165 (209)
                      ....|+.+-.+|.+.|++++|...++...   ..+...|..+-.+|.+.|++++|++.|... .+.|+..
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~  145 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDK  145 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCH
Confidence            34567777888888999999998888873   245778888888889999999999888888 6666543

>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=97.18  E-value=0.0036  Score=46.33  Aligned_cols=136  Identities=7%  Similarity=0.009  Sum_probs=69.4

Q ss_pred             CCccchHHHHHHhhhCCCCCCHHH-HH---HHHHHH-------hccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHh
Q 045511           45 STPQNAIPLYNKMLNCPSSYNHYT-FT---QALKAC-------SLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVT  113 (209)
Q Consensus        45 g~~~~a~~l~~~m~~~g~~p~~~t-~~---~ll~~~-------~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  113 (209)
                      +..++|.+++++..+.  .|+..+ |+   .++...       ...|+++++...++...+.. +.+...|..+..++..
T Consensus        43 ~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~  119 (334)
T d1dcea1          43 ELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSR  119 (334)
T ss_dssp             CCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHH
Confidence            3345677777666653  355433 21   112222       22344566666666666543 3344555555555544


Q ss_pred             CC--ChhhHHHHHHhcC---CCcHhHHHHHH-HHHHhCCChHHHHHHHhhC-CCCCC-HHhHHHHHHHhccccchhHH
Q 045511          114 VK--DIFSAHQIFNSVV---FPDVVTWTTII-SGLSKCGFHKEAIDMFCGI-DVKPN-ANTLVSVLSACSSLGSRKLG  183 (209)
Q Consensus       114 ~g--~~~~a~~~~~~~~---~~~~~~~~~li-~~~~~~g~~~~a~~~~~~m-~~~p~-~~t~~~li~~~~~~g~~~~a  183 (209)
                      .+  +.++|...+....   .++...+...+ ..+-..+.+++|+..++.. ...|+ ...|..+-..+.+.|++++|
T Consensus       120 ~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A  197 (334)
T d1dcea1         120 LPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDS  197 (334)
T ss_dssp             CSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCS
T ss_pred             hccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHH
Confidence            44  3566666666652   23344443332 4555566677777776666 44553 34455555555555554433

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.04  E-value=0.0008  Score=48.82  Aligned_cols=116  Identities=9%  Similarity=-0.065  Sum_probs=75.0

Q ss_pred             HHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhH
Q 045511           41 LTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSA  120 (209)
Q Consensus        41 ~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a  120 (209)
                      ..+.|++++|...+++..+.. +-|...+..+...++..|++++|...++...+.. +-+...+..+-..+...+..+++
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 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLF-PEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHhccccHHH
Confidence            346788889998888888764 3466888888888899999999988888887754 22234444444444333333333


Q ss_pred             HHHHHhc---CCC-cHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          121 HQIFNSV---VFP-DVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       121 ~~~~~~~---~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ..-...-   ..| +...+......+...|+.++|.+.+.+.
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a  125 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQI  125 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            2221111   122 2344445566777889999999888877

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.82  E-value=0.0056  Score=40.69  Aligned_cols=108  Identities=11%  Similarity=-0.002  Sum_probs=78.6

Q ss_pred             HHHHHHHHHcCCCccchHHHHHHhhhC--------------CCC-CCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccC
Q 045511           34 LNTLLKLLTQSSTPQNAIPLYNKMLNC--------------PSS-YNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHL   98 (209)
Q Consensus        34 ~~~li~~~~~~g~~~~a~~l~~~m~~~--------------g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~   98 (209)
                      +...-..+.+.|++++|...|++..+.              -+. .+...|..+-.++.+.|++++|...++..++.. +
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            344556677889999998888776431              011 233456667778889999999999999998865 4


Q ss_pred             ccHhHHHHHHHHHHhCCChhhHHHHHHhcC--CC-cHhHHHHHHHHH
Q 045511           99 HDIFIQNSLLHFYVTVKDIFSAHQIFNSVV--FP-DVVTWTTIISGL  142 (209)
Q Consensus        99 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~  142 (209)
                      .++..|..+-.+|.+.|++++|.+.|....  .| +......+-...
T Consensus       109 ~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~~~~l~~~~  155 (169)
T d1ihga1         109 SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVK  155 (169)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            567899999999999999999999998873  23 444454444433

>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=96.68  E-value=0.022  Score=37.09  Aligned_cols=83  Identities=13%  Similarity=0.083  Sum_probs=46.4

Q ss_pred             HhccccHHHHHHHHHHHHHhcc-Cc----------cHhHHHHHHHHHHhCCChhhHHHHHHhcC-------C--C-----
Q 045511           76 CSLAHAHQKGLEIHAHVIKYGH-LH----------DIFIQNSLLHFYVTVKDIFSAHQIFNSVV-------F--P-----  130 (209)
Q Consensus        76 ~~~~~~~~~a~~~~~~m~~~g~-~~----------~~~~~~~ll~~~~~~g~~~~a~~~~~~~~-------~--~-----  130 (209)
                      +.+.|++++|.+.|++.++... .|          ...+|+.+-.+|.+.|++++|.+.+++..       .  +     
T Consensus        19 ~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~   98 (156)
T d2hr2a1          19 QLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKL   98 (156)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccch
Confidence            3444666666666665554321 01          13456666666777777766666665541       1  1     


Q ss_pred             cHhHHHHHHHHHHhCCChHHHHHHHhhC
Q 045511          131 DVVTWTTIISGLSKCGFHKEAIDMFCGI  158 (209)
Q Consensus       131 ~~~~~~~li~~~~~~g~~~~a~~~~~~m  158 (209)
                      ....++.+-.+|...|++++|+..|++.
T Consensus        99 ~~~a~~~~g~~~~~lg~~eeA~~~~~~A  126 (156)
T d2hr2a1          99 WISAVYSRALALDGLGRGAEAMPEFKKV  126 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            1224555666677777777777666664

>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=96.56  E-value=0.022  Score=37.11  Aligned_cols=91  Identities=12%  Similarity=0.035  Sum_probs=68.3

Q ss_pred             hHHHHH--HHHHHhCCChhhHHHHHHhcCC-----C----------cHhHHHHHHHHHHhCCChHHHHHHHhhC------
Q 045511          102 FIQNSL--LHFYVTVKDIFSAHQIFNSVVF-----P----------DVVTWTTIISGLSKCGFHKEAIDMFCGI------  158 (209)
Q Consensus       102 ~~~~~l--l~~~~~~g~~~~a~~~~~~~~~-----~----------~~~~~~~li~~~~~~g~~~~a~~~~~~m------  158 (209)
                      .+|..+  -..+...|++++|.+.|++..+     |          ....|+.+-.+|...|++++|..-+.+.      
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            456655  4456678999999999987621     1          1467889999999999999999888776      


Q ss_pred             --CCCCCH-----HhHHHHHHHhccccchhHHHHHHHHHHH
Q 045511          159 --DVKPNA-----NTLVSVLSACSSLGSRKLGKAIHAHSLR  192 (209)
Q Consensus       159 --~~~p~~-----~t~~~li~~~~~~g~~~~a~~~~~~~~~  192 (209)
                        ...++.     ..+..+-.++...|++++|.+.|+...+
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              222222     2466677889999999999999997644

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=96.42  E-value=0.014  Score=38.73  Aligned_cols=59  Identities=12%  Similarity=-0.026  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           68 TFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        68 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .|..+-.++.+.|++++|.+.++..++.. +.+..+|..+-.+|...|++++|.+.|...
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~a  124 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKV  124 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            35556666777788888888877777654 456677777777888888888888888776

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.31  E-value=0.0032  Score=49.65  Aligned_cols=107  Identities=7%  Similarity=-0.157  Sum_probs=52.9

Q ss_pred             cHhHHHHHHHHHHhCCChhhHHHHHHhcCCCc-HhHHHHHHHHHHhCCChHHHHHHHhhC-CCCCCH-HhHHHHHHHhcc
Q 045511          100 DIFIQNSLLHFYVTVKDIFSAHQIFNSVVFPD-VVTWTTIISGLSKCGFHKEAIDMFCGI-DVKPNA-NTLVSVLSACSS  176 (209)
Q Consensus       100 ~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m-~~~p~~-~t~~~li~~~~~  176 (209)
                      +...+..+-..+.+.|+.++|...+.....++ ..++..+-..+...|++++|...|.+. .+.|+. .+|+.+-..+..
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~  198 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASS  198 (497)
T ss_dssp             ------------------------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHH
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHH
Confidence            34456666666677777777766665543322 234555666777777888888777777 666655 577777777777


Q ss_pred             ccchhHHHHHHHHHHHhccCCCchhHhHhhh
Q 045511          177 LGSRKLGKAIHAHSLRNLNENNIILDNAVLD  207 (209)
Q Consensus       177 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~li~  207 (209)
                      .|+..+|...|.+..... .|.+..+..|.+
T Consensus       199 ~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~  228 (497)
T d1ya0a1         199 KGDHLTTIFYYCRSIAVK-FPFPAASTNLQK  228 (497)
T ss_dssp             TTCHHHHHHHHHHHHSSS-BCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhCC-CCCHHHHHHHHH
Confidence            777777777776665543 344445555543

>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=96.14  E-value=0.16  Score=37.66  Aligned_cols=142  Identities=11%  Similarity=0.002  Sum_probs=84.9

Q ss_pred             cHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHH
Q 045511           33 ILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYV  112 (209)
Q Consensus        33 ~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  112 (209)
                      -|.-++..+.+.++++.|.+.+++.      -+..+|..+..+|.+......+     .+...+...++.....++..|-
T Consensus        42 d~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye  110 (336)
T d1b89a_          42 NFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQ  110 (336)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHH
Confidence            3444555555555555555554433      1334555566665555444321     2222223345555567888888


Q ss_pred             hCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhCCChHHHHHHHhhCCCCCCHHhHHHHHHHhccccchhHHHHHHHH
Q 045511          113 TVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKCGFHKEAIDMFCGIDVKPNANTLVSVLSACSSLGSRKLGKAIHAH  189 (209)
Q Consensus       113 ~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~  189 (209)
                      ..|.+++...+++..   ...+...++-++..|++.+ .++..+.++...   +..-..-+++.|.+.+-+.++.-++..
T Consensus       111 ~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~-~~kl~e~l~~~s---~~y~~~k~~~~c~~~~l~~elv~Ly~~  186 (336)
T d1b89a_         111 DRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK-PQKMREHLELFW---SRVNIPKVLRAAEQAHLWAELVFLYDK  186 (336)
T ss_dssp             HTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTC-HHHHHHHHHHHS---TTSCHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhC-hHHHHHHHHhcc---ccCCHHHHHHHHHHcCChHHHHHHHHh
Confidence            888888888888865   3456777888888888765 455555555531   223344567888888888887777764

>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=95.63  E-value=0.27  Score=36.35  Aligned_cols=156  Identities=6%  Similarity=-0.021  Sum_probs=96.0

Q ss_pred             CCcccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHH
Q 045511           29 PQPHILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLL  108 (209)
Q Consensus        29 p~~~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  108 (209)
                      -+..+|..+...|.+......+     .+...+...+......++..|-..|.+++...+++..... -.++...++.++
T Consensus        67 ~~~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~  140 (336)
T d1b89a_          67 NSTRTWKEVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELA  140 (336)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHH
Confidence            4456777777777666544322     2223334456677788999999999999988888876533 256777889999


Q ss_pred             HHHHhCCChhhHHHHHHhcCCCcHhHHHHHHHHHHhCCChHHHHHHHhhC-----------CCCCCHHhHHHHHHHhccc
Q 045511          109 HFYVTVKDIFSAHQIFNSVVFPDVVTWTTIISGLSKCGFHKEAIDMFCGI-----------DVKPNANTLVSVLSACSSL  177 (209)
Q Consensus       109 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m-----------~~~p~~~t~~~li~~~~~~  177 (209)
                      ..|++.+. +...+.+....  +.....-++..|-+.+.|.++.-++..+           ...|+..-...++..+.+.
T Consensus       141 ~lyak~~~-~kl~e~l~~~s--~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~  217 (336)
T d1b89a_         141 ILYSKFKP-QKMREHLELFW--SRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKV  217 (336)
T ss_dssp             HHHHTTCH-HHHHHHHHHHS--TTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHC
T ss_pred             HHHHHhCh-HHHHHHHHhcc--ccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHcc
Confidence            99998754 34444443321  1222233344444455555555555444           1234444455567778888


Q ss_pred             cchhHHHHHHHHHHHh
Q 045511          178 GSRKLGKAIHAHSLRN  193 (209)
Q Consensus       178 g~~~~a~~~~~~~~~~  193 (209)
                      ++.+...++.....+.
T Consensus       218 ~N~e~~~~~i~~yL~~  233 (336)
T d1b89a_         218 ANVELYYRAIQFYLEF  233 (336)
T ss_dssp             SSTHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHc
Confidence            8888877777766654

>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=95.27  E-value=0.034  Score=32.95  Aligned_cols=56  Identities=9%  Similarity=-0.098  Sum_probs=29.7

Q ss_pred             HHHHHhccccHHHHHHHHHHHHHhcc-----Ccc-HhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           72 ALKACSLAHAHQKGLEIHAHVIKYGH-----LHD-IFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        72 ll~~~~~~~~~~~a~~~~~~m~~~g~-----~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      +=..+.+.|+++.|..+|++..+...     .++ ..+++.|-.+|.+.|++++|.+.+++.
T Consensus        11 lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~a   72 (95)
T d1tjca_          11 LGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKL   72 (95)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHH
Confidence            33445566666666666665544321     111 235555555666666666666665554

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.18  E-value=0.1  Score=31.08  Aligned_cols=60  Identities=13%  Similarity=0.051  Sum_probs=48.5

Q ss_pred             chHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHH
Q 045511           49 NAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLH  109 (209)
Q Consensus        49 ~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  109 (209)
                      ++.+-++.+....+.|+.....+.+++|.+.+++..|..+|+.++.+. .++..+|..++.
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yilq   83 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHHH
Confidence            456667778888899999999999999999999999999999888553 334667776664

>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=94.82  E-value=0.17  Score=29.60  Aligned_cols=58  Identities=10%  Similarity=-0.016  Sum_probs=27.4

Q ss_pred             HHHHHcCCCccchHHHHHHhhhCC-----CCCC-HHHHHHHHHHHhccccHHHHHHHHHHHHHh
Q 045511           38 LKLLTQSSTPQNAIPLYNKMLNCP-----SSYN-HYTFTQALKACSLAHAHQKGLEIHAHVIKY   95 (209)
Q Consensus        38 i~~~~~~g~~~~a~~l~~~m~~~g-----~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~   95 (209)
                      =..+.+.|+++.|...|++..+..     ..++ ..+|..+-.++.+.|++++|.+.+++.++.
T Consensus        12 G~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_          12 GKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            334445555555555555443311     1111 234555555555555555555555555544

>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=94.56  E-value=0.046  Score=42.79  Aligned_cols=110  Identities=10%  Similarity=-0.010  Sum_probs=59.3

Q ss_pred             ccHHHHHHHHHcCCCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHH
Q 045511           32 HILNTLLKLLTQSSTPQNAIPLYNKMLNCPSSYNHYTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFY  111 (209)
Q Consensus        32 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  111 (209)
                      ..+..+-..+.+.|+.+.|...++...+..   ...++..+-..+...+++++|.+.|....+.. +-+..+|+.|-..+
T Consensus       121 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~  196 (497)
T d1ya0a1         121 VKSSQLGIISNKQTHTSAIVKPQSSSCSYI---CQHCLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAILA  196 (497)
T ss_dssp             ----------------------CCHHHHHH---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHHHH
T ss_pred             HHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHHHH
Confidence            445555555555666666655544433211   12456666667777788888888888777654 34456888888888


Q ss_pred             HhCCChhhHHHHHHhc---CCCcHhHHHHHHHHHHhC
Q 045511          112 VTVKDIFSAHQIFNSV---VFPDVVTWTTIISGLSKC  145 (209)
Q Consensus       112 ~~~g~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~  145 (209)
                      ...|+..+|...|.+.   ..|-..+++.|...+.+.
T Consensus       197 ~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~  233 (497)
T d1ya0a1         197 SSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKA  233 (497)
T ss_dssp             HHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence            8888888888888765   345666777777766543

>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=94.48  E-value=0.29  Score=30.72  Aligned_cols=66  Identities=12%  Similarity=0.073  Sum_probs=57.3

Q ss_pred             cHhHHHHHHHHHHhCCChHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhccC
Q 045511          131 DVVTWTTIISGLSKCGFHKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLNE  196 (209)
Q Consensus       131 ~~~~~~~li~~~~~~g~~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  196 (209)
                      +..-++.-++.+..+|.-++-.++++++  .-+|++...-.+-.+|.+.|+..++.+++.+.-++|++
T Consensus        85 ~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          85 LNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            3445677788999999999999999996  77889999999999999999999999999999998865

>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=93.97  E-value=0.079  Score=33.97  Aligned_cols=96  Identities=8%  Similarity=-0.066  Sum_probs=53.2

Q ss_pred             CCccchHHHHHHhhhCCCCCCHHHHHHHHHHHhc----------cccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhC
Q 045511           45 STPQNAIPLYNKMLNCPSSYNHYTFTQALKACSL----------AHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTV  114 (209)
Q Consensus        45 g~~~~a~~l~~~m~~~g~~p~~~t~~~ll~~~~~----------~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  114 (209)
                      +.+++|...|+...+.. +-+...+..+=.++..          .+.+++|...|+...+.. +.+..+|..+-..|...
T Consensus        11 ~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~y~~~   88 (145)
T d1zu2a1          11 LLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYTSF   88 (145)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHHHHHc
Confidence            34555666666655533 1233344444333332          244567777777777654 44566777777777665


Q ss_pred             CC-----------hhhHHHHHHhc--CCCcHhHHHHHHHHH
Q 045511          115 KD-----------IFSAHQIFNSV--VFPDVVTWTTIISGL  142 (209)
Q Consensus       115 g~-----------~~~a~~~~~~~--~~~~~~~~~~li~~~  142 (209)
                      |+           +++|.+.|+..  ..|+...|..-+..+
T Consensus        89 g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~  129 (145)
T d1zu2a1          89 AFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT  129 (145)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             ccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH
Confidence            43           46677777665  346655555444433

>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=93.53  E-value=0.17  Score=31.85  Aligned_cols=59  Identities=17%  Similarity=0.074  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHh
Q 045511           67 YTFTQALKACSLAHAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNS  126 (209)
Q Consensus        67 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~  126 (209)
                      ..++..+....++|+-+.-.+++..+.+.+ +|++...-.+-.+|.+.|...++-+++.+
T Consensus        87 e~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~  145 (161)
T d1wy6a1          87 EHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIE  145 (161)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHH
Confidence            334444444445555444444544444433 44444444444455555555554444443

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=89.56  E-value=1.4  Score=27.08  Aligned_cols=17  Identities=12%  Similarity=0.061  Sum_probs=8.3

Q ss_pred             ccHHHHHHHHHHHHHhc
Q 045511           80 HAHQKGLEIHAHVIKYG   96 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g   96 (209)
                      .+.+++.++++...+.|
T Consensus        37 ~~~~~a~~~~~~aa~~g   53 (133)
T d1klxa_          37 INKQKLFQYLSKACELN   53 (133)
T ss_dssp             SCHHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHHhhhhccc
Confidence            34455555555544444

>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=89.40  E-value=0.46  Score=29.52  Aligned_cols=48  Identities=10%  Similarity=0.036  Sum_probs=23.7

Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhc
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSV  127 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~  127 (209)
                      .+.+.+..+++...+.+...-...+-.|--+|.+.|++++|.+.++..
T Consensus        52 ~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~   99 (124)
T d2pqrb1          52 NDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTL   99 (124)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            445556666665554331111223334444555666666666666554

>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=89.27  E-value=1.3  Score=26.20  Aligned_cols=71  Identities=14%  Similarity=0.094  Sum_probs=53.3

Q ss_pred             HHHHHHHhccc-cHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcC---CCcHhHHHHHHH
Q 045511           70 TQALKACSLAH-AHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVV---FPDVVTWTTIIS  140 (209)
Q Consensus        70 ~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~  140 (209)
                      ......+-+.. +.-++.+-++.+....+.|++.+..+.+++|-|.+++.-|.++|+.+.   ..+...|.-++.
T Consensus         9 aRy~~~F~~~~iD~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yilq   83 (105)
T d1v54e_           9 ARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             HHHHHHhcCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            34455555554 566677778888877899999999999999999999999999998873   234455665554

>d1khda1 a.46.2.1 (A:12-80) Anthranilate phosphoribosyltransferase (TrpD) {Pectobacterium carotovorum [TaxId: 554]}

class: All alpha proteins
fold: Methionine synthase domain-like
superfamily: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
family: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
domain: Anthranilate phosphoribosyltransferase (TrpD)
species: Pectobacterium carotovorum [TaxId: 554]

Probab=85.90  E-value=1.5  Score=23.79  Aligned_cols=62  Identities=15%  Similarity=0.101  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhCCC--hHHHHHHHhhC--CCCCCHHhHHHHHHHhccccchhHHHHHHHHHHHhcc
Q 045511          134 TWTTIISGLSKCGF--HKEAIDMFCGI--DVKPNANTLVSVLSACSSLGSRKLGKAIHAHSLRNLN  195 (209)
Q Consensus       134 ~~~~li~~~~~~g~--~~~a~~~~~~m--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~~~~~~~  195 (209)
                      ||..+|+.+...++  .+++..+++.+  |--+|...-.-|+....+.-..++...+.+-|++++.
T Consensus         1 t~~~il~kl~~g~~Ls~ee~~~~~~~i~~g~~~d~qiaafL~al~~kg~t~dEi~g~~~am~~~~~   66 (69)
T d1khda1           1 THQPILEKLFKSQSMTQEESHQLFAAIVRGELEDSQLAAALISMKMRGERPEEIAGAASALLADAQ   66 (69)
T ss_dssp             CCHHHHHHHHTTCCCCHHHHHHHHHHHTTTCSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTSC
T ss_pred             CHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCC
Confidence            46778888877665  56788888888  5555555544455555566677888888888887763

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=81.66  E-value=3.9  Score=24.85  Aligned_cols=110  Identities=7%  Similarity=-0.036  Sum_probs=66.0

Q ss_pred             ccHHHHHHHHHHHHHhccCccHhHHHHHHHHHHhCCChhhHHHHHHhcCC-CcHhHHHHHHHHHHh----CCChHHHHHH
Q 045511           80 HAHQKGLEIHAHVIKYGHLHDIFIQNSLLHFYVTVKDIFSAHQIFNSVVF-PDVVTWTTIISGLSK----CGFHKEAIDM  154 (209)
Q Consensus        80 ~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~~-~~~~~~~~li~~~~~----~g~~~~a~~~  154 (209)
                      .++++|.++|+.-.+.|   ++..+..|.  .....+.++|.+++.+..+ -+......|-..|..    ..+.++|.+.
T Consensus         7 kd~~~A~~~~~kaa~~g---~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~   81 (133)
T d1klxa_           7 KDLKKAIQYYVKACELN---EMFGCLSLV--SNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQY   81 (133)
T ss_dssp             HHHHHHHHHHHHHHHTT---CTTHHHHHH--TCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHCC---Chhhhhhhc--cccccCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHH
Confidence            36677888888777776   223333332  2345678888888887633 344444444444433    5678899999


Q ss_pred             HhhC-CCCCCHHhHHHHHHHhcc----ccchhHHHHHHHHHHHhcc
Q 045511          155 FCGI-DVKPNANTLVSVLSACSS----LGSRKLGKAIHAHSLRNLN  195 (209)
Q Consensus       155 ~~~m-~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~~~~~~~  195 (209)
                      |++- ... +...+..|-..|..    ..|.++|.+.+....+.|.
T Consensus        82 ~~~aa~~g-~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          82 YSKACGLN-DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHTT-CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HhhhhccC-cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            9887 111 22223333333332    4578899999988887774