Citrus Sinensis ID: 042039

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370------
Protein Sequence
MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDLL
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHccc
Coil and Loop (DISEMBL)
mangngeigvvckpntvtYNTIIDGLCKEGFVDKAKALFLQMkgeninpdvvtyNSLIHGLCHANDWNEAKRLFFEMmdqgvqpsvVTFNVIMDELCKNGKMDEASRLLDLMVQrdvrpnaftystlmdgfcltgKINRAEELFgsmesmgckhddvsyNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQrddvaadtstynTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLcndgqmdkAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKekkvmpdasIVSMVVDLL
Flexible Loop (DISEMBL)
mangngeigvvckpntvTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAftystlmdgfCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELfrslprrvlVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKmkekkvmpdasiVSMVVDLL
Low Complexity Region (SEG)
MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDLL
Disordered region (IsUnstruct)
******EIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKM*******************
Disordered Region (DISOPRED)
M****G*IGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDLL
Disordered Region (DISEMBL)
MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDLL
Disordered Region (DISPRO)
MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDLL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDLL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	376	2.2.26 [Sep-21-2011]
Q9CAN5	614	Pentatricopeptide repeat-	yes	no	0.965	0.591	0.398	2e-78
Q9SXD1	630	Pentatricopeptide repeat-	no	no	0.957	0.571	0.406	3e-78
Q9LQ14	629	Pentatricopeptide repeat-	no	no	0.957	0.572	0.403	3e-77
Q9CAN0	630	Pentatricopeptide repeat-	no	no	0.765	0.457	0.392	3e-76
Q9SXD8	634	Pentatricopeptide repeat-	no	no	0.875	0.518	0.390	1e-75
Q9LQ16	632	Pentatricopeptide repeat-	no	no	0.906	0.539	0.390	9e-75
Q9LPX2	644	Pentatricopeptide repeat-	no	no	0.949	0.554	0.395	2e-74
P0C7Q7	602	Putative pentatricopeptid	no	no	0.875	0.546	0.387	3e-74
Q6NQ83	619	Pentatricopeptide repeat-	no	no	0.946	0.575	0.390	3e-74
Q9C8T7	559	Pentatricopeptide repeat-	no	no	0.875	0.588	0.384	4e-74

>sp|Q9CAN5|PPR98_ARATH Pentatricopeptide repeat-containing protein At1g63080, mitochondrial OS=Arabidopsis thaliana GN=At1g63080 PE=2 SV=1

 Score =  292 bits (748), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 145/364 (39%), Positives = 225/364 (61%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           + + V Y+T+ID LCK   VD A  LF +M  + I PDV TY+SLI  LC+   W++A R
Sbjct: 237 EADVVIYSTVIDSLCKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDASR 296

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P+VVTFN ++D   K GK+ EA +L D M+QR + PN  TY++L++GFC
Sbjct: 297 LLSDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTYNSLINGFC 356

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  +++ A+++F  M S  C  D V+YN LING+CK K+V + + L+R+M  +G+    V
Sbjct: 357 MHDRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSRRGLVGNTV 416

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TY TL  G F+    ++A  +F++M  D V  +  TYNT +DGLCKNG + +A+ +F  L
Sbjct: 417 TYTTLIHGFFQASDCDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVFEYL 476

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              K E DI  YN + +G+CK+G++E   +LF SL  + +  DV+ YN MI G C  G  
Sbjct: 477 QKSKMEPDIYTYNIMSEGMCKAGKVEDGWDLFCSLSLKGVKPDVIAYNTMISGFCKKGLK 536

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
           ++A+ LF+ M+E+   P+   + TLI   +R    +   EL+ +M+  +   DAS   +V
Sbjct: 537 EEAYTLFIKMKEDGPLPDSGTYNTLIRAHLRDGDKAASAELIKEMRSCRFAGDASTYGLV 596

Query: 373 VDLL 376
            D+L
Sbjct: 597 TDML 600

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SXD1|PPR91_ARATH Pentatricopeptide repeat-containing protein At1g62670, mitochondrial OS=Arabidopsis thaliana GN=At1g62670 PE=2 SV=2

 Score =  292 bits (748), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 148/364 (40%), Positives = 224/364 (61%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           +P  + YNTIIDGLCK   +D A  LF +M+ + I P+VVTY+SLI  LC+   W++A R
Sbjct: 253 EPGVLIYNTIIDGLCKYKHMDDALNLFKEMETKGIRPNVVTYSSLISCLCNYGRWSDASR 312

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P V TF+ ++D   K GK+ EA +L D MV+R + P+  TYS+L++GFC
Sbjct: 313 LLSDMIERKINPDVFTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTYSSLINGFC 372

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  +++ A+++F  M S  C  D V+YN LI G+CK K VEE + ++REM  +G+    V
Sbjct: 373 MHDRLDEAKQMFEFMVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTV 432

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TYN L  GLF+    + A ++F+EM  D V  +  TYNT +DGLCKNG + +A+ +F  L
Sbjct: 433 TYNILIQGLFQAGDCDMAQEIFKEMVSDGVPPNIMTYNTLLDGLCKNGKLEKAMVVFEYL 492

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              K E  I  YN +I+G+CK+G++E   +LF +L  + +  DVV YN MI G C  G  
Sbjct: 493 QRSKMEPTIYTYNIMIEGMCKAGKVEDGWDLFCNLSLKGVKPDVVAYNTMISGFCRKGSK 552

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
           ++A  LF +M+E+   PN   + TLI   +R        EL+ +M+      DAS + +V
Sbjct: 553 EEADALFKEMKEDGTLPNSGCYNTLIRARLRDGDREASAELIKEMRSCGFAGDASTIGLV 612

Query: 373 VDLL 376
            ++L
Sbjct: 613 TNML 616

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ14|PPR96_ARATH Pentatricopeptide repeat-containing protein At1g62930, chloroplastic OS=Arabidopsis thaliana GN=At1g62930 PE=2 SV=2

 Score =  289 bits (739), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 147/364 (40%), Positives = 225/364 (61%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           + + V Y TIID LC    V+ A  LF +M  + I P+VVTYNSLI  LC+   W++A R
Sbjct: 252 EADVVIYTTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWSDASR 311

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P+VVTF+ ++D   K GK+ EA +L D M++R + P+ FTYS+L++GFC
Sbjct: 312 LLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFC 371

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  +++ A+ +F  M S  C  + V+YN LI G+CK K VEE + L+REM  +G+    V
Sbjct: 372 MHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQRGLVGNTV 431

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TYNTL  GLF+    + A K+F++M  D V  D  TY+  +DGLCK G + +A+ +F  L
Sbjct: 432 TYNTLIQGLFQAGDCDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLEKALVVFEYL 491

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              K E DI  YN +I+G+CK+G++E   +LF SL  + +  +V+ Y  MI G C  G  
Sbjct: 492 QKSKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVIIYTTMISGFCRKGLK 551

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
           ++A  LF +M+E+   PN   + TLI   +R    +   EL+ +M+    + DAS +SMV
Sbjct: 552 EEADALFREMKEDGTLPNSGTYNTLIRARLRDGDKAASAELIKEMRSCGFVGDASTISMV 611

Query: 373 VDLL 376
           +++L
Sbjct: 612 INML 615

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAN0|PPR99_ARATH Pentatricopeptide repeat-containing protein At1g63130, mitochondrial OS=Arabidopsis thaliana GN=At1g63130 PE=2 SV=1

 Score =  286 bits (731), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 143/364 (39%), Positives = 223/364 (61%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           +P  V YNTIID LC    V+ A  LF +M  + I P+VVTYNSLI  LC+   W++A R
Sbjct: 253 EPGVVIYNTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWSDASR 312

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P+VVTF+ ++D   K GK+ EA +L D M++R + P+ FTYS+L++GFC
Sbjct: 313 LLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFC 372

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  +++ A+ +F  M S  C  + V+YN LI G+CK K V+E + L+REM  +G+    V
Sbjct: 373 MHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVDEGMELFREMSQRGLVGNTV 432

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TY TL  G F+  + ++A  +F++M  D V  D  TY+  +DGLC NG +  A+ +F  L
Sbjct: 433 TYTTLIHGFFQARECDNAQIVFKQMVSDGVLPDIMTYSILLDGLCNNGKVETALVVFEYL 492

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              K E DI  YN +I+G+CK+G++E   +LF SL  + +  +VVTY  M+ G C  G  
Sbjct: 493 QRSKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVVTYTTMMSGFCRKGLK 552

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
           ++A  LF +M+E    P+   + TLI   +R    +   EL+ +M+  + + DAS + +V
Sbjct: 553 EEADALFREMKEEGPLPDSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLV 612

Query: 373 VDLL 376
            ++L
Sbjct: 613 TNML 616

Arabidopsis thaliana (taxid: 3702)

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

 Score =  283 bits (725), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 142/364 (39%), Positives = 229/364 (62%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           + + V +NTIID LCK   VD A  LF +M+ + I P+VVTY+SLI  LC    W++A +
Sbjct: 257 EADVVIFNTIIDSLCKYRHVDDALNLFKEMETKGIRPNVVTYSSLISCLCSYGRWSDASQ 316

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P++VTFN ++D   K GK  EA +L D M++R + P+ FTY++L++GFC
Sbjct: 317 LLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLYDDMIKRSIDPDIFTYNSLVNGFC 376

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  ++++A+++F  M S  C  D V+YN LI G+CK+K VE+   L+REM  +G+    V
Sbjct: 377 MHDRLDKAKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKRVEDGTELFREMSHRGLVGDTV 436

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TY TL  GLF     ++A K+F++M  D V  D  TY+  +DGLC NG + +A+E+F  +
Sbjct: 437 TYTTLIQGLFHDGDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLEKALEVFDYM 496

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              + +LDI  Y  +I+G+CK+G+++   +LF SL  + +  +VVTYN MI GLC+   +
Sbjct: 497 QKSEIKLDIYIYTTMIEGMCKAGKVDDGWDLFCSLSLKGVKPNVVTYNTMISGLCSKRLL 556

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
            +A+ L   M+E+   PN   + TLI   +R    +   EL+ +M+  + + DAS + +V
Sbjct: 557 QEAYALLKKMKEDGPLPNSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLV 616

Query: 373 VDLL 376
            ++L
Sbjct: 617 ANML 620

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ16|PPR94_ARATH Pentatricopeptide repeat-containing protein At1g62910 OS=Arabidopsis thaliana GN=At1g62910 PE=2 SV=1

 Score =  280 bits (717), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 142/364 (39%), Positives = 219/364 (60%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           + + V YNTIIDGLCK   +D A  LF +M  + I PDV TY+SLI  LC+   W++A R
Sbjct: 255 EADVVIYNTIIDGLCKYKHMDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDASR 314

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P+VVTF+ ++D   K GK+ EA +L D M++R + P+ FTYS+L++GFC
Sbjct: 315 LLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFC 374

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  +++ A+ +F  M S  C  + V+Y+ LI G+CK K VEE + L+REM  +G+    V
Sbjct: 375 MHDRLDEAKHMFELMISKDCFPNVVTYSTLIKGFCKAKRVEEGMELFREMSQRGLVGNTV 434

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TY TL  G F+    ++A  +F++M    V  +  TYN  +DGLCKNG + +A+ +F  L
Sbjct: 435 TYTTLIHGFFQARDCDNAQMVFKQMVSVGVHPNILTYNILLDGLCKNGKLAKAMVVFEYL 494

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                E DI  YN +I+G+CK+G++E   ELF +L  + +  +V+ YN MI G C  G  
Sbjct: 495 QRSTMEPDIYTYNIMIEGMCKAGKVEDGWELFCNLSLKGVSPNVIAYNTMISGFCRKGSK 554

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
           ++A  L   M+E+   PN   + TLI   +R        EL+ +M+      DAS + +V
Sbjct: 555 EEADSLLKKMKEDGPLPNSGTYNTLIRARLRDGDREASAELIKEMRSCGFAGDASTIGLV 614

Query: 373 VDLL 376
            ++L
Sbjct: 615 TNML 618

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LPX2|PPR39_ARATH Pentatricopeptide repeat-containing protein At1g12775, mitochondrial OS=Arabidopsis thaliana GN=At1g12775 PE=2 SV=1

 Score =  280 bits (715), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 144/364 (39%), Positives = 218/364 (59%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           K + V Y+ IIDGLCK+G +D A  LF +M+ +    D++TYN+LI G C+A  W++  +
Sbjct: 260 KLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIITYNTLIGGFCNAGRWDDGAK 319

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+ + + P+VVTF+V++D   K GK+ EA +LL  M+QR + PN  TY++L+DGFC
Sbjct: 320 LLRDMIKRKISPNVVTFSVLIDSFVKEGKLREADQLLKEMMQRGIAPNTITYNSLIDGFC 379

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
              ++  A ++   M S GC  D +++NILINGYCK   +++ L L+REM  +G+    V
Sbjct: 380 KENRLEEAIQMVDLMISKGCDPDIMTFNILINGYCKANRIDDGLELFREMSLRGVIANTV 439

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TYNTL  G  +  ++E A KLF+EM    V  D  +Y   +DGLC NG + +A+E+F  +
Sbjct: 440 TYNTLVQGFCQSGKLEVAKKLFQEMVSRRVRPDIVSYKILLDGLCDNGELEKALEIFGKI 499

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              K ELDI  Y  +I G+C + +++ A +LF SLP + +  D   YNIMI  LC    +
Sbjct: 500 EKSKMELDIGIYMIIIHGMCNASKVDDAWDLFCSLPLKGVKLDARAYNIMISELCRKDSL 559

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
            KA  LF  M E   AP+ + +  LI   +  +  +   EL+ +MK      D S V MV
Sbjct: 560 SKADILFRKMTEEGHAPDELTYNILIRAHLGDDDATTAAELIEEMKSSGFPADVSTVKMV 619

Query: 373 VDLL 376
           +++L
Sbjct: 620 INML 623

Arabidopsis thaliana (taxid: 3702)

>sp|P0C7Q7|PPR38_ARATH Putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial OS=Arabidopsis thaliana GN=At1g12700 PE=3 SV=1

 Score =  279 bits (713), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 141/364 (38%), Positives = 217/364 (59%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           K +  TY+TIID LC++G +D A +LF +M+ + I   VVTYNSL+ GLC A  WN+   
Sbjct: 225 KADVFTYSTIIDSLCRDGCIDAAISLFKEMETKGIKSSVVTYNSLVRGLCKAGKWNDGAL 284

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+ + + P+V+TFNV++D   K GK+ EA+ L   M+ R + PN  TY+TLMDG+C
Sbjct: 285 LLKDMVSREIVPNVITFNVLLDVFVKEGKLQEANELYKEMITRGISPNIITYNTLMDGYC 344

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  +++ A  +   M    C  D V++  LI GYC  K V++ + ++R +  +G+    V
Sbjct: 345 MQNRLSEANNMLDLMVRNKCSPDIVTFTSLIKGYCMVKRVDDGMKVFRNISKRGLVANAV 404

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TY+ L  G  +  +++ A +LF+EM    V  D  TY   +DGLC NG + +A+E+F  L
Sbjct: 405 TYSILVQGFCQSGKIKLAEELFQEMVSHGVLPDVMTYGILLDGLCDNGKLEKALEIFEDL 464

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              K +L I  Y  +I+G+CK G++E A  LF SLP + +  +V+TY +MI GLC  G +
Sbjct: 465 QKSKMDLGIVMYTTIIEGMCKGGKVEDAWNLFCSLPCKGVKPNVMTYTVMISGLCKKGSL 524

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
            +A+ L   MEE+  APN   + TLI   +R    +   +L+ +MK      DAS + MV
Sbjct: 525 SEANILLRKMEEDGNAPNDCTYNTLIRAHLRDGDLTASAKLIEEMKSCGFSADASSIKMV 584

Query: 373 VDLL 376
           +D+L
Sbjct: 585 IDML 588

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQ83|PP247_ARATH Pentatricopeptide repeat-containing protein At3g22470, mitochondrial OS=Arabidopsis thaliana GN=At3g22470 PE=2 SV=1

 Score =  278 bits (712), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 142/364 (39%), Positives = 220/364 (60%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           K + V Y+ +ID LCK+G  D A +LF +M+ + I  DVVTY+SLI GLC+   W++  +
Sbjct: 242 KASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGLCNDGKWDDGAK 301

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           +  EM+ + + P VVTF+ ++D   K GK+ EA  L + M+ R + P+  TY++L+DGFC
Sbjct: 302 MLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPDTITYNSLIDGFC 361

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
               ++ A ++F  M S GC+ D V+Y+ILIN YCK K V++ + L+RE+ SKG+ P  +
Sbjct: 362 KENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFREISSKGLIPNTI 421

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TYNTL LG  +  ++  A +LF+EM    V     TY   +DGLC NG + +A+E+F  +
Sbjct: 422 TYNTLVLGFCQSGKLNAAKELFQEMVSRGVPPSVVTYGILLDGLCDNGELNKALEIFEKM 481

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              +  L I  YN +I G+C + +++ A  LF SL  + +  DVVTYN+MI GLC  G +
Sbjct: 482 QKSRMTLGIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNVMIGGLCKKGSL 541

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
            +A  LF  M+E+   P+   +  LI   +  +     +EL+ +MK      D+S + MV
Sbjct: 542 SEADMLFRKMKEDGCTPDDFTYNILIRAHLGGSGLISSVELIEEMKVCGFSADSSTIKMV 601

Query: 373 VDLL 376
           +D+L
Sbjct: 602 IDML 605

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C8T7|PP101_ARATH Pentatricopeptide repeat-containing protein At1g63330 OS=Arabidopsis thaliana GN=At1g63330 PE=2 SV=2

 Score =  278 bits (712), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 140/364 (38%), Positives = 228/364 (62%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           + + V +NTIID LCK   VD A  LF +M+ + I P+VVTY+SLI  LC    W++A +
Sbjct: 182 EADVVIFNTIIDSLCKYRHVDDALNLFKEMETKGIRPNVVTYSSLISCLCSYGRWSDASQ 241

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           L  +M+++ + P++VTFN ++D   K GK  EA +L D M++R + P+ FTY++L++GFC
Sbjct: 242 LLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLHDDMIKRSIDPDIFTYNSLINGFC 301

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
           +  ++++A+++F  M S  C  D  +YN LI G+CK+K VE+   L+REM  +G+    V
Sbjct: 302 MHDRLDKAKQMFEFMVSKDCFPDLDTYNTLIKGFCKSKRVEDGTELFREMSHRGLVGDTV 361

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
           TY TL  GLF     ++A K+F++M  D V  D  TY+  +DGLC NG + +A+E+F  +
Sbjct: 362 TYTTLIQGLFHDGDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLEKALEVFDYM 421

Query: 253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
              + +LDI  Y  +I+G+CK+G+++   +LF SL  + +  +VVTYN MI GLC+   +
Sbjct: 422 QKSEIKLDIYIYTTMIEGMCKAGKVDDGWDLFCSLSLKGVKPNVVTYNTMISGLCSKRLL 481

Query: 313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
            +A+ L   M+E+   P+   + TLI   +R    +   EL+ +M+  + + DAS + +V
Sbjct: 482 QEAYALLKKMKEDGPLPDSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLV 541

Query: 373 VDLL 376
            ++L
Sbjct: 542 ANML 545

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	376
359479583	627	PREDICTED: pentatricopeptide repeat-cont	0.984	0.590	0.563	1e-118
449529622	618	PREDICTED: pentatricopeptide repeat-cont	0.968	0.588	0.521	1e-108
449520325	605	PREDICTED: pentatricopeptide repeat-cont	0.968	0.601	0.497	1e-104
255559961	628	pentatricopeptide repeat-containing prot	0.973	0.582	0.498	1e-103
449520323	605	PREDICTED: pentatricopeptide repeat-cont	0.949	0.590	0.504	1e-100
449462477	597	PREDICTED: pentatricopeptide repeat-cont	0.960	0.604	0.493	2e-95
449462479	580	PREDICTED: pentatricopeptide repeat-cont	0.970	0.629	0.464	2e-92
449491568	412	PREDICTED: pentatricopeptide repeat-cont	0.914	0.834	0.483	6e-91
449444222	588	PREDICTED: pentatricopeptide repeat-cont	0.970	0.620	0.466	2e-90
449444228	585	PREDICTED: pentatricopeptide repeat-cont	0.970	0.623	0.463	1e-87

>gi|359479583|ref|XP_002275680.2| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Vitis vinifera] gi|297735515|emb|CBI17955.3| unnamed protein product [Vitis vinifera]

 Score =  432 bits (1110), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 212/376 (56%), Positives = 268/376 (71%)

Query: 1   MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHG 60
           M NGNG  GV  KPN V Y TIID LCK+G +DK K LFL+MKG  I+PDVV Y+S+IHG
Sbjct: 223 MLNGNGGFGVTIKPNLVCYCTIIDSLCKDGLIDKGKELFLEMKGRGISPDVVAYSSIIHG 282

Query: 61  LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
           +CH   W  AK LF EM+D+GV P+VVTFNV++D LCK GKM+EA+ LL LM+QR   P+
Sbjct: 283 MCHTGRWEGAKGLFNEMVDEGVHPNVVTFNVLIDALCKAGKMEEANHLLKLMIQRGESPD 342

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 180
            FTY+TL+DGFCL G+I+ A +LF SMES G + D VSYN+LINGYCK+  + EA  LYR
Sbjct: 343 TFTYNTLIDGFCLEGRIDDARDLFVSMESKGIETDAVSYNVLINGYCKSGRMVEAKKLYR 402

Query: 181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG 240
           EM+ K I PTV+TYNTL  GLF   +V  A  LF EM+  D+  ++ TYN  +DGLCKN 
Sbjct: 403 EMMCKEIMPTVITYNTLLTGLFREGKVRDAWNLFGEMKVHDLTPESCTYNILLDGLCKNN 462

Query: 241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYN 300
           ++ EA+ELF  L     +  IQ +NCLIDGLCK+ ++EIA ELF  L    L  +V+TY 
Sbjct: 463 HLSEAMELFHYLENHDFQPSIQIFNCLIDGLCKARKIEIARELFNRLSHEGLEPNVITYT 522

Query: 301 IMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK 360
           +MIHGLC  GQ++ A DLFL MEE   APN++ F TL+ GF + ++  KV+ELL +M EK
Sbjct: 523 VMIHGLCKSGQLENAKDLFLGMEEKGCAPNLVTFNTLMRGFCQNDEMQKVVELLQEMAEK 582

Query: 361 KVMPDASIVSMVVDLL 376
              PDAS +S+VVDLL
Sbjct: 583 DFSPDASTISIVVDLL 598

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449529622|ref|XP_004171797.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  398 bits (1022), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 196/376 (52%), Positives = 264/376 (70%)

Query: 1   MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHG 60
           M N   + GV CKP  +TY+ IIDGLCK G  D+AK LF +MK + + PDV++Y++LIHG
Sbjct: 222 MLNDASQYGVNCKPGVITYSIIIDGLCKVGREDEAKELFEEMKAQGMIPDVISYSTLIHG 281

Query: 61  LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
            C A  W+++K LF EM+DQGVQP +VTF+V++D LCK GK+ EA +LL++M+QR + PN
Sbjct: 282 FCCAGKWDQSKHLFDEMVDQGVQPDMVTFSVLIDTLCKEGKVTEAKKLLEVMIQRGIVPN 341

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 180
             TY++L+DGFC+ G +N A ELF SM S G + D++SY  LINGYCK  +V+EA++LY 
Sbjct: 342 LITYNSLIDGFCMVGDLNSARELFLSMPSKGLEPDEISYTTLINGYCKTWKVKEAMNLYN 401

Query: 181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG 240
           EM+  G  P V TY TL  GLF+  +V  A KLF  M+   V+A++  Y  F+DGLCKN 
Sbjct: 402 EMLQVGKSPNVTTYGTLLKGLFQKGKVGDAKKLFGVMKTYGVSANSQIYGIFLDGLCKND 461

Query: 241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYN 300
            + EA+ELF  L     +L+I+ Y+CLIDGLCK+G+LE A ELF  L +  L  DVVTYN
Sbjct: 462 CLFEAMELFNELKSYNFKLNIENYSCLIDGLCKAGKLETAWELFEKLSQEGLQPDVVTYN 521

Query: 301 IMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK 360
           IMIHG C  GQ+D A+ LF  MEEN   P++I + TL+ GF   NK  +VI+LLHKM +K
Sbjct: 522 IMIHGFCKVGQVDNANILFEKMEENGCTPDIIAYNTLLCGFCEGNKLEEVIKLLHKMVQK 581

Query: 361 KVMPDASIVSMVVDLL 376
            V P+A+  ++VVD+L
Sbjct: 582 DVSPNAASCTIVVDML 597

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520325|ref|XP_004167184.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 187/376 (49%), Positives = 257/376 (68%)

Query: 1   MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHG 60
           M N      + CKPN +TYN I+DGLCK G  D+AK LF +MK + + P +++YNSLIHG
Sbjct: 200 MLNDISRYEINCKPNVITYNIIVDGLCKVGREDEAKQLFEEMKTQGMIPSIISYNSLIHG 259

Query: 61  LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
            C A  W E+KRL  EM+DQG+QP +VTFNV++D LCK GK+ EA +LL +M++  + P+
Sbjct: 260 FCCAGKWEESKRLLDEMLDQGLQPDMVTFNVLIDTLCKEGKVIEAKKLLGVMIESGIVPD 319

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 180
             TY++L++GFC+ G +N A ELF SM S GC+ D +SYN+LINGY K  +VEEA+ LY 
Sbjct: 320 LVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDVISYNVLINGYSKTLKVEEAMKLYN 379

Query: 181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG 240
           EM+  G +P V+TY++L  G+F   +V+ A KLF  M+   +A ++ TY  F+DGLCKN 
Sbjct: 380 EMLLVGKRPNVITYDSLLKGIFLAGKVDDAKKLFSVMKAHGIAENSYTYGIFLDGLCKND 439

Query: 241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYN 300
            + EA++LF  L     +L+I+  NCLIDGLCK+G+LE A ELF  L       +VVTY 
Sbjct: 440 CLFEAMKLFTELKSSNFKLEIENLNCLIDGLCKAGKLETAWELFEKLSNEGHEPNVVTYT 499

Query: 301 IMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK 360
           IMIHG C +GQ+DKA+ L   ME N   P++I + TL+ GF   NK  +V++LLH+M +K
Sbjct: 500 IMIHGFCREGQVDKANVLIQKMEANGCTPDIITYNTLMRGFYESNKLEEVVQLLHRMAQK 559

Query: 361 KVMPDASIVSMVVDLL 376
            V PDA   S+VVD+L
Sbjct: 560 DVSPDAITCSIVVDML 575

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559961|ref|XP_002520999.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223539836|gb|EEF41416.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 189/379 (49%), Positives = 262/379 (69%), Gaps = 13/379 (3%)

Query: 1   MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHG 60
           M NGN + G+ CKP  V+Y+ IID LCK+G V++AK  F++MK + I P+VVTY SL+HG
Sbjct: 238 MINGNSDFGINCKPTVVSYSCIIDSLCKDGLVERAKEFFVEMKEKGIFPNVVTYTSLLHG 297

Query: 61  LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
           LC A++W EAKRLF EM+D G+ P VVTF+V++  LCK GK+ EAS L DLMVQR V P+
Sbjct: 298 LCSASEWEEAKRLFIEMVDHGLLPDVVTFSVLIGALCKVGKVKEASGLFDLMVQRYVEPS 357

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 180
             TY+ L++G+CL G ++  +++F SM +  C+HD  SY+IL+  YCK+ EV  A+ LYR
Sbjct: 358 TRTYNILIEGYCLAGMVDEGKKIFLSMVNKRCQHDAGSYSILMKAYCKDSEVHGAMILYR 417

Query: 181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT---STYNTFIDGLC 237
           EM+ +GI+PTV+TY+          +V  A KLF E+Q  D+  D+   S YN ++DGLC
Sbjct: 418 EMMDRGIQPTVITYS----------KVGDARKLFGEIQFQDMVLDSISYSIYNVYLDGLC 467

Query: 238 KNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVV 297
           KNG + EA+++F  L   K   ++  +N LI+G+C+S +LEIA ELF  L    L  DVV
Sbjct: 468 KNGCVSEALDVFYGLENCKFASNVAIFNSLINGMCRSEKLEIAWELFNRLCNEALQPDVV 527

Query: 298 TYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKM 357
           TY IMI+GLC  GQ  KA+DLFL+MEE   APNV+ F TL+ G    ++  K++ELLHKM
Sbjct: 528 TYTIMIYGLCKVGQPQKAYDLFLEMEEKGCAPNVVTFNTLMRGLCLNSERPKIVELLHKM 587

Query: 358 KEKKVMPDASIVSMVVDLL 376
             +K+ PDAS + +V+D+L
Sbjct: 588 AARKLSPDASTLLIVMDIL 606

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520323|ref|XP_004167183.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/369 (50%), Positives = 245/369 (66%)

Query: 1   MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHG 60
           M N +   G+  KP  ++Y+ IID LCK+   D+A+ LF +MK + + P V++Y SLIHG
Sbjct: 227 MLNDSSLYGINFKPVVISYSIIIDALCKDRREDEARDLFEEMKVQGMTPTVISYTSLIHG 286

Query: 61  LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
            C    W EAKRLF EM++QGVQP+VVTFNV++D LCK GK+ EA  LL++M+QR + PN
Sbjct: 287 FCCGGKWEEAKRLFNEMVNQGVQPNVVTFNVLIDVLCKEGKVIEAKDLLEVMIQRGIVPN 346

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 180
             TY++L++GFCL G +N A ELF SM S GC+ D + Y +LINGYCK  +VEEA+ LY 
Sbjct: 347 LLTYNSLIEGFCLVGDLNSARELFVSMPSKGCEPDVICYTVLINGYCKTSKVEEAMKLYN 406

Query: 181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG 240
            M+  G +P V TY  L  GLF+  +V  A KLF  M+   +  D   Y  F++GLCKNG
Sbjct: 407 GMLQVGKRPDVKTYGALLTGLFQGGKVGDAKKLFGVMKVYGIPGDLYIYGIFLNGLCKNG 466

Query: 241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYN 300
            + EA+ELF  L     +LDI+ +NCLIDGLCK+G+LE A ELF  LP+  L  DVVTYN
Sbjct: 467 CLFEAMELFNKLKSYNIKLDIECFNCLIDGLCKAGKLETAWELFEKLPQEELQPDVVTYN 526

Query: 301 IMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK 360
           IMIH  C  GQ+ KA+ LF  ME+N   P+ I + TLI GF    K  KV+ELLH M ++
Sbjct: 527 IMIHEFCRGGQVVKANILFQKMEKNGCTPDKITYATLIRGFFESKKLEKVVELLHMMVQR 586

Query: 361 KVMPDASIV 369
            V  D +I+
Sbjct: 587 DVSLDVNIL 595

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462477|ref|XP_004148967.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  355 bits (911), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 182/369 (49%), Positives = 242/369 (65%), Gaps = 8/369 (2%)

Query: 1   MANGNGEIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHG 60
           M N +   G+  KP  ++Y+ IID LCK+   D+A+ LF +MK + + P V++Y SL+  
Sbjct: 227 MLNDSSLYGINFKPVVISYSIIIDALCKDRREDEARDLFEEMKVQGMTPTVISYTSLM-- 284

Query: 61  LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
                 W EAKRLF EM++QGVQP+VVTFNV++D LCK GK+ EA  LL++M+QR + PN
Sbjct: 285 ------WEEAKRLFNEMVNQGVQPNVVTFNVLIDVLCKEGKVIEAKDLLEVMIQRGIVPN 338

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 180
             TY++L++GFCL G +N A ELF SM S GC+ D + Y +LINGYCK  +VEEA+ LY 
Sbjct: 339 LLTYNSLIEGFCLVGDLNSARELFVSMPSKGCEPDVICYTVLINGYCKTSKVEEAMKLYN 398

Query: 181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG 240
            M+  G +P V TY  L  GLF+  +V  A KLF  M+   +  D   Y  F++GLCKNG
Sbjct: 399 GMLQVGKRPDVKTYGALLTGLFQGGKVGDAKKLFGVMKVYGIPGDLYIYGIFLNGLCKNG 458

Query: 241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYN 300
            + EA+ELF  L     +LDI+ +NCLIDGLCK+G+LE A ELF  LP+  L  DVVTYN
Sbjct: 459 CLFEAMELFNKLKSYNIKLDIECFNCLIDGLCKAGKLETAWELFEKLPQEELQPDVVTYN 518

Query: 301 IMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK 360
           IMIH  C  GQ+ KA+ LF  ME+N   P+ I + TLI GF    K  KV+ELLH M ++
Sbjct: 519 IMIHEFCRGGQVVKANILFQKMEKNGCTPDKITYATLIRGFFESKKLEKVVELLHMMVQR 578

Query: 361 KVMPDASIV 369
            V  D +I+
Sbjct: 579 DVSLDVNIL 587

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462479|ref|XP_004148968.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  345 bits (884), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 177/381 (46%), Positives = 248/381 (65%), Gaps = 16/381 (4%)

Query: 12  CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGE------NINPDVVTYNSLIHGLCHAN 65
           C P+ VTY T+I GLC  G ++ A  L  +M  +      N  P+V+TYN ++ GLC   
Sbjct: 170 CTPDVVTYGTLIKGLCGTGNINIALKLHQEMLNDISRYEINCKPNVITYNIIVDGLCKVG 229

Query: 66  DWNEAKRLF----------FEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR 115
             +EAK+LF           EM+DQG+QP +VTFNV++D LCK GK+ EA +LL +M++ 
Sbjct: 230 REDEAKQLFEEMKTQGMIPNEMLDQGLQPDMVTFNVLIDTLCKEGKVIEAKKLLGVMIES 289

Query: 116 DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA 175
            + P+  TY++L++GFC+ G +N A ELF SM S GC+ D +SYN+LINGY K  +VEEA
Sbjct: 290 GIVPDLVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDVISYNVLINGYSKTLKVEEA 349

Query: 176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDG 235
           + LY EM+  G +P V+TY++L  G+F   +V+ A KLF  M+   +A ++ TY  F+DG
Sbjct: 350 MKLYNEMLLVGKRPNVITYDSLLKGIFLAGKVDDAKKLFSVMKAHGIAENSYTYGIFLDG 409

Query: 236 LCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD 295
           LCKN  + EA++LF  L     +L+I+  NCLIDGLCK+G+LE A ELF  L       +
Sbjct: 410 LCKNDCLFEAMKLFTELKSSNFKLEIENLNCLIDGLCKAGKLETAWELFEKLSNEGHEPN 469

Query: 296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLH 355
           VVTY IMIHG C +GQ+DKA+ L   ME N   P++I + TL+ GF   NK  +V++LLH
Sbjct: 470 VVTYTIMIHGFCREGQVDKANVLIQKMEANGCTPDIITYNTLMRGFYESNKLEEVVQLLH 529

Query: 356 KMKEKKVMPDASIVSMVVDLL 376
           +M +K V PDA   S+VVD+L
Sbjct: 530 RMAQKDVSPDAITCSIVVDML 550

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449491568|ref|XP_004158939.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  340 bits (872), Expect = 6e-91,   Method: Compositional matrix adjust.
 Identities = 176/364 (48%), Positives = 242/364 (66%), Gaps = 20/364 (5%)

Query: 14  PNTVTYNT-----------------IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNS 56
           P+ VTYNT                 IIDGLCK G  D+AK +F +MK + + P+V++Y+S
Sbjct: 43  PDIVTYNTLIKGLCRVHRISVATCIIIDGLCKVGHEDEAKEIFEEMKAQGMIPNVISYSS 102

Query: 57  LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD 116
           L+HG C A    E+KRLF EM+DQGVQP++V FNV++D LCK GK+ EA +LL++ +QR 
Sbjct: 103 LVHGFCCAGKLEESKRLFNEMVDQGVQPNLVQFNVLIDILCKEGKVIEAKKLLEVTIQRG 162

Query: 117 VRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL 176
           +  +  TY++L+DGFC  G ++ A +LF SM S GC+H+++SY ILINGYCK  +VEEA+
Sbjct: 163 IILDLVTYNSLIDGFCKIGDLSSARKLFLSMPSKGCEHNEISYTILINGYCKIWKVEEAM 222

Query: 177 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGL 236
           +LY EM   G +P V TY+TL  GL +  +V  A KLF  M+   ++ D+  Y  F+DGL
Sbjct: 223 NLYNEMPQVGKRPNVKTYSTLLTGLLQTGKVGDANKLFGVMKASGISVDSCIYVIFLDGL 282

Query: 237 CKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV 296
           CKNG + EA+ELF  L     +LD ++Y+ LIDGLCK+G++EIA E F+ L +  L  +V
Sbjct: 283 CKNGVLFEAMELFNELKSYNFKLDFESYSRLIDGLCKAGKVEIAWEFFKQLSQEGLQPNV 342

Query: 297 VTYNIMIHGLCNDGQMDKAHDLF---LDMEENAVAPNVIIFVTLIHGFVRINKPSKVIEL 353
           VT NIMIHG C   Q+DKA+ LF     MEEN   P++I + TL+ GF   NK  +V+ L
Sbjct: 343 VTCNIMIHGFCRVEQVDKANILFEKMEKMEENGCTPDIITYNTLLRGFCESNKLEEVVNL 402

Query: 354 LHKM 357
           LHKM
Sbjct: 403 LHKM 406

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444222|ref|XP_004139874.1| PREDICTED: pentatricopeptide repeat-containing protein At1g62910-like [Cucumis sativus] gi|449492651|ref|XP_004159061.1| PREDICTED: pentatricopeptide repeat-containing protein At1g62910-like [Cucumis sativus]

 Score =  339 bits (869), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 173/371 (46%), Positives = 241/371 (64%), Gaps = 6/371 (1%)

Query: 12  CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGE------NINPDVVTYNSLIHGLCHAN 65
           C PN VTY T+I GLC  G ++ A     +M  +      N  P+V++Y+ +I GLC   
Sbjct: 192 CTPNVVTYGTLIKGLCALGNINIALKWHQEMLNDTSPYVFNCRPNVISYSIIIDGLCKVG 251

Query: 66  DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYS 125
           +W EA  LF EM+DQGVQP+VVTF+V++D LCK G++ +A +LL++M+Q  + PN FTY+
Sbjct: 252 NWEEAICLFNEMVDQGVQPNVVTFSVLIDMLCKEGQVIKAKKLLEMMIQIGIVPNLFTYT 311

Query: 126 TLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK 185
           +L+ GFCL G +N A+ELF SM S G + D +SYN+LINGYCK  +VEEA+ L+ EM+  
Sbjct: 312 SLIKGFCLVGDLNSAKELFVSMPSKGYEPDVISYNMLINGYCKTLKVEEAMKLFNEMLHV 371

Query: 186 GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEA 245
           G+ P V T   L   LF   +V+ A +LF  ++   +  D      F+DGLCKNGYI EA
Sbjct: 372 GMWPDVKTSGVLLKALFLAGKVDDAKELFRVIKPYAMPKDLCICCIFLDGLCKNGYIFEA 431

Query: 246 VELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHG 305
           ++LF  L     +LDI+ + CLIDGLCK+G+LE A ELF  L    +  D + Y+ MIHG
Sbjct: 432 MKLFNELESYNMKLDIETFGCLIDGLCKAGKLETAWELFEKLYEEGIQPDAMAYSSMIHG 491

Query: 306 LCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPD 365
            C  GQ+DKA+ LF  MEEN  +P++I +  L+ GF   NK  KV++LLH+M EK V PD
Sbjct: 492 FCKKGQVDKANILFQKMEENGCSPDLITYSILMRGFYESNKLEKVVQLLHRMIEKDVWPD 551

Query: 366 ASIVSMVVDLL 376
             I ++V D++
Sbjct: 552 DGIYAIVEDMV 562

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444228|ref|XP_004139877.1| PREDICTED: pentatricopeptide repeat-containing protein At1g62910-like [Cucumis sativus] gi|449492643|ref|XP_004159059.1| PREDICTED: pentatricopeptide repeat-containing protein At1g62910-like [Cucumis sativus]

 Score =  329 bits (844), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 172/371 (46%), Positives = 239/371 (64%), Gaps = 6/371 (1%)

Query: 12  CKPNTVTYNTIIDGLCKEGFVDKAKALFLQM------KGENINPDVVTYNSLIHGLCHAN 65
           C PN VTY T+I GLC+ G ++ A  L  +M         N  P++ +YN +I  LC   
Sbjct: 192 CWPNVVTYGTLIKGLCRTGNINLALKLHQEMLNGTSPYAINCKPNIFSYNIIIDELCKIG 251

Query: 66  DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYS 125
            W EAKRLF EM+DQGV+P VVTF+ ++D LCK G + EA + L+ M+ R + P+ FT++
Sbjct: 252 KWKEAKRLFNEMVDQGVRPDVVTFSALIDTLCKEGMVIEAKKFLETMMLRGIVPDLFTFT 311

Query: 126 TLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK 185
           +L++GFCL G ++ A+ELF SM S G + D +SY +LI GYCK   VEEA+ LY EM+  
Sbjct: 312 SLIEGFCLVGDLDSAKELFLSMPSKGYEPDVISYTVLIYGYCKTFNVEEAMKLYNEMLRV 371

Query: 186 GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEA 245
           G  P + T+  L  GLF   +V  A KLF  ++   V  +    + F+DGLCKNG + EA
Sbjct: 372 GKWPDMKTFCVLLKGLFLAGKVGDAKKLFGVVKPHAVPKNLYICSVFLDGLCKNGCLFEA 431

Query: 246 VELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHG 305
           +ELF  L     +LDI+++NCLIDGLCK+ +LE A ELF  L +  L  DVVTY IMI+G
Sbjct: 432 MELFNELKSYNMKLDIESFNCLIDGLCKARKLETAWELFEKLSQEGLQPDVVTYCIMING 491

Query: 306 LCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPD 365
            C +GQ+D A+ LF  MEEN   PN++ +  L+HGF + NK  +V++LLHKM +K V   
Sbjct: 492 FCKNGQVDNANILFQMMEENGCTPNLLTYSALLHGFYKNNKLEEVVKLLHKMIQKDVSLA 551

Query: 366 ASIVSMVVDLL 376
           ASI ++V D++
Sbjct: 552 ASIYTIVEDMV 562

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	376
TAIR|locus:2015228	614	AT1G63080 [Arabidopsis thalian	0.962	0.589	0.400	1.1e-73
TAIR|locus:2026192	630	RPF2 "rna processing factor 2"	0.968	0.577	0.406	2.8e-73
TAIR|locus:2015494	629	RPF3 "RNA processing factor 3"	0.962	0.575	0.406	3.2e-72
TAIR|locus:2015208	630	AT1G63130 [Arabidopsis thalian	0.968	0.577	0.392	1.4e-71
TAIR|locus:2203916	634	AT1G62590 [Arabidopsis thalian	0.962	0.570	0.392	2.9e-71
TAIR|locus:1009023134	644	AT1G12775 [Arabidopsis thalian	0.968	0.565	0.395	2.1e-70
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.968	0.588	0.390	3.3e-70
TAIR|locus:2034760	637	AT1G12300 [Arabidopsis thalian	0.968	0.571	0.390	1.1e-69
TAIR|locus:2015213	629	AT1G63150 [Arabidopsis thalian	0.960	0.573	0.395	1.8e-69
TAIR|locus:2195047	621	AT1G12620 [Arabidopsis thalian	0.968	0.586	0.392	4.9e-69

TAIR|locus:2015228 AT1G63080 [Arabidopsis thaliana (taxid:3702)]

 Score = 744 (267.0 bits), Expect = 1.1e-73, P = 1.1e-73
 Identities = 145/362 (40%), Positives = 224/362 (61%)

Query:    15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLF 74
             + V Y+T+ID LCK   VD A  LF +M  + I PDV TY+SLI  LC+   W++A RL 
Sbjct:   239 DVVIYSTVIDSLCKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDASRLL 298

Query:    75 FEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT 134
              +M+++ + P+VVTFN ++D   K GK+ EA +L D M+QR + PN  TY++L++GFC+ 
Sbjct:   299 SDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTYNSLINGFCMH 358

Query:   135 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTY 194
              +++ A+++F  M S  C  D V+YN LING+CK K+V + + L+R+M  +G+    VTY
Sbjct:   359 DRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSRRGLVGNTVTY 418

Query:   195 NTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI 254
              TL  G F+    ++A  +F++M  D V  +  TYNT +DGLCKNG + +A+ +F  L  
Sbjct:   419 TTLIHGFFQASDCDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVFEYLQK 478

Query:   255 LKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDK 314
              K E DI  YN + +G+CK+G++E   +LF SL  + +  DV+ YN MI G C  G  ++
Sbjct:   479 SKMEPDIYTYNIMSEGMCKAGKVEDGWDLFCSLSLKGVKPDVIAYNTMISGFCKKGLKEE 538

Query:   315 AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVD 374
             A+ LF+ M+E+   P+   + TLI   +R    +   EL+ +M+  +   DAS   +V D
Sbjct:   539 AYTLFIKMKEDGPLPDSGTYNTLIRAHLRDGDKAASAELIKEMRSCRFAGDASTYGLVTD 598

Query:   375 LL 376
             +L
Sbjct:   599 ML 600

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2026192 RPF2 "rna processing factor 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 740 (265.6 bits), Expect = 2.8e-73, P = 2.8e-73
 Identities = 148/364 (40%), Positives = 224/364 (61%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             +P  + YNTIIDGLCK   +D A  LF +M+ + I P+VVTY+SLI  LC+   W++A R
Sbjct:   253 EPGVLIYNTIIDGLCKYKHMDDALNLFKEMETKGIRPNVVTYSSLISCLCNYGRWSDASR 312

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             L  +M+++ + P V TF+ ++D   K GK+ EA +L D MV+R + P+  TYS+L++GFC
Sbjct:   313 LLSDMIERKINPDVFTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTYSSLINGFC 372

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
             +  +++ A+++F  M S  C  D V+YN LI G+CK K VEE + ++REM  +G+    V
Sbjct:   373 MHDRLDEAKQMFEFMVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTV 432

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TYN L  GLF+    + A ++F+EM  D V  +  TYNT +DGLCKNG + +A+ +F  L
Sbjct:   433 TYNILIQGLFQAGDCDMAQEIFKEMVSDGVPPNIMTYNTLLDGLCKNGKLEKAMVVFEYL 492

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                K E  I  YN +I+G+CK+G++E   +LF +L  + +  DVV YN MI G C  G  
Sbjct:   493 QRSKMEPTIYTYNIMIEGMCKAGKVEDGWDLFCNLSLKGVKPDVVAYNTMISGFCRKGSK 552

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
             ++A  LF +M+E+   PN   + TLI   +R        EL+ +M+      DAS + +V
Sbjct:   553 EEADALFKEMKEDGTLPNSGCYNTLIRARLRDGDREASAELIKEMRSCGFAGDASTIGLV 612

Query:   373 VDLL 376
              ++L
Sbjct:   613 TNML 616

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0000966 "RNA 5'-end processing" evidence=IMP

GO:0003723 "RNA binding" evidence=IDA

TAIR|locus:2015494 RPF3 "RNA processing factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 730 (262.0 bits), Expect = 3.2e-72, P = 3.2e-72
 Identities = 147/362 (40%), Positives = 224/362 (61%)

Query:    15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLF 74
             + V Y TIID LC    V+ A  LF +M  + I P+VVTYNSLI  LC+   W++A RL 
Sbjct:   254 DVVIYTTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWSDASRLL 313

Query:    75 FEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT 134
              +M+++ + P+VVTF+ ++D   K GK+ EA +L D M++R + P+ FTYS+L++GFC+ 
Sbjct:   314 SDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFCMH 373

Query:   135 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTY 194
              +++ A+ +F  M S  C  + V+YN LI G+CK K VEE + L+REM  +G+    VTY
Sbjct:   374 DRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQRGLVGNTVTY 433

Query:   195 NTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI 254
             NTL  GLF+    + A K+F++M  D V  D  TY+  +DGLCK G + +A+ +F  L  
Sbjct:   434 NTLIQGLFQAGDCDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLEKALVVFEYLQK 493

Query:   255 LKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDK 314
              K E DI  YN +I+G+CK+G++E   +LF SL  + +  +V+ Y  MI G C  G  ++
Sbjct:   494 SKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVIIYTTMISGFCRKGLKEE 553

Query:   315 AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVD 374
             A  LF +M+E+   PN   + TLI   +R    +   EL+ +M+    + DAS +SMV++
Sbjct:   554 ADALFREMKEDGTLPNSGTYNTLIRARLRDGDKAASAELIKEMRSCGFVGDASTISMVIN 613

Query:   375 LL 376
             +L
Sbjct:   614 ML 615

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006397 "mRNA processing" evidence=IMP

TAIR|locus:2015208 AT1G63130 [Arabidopsis thaliana (taxid:3702)]

 Score = 724 (259.9 bits), Expect = 1.4e-71, P = 1.4e-71
 Identities = 143/364 (39%), Positives = 223/364 (61%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             +P  V YNTIID LC    V+ A  LF +M  + I P+VVTYNSLI  LC+   W++A R
Sbjct:   253 EPGVVIYNTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWSDASR 312

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             L  +M+++ + P+VVTF+ ++D   K GK+ EA +L D M++R + P+ FTYS+L++GFC
Sbjct:   313 LLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFC 372

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
             +  +++ A+ +F  M S  C  + V+YN LI G+CK K V+E + L+REM  +G+    V
Sbjct:   373 MHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVDEGMELFREMSQRGLVGNTV 432

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TY TL  G F+  + ++A  +F++M  D V  D  TY+  +DGLC NG +  A+ +F  L
Sbjct:   433 TYTTLIHGFFQARECDNAQIVFKQMVSDGVLPDIMTYSILLDGLCNNGKVETALVVFEYL 492

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                K E DI  YN +I+G+CK+G++E   +LF SL  + +  +VVTY  M+ G C  G  
Sbjct:   493 QRSKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVVTYTTMMSGFCRKGLK 552

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
             ++A  LF +M+E    P+   + TLI   +R    +   EL+ +M+  + + DAS + +V
Sbjct:   553 EEADALFREMKEEGPLPDSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLV 612

Query:   373 VDLL 376
              ++L
Sbjct:   613 TNML 616

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2203916 AT1G62590 [Arabidopsis thaliana (taxid:3702)]

 Score = 721 (258.9 bits), Expect = 2.9e-71, P = 2.9e-71
 Identities = 142/362 (39%), Positives = 228/362 (62%)

Query:    15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLF 74
             + V +NTIID LCK   VD A  LF +M+ + I P+VVTY+SLI  LC    W++A +L 
Sbjct:   259 DVVIFNTIIDSLCKYRHVDDALNLFKEMETKGIRPNVVTYSSLISCLCSYGRWSDASQLL 318

Query:    75 FEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT 134
              +M+++ + P++VTFN ++D   K GK  EA +L D M++R + P+ FTY++L++GFC+ 
Sbjct:   319 SDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLYDDMIKRSIDPDIFTYNSLVNGFCMH 378

Query:   135 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTY 194
              ++++A+++F  M S  C  D V+YN LI G+CK+K VE+   L+REM  +G+    VTY
Sbjct:   379 DRLDKAKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKRVEDGTELFREMSHRGLVGDTVTY 438

Query:   195 NTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI 254
              TL  GLF     ++A K+F++M  D V  D  TY+  +DGLC NG + +A+E+F  +  
Sbjct:   439 TTLIQGLFHDGDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLEKALEVFDYMQK 498

Query:   255 LKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDK 314
              + +LDI  Y  +I+G+CK+G+++   +LF SL  + +  +VVTYN MI GLC+   + +
Sbjct:   499 SEIKLDIYIYTTMIEGMCKAGKVDDGWDLFCSLSLKGVKPNVVTYNTMISGLCSKRLLQE 558

Query:   315 AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVD 374
             A+ L   M+E+   PN   + TLI   +R    +   EL+ +M+  + + DAS + +V +
Sbjct:   559 AYALLKKMKEDGPLPNSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLVAN 618

Query:   375 LL 376
             +L
Sbjct:   619 ML 620

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:1009023134 AT1G12775 [Arabidopsis thaliana (taxid:3702)]

 Score = 713 (256.0 bits), Expect = 2.1e-70, P = 2.1e-70
 Identities = 144/364 (39%), Positives = 218/364 (59%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             K + V Y+ IIDGLCK+G +D A  LF +M+ +    D++TYN+LI G C+A  W++  +
Sbjct:   260 KLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIITYNTLIGGFCNAGRWDDGAK 319

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             L  +M+ + + P+VVTF+V++D   K GK+ EA +LL  M+QR + PN  TY++L+DGFC
Sbjct:   320 LLRDMIKRKISPNVVTFSVLIDSFVKEGKLREADQLLKEMMQRGIAPNTITYNSLIDGFC 379

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
                ++  A ++   M S GC  D +++NILINGYCK   +++ L L+REM  +G+    V
Sbjct:   380 KENRLEEAIQMVDLMISKGCDPDIMTFNILINGYCKANRIDDGLELFREMSLRGVIANTV 439

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TYNTL  G  +  ++E A KLF+EM    V  D  +Y   +DGLC NG + +A+E+F  +
Sbjct:   440 TYNTLVQGFCQSGKLEVAKKLFQEMVSRRVRPDIVSYKILLDGLCDNGELEKALEIFGKI 499

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                K ELDI  Y  +I G+C + +++ A +LF SLP + +  D   YNIMI  LC    +
Sbjct:   500 EKSKMELDIGIYMIIIHGMCNASKVDDAWDLFCSLPLKGVKLDARAYNIMISELCRKDSL 559

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
              KA  LF  M E   AP+ + +  LI   +  +  +   EL+ +MK      D S V MV
Sbjct:   560 SKADILFRKMTEEGHAPDELTYNILIRAHLGDDDATTAAELIEEMKSSGFPADVSTVKMV 619

Query:   373 VDLL 376
             +++L
Sbjct:   620 INML 623

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2077061 AT3G22470 "AT3G22470" [Arabidopsis thaliana (taxid:3702)]

 Score = 711 (255.3 bits), Expect = 3.3e-70, P = 3.3e-70
 Identities = 142/364 (39%), Positives = 220/364 (60%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             K + V Y+ +ID LCK+G  D A +LF +M+ + I  DVVTY+SLI GLC+   W++  +
Sbjct:   242 KASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGLCNDGKWDDGAK 301

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             +  EM+ + + P VVTF+ ++D   K GK+ EA  L + M+ R + P+  TY++L+DGFC
Sbjct:   302 MLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPDTITYNSLIDGFC 361

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
                 ++ A ++F  M S GC+ D V+Y+ILIN YCK K V++ + L+RE+ SKG+ P  +
Sbjct:   362 KENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFREISSKGLIPNTI 421

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TYNTL LG  +  ++  A +LF+EM    V     TY   +DGLC NG + +A+E+F  +
Sbjct:   422 TYNTLVLGFCQSGKLNAAKELFQEMVSRGVPPSVVTYGILLDGLCDNGELNKALEIFEKM 481

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                +  L I  YN +I G+C + +++ A  LF SL  + +  DVVTYN+MI GLC  G +
Sbjct:   482 QKSRMTLGIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNVMIGGLCKKGSL 541

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
              +A  LF  M+E+   P+   +  LI   +  +     +EL+ +MK      D+S + MV
Sbjct:   542 SEADMLFRKMKEDGCTPDDFTYNILIRAHLGGSGLISSVELIEEMKVCGFSADSSTIKMV 601

Query:   373 VDLL 376
             +D+L
Sbjct:   602 IDML 605

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2034760 AT1G12300 [Arabidopsis thaliana (taxid:3702)]

 Score = 706 (253.6 bits), Expect = 1.1e-69, P = 1.1e-69
 Identities = 142/364 (39%), Positives = 220/364 (60%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             K + V Y+ IIDGLCK G +D A  LF +M+ + I  +++TYN LI G C+A  W++  +
Sbjct:   260 KLDAVKYSIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGFCNAGRWDDGAK 319

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             L  +M+ + + P+VVTF+V++D   K GK+ EA  L   M+ R + P+  TY++L+DGFC
Sbjct:   320 LLRDMIKRKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDTITYTSLIDGFC 379

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
                 +++A ++   M S GC  +  ++NILINGYCK   +++ L L+R+M  +G+    V
Sbjct:   380 KENHLDKANQMVDLMVSKGCDPNIRTFNILINGYCKANRIDDGLELFRKMSLRGVVADTV 439

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TYNTL  G  E+ ++  A +LF+EM    V  +  TY   +DGLC NG   +A+E+F  +
Sbjct:   440 TYNTLIQGFCELGKLNVAKELFQEMVSRKVPPNIVTYKILLDGLCDNGESEKALEIFEKI 499

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                K ELDI  YN +I G+C + +++ A +LF SLP + +   V TYNIMI GLC  G +
Sbjct:   500 EKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPGVKTYNIMIGGLCKKGPL 559

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
              +A  LF  MEE+  AP+   +  LI   +     +K ++L+ ++K      DAS + MV
Sbjct:   560 SEAELLFRKMEEDGHAPDGWTYNILIRAHLGDGDATKSVKLIEELKRCGFSVDASTIKMV 619

Query:   373 VDLL 376
             +D+L
Sbjct:   620 IDML 623

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015213 AT1G63150 [Arabidopsis thaliana (taxid:3702)]

 Score = 704 (252.9 bits), Expect = 1.8e-69, P = 1.8e-69
 Identities = 144/364 (39%), Positives = 224/364 (61%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             K N V +NTIID LCK   V+ A  LF +M+ + I P+VVTYNSLI+ LC+   W++A R
Sbjct:   255 KANVVIFNTIIDSLCKYRHVEVAVDLFTEMETKGIRPNVVTYNSLINCLCNYGRWSDASR 314

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             L   M+++ + P+VVTFN ++D   K GK+ EA +L + M+QR + P+  TY+ L++GFC
Sbjct:   315 LLSNMLEKKINPNVVTFNALIDAFFKEGKLVEAEKLHEEMIQRSIDPDTITYNLLINGFC 374

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
             +  +++ A+++F  M S  C  +  +YN LING+CK K VE+ + L+REM  +G+    V
Sbjct:   375 MHNRLDEAKQMFKFMVSKDCLPNIQTYNTLINGFCKCKRVEDGVELFREMSQRGLVGNTV 434

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TY T+  G F+    + A  +F++M  + V  D  TY+  + GLC  G +  A+ +F+ L
Sbjct:   435 TYTTIIQGFFQAGDCDSAQMVFKQMVSNRVPTDIMTYSILLHGLCSYGKLDTALVIFKYL 494

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                + EL+I  YN +I+G+CK+G++  A +LF SL    +  DVVTYN MI GLC+   +
Sbjct:   495 QKSEMELNIFIYNTMIEGMCKAGKVGEAWDLFCSLS---IKPDVVTYNTMISGLCSKRLL 551

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
              +A DLF  M+E+   PN   + TLI   +R    +   EL+ +M+    + DAS +S+V
Sbjct:   552 QEADDLFRKMKEDGTLPNSGTYNTLIRANLRDCDRAASAELIKEMRSSGFVGDASTISLV 611

Query:   373 VDLL 376
              ++L
Sbjct:   612 TNML 615

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2195047 AT1G12620 [Arabidopsis thaliana (taxid:3702)]

 Score = 700 (251.5 bits), Expect = 4.9e-69, P = 4.9e-69
 Identities = 143/364 (39%), Positives = 218/364 (59%)

Query:    13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
             K + V Y+ IIDGLCK+G +D A  LF +M+ +    D++ Y +LI G C+A  W++  +
Sbjct:   244 KLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIIIYTTLIRGFCYAGRWDDGAK 303

Query:    73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
             L  +M+ + + P VV F+ ++D   K GK+ EA  L   M+QR + P+  TY++L+DGFC
Sbjct:   304 LLRDMIKRKITPDVVAFSALIDCFVKEGKLREAEELHKEMIQRGISPDTVTYTSLIDGFC 363

Query:   133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
                ++++A  +   M S GC  +  ++NILINGYCK   +++ L L+R+M  +G+    V
Sbjct:   364 KENQLDKANHMLDLMVSKGCGPNIRTFNILINGYCKANLIDDGLELFRKMSLRGVVADTV 423

Query:   193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL 252
             TYNTL  G  E+ ++E A +LF+EM    V  D  +Y   +DGLC NG   +A+E+F  +
Sbjct:   424 TYNTLIQGFCELGKLEVAKELFQEMVSRRVRPDIVSYKILLDGLCDNGEPEKALEIFEKI 483

Query:   253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
                K ELDI  YN +I G+C + +++ A +LF SLP + +  DV TYNIMI GLC  G +
Sbjct:   484 EKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPDVKTYNIMIGGLCKKGSL 543

Query:   313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV 372
              +A  LF  MEE+  +PN   +  LI   +     +K  +L+ ++K      DAS V MV
Sbjct:   544 SEADLLFRKMEEDGHSPNGCTYNILIRAHLGEGDATKSAKLIEEIKRCGFSVDASTVKMV 603

Query:   373 VDLL 376
             VD+L
Sbjct:   604 VDML 607

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	376
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	7e-28
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-27
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-27
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	3e-26
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	5e-24
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-20
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-19
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-18
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-18
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-17
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-17
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	6e-16
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-14
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-12
pfam13041	50	pfam13041, PPR_2, PPR repeat family	5e-11
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-11
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-10
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-10
pfam12854	34	pfam12854, PPR_1, PPR repeat	8e-10
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	9e-10
pfam01535	31	pfam01535, PPR, PPR repeat	5e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	7e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-08
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-08
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-08
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-08
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	9e-08
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	8e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-06
pfam01535	31	pfam01535, PPR, PPR repeat	1e-06
pfam01535	31	pfam01535, PPR, PPR repeat	3e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-06
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	4e-06
pfam01535	31	pfam01535, PPR, PPR repeat	5e-06
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	5e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-05
pfam01535	31	pfam01535, PPR, PPR repeat	4e-05
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-04
pfam01535	31	pfam01535, PPR, PPR repeat	7e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	8e-04
pfam01535	31	pfam01535, PPR, PPR repeat	0.001
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.002
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.003
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.003
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.004
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.004

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

 Score =  114 bits (288), Expect = 7e-28
 Identities = 79/367 (21%), Positives = 162/367 (44%), Gaps = 8/367 (2%)

Query: 14  PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRL 73
           P   T+N ++        +D A  +   ++   +  D   Y +LI     +   +    +
Sbjct: 435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEV 494

Query: 74  FFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL 133
           F EM++ GV+ +V TF  ++D   + G++ +A     +M  ++V+P+   ++ L+     
Sbjct: 495 FHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

Query: 134 TGKINRAEELFGSM--ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 191
           +G ++RA ++   M  E+     D ++   L+       +V+ A  +Y+ +    IK T 
Sbjct: 555 SGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTP 614

Query: 192 VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELF-- 249
             Y        +    + AL ++++M++  V  D   ++  +D     G + +A E+   
Sbjct: 615 EVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQD 674

Query: 250 -RTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN 308
            R  GI   +L   +Y+ L+     +   + ALEL+  +    L   V T N +I  LC 
Sbjct: 675 ARKQGI---KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCE 731

Query: 309 DGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASI 368
             Q+ KA ++  +M+   + PN I +  L+    R +     ++LL + KE  + P+  +
Sbjct: 732 GNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVM 791

Query: 369 VSMVVDL 375
              +  L
Sbjct: 792 CRCITGL 798

Length = 1060

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

 Score =  113 bits (285), Expect = 2e-27
 Identities = 78/328 (23%), Positives = 149/328 (45%), Gaps = 2/328 (0%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           K +   Y T+I    K G VD    +F +M    +  +V T+ +LI G   A    +A  
Sbjct: 469 KADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFG 528

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMV--QRDVRPNAFTYSTLMDG 130
            +  M  + V+P  V FN ++    ++G +D A  +L  M      + P+  T   LM  
Sbjct: 529 AYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKA 588

Query: 131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT 190
               G+++RA+E++  +     K     Y I +N   +  + + ALS+Y +M  KG+KP 
Sbjct: 589 CANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPD 648

Query: 191 VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR 250
            V ++ L         ++ A ++ ++ ++  +   T +Y++ +          +A+EL+ 
Sbjct: 649 EVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYE 708

Query: 251 TLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDG 310
            +  +K    +   N LI  LC+  +L  ALE+   + R  L  + +TY+I++       
Sbjct: 709 DIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKD 768

Query: 311 QMDKAHDLFLDMEENAVAPNVIIFVTLI 338
             D   DL    +E+ + PN+++   + 
Sbjct: 769 DADVGLDLLSQAKEDGIKPNLVMCRCIT 796

Length = 1060

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

 Score =  112 bits (282), Expect = 4e-27
 Identities = 103/427 (24%), Positives = 173/427 (40%), Gaps = 87/427 (20%)

Query: 20  NTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMD 79
           N +I    K G V  A+ +F +M       D +++N++I G     +  E   LFF M +
Sbjct: 226 NALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFFTMRE 281

Query: 80  QGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINR 139
             V P ++T   ++      G       +   +V+     +    ++L+  +   G    
Sbjct: 282 LSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGE 341

Query: 140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLF- 198
           AE++F  ME    K D VS+  +I+GY KN   ++AL  Y  M    + P  +T  ++  
Sbjct: 342 AEKVFSRME---TK-DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLS 397

Query: 199 ----LGLF----EIHQ--------------------------VEHALKLFEEMQRDDVAA 224
               LG      ++H+                          ++ AL++F  +   DV +
Sbjct: 398 ACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVIS 457

Query: 225 DTSTYNTFIDGLCKNGYIVEAVELFRTL---------------------GILKCELDIQA 263
            TS     I GL  N    EA+  FR +                     G L C  +I A
Sbjct: 458 WTS----IIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHA 513

Query: 264 Y-------------NCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDG 310
           +             N L+D   + GR+  A   F S  +     DVV++NI++ G    G
Sbjct: 514 HVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHG 568

Query: 311 QMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK-KVMPDASIV 369
           +   A +LF  M E+ V P+ + F++L+    R    ++ +E  H M+EK  + P+    
Sbjct: 569 KGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHY 628

Query: 370 SMVVDLL 376
           + VVDLL
Sbjct: 629 ACVVDLL 635

Length = 857

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

 Score =  110 bits (276), Expect = 3e-26
 Identities = 68/264 (25%), Positives = 129/264 (48%), Gaps = 5/264 (1%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGEN--INPDVVTYNSLIHGLCHANDWNEA 70
           KP+ V +N +I    + G VD+A  +  +MK E   I+PD +T  +L+    +A   + A
Sbjct: 539 KPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRA 598

Query: 71  KRLFFEMMDQ-GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD 129
           K ++ +M+ +  ++ +   + + ++   + G  D A  + D M ++ V+P+   +S L+D
Sbjct: 599 KEVY-QMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVD 657

Query: 130 GFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP 189
                G +++A E+       G K   VSY+ L+      K  ++AL LY ++ S  ++P
Sbjct: 658 VAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRP 717

Query: 190 TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELF 249
           TV T N L   L E +Q+  AL++  EM+R  +  +T TY+  +    +       ++L 
Sbjct: 718 TVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLL 777

Query: 250 RTLGILKCELDIQAYNCLIDGLCK 273
                   + ++    C+  GLC 
Sbjct: 778 SQAKEDGIKPNLVMCRCIT-GLCL 800

Length = 1060

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

 Score =  103 bits (258), Expect = 5e-24
 Identities = 84/330 (25%), Positives = 139/330 (42%), Gaps = 57/330 (17%)

Query: 14  PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRL 73
           P+    N ++    K G +  A+ LF +M   N+     ++ ++I GL  A ++ EA  L
Sbjct: 156 PDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNL----ASWGTIIGGLVDAGNYREAFAL 211

Query: 74  FFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL 133
           F EM + G      TF V++      G      +L   +++  V  + F    L+D +  
Sbjct: 212 FREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSK 271

Query: 134 TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT 193
            G I  A  +F  M     +   V++N ++ GY  +   EEAL LY EM   G+     T
Sbjct: 272 CGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFT 327

Query: 194 YNTLF-----LGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVEL 248
           ++ +      L L E  +  HA                        GL + G+       
Sbjct: 328 FSIMIRIFSRLALLEHAKQAHA------------------------GLIRTGF------- 356

Query: 249 FRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN 308
                     LDI A   L+D   K GR+E A  +F  +PR+    +++++N +I G  N
Sbjct: 357 ---------PLDIVANTALVDLYSKWGRMEDARNVFDRMPRK----NLISWNALIAGYGN 403

Query: 309 DGQMDKAHDLFLDMEENAVAPNVIIFVTLI 338
            G+  KA ++F  M    VAPN + F+ ++
Sbjct: 404 HGRGTKAVEMFERMIAEGVAPNHVTFLAVL 433

Length = 697

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

 Score = 82.5 bits (205), Expect = 3e-20
 Identities = 28/50 (56%), Positives = 36/50 (72%)

Query: 14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH 63
          P+ VTYNT+IDG CK+G V++A  LF +MK   I P+V TY+ LI GLC 
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 90.7 bits (225), Expect = 1e-19
 Identities = 65/282 (23%), Positives = 116/282 (41%), Gaps = 40/282 (14%)

Query: 7   EIGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND 66
           + GV  KP+ V ++ ++D     G +DKA  +    + + I    V+Y+SL+    +A +
Sbjct: 642 KKGV--KPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKN 699

Query: 67  WNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYST 126
           W +A  L+ ++    ++P+V T N ++  LC+  ++ +A  +L  M +  + PN  TYS 
Sbjct: 700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSI 759

Query: 127 LMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNIL----INGYCK-------------- 168
           L+         +   +L         K D +  N++    I G C               
Sbjct: 760 LLVASERKDDADVGLDLL-----SQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVV 814

Query: 169 ----------NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQ 218
                     NK    AL +YRE +S G  PT+   + +   L   H      +L E + 
Sbjct: 815 SFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLG 874

Query: 219 RDDVAADTSTYNTFIDGLCKNGYIVEAVELFR---TLGILKC 257
               +   S  +T +DG  +  Y   A  L     +LG++  
Sbjct: 875 ISADSQKQSNLSTLVDGFGE--YDPRAFSLLEEAASLGVVPS 914

Length = 1060

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

 Score = 85.3 bits (211), Expect = 5e-18
 Identities = 84/360 (23%), Positives = 137/360 (38%), Gaps = 59/360 (16%)

Query: 55  NSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEA-----SRLL 109
           NS +  LC      +A +L   M +  V      + V +  LC+  +  E      SR L
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAY-VALFRLCEWKRAVEEGSRVCSRAL 113

Query: 110 DLMVQRDVR-PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK 168
                  VR  NA      +  F   G++  A  +FG M     + D  S+N+L+ GY K
Sbjct: 114 SSHPSLGVRLGNAM-----LSMFVRFGELVHAWYVFGKMP----ERDLFSWNVLVGGYAK 164

Query: 169 NKEVEEALSLYREMVSKGIKPTVVTY---------------------------------- 194
               +EAL LY  M+  G++P V T+                                  
Sbjct: 165 AGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDV 224

Query: 195 -NTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLG 253
            N L     +   V  A  +F+ M R D      ++N  I G  +NG  +E +ELF T+ 
Sbjct: 225 VNALITMYVKCGDVVSARLVFDRMPRRDCI----SWNAMISGYFENGECLEGLELFFTMR 280

Query: 254 ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMD 313
            L  + D+     +I      G   +  E+   + +     DV   N +I    + G   
Sbjct: 281 ELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWG 340

Query: 314 KAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVV 373
           +A  +F  ME      + + +  +I G+ +   P K +E    M++  V PD   ++ V+
Sbjct: 341 EAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVL 396

Length = 857

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

 Score = 75.9 bits (188), Expect = 8e-18
 Identities = 24/49 (48%), Positives = 36/49 (73%)

Query: 84  PSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
           P VVT+N ++D  CK GK++EA +L + M +R ++PN +TYS L+DG C
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 75.1 bits (186), Expect = 2e-17
 Identities = 28/47 (59%), Positives = 34/47 (72%)

Query: 155 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL 201
           D V+YN LI+GYCK  +VEEAL L+ EM  +GIKP V TY+ L  GL
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 74.0 bits (183), Expect = 4e-17
 Identities = 25/50 (50%), Positives = 36/50 (72%)

Query: 49 PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK 98
          PDVVTYN+LI G C      EA +LF EM  +G++P+V T+++++D LCK
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 81.4 bits (201), Expect = 1e-16
 Identities = 65/244 (26%), Positives = 103/244 (42%), Gaps = 21/244 (8%)

Query: 17  VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFE 76
           V  N +I+   K   +DKA  +F  +       DV+++ S+I GL   N   EA  +FF 
Sbjct: 425 VVANALIEMYSKCKCIDKALEVFHNIP----EKDVISWTSIIAGLRLNNRCFEA-LIFFR 479

Query: 77  MMDQGVQPSVVTFNVIMDELCK-----NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF 131
            M   ++P+ VT    +    +      GK   A  L   +      PNA     L+D +
Sbjct: 480 QMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNA-----LLDLY 534

Query: 132 CLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 191
              G++N A   F S      + D VS+NIL+ GY  + +   A+ L+  MV  G+ P  
Sbjct: 535 VRCGRMNYAWNQFNS-----HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDE 589

Query: 192 VTYNTLFLGLFEIHQVEHALKLFEEMQRD-DVAADTSTYNTFIDGLCKNGYIVEAVELFR 250
           VT+ +L         V   L+ F  M+    +  +   Y   +D L + G + EA     
Sbjct: 590 VTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFIN 649

Query: 251 TLGI 254
            + I
Sbjct: 650 KMPI 653

Length = 857

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

 Score = 70.9 bits (175), Expect = 6e-16
 Identities = 23/50 (46%), Positives = 34/50 (68%)

Query: 119 PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK 168
           P+  TY+TL+DG+C  GK+  A +LF  M+  G K +  +Y+ILI+G CK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 76.8 bits (189), Expect = 3e-15
 Identities = 76/366 (20%), Positives = 141/366 (38%), Gaps = 50/366 (13%)

Query: 15  NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLF 74
           +  ++N ++ G  K G+ D+A  L+ +M    + PDV T+  ++       D    + + 
Sbjct: 151 DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVH 210

Query: 75  FEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD-VRPNAFTYSTLMDGFCL 133
             ++  G +  V   N ++    K G +  A  + D M +RD +  NA       +G CL
Sbjct: 211 AHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECL 270

Query: 134 TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT 193
            G      ELF +M  +    D ++   +I+      +      ++  +V  G    V  
Sbjct: 271 EGL-----ELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSV 325

Query: 194 YNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL- 252
            N+L      +     A K+F  M+  D      ++   I G  KNG   +A+E +  + 
Sbjct: 326 CNSLIQMYLSLGSWGEAEKVFSRMETKDAV----SWTAMISGYEKNGLPDKALETYALME 381

Query: 253 --------------------------GILKCELDIQA--------YNCLIDGLCKSGRLE 278
                                     G+   EL  +          N LI+   K   ++
Sbjct: 382 QDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCID 441

Query: 279 IALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLI 338
            ALE+F ++P +    DV+++  +I GL  + +  +A   F  M    + PN +  +  +
Sbjct: 442 KALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAAL 496

Query: 339 HGFVRI 344
               RI
Sbjct: 497 SACARI 502

Length = 857

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

 Score = 67.4 bits (166), Expect = 9e-15
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query: 295 DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR 343
           DVVTYN +I G C  G++++A  LF +M++  + PNV  +  LI G  +
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

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

 Score = 66.7 bits (164), Expect = 2e-14
 Identities = 24/49 (48%), Positives = 34/49 (69%)

Query: 260 DIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN 308
           D+  YN LIDG CK G++E AL+LF  + +R +  +V TY+I+I GLC 
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

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

 Score = 69.1 bits (169), Expect = 1e-12
 Identities = 64/310 (20%), Positives = 122/310 (39%), Gaps = 44/310 (14%)

Query: 15  NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINP------------------------- 49
           N  ++ TII GL   G   +A ALF +M  +  +                          
Sbjct: 188 NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLH 247

Query: 50  ----------DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN 99
                     D     +LI       D  +A+ +F    D   + + V +N ++     +
Sbjct: 248 CCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVF----DGMPEKTTVAWNSMLAGYALH 303

Query: 100 GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSY 159
           G  +EA  L   M    V  + FT+S ++  F     +  A++    +   G   D V+ 
Sbjct: 304 GYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVAN 363

Query: 160 NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR 219
             L++ Y K   +E+A +++  M  K +    +++N L  G     +   A+++FE M  
Sbjct: 364 TALVDLYSKWGRMEDARNVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVEMFERMIA 419

Query: 220 DDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLG-ILKCELDIQAYNCLIDGLCKSGRLE 278
           + VA +  T+   +     +G   +  E+F+++    + +     Y C+I+ L + G L+
Sbjct: 420 EGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLD 479

Query: 279 IALELFRSLP 288
            A  + R  P
Sbjct: 480 EAYAMIRRAP 489

Length = 697

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

 Score = 57.0 bits (139), Expect = 5e-11
 Identities = 23/49 (46%), Positives = 31/49 (63%)

Query: 225 DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCK 273
           D  TYNT IDG CK G + EA++LF  +     + ++  Y+ LIDGLCK
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

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 56.6 bits (138), Expect = 5e-11
 Identities = 18/32 (56%), Positives = 24/32 (75%)

Query: 12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMK 43
           KP+ VTYNT+IDGLC+ G VD+A  L  +M+
Sbjct: 3  LKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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

 Score = 62.6 bits (152), Expect = 1e-10
 Identities = 58/254 (22%), Positives = 101/254 (39%), Gaps = 21/254 (8%)

Query: 100 GKMDEASRLLDLMVQR-DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVS 158
           G+  EA  L +++         A TY  L++       I   + ++  +ES G + D   
Sbjct: 101 GRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYM 160

Query: 159 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQ 218
            N ++  + K   + +A  L+ EM  + +     ++ T+  GL +      A  LF EM 
Sbjct: 161 MNRVLLMHVKCGMLIDARRLFDEMPERNL----ASWGTIIGGLVDAGNYREAFALFREMW 216

Query: 219 RDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYN-----C-LIDGLC 272
            D   A+  T+   +      G      +L        C L           C LID   
Sbjct: 217 EDGSDAEPRTFVVMLRASAGLGSARAGQQLH------CCVLKTGVVGDTFVSCALIDMYS 270

Query: 273 KSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVI 332
           K G +E A  +F  +P +  VA    +N M+ G    G  ++A  L+ +M ++ V+ +  
Sbjct: 271 KCGDIEDARCVFDGMPEKTTVA----WNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQF 326

Query: 333 IFVTLIHGFVRINK 346
            F  +I  F R+  
Sbjct: 327 TFSIMIRIFSRLAL 340

Length = 697

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

 Score = 61.8 bits (150), Expect = 3e-10
 Identities = 61/254 (24%), Positives = 104/254 (40%), Gaps = 46/254 (18%)

Query: 121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE-VEEALSLY 179
             + S L    C  G++ +A +L  SM+ +    D+ +Y  L    C+ K  VEE   + 
Sbjct: 52  HDSNSQLR-ALCSHGQLEQALKLLESMQELRVPVDEDAYVALFR-LCEWKRAVEEGSRVC 109

Query: 180 REMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKN 239
              +S      V   N +        ++ HA  +F +M   D+     ++N  + G  K 
Sbjct: 110 SRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLF----SWNVLVGGYAKA 165

Query: 240 GYIVEAVELF-------------------RTLG--------------ILK--CELDIQAY 264
           GY  EA+ L+                   RT G              +++   ELD+   
Sbjct: 166 GYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVV 225

Query: 265 NCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE 324
           N LI    K G +  A  +F  +PRR    D +++N MI G   +G+  +  +LF  M E
Sbjct: 226 NALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFFTMRE 281

Query: 325 NAVAPNVIIFVTLI 338
            +V P+++   ++I
Sbjct: 282 LSVDPDLMTITSVI 295

Length = 857

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 53.1 bits (129), Expect = 8e-10
 Identities = 16/34 (47%), Positives = 21/34 (61%)

Query: 150 MGCKHDDVSYNILINGYCKNKEVEEALSLYREMV 183
            G K D V+YN LI+G C+   V+EA+ L  EM 
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 52.8 bits (128), Expect = 9e-10
 Identities = 20/35 (57%), Positives = 26/35 (74%)

Query: 157 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 191
           V+YN LI+G CK   VEEAL L++EM  +GI+P V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

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

 Score = 50.9 bits (123), Expect = 5e-09
 Identities = 18/31 (58%), Positives = 25/31 (80%)

Query: 157 VSYNILINGYCKNKEVEEALSLYREMVSKGI 187
           V+YN LI+GYCK  ++EEAL L++EM  KG+
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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|205109 pfam12854, PPR_1, PPR repeat

 Score = 50.4 bits (122), Expect = 7e-09
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 80  QGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMV 113
           +G++P VVT+N ++D LC+ G++DEA  LLD M 
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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|205109 pfam12854, PPR_1, PPR repeat

 Score = 49.3 bits (119), Expect = 2e-08
 Identities = 17/32 (53%), Positives = 23/32 (71%)

Query: 292 LVADVVTYNIMIHGLCNDGQMDKAHDLFLDME 323
           L  DVVTYN +I GLC  G++D+A +L  +ME
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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|205109 pfam12854, PPR_1, PPR repeat

 Score = 48.9 bits (118), Expect = 2e-08
 Identities = 18/32 (56%), Positives = 21/32 (65%)

Query: 46 NINPDVVTYNSLIHGLCHANDWNEAKRLFFEM 77
           + PDVVTYN+LI GLC A   +EA  L  EM
Sbjct: 2  GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 49.0 bits (118), Expect = 2e-08
 Identities = 19/35 (54%), Positives = 24/35 (68%)

Query: 52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV 86
          VTYN+LI GLC A    EA  LF EM ++G++P V
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 48.5 bits (117), Expect = 4e-08
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 115 RDVRPNAFTYSTLMDGFCLTGKINRAEELFGSME 148
           + ++P+  TY+TL+DG C  G+++ A EL   ME
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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

 Score = 53.7 bits (129), Expect = 9e-08
 Identities = 30/129 (23%), Positives = 65/129 (50%), Gaps = 6/129 (4%)

Query: 14  PNTVTYNT-IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR 72
           P  +  NT ++D   K G ++ A+ +F +M  +N+    +++N+LI G  +     +A  
Sbjct: 357 PLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVE 412

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQ-RDVRPNAFTYSTLMDGF 131
           +F  M+ +GV P+ VTF  ++     +G  ++   +   M +   ++P A  Y+ +++  
Sbjct: 413 MFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELL 472

Query: 132 CLTGKINRA 140
              G ++ A
Sbjct: 473 GREGLLDEA 481

Length = 697

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

 Score = 46.7 bits (112), Expect = 2e-07
 Identities = 22/35 (62%), Positives = 26/35 (74%)

Query: 17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDV 51
          VTYNT+IDGLCK G V++A  LF +MK   I PDV
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 44.6 bits (107), Expect = 8e-07
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 220 DDVAADTSTYNTFIDGLCKNGYIVEAVELFR 250
             +  D  TYNT IDGLC+ G + EAVEL  
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLD 31

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|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 49.8 bits (119), Expect = 1e-06
 Identities = 42/185 (22%), Positives = 82/185 (44%), Gaps = 19/185 (10%)

Query: 11  VCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEA 70
             + + V++N ++ G    G    A  LF +M    +NPD VT+ SL+     +    + 
Sbjct: 549 SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQG 608

Query: 71  KRLFFEMMDQ-GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD 129
              F  M ++  + P++  +  ++D L + GK+ EA   ++ M    + P+   +  L++
Sbjct: 609 LEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWGALLN 665

Query: 130 GFCLTGKINRAEELFGSMESMGCKH------DDVSYNILI-NGYCKNKEVEEALSLYREM 182
             C   +I+R  EL      +  +H      + V Y IL+ N Y    + +E   + + M
Sbjct: 666 A-C---RIHRHVEL----GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTM 717

Query: 183 VSKGI 187
              G+
Sbjct: 718 RENGL 722

Length = 857

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

 Score = 44.4 bits (106), Expect = 1e-06
 Identities = 16/35 (45%), Positives = 26/35 (74%)

Query: 297 VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV 331
           VTYN +I GLC  G++++A +LF +M+E  + P+V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

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

 Score = 44.0 bits (105), Expect = 1e-06
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENI 47
          VTYN++I G CK G +++A  LF +MK + +
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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|144943 pfam01535, PPR, PPR repeat

 Score = 43.2 bits (103), Expect = 3e-06
 Identities = 18/31 (58%), Positives = 20/31 (64%)

Query: 52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGV 82
          VTYNSLI G C A    EA  LF EM ++GV
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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|205109 pfam12854, PPR_1, PPR repeat

 Score = 42.7 bits (102), Expect = 4e-06
 Identities = 14/29 (48%), Positives = 21/29 (72%)

Query: 257 CELDIQAYNCLIDGLCKSGRLEIALELFR 285
            + D+  YN LIDGLC++GR++ A+EL  
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELLD 31

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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 42.9 bits (102), Expect = 4e-06
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQP 84
          + TYN+L+  L  A D + A  +  EM   G++P
Sbjct: 1  LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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 = 42.4 bits (101), Expect = 5e-06
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 297 VTYNIMIHGLCNDGQMDKAHDLFLDMEEN 325
           VTYN +I G C  G++++A +LF +M+E 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEK 29

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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 157 VSYNILINGYCKNKEVEEALSLYREMVSKGIKP 189
            +YN L+    K  + + AL++  EM + G+KP
Sbjct: 2   ETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 41.7 bits (99), Expect = 1e-05
 Identities = 15/35 (42%), Positives = 21/35 (60%)

Query: 122 FTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDD 156
            TY+TL+DG C  G++  A ELF  M+  G + D 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

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

 Score = 41.3 bits (98), Expect = 1e-05
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 87  VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA 121
           VT+N ++D LCK G+++EA  L   M +R + P+ 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

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

 Score = 39.7 bits (94), Expect = 4e-05
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 122 FTYSTLMDGFCLTGKINRAEELFGSMESMGC 152
            TY++L+ G+C  GK+  A ELF  M+  G 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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|144943 pfam01535, PPR, PPR repeat

 Score = 38.2 bits (90), Expect = 2e-04
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 87  VTFNVIMDELCKNGKMDEASRLLDLMVQRDV 117
           VT+N ++   CK GK++EA  L   M ++ V
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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 = 36.6 bits (86), Expect = 7e-04
 Identities = 11/17 (64%), Positives = 13/17 (76%)

Query: 12 CKPNTVTYNTIIDGLCK 28
           KPN  TY+ +IDGLCK
Sbjct: 34 IKPNVYTYSILIDGLCK 50

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

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

 Score = 36.3 bits (85), Expect = 7e-04
 Identities = 13/24 (54%), Positives = 17/24 (70%)

Query: 227 STYNTFIDGLCKNGYIVEAVELFR 250
            TYN+ I G CK G + EA+ELF+
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFK 24

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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 36.3 bits (85), Expect = 8e-04
 Identities = 20/34 (58%), Positives = 25/34 (73%)

Query: 263 AYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV 296
            YN LIDGLCK+GR+E ALELF+ +  R +  DV
Sbjct: 2   TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

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

 Score = 35.9 bits (84), Expect = 0.001
 Identities = 15/28 (53%), Positives = 20/28 (71%)

Query: 263 AYNCLIDGLCKSGRLEIALELFRSLPRR 290
            YN LI G CK+G+LE ALELF+ +  +
Sbjct: 2   TYNSLISGYCKAGKLEEALELFKEMKEK 29

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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 35.1 bits (82), Expect = 0.002
 Identities = 11/35 (31%), Positives = 20/35 (57%)

Query: 332 IIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA 366
           + + TLI G  +  +  + +EL  +MKE+ + PD 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

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

 Score = 34.7 bits (81), Expect = 0.003
 Identities = 18/34 (52%), Positives = 23/34 (67%)

Query: 228 TYNTFIDGLCKNGYIVEAVELFRTLGILKCELDI 261
           TYNT IDGLCK G + EA+ELF+ +     E D+
Sbjct: 2   TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 34.8 bits (81), Expect = 0.003
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP 329
           + TYN ++  L   G  D A  +  +M+ + + P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 34.4 bits (80), Expect = 0.004
 Identities = 17/35 (48%), Positives = 23/35 (65%)

Query: 192 VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT 226
           VTYNTL  GL +  +VE AL+LF+EM+   +  D 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 86  VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRP 119
           + T+N ++  L K G  D A  +L+ M    ++P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	376
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.97
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.97
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.96
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.96
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.95
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.95
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.94
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.94
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.94
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.94
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.93
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.93
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.91
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.89
KOG2076	895	consensus RNA polymerase III transcription factor	99.85
PRK14574	822	hmsH outer membrane protein; Provisional	99.85
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.84
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.83
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.83
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.83
PRK14574	822	hmsH outer membrane protein; Provisional	99.83
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.83
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.82
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.82
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.82
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.82
KOG1126	638	consensus DNA-binding cell division cycle control	99.82
KOG1126	638	consensus DNA-binding cell division cycle control	99.81
KOG2003	840	consensus TPR repeat-containing protein [General f	99.81
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.81
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.8
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.8
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.8
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.79
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.79
KOG2076	895	consensus RNA polymerase III transcription factor	99.79
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.77
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.77
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.75
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.75
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.75
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.73
KOG2003	840	consensus TPR repeat-containing protein [General f	99.71
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.71
KOG1129	478	consensus TPR repeat-containing protein [General f	99.7
PRK12370	553	invasion protein regulator; Provisional	99.69
KOG1129	478	consensus TPR repeat-containing protein [General f	99.69
PRK12370	553	invasion protein regulator; Provisional	99.68
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.68
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.68
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.66
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.64
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.63
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.59
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.59
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.59
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.58
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.57
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.56
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.55
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.55
PRK11189	296	lipoprotein NlpI; Provisional	99.54
PRK11189	296	lipoprotein NlpI; Provisional	99.54
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.53
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.53
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.53
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.48
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.48
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.46
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.46
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.46
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.45
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.44
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.41
KOG1125	579	consensus TPR repeat-containing protein [General f	99.41
PF13041	50	PPR_2: PPR repeat family	99.4
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.4
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.4
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.38
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.36
PF13041	50	PPR_2: PPR repeat family	99.32
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.31
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.31
KOG1125	579	consensus TPR repeat-containing protein [General f	99.31
PRK04841	903	transcriptional regulator MalT; Provisional	99.29
PLN02789	320	farnesyltranstransferase	99.26
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.25
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.23
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.23
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.23
PLN02789	320	farnesyltranstransferase	99.21
KOG1128	777	consensus Uncharacterized conserved protein, conta	99.2
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.18
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.18
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.17
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.16
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	99.15
PRK04841	903	transcriptional regulator MalT; Provisional	99.13
PRK14720	906	transcript cleavage factor/unknown domain fusion p	99.11
KOG1128	777	consensus Uncharacterized conserved protein, conta	99.1
PRK10370	198	formate-dependent nitrite reductase complex subuni	99.08
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	99.07
PRK14720	906	transcript cleavage factor/unknown domain fusion p	99.07
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	99.07
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.05
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	99.04
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.04
PRK10370	198	formate-dependent nitrite reductase complex subuni	99.03
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.02
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	99.0
PRK15359	144	type III secretion system chaperone protein SscB;	99.0
PRK15359	144	type III secretion system chaperone protein SscB;	99.0
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.99
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.99
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.95
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.94
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.93
PF12854	34	PPR_1: PPR repeat	98.92
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.9
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.89
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.85
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.85
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.83
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.81
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.77
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.76
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.75
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.71
PF12854	34	PPR_1: PPR repeat	98.68
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.68
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.66
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.65
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.65
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.62
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.61
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.61
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.47
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.47
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.44
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.42
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.42
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	98.41
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.39
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.38
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	98.38
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.37
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.36
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.34
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.34
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.33
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.32
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.31
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.29
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.29
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.29
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.28
PF12688	120	TPR_5: Tetratrico peptide repeat	98.27
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.26
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	98.26
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.23
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.23
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	98.23
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.22
KOG0553	304	consensus TPR repeat-containing protein [General f	98.22
KOG0553	304	consensus TPR repeat-containing protein [General f	98.21
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.2
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	98.2
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	98.18
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.17
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.16
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.14
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	98.13
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.11
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	98.1
COG3898	531	Uncharacterized membrane-bound protein [Function u	98.1
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	98.09
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	98.08
PF12688	120	TPR_5: Tetratrico peptide repeat	98.08
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	98.07
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	98.07
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	98.06
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	98.03
COG4700	251	Uncharacterized protein conserved in bacteria cont	98.02
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.0
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.0
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.99
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.96
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.95
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.95
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.89
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.85
PRK10803	263	tol-pal system protein YbgF; Provisional	97.84
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.82
PRK15331	165	chaperone protein SicA; Provisional	97.81
PRK10803	263	tol-pal system protein YbgF; Provisional	97.81
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.78
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.76
PRK15331	165	chaperone protein SicA; Provisional	97.76
PF13371	73	TPR_9: Tetratricopeptide repeat	97.75
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.73
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.68
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.64
PF13371	73	TPR_9: Tetratricopeptide repeat	97.6
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.55
KOG1585	308	consensus Protein required for fusion of vesicles	97.53
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.53
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.53
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.51
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.46
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	97.41
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.38
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.37
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	97.35
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	97.31
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.3
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	97.26
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	97.25
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	97.23
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.21
KOG1258	577	consensus mRNA processing protein [RNA processing	97.21
KOG2610	491	consensus Uncharacterized conserved protein [Funct	97.21
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.21
PF13512	142	TPR_18: Tetratricopeptide repeat	97.2
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	97.2
COG3118	304	Thioredoxin domain-containing protein [Posttransla	97.2
COG4105	254	ComL DNA uptake lipoprotein [General function pred	97.16
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	97.14
PRK11906	458	transcriptional regulator; Provisional	97.14
PRK11906	458	transcriptional regulator; Provisional	97.12
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.1
KOG1585	308	consensus Protein required for fusion of vesicles	97.07
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.07
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	97.05
PF13428	44	TPR_14: Tetratricopeptide repeat	96.96
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.96
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.88
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.86
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.85
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.85
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.81
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.8
KOG4555	175	consensus TPR repeat-containing protein [Function	96.79
PF13428	44	TPR_14: Tetratricopeptide repeat	96.69
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	96.69
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.68
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.62
KOG4555	175	consensus TPR repeat-containing protein [Function	96.6
COG0457	291	NrfG FOG: TPR repeat [General function prediction	96.55
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.49
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.48
COG0457	291	NrfG FOG: TPR repeat [General function prediction	96.45
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	96.43
KOG1550	552	consensus Extracellular protein SEL-1 and related	96.39
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	96.35
KOG1258	577	consensus mRNA processing protein [RNA processing	96.17
COG3629	280	DnrI DNA-binding transcriptional activator of the	96.06
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	96.03
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.97
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.92
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.81
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	95.69
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	95.69
PF13431	34	TPR_17: Tetratricopeptide repeat	95.69
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	95.68
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	95.66
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.65
PF13431	34	TPR_17: Tetratricopeptide repeat	95.63
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.63
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	95.5
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.47
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.45
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.42
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.38
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	95.26
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.26
KOG3941	406	consensus Intermediate in Toll signal transduction	95.16
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	95.07
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	95.04
PF13512	142	TPR_18: Tetratricopeptide repeat	95.03
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.03
KOG1550	552	consensus Extracellular protein SEL-1 and related	94.82
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.69
KOG4234	271	consensus TPR repeat-containing protein [General f	94.67
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	94.53
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	94.51
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	94.42
KOG3941	406	consensus Intermediate in Toll signal transduction	94.36
KOG4234	271	consensus TPR repeat-containing protein [General f	94.35
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	94.32
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	94.3
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.3
KOG4648	536	consensus Uncharacterized conserved protein, conta	94.22
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	94.22
KOG2471	696	consensus TPR repeat-containing protein [General f	94.2
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	94.16
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	94.1
PF07575	566	Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR0	94.06
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	93.84
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	93.75
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	93.73
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	93.66
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	93.62
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	93.38
COG4455	273	ImpE Protein of avirulence locus involved in tempe	93.18
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	93.1
KOG4648	536	consensus Uncharacterized conserved protein, conta	93.0
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.86
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	92.85
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.8
PRK11619	644	lytic murein transglycosylase; Provisional	92.77
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	92.66
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	92.44
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	92.4
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	92.37
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	92.26
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	92.2
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	92.2
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	91.86
KOG4642	284	consensus Chaperone-dependent E3 ubiquitin protein	91.84
COG1747	711	Uncharacterized N-terminal domain of the transcrip	91.8
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	91.55
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	91.31
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	91.3
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	91.26
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	91.23
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	91.23
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	91.23
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.17
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	90.96
COG0790	292	FOG: TPR repeat, SEL1 subfamily [General function	90.9
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.68
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	90.59
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	90.43
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	90.25
KOG4507	886	consensus Uncharacterized conserved protein, conta	90.15
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	90.04
KOG4507	886	consensus Uncharacterized conserved protein, conta	89.89
KOG1308	377	consensus Hsp70-interacting protein Hip/Transient	89.42
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	89.35
PRK09687	280	putative lyase; Provisional	88.93
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	88.64
COG4455	273	ImpE Protein of avirulence locus involved in tempe	88.52
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	88.18
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	88.13
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	88.08
PRK11619	644	lytic murein transglycosylase; Provisional	87.97
KOG1586	288	consensus Protein required for fusion of vesicles	87.93
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	87.8
COG1747	711	Uncharacterized N-terminal domain of the transcrip	87.73
KOG4570	418	consensus Uncharacterized conserved protein [Funct	87.35
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	87.35
COG3947	361	Response regulator containing CheY-like receiver a	87.26
COG3947	361	Response regulator containing CheY-like receiver a	86.67
KOG4642	284	consensus Chaperone-dependent E3 ubiquitin protein	86.59
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	86.55
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	86.49
PRK12798	421	chemotaxis protein; Reviewed	85.6
PRK09687	280	putative lyase; Provisional	85.46
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	85.34
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	84.95
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	84.92
COG0790	292	FOG: TPR repeat, SEL1 subfamily [General function	84.9
PRK10941	269	hypothetical protein; Provisional	84.59
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	84.32
PRK10941	269	hypothetical protein; Provisional	83.47
PF10579	80	Rapsyn_N: Rapsyn N-terminal myristoylation and lin	83.35
PF13929	292	mRNA_stabil: mRNA stabilisation	83.1
PF09670	379	Cas_Cas02710: CRISPR-associated protein (Cas_Cas02	82.89
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	82.72
COG4259	121	Uncharacterized protein conserved in bacteria [Fun	82.7
KOG3364	149	consensus Membrane protein involved in organellar	82.22
PF04190	260	DUF410: Protein of unknown function (DUF410) ; Int	82.21
KOG3364	149	consensus Membrane protein involved in organellar	82.16
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	82.09
KOG0686	466	consensus COP9 signalosome, subunit CSN1 [Posttran	80.86
KOG1586	288	consensus Protein required for fusion of vesicles	80.71
KOG0545	329	consensus Aryl-hydrocarbon receptor-interacting pr	80.2
KOG1308	377	consensus Hsp70-interacting protein Hip/Transient	80.19
KOG0376	476	consensus Serine-threonine phosphatase 2A, catalyt	80.14
PF12862	94	Apc5: Anaphase-promoting complex subunit 5	80.06

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1e-59  Score=426.34  Aligned_cols=363  Identities=21%  Similarity=0.373  Sum_probs=355.8

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      .||..+|+.++.+|++.|+++.|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.+
T Consensus       434 ~pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaL  513 (1060)
T PLN03218        434 NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGAL  513 (1060)
T ss_pred             CCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            39999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHh--cCCCCChhhHHHHHHHHHccC
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMES--MGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      +.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|..  .++.|+..+|+.++.+|++.|
T Consensus       514 I~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G  593 (1060)
T PLN03218        514 IDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAG  593 (1060)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCC
Confidence            999999999999999999999999999999999999999999999999999999976  578899999999999999999


Q ss_pred             cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          171 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      ++++|.++|+.|.+.|+.|+..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+|++.|++++|.++++
T Consensus       594 ~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~  673 (1060)
T PLN03218        594 QVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQ  673 (1060)
T ss_pred             CHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc
Q 042039          251 TLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       251 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  330 (376)
                      .|.+.+..|+..+|+.++.+|++.|++++|.++|++|...+..||..+|+.++.+|++.|++++|.++|++|.+.|+.||
T Consensus       674 eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd  753 (1060)
T PLN03218        674 DARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPN  753 (1060)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHHhh
Q 042039          331 VIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDL  375 (376)
Q Consensus       331 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  375 (376)
                      ..+|+.++.+|.+.|+.++|.+++++|.+.|+.||..+|++++..
T Consensus       754 ~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIgl  798 (1060)
T PLN03218        754 TITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGL  798 (1060)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999998753

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=7.6e-59  Score=420.70  Aligned_cols=368  Identities=23%  Similarity=0.378  Sum_probs=353.8

Q ss_pred             cccccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchH
Q 042039            8 IGVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVV   87 (376)
Q Consensus         8 ~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~   87 (376)
                      ...|+.||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..
T Consensus       464 ~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~v  543 (1060)
T PLN03218        464 QEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRV  543 (1060)
T ss_pred             HHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHH
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHh--cCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQ--RDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILING  165 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  165 (376)
                      +|+.++.+|++.|++++|.+++++|..  .++.||..+|+.++.+|++.|++++|.++|+.|.+.+++|+..+|+.++.+
T Consensus       544 TYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~a  623 (1060)
T PLN03218        544 VFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS  623 (1060)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHH
Confidence            999999999999999999999999986  578999999999999999999999999999999999999999999999999


Q ss_pred             HHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHH
Q 042039          166 YCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEA  245 (376)
Q Consensus       166 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  245 (376)
                      |++.|++++|.++|++|.+.|+.||..+|+.++.+|.+.|++++|.++++.|.+.+..|+..+|+.++.+|++.|++++|
T Consensus       624 y~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA  703 (1060)
T PLN03218        624 CSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKA  703 (1060)
T ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          246 VELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      .++|+.|...+..|+..+|+.++.+|++.|++++|.++|++|...|+.||..+|+.++.+|.+.|++++|.+++++|.+.
T Consensus       704 ~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~  783 (1060)
T PLN03218        704 LELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKED  783 (1060)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcHHHHHHHHHHHhh----c-------------------CChhhHHHHHHHHHhCCCCCchHHHHHHHhh
Q 042039          326 AVAPNVIIFVTLIHGFVR----I-------------------NKPSKVIELLHKMKEKKVMPDASIVSMVVDL  375 (376)
Q Consensus       326 ~~~~~~~~~~~l~~~~~~----~-------------------g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  375 (376)
                      |+.||..+|+.++..|.+    .                   +..+.|..+|++|.+.|+.||..||+.+|.+
T Consensus       784 Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~c  856 (1060)
T PLN03218        784 GIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGC  856 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Confidence            999999999999865432    1                   2246799999999999999999999999865

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

Probab=100.00  E-value=3.6e-53  Score=380.87  Aligned_cols=350  Identities=22%  Similarity=0.359  Sum_probs=267.5

Q ss_pred             ccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHH
Q 042039           11 VCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFN   90 (376)
Q Consensus        11 ~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   90 (376)
                      |+.||+.+|+.++..|++.|++++|.++|++|.    .||..+|+.++.+|++.|++++|.++|++|.+.|..|+..+|.
T Consensus       153 g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~  228 (697)
T PLN03081        153 GFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFV  228 (697)
T ss_pred             CCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHH
Confidence            445555555555555555555555555555554    2455555555555555555555555555555555555555555


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      .++.++...|..+.+.+++..+.+.|..||..+++.++.+|++.|++++|.++|+.|.    +++..+|+.++.+|++.|
T Consensus       229 ~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~~~vt~n~li~~y~~~g  304 (697)
T PLN03081        229 VMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHG  304 (697)
T ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCC
Confidence            5555555555555555555555566666667777778888888888888888888775    357788888888888888


Q ss_pred             cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          171 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      ++++|+++|++|.+.|+.||..+|..++.+|++.|+++.|.+++..|.+.+.+|+..+++.++.+|++.|++++|.++|+
T Consensus       305 ~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~  384 (697)
T PLN03081        305 YSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFD  384 (697)
T ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHH
Confidence            88888888888888888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             HhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH-cCCCC
Q 042039          251 TLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE-NAVAP  329 (376)
Q Consensus       251 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~  329 (376)
                      .|.+    ||..+|+.++.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|..++|.++|+.|.+ .|+.|
T Consensus       385 ~m~~----~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p  460 (697)
T PLN03081        385 RMPR----KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKP  460 (697)
T ss_pred             hCCC----CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCC
Confidence            8763    577788888888888888888888888888888888888888888888888888888888888875 57888


Q ss_pred             cHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHHhh
Q 042039          330 NVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDL  375 (376)
Q Consensus       330 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  375 (376)
                      +..+|+.++.+|.+.|+.++|.+++++|   ++.|+..+|++++.+
T Consensus       461 ~~~~y~~li~~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~Ll~a  503 (697)
T PLN03081        461 RAMHYACMIELLGREGLLDEAYAMIRRA---PFKPTVNMWAALLTA  503 (697)
T ss_pred             CccchHhHHHHHHhcCCHHHHHHHHHHC---CCCCCHHHHHHHHHH
Confidence            8888888888888888888888887765   678888888888765

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

Probab=100.00  E-value=1.5e-52  Score=376.91  Aligned_cols=354  Identities=23%  Similarity=0.342  Sum_probs=332.1

Q ss_pred             ccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHH
Q 042039           11 VCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFN   90 (376)
Q Consensus        11 ~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   90 (376)
                      +..||..+|+.++.+|.+.++++.+.+++..|.+.|+.||..+|+.++.+|.+.|++++|.++|++|.    .||..+|+
T Consensus       118 ~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~~~~t~n  193 (697)
T PLN03081        118 PFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMP----ERNLASWG  193 (697)
T ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCC----CCCeeeHH
Confidence            45788999999999999999999999999999998988999999999999999999999999998885    36888999


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      .++.+|++.|++++|.++|++|.+.|..|+..+|..++.+++..|..+.+.+++..+.+.|..++..+++.++.+|++.|
T Consensus       194 ~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g  273 (697)
T PLN03081        194 TIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCG  273 (697)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCC
Confidence            99999999999999999999999988899999999999999999999999999999999998999999999999999999


Q ss_pred             cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          171 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      ++++|.++|+.|..    ++..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+|++.|++++|.+++.
T Consensus       274 ~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~  349 (697)
T PLN03081        274 DIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHA  349 (697)
T ss_pred             CHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHH
Confidence            99999999999854    58899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc
Q 042039          251 TLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       251 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  330 (376)
                      .+.+.+..|+..+++.++.+|++.|++++|.++|++|.+    ||..+|+.++.+|++.|+.++|.++|++|.+.|+.||
T Consensus       350 ~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd  425 (697)
T PLN03081        350 GLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPN  425 (697)
T ss_pred             HHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCC
Confidence            999999999999999999999999999999999999965    5889999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCChhhHHHHHHHHHh-CCCCCchHHHHHHHhhC
Q 042039          331 VIIFVTLIHGFVRINKPSKVIELLHKMKE-KKVMPDASIVSMVVDLL  376 (376)
Q Consensus       331 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-~~~~p~~~~~~~ll~~l  376 (376)
                      ..||+.++.+|.+.|+.++|.++|+.|.+ .|+.|+..+|++++++|
T Consensus       426 ~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l  472 (697)
T PLN03081        426 HVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELL  472 (697)
T ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHH
Confidence            99999999999999999999999999986 59999999999999875

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.5e-51  Score=377.42  Aligned_cols=354  Identities=24%  Similarity=0.369  Sum_probs=217.2

Q ss_pred             cccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhH
Q 042039           10 VVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTF   89 (376)
Q Consensus        10 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   89 (376)
                      .|+.||+.+|+.++..|++.|++++|.++|++|.    .||..+|+.++.+|.+.|++++|.++|++|...|+.||..+|
T Consensus       216 ~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty  291 (857)
T PLN03077        216 FGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTI  291 (857)
T ss_pred             cCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHH
Confidence            3556666666666666666666666666666665    345556666666666666666666666666666666666666


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      +.++.++.+.|+.+.+.+++..+.+.|..||..+|+.++.+|++.|++++|.++|++|.    .|+..+|+.++.+|.+.
T Consensus       292 ~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~d~~s~n~li~~~~~~  367 (857)
T PLN03077        292 TSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME----TKDAVSWTAMISGYEKN  367 (857)
T ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC----CCCeeeHHHHHHHHHhC
Confidence            66666666666666666666666666666666666666666666666666666665553    24555566666666666


Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELF  249 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  249 (376)
                      |++++|+++|++|.+.|+.|+..+|..++.++++.|+++.+.++++.+.+.|..++..+++.++.+|.+.|++++|.++|
T Consensus       368 g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf  447 (857)
T PLN03077        368 GLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVF  447 (857)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            66666666666665555555555555555555555555555555555555555555555555555555555555544444


Q ss_pred             HHhccc------------------------------CCCchHHHHHHHH-------------------------------
Q 042039          250 RTLGIL------------------------------KCELDIQAYNCLI-------------------------------  268 (376)
Q Consensus       250 ~~~~~~------------------------------~~~~~~~~~~~l~-------------------------------  268 (376)
                      +.|.+.                              +..||..+|..++                               
T Consensus       448 ~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~  527 (857)
T PLN03077        448 HNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLP  527 (857)
T ss_pred             HhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceec
Confidence            443221                              2355555544433                               


Q ss_pred             ----HHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhc
Q 042039          269 ----DGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRI  344 (376)
Q Consensus       269 ----~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  344 (376)
                          .+|.+.|++++|.++|+.+     .+|..+|+.++.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.
T Consensus       528 naLi~~y~k~G~~~~A~~~f~~~-----~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~  602 (857)
T PLN03077        528 NALLDLYVRCGRMNYAWNQFNSH-----EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRS  602 (857)
T ss_pred             hHHHHHHHHcCCHHHHHHHHHhc-----CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhc
Confidence                4445555555555555544     3566677777777777777777777777777777777777777777777777


Q ss_pred             CChhhHHHHHHHHH-hCCCCCchHHHHHHHhhC
Q 042039          345 NKPSKVIELLHKMK-EKKVMPDASIVSMVVDLL  376 (376)
Q Consensus       345 g~~~~a~~~~~~~~-~~~~~p~~~~~~~ll~~l  376 (376)
                      |++++|.++|+.|. +.|+.|+..+|++++++|
T Consensus       603 g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l  635 (857)
T PLN03077        603 GMVTQGLEYFHSMEEKYSITPNLKHYACVVDLL  635 (857)
T ss_pred             ChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHH
Confidence            77777777777777 457777777777776653

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.5e-51  Score=375.68  Aligned_cols=355  Identities=21%  Similarity=0.274  Sum_probs=328.5

Q ss_pred             ccccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHh
Q 042039            9 GVVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVT   88 (376)
Q Consensus         9 ~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   88 (376)
                      ..|++||..+|+.++.+|...+++..+.+++..+.+.|..||..+++.++.+|.+.|++++|.++|++|.    .||..+
T Consensus       180 ~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~d~~s  255 (857)
T PLN03077        180 WAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCIS  255 (857)
T ss_pred             HcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCC----CCCcch
Confidence            4589999999999999999999999999999999999999999999999999999999999999999986    468899


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  168 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  168 (376)
                      |+.++.+|++.|++++|.++|.+|.+.|+.||..+|+.++.+|++.|+.+.+.+++..+...|+.|+..+|+.++.+|.+
T Consensus       256 ~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k  335 (857)
T PLN03077        256 WNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLS  335 (857)
T ss_pred             hHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHH
Q 042039          169 NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVEL  248 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  248 (376)
                      .|++++|.++|++|.    .|+..+|+.++.+|.+.|++++|.++|++|.+.++.|+..+|..++.+|++.|++++|.++
T Consensus       336 ~g~~~~A~~vf~~m~----~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l  411 (857)
T PLN03077        336 LGSWGEAEKVFSRME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKL  411 (857)
T ss_pred             cCCHHHHHHHHhhCC----CCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHH
Confidence            999999999999986    3688999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC-
Q 042039          249 FRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV-  327 (376)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-  327 (376)
                      ++.+.+.|..|+..+++.++.+|.+.|++++|.++|++|.+.    |..+|+.++.+|.+.|+.++|..+|++|... + 
T Consensus       412 ~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~----d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~-~~  486 (857)
T PLN03077        412 HELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LK  486 (857)
T ss_pred             HHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCC----CeeeHHHHHHHHHHCCCHHHHHHHHHHHHhC-CC
Confidence            999999999999999999999999999999999999998653    5566666666666666666666666666532 3 


Q ss_pred             ----------------------------------------------------------------CCcHHHHHHHHHHHhh
Q 042039          328 ----------------------------------------------------------------APNVIIFVTLIHGFVR  343 (376)
Q Consensus       328 ----------------------------------------------------------------~~~~~~~~~l~~~~~~  343 (376)
                                                                                      .||..+|+.++.+|.+
T Consensus       487 pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~  566 (857)
T PLN03077        487 PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVA  566 (857)
T ss_pred             CCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHH
Confidence                                                                            3456678888899999


Q ss_pred             cCChhhHHHHHHHHHhCCCCCchHHHHHHHhhC
Q 042039          344 INKPSKVIELLHKMKEKKVMPDASIVSMVVDLL  376 (376)
Q Consensus       344 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~l  376 (376)
                      .|+.++|+++|++|.+.|+.||..||+.+|.++
T Consensus       567 ~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~  599 (857)
T PLN03077        567 HGKGSMAVELFNRMVESGVNPDEVTFISLLCAC  599 (857)
T ss_pred             cCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHH
Confidence            999999999999999999999999999999764

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

Probab=99.97  E-value=3.9e-27  Score=221.82  Aligned_cols=349  Identities=12%  Similarity=0.069  Sum_probs=264.9

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +.+..++..+...+.+.|++++|...++++...+ +.+...+..++..+...|++++|.++++++.+.. +.+...|..+
T Consensus       530 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l  607 (899)
T TIGR02917       530 PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLML  607 (899)
T ss_pred             cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHH
Confidence            3456778888888888888888888888887765 5567777788888888888888888888887653 3366778888


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      +.++...|++++|...++.+.+.. +.+...+..++.++...|++++|..+++++.... |.+..++..++..+...|++
T Consensus       608 ~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~  685 (899)
T TIGR02917       608 GRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRT  685 (899)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCH
Confidence            888888888888888888887764 3456677778888888888888888888887765 55677788888888888888


Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      ++|.++++.+.... +.+...+..+...+...|++++|.+.+..+....  |+..++..++.++.+.|++++|...++.+
T Consensus       686 ~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  762 (899)
T TIGR02917       686 ESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAW  762 (899)
T ss_pred             HHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            88888888887763 4466677777788888888888888888887764  34466777778888888888888888887


Q ss_pred             cccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHH
Q 042039          253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVI  332 (376)
Q Consensus       253 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  332 (376)
                      .... +.+...+..++..|...|++++|...|+++.+. .++++.++..++..+...|+ .+|+.+++++.+... .+..
T Consensus       763 l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~-~~~~  838 (899)
T TIGR02917       763 LKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKK-APDNAVVLNNLAWLYLELKD-PRALEYAEKALKLAP-NIPA  838 (899)
T ss_pred             HHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCC-CCcH
Confidence            7655 346777788888888888888888888887766 45567777788888888888 778888888776532 2455


Q ss_pred             HHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHH
Q 042039          333 IFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVV  373 (376)
Q Consensus       333 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll  373 (376)
                      ++..+...+...|++++|.++++++.+.+.. +..++..+.
T Consensus       839 ~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~  878 (899)
T TIGR02917       839 ILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLA  878 (899)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHH
Confidence            6667777778888888888888888876543 555555443

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=99.97  E-value=1.8e-26  Score=217.34  Aligned_cols=330  Identities=15%  Similarity=0.104  Sum_probs=152.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ..+..++..+.+.|++++|..+++.+.+.. +.+..+|..++.++...|++++|...|+++.+... .+...+..+..++
T Consensus       568 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~  645 (899)
T TIGR02917       568 EPALALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP-DSALALLLLADAY  645 (899)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHH
Confidence            344444444445555555555555444332 33444444445555555555555555554444321 1333444444444


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHH
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL  176 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  176 (376)
                      ...|++++|...++++.+.. +.+..++..++..+...|++++|.++++.+.... +.+...+..++.++...|++++|.
T Consensus       646 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~  723 (899)
T TIGR02917       646 AVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAI  723 (899)
T ss_pred             HHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHH
Confidence            44555555555555444432 2234444444444455555555555555444443 333444444444444555555555


Q ss_pred             HHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC
Q 042039          177 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK  256 (376)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  256 (376)
                      ..|+.+...  .|+..++..++.++...|++++|.+.++.+.+.. +.+...+..++..|...|++++|..+|+++....
T Consensus       724 ~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  800 (899)
T TIGR02917       724 QAYRKALKR--APSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA  800 (899)
T ss_pred             HHHHHHHhh--CCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC
Confidence            555544443  2222344444444444555555555554444432 3334444444444444555555555555444433


Q ss_pred             CCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHH
Q 042039          257 CELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVT  336 (376)
Q Consensus       257 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  336 (376)
                       +.++..+..++..+...|+ .+|+.+++++... .+.+..++..++..+...|++++|...++++.+.+.. +..++..
T Consensus       801 -p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~  876 (899)
T TIGR02917       801 -PDNAVVLNNLAWLYLELKD-PRALEYAEKALKL-APNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYH  876 (899)
T ss_pred             -CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhh-CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHH
Confidence             2244444444444444444 4455554444433 2223344444444444455555555555555444322 4444444


Q ss_pred             HHHHHhhcCChhhHHHHHHHH
Q 042039          337 LIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       337 l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      ++.++.+.|++++|.+++++|
T Consensus       877 l~~~~~~~g~~~~A~~~~~~~  897 (899)
T TIGR02917       877 LALALLATGRKAEARKELDKL  897 (899)
T ss_pred             HHHHHHHcCCHHHHHHHHHHH
Confidence            444555555555555555444

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.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.96  E-value=2.9e-25  Score=188.46  Aligned_cols=307  Identities=16%  Similarity=0.146  Sum_probs=225.7

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC---hhhHHHHHHH
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN---AFTYSTLMDG  130 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~  130 (376)
                      ....+..+...|++++|...|+++.+.++ .+..++..+...+...|++++|..+++.++.....++   ...+..++..
T Consensus        38 ~y~~g~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~  116 (389)
T PRK11788         38 DYFKGLNFLLNEQPDKAIDLFIEMLKVDP-ETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQD  116 (389)
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            33345556677888888888888887643 2556777777888888888888888888776432211   2456677888


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC----HhHHHHHHHHHHhccc
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT----VVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~  206 (376)
                      |...|++++|..+|+++.+.. +.+..++..++.++...|++++|.+.++.+.+.+..+.    ...+..++..+...|+
T Consensus       117 ~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~  195 (389)
T PRK11788        117 YLKAGLLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGD  195 (389)
T ss_pred             HHHCCCHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCC
Confidence            888888888888888887654 45667788888888888888888888888877543222    1234556677778888


Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhc
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  286 (376)
                      +++|...++++.+.. +.+...+..++..+.+.|++++|.++++++...+......++..++.+|...|++++|...+++
T Consensus       196 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~  274 (389)
T PRK11788        196 LDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRR  274 (389)
T ss_pred             HHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            888888888887764 4455677778888888888888888888887654333345677888888888899999888888


Q ss_pred             ccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh---cCChhhHHHHHHHHHhCCCC
Q 042039          287 LPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR---INKPSKVIELLHKMKEKKVM  363 (376)
Q Consensus       287 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~~~~  363 (376)
                      +.+.  .|+...+..++..+.+.|++++|..+++++.+.  .|+...+..++..+..   .|+.+++..++++|.++++.
T Consensus       275 ~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~  350 (389)
T PRK11788        275 ALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLK  350 (389)
T ss_pred             HHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHh
Confidence            7765  355566678888888889999999988888775  5777777777766554   45888888888888887666


Q ss_pred             CchH
Q 042039          364 PDAS  367 (376)
Q Consensus       364 p~~~  367 (376)
                      |++.
T Consensus       351 ~~p~  354 (389)
T PRK11788        351 RKPR  354 (389)
T ss_pred             CCCC
Confidence            6553

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.96  E-value=3.8e-24  Score=190.09  Aligned_cols=334  Identities=11%  Similarity=0.028  Sum_probs=278.6

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      -...++..+.+.|++++|..+++...... +.+...+..++.+....|++++|...++++....+. +...+..+...+.
T Consensus        44 ~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~-~~~a~~~la~~l~  121 (656)
T PRK15174         44 NIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVC-QPEDVLLVASVLL  121 (656)
T ss_pred             CHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHH
Confidence            34556778889999999999999998875 666778888888889999999999999999987443 6778888999999


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      ..|++++|...++++++.. +.+...+..++.++...|++++|...++.+.... +.+...+..+ ..+...|++++|..
T Consensus       122 ~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~-P~~~~a~~~~-~~l~~~g~~~eA~~  198 (656)
T PRK15174        122 KSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQAQEV-PPRGDMIATC-LSFLNKSRLPEDHD  198 (656)
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-CCCHHHHHHH-HHHHHcCCHHHHHH
Confidence            9999999999999999863 4457788899999999999999999999887764 3444455444 34788999999999


Q ss_pred             HHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHH----HHHHHHHhc
Q 042039          178 LYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVE----AVELFRTLG  253 (376)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~  253 (376)
                      .++.+.+....++......+...+...|++++|...++++.... +.+...+..++..+...|++++    |...++++.
T Consensus       199 ~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al  277 (656)
T PRK15174        199 LARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHAL  277 (656)
T ss_pred             HHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHH
Confidence            99998876433445555566788889999999999999999875 5567788889999999999986    899999998


Q ss_pred             ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcH-H
Q 042039          254 ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV-I  332 (376)
Q Consensus       254 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~  332 (376)
                      ...+ .+...+..++..+...|++++|...++++... .+.+...+..++.++.+.|++++|+..++++.+.+  |+. .
T Consensus       278 ~l~P-~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l-~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~--P~~~~  353 (656)
T PRK15174        278 QFNS-DNVRIVTLYADALIRTGQNEKAIPLLQQSLAT-HPDLPYVRAMYARALRQVGQYTAASDEFVQLAREK--GVTSK  353 (656)
T ss_pred             hhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--ccchH
Confidence            8763 37889999999999999999999999998876 45567788889999999999999999999998763  443 3


Q ss_pred             HHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          333 IFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       333 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      .+..+..++...|++++|...|++..+..
T Consensus       354 ~~~~~a~al~~~G~~deA~~~l~~al~~~  382 (656)
T PRK15174        354 WNRYAAAALLQAGKTSEAESVFEHYIQAR  382 (656)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            34445678899999999999999988653

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.95  E-value=8.5e-25  Score=185.65  Aligned_cols=307  Identities=14%  Similarity=0.095  Sum_probs=254.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc---hHhHHHHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS---VVTFNVIMDE   95 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~   95 (376)
                      .......+...|++++|+..|+++.+.+ +.+..++..++..+...|++++|..+++.+...+..++   ...+..++..
T Consensus        38 ~y~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~  116 (389)
T PRK11788         38 DYFKGLNFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQD  116 (389)
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            3334456678899999999999999886 66778999999999999999999999999987643222   2467888999


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCC----hhhHHHHHHHHHccCc
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHD----DVSYNILINGYCKNKE  171 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~  171 (376)
                      +...|++++|..+|+++.+.. +.+..++..++..+...|++++|.+.++.+...+..+.    ...+..++..+.+.|+
T Consensus       117 ~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~  195 (389)
T PRK11788        117 YLKAGLLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGD  195 (389)
T ss_pred             HHHCCCHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCC
Confidence            999999999999999999863 45678899999999999999999999999987652222    1245677888899999


Q ss_pred             HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHH
Q 042039          172 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRT  251 (376)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  251 (376)
                      +++|...++++.+.. +.+...+..++..+...|++++|.+.++++...+......++..++.+|...|++++|...+++
T Consensus       196 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~  274 (389)
T PRK11788        196 LDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRR  274 (389)
T ss_pred             HHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999999998863 3356678888999999999999999999998765333346678899999999999999999999


Q ss_pred             hcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHc---cCChhHHHHHHHHHHHcCCC
Q 042039          252 LGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN---DGQMDKAHDLFLDMEENAVA  328 (376)
Q Consensus       252 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~  328 (376)
                      +....  |+...+..++..+.+.|++++|..+++++.+.  .|+...+..++..+..   .|+.+++..+++++.+.++.
T Consensus       275 ~~~~~--p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~  350 (389)
T PRK11788        275 ALEEY--PGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLK  350 (389)
T ss_pred             HHHhC--CCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHh
Confidence            88764  45556688999999999999999999998875  5777788877777664   56899999999999987776


Q ss_pred             CcHH
Q 042039          329 PNVI  332 (376)
Q Consensus       329 ~~~~  332 (376)
                      |++.
T Consensus       351 ~~p~  354 (389)
T PRK11788        351 RKPR  354 (389)
T ss_pred             CCCC
Confidence            6665

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

Probab=99.95  E-value=7.1e-25  Score=179.81  Aligned_cols=336  Identities=18%  Similarity=0.164  Sum_probs=256.7

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchH-------
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVV-------   87 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------   87 (376)
                      -..+|..+...+-..|++++|+.+++.+.+.. +.....|..+..++...|+.+.|.+.|.+.++.  .|+..       
T Consensus       115 ~ae~ysn~aN~~kerg~~~~al~~y~~aiel~-p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lg  191 (966)
T KOG4626|consen  115 GAEAYSNLANILKERGQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLG  191 (966)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--Ccchhhhhcchh
Confidence            35789999999999999999999999999875 567889999999999999999999998888775  33222       


Q ss_pred             ----------------------------hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHhcCcHH
Q 042039           88 ----------------------------TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFCLTGKIN  138 (376)
Q Consensus        88 ----------------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~  138 (376)
                                                  .|..|...+-.+|+...|+..|++.++.  .|+ ...|..+...|...+.++
T Consensus       192 nLlka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~~d  269 (966)
T KOG4626|consen  192 NLLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARIFD  269 (966)
T ss_pred             HHHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhcch
Confidence                                        2333333344455555555555555553  333 556667777777777777


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC-HhHHHHHHHHHHhccchHHHHHHHHHH
Q 042039          139 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHALKLFEEM  217 (376)
Q Consensus       139 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~  217 (376)
                      .|...|.++.... |....++.++...|...|+.+-|+..|++.++.  .|+ +..|+.+..++-..|++.+|.+.+.+.
T Consensus       270 ~Avs~Y~rAl~lr-pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cYnka  346 (966)
T KOG4626|consen  270 RAVSCYLRALNLR-PNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCYNKA  346 (966)
T ss_pred             HHHHHHHHHHhcC-CcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHHHHH
Confidence            7777777766654 455666777777777777788888888877774  343 678888888888888888888888888


Q ss_pred             HhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC-H
Q 042039          218 QRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD-V  296 (376)
Q Consensus       218 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~  296 (376)
                      +... +......+.++..|...|.+++|..+|....+.... -...++.|+..|.++|++++|+..|+++++.  .|+ .
T Consensus       347 L~l~-p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~-~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI--~P~fA  422 (966)
T KOG4626|consen  347 LRLC-PNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPE-FAAAHNNLASIYKQQGNLDDAIMCYKEALRI--KPTFA  422 (966)
T ss_pred             HHhC-CccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChh-hhhhhhhHHHHHHhcccHHHHHHHHHHHHhc--CchHH
Confidence            8774 556777888888888888899998888887765422 3567888888999999999999999988874  444 5


Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc-HHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCch
Q 042039          297 VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN-VIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA  366 (376)
Q Consensus       297 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  366 (376)
                      ..++.++..|-..|+.+.|+..+.+++..  .|. ...++.|...|...|+..+|+.-++...+  +.||.
T Consensus       423 da~~NmGnt~ke~g~v~~A~q~y~rAI~~--nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDf  489 (966)
T KOG4626|consen  423 DALSNMGNTYKEMGDVSAAIQCYTRAIQI--NPTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDF  489 (966)
T ss_pred             HHHHhcchHHHHhhhHHHHHHHHHHHHhc--CcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCC
Confidence            68888999999999999999999988874  444 56788899999999999999999999885  45554

>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=99.94  E-value=9.3e-23  Score=181.89  Aligned_cols=255  Identities=14%  Similarity=0.031  Sum_probs=160.7

Q ss_pred             ChHHHHHHHHHHHhcC-CCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHH
Q 042039          101 KMDEASRLLDLMVQRD-VRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSL  178 (376)
Q Consensus       101 ~~~~a~~~~~~~~~~~-~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  178 (376)
                      ++++|...|+..++.+ ..| ....+..+...+...|++++|...+++..... |.....|..++.++...|++++|+..
T Consensus       309 ~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~  387 (615)
T TIGR00990       309 SYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD-PRVTQSYIKRASMNLELGDPDKAEED  387 (615)
T ss_pred             hHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4445555555555432 112 23445556666666777777777777776654 34455666777777777777777777


Q ss_pred             HHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC
Q 042039          179 YREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE  258 (376)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  258 (376)
                      ++++++.. +.+..++..+...+...|++++|...|++.++.. +.+...+..++.++.+.|++++|+..++++.... +
T Consensus       388 ~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P  464 (615)
T TIGR00990       388 FDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-P  464 (615)
T ss_pred             HHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-C
Confidence            77776642 3346667777777777777777777777777664 4455566667777777777777777777766543 3


Q ss_pred             chHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCH------HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHH
Q 042039          259 LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV------VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVI  332 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  332 (376)
                      .++..+..++.++...|++++|+..|+++.......+.      ..+...+..+...|++++|..+++++.+... .+..
T Consensus       465 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p-~~~~  543 (615)
T TIGR00990       465 EAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDP-ECDI  543 (615)
T ss_pred             CChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCC-CcHH
Confidence            35666777777777777777777777776553211111      0111122223345777777777777766532 2344


Q ss_pred             HHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          333 IFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       333 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      .+..+...+.+.|++++|++.|++..+.
T Consensus       544 a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       544 AVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            6677777788888888888888777654

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

Probab=99.94  E-value=5.3e-24  Score=174.76  Aligned_cols=324  Identities=13%  Similarity=0.078  Sum_probs=262.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCC---------------------------------CCChhhHHHHHHHHh
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENI---------------------------------NPDVVTYNSLIHGLC   62 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~---------------------------------~~~~~~~~~l~~~~~   62 (376)
                      +..|..+..++...|+.+.|.+.|.+.++.+.                                 +--..+|..|...+-
T Consensus       150 ida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnLlka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~  229 (966)
T KOG4626|consen  150 IDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNLLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFN  229 (966)
T ss_pred             hHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHHHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHh
Confidence            45566666666666666666666666555431                                 111334556666666


Q ss_pred             cCCChHHHHHHHHHHHhcCCCCc-hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHH
Q 042039           63 HANDWNEAKRLFFEMMDQGVQPS-VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAE  141 (376)
Q Consensus        63 ~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  141 (376)
                      .+|+...|++.|++..+.  .|+ ...|..|...|...+.+++|...|.+..... +.....+..+...|..+|.++.|+
T Consensus       230 ~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lr-pn~A~a~gNla~iYyeqG~ldlAI  306 (966)
T KOG4626|consen  230 AQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARIFDRAVSCYLRALNLR-PNHAVAHGNLACIYYEQGLLDLAI  306 (966)
T ss_pred             hcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhcC-CcchhhccceEEEEeccccHHHHH
Confidence            777888888888887775  444 5689999999999999999999999998863 334778889999999999999999


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          142 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                      ..|++..+.. |.-+.+|++|..++-..|+..+|.+.|.+.+.. .+....+.+.+..++...|.++.|..+|....+-.
T Consensus       307 ~~Ykral~~~-P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l-~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~  384 (966)
T KOG4626|consen  307 DTYKRALELQ-PNFPDAYNNLANALKDKGSVTEAVDCYNKALRL-CPNHADAMNNLGNIYREQGKIEEATRLYLKALEVF  384 (966)
T ss_pred             HHHHHHHhcC-CCchHHHhHHHHHHHhccchHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhC
Confidence            9999999886 667789999999999999999999999999986 33457889999999999999999999999998764


Q ss_pred             CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHH
Q 042039          222 VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNI  301 (376)
Q Consensus       222 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  301 (376)
                       +.-...++.++..|-++|++++|+..|+++.+.. +.-...++.++..|...|+...|++.+.+++.. .|.-...++.
T Consensus       385 -p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~-P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~-nPt~AeAhsN  461 (966)
T KOG4626|consen  385 -PEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIK-PTFADALSNMGNTYKEMGDVSAAIQCYTRAIQI-NPTFAEAHSN  461 (966)
T ss_pred             -hhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcC-chHHHHHHhcchHHHHhhhHHHHHHHHHHHHhc-CcHHHHHHhh
Confidence             4456789999999999999999999999998775 224689999999999999999999999998875 2334678899


Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCCCc-HHHHHHHHHHHhhcCChhh
Q 042039          302 MIHGLCNDGQMDKAHDLFLDMEENAVAPN-VIIFVTLIHGFVRINKPSK  349 (376)
Q Consensus       302 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~  349 (376)
                      |...|-..|+..+|+.-++..++.  +|| +..+..++.+..-..+|..
T Consensus       462 Lasi~kDsGni~~AI~sY~~aLkl--kPDfpdA~cNllh~lq~vcdw~D  508 (966)
T KOG4626|consen  462 LASIYKDSGNIPEAIQSYRTALKL--KPDFPDAYCNLLHCLQIVCDWTD  508 (966)
T ss_pred             HHHHhhccCCcHHHHHHHHHHHcc--CCCCchhhhHHHHHHHHHhcccc
Confidence            999999999999999999999985  555 5667777776544444444

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.94  E-value=3.7e-22  Score=177.51  Aligned_cols=337  Identities=12%  Similarity=0.066  Sum_probs=267.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +...+..++.++...|++++|+..++++.... |.+...+..+...+...|++++|...++++....+. +...+..++.
T Consensus        75 ~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~-~~~a~~~la~  152 (656)
T PRK15174         75 GRDLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSG-NSQIFALHLR  152 (656)
T ss_pred             chhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHH
Confidence            45567777788888999999999999999886 677889999999999999999999999999986433 6778888999


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  174 (376)
                      ++...|++++|...++.+..... .+...+..+ ..+...|++++|...++.+......++......++..+...|++++
T Consensus       153 ~l~~~g~~~eA~~~~~~~~~~~P-~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~e  230 (656)
T PRK15174        153 TLVLMDKELQAISLARTQAQEVP-PRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQE  230 (656)
T ss_pred             HHHHCCChHHHHHHHHHHHHhCC-CCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHH
Confidence            99999999999999998877642 233344333 3478899999999999998876533444455666788999999999


Q ss_pred             HHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHH----HHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          175 ALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH----ALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       175 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      |+..++++.... +.+...+..+...+...|++++    |...++++.+.. +.+...+..++..+...|++++|...++
T Consensus       231 A~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~  308 (656)
T PRK15174        231 AIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQ  308 (656)
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            999999999863 4467788889999999999985    899999998875 5577889999999999999999999999


Q ss_pred             HhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc
Q 042039          251 TLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       251 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  330 (376)
                      ++....+. ++..+..++.++...|++++|...++.+... .+.+...+..++.++...|++++|...|+++.+....-.
T Consensus       309 ~al~l~P~-~~~a~~~La~~l~~~G~~~eA~~~l~~al~~-~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~~~  386 (656)
T PRK15174        309 QSLATHPD-LPYVRAMYARALRQVGQYTAASDEFVQLARE-KGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQARASHL  386 (656)
T ss_pred             HHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChhhc
Confidence            99887633 6778888999999999999999999998875 222334455567889999999999999999987532211


Q ss_pred             HH----HHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          331 VI----IFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       331 ~~----~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      ..    ....+-.++...+.+++...+..++.-
T Consensus       387 ~~~~~ea~~~~~~~~~~~~~~~~~~~W~~~~~~  419 (656)
T PRK15174        387 PQSFEEGLLALDGQISAVNLPPERLDWAWEVAG  419 (656)
T ss_pred             hhhHHHHHHHHHHHHHhcCCccchhhHHHHHhc
Confidence            22    233333444445555555456666543

>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=99.94  E-value=6.5e-22  Score=176.49  Aligned_cols=337  Identities=15%  Similarity=0.049  Sum_probs=266.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .+......+.+.|++++|+..|++.+..  .|+...|..+..+|...|++++|++.+++.++..+. +...+..+..++.
T Consensus       129 ~~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~-~~~a~~~~a~a~~  205 (615)
T TIGR00990       129 KLKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELDPD-YSKALNRRANAYD  205 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHH
Confidence            3556778899999999999999999876  567889999999999999999999999999987433 6778899999999


Q ss_pred             hCCChHHHHHHHHHHHhcCC-----------------------------CCChhhHHHHHHH------------------
Q 042039           98 KNGKMDEASRLLDLMVQRDV-----------------------------RPNAFTYSTLMDG------------------  130 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~-----------------------------~~~~~~~~~l~~~------------------  130 (376)
                      ..|++++|...+..+...+.                             +++...+..+...                  
T Consensus       206 ~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  285 (615)
T TIGR00990       206 GLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNE  285 (615)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccc
Confidence            99999999876654432110                             0110011111000                  


Q ss_pred             ------------H------HhcCcHHHHHHHHHHHHhcC--CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC
Q 042039          131 ------------F------CLTGKINRAEELFGSMESMG--CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT  190 (376)
Q Consensus       131 ------------~------~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  190 (376)
                                  .      ...+++++|.+.|+.....+  .+.....+..++.++...|++++|+..+++.+... +..
T Consensus       286 ~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~-P~~  364 (615)
T TIGR00990       286 LDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD-PRV  364 (615)
T ss_pred             cccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCc
Confidence                        0      12257889999999998764  23455678889999999999999999999999852 234


Q ss_pred             HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHH
Q 042039          191 VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG  270 (376)
Q Consensus       191 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  270 (376)
                      ...|..+...+...|++++|...++.+++.+ +.+..++..++..+...|++++|...|+++....+ .+...+..++.+
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P-~~~~~~~~la~~  442 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDP-DFIFSHIQLGVT  442 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCc-cCHHHHHHHHHH
Confidence            6688899999999999999999999998875 56778999999999999999999999999988763 367788899999


Q ss_pred             HHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcH------HHHHHHHHHHhhc
Q 042039          271 LCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV------IIFVTLIHGFVRI  344 (376)
Q Consensus       271 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~  344 (376)
                      +.+.|++++|+..+++..+. .+.+...+..++.++...|++++|++.|+++.+.....+.      ..+......+...
T Consensus       443 ~~~~g~~~eA~~~~~~al~~-~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~  521 (615)
T TIGR00990       443 QYKEGSIASSMATFRRCKKN-FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWK  521 (615)
T ss_pred             HHHCCCHHHHHHHHHHHHHh-CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHh
Confidence            99999999999999998876 4567889999999999999999999999999875322111      1122222334457


Q ss_pred             CChhhHHHHHHHHHhCC
Q 042039          345 NKPSKVIELLHKMKEKK  361 (376)
Q Consensus       345 g~~~~a~~~~~~~~~~~  361 (376)
                      |++++|..++++..+..
T Consensus       522 ~~~~eA~~~~~kAl~l~  538 (615)
T TIGR00990       522 QDFIEAENLCEKALIID  538 (615)
T ss_pred             hhHHHHHHHHHHHHhcC
Confidence            99999999999988654

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.93  E-value=2e-21  Score=184.22  Aligned_cols=338  Identities=15%  Similarity=0.087  Sum_probs=180.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCC-ChhhH------------HHHHHHHhcCCChHHHHHHHHHHHhcC
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINP-DVVTY------------NSLIHGLCHANDWNEAKRLFFEMMDQG   81 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~------------~~l~~~~~~~~~~~~a~~~~~~~~~~~   81 (376)
                      +..++..+...+.+.|++++|+..|++..+..... ....|            ......+...|++++|+..|+++++..
T Consensus       302 ~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~  381 (1157)
T PRK11447        302 DSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVD  381 (1157)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            44455555555555555555555555555442111 10111            112334445555555555555555542


Q ss_pred             CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH----------------------------------
Q 042039           82 VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL----------------------------------  127 (376)
Q Consensus        82 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l----------------------------------  127 (376)
                      +. +...+..+..++...|++++|++.|+++++.. +.+...+..+                                  
T Consensus       382 P~-~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~~~~~~~A~~~l~~l~~~~~~~~~~~~~~l  459 (1157)
T PRK11447        382 NT-DSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYRQQSPEKALAFIASLSASQRRSIDDIERSL  459 (1157)
T ss_pred             CC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            22 34445555556666666666666666665542 1122222111                                  


Q ss_pred             --------HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 042039          128 --------MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL  199 (376)
Q Consensus       128 --------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  199 (376)
                              ...+...|++++|.+.|+++.+.. |.+...+..++.+|.+.|++++|...++++.+.. +.+...+..+..
T Consensus       460 ~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~-P~~~~~~~a~al  537 (1157)
T PRK11447        460 QNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQK-PNDPEQVYAYGL  537 (1157)
T ss_pred             hhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHH
Confidence                    222334455666666666655543 3344555556666666666666666666655431 112222222222


Q ss_pred             HHHhccchHHHHHHHHHHHhc---------------------------------------CCCCCcchHHHHHHHHHhCC
Q 042039          200 GLFEIHQVEHALKLFEEMQRD---------------------------------------DVAADTSTYNTFIDGLCKNG  240 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~---------------------------------------~~~~~~~~~~~l~~~~~~~~  240 (376)
                      .+...++.++|...++.+...                                       ..+.+...+..++..+.+.|
T Consensus       538 ~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g  617 (1157)
T PRK11447        538 YLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRG  617 (1157)
T ss_pred             HHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcC
Confidence            222233333333322221000                                       01334445556666677777


Q ss_pred             CHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHH
Q 042039          241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFL  320 (376)
Q Consensus       241 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  320 (376)
                      ++++|+..|+.+.... +.++..+..++..+...|++++|++.++.+.+. .+.+......+..++...|++++|.++++
T Consensus       618 ~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~-~p~~~~~~~~la~~~~~~g~~~eA~~~~~  695 (1157)
T PRK11447        618 DYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPAT-ANDSLNTQRRVALAWAALGDTAAAQRTFN  695 (1157)
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc-CCCChHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            7777777777776665 335677777777777777777777777766654 23345566667777777777777777777


Q ss_pred             HHHHcCCC--C---cHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          321 DMEENAVA--P---NVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       321 ~~~~~~~~--~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      ++.+....  |   +...+..+...+...|++++|+..|++..
T Consensus       696 ~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al  738 (1157)
T PRK11447        696 RLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAM  738 (1157)
T ss_pred             HHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            77654221  1   22345555667777777888877777765

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.93  E-value=5.9e-21  Score=181.10  Aligned_cols=331  Identities=14%  Similarity=0.064  Sum_probs=248.0

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc-hHhH------------
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS-VVTF------------   89 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~------------   89 (376)
                      ...+...|++++|+..|++..+.. |.+..++..+..++.+.|++++|+..|++.++...... ...|            
T Consensus       276 G~~~~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        276 GLAAVDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            566778999999999999999875 66889999999999999999999999999998644321 1111            


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHH------
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILI------  163 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~------  163 (376)
                      ......+.+.|++++|...|+++++.. +.+...+..+..++...|++++|++.|+++.+.. +.+...+..+.      
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~~~  432 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYRQQ  432 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhc
Confidence            123456778999999999999999874 4467788889999999999999999999998765 33444433332      


Q ss_pred             ------------------------------------HHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccch
Q 042039          164 ------------------------------------NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV  207 (376)
Q Consensus       164 ------------------------------------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  207 (376)
                                                          ..+...|++++|++.|+++++.. +.+...+..+...+.+.|++
T Consensus       433 ~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~  511 (1157)
T PRK11447        433 SPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQR  511 (1157)
T ss_pred             CHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence                                                33456788888888888888752 33566777888889999999


Q ss_pred             HHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc--------------------------------
Q 042039          208 EHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL--------------------------------  255 (376)
Q Consensus       208 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--------------------------------  255 (376)
                      ++|...++++.+.. +.+...+..+...+...++.++|...++.+...                                
T Consensus       512 ~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~  590 (1157)
T PRK11447        512 SQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEA  590 (1157)
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHH
Confidence            99999999887754 334444443333344444444444444432111                                


Q ss_pred             -------CCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 042039          256 -------KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVA  328 (376)
Q Consensus       256 -------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  328 (376)
                             ..+.++..+..++..+.+.|++++|+..|+++.+. .|.+...+..++..+...|++++|++.++.+.+.. +
T Consensus       591 eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~-~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~-p  668 (1157)
T PRK11447        591 EAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTR-EPGNADARLGLIEVDIAQGDLAAARAQLAKLPATA-N  668 (1157)
T ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccC-C
Confidence                   01334556677888888889999999999988876 45677888889999999999999999999887643 2


Q ss_pred             CcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          329 PNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       329 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      .+...+..+..++...|++++|.++++++.+.
T Consensus       669 ~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        669 DSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            24566777788888899999999999998765

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.91  E-value=1.3e-19  Score=164.67  Aligned_cols=340  Identities=12%  Similarity=0.033  Sum_probs=245.9

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      .+...+..+...+.+.|++++|.++|++..+.. |.+...+..++.++...|++++|+..++++++..+. +.. +..+.
T Consensus        47 ~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~P~-~~~-~~~la  123 (765)
T PRK10049         47 LPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAGQYDEALVKAKQLVSGAPD-KAN-LLALA  123 (765)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHH-HHHHH
Confidence            344568888899999999999999999988775 667778888889999999999999999999887333 555 88888


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHH----------------------------
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFG----------------------------  145 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~----------------------------  145 (376)
                      .++...|+.++|+..++++.+.. +.+...+..++.++...+..+.|.+.++                            
T Consensus       124 ~~l~~~g~~~~Al~~l~~al~~~-P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~  202 (765)
T PRK10049        124 YVYKRAGRHWDELRAMTQALPRA-PQTQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPT  202 (765)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccc
Confidence            88999999999999999999874 3345555666666666566554443333                            


Q ss_pred             ------------------HHHhc-CCCCChh-hH----HHHHHHHHccCcHHHHHHHHHHHHHCCCC-CCHhHHHHHHHH
Q 042039          146 ------------------SMESM-GCKHDDV-SY----NILINGYCKNKEVEEALSLYREMVSKGIK-PTVVTYNTLFLG  200 (376)
Q Consensus       146 ------------------~~~~~-~~~~~~~-~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~  200 (376)
                                        .+... ...|+.. .+    ...+..+...|++++|+..|+.+.+.+.+ |+ .....+..+
T Consensus       203 ~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~-~a~~~la~~  281 (765)
T PRK10049        203 RSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPP-WAQRWVASA  281 (765)
T ss_pred             cChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCH-HHHHHHHHH
Confidence                              33322 0111111 11    11122345668889999999998876422 22 122335678


Q ss_pred             HHhccchHHHHHHHHHHHhcCCCC---CcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC-----------Cch---HHH
Q 042039          201 LFEIHQVEHALKLFEEMQRDDVAA---DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC-----------ELD---IQA  263 (376)
Q Consensus       201 ~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~---~~~  263 (376)
                      +...|++++|...|+.+.+.....   .......+..++...|++++|..+++.+....+           .|+   ...
T Consensus       282 yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a  361 (765)
T PRK10049        282 YLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQG  361 (765)
T ss_pred             HHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHH
Confidence            888999999999999887653111   123455666678889999999999888865531           122   234


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh
Q 042039          264 YNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR  343 (376)
Q Consensus       264 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  343 (376)
                      +..++..+...|++++|+++++++... .|.+...+..++..+...|++++|++.++++.+.. +.+...+...+..+.+
T Consensus       362 ~~~~a~~l~~~g~~~eA~~~l~~al~~-~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~-Pd~~~l~~~~a~~al~  439 (765)
T PRK10049        362 QSLLSQVAKYSNDLPQAEMRARELAYN-APGNQGLRIDYASVLQARGWPRAAENELKKAEVLE-PRNINLEVEQAWTALD  439 (765)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhC-CCChHHHHHHHHHHHH
Confidence            566777888889999999999988776 56678888888999999999999999999988854 2245666677778888


Q ss_pred             cCChhhHHHHHHHHHhC
Q 042039          344 INKPSKVIELLHKMKEK  360 (376)
Q Consensus       344 ~g~~~~a~~~~~~~~~~  360 (376)
                      .|++++|..+++++.+.
T Consensus       440 ~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        440 LQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             hCCHHHHHHHHHHHHHh
Confidence            89999999999998864

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.89  E-value=1.4e-18  Score=158.09  Aligned_cols=346  Identities=10%  Similarity=0.029  Sum_probs=261.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      -++....-.+......|+.++|+++|++..... +.+...+..++..+...|++++|.++|+++++..+ .+...+..++
T Consensus        13 ~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~la   90 (765)
T PRK10049         13 LSNNQIADWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEP-QNDDYQRGLI   90 (765)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHH
Confidence            344455566677889999999999999998643 56677899999999999999999999999988733 3567778888


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHH
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  173 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  173 (376)
                      .++...|++++|...++++++.. +.+.. +..+..++...|+.++|...++++.... |.+...+..++.++...+..+
T Consensus        91 ~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~-P~~~~~~~~la~~l~~~~~~e  167 (765)
T PRK10049         91 LTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRA-PQTQQYPTEYVQALRNNRLSA  167 (765)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCChH
Confidence            89999999999999999999873 44566 8889999999999999999999999886 556667777777777666666


Q ss_pred             HHHHHHH----------------------------------------------HHHHC-CCCCCHh-HHH----HHHHHH
Q 042039          174 EALSLYR----------------------------------------------EMVSK-GIKPTVV-TYN----TLFLGL  201 (376)
Q Consensus       174 ~a~~~~~----------------------------------------------~~~~~-~~~~~~~-~~~----~l~~~~  201 (376)
                      +|+..++                                              .+.+. ...|+.. .+.    ..+..+
T Consensus       168 ~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~L  247 (765)
T PRK10049        168 PALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGAL  247 (765)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHH
Confidence            5554444                                              33321 1112111 111    113345


Q ss_pred             HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc---hHHHHHHHHHHHHhCCChH
Q 042039          202 FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCEL---DIQAYNCLIDGLCKSGRLE  278 (376)
Q Consensus       202 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~  278 (376)
                      ...+++++|+..|+.+.+.+.+........+..+|...|++++|+..|+++.......   .......+..++...|+++
T Consensus       248 l~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~  327 (765)
T PRK10049        248 LARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYP  327 (765)
T ss_pred             HHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHH
Confidence            6778999999999999887522112233346778999999999999999987654221   1345666777889999999


Q ss_pred             HHHHHHhcccccCC-----------CCC---HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhc
Q 042039          279 IALELFRSLPRRVL-----------VAD---VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRI  344 (376)
Q Consensus       279 ~a~~~~~~~~~~~~-----------~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  344 (376)
                      +|...++.+.....           .|+   ...+..++..+...|++++|+++++++.... +.+...+..+...+...
T Consensus       328 eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~  406 (765)
T PRK10049        328 GALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQAR  406 (765)
T ss_pred             HHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhc
Confidence            99999998876421           122   2345677888999999999999999998864 33678888999999999


Q ss_pred             CChhhHHHHHHHHHhCCCCCchH
Q 042039          345 NKPSKVIELLHKMKEKKVMPDAS  367 (376)
Q Consensus       345 g~~~~a~~~~~~~~~~~~~p~~~  367 (376)
                      |++++|++.+++..+.  .|+..
T Consensus       407 g~~~~A~~~l~~al~l--~Pd~~  427 (765)
T PRK10049        407 GWPRAAENELKKAEVL--EPRNI  427 (765)
T ss_pred             CCHHHHHHHHHHHHhh--CCCCh
Confidence            9999999999999864  46653

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

Probab=99.85  E-value=5e-17  Score=139.58  Aligned_cols=338  Identities=15%  Similarity=0.132  Sum_probs=261.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ....-.....+...|++++|.+++.++++.. +.+...|..|..+|-+.|+.+++...+-.+...+++ |...|..+...
T Consensus       139 l~~ll~eAN~lfarg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~-d~e~W~~ladl  216 (895)
T KOG2076|consen  139 LRQLLGEANNLFARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPK-DYELWKRLADL  216 (895)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCC-ChHHHHHHHHH
Confidence            3444444555666799999999999999886 778899999999999999999999998777665444 67899999999


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChh----hHHHHHHHHHccCc
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDV----SYNILINGYCKNKE  171 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~  171 (376)
                      ..+.|+++.|.-+|.++++.. +++......-+..|-+.|+...|...|.++.....+.+..    .-...+..+...++
T Consensus       217 s~~~~~i~qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~  295 (895)
T KOG2076|consen  217 SEQLGNINQARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNE  295 (895)
T ss_pred             HHhcccHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhH
Confidence            999999999999999999985 5566666777889999999999999999998875322322    23345667777888


Q ss_pred             HHHHHHHHHHHHHC-CCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC---------------------------CC
Q 042039          172 VEEALSLYREMVSK-GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD---------------------------VA  223 (376)
Q Consensus       172 ~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------------------~~  223 (376)
                      -+.|.+.++..... +-..+...++.++..+....+++.+......+....                           ..
T Consensus       296 ~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s  375 (895)
T KOG2076|consen  296 RERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELS  375 (895)
T ss_pred             HHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCC
Confidence            89999999988773 223355667788888889999999988887776511                           11


Q ss_pred             CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC--CCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHH
Q 042039          224 ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK--CELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNI  301 (376)
Q Consensus       224 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  301 (376)
                      ++..+ ..+..++......+....+........  +.-+...+..+..++...|++.+|+.+|..+.......+...|..
T Consensus       376 ~~l~v-~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~  454 (895)
T KOG2076|consen  376 YDLRV-IRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYK  454 (895)
T ss_pred             ccchh-HhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHH
Confidence            12222 123333444444444444444444444  334578899999999999999999999999987755566789999


Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          302 MIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       302 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      ++.+|...|.+++|.+.|++++... +.+...-..|...+.+.|++++|.+.+..+.
T Consensus       455 ~a~c~~~l~e~e~A~e~y~kvl~~~-p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  455 LARCYMELGEYEEAIEFYEKVLILA-PDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHhcC-CCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            9999999999999999999999863 2255666677788999999999999999875

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.85  E-value=2.3e-16  Score=141.46  Aligned_cols=158  Identities=15%  Similarity=0.150  Sum_probs=93.6

Q ss_pred             HHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC-----CchHHHHHHHHHHHHhC
Q 042039          200 GLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC-----ELDIQAYNCLIDGLCKS  274 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~  274 (376)
                      ++...++..++++.++.+...+.+....+...++.+|...+.+++|..+++.+.....     +++......|..++...
T Consensus       301 aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~  380 (822)
T PRK14574        301 ALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNES  380 (822)
T ss_pred             HHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhc
Confidence            3444555566666666665555443444566666677777777777777776644321     12233345666677777


Q ss_pred             CChHHHHHHHhcccccCC-----------CCCH---HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 042039          275 GRLEIALELFRSLPRRVL-----------VADV---VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHG  340 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~-----------~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  340 (376)
                      +++++|..+++++.+...           .||+   ..+..++..+...|++.+|++.++++.... +-|......+...
T Consensus       381 e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~v  459 (822)
T PRK14574        381 EQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTA-PANQNLRIALASI  459 (822)
T ss_pred             ccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            777777777776654211           1111   233445556666777777777777776543 2366666666777


Q ss_pred             HhhcCChhhHHHHHHHHH
Q 042039          341 FVRINKPSKVIELLHKMK  358 (376)
Q Consensus       341 ~~~~g~~~~a~~~~~~~~  358 (376)
                      +...|.+..|...++...
T Consensus       460 ~~~Rg~p~~A~~~~k~a~  477 (822)
T PRK14574        460 YLARDLPRKAEQELKAVE  477 (822)
T ss_pred             HHhcCCHHHHHHHHHHHh
Confidence            777777777777775554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.84  E-value=2.6e-16  Score=143.99  Aligned_cols=320  Identities=10%  Similarity=0.019  Sum_probs=192.4

Q ss_pred             CChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc-C-CCCchHhHHHHHHHHHhCCC---hHH
Q 042039           30 GFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ-G-VQPSVVTFNVIMDELCKNGK---MDE  104 (376)
Q Consensus        30 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~~~---~~~  104 (376)
                      +...++.+.+..+.+.. +-+......+.....+.|+.++|.++|+..... + ..++......++..|.+.+.   ..+
T Consensus       356 ~~~~~~~~~~~~~y~~~-~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~  434 (987)
T PRK09782        356 RNKAEALRLARLLYQQE-PANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAK  434 (987)
T ss_pred             CchhHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHH
Confidence            55555666666555542 345566666666667777777777777776652 1 11223333355555555544   222


Q ss_pred             HHHH----------------------HHHHHhc-C-CCC--ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhh
Q 042039          105 ASRL----------------------LDLMVQR-D-VRP--NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVS  158 (376)
Q Consensus       105 a~~~----------------------~~~~~~~-~-~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  158 (376)
                      +..+                      +...... + .++  +...+..+..++.. ++.++|...+.+.....  |+...
T Consensus       435 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~  511 (987)
T PRK09782        435 VAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQ  511 (987)
T ss_pred             HHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHH
Confidence            2111                      1111111 0 123  45566666666665 66777777666666553  34333


Q ss_pred             HHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          159 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       159 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                      ...++..+...|++++|...++++...  +|+...+..+...+...|+.+.|...++..++.+ +.....+..+......
T Consensus       512 ~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~  588 (987)
T PRK09782        512 HRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYI  588 (987)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHh
Confidence            333444445677777777777776553  3444445566666777777777777777776654 2233333333334445


Q ss_pred             CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHH
Q 042039          239 NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDL  318 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  318 (376)
                      .|++++|...++++....  |+...+..++.++.+.|++++|+..++++... .|.+...+..+..++...|++++|+..
T Consensus       589 ~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l-~Pd~~~a~~nLG~aL~~~G~~eeAi~~  665 (987)
T PRK09782        589 PGQPELALNDLTRSLNIA--PSANAYVARATIYRQRHNVPAAVSDLRAALEL-EPNNSNYQAALGYALWDSGDIAQSREM  665 (987)
T ss_pred             CCCHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            577777777777776654  34666777777777777777777777777665 345566777777777777777777777


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          319 FLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      ++++.+..+ .+...+..+..++...|++++|+..+++..+.
T Consensus       666 l~~AL~l~P-~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l  706 (987)
T PRK09782        666 LERAHKGLP-DDPALIRQLAYVNQRLDDMAATQHYARLVIDD  706 (987)
T ss_pred             HHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            777776532 25566777777777777777777777777643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.83  E-value=1.2e-16  Score=134.65  Aligned_cols=285  Identities=11%  Similarity=0.071  Sum_probs=223.4

Q ss_pred             hcCCChHHHHHHHHHHHhcCCCCchHh-HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhH--HHHHHHHHhcCcHH
Q 042039           62 CHANDWNEAKRLFFEMMDQGVQPSVVT-FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTY--STLMDGFCLTGKIN  138 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~  138 (376)
                      ...|++++|.+.+....+..  +++.. +.....+..+.|+++.|..++.++.+.  .|+....  ......+...|+++
T Consensus        95 ~~eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~  170 (398)
T PRK10747         95 LAEGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENH  170 (398)
T ss_pred             HhCCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHH
Confidence            34699999998888766542  22333 333355558999999999999999875  4444322  24477889999999


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCH-------hHHHHHHHHHHhccchHHHH
Q 042039          139 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV-------VTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       139 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~  211 (376)
                      .|...++++.+.. |.++.....+...|.+.|++++|.+++..+.+.+..++.       .+|..++.......+.+...
T Consensus       171 ~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~  249 (398)
T PRK10747        171 AARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLK  249 (398)
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            9999999999887 778889999999999999999999999999987554322       12333344344445556666


Q ss_pred             HHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC
Q 042039          212 KLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV  291 (376)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  291 (376)
                      ++++.+.+. .+.++.....++..+...|+.++|...+++..+.  ++++....  +.+....++.+++.+..+...+. 
T Consensus       250 ~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~~--l~~~l~~~~~~~al~~~e~~lk~-  323 (398)
T PRK10747        250 RWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLVL--LIPRLKTNNPEQLEKVLRQQIKQ-  323 (398)
T ss_pred             HHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHH--HHhhccCCChHHHHHHHHHHHhh-
Confidence            666666443 3567888999999999999999999999998774  44554332  33334569999999999998876 


Q ss_pred             CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          292 LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       292 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .|.|+..+..++..+.+.+++++|.+.|+.+.+.  .|+...+..+...+.+.|+.++|.+++++...
T Consensus       324 ~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        324 HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            5677888999999999999999999999999985  68989989999999999999999999998764

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.83  E-value=5.2e-16  Score=142.08  Aligned_cols=333  Identities=13%  Similarity=-0.008  Sum_probs=254.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhC-C-CCCChhhHHHHHHHHhcCCC---hHHHHHH----------------
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGE-N-INPDVVTYNSLIHGLCHAND---WNEAKRL----------------   73 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~~~---~~~a~~~----------------   73 (376)
                      +......+.-...+.|+.++|.++++..... + ...+......++..|.+.+.   ..++..+                
T Consensus       375 ~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  454 (987)
T PRK09782        375 NLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQL  454 (987)
T ss_pred             CHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhccccccchhHHHHhhh
Confidence            4444455555677899999999999998763 1 12344455577777777765   3333222                


Q ss_pred             ------HHHHHhc-CC-CC--chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHH
Q 042039           74 ------FFEMMDQ-GV-QP--SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEEL  143 (376)
Q Consensus        74 ------~~~~~~~-~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  143 (376)
                            ++..... +. ++  +...|..+..++.. +++++|...+.+....  .|+......++..+...|++++|...
T Consensus       455 ~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~  531 (987)
T PRK09782        455 PGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAA  531 (987)
T ss_pred             hhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHH
Confidence                  2222221 11 23  56678888887776 8999999988888876  35555555556666789999999999


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCC
Q 042039          144 FGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVA  223 (376)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  223 (376)
                      |+++...  +|+...+..++.++.+.|++++|...+++.++.. +.....+..+.......|++++|...+++.++..  
T Consensus       532 ~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--  606 (987)
T PRK09782        532 WQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--  606 (987)
T ss_pred             HHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--
Confidence            9998665  4555667788889999999999999999999863 3333444444445556699999999999999875  


Q ss_pred             CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHH
Q 042039          224 ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMI  303 (376)
Q Consensus       224 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  303 (376)
                      |+...+..++.++.+.|++++|+..++++....+ .+...+..++.++...|++++|+..++++.+. .|.+...+..+.
T Consensus       607 P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~P-d~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l-~P~~~~a~~nLA  684 (987)
T PRK09782        607 PSANAYVARATIYRQRHNVPAAVSDLRAALELEP-NNSNYQAALGYALWDSGDIAQSREMLERAHKG-LPDDPALIRQLA  684 (987)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHH
Confidence            4678899999999999999999999999998874 37889999999999999999999999999886 456788999999


Q ss_pred             HHHHccCChhHHHHHHHHHHHcCCCCc-HHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          304 HGLCNDGQMDKAHDLFLDMEENAVAPN-VIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       304 ~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .++...|++++|+..++++.+..  |+ ..+.........+..+++.+.+-+++...
T Consensus       685 ~al~~lGd~~eA~~~l~~Al~l~--P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~~  739 (987)
T PRK09782        685 YVNQRLDDMAATQHYARLVIDDI--DNQALITPLTPEQNQQRFNFRRLHEEVGRRWT  739 (987)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhcC--CCCchhhhhhhHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999864  43 35555566667777778888887777654

>TIGR00540 hemY_coli hemY protein

Probab=99.83  E-value=7.8e-17  Score=136.43  Aligned_cols=296  Identities=10%  Similarity=0.033  Sum_probs=219.4

Q ss_pred             HHhcCCChHHHHHHHHHHHhcCCCCc-hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHH
Q 042039           60 GLCHANDWNEAKRLFFEMMDQGVQPS-VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKIN  138 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  138 (376)
                      .....|+++.|.+.+.+..+..  |+ ...+-....+....|+++.|..++.+..+....+...........+...|+++
T Consensus        93 la~~~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~  170 (409)
T TIGR00540        93 LKLAEGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELH  170 (409)
T ss_pred             HHHhCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHH
Confidence            3456799999999999887753  44 33445556788899999999999999987532222234445688899999999


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHH---HHhccchHHHHHHHH
Q 042039          139 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLG---LFEIHQVEHALKLFE  215 (376)
Q Consensus       139 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~a~~~~~  215 (376)
                      .|...++.+.+.. |.++.++..+...+...|++++|.+.+..+.+.+..+..........+   ....+..+.+.+.+.
T Consensus       171 ~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~  249 (409)
T TIGR00540       171 AARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLL  249 (409)
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            9999999999886 678889999999999999999999999999998654332221111111   133333344444555


Q ss_pred             HHHhcCC---CCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHH-HHHHHHHHhCCChHHHHHHHhcccccC
Q 042039          216 EMQRDDV---AADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAY-NCLIDGLCKSGRLEIALELFRSLPRRV  291 (376)
Q Consensus       216 ~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~  291 (376)
                      .+.....   +.+...+..++..+...|+.++|.+.+++..+..+......+ ..........++.+.+.+.++...+. 
T Consensus       250 ~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~-  328 (409)
T TIGR00540       250 NWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN-  328 (409)
T ss_pred             HHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh-
Confidence            5554421   247788899999999999999999999999886533221111 11122223457888899999887765 


Q ss_pred             CCCCH--HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          292 LVADV--VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       292 ~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .|.|+  .....++..+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.+++++...
T Consensus       329 ~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       329 VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45566  677899999999999999999999654444578888888999999999999999999998653

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.83  E-value=1.1e-15  Score=137.26  Aligned_cols=332  Identities=12%  Similarity=0.044  Sum_probs=236.7

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCCh
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKM  102 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  102 (376)
                      ...+...|++++|+++|+++.+.. |.++..+..++..+...++.++|++.++++...  .|+...+..++..+...++.
T Consensus       109 A~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~  185 (822)
T PRK14574        109 ARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRN  185 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchH
Confidence            446667788888888888887775 556677777777778888888888888887765  34444444444444445556


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHH--------------------------------------
Q 042039          103 DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELF--------------------------------------  144 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~--------------------------------------  144 (376)
                      .+|+..++++.+.. +.+...+..+..++.+.|-...|.++.                                      
T Consensus       186 ~~AL~~~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~  264 (822)
T PRK14574        186 YDALQASSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERF  264 (822)
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhH
Confidence            56888888887763 334555555555554444333332222                                      


Q ss_pred             ----------HHHHhc-C-CCCChhh----HHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchH
Q 042039          145 ----------GSMESM-G-CKHDDVS----YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVE  208 (376)
Q Consensus       145 ----------~~~~~~-~-~~~~~~~----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  208 (376)
                                +.+... + .|+....    ..-.+-++...+++.++++.|+.+...+.+....+-..+..+|...++++
T Consensus       265 ~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~  344 (822)
T PRK14574        265 DIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPE  344 (822)
T ss_pred             HHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcH
Confidence                      222221 0 1111111    12334566778889999999999998876656668888999999999999


Q ss_pred             HHHHHHHHHHhcCC-----CCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC-----------Cch---HHHHHHHHH
Q 042039          209 HALKLFEEMQRDDV-----AADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC-----------ELD---IQAYNCLID  269 (376)
Q Consensus       209 ~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~---~~~~~~l~~  269 (376)
                      +|..++..+.....     +++......|.-++...+++++|..+++.+....+           .|+   ......++.
T Consensus       345 kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~  424 (822)
T PRK14574        345 KAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQ  424 (822)
T ss_pred             HHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHH
Confidence            99999999977531     22233357789999999999999999999876322           122   234455677


Q ss_pred             HHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhh
Q 042039          270 GLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSK  349 (376)
Q Consensus       270 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  349 (376)
                      .+...|++.+|++.++.+... .|-|......+...+...|.+.+|+..++.+.... +-+..+....+.++...|++++
T Consensus       425 ~~~~~gdl~~Ae~~le~l~~~-aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~-P~~~~~~~~~~~~al~l~e~~~  502 (822)
T PRK14574        425 SLVALNDLPTAQKKLEDLSST-APANQNLRIALASIYLARDLPRKAEQELKAVESLA-PRSLILERAQAETAMALQEWHQ  502 (822)
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhC-CccHHHHHHHHHHHHhhhhHHH
Confidence            788999999999999999776 67799999999999999999999999998877653 2256677788888999999999


Q ss_pred             HHHHHHHHHhC
Q 042039          350 VIELLHKMKEK  360 (376)
Q Consensus       350 a~~~~~~~~~~  360 (376)
                      |..+.+++.+.
T Consensus       503 A~~~~~~l~~~  513 (822)
T PRK14574        503 MELLTDDVISR  513 (822)
T ss_pred             HHHHHHHHHhh
Confidence            99999888764

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

Probab=99.83  E-value=1.3e-19  Score=146.01  Aligned_cols=262  Identities=18%  Similarity=0.201  Sum_probs=106.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCC-CCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGEN-INPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN   99 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   99 (376)
                      .+...+.+.|++++|++++++..... .+.+...|..+.......++++.|.+.++++...+.. ++..+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            55778888899999999986554443 2456667777777888888999999999988876544 56667777776 688


Q ss_pred             CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CCCChhhHHHHHHHHHccCcHHHHHHH
Q 042039          100 GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG-CKHDDVSYNILINGYCKNKEVEEALSL  178 (376)
Q Consensus       100 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~  178 (376)
                      +++++|..++....+..  +++..+..++..+...++++++.++++.+.... .+.+...|..++.++.+.|++++|++.
T Consensus        91 ~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~  168 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRD  168 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             ccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            88899888888776653  455667778888888899999988888876532 245667788888888889999999999


Q ss_pred             HHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC
Q 042039          179 YREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE  258 (376)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  258 (376)
                      ++++++.. +.+......++..+...|+.+++..++....+.. +.++..+..++.++...|+.++|..++++..... +
T Consensus       169 ~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p  245 (280)
T PF13429_consen  169 YRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-P  245 (280)
T ss_dssp             HHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-T
T ss_pred             HHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-c
Confidence            99988852 3357777888888888888888888888877664 5666777888888888899999999988887765 4


Q ss_pred             chHHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          259 LDIQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                      .|+.....++.++...|+.++|.++.+++.+
T Consensus       246 ~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  246 DDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             T-HHHHHHHHHHHT-----------------
T ss_pred             ccccccccccccccccccccccccccccccc
Confidence            4788888888888888998888888877654

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

Probab=99.82  E-value=8.2e-17  Score=139.34  Aligned_cols=342  Identities=16%  Similarity=0.165  Sum_probs=168.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCC--CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENI--NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      |+.+.+.|...+.-.|++..++.+.+.+.....  ..-...|..++++|...|++++|...|.+..+....-....+.-+
T Consensus       269 nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~Gl  348 (1018)
T KOG2002|consen  269 NPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGL  348 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccch
Confidence            455566666666666666666666665554421  112334556666666666666666666555554222113334445


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC----cHHHH----------------------------
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG----KINRA----------------------------  140 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a----------------------------  140 (376)
                      .+.+.+.|+++.+...|+.+.+.. +.+..+...++..|...+    ..+.|                            
T Consensus       349 gQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~  427 (1018)
T KOG2002|consen  349 GQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQT  427 (1018)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhc
Confidence            556666666666666665555542 223344444444444332    22233                            


Q ss_pred             -----HHHHHHH----HhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC---CCCCC------HhHHHHHHHHHH
Q 042039          141 -----EELFGSM----ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK---GIKPT------VVTYNTLFLGLF  202 (376)
Q Consensus       141 -----~~~~~~~----~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~------~~~~~~l~~~~~  202 (376)
                           +.+|..+    ...+.++.+...|+++..+...|++++|...|......   ...++      ..+-..+...+-
T Consensus       428 d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E  507 (1018)
T KOG2002|consen  428 DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLE  507 (1018)
T ss_pred             ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHH
Confidence                 3333322    22333455566666666667777777777777666543   11111      122333444444


Q ss_pred             hccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC--------------------------
Q 042039          203 EIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK--------------------------  256 (376)
Q Consensus       203 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------------------------  256 (376)
                      ..++.+.|.+.|..+.+.. |.-...|..++......+...+|...++.+...+                          
T Consensus       508 ~l~~~~~A~e~Yk~Ilkeh-p~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~  586 (1018)
T KOG2002|consen  508 ELHDTEVAEEMYKSILKEH-PGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKK  586 (1018)
T ss_pred             hhhhhhHHHHHHHHHHHHC-chhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccH
Confidence            4445555555555544432 1112222222212222233333333333331111                          


Q ss_pred             ---------CCchHHHHHHHHHHHHh------------CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHH
Q 042039          257 ---------CELDIQAYNCLIDGLCK------------SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKA  315 (376)
Q Consensus       257 ---------~~~~~~~~~~l~~~~~~------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  315 (376)
                               ..+|+.+...|+..|.+            .+..++|+++|.++++. .|.|...-+-++-+++..|++.+|
T Consensus       587 f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~-dpkN~yAANGIgiVLA~kg~~~~A  665 (1018)
T KOG2002|consen  587 FETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRN-DPKNMYAANGIGIVLAEKGRFSEA  665 (1018)
T ss_pred             HHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhc-CcchhhhccchhhhhhhccCchHH
Confidence                     01233333444443321            23355666666666554 344555555566666666666666


Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          316 HDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      ..+|.++.+... ....+|..+.++|..+|++..|+++|+...++
T Consensus       666 ~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  666 RDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             HHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666665432 24455666666666666666666666665543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.82  E-value=1.9e-15  Score=119.70  Aligned_cols=344  Identities=17%  Similarity=0.232  Sum_probs=260.5

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +.+..+|..+|.++++-...++|.+++++......+.+..+|+.+|.+-.-.    ...++..+|......||..|+|.+
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~----~~K~Lv~EMisqkm~Pnl~TfNal  279 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYS----VGKKLVAEMISQKMTPNLFTFNAL  279 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhh----ccHHHHHHHHHhhcCCchHhHHHH
Confidence            4567899999999999999999999999998887788999999998765433    237899999999999999999999


Q ss_pred             HHHHHhCCChHH----HHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHH-HHHHHHHHHhc----C----CCCChhhH
Q 042039           93 MDELCKNGKMDE----ASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINR-AEELFGSMESM----G----CKHDDVSY  159 (376)
Q Consensus        93 ~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~----~----~~~~~~~~  159 (376)
                      +.+..+.|+++.    |.+++.+|.+.|+.|...+|..++..+++.++..+ +..++.++...    .    .+.+...|
T Consensus       280 L~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF  359 (625)
T KOG4422|consen  280 LSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFF  359 (625)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHH
Confidence            999999998765    56678889999999999999999999998887644 45555555332    1    23344567


Q ss_pred             HHHHHHHHccCcHHHHHHHHHHHHHCC----CCCC---HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHH
Q 042039          160 NILINGYCKNKEVEEALSLYREMVSKG----IKPT---VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTF  232 (376)
Q Consensus       160 ~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  232 (376)
                      ...+..|.+..+.+-|.++-.-+....    +.|+   ..-|..+....++....+.....|+.+...-.-|+..+...+
T Consensus       360 ~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~  439 (625)
T KOG4422|consen  360 QSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHL  439 (625)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHH
Confidence            778888889999999988876655421    3333   334666777788889999999999999988788899999999


Q ss_pred             HHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCC-Ch--------H-----HHHHHHh-------cccccC
Q 042039          233 IDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSG-RL--------E-----IALELFR-------SLPRRV  291 (376)
Q Consensus       233 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~--------~-----~a~~~~~-------~~~~~~  291 (376)
                      +++....|.++-.-+++.+++..|..........+...+++.+ ..        .     -|..+++       ++.+  
T Consensus       440 lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r~--  517 (625)
T KOG4422|consen  440 LRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQRA--  517 (625)
T ss_pred             HHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHHh--
Confidence            9999999999999999988877765544444444444444433 11        0     0111111       1222  


Q ss_pred             CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcC----CCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCC
Q 042039          292 LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA----VAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKV  362 (376)
Q Consensus       292 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  362 (376)
                      ........+..+-.+.+.|+.++|.+++..+.+.+    ..|.......++..-.+.+++..|...++-|.+.+.
T Consensus       518 ~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a~~~n~  592 (625)
T KOG4422|consen  518 QDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLASAFNL  592 (625)
T ss_pred             ccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCc
Confidence            33456677888888999999999999999986542    234444555777777888999999999999876543

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

Probab=99.82  E-value=1e-19  Score=146.64  Aligned_cols=261  Identities=15%  Similarity=0.146  Sum_probs=85.4

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcC-CCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRD-VRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      .+...+...|++++|+++++...... .+.+...|..+...+...++++.|.+.++++...+ +.++..+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-~~~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-KANPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccc-ccc
Confidence            34555666666666666665443332 12234444555555566666666666666666554 3344555555555 566


Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHhCCCHHHHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD-VAADTSTYNTFIDGLCKNGYIVEAVEL  248 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~  248 (376)
                      +++++|.+++....+.  .+++..+..++..+...++++++..+++.+.... .+.+...+..++..+.+.|+.++|+..
T Consensus        91 ~~~~~A~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~  168 (280)
T PF13429_consen   91 GDPEEALKLAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRD  168 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             cccccccccccccccc--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            6667777666665543  2344555566666666677777777666655432 234455566666667777777777777


Q ss_pred             HHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 042039          249 FRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVA  328 (376)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  328 (376)
                      ++++....+. ++.....++..+...|+.+++..++....+. .+.|+..+..++.++...|++++|...|++..+.. +
T Consensus       169 ~~~al~~~P~-~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~-~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p  245 (280)
T PF13429_consen  169 YRKALELDPD-DPDARNALAWLLIDMGDYDEAREALKRLLKA-APDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-P  245 (280)
T ss_dssp             HHHHHHH-TT--HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-T
T ss_pred             HHHHHHcCCC-CHHHHHHHHHHHHHCCChHHHHHHHHHHHHH-CcCHHHHHHHHHHHhcccccccccccccccccccc-c
Confidence            7777666422 5666666777777777777766666665554 24455566667777777777777777777776643 2


Q ss_pred             CcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          329 PNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       329 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      .|+.....+..++.+.|+.++|.++.+++.
T Consensus       246 ~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  246 DDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             T-HHHHHHHHHHHT----------------
T ss_pred             cccccccccccccccccccccccccccccc
Confidence            266666667777777777777777666654

>TIGR00540 hemY_coli hemY protein

Probab=99.82  E-value=2.5e-16  Score=133.35  Aligned_cols=301  Identities=12%  Similarity=0.045  Sum_probs=222.3

Q ss_pred             HHHHHHHH--HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           19 YNTIIDGL--CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        19 ~~~l~~~~--~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ...+.++.  ...|+++.|.+.+.+..+.. +.....+.....+..+.|+++.|.+.+.+..+....+...........+
T Consensus        85 ~~~~~~glla~~~g~~~~A~~~l~~~~~~~-~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~  163 (409)
T TIGR00540        85 QKQTEEALLKLAEGDYAKAEKLIAKNADHA-AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRIL  163 (409)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhhcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHH
Confidence            34444443  45799999999999887763 2234455566788899999999999999988764333333444468888


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHH-HHHHHH---HccCcH
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYN-ILINGY---CKNKEV  172 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~---~~~~~~  172 (376)
                      ...|+++.|...++.+.+.. +-+..+...+...+...|++++|.+.+..+.+.+.. +...+. .-...+   ...+..
T Consensus       164 l~~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~  241 (409)
T TIGR00540       164 LAQNELHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMA  241 (409)
T ss_pred             HHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999985 446788899999999999999999999999988643 333332 111221   233333


Q ss_pred             HHHHHHHHHHHHCCC---CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchH--HHHHHHHHhCCCHHHHHH
Q 042039          173 EEALSLYREMVSKGI---KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTY--NTFIDGLCKNGYIVEAVE  247 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~  247 (376)
                      +++.+.+..+.+...   +.+...+..+...+...|+.++|.+.+++..+... .+....  ..........++.+.+.+
T Consensus       242 ~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~p-d~~~~~~~~l~~~~~l~~~~~~~~~~  320 (409)
T TIGR00540       242 DEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLG-DDRAISLPLCLPIPRLKPEDNEKLEK  320 (409)
T ss_pred             hcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCC-CcccchhHHHHHhhhcCCCChHHHHH
Confidence            444445555555421   23788889999999999999999999999998752 222211  112222334578889999


Q ss_pred             HHHHhcccCCCchH--HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          248 LFRTLGILKCELDI--QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       248 ~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      .++...+.. +-++  .....++..+.+.|++++|.+.|+........|+...+..++..+.+.|+.++|.+++++...
T Consensus       321 ~~e~~lk~~-p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       321 LIEKQAKNV-DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             HHHHHHHhC-CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            998887765 3366  778899999999999999999999544433568888889999999999999999999998754

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.

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

Probab=99.82  E-value=1.4e-17  Score=138.59  Aligned_cols=289  Identities=13%  Similarity=0.072  Sum_probs=162.7

Q ss_pred             ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCC--CCChhhHHHHHHHHHhcCcHHHHHHH
Q 042039           66 DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDV--RPNAFTYSTLMDGFCLTGKINRAEEL  143 (376)
Q Consensus        66 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~  143 (376)
                      +..+|+..|.++... +.-+..+...+.++|...+++++|.++|+.+.+...  --+..+|.+.+..+-+    +-+...
T Consensus       334 ~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~----~v~Ls~  408 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQD----EVALSY  408 (638)
T ss_pred             HHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHh----hHHHHH
Confidence            345666666664433 222334555566666666666666666666655320  0123444444433211    112222


Q ss_pred             H-HHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          144 F-GSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       144 ~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                      + +.+.+.. +..+.+|-.++++|.-+++.+.|++.|+++++.  .| ...+|+.+..-+.....+|.|...|+..+..+
T Consensus       409 Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~  485 (638)
T KOG1126|consen  409 LAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVD  485 (638)
T ss_pred             HHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCC
Confidence            2 2222222 455566666666666666666666666666653  33 45566666666666666666666666665543


Q ss_pred             CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHH
Q 042039          222 VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNI  301 (376)
Q Consensus       222 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  301 (376)
                       +-+..+|..++..|.+.++++.|+-.|+.+...++. +......++..+.+.|+.++|+++++++... .+.|+..-..
T Consensus       486 -~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~-nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l-d~kn~l~~~~  562 (638)
T KOG1126|consen  486 -PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPS-NSVILCHIGRIQHQLKRKDKALQLYEKAIHL-DPKNPLCKYH  562 (638)
T ss_pred             -chhhHHHHhhhhheeccchhhHHHHHHHhhhcCCcc-chhHHhhhhHHHHHhhhhhHHHHHHHHHHhc-CCCCchhHHH
Confidence             334455566666666666666666666666665532 5556666666666666666666666666554 2334555555


Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCch
Q 042039          302 MIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA  366 (376)
Q Consensus       302 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  366 (376)
                      .+..+...+++++|+..++++.+. ++.+...+..+.+.|.+.|+.+.|+.-|--+.+...+++.
T Consensus       563 ~~~il~~~~~~~eal~~LEeLk~~-vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  563 RASILFSLGRYVEALQELEELKEL-VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             HHHHHHhhcchHHHHHHHHHHHHh-CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            566666666666666666666664 2224455556666666666666666666666654444333

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

Probab=99.81  E-value=2.8e-17  Score=136.80  Aligned_cols=292  Identities=13%  Similarity=0.060  Sum_probs=239.0

Q ss_pred             CChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC--CCchHhHHHHHHHHHhCCChHHHHH
Q 042039           30 GFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV--QPSVVTFNVIMDELCKNGKMDEASR  107 (376)
Q Consensus        30 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~  107 (376)
                      -+.++|+..|+.+... +..+.++...++.+|...+++++|.++|+.+.+..+  -.+..+|...+..+-   +.-+---
T Consensus       333 y~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq---~~v~Ls~  408 (638)
T KOG1126|consen  333 YNCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQ---DEVALSY  408 (638)
T ss_pred             HHHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHH---hhHHHHH
Confidence            4578999999995544 355668889999999999999999999999988632  125667776665432   2222223


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCC
Q 042039          108 LLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGI  187 (376)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  187 (376)
                      +-+.+.+.+ +-.+.+|..++.+|..+++.+.|++.|+++.+.+ +....+|..++.-+....++|.|...|+.++... 
T Consensus       409 Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQld-p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~-  485 (638)
T KOG1126|consen  409 LAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLD-PRFAYAYTLLGHESIATEEFDKAMKSFRKALGVD-  485 (638)
T ss_pred             HHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccC-CccchhhhhcCChhhhhHHHHhHHHHHHhhhcCC-
Confidence            334455443 4468999999999999999999999999999986 5578899999999999999999999999988752 


Q ss_pred             CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHH
Q 042039          188 KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCL  267 (376)
Q Consensus       188 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  267 (376)
                      +.+-.+|.-++..|.+.++++.|.-.|+++.+.+ |.+......++..+.+.|+.++|+++++++...+.. ++-.-...
T Consensus       486 ~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~~~~  563 (638)
T KOG1126|consen  486 PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCKYHR  563 (638)
T ss_pred             chhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhHHHH
Confidence            2245667778899999999999999999999887 667778888899999999999999999999888744 66666777


Q ss_pred             HHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcH
Q 042039          268 IDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV  331 (376)
Q Consensus       268 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  331 (376)
                      +..+...+++++|+..++++.+. ++.+...|..++..|.+.|+.+.|+.-|--+.+...++..
T Consensus       564 ~~il~~~~~~~eal~~LEeLk~~-vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  564 ASILFSLGRYVEALQELEELKEL-VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             HHHHHhhcchHHHHHHHHHHHHh-CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            88888999999999999999886 6667788999999999999999999999988886554433

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

Probab=99.81  E-value=1.9e-16  Score=126.43  Aligned_cols=350  Identities=17%  Similarity=0.148  Sum_probs=238.8

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC------------C
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ------------P   84 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------------~   84 (376)
                      ...+.+.-.+.+.|+++.|+..|+...+.  .|+..+-..|+.++...|+-++..+.|.+++.....            |
T Consensus       277 kil~nigvtfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp  354 (840)
T KOG2003|consen  277 KILNNIGVTFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDP  354 (840)
T ss_pred             HHHhhcCeeEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCc
Confidence            34555555677889999999999988776  567766667777777888888888889888764222            2


Q ss_pred             chHhHHHHH-----HHHHhCC--ChHHHHHHHHHHHhcCCCCCh---------------------hhHHHHHHHHHhcCc
Q 042039           85 SVVTFNVIM-----DELCKNG--KMDEASRLLDLMVQRDVRPNA---------------------FTYSTLMDGFCLTGK  136 (376)
Q Consensus        85 ~~~~~~~l~-----~~~~~~~--~~~~a~~~~~~~~~~~~~~~~---------------------~~~~~l~~~~~~~~~  136 (376)
                      +....+..+     +-.-+.+  +-++++..--+++.--+.|+-                     ..-..-..-+.+.|+
T Consensus       355 ~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d  434 (840)
T KOG2003|consen  355 DDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGD  434 (840)
T ss_pred             chHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccC
Confidence            222221111     1111111  111121111111111111110                     000112335667777


Q ss_pred             HHHHHHHHHHHHhcCCC------------------------------------CChhhHHHHHHHHHccCcHHHHHHHHH
Q 042039          137 INRAEELFGSMESMGCK------------------------------------HDDVSYNILINGYCKNKEVEEALSLYR  180 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~------------------------------------~~~~~~~~l~~~~~~~~~~~~a~~~~~  180 (376)
                      ++.|.+++.-..+..-+                                    .++.....-.......|++++|.+.|+
T Consensus       435 ~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~dka~~~yk  514 (840)
T KOG2003|consen  435 IEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDLDKAAEFYK  514 (840)
T ss_pred             HHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcHHHHHHHHH
Confidence            77777777665443211                                    111111222222344788999999999


Q ss_pred             HHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCch
Q 042039          181 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELD  260 (376)
Q Consensus       181 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  260 (376)
                      +.+..+.. .......+...+...|+.++|++.|-++... ...+..++..+...|....++.+|++++-++...- +.|
T Consensus       515 eal~ndas-c~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~sli-p~d  591 (840)
T KOG2003|consen  515 EALNNDAS-CTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQANSLI-PND  591 (840)
T ss_pred             HHHcCchH-HHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcccC-CCC
Confidence            98876322 3444445556677889999999999887654 24577888889999999999999999999886553 558


Q ss_pred             HHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 042039          261 IQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHG  340 (376)
Q Consensus       261 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  340 (376)
                      +..+..++..|-+.|+-.+|.+.+-.--+. +|.+..+...|..-|....-+++++.+|+++.-  +.|+..-|..++..
T Consensus       592 p~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlmias  668 (840)
T KOG2003|consen  592 PAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLMIAS  668 (840)
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHHHHH
Confidence            999999999999999999999987765554 778999999999999999999999999999865  68999999988865


Q ss_pred             -HhhcCChhhHHHHHHHHHhCCCCCchHHHHHHHhh
Q 042039          341 -FVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDL  375 (376)
Q Consensus       341 -~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  375 (376)
                       +.+.|++++|.+++++..++ ++-|...+..+++.
T Consensus       669 c~rrsgnyqka~d~yk~~hrk-fpedldclkflvri  703 (840)
T KOG2003|consen  669 CFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRI  703 (840)
T ss_pred             HHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHH
Confidence             46689999999999998764 66677777766653

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.81  E-value=6e-16  Score=130.34  Aligned_cols=285  Identities=12%  Similarity=0.045  Sum_probs=221.7

Q ss_pred             hcCChhHHHHHHHHhhhCCCCCChhh-HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhH--HHHHHHHHhCCChHH
Q 042039           28 KEGFVDKAKALFLQMKGENINPDVVT-YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTF--NVIMDELCKNGKMDE  104 (376)
Q Consensus        28 ~~g~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~  104 (376)
                      -.|++++|.+.+....+..  +++.. |........+.|+++.|.+.+.++.+.  .|+....  ......+...|+++.
T Consensus        96 ~eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~  171 (398)
T PRK10747         96 AEGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHA  171 (398)
T ss_pred             hCCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHH
Confidence            3699999998888766542  23333 333355658999999999999999875  4444322  244678899999999


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChh-------hHHHHHHHHHccCcHHHHHH
Q 042039          105 ASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDV-------SYNILINGYCKNKEVEEALS  177 (376)
Q Consensus       105 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~l~~~~~~~~~~~~a~~  177 (376)
                      |...++++.+.. +-++.....+...|.+.|++++|.+++..+.+....++..       +|..++.......+.+...+
T Consensus       172 Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~  250 (398)
T PRK10747        172 ARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKR  250 (398)
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            999999999875 4468888999999999999999999999999876432221       22333333344455566666


Q ss_pred             HHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC
Q 042039          178 LYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC  257 (376)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  257 (376)
                      +++.+.+. .+.++.....+...+...|+.++|.+.+++..+.  +++....  ++.+....++++++.+..+...+..+
T Consensus       251 ~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~~P  325 (398)
T PRK10747        251 WWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQHG  325 (398)
T ss_pred             HHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHHHHHHhhCC
Confidence            66665443 3557888899999999999999999999999874  4444322  23344466999999999999887764


Q ss_pred             CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          258 ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       258 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                       -|+..+..++..+.+.+++++|.+.|+.+.+.  .|+...+..+..++.+.|+.++|.+++++....
T Consensus       326 -~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~  390 (398)
T PRK10747        326 -DTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLML  390 (398)
T ss_pred             -CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             47888999999999999999999999999874  689999999999999999999999999988653

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

Probab=99.80  E-value=1.2e-15  Score=116.28  Aligned_cols=291  Identities=16%  Similarity=0.195  Sum_probs=229.2

Q ss_pred             cCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC---hhhHHHHHHHHHhcCcHHH
Q 042039           63 HANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN---AFTYSTLMDGFCLTGKINR  139 (376)
Q Consensus        63 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~  139 (376)
                      -.++.++|.+.|-+|.+.... +..+...|.+.+.+.|..+.|+++.+.+.++..-+.   ......+.+-|...|-+|.
T Consensus        47 Ls~Q~dKAvdlF~e~l~~d~~-t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DR  125 (389)
T COG2956          47 LSNQPDKAVDLFLEMLQEDPE-TFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDR  125 (389)
T ss_pred             hhcCcchHHHHHHHHHhcCch-hhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhH
Confidence            356889999999999885322 566677888999999999999999999987521111   3355677888999999999


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC----HhHHHHHHHHHHhccchHHHHHHHH
Q 042039          140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT----VVTYNTLFLGLFEIHQVEHALKLFE  215 (376)
Q Consensus       140 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~  215 (376)
                      |+.+|..+.+.+ ..-..+...|+..|-...+|++|+++-+++.+.+..+.    ...|..+...+....++++|...+.
T Consensus       126 AE~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~  204 (389)
T COG2956         126 AEDIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLK  204 (389)
T ss_pred             HHHHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            999999998865 45667888899999999999999999999988654443    3456777777778889999999999


Q ss_pred             HHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC
Q 042039          216 EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD  295 (376)
Q Consensus       216 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  295 (376)
                      +..+.+ +....+-..+++.....|+++.|++.++.+.+.++..-+.+...+..+|.+.|+.++...++..+.+..  +.
T Consensus       205 kAlqa~-~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~--~g  281 (389)
T COG2956         205 KALQAD-KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN--TG  281 (389)
T ss_pred             HHHhhC-ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc--CC
Confidence            998886 556777778889999999999999999999988776667888999999999999999999999988753  34


Q ss_pred             HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh---cCChhhHHHHHHHHHhC
Q 042039          296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR---INKPSKVIELLHKMKEK  360 (376)
Q Consensus       296 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~  360 (376)
                      ...-..+...-....-.+.|...+.+-+..  +|+...+..++.....   -|...+-+..+++|...
T Consensus       282 ~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge  347 (389)
T COG2956         282 ADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGE  347 (389)
T ss_pred             ccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHH
Confidence            444455555555556667777666665553  6899999999886654   34567777888888754

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

Probab=99.80  E-value=5.5e-16  Score=134.31  Aligned_cols=348  Identities=13%  Similarity=0.057  Sum_probs=222.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC----ChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN----DWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +.-+...+.+.|+++.+...|+.+.... |.+..+...|+..|...+    ..+.|..++.+..+.- +.|...|..+..
T Consensus       345 ~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-~~d~~a~l~laq  422 (1018)
T KOG2002|consen  345 LVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-PVDSEAWLELAQ  422 (1018)
T ss_pred             ccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-cccHHHHHHHHH
Confidence            4456677888888888888888877765 556677777777776664    4455555555555442 224555555554


Q ss_pred             HHHhCCChHHHHHHHHHHH----hcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc---CCC------CChhhHHH
Q 042039           95 ELCKNGKMDEASRLLDLMV----QRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM---GCK------HDDVSYNI  161 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~------~~~~~~~~  161 (376)
                      .+....-+.. +.+|..+.    ..+..+.+...+.++..+...|++..|...|......   ...      ++..+-.+
T Consensus       423 l~e~~d~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YN  501 (1018)
T KOG2002|consen  423 LLEQTDPWAS-LDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYN  501 (1018)
T ss_pred             HHHhcChHHH-HHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHH
Confidence            4443332222 44444333    2222344455555555555556655555555555433   001      11112333


Q ss_pred             HHHHHHccCcHHHHHHHHH----------------------------------HHHHCCCCCCHhHHHHHHHHHHhccch
Q 042039          162 LINGYCKNKEVEEALSLYR----------------------------------EMVSKGIKPTVVTYNTLFLGLFEIHQV  207 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~----------------------------------~~~~~~~~~~~~~~~~l~~~~~~~~~~  207 (376)
                      +..++-..++.+.|.+.|.                                  ..... ...++..+..+...+.....+
T Consensus       502 larl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~-d~~np~arsl~G~~~l~k~~~  580 (1018)
T KOG2002|consen  502 LARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNI-DSSNPNARSLLGNLHLKKSEW  580 (1018)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhc-ccCCcHHHHHHHHHHHhhhhh
Confidence            4444444444444444444                                  44433 222444455555556666666


Q ss_pred             HHHHHHHHHHHhcC-CCCCcchHHHHHHHHHh------------CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhC
Q 042039          208 EHALKLFEEMQRDD-VAADTSTYNTFIDGLCK------------NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKS  274 (376)
Q Consensus       208 ~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  274 (376)
                      ..|.+-|..+.+.- ..+|+.+...|+..|.+            .+..++|+++|.++.... +.+...-+.++.+++..
T Consensus       581 ~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~k  659 (1018)
T KOG2002|consen  581 KPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEK  659 (1018)
T ss_pred             cccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhc
Confidence            66666555554431 12344445555554442            345788999999988876 34788889999999999


Q ss_pred             CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc-CCCCcHHHHHHHHHHHhhcCChhhHHHH
Q 042039          275 GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN-AVAPNVIIFVTLIHGFVRINKPSKVIEL  353 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~  353 (376)
                      |++.+|..+|.+..+. ......+|..++++|..+|+|..|+++|+...+. ....+..+...|.+++.+.|++.+|.+.
T Consensus       660 g~~~~A~dIFsqVrEa-~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~  738 (1018)
T KOG2002|consen  660 GRFSEARDIFSQVREA-TSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEA  738 (1018)
T ss_pred             cCchHHHHHHHHHHHH-HhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHH
Confidence            9999999999999876 3346778999999999999999999999998765 4455788899999999999999999999


Q ss_pred             HHHHHhCCCCCchHHHHHH
Q 042039          354 LHKMKEKKVMPDASIVSMV  372 (376)
Q Consensus       354 ~~~~~~~~~~p~~~~~~~l  372 (376)
                      +.......+.-....++..
T Consensus       739 ll~a~~~~p~~~~v~FN~a  757 (1018)
T KOG2002|consen  739 LLKARHLAPSNTSVKFNLA  757 (1018)
T ss_pred             HHHHHHhCCccchHHhHHH
Confidence            9998877665555566543

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

Probab=99.80  E-value=8.6e-16  Score=122.67  Aligned_cols=291  Identities=12%  Similarity=0.070  Sum_probs=179.2

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--CchHhHHHHHHHHHhCCC
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~  101 (376)
                      .++....+.++++.-.+.....|.+.+...-+..+.+.....++++|+.+|+++.+..+-  .|..+|..++-  .+..+
T Consensus       235 ~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LY--v~~~~  312 (559)
T KOG1155|consen  235 KAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLY--VKNDK  312 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHH--HHhhh
Confidence            344445566666666666676666655555555566666667777777777777765221  13445554432  22211


Q ss_pred             hHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHH
Q 042039          102 MDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                        ..+.++.+-.-.-.+-.+.|+..+++-|.-.++.++|...|++..+.+ |....+|..+++-|....+...|++.|+.
T Consensus       313 --skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRr  389 (559)
T KOG1155|consen  313 --SKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRR  389 (559)
T ss_pred             --HHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHH
Confidence              112222221111112234566667777777777777777777777776 55666777777777777777777777777


Q ss_pred             HHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchH
Q 042039          182 MVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDI  261 (376)
Q Consensus       182 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  261 (376)
                      +++- .+.|-..|-.++++|.-.+.+.=|+-.|++..... |.|+..+..++.+|.+.++.++|++.|+++...+ ..+.
T Consensus       390 Avdi-~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~  466 (559)
T KOG1155|consen  390 AVDI-NPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEG  466 (559)
T ss_pred             HHhc-CchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccch
Confidence            7775 34466777777777777777777777777777664 5667777777777777777777777777776655 2255


Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhccccc----C-CCC-CHHHHHHHHHHHHccCChhHHHHHHHHH
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPRR----V-LVA-DVVTYNIMIHGLCNDGQMDKAHDLFLDM  322 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~  322 (376)
                      ..+..++..|.+.++.++|.+.|.+.++.    | ..| .......|..-+.+.+++++|.......
T Consensus       467 ~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~  533 (559)
T KOG1155|consen  467 SALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLV  533 (559)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            67777777777777777777777665432    1 111 1222333555556666666665544433

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

Probab=99.79  E-value=7.5e-15  Score=117.42  Aligned_cols=351  Identities=12%  Similarity=0.055  Sum_probs=224.1

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHH-----------------------------HHh
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIH-----------------------------GLC   62 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~-----------------------------~~~   62 (376)
                      ...|+..+......+.+.|....|++.|......- |-.-.+|..|..                             ++.
T Consensus       160 ~~~D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~~-P~~W~AWleL~~lit~~e~~~~l~~~l~~~~h~M~~~F~~~a~~  238 (559)
T KOG1155|consen  160 GEKDEFLLYLYGVVLKELGLLSLAIDSFVEVVNRY-PWFWSAWLELSELITDIEILSILVVGLPSDMHWMKKFFLKKAYQ  238 (559)
T ss_pred             ccchhHHHHHHHHHHHhhchHHHHHHHHHHHHhcC-CcchHHHHHHHHhhchHHHHHHHHhcCcccchHHHHHHHHHHHH
Confidence            34455566666666778888888888888776542 333333333222                             222


Q ss_pred             cCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC--CChhhHHHHHHHHHhcCcHHHH
Q 042039           63 HANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR--PNAFTYSTLMDGFCLTGKINRA  140 (376)
Q Consensus        63 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a  140 (376)
                      ...+.+++.+-.+.....|.+-+...-+..+.+.....++++|+..|+++.+.++-  .|..+|..++-.-...   .+.
T Consensus       239 el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~---skL  315 (559)
T KOG1155|consen  239 ELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDK---SKL  315 (559)
T ss_pred             HHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhh---HHH
Confidence            22344444444455555555444444444445555566666666666666655210  1233444333221111   111


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          141 EELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      .-+-+.....+ +-.+.+...+++.|.-.++.++|...|++.++.+ +.....|..++.-|....+...|+..++.+++.
T Consensus       316 s~LA~~v~~id-KyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi  393 (559)
T KOG1155|consen  316 SYLAQNVSNID-KYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDI  393 (559)
T ss_pred             HHHHHHHHHhc-cCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhc
Confidence            11111111111 2344555666777777888888999998888853 224677888888888888888999999888887


Q ss_pred             CCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHH
Q 042039          221 DVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYN  300 (376)
Q Consensus       221 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  300 (376)
                      + |.|...|..++++|.-.+.+.-|.-.|+++.... +-|+..|..|+.+|.+.++.++|++.|..+...+. .+...+.
T Consensus       394 ~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d-te~~~l~  470 (559)
T KOG1155|consen  394 N-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD-TEGSALV  470 (559)
T ss_pred             C-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc-cchHHHH
Confidence            6 6688888889999988888888888888888776 44788889999999999999999999988877643 3567888


Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHc----C-CCC-cHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHH
Q 042039          301 IMIHGLCNDGQMDKAHDLFLDMEEN----A-VAP-NVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVV  373 (376)
Q Consensus       301 ~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll  373 (376)
                      .++..|-+.++..+|...|++.++.    | +.| ......-|..-+.+.+++++|..........  .+...--+.++
T Consensus       471 ~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~~--~~e~eeak~Ll  547 (559)
T KOG1155|consen  471 RLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLVLKG--ETECEEAKALL  547 (559)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhcC--CchHHHHHHHH
Confidence            8888888888988888888877652    2 223 2223333556677788888887766655433  44444444443

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

Probab=99.79  E-value=3.5e-15  Score=117.23  Aligned_cols=292  Identities=13%  Similarity=0.126  Sum_probs=237.1

Q ss_pred             cCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHH
Q 042039           63 HANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEE  142 (376)
Q Consensus        63 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  142 (376)
                      ..|+|.+|++...+..+.+.. ....|..-+++.-..|+.+.+-.++.++-+....++........+.....|+++.|..
T Consensus        96 ~eG~~~qAEkl~~rnae~~e~-p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~  174 (400)
T COG3071          96 FEGDFQQAEKLLRRNAEHGEQ-PVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARE  174 (400)
T ss_pred             hcCcHHHHHHHHHHhhhcCcc-hHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHH
Confidence            468999999999998877655 3455666677888899999999999999886445567777788889999999999999


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC-------HhHHHHHHHHHHhccchHHHHHHHH
Q 042039          143 LFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-------VVTYNTLFLGLFEIHQVEHALKLFE  215 (376)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~  215 (376)
                      -+.++...+ +.++.+......+|.+.|++.....++..+.+.+.-.+       ..+|..++.-....+..+.-...|+
T Consensus       175 ~v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~  253 (400)
T COG3071         175 NVDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWK  253 (400)
T ss_pred             HHHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHH
Confidence            999999887 77888999999999999999999999999999876555       3455666666666666666566666


Q ss_pred             HHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC
Q 042039          216 EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD  295 (376)
Q Consensus       216 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  295 (376)
                      ...+. .+.++..-..++.-+.++|+.++|.++.++..+....|.   . .....+.+.++.+.-++..++..+. .+.+
T Consensus       254 ~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L-~~~~~~l~~~d~~~l~k~~e~~l~~-h~~~  327 (400)
T COG3071         254 NQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR---L-CRLIPRLRPGDPEPLIKAAEKWLKQ-HPED  327 (400)
T ss_pred             hccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh---H-HHHHhhcCCCCchHHHHHHHHHHHh-CCCC
Confidence            66544 356777888889999999999999999999988876554   2 2223456778888888888776655 5567


Q ss_pred             HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCC
Q 042039          296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMP  364 (376)
Q Consensus       296 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p  364 (376)
                      +..+..++..|.+.+.|.+|...|+...+.  .|+..+|..+.+++.+.|++.+|.+..++....-..|
T Consensus       328 p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~  394 (400)
T COG3071         328 PLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREALLLTRQP  394 (400)
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCC
Confidence            789999999999999999999999988874  7899999999999999999999999999876443333

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

Probab=99.79  E-value=5.7e-15  Score=127.24  Aligned_cols=344  Identities=16%  Similarity=0.135  Sum_probs=269.9

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV   91 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   91 (376)
                      .+.+...|..|...|-+.|+.+++...+-.+...+ |.|...|..+.....+.|.+++|.-+|.++++..+. +...+..
T Consensus       169 dp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~p~-n~~~~~e  246 (895)
T KOG2076|consen  169 DPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGNINQARYCYSRAIQANPS-NWELIYE  246 (895)
T ss_pred             CccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCc-chHHHHH
Confidence            35677899999999999999999999988777665 678899999999999999999999999999998543 6666666


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCCCCh----hhHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CCCChhhHHHHHHHH
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDVRPNA----FTYSTLMDGFCLTGKINRAEELFGSMESMG-CKHDDVSYNILINGY  166 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~  166 (376)
                      -...|-+.|+...|.+.|.++.+...+.+.    .....++..+...++-+.|.+.++.....+ -..+...++.++..+
T Consensus       247 rs~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~  326 (895)
T KOG2076|consen  247 RSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELF  326 (895)
T ss_pred             HHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHH
Confidence            778899999999999999999987532222    233445667777888899999998887632 234556788999999


Q ss_pred             HccCcHHHHHHHHHHHHHCC---------------------------CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          167 CKNKEVEEALSLYREMVSKG---------------------------IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       167 ~~~~~~~~a~~~~~~~~~~~---------------------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      .+...++.+...........                           ..++..+ ..+.-++.+.+..+....+......
T Consensus       327 l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v-~rl~icL~~L~~~e~~e~ll~~l~~  405 (895)
T KOG2076|consen  327 LKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRV-IRLMICLVHLKERELLEALLHFLVE  405 (895)
T ss_pred             HHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchh-HhHhhhhhcccccchHHHHHHHHHH
Confidence            99999999999888877621                           1222222 2344455666666666666666666


Q ss_pred             cC--CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHH
Q 042039          220 DD--VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVV  297 (376)
Q Consensus       220 ~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  297 (376)
                      .+  +..+...|..+..++...|++.+|+.++..+......-+...|..++++|...|.+++|.+.|+.++.. .|.+..
T Consensus       406 ~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~-~p~~~D  484 (895)
T KOG2076|consen  406 DNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLIL-APDNLD  484 (895)
T ss_pred             hcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhc-CCCchh
Confidence            65  334566899999999999999999999999987655556789999999999999999999999999876 455677


Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHH--------cCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEE--------NAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~--------~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .-..|...+.+.|+.++|.+.+..+..        .+..|+..........+.+.|+.++-+..-..|+.
T Consensus       485 ~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~E~fi~t~~~Lv~  554 (895)
T KOG2076|consen  485 ARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKREEFINTASTLVD  554 (895)
T ss_pred             hhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            777888999999999999999998542        23556666666677788889998886666555543

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

Probab=99.77  E-value=1.3e-14  Score=114.13  Aligned_cols=299  Identities=12%  Similarity=0.079  Sum_probs=238.9

Q ss_pred             HHHHHH--hcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC
Q 042039           22 IIDGLC--KEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN   99 (376)
Q Consensus        22 l~~~~~--~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   99 (376)
                      +.++..  -.|+|.+|+++..+..+.+ +.....|..-+.+.-+.|+.+.+-.++.++.+....++....-...+.....
T Consensus        88 ~~egl~~l~eG~~~qAEkl~~rnae~~-e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~  166 (400)
T COG3071          88 LNEGLLKLFEGDFQQAEKLLRRNAEHG-EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNR  166 (400)
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHhhhcC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhC
Confidence            444444  3699999999999988776 4445667777788889999999999999998875566777778888899999


Q ss_pred             CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChh-------hHHHHHHHHHccCcH
Q 042039          100 GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDV-------SYNILINGYCKNKEV  172 (376)
Q Consensus       100 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~l~~~~~~~~~~  172 (376)
                      |+...|..-+.++.+.+ +.++.......++|.+.|++.....++..+.+.+.-.+..       +|..++.-....+..
T Consensus       167 ~d~~aA~~~v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~  245 (400)
T COG3071         167 RDYPAARENVDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGS  245 (400)
T ss_pred             CCchhHHHHHHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccc
Confidence            99999999999999886 4467888999999999999999999999999988655543       566666666666666


Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      +.-...++...++ .+-++..-..++.-+.++|+.+.|.++..+..+.+..+.   . .....+.+.++...-++..+..
T Consensus       246 ~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L-~~~~~~l~~~d~~~l~k~~e~~  320 (400)
T COG3071         246 EGLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR---L-CRLIPRLRPGDPEPLIKAAEKW  320 (400)
T ss_pred             hHHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh---H-HHHHhhcCCCCchHHHHHHHHH
Confidence            6655566665544 455677778888999999999999999999998865554   2 2223456778888877777776


Q ss_pred             cccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc
Q 042039          253 GILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       253 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  330 (376)
                      .... +.++..+..++..|.+.+.|.+|...|+...+  ..|+..+|..+..++.+.|+..+|.++.++....-.+|+
T Consensus       321 l~~h-~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~  395 (400)
T COG3071         321 LKQH-PEDPLLLSTLGRLALKNKLWGKASEALEAALK--LRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPN  395 (400)
T ss_pred             HHhC-CCChhHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCC
Confidence            6554 33678999999999999999999999998776  478999999999999999999999999998875433333

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

Probab=99.77  E-value=5.2e-15  Score=119.10  Aligned_cols=331  Identities=17%  Similarity=0.149  Sum_probs=185.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC-hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc-hHhHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPD-VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS-VVTFNVIMDE   95 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~   95 (376)
                      .+-...+-|.++|++++|++.|.+.+..  .|+ +..|.....+|...|+|+++.+...+.++.  .|+ +..+..-..+
T Consensus       117 ~lK~~GN~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl--~P~Y~KAl~RRA~A  192 (606)
T KOG0547|consen  117 ALKTKGNKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAACYESLGDWEKVIEDCTKALEL--NPDYVKALLRRASA  192 (606)
T ss_pred             HHHhhhhhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhc--CcHHHHHHHHHHHH
Confidence            4555667789999999999999999987  566 888999999999999999999988888775  333 3344444555


Q ss_pred             HHhCCChHHHHHHH------------------HHHH------------h-cC--CCCChhhHHHHHHHH-----------
Q 042039           96 LCKNGKMDEASRLL------------------DLMV------------Q-RD--VRPNAFTYSTLMDGF-----------  131 (376)
Q Consensus        96 ~~~~~~~~~a~~~~------------------~~~~------------~-~~--~~~~~~~~~~l~~~~-----------  131 (376)
                      +-..|++.+|+.-.                  ++.+            + .+  +-|......+....+           
T Consensus       193 ~E~lg~~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~  272 (606)
T KOG0547|consen  193 HEQLGKFDEALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNK  272 (606)
T ss_pred             HHhhccHHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCC
Confidence            55556655543211                  1111            0 01  111211111111111           


Q ss_pred             ----------------------------------------------------------------HhcCcHHHHHHHHHHH
Q 042039          132 ----------------------------------------------------------------CLTGKINRAEELFGSM  147 (376)
Q Consensus       132 ----------------------------------------------------------------~~~~~~~~a~~~~~~~  147 (376)
                                                                                      .-.|+.-.|.+-|+..
T Consensus       273 ~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~  352 (606)
T KOG0547|consen  273 SDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAA  352 (606)
T ss_pred             CccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHH
Confidence                                                                            1123333333444444


Q ss_pred             HhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcc
Q 042039          148 ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTS  227 (376)
Q Consensus       148 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  227 (376)
                      +... +.+...|..+..+|...++.++....|....+.+ +-++.+|..-.+...-.++++.|..-|++.+..+ +.+..
T Consensus       353 I~l~-~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~-pe~~~  429 (606)
T KOG0547|consen  353 IKLD-PAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQYEEAIADFQKAISLD-PENAY  429 (606)
T ss_pred             HhcC-cccchHHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcC-hhhhH
Confidence            4332 2222235555555666666666666666655542 2245556556666666666666666666665553 33444


Q ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCC-----CCHHH--HH
Q 042039          228 TYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLV-----ADVVT--YN  300 (376)
Q Consensus       228 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~--~~  300 (376)
                      .|..+.-+..+.+.++++...|+.....- +..+..|+..+..+...+++++|.+.|+..++....     .++..  .-
T Consensus       430 ~~iQl~~a~Yr~~k~~~~m~~Fee~kkkF-P~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~K  508 (606)
T KOG0547|consen  430 AYIQLCCALYRQHKIAESMKTFEEAKKKF-PNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHK  508 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhh
Confidence            45555555556666666666666655442 324556666666666666666666666655442100     01111  11


Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          301 IMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       301 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      .++ .+.-.+++..|..++.++.+.+.+ ....+..|...-.+.|+.++|+++|++..
T Consensus       509 a~l-~~qwk~d~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  509 ALL-VLQWKEDINQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             hHh-hhchhhhHHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            111 111235666666666666664322 34556777777777788888888877654

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

Probab=99.75  E-value=7.7e-14  Score=116.46  Aligned_cols=336  Identities=13%  Similarity=0.057  Sum_probs=261.9

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      -.+|+.-.+.|.+.+-++-|+.+|...++.- +.+...|......--..|..++-..+++++...- +-....|......
T Consensus       516 ~~tw~~da~~~~k~~~~~carAVya~alqvf-p~k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake  593 (913)
T KOG0495|consen  516 KSTWLDDAQSCEKRPAIECARAVYAHALQVF-PCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKE  593 (913)
T ss_pred             HhHHhhhHHHHHhcchHHHHHHHHHHHHhhc-cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHH
Confidence            4578888888888888888888888888764 5567778877777777888888888888888763 3245566666677


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      +-..|+...|..++.+..+.. +.+...|...+..-....+++.|..+|.+....  .++..+|..-+....-.++.++|
T Consensus       594 ~w~agdv~~ar~il~~af~~~-pnseeiwlaavKle~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld~~eeA  670 (913)
T KOG0495|consen  594 KWKAGDVPAARVILDQAFEAN-PNSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLDNVEEA  670 (913)
T ss_pred             HHhcCCcHHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhhhHHHH
Confidence            777899999999998888864 336778888888888888999999999888775  57778888878887888889999


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      ++++++.++. ++.-...|..+.+.+-+.++.+.|...|..-.+. .|.....+..+...--+.|.+-.|..++++....
T Consensus       671 ~rllEe~lk~-fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlk  748 (913)
T KOG0495|consen  671 LRLLEEALKS-FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLK  748 (913)
T ss_pred             HHHHHHHHHh-CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhc
Confidence            9999888885 4444677888888888888888888888877665 3556667777778778888899999999988777


Q ss_pred             CCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc----C-------------------------CCCCHHHHHHHHHHH
Q 042039          256 KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR----V-------------------------LVADVVTYNIMIHGL  306 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-------------------------~~~~~~~~~~l~~~~  306 (376)
                      ++. +...|...+++-.+.|+.+.|..++.++++.    |                         ...|+.+...+...|
T Consensus       749 NPk-~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lf  827 (913)
T KOG0495|consen  749 NPK-NALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLF  827 (913)
T ss_pred             CCC-cchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHH
Confidence            643 7888888899989999988888877665443    0                         223555666677777


Q ss_pred             HccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          307 CNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       307 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      ....++++|.+.|.+.++.+.. +..+|..+...+.++|.-+.-.+++++....
T Consensus       828 w~e~k~~kar~Wf~Ravk~d~d-~GD~wa~fykfel~hG~eed~kev~~~c~~~  880 (913)
T KOG0495|consen  828 WSEKKIEKAREWFERAVKKDPD-NGDAWAWFYKFELRHGTEEDQKEVLKKCETA  880 (913)
T ss_pred             HHHHHHHHHHHHHHHHHccCCc-cchHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            7788888888888888876432 5678888888888888888888888887653

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

Probab=99.75  E-value=2.4e-14  Score=109.42  Aligned_cols=299  Identities=15%  Similarity=0.146  Sum_probs=228.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc---hHhHHHHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS---VVTFNVIMDE   95 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~   95 (376)
                      |..=++.+ -+.+.++|.++|-+|.+.. +.+.++...|...+.+.|..+.|+.+.+.+.++..-+.   ......|.+-
T Consensus        39 Yv~GlNfL-Ls~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~D  116 (389)
T COG2956          39 YVKGLNFL-LSNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRD  116 (389)
T ss_pred             HHhHHHHH-hhcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHH
Confidence            44434433 4568999999999999865 66778889999999999999999999999987521111   2345567788


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCCh----hhHHHHHHHHHccCc
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDD----VSYNILINGYCKNKE  171 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~  171 (376)
                      |...|-++.|+.+|..+.+.+ .--......++..|-...+|++|+++-+++...+..+..    ..|--+...+....+
T Consensus       117 ym~aGl~DRAE~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~  195 (389)
T COG2956         117 YMAAGLLDRAEDIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSD  195 (389)
T ss_pred             HHHhhhhhHHHHHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhh
Confidence            999999999999999998864 334677889999999999999999999999887633321    244556666667889


Q ss_pred             HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHH
Q 042039          172 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRT  251 (376)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  251 (376)
                      .+.|...+.+..+.+ +.+...-..+.......|+++.|.+.++.+.+.+..--+.+...+..+|.+.|+.++....+.+
T Consensus       196 ~d~A~~~l~kAlqa~-~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~  274 (389)
T COG2956         196 VDRARELLKKALQAD-KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRR  274 (389)
T ss_pred             HHHHHHHHHHHHhhC-ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            999999999999863 3345556677888999999999999999999988666778899999999999999999999999


Q ss_pred             hcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHc---cCChhHHHHHHHHHHHc
Q 042039          252 LGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN---DGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       252 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~  325 (376)
                      +.+....  ...-..+........-.+.|...+.+-+++  .|+...+..++..-..   .|...+-..++++|...
T Consensus       275 ~~~~~~g--~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge  347 (389)
T COG2956         275 AMETNTG--ADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGE  347 (389)
T ss_pred             HHHccCC--ccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHH
Confidence            8876433  334444444444445566666666555543  6899999999887654   34466667777777643

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.75  E-value=4.7e-14  Score=112.03  Aligned_cols=321  Identities=17%  Similarity=0.233  Sum_probs=241.0

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      |.+..++..+|.++++--..+.|.+++++......+.+..+||.++.+..-...    .+++.+|......||..|++.+
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNal  279 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNAL  279 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHH
Confidence            556789999999999999999999999999888788899999999886543322    7889999999999999999999


Q ss_pred             HHHHHhcCcHHH----HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH-HHHHHHHHHHC----CC----CCCHhHH
Q 042039          128 MDGFCLTGKINR----AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE-ALSLYREMVSK----GI----KPTVVTY  194 (376)
Q Consensus       128 ~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~----~~----~~~~~~~  194 (376)
                      +.+..+.|+++.    |.+++.+|.+.|+.|...+|..++..+.+.++..+ +..++.++...    .+    +.+...|
T Consensus       280 L~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF  359 (625)
T KOG4422|consen  280 LSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFF  359 (625)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHH
Confidence            999999998765    56778889999999999999999999999888754 55555555442    12    2245567


Q ss_pred             HHHHHHHHhccchHHHHHHHHHHHhcC----CCCC---cchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHH
Q 042039          195 NTLFLGLFEIHQVEHALKLFEEMQRDD----VAAD---TSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCL  267 (376)
Q Consensus       195 ~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  267 (376)
                      ...+..|.+..+.+.|.++..-.....    +.++   ..-|..+..+.++....+.-..+|+.++..-.-|++.+...+
T Consensus       360 ~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~  439 (625)
T KOG4422|consen  360 QSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHL  439 (625)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHH
Confidence            777888889999998888776654331    1222   123556677778888899999999999988888899999999


Q ss_pred             HHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccC-Ch--------hH-----HHHHHH-------HHHHcC
Q 042039          268 IDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDG-QM--------DK-----AHDLFL-------DMEENA  326 (376)
Q Consensus       268 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~--------~~-----a~~~~~-------~~~~~~  326 (376)
                      +++..-.+.++-..++|..+...|...+...-..+...+++.+ ..        ..     |..+++       ++..  
T Consensus       440 lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r~--  517 (625)
T KOG4422|consen  440 LRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQRA--  517 (625)
T ss_pred             HHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHHh--
Confidence            9999999999999999999988775555555555555555544 11        11     111211       1222  


Q ss_pred             CCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC-CCCCchHHHHHHHh
Q 042039          327 VAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK-KVMPDASIVSMVVD  374 (376)
Q Consensus       327 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~p~~~~~~~ll~  374 (376)
                      ........+..+-.+.+.|..++|.+++.-+.++ .-.|-....+++++
T Consensus       518 ~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~E  566 (625)
T KOG4422|consen  518 QDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAE  566 (625)
T ss_pred             ccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHH
Confidence            2334555667777788999999999999999655 34455555554443

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

Probab=99.73  E-value=2.2e-13  Score=113.84  Aligned_cols=315  Identities=11%  Similarity=0.018  Sum_probs=222.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +...|...+..--..|..++-..+|+++...- |.....|......+-..|+...|..++.++.+.... +...|...+.
T Consensus       549 k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavK  626 (913)
T KOG0495|consen  549 KKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVK  626 (913)
T ss_pred             hhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHH
Confidence            44556666665556677777777777777552 445556666666677778888888888777776444 6667777777


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  174 (376)
                      ......++++|..+|.+....  .|+..+|..-+..-...+..++|.+++++..+. +|.-...|..++..+-+.++.+.
T Consensus       627 le~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~-fp~f~Kl~lmlGQi~e~~~~ie~  703 (913)
T KOG0495|consen  627 LEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLDNVEEALRLLEEALKS-FPDFHKLWLMLGQIEEQMENIEM  703 (913)
T ss_pred             HhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh-CCchHHHHHHHhHHHHHHHHHHH
Confidence            777777788888887777664  456677776666666777778888887777765 24445567777777777777777


Q ss_pred             HHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcc
Q 042039          175 ALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI  254 (376)
Q Consensus       175 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  254 (376)
                      |...|..-.+. ++-....|..+...--+.|++-+|..++++..-.+ |.+...|...+++-.+.|..+.|..+..++..
T Consensus       704 aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQ  781 (913)
T KOG0495|consen  704 AREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQ  781 (913)
T ss_pred             HHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            77777766654 45456666666666667777777777777776665 55667777777777777777777766655522


Q ss_pred             cC-----------------------------CCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHH
Q 042039          255 LK-----------------------------CELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHG  305 (376)
Q Consensus       255 ~~-----------------------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  305 (376)
                      .-                             +.-|+.+...++..+....++++|.+.|.+..+. .+.+..+|..+...
T Consensus       782 ecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~-d~d~GD~wa~fykf  860 (913)
T KOG0495|consen  782 ECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKK-DPDNGDAWAWFYKF  860 (913)
T ss_pred             hCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHcc-CCccchHHHHHHHH
Confidence            11                             1235666777888888889999999999999887 45567899999999


Q ss_pred             HHccCChhHHHHHHHHHHHcCCCCcHHHHHHHH
Q 042039          306 LCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLI  338 (376)
Q Consensus       306 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  338 (376)
                      +...|.-+.-.+++.+.....+. ....|..+-
T Consensus       861 el~hG~eed~kev~~~c~~~EP~-hG~~W~avS  892 (913)
T KOG0495|consen  861 ELRHGTEEDQKEVLKKCETAEPT-HGELWQAVS  892 (913)
T ss_pred             HHHhCCHHHHHHHHHHHhccCCC-CCcHHHHHh
Confidence            99999999999999988875322 234454443

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

Probab=99.71  E-value=1.6e-14  Score=115.69  Aligned_cols=279  Identities=13%  Similarity=0.136  Sum_probs=210.8

Q ss_pred             HHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc--CCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCCh
Q 042039           25 GLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH--ANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKM  102 (376)
Q Consensus        25 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  102 (376)
                      .+.++|+++.|++++.-+.+.+.+....+-+.|-..+.-  -.++.+|.++-+..+... .-+......-.......|++
T Consensus       428 ~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~d-ryn~~a~~nkgn~~f~ngd~  506 (840)
T KOG2003|consen  428 ELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNID-RYNAAALTNKGNIAFANGDL  506 (840)
T ss_pred             HHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhccc-ccCHHHhhcCCceeeecCcH
Confidence            477899999999998887766534333344444333333  347888888887776542 22444444444555677899


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          103 DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      ++|.+.|++.+..+. ........+...+-..|++++|+++|-++...- ..+..+...+...|....++.+|++++-+.
T Consensus       507 dka~~~ykeal~nda-sc~ealfniglt~e~~~~ldeald~f~klh~il-~nn~evl~qianiye~led~aqaie~~~q~  584 (840)
T KOG2003|consen  507 DKAAEFYKEALNNDA-SCTEALFNIGLTAEALGNLDEALDCFLKLHAIL-LNNAEVLVQIANIYELLEDPAQAIELLMQA  584 (840)
T ss_pred             HHHHHHHHHHHcCch-HHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHhhCHHHHHHHHHHh
Confidence            999999999987642 233444555666778899999999998876542 457778888899999999999999999887


Q ss_pred             HHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHH
Q 042039          183 VSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQ  262 (376)
Q Consensus       183 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  262 (376)
                      ... ++.++.+...+...|-+.|+..+|.+.+-+--+. ++.+..+...+...|....-+++++.+|+++.-.  .|+..
T Consensus       585 ~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaali--qp~~~  660 (840)
T KOG2003|consen  585 NSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAALI--QPNQS  660 (840)
T ss_pred             ccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhc--CccHH
Confidence            775 6667888999999999999999999887766554 4778888999999999999999999999987544  67877


Q ss_pred             HHHHHHHHH-HhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCC
Q 042039          263 AYNCLIDGL-CKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQ  311 (376)
Q Consensus       263 ~~~~l~~~~-~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  311 (376)
                      -|..++..| .+.|++.+|.++|+...+. +|.|......|++.+...|-
T Consensus       661 kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  661 KWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccc
Confidence            787776554 5679999999999998776 78888888888888877663

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

Probab=99.71  E-value=4e-14  Score=116.05  Aligned_cols=284  Identities=14%  Similarity=0.096  Sum_probs=206.0

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      +.........-+...+++.+..++.+.+.+. .+++...+..-+.++...|+..+-..+=.++++.. +..+.+|..++-
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~  320 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGC  320 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHH
Confidence            4445555566677778888888888888776 34456666666667888888887777777777763 445778888888


Q ss_pred             HHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHH
Q 042039          130 GFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH  209 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  209 (376)
                      .|.-.|..++|.++|.+....+ +.-...|..++..|.-.+..++|...|..+-+. ++-...-+.-+..-|.+.++.+.
T Consensus       321 YYl~i~k~seARry~SKat~lD-~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kL  398 (611)
T KOG1173|consen  321 YYLMIGKYSEARRYFSKATTLD-PTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKL  398 (611)
T ss_pred             HHHHhcCcHHHHHHHHHHhhcC-ccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHH
Confidence            8888888888888888887765 445567888888888888888888888877764 22222223344556777888888


Q ss_pred             HHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc----CC--CchHHHHHHHHHHHHhCCChHHHHHH
Q 042039          210 ALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL----KC--ELDIQAYNCLIDGLCKSGRLEIALEL  283 (376)
Q Consensus       210 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~--~~~~~~~~~l~~~~~~~~~~~~a~~~  283 (376)
                      |.+.|....... |.++..++.++......+.+.+|..+|+.....    ..  ..-..+++.++.+|.+.+.+++|+..
T Consensus       399 Ae~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~  477 (611)
T KOG1173|consen  399 AEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDY  477 (611)
T ss_pred             HHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHH
Confidence            888888887764 667777788877777788888888888776511    00  11345678888888888888888888


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 042039          284 FRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGF  341 (376)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  341 (376)
                      +++.+.. .+.+..++..++-.|...|+++.|++.|.+.+-  +.|+-.+...++..+
T Consensus       478 ~q~aL~l-~~k~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  478 YQKALLL-SPKDASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKLA  532 (611)
T ss_pred             HHHHHHc-CCCchhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHHH
Confidence            8887766 566788888888888888888888888888776  456665555555543

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

Probab=99.70  E-value=7.7e-15  Score=112.33  Aligned_cols=230  Identities=13%  Similarity=0.044  Sum_probs=203.0

Q ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc
Q 042039          125 STLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       125 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  204 (376)
                      ..+.++|.+.|.+.+|.+.++.....  .|-+.+|..|...|.+..+++.|+.++.+-++. .+.+........+.+...
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHHH
Confidence            57899999999999999999998876  577889999999999999999999999999886 555666667788889999


Q ss_pred             cchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHH
Q 042039          205 HQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELF  284 (376)
Q Consensus       205 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  284 (376)
                      ++.++|.++++.+.+.+ +.+.+....+...|.-.++++-|...|+++...|.. ++..|+.++-+|...++++-++..|
T Consensus       304 ~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf  381 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSF  381 (478)
T ss_pred             HhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHH
Confidence            99999999999999886 667888888888899999999999999999999976 8999999999999999999999999


Q ss_pred             hcccccCCCCC--HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          285 RSLPRRVLVAD--VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       285 ~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      +++...-..|+  ..+|..+.......|++..|.+.|+-.+.++.. +...++.|.-.-.+.|+.++|..+++.....
T Consensus       382 ~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  382 QRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             HHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHHHhhhh
Confidence            98876533343  568999999999999999999999999887533 6788999988889999999999999998754

>PRK12370 invasion protein regulator; Provisional

Probab=99.69  E-value=9e-14  Score=122.36  Aligned_cols=269  Identities=13%  Similarity=0.059  Sum_probs=191.6

Q ss_pred             CCChhhHHHHHHHHhc-----CCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH---------hCCChHHHHHHHHHHH
Q 042039           48 NPDVVTYNSLIHGLCH-----ANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC---------KNGKMDEASRLLDLMV  113 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~~~~~~~a~~~~~~~~  113 (376)
                      +.+...|...+.+...     .+++++|...|++.++..+. +...|..+..++.         ..+++++|...+++++
T Consensus       253 ~~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP~-~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al  331 (553)
T PRK12370        253 LNSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPN-SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKAT  331 (553)
T ss_pred             CCChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHH
Confidence            3455555555544321     23577999999999986433 4556666665544         2245899999999999


Q ss_pred             hcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhH
Q 042039          114 QRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT  193 (376)
Q Consensus       114 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  193 (376)
                      +.+ +.+...+..+...+...|++++|...|+++.+.+ |.+...+..++.++...|++++|+..++++.+.... +...
T Consensus       332 ~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-~~~~  408 (553)
T PRK12370        332 ELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-RAAA  408 (553)
T ss_pred             hcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-Chhh
Confidence            875 4467888888999999999999999999999886 667788999999999999999999999999986322 2333


Q ss_pred             HHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHh
Q 042039          194 YNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCK  273 (376)
Q Consensus       194 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  273 (376)
                      +..++..+...|++++|...++++.....+.++..+..+..++...|+.++|...+.++.... +.+......+...|..
T Consensus       409 ~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~-~~~~~~~~~l~~~~~~  487 (553)
T PRK12370        409 GITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQE-ITGLIAVNLLYAEYCQ  487 (553)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhcc-chhHHHHHHHHHHHhc
Confidence            344455577789999999999998876433355567888889999999999999999876543 2244555666667777


Q ss_pred             CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          274 SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       274 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      .|  ++|...++.+.+.. .-.......+...+.-.|+.+.+..+ +++.+.
T Consensus       488 ~g--~~a~~~l~~ll~~~-~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~  535 (553)
T PRK12370        488 NS--ERALPTIREFLESE-QRIDNNPGLLPLVLVAHGEAIAEKMW-NKFKNE  535 (553)
T ss_pred             cH--HHHHHHHHHHHHHh-hHhhcCchHHHHHHHHHhhhHHHHHH-HHhhcc
Confidence            77  47777777765431 11111122244556666777776666 777764

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

Probab=99.69  E-value=5.2e-15  Score=113.23  Aligned_cols=231  Identities=13%  Similarity=0.060  Sum_probs=167.9

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL  133 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  133 (376)
                      -+.+..+|.+.|-+.+|.+.++..++.  .|.+.||..|.+.|.+..+++.|+.++.+.++. .+-++.....+.+.+-.
T Consensus       226 k~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~ea  302 (478)
T KOG1129|consen  226 KQQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEA  302 (478)
T ss_pred             HHHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHH
Confidence            356777888888888888888777765  556677777778888888888888888777765 23345445567777777


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHH
Q 042039          134 TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKL  213 (376)
Q Consensus       134 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  213 (376)
                      .++.++|.++|+...+.. +.++.+...+...|.-.++++-|+.+|+++++.|+. ++..|..+.-+|.-.++++-++..
T Consensus       303 m~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~s  380 (478)
T KOG1129|consen  303 MEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPS  380 (478)
T ss_pred             HHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHH
Confidence            788888888888777664 556666666777777778888888888888887765 667777777777778888888777


Q ss_pred             HHHHHhcCCCC--CcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          214 FEEMQRDDVAA--DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       214 ~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      |.+....-..|  ...+|..+.......||+..|.+.|+-....+.. +...++.++..-.+.|+.++|..+++.+...
T Consensus       381 f~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  381 FQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             HHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHHHhhhh
Confidence            77776543222  3446777777777778888888888777766533 5677777777777888888888888776543

>PRK12370 invasion protein regulator; Provisional

Probab=99.68  E-value=1.4e-13  Score=121.13  Aligned_cols=267  Identities=15%  Similarity=0.089  Sum_probs=192.3

Q ss_pred             chHhHHHHHHHHHh-----CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHH---------hcCcHHHHHHHHHHHHhc
Q 042039           85 SVVTFNVIMDELCK-----NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC---------LTGKINRAEELFGSMESM  150 (376)
Q Consensus        85 ~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~~~~~~~a~~~~~~~~~~  150 (376)
                      +...|...+++...     .+++++|..++++.++.+ +.+...+..+..++.         ..+++++|...++++.+.
T Consensus       255 ~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ld-P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l  333 (553)
T PRK12370        255 SIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMS-PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL  333 (553)
T ss_pred             ChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc
Confidence            44555555554322     234679999999999874 334566666665554         234589999999999988


Q ss_pred             CCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHH
Q 042039          151 GCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYN  230 (376)
Q Consensus       151 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  230 (376)
                      + |.+..++..+..++...|++++|...++++++.+ +.+...+..+...+...|++++|...++++.+.+ +.+...+.
T Consensus       334 d-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~-P~~~~~~~  410 (553)
T PRK12370        334 D-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLD-PTRAAAGI  410 (553)
T ss_pred             C-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCChhhHH
Confidence            6 6788889999999999999999999999999863 3357778888999999999999999999999875 33333444


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccC
Q 042039          231 TFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDG  310 (376)
Q Consensus       231 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  310 (376)
                      .++..+...|++++|+..++++.....+.++..+..++.++...|++++|...+.++... .+.+....+.+...|...|
T Consensus       411 ~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g  489 (553)
T PRK12370        411 TKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ-EITGLIAVNLLYAEYCQNS  489 (553)
T ss_pred             HHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc-cchhHHHHHHHHHHHhccH
Confidence            455567778999999999999876543335666788888999999999999999887654 2334445566666777777


Q ss_pred             ChhHHHHHHHHHHHcC-CCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          311 QMDKAHDLFLDMEENA-VAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       311 ~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                        ++|...++.+.+.. ..+....+  +...|.-.|+.+.+..+ +++.+.+
T Consensus       490 --~~a~~~l~~ll~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        490 --ERALPTIREFLESEQRIDNNPGL--LPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             --HHHHHHHHHHHHHhhHhhcCchH--HHHHHHHHhhhHHHHHH-HHhhccc
Confidence              47777777766431 12222222  33445557787777776 8887653

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.68  E-value=1.2e-13  Score=108.89  Aligned_cols=198  Identities=13%  Similarity=0.020  Sum_probs=101.0

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..++..+...|++++|.+.++++++... .+...+..+...+...|++++|...+++..+.. +.+...+..+...
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~  108 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDP-DDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH
Confidence            34455555555555555555555555554321 134444555555555555555555555555442 2233444455555


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCC-CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHH
Q 042039          131 FCLTGKINRAEELFGSMESMGC-KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH  209 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  209 (376)
                      +...|++++|.+.++++..... +.....+..++.++...|++++|...+++..+.. +.+...+..+...+...|++++
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHH
Confidence            5555555555555555544311 1223344445555555566666666665555531 2234445555555555566666


Q ss_pred             HHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          210 ALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       210 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      |...+++..... +.+...+..++..+...|+.++|..+.+.+
T Consensus       188 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  229 (234)
T TIGR02521       188 ARAYLERYQQTY-NQTAESLWLGIRIARALGDVAAAQRYGAQL  229 (234)
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            666555555442 333444444555555556666665555544

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.

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

Probab=99.68  E-value=2.5e-13  Score=111.54  Aligned_cols=282  Identities=12%  Similarity=0.035  Sum_probs=231.9

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      ++........-+...+++.+..++.+.+.+.. ++....+..-+.++...|+..+-..+=.++.+.- |..+.+|..++.
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~  320 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGC  320 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHH
Confidence            44445555667778899999999999999875 6666777777778889999888888888888764 778889999999


Q ss_pred             HHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHH
Q 042039          165 GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVE  244 (376)
Q Consensus       165 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  244 (376)
                      .|...|+.++|.+.|.+....+. .-...|..++..+.-.+..++|+..+..+.+.- +-....+..++.-|.+.+..+.
T Consensus       321 YYl~i~k~seARry~SKat~lD~-~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~-~G~hlP~LYlgmey~~t~n~kL  398 (611)
T KOG1173|consen  321 YYLMIGKYSEARRYFSKATTLDP-TFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLM-PGCHLPSLYLGMEYMRTNNLKL  398 (611)
T ss_pred             HHHHhcCcHHHHHHHHHHhhcCc-cccHHHHHHhHHhhhcchHHHHHHHHHHHHHhc-cCCcchHHHHHHHHHHhccHHH
Confidence            99999999999999999877422 125678889999999999999999998887652 3344445666777889999999


Q ss_pred             HHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC------CCCCHHHHHHHHHHHHccCChhHHHHH
Q 042039          245 AVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV------LVADVVTYNIMIHGLCNDGQMDKAHDL  318 (376)
Q Consensus       245 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~  318 (376)
                      |.+.|..+.... |.|+...+.++-+....+.+.+|..+|+..+..-      .+....+++.++++|.+.+.+++|+..
T Consensus       399 Ae~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~  477 (611)
T KOG1173|consen  399 AEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDY  477 (611)
T ss_pred             HHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHH
Confidence            999999988766 4588999999999889999999999998865210      112455789999999999999999999


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHHh
Q 042039          319 FLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVD  374 (376)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  374 (376)
                      +++.+... +.+..++..+.-.|...|+++.|.+.|.+..  .+.|+..+.+.+|+
T Consensus       478 ~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~  530 (611)
T KOG1173|consen  478 YQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLK  530 (611)
T ss_pred             HHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHH
Confidence            99999874 3488999999999999999999999999987  57899888777765

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

Probab=99.66  E-value=1.7e-11  Score=99.07  Aligned_cols=341  Identities=9%  Similarity=0.078  Sum_probs=231.1

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc-CC-CCchHhH
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ-GV-QPSVVTF   89 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~-~~~~~~~   89 (376)
                      ..|+..+|.+.|..=.+...++.|..++++..-.  .|++.+|...+..=-+.|...-|..+|+.+++. |- ..+...+
T Consensus       170 w~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lf  247 (677)
T KOG1915|consen  170 WEPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEILF  247 (677)
T ss_pred             CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            4566666666666666666666666666666544  466666666666666666666666666666553 10 0112233


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCC--hhhHHHHHHHHHhcCcHHHHHHH--------HHHHHhcCCCCChhhH
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPN--AFTYSTLMDGFCLTGKINRAEEL--------FGSMESMGCKHDDVSY  159 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~--------~~~~~~~~~~~~~~~~  159 (376)
                      ...+..-..+..++.|..+|+-.++. ++.+  ...|..+...--+.|+.......        ++.....+ |.+-.+|
T Consensus       248 vaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~n-p~nYDsW  325 (677)
T KOG1915|consen  248 VAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKN-PYNYDSW  325 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhC-CCCchHH
Confidence            33333334455666666666666654 2222  23344444433444554433332        33444444 5677788


Q ss_pred             HHHHHHHHccCcHHHHHHHHHHHHHCCCCCCH--hHHHHHH-----HHH---HhccchHHHHHHHHHHHhcCCCCCcchH
Q 042039          160 NILINGYCKNKEVEEALSLYREMVSKGIKPTV--VTYNTLF-----LGL---FEIHQVEHALKLFEEMQRDDVAADTSTY  229 (376)
Q Consensus       160 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~-----~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~  229 (376)
                      ...+..-...|+.+...++|++++.. ++|-.  ..|...+     .++   ....+.+.+.++++..++. +|....++
T Consensus       326 fdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l-IPHkkFtF  403 (677)
T KOG1915|consen  326 FDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL-IPHKKFTF  403 (677)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-cCcccchH
Confidence            88888888899999999999999986 55531  1222222     111   3567899999999998884 45555665


Q ss_pred             HHHHHH----HHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHH
Q 042039          230 NTFIDG----LCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHG  305 (376)
Q Consensus       230 ~~l~~~----~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  305 (376)
                      ..+-..    -.++.+...|.+++..++..  -|...+|...+..-.+.++++.+..++++.++. .|.+..+|...+..
T Consensus       404 aKiWlmyA~feIRq~~l~~ARkiLG~AIG~--cPK~KlFk~YIelElqL~efDRcRkLYEkfle~-~Pe~c~~W~kyaEl  480 (677)
T KOG1915|consen  404 AKIWLMYAQFEIRQLNLTGARKILGNAIGK--CPKDKLFKGYIELELQLREFDRCRKLYEKFLEF-SPENCYAWSKYAEL  480 (677)
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHhcc--CCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhc-ChHhhHHHHHHHHH
Confidence            554444    45788999999999997654  567788999999999999999999999999987 45577888888888


Q ss_pred             HHccCChhHHHHHHHHHHHcC-CCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          306 LCNDGQMDKAHDLFLDMEENA-VAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       306 ~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      =...|+.+.|..+|.-+++.. .......|...+..-...|.+++|..+++++.+..
T Consensus       481 E~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt  537 (677)
T KOG1915|consen  481 ETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRT  537 (677)
T ss_pred             HHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhc
Confidence            889999999999999998752 22234556777777778999999999999998764

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.64  E-value=3.8e-13  Score=106.07  Aligned_cols=198  Identities=12%  Similarity=0.046  Sum_probs=110.4

Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHH
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLC  237 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  237 (376)
                      .+..++..+...|++++|...++++.+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..++..+.
T Consensus        33 ~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~  110 (234)
T TIGR02521        33 IRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLC  110 (234)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHH
Confidence            34444455555555555555555544431 2233444444555555555555555555554443 223344455555555


Q ss_pred             hCCCHHHHHHHHHHhcccCC-CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHH
Q 042039          238 KNGYIVEAVELFRTLGILKC-ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAH  316 (376)
Q Consensus       238 ~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  316 (376)
                      ..|++++|...++++..... +.....+..++..+...|++++|...+.+.... .+.+...+..++..+...|++++|.
T Consensus       111 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~la~~~~~~~~~~~A~  189 (234)
T TIGR02521       111 QQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQI-DPQRPESLLELAELYYLRGQYKDAR  189 (234)
T ss_pred             HcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CcCChHHHHHHHHHHHHcCCHHHHH
Confidence            55666666665555543221 112344555666666777777777777766654 2334556666777777777777777


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          317 DLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      ..++++.+. .+.+...+..+...+...|+.++|..+.+.+.+
T Consensus       190 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       190 AYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            777776665 233455555566666677777777777666543

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.

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

Probab=99.63  E-value=3e-12  Score=103.51  Aligned_cols=219  Identities=17%  Similarity=0.169  Sum_probs=175.5

Q ss_pred             CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHH
Q 042039          100 GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLY  179 (376)
Q Consensus       100 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  179 (376)
                      |+.-.|..-|+..++.... +...|..+..+|....+.++..+.|..+.+.+ |.++.+|..-+..+.-.+++++|..-|
T Consensus       340 g~~~~a~~d~~~~I~l~~~-~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q~e~A~aDF  417 (606)
T KOG0547|consen  340 GDSLGAQEDFDAAIKLDPA-FNSLYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQYEEAIADF  417 (606)
T ss_pred             CCchhhhhhHHHHHhcCcc-cchHHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHHHHHHHHHH
Confidence            4444555555555554322 23347778889999999999999999999987 778899999999999999999999999


Q ss_pred             HHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC-
Q 042039          180 REMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE-  258 (376)
Q Consensus       180 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-  258 (376)
                      ++.++.. +.+...|..+.-+..+.+.++++...|++.++. .|..+..|+..+..+...+++++|.+.|+.+.+.... 
T Consensus       418 ~Kai~L~-pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~  495 (606)
T KOG0547|consen  418 QKAISLD-PENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPRE  495 (606)
T ss_pred             HHHhhcC-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhcccc
Confidence            9999852 335777888888889999999999999999887 5778899999999999999999999999998766432 


Q ss_pred             ------chHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          259 ------LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       259 ------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                            +.+.+.-.++. +.-.+++..|..+++++.+. .|.....+..|+..-.+.|+.++|+++|++...
T Consensus       496 ~~~~v~~~plV~Ka~l~-~qwk~d~~~a~~Ll~KA~e~-Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  496 HLIIVNAAPLVHKALLV-LQWKEDINQAENLLRKAIEL-DPKCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             ccccccchhhhhhhHhh-hchhhhHHHHHHHHHHHHcc-CchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                  11222222222 22458999999999999886 344567899999999999999999999998865

>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=99.59  E-value=4.6e-11  Score=102.10  Aligned_cols=295  Identities=17%  Similarity=0.114  Sum_probs=213.6

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC-
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN-   99 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-   99 (376)
                      -....+...|++++|++.++.-... +..........+..+.+.|+.++|..+|..+++.++. +..-|..+..+..-. 
T Consensus         9 Y~~~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPd-n~~Yy~~L~~~~g~~~   86 (517)
T PF12569_consen    9 YKNSILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPD-NYDYYRGLEEALGLQL   86 (517)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHhhhc
Confidence            3446678899999999999876544 3445677788899999999999999999999998543 455555555555222 


Q ss_pred             ----CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHH-HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH
Q 042039          100 ----GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKIN-RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus       100 ----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  174 (376)
                          .+.+....+|+++...-  |.......+.-.+.....+. .+..++......|+|   .+|..+-..|......+-
T Consensus        87 ~~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~Ly~d~~K~~~  161 (517)
T PF12569_consen   87 QLSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKPLYKDPEKAAI  161 (517)
T ss_pred             ccccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHHHHcChhHHHH
Confidence                35778888999887753  44444333333333333343 455666777777754   457777777776655555


Q ss_pred             HHHHHHHHHHC----C----------CCCCH--hHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          175 ALSLYREMVSK----G----------IKPTV--VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       175 a~~~~~~~~~~----~----------~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                      ..+++......    +          -+|+.  .++..+...|...|++++|..++++.+... |..+..|..-++.+-+
T Consensus       162 i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~ely~~KarilKh  240 (517)
T PF12569_consen  162 IESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVELYMTKARILKH  240 (517)
T ss_pred             HHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHH
Confidence            55666655432    1          12333  244566788889999999999999999875 4457788999999999


Q ss_pred             CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHH------HH--HHHHHHHHccC
Q 042039          239 NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVV------TY--NIMIHGLCNDG  310 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------~~--~~l~~~~~~~~  310 (376)
                      .|++.+|.+.++.+...+.. |...-+..+..+.+.|+.++|.+++..+.+.+..|...      .|  ...+.+|.+.|
T Consensus       241 ~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~  319 (517)
T PF12569_consen  241 AGDLKEAAEAMDEARELDLA-DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQG  319 (517)
T ss_pred             CCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999888744 77888888899999999999999999987765433221      22  34567899999


Q ss_pred             ChhHHHHHHHHHHH
Q 042039          311 QMDKAHDLFLDMEE  324 (376)
Q Consensus       311 ~~~~a~~~~~~~~~  324 (376)
                      ++..|++.|..+.+
T Consensus       320 ~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  320 DYGLALKRFHAVLK  333 (517)
T ss_pred             hHHHHHHHHHHHHH
Confidence            99999888877654

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=99.59  E-value=1.9e-11  Score=104.44  Aligned_cols=299  Identities=16%  Similarity=0.110  Sum_probs=211.3

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      +........+...|++++|++.++.-... +..........+..+.+.|+.++|..+|..+++.+ +.|..-|..+..+.
T Consensus         5 E~lLY~~~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN-Pdn~~Yy~~L~~~~   82 (517)
T PF12569_consen    5 ELLLYKNSILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN-PDNYDYYRGLEEAL   82 (517)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHH
Confidence            34444566778999999999999886554 44456677788899999999999999999999985 33444455555554


Q ss_pred             Hhc-----CcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH-HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhcc
Q 042039          132 CLT-----GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV-EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH  205 (376)
Q Consensus       132 ~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  205 (376)
                      ...     .+.+...++|+++...-  |...+...+.-.+.....+ ..+..++..++.+|+|+   +|..+-..|....
T Consensus        83 g~~~~~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~  157 (517)
T PF12569_consen   83 GLQLQLSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPE  157 (517)
T ss_pred             hhhcccccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChh
Confidence            222     35778888998887653  3333333333333332333 34555667777777653   4555555555555


Q ss_pred             chHHHHHHHHHHHhc----C----------CCCCc--chHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHH
Q 042039          206 QVEHALKLFEEMQRD----D----------VAADT--STYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLID  269 (376)
Q Consensus       206 ~~~~a~~~~~~~~~~----~----------~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  269 (376)
                      ...-..+++......    +          -+|..  .++..+...|...|++++|..+++.++... |..+..|..-++
T Consensus       158 K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~ely~~Kar  236 (517)
T PF12569_consen  158 KAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVELYMTKAR  236 (517)
T ss_pred             HHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHHHHHHHH
Confidence            555555555554332    1          12222  355777888999999999999999998886 335889999999


Q ss_pred             HHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHH------H--HHHHHHHH
Q 042039          270 GLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVI------I--FVTLIHGF  341 (376)
Q Consensus       270 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------~--~~~l~~~~  341 (376)
                      .+.+.|++.+|...++.+... ..-|...-+..+..+.+.|+.++|.+++......+..|...      .  ......+|
T Consensus       237 ilKh~G~~~~Aa~~~~~Ar~L-D~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~  315 (517)
T PF12569_consen  237 ILKHAGDLKEAAEAMDEAREL-DLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAY  315 (517)
T ss_pred             HHHHCCCHHHHHHHHHHHHhC-ChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHH
Confidence            999999999999999998876 33466667778888999999999999999987765433221      2  24446789


Q ss_pred             hhcCChhhHHHHHHHHHh
Q 042039          342 VRINKPSKVIELLHKMKE  359 (376)
Q Consensus       342 ~~~g~~~~a~~~~~~~~~  359 (376)
                      .+.|++..|++.|..+.+
T Consensus       316 ~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  316 LRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HHHhhHHHHHHHHHHHHH
Confidence            999999999988877654

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 [], [].

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.59  E-value=1.3e-12  Score=110.05  Aligned_cols=238  Identities=18%  Similarity=0.146  Sum_probs=180.0

Q ss_pred             hhhHHHHHHHHHhcCcHHHHHHHHHHHHhc-------CCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC-----C-C
Q 042039          121 AFTYSTLMDGFCLTGKINRAEELFGSMESM-------GCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK-----G-I  187 (376)
Q Consensus       121 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~  187 (376)
                      ..+...+...|...|+++.|+.+++...+.       ..+.=....+.+...|...+++++|..+|++++..     | .
T Consensus       199 ~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~  278 (508)
T KOG1840|consen  199 LRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGED  278 (508)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCC
Confidence            556777999999999999999999988765       21212223455888999999999999999998763     2 1


Q ss_pred             CC-CHhHHHHHHHHHHhccchHHHHHHHHHHHhc-----CC-CC-CcchHHHHHHHHHhCCCHHHHHHHHHHhcccC---
Q 042039          188 KP-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRD-----DV-AA-DTSTYNTFIDGLCKNGYIVEAVELFRTLGILK---  256 (376)
Q Consensus       188 ~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---  256 (376)
                      .| -..++..|...|.+.|++++|...++.+.+.     +. .+ -...+..++..+...+++++|..+++...+.-   
T Consensus       279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~  358 (508)
T KOG1840|consen  279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA  358 (508)
T ss_pred             CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence            12 2567788888999999999999888876543     10 11 12346777788889999999999888763311   


Q ss_pred             CC----chHHHHHHHHHHHHhCCChHHHHHHHhcccccC-------CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          257 CE----LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV-------LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       257 ~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      +.    .-..++..++..|...|++++|.+++++++...       ..-....++.+...|.+.+++.+|.++|.+....
T Consensus       359 ~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i  438 (508)
T KOG1840|consen  359 PGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDI  438 (508)
T ss_pred             ccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHH
Confidence            11    125688999999999999999999999876431       1222457788999999999999999999887532


Q ss_pred             ----CCC-C-cHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          326 ----AVA-P-NVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       326 ----~~~-~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                          |+. | ...+|..|...|.+.|++++|.++.+.+.
T Consensus       439 ~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  439 MKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence                321 2 34679999999999999999999988876

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

Probab=99.58  E-value=1.5e-10  Score=93.67  Aligned_cols=160  Identities=9%  Similarity=0.062  Sum_probs=77.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .|-.....=..++++..|.++|++.+..+ ..+...|...+.+=.+......|..++++++..=+. -...|...+.+--
T Consensus        75 ~WikYaqwEesq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPR-VdqlWyKY~ymEE  152 (677)
T KOG1915|consen   75 VWIKYAQWEESQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPR-VDQLWYKYIYMEE  152 (677)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcch-HHHHHHHHHHHHH
Confidence            34444444444555666666666666544 345555555555555555555555555555543111 1223333333333


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      ..|++..|.++|++-.+.  .|+...|.+.+..-.+...++.|..++++..-.  .|+...|......-.+.|+...|..
T Consensus       153 ~LgNi~gaRqiferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~  228 (677)
T KOG1915|consen  153 MLGNIAGARQIFERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARS  228 (677)
T ss_pred             HhcccHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHH
Confidence            445555555555554443  445555555555555555555555555554433  2444444444444444444444444


Q ss_pred             HHHHHH
Q 042039          178 LYREMV  183 (376)
Q Consensus       178 ~~~~~~  183 (376)
                      +|+.+.
T Consensus       229 VyerAi  234 (677)
T KOG1915|consen  229 VYERAI  234 (677)
T ss_pred             HHHHHH
Confidence            444443

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.57  E-value=3.9e-11  Score=93.49  Aligned_cols=224  Identities=13%  Similarity=0.135  Sum_probs=114.2

Q ss_pred             HHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHH-HHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc
Q 042039          126 TLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYN-ILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       126 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  204 (376)
                      +++......-++++|++++.++...+  |.-...+ .+.-+|.+..-++-+.+++.-.++. ++.++...+..+....+.
T Consensus       156 SLAsvhYmR~HYQeAIdvYkrvL~dn--~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q-~pdStiA~NLkacn~fRl  232 (557)
T KOG3785|consen  156 SLASVHYMRMHYQEAIDVYKRVLQDN--PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ-FPDSTIAKNLKACNLFRL  232 (557)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcC--hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh-CCCcHHHHHHHHHHHhhh
Confidence            34445555557888888888887653  3333333 4556677777778888888777664 232333333222222221


Q ss_pred             cchHHHHH--------------HHHHHHhcC-----------------CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhc
Q 042039          205 HQVEHALK--------------LFEEMQRDD-----------------VAADTSTYNTFIDGLCKNGYIVEAVELFRTLG  253 (376)
Q Consensus       205 ~~~~~a~~--------------~~~~~~~~~-----------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  253 (376)
                      =.-..|.+              ..+.+.+.+                 ...-+..-..++..|.+.++..+|..+.+++.
T Consensus       233 ~ngr~ae~E~k~ladN~~~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~  312 (557)
T KOG3785|consen  233 INGRTAEDEKKELADNIDQEYPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLD  312 (557)
T ss_pred             hccchhHHHHHHHHhcccccchhHHHHHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcC
Confidence            11011111              111111111                 00112334445556777888888887777653


Q ss_pred             ccCCCchHHHHHHHHHHHH-------------------------------------------hCCChHHHHHHHhccccc
Q 042039          254 ILKCELDIQAYNCLIDGLC-------------------------------------------KSGRLEIALELFRSLPRR  290 (376)
Q Consensus       254 ~~~~~~~~~~~~~l~~~~~-------------------------------------------~~~~~~~a~~~~~~~~~~  290 (376)
                      ..    ++.-|..-+....                                           -..++++++.++..+...
T Consensus       313 Pt----tP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sY  388 (557)
T KOG3785|consen  313 PT----TPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESY  388 (557)
T ss_pred             CC----ChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            21    2222221111122                                           222233333333333322


Q ss_pred             CCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          291 VLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       291 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                       +..|...-..+.++.+..|++.+|+++|-++....++.+......|.++|.+.++++-|.+++-++
T Consensus       389 -F~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  389 -FTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             -hcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhc
Confidence             222222223466777778888888888877765545533334455567888888888777665544

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

Probab=99.56  E-value=1.8e-11  Score=89.60  Aligned_cols=199  Identities=14%  Similarity=0.022  Sum_probs=128.6

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      .+...|...|.+.|++..|..-+++.++..+. +..+|..+...|.+.|+.+.|.+.|++.++.. +.+..+.+.....+
T Consensus        36 ~arlqLal~YL~~gd~~~A~~nlekAL~~DPs-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FL  113 (250)
T COG3063          36 KARLQLALGYLQQGDYAQAKKNLEKALEHDPS-YYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFL  113 (250)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHH
Confidence            34555666777777777777777777765332 45566666777777777777777777777653 33566667777777


Q ss_pred             HhcCcHHHHHHHHHHHHhcC-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHH
Q 042039          132 CLTGKINRAEELFGSMESMG-CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  210 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  210 (376)
                      |..|++++|...|++..... .+....+|.+++-|..+.|+++.|...|++.++.. +-...+...+.......|++-.|
T Consensus       114 C~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~A  192 (250)
T COG3063         114 CAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPA  192 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHH
Confidence            77777777777777766542 12234566777777777777777777777777652 22345566666677777777777


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcc
Q 042039          211 LKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI  254 (376)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  254 (376)
                      ...++.....+ .++...+-..++.--..|+-+.+-++=..+..
T Consensus       193 r~~~~~~~~~~-~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r  235 (250)
T COG3063         193 RLYLERYQQRG-GAQAESLLLGIRIAKRLGDRAAAQRYQAQLQR  235 (250)
T ss_pred             HHHHHHHHhcc-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            77777766655 35666666666666666776666665555443

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

Probab=99.55  E-value=1.3e-11  Score=90.32  Aligned_cols=199  Identities=14%  Similarity=0.045  Sum_probs=162.5

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYC  167 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  167 (376)
                      +...+.-.|...|+...|..-+++.++.+ +.+..+|..+...|.+.|+.+.|.+.|++..+.. |.+..+.|+.+..+|
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC  114 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFLC  114 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHHH
Confidence            45567778899999999999999999875 4467888899999999999999999999998886 677888999999999


Q ss_pred             ccCcHHHHHHHHHHHHHCCC-CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHH
Q 042039          168 KNKEVEEALSLYREMVSKGI-KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAV  246 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  246 (376)
                      ..|++++|...|++...... .....+|..+.-+..+.|+.+.|...|++.++.+ +..+.....+.....+.|++-.|.
T Consensus       115 ~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar  193 (250)
T COG3063         115 AQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPAR  193 (250)
T ss_pred             hCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHH
Confidence            99999999999999887532 2236788888888888999999999999888876 556677788888888889998898


Q ss_pred             HHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          247 ELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      ..++.....+. ++..++...++.-...|+-+.+.++=.++.+.
T Consensus       194 ~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         194 LYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             HHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            88888877664 67777777777778888888777766665553

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

Probab=99.55  E-value=8.4e-11  Score=93.45  Aligned_cols=292  Identities=13%  Similarity=0.051  Sum_probs=210.0

Q ss_pred             HhcCChhHHHHHHHHhhhC-CCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHH
Q 042039           27 CKEGFVDKAKALFLQMKGE-NINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEA  105 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  105 (376)
                      +..++-..|...+-.+... -.+.|+.....+..++...|+..+|+..|++....++. +..........+...|+.+..
T Consensus       207 ~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy-~i~~MD~Ya~LL~~eg~~e~~  285 (564)
T KOG1174|consen  207 MFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPD-NVEAMDLYAVLLGQEGGCEQD  285 (564)
T ss_pred             HHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChh-hhhhHHHHHHHHHhccCHhhH
Confidence            3345544554444433322 24667888888999999999999999999888765322 333444455566778888888


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          106 SRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      ..+...+.... +.+...|..-+.......++..|+.+-++.++.+ +.+...+..-+..+...+++++|.-.|+.+...
T Consensus       286 ~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~-~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~L  363 (564)
T KOG1174|consen  286 SALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSE-PRNHEALILKGRLLIALERHTQAVIAFRTAQML  363 (564)
T ss_pred             HHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccC-cccchHHHhccHHHHhccchHHHHHHHHHHHhc
Confidence            88877776643 2344555555666667788889998888888876 567777777788888899999999999888774


Q ss_pred             CCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHH-HHH-HhCCCHHHHHHHHHHhcccCCCchHHH
Q 042039          186 GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFI-DGL-CKNGYIVEAVELFRTLGILKCELDIQA  263 (376)
Q Consensus       186 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~~-~~~~~~~~a~~~~~~~~~~~~~~~~~~  263 (376)
                       -+.+...|.-++.+|...|.+.+|.-.-....+. .+.+..++..+. ..+ ....--++|.++++......+. -...
T Consensus       364 -ap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~-Y~~A  440 (564)
T KOG1174|consen  364 -APYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPI-YTPA  440 (564)
T ss_pred             -chhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCc-cHHH
Confidence             2346788999999999999998888777766554 244555555553 222 2233457888888887766422 3556


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 042039          264 YNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA  326 (376)
Q Consensus       264 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  326 (376)
                      ...++..+...|..+.++.++++...  ..||....+.|+..+...+.+++|.+.|..+...+
T Consensus       441 V~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~d  501 (564)
T KOG1174|consen  441 VNLIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQD  501 (564)
T ss_pred             HHHHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            77788888888999999999988776  36788888889999999999999999888887754

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.54  E-value=2.8e-11  Score=97.92  Aligned_cols=150  Identities=10%  Similarity=-0.100  Sum_probs=82.1

Q ss_pred             CChHHHHHHHHHHHhcCC-CC--chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHH
Q 042039           65 NDWNEAKRLFFEMMDQGV-QP--SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAE  141 (376)
Q Consensus        65 ~~~~~a~~~~~~~~~~~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  141 (376)
                      ++.+.++.-+.+++.... .|  ....|..+...+...|++++|...|++.++.. +.+...|..++..+...|++++|.
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            344555666656554311 11  12345555666666666666666666666653 234566666666666666666666


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHH
Q 042039          142 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  218 (376)
                      ..|++..+.. |.+..++..++.++...|++++|++.+++..+.  .|+..............++.++|...+.+..
T Consensus       119 ~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        119 EAFDSVLELD-PTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            6666666554 344556666666666666666666666666653  2222111111122233455666666665443

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.54  E-value=2.7e-11  Score=97.97  Aligned_cols=220  Identities=12%  Similarity=0.039  Sum_probs=158.8

Q ss_pred             cCChhHHHHHHHHhhhCCC-C--CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHH
Q 042039           29 EGFVDKAKALFLQMKGENI-N--PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEA  105 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~-~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  105 (376)
                      .+..+.++..+.+++.... .  .....|..++..+...|++++|...|++.++..+. +...|+.+...+...|++++|
T Consensus        39 ~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~~~~~g~~~~A  117 (296)
T PRK11189         39 TLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPD-MADAYNYLGIYLTQAGNFDAA  117 (296)
T ss_pred             chHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHCCCHHHH
Confidence            4566778888888886431 1  12466888999999999999999999999997544 688999999999999999999


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          106 SRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      ...|++.++.. +.+..++..++.++...|++++|.+.+++..... |.+. ........+...+++++|...+.+....
T Consensus       118 ~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~-P~~~-~~~~~~~l~~~~~~~~~A~~~l~~~~~~  194 (296)
T PRK11189        118 YEAFDSVLELD-PTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDD-PNDP-YRALWLYLAESKLDPKQAKENLKQRYEK  194 (296)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCH-HHHHHHHHHHccCCHHHHHHHHHHHHhh
Confidence            99999999864 3357788889999999999999999999999875 3333 2233333455678899999999776643


Q ss_pred             CCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc---CC---CCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC
Q 042039          186 GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD---DV---AADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC  257 (376)
Q Consensus       186 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  257 (376)
                       ..|+...+   .......|+...+ ..+..+.+.   .+   +.....|..++..+.+.|++++|+..|+++...++
T Consensus       195 -~~~~~~~~---~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        195 -LDKEQWGW---NIVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             -CCccccHH---HHHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence             23332221   2333345555443 344444322   10   12335678888888888888888888888877653

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

Probab=99.53  E-value=2.5e-11  Score=96.34  Aligned_cols=273  Identities=15%  Similarity=0.077  Sum_probs=218.9

Q ss_pred             cccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhH
Q 042039           10 VVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTF   89 (376)
Q Consensus        10 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   89 (376)
                      ...+-|+.....+...+...|+.++|+..|++..-.+ +-+..........+.+.|+.++...+...+.... +-+...|
T Consensus       226 ~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~d-py~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~w  303 (564)
T KOG1174|consen  226 TTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCAN-PDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHW  303 (564)
T ss_pred             ccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCC-hhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhh
Confidence            4557788899999999999999999999999988775 4455556666677788899999988888887652 2245556


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      ..-+.......+++.|+.+-++.++.+ +.+...+..-+..+...++.++|.-.|+.+.... |.+..+|..|+.+|...
T Consensus       304 fV~~~~l~~~K~~~rAL~~~eK~I~~~-~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~  381 (564)
T KOG1174|consen  304 FVHAQLLYDEKKFERALNFVEKCIDSE-PRNHEALILKGRLLIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQ  381 (564)
T ss_pred             hhhhhhhhhhhhHHHHHHHHHHHhccC-cccchHHHhccHHHHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhh
Confidence            555666777889999999999998864 3456677777888899999999999999998875 67889999999999999


Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHH-HHH-HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLF-LGL-FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVE  247 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~~-~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  247 (376)
                      |.+.+|.-.-+...+. .+.+..+...+. ..+ .....-++|.++++..++.. |.-......++..+...|..+.++.
T Consensus       382 ~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~-P~Y~~AV~~~AEL~~~Eg~~~D~i~  459 (564)
T KOG1174|consen  382 KRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKIN-PIYTPAVNLIAELCQVEGPTKDIIK  459 (564)
T ss_pred             chHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccC-CccHHHHHHHHHHHHhhCccchHHH
Confidence            9999999888777664 344555555553 222 23344678999999988764 3445567788889999999999999


Q ss_pred             HHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          248 LFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      ++++....  .||......++..+...+.+.+|...|..+.+.
T Consensus       460 LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~  500 (564)
T KOG1174|consen  460 LLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQ  500 (564)
T ss_pred             HHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            99998755  678899999999999999999999999998875

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.53  E-value=2.5e-10  Score=97.64  Aligned_cols=344  Identities=14%  Similarity=0.067  Sum_probs=209.0

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc-hHhHH
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS-VVTFN   90 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~   90 (376)
                      +.-|+..|..+.-++...|+++.+.+.|++....- -...+.|+.+...+...|.-..|+.+++........|+ +..+.
T Consensus       319 ~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~L  397 (799)
T KOG4162|consen  319 FQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLL  397 (799)
T ss_pred             hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHH
Confidence            34577888888888888899999988888876442 33456777777777777777777777776655432232 22222


Q ss_pred             HHHHHHH-hCCChHHHHHHHHHHHh--------------------------------------------------cCCCC
Q 042039           91 VIMDELC-KNGKMDEASRLLDLMVQ--------------------------------------------------RDVRP  119 (376)
Q Consensus        91 ~l~~~~~-~~~~~~~a~~~~~~~~~--------------------------------------------------~~~~~  119 (376)
                      .....|. +.+..++++.+-.+++.                                                  .+ +.
T Consensus       398 masklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d-~~  476 (799)
T KOG4162|consen  398 MASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFD-PT  476 (799)
T ss_pred             HHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcC-CC
Confidence            2222222 23444444444444433                                                  32 22


Q ss_pred             ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC-CCCC---------
Q 042039          120 NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK-GIKP---------  189 (376)
Q Consensus       120 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~---------  189 (376)
                      |+.+...+.--|+..++++.|.+..++..+.+...+...|..+..++...+++.+|+.+.+..... |...         
T Consensus       477 dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i  556 (799)
T KOG4162|consen  477 DPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHI  556 (799)
T ss_pred             CchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhh
Confidence            333333444445555666666666666655543555566666666666666666666666655543 1000         


Q ss_pred             ---------CHhHHHHHHHHHHh-----------------------ccchHHHHHHHHHHH--------hcC--------
Q 042039          190 ---------TVVTYNTLFLGLFE-----------------------IHQVEHALKLFEEMQ--------RDD--------  221 (376)
Q Consensus       190 ---------~~~~~~~l~~~~~~-----------------------~~~~~~a~~~~~~~~--------~~~--------  221 (376)
                               ...|...++..+-.                       .++..++.+....+.        ..+        
T Consensus       557 ~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s  636 (799)
T KOG4162|consen  557 ELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSS  636 (799)
T ss_pred             hhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcc
Confidence                     01111111111110                       001111111111100        000        


Q ss_pred             -CCCCc--------chHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCC
Q 042039          222 -VAADT--------STYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVL  292 (376)
Q Consensus       222 -~~~~~--------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  292 (376)
                       ..|..        ..+......+.+.+..++|...+.++.... +.....|...+..+...|++++|.+.|...... .
T Consensus       637 ~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~l-d  714 (799)
T KOG4162|consen  637 TVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLLLEVKGQLEEAKEAFLVALAL-D  714 (799)
T ss_pred             cccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhc-C
Confidence             00010        123344556667777788877777766554 446777888888888999999999999988775 3


Q ss_pred             CCCHHHHHHHHHHHHccCChhHHHH--HHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          293 VADVVTYNIMIHGLCNDGQMDKAHD--LFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       293 ~~~~~~~~~l~~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      |.++.....++.++.+.|+..-|..  ++..+.+.+.. +...|..+...+.+.|+.+.|.+.|....+-
T Consensus       715 P~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~-n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  715 PDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPL-NHEAWYYLGEVFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             CCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHccchHHHHHHHHHHHhh
Confidence            5567788899999999998888887  99999987644 8899999999999999999999999988754

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.53  E-value=9.4e-12  Score=104.98  Aligned_cols=236  Identities=18%  Similarity=0.136  Sum_probs=115.6

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhc-----C-CCCChhh-HHHHHHHHHhcCcHHHHHHHHHHHHhc-----C--CC
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQR-----D-VRPNAFT-YSTLMDGFCLTGKINRAEELFGSMESM-----G--CK  153 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~  153 (376)
                      +...+...|...|+++.|..+++..++.     | ..|...+ ...++..|...+++++|..+|+++...     |  .+
T Consensus       201 ~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~  280 (508)
T KOG1840|consen  201 TLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHP  280 (508)
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            3333444555555555555554444432     1 0122221 222444555555555555555554321     1  11


Q ss_pred             CChhhHHHHHHHHHccCcHHHHHHHHHHHHHC-----CC-CCC-HhHHHHHHHHHHhccchHHHHHHHHHHHhc---CCC
Q 042039          154 HDDVSYNILINGYCKNKEVEEALSLYREMVSK-----GI-KPT-VVTYNTLFLGLFEIHQVEHALKLFEEMQRD---DVA  223 (376)
Q Consensus       154 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~  223 (376)
                      .-..+++.|..+|.+.|++++|...++.+.+-     +. .|. ...+..+...+...+++++|..++....+.   -+.
T Consensus       281 ~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g  360 (508)
T KOG1840|consen  281 AVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPG  360 (508)
T ss_pred             HHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhcc
Confidence            12234445555555555555555555444321     11 111 223344444555555555555555543322   011


Q ss_pred             ----CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC-------CCchHHHHHHHHHHHHhCCChHHHHHHHhcccc---
Q 042039          224 ----ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK-------CELDIQAYNCLIDGLCKSGRLEIALELFRSLPR---  289 (376)
Q Consensus       224 ----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---  289 (376)
                          .-..++..+...|...|++++|.++++.++...       .......++.++..|.+.+++++|.++|.+...   
T Consensus       361 ~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~  440 (508)
T KOG1840|consen  361 EDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMK  440 (508)
T ss_pred             ccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHH
Confidence                123456666666666666666666666653211       111234556666666666666666666655321   


Q ss_pred             -cC--CCCCHHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          290 -RV--LVADVVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       290 -~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                       .|  .+....+|..|+.+|...|+++.|+++.+.+.
T Consensus       441 ~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  441 LCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence             11  22234567777777777777777777776665

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.48  E-value=1.6e-09  Score=91.21  Aligned_cols=98  Identities=18%  Similarity=0.160  Sum_probs=60.8

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHh
Q 042039          263 AYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFV  342 (376)
Q Consensus       263 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  342 (376)
                      ++..++..+-..|+++.|..+++.+..+ .|.-+..|..-.+.+...|++++|..+++++.+.+ .+|...-..-+....
T Consensus       373 t~y~laqh~D~~g~~~~A~~yId~AIdH-TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INsKcAKYmL  450 (700)
T KOG1156|consen  373 TLYFLAQHYDKLGDYEVALEYIDLAIDH-TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINSKCAKYML  450 (700)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHhcc-CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHHHHHHHHH
Confidence            3345566666777777777777776665 22223444445566777777777777777777653 234433334455556


Q ss_pred             hcCChhhHHHHHHHHHhCCC
Q 042039          343 RINKPSKVIELLHKMKEKKV  362 (376)
Q Consensus       343 ~~g~~~~a~~~~~~~~~~~~  362 (376)
                      +.++.++|.++.....+.|.
T Consensus       451 rAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  451 RANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             HccccHHHHHHHHHhhhccc
Confidence            67777777777777766653

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.48  E-value=1.6e-10  Score=88.06  Aligned_cols=296  Identities=14%  Similarity=0.085  Sum_probs=208.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH-HHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV-IMDE   95 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~   95 (376)
                      --+.+++..+.+..++..|++++..-.++. +.+......|..+|....++..|-+.|+++...  .|...-|.. -...
T Consensus        11 Geftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQS   87 (459)
T KOG4340|consen   11 GEFTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQS   87 (459)
T ss_pred             CchHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHH
Confidence            347778888889999999999999888775 557888999999999999999999999999775  455444433 3567


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      +.+.+.+..|+++...|.... ..-......-.......+++..+..+.++....+   +..+.+..+....+.|+++.|
T Consensus        88 LY~A~i~ADALrV~~~~~D~~-~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegqyEaA  163 (459)
T KOG4340|consen   88 LYKACIYADALRVAFLLLDNP-ALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQYEAA  163 (459)
T ss_pred             HHHhcccHHHHHHHHHhcCCH-HHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccccHHHH
Confidence            788899999999998886531 1112222222333456788888888888876533   556677777788899999999


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcc----------------------------
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTS----------------------------  227 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----------------------------  227 (376)
                      .+-|+...+-+---....| .+.-+..+.++++.|.+...++++.|++..+.                            
T Consensus       164 vqkFqaAlqvsGyqpllAY-niALaHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~e  242 (459)
T KOG4340|consen  164 VQKFQAALQVSGYQPLLAY-NLALAHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVE  242 (459)
T ss_pred             HHHHHHHHhhcCCCchhHH-HHHHHHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHH
Confidence            9999998885333233444 44556778899999999999988876443211                            


Q ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHhcccC-CCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHH
Q 042039          228 TYNTFIDGLCKNGYIVEAVELFRTLGILK-CELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGL  306 (376)
Q Consensus       228 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  306 (376)
                      .++.-...+.+.++++.|.+.+..|.... ...|+.+...+.-.-. .+++....+-++-+... .|....||..++-.|
T Consensus       243 AfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~-nPfP~ETFANlLlly  320 (459)
T KOG4340|consen  243 AFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQ-NPFPPETFANLLLLY  320 (459)
T ss_pred             HhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhc-CCCChHHHHHHHHHH
Confidence            12333334567889999998888875432 2456777766654432 33444444444444443 234578899999999


Q ss_pred             HccCChhHHHHHHHHH
Q 042039          307 CNDGQMDKAHDLFLDM  322 (376)
Q Consensus       307 ~~~~~~~~a~~~~~~~  322 (376)
                      ++..-++-|.+++.+-
T Consensus       321 CKNeyf~lAADvLAEn  336 (459)
T KOG4340|consen  321 CKNEYFDLAADVLAEN  336 (459)
T ss_pred             hhhHHHhHHHHHHhhC
Confidence            9999999888887653

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

Probab=99.46  E-value=1.7e-09  Score=91.03  Aligned_cols=198  Identities=15%  Similarity=0.059  Sum_probs=116.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD---VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      ..|..+...+...|+.+.+...+....+.. +++   ..........+...|++++|.+.+++.....+. +...+.. .
T Consensus         7 ~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~-~~~a~~~-~   83 (355)
T cd05804           7 LGHAAAALLLLLGGERPAAAAKAAAAAQAL-AARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPR-DLLALKL-H   83 (355)
T ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHHh-ccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHH-h
Confidence            445666666666777777766666655443 222   222333445566778888888888887765322 3333332 1


Q ss_pred             HHHH----hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           94 DELC----KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        94 ~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      ..+.    ..+....+.+.+.... ...+........+...+...|++++|...+++..+.. |.+...+..+..++...
T Consensus        84 ~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~  161 (355)
T cd05804          84 LGAFGLGDFSGMRDHVARVLPLWA-PENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQ  161 (355)
T ss_pred             HHHHHhcccccCchhHHHHHhccC-cCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHc
Confidence            1222    2344444444444311 1112223344455667777788888888888877765 55566677777778888


Q ss_pred             CcHHHHHHHHHHHHHCCC-CCC--HhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          170 KEVEEALSLYREMVSKGI-KPT--VVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~-~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      |++++|...+++...... .|+  ...|..+...+...|++++|..++++...
T Consensus       162 g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         162 GRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             CCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            888888888877766421 122  12344566777777777777777777643

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.

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.46  E-value=7.6e-09  Score=86.28  Aligned_cols=342  Identities=13%  Similarity=0.028  Sum_probs=183.8

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCC
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG  100 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  100 (376)
                      +=++.+.+.|++++|.....+++..+ +.+..++..-+.++++.+++++|+.+.+.-...  ..+...+..-+.+..+.+
T Consensus        17 t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~~fEKAYc~Yrln   93 (652)
T KOG2376|consen   17 TDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSFFFEKAYCEYRLN   93 (652)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchhhHHHHHHHHHcc
Confidence            33466777888999999999888776 667778888888888888888888655432211  101111112223344556


Q ss_pred             ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC---------------------------
Q 042039          101 KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCK---------------------------  153 (376)
Q Consensus       101 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---------------------------  153 (376)
                      ..++|+..++-+.    +.+..+...-...+.+.|++++|..+|+.+.+.+.+                           
T Consensus        94 k~Dealk~~~~~~----~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~  169 (652)
T KOG2376|consen   94 KLDEALKTLKGLD----RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPE  169 (652)
T ss_pred             cHHHHHHHHhccc----ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccC
Confidence            6666666665111    112334445555566666666666666665332110                           


Q ss_pred             -C--ChhhHHHHHHHHHccCcHHHHHHHHHHHHHC-------CCCCC-------HhHHHHHHHHHHhccchHHHHHHHHH
Q 042039          154 -H--DDVSYNILINGYCKNKEVEEALSLYREMVSK-------GIKPT-------VVTYNTLFLGLFEIHQVEHALKLFEE  216 (376)
Q Consensus       154 -~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~  216 (376)
                       |  +-..+.+....+...|++.+|+++++...+.       +-.-+       ...-..+..++...|+..+|..++..
T Consensus       170 v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~  249 (652)
T KOG2376|consen  170 VPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVD  249 (652)
T ss_pred             CCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHH
Confidence             0  1112223344455566666666666665221       00000       11123334445556666666666665


Q ss_pred             HHhcCCCCCcc---------------------------------------------------------------------
Q 042039          217 MQRDDVAADTS---------------------------------------------------------------------  227 (376)
Q Consensus       217 ~~~~~~~~~~~---------------------------------------------------------------------  227 (376)
                      .++.+. +|..                                                                     
T Consensus       250 ~i~~~~-~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~tnk~~q~r~  328 (652)
T KOG2376|consen  250 IIKRNP-ADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFTNKMDQVRE  328 (652)
T ss_pred             HHHhcC-CCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence            555431 1110                                                                     


Q ss_pred             ------------hHHHHHHHHHh--CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHh--------
Q 042039          228 ------------TYNTFIDGLCK--NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFR--------  285 (376)
Q Consensus       228 ------------~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~--------  285 (376)
                                  .+..++..+.+  ...+.++..++.........-...+....+......|+++.|.+++.        
T Consensus       329 ~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~s  408 (652)
T KOG2376|consen  329 LSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKS  408 (652)
T ss_pred             HHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhh
Confidence                        11111111111  11233344444443333222223445556666778899999999888        


Q ss_pred             cccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc------CCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          286 SLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN------AVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       286 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .+.+.+.  .+.+...+...+.+.++-+.|..++.+++..      +-.--..++..++..-.+.|+.++|..+++++.+
T Consensus       409 s~~~~~~--~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k  486 (652)
T KOG2376|consen  409 SILEAKH--LPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVK  486 (652)
T ss_pred             hhhhhcc--ChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHH
Confidence            4444333  3445556677777777777777777776542      1111123445555556678999999999999987


Q ss_pred             CCCCCchHHHHHHH
Q 042039          360 KKVMPDASIVSMVV  373 (376)
Q Consensus       360 ~~~~p~~~~~~~ll  373 (376)
                      .. ++|..+...++
T Consensus       487 ~n-~~d~~~l~~lV  499 (652)
T KOG2376|consen  487 FN-PNDTDLLVQLV  499 (652)
T ss_pred             hC-CchHHHHHHHH
Confidence            53 44555554444

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

Probab=99.46  E-value=2.3e-09  Score=90.13  Aligned_cols=309  Identities=10%  Similarity=0.002  Sum_probs=195.8

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC-CCch-HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV-QPSV-VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYS  125 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  125 (376)
                      |.....|..+...+...|+.+.+.+.+.+..+... .++. .........+...|++++|..++++..+.. +.+...+.
T Consensus         3 p~~~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~   81 (355)
T cd05804           3 PDFALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALK   81 (355)
T ss_pred             CccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHH
Confidence            33466778888888888999998888877765422 1222 223333446678899999999999998863 33444443


Q ss_pred             HHHHHHH----hcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHH
Q 042039          126 TLMDGFC----LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL  201 (376)
Q Consensus       126 ~l~~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  201 (376)
                      . ...+.    ..+..+.+.+.++.... ..+........+..++...|++++|...+++..+.. +.+...+..+..++
T Consensus        82 ~-~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~  158 (355)
T cd05804          82 L-HLGAFGLGDFSGMRDHVARVLPLWAP-ENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVL  158 (355)
T ss_pred             H-hHHHHHhcccccCchhHHHHHhccCc-CCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHH
Confidence            2 22222    24555556666554211 123334455567788999999999999999999963 44567788889999


Q ss_pred             HhccchHHHHHHHHHHHhcCCC-CCc--chHHHHHHHHHhCCCHHHHHHHHHHhcccCC-CchHHHH-H--HHHHHHHhC
Q 042039          202 FEIHQVEHALKLFEEMQRDDVA-ADT--STYNTFIDGLCKNGYIVEAVELFRTLGILKC-ELDIQAY-N--CLIDGLCKS  274 (376)
Q Consensus       202 ~~~~~~~~a~~~~~~~~~~~~~-~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~-~--~l~~~~~~~  274 (376)
                      ...|++++|...+++....... +..  ..+..++..+...|++++|..+++++..... .+..... .  .++..+...
T Consensus       159 ~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (355)
T cd05804         159 EMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELA  238 (355)
T ss_pred             HHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhc
Confidence            9999999999999998876421 222  2345688889999999999999999864432 1111111 1  223333444


Q ss_pred             CChHHHHHH---Hhccccc-CCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCC------C--cHHHHHHHHHHHh
Q 042039          275 GRLEIALEL---FRSLPRR-VLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVA------P--NVIIFVTLIHGFV  342 (376)
Q Consensus       275 ~~~~~a~~~---~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~--~~~~~~~l~~~~~  342 (376)
                      |....+.+.   ....... ..............++...|+.++|..+++.+......      .  ..........++.
T Consensus       239 g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~  318 (355)
T cd05804         239 GHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAF  318 (355)
T ss_pred             CCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHH
Confidence            433333322   1111111 00111222235677788999999999999988653211      0  1122222334567


Q ss_pred             hcCChhhHHHHHHHHHhC
Q 042039          343 RINKPSKVIELLHKMKEK  360 (376)
Q Consensus       343 ~~g~~~~a~~~~~~~~~~  360 (376)
                      ..|++++|.+.+......
T Consensus       319 ~~g~~~~A~~~L~~al~~  336 (355)
T cd05804         319 AEGNYATALELLGPVRDD  336 (355)
T ss_pred             HcCCHHHHHHHHHHHHHH
Confidence            899999999999988754

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.

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.45  E-value=3.5e-09  Score=82.47  Aligned_cols=304  Identities=12%  Similarity=0.049  Sum_probs=220.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHh-HHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVT-FNVIM   93 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~   93 (376)
                      ++.--.-+...+...|++..|+.-|....+-+ |.+-.++..-...|...|+-..|+.-+.+.++.  +||-.. -..-.
T Consensus        37 dvekhlElGk~lla~~Q~sDALt~yHaAve~d-p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQRg  113 (504)
T KOG0624|consen   37 DVEKHLELGKELLARGQLSDALTHYHAAVEGD-PNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQRG  113 (504)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC-chhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHhc
Confidence            34444556777888899999999998888654 445556666678888999999999999998875  666432 22344


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCC--hh------------hHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhH
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPN--AF------------TYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSY  159 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  159 (376)
                      ..+.++|.++.|..-|+.+++.....+  ..            .....+..+...|+...|+.....+.+.. +.+...+
T Consensus       114 ~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~  192 (504)
T KOG0624|consen  114 VVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLR  192 (504)
T ss_pred             hhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHH
Confidence            567889999999999999988742211  11            12233455667789999999999998876 7788888


Q ss_pred             HHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchH----HHH---
Q 042039          160 NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTY----NTF---  232 (376)
Q Consensus       160 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----~~l---  232 (376)
                      ..-..+|...|++..|+.-++...+. ...+...+..+...+...|+.+.++...++.++.+  |+....    ..+   
T Consensus       193 ~~Rakc~i~~~e~k~AI~Dlk~askL-s~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKld--pdHK~Cf~~YKklkKv  269 (504)
T KOG0624|consen  193 QARAKCYIAEGEPKKAIHDLKQASKL-SQDNTEGHYKISQLLYTVGDAENSLKEIRECLKLD--PDHKLCFPFYKKLKKV  269 (504)
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHhc-cccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccC--cchhhHHHHHHHHHHH
Confidence            88899999999999999888887765 23466777778888889999999998888887764  333221    111   


Q ss_pred             ------HHHHHhCCCHHHHHHHHHHhcccCCCch---HHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHH
Q 042039          233 ------IDGLCKNGYIVEAVELFRTLGILKCELD---IQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMI  303 (376)
Q Consensus       233 ------~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  303 (376)
                            +......+++.++.+..+...+..+...   ...+..+-.++...+++.+|++.-.++++. .+.|..++..-.
T Consensus       270 ~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~-d~~dv~~l~dRA  348 (504)
T KOG0624|consen  270 VKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI-DPDDVQVLCDRA  348 (504)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc-CchHHHHHHHHH
Confidence                  1223456677777777777665543311   233445556677788899999988888775 344588888888


Q ss_pred             HHHHccCChhHHHHHHHHHHHcC
Q 042039          304 HGLCNDGQMDKAHDLFLDMEENA  326 (376)
Q Consensus       304 ~~~~~~~~~~~a~~~~~~~~~~~  326 (376)
                      .+|.-...++.|+.-|+.+.+.+
T Consensus       349 eA~l~dE~YD~AI~dye~A~e~n  371 (504)
T KOG0624|consen  349 EAYLGDEMYDDAIHDYEKALELN  371 (504)
T ss_pred             HHHhhhHHHHHHHHHHHHHHhcC
Confidence            89999999999999999887754

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

Probab=99.44  E-value=1.1e-08  Score=86.16  Aligned_cols=27  Identities=15%  Similarity=0.364  Sum_probs=16.4

Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHh
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMES  149 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  149 (376)
                      .|..|+..|.+.|++++|..+|++...
T Consensus       250 Lw~SLAdYYIr~g~~ekarDvyeeai~  276 (835)
T KOG2047|consen  250 LWCSLADYYIRSGLFEKARDVYEEAIQ  276 (835)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            355666666666666666666665443

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

Probab=99.41  E-value=1.2e-08  Score=86.13  Aligned_cols=345  Identities=14%  Similarity=0.168  Sum_probs=206.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcC----------------C------ChHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHA----------------N------DWNEAKRLF   74 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------------~------~~~~a~~~~   74 (376)
                      ..|++|.+.|.+.|.+++|.++|++..+.  ..++.-|..+...|++-                +      +++-...-|
T Consensus       249 ~Lw~SLAdYYIr~g~~ekarDvyeeai~~--v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~  326 (835)
T KOG2047|consen  249 FLWCSLADYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARF  326 (835)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHH
Confidence            46889999999999999999999988765  22333344444433321                1      122333444


Q ss_pred             HHHHhcCC-----------CCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC------hhhHHHHHHHHHhcCcH
Q 042039           75 FEMMDQGV-----------QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN------AFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        75 ~~~~~~~~-----------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~  137 (376)
                      +.+.....           +.++..|..-.  -+..|+..+....|.++++. +.|.      ...|..+...|-..|++
T Consensus       327 e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV--~l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l  403 (835)
T KOG2047|consen  327 ESLMNRRPLLLNSVLLRQNPHNVEEWHKRV--KLYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDL  403 (835)
T ss_pred             HHHHhccchHHHHHHHhcCCccHHHHHhhh--hhhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcH
Confidence            44433211           11333343322  23456677777888887764 2222      34577888888999999


Q ss_pred             HHHHHHHHHHHhcCCCCC---hhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCC-----------------CHhHHHHH
Q 042039          138 NRAEELFGSMESMGCKHD---DVSYNILINGYCKNKEVEEALSLYREMVSKGIKP-----------------TVVTYNTL  197 (376)
Q Consensus       138 ~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------------~~~~~~~l  197 (376)
                      +.|..+|++......+.-   ..+|...+..-.+..+++.|+++++.+....-.|                 +...|...
T Consensus       404 ~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y  483 (835)
T KOG2047|consen  404 DDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMY  483 (835)
T ss_pred             HHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHH
Confidence            999999999887653322   3466667777778888899999888776431111                 23345555


Q ss_pred             HHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchH-HHHHHHHHHHHh---
Q 042039          198 FLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDI-QAYNCLIDGLCK---  273 (376)
Q Consensus       198 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~---  273 (376)
                      +...-..|-++....++++++...+ .++......+..+..+..++++.+.|++-+..-..|+. ..|+..+.-+.+   
T Consensus       484 ~DleEs~gtfestk~vYdriidLri-aTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~ryg  562 (835)
T KOG2047|consen  484 ADLEESLGTFESTKAVYDRIIDLRI-ATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYG  562 (835)
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhc
Confidence            5555567788888888888887753 34555555555666777788888888887665544443 455555444433   


Q ss_pred             CCChHHHHHHHhcccccCCCCCHH-H-HHHHHHHHHccCChhHHHHHHHHHHHcCCCCc--HHHHHHHHHHHhhcCChhh
Q 042039          274 SGRLEIALELFRSLPRRVLVADVV-T-YNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN--VIIFVTLIHGFVRINKPSK  349 (376)
Q Consensus       274 ~~~~~~a~~~~~~~~~~~~~~~~~-~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~  349 (376)
                      ...++.|..+|+++++ +.||... + |......=-+.|-...|..+++++... +++.  ...|+..+.--...--...
T Consensus       563 g~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~~-v~~a~~l~myni~I~kaae~yGv~~  640 (835)
T KOG2047|consen  563 GTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATSA-VKEAQRLDMYNIYIKKAAEIYGVPR  640 (835)
T ss_pred             CCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHHhCCcc
Confidence            3468888888888887 4555432 2 222222223456677777787776543 2222  2345555543333333444


Q ss_pred             HHHHHHHHHhCCCCCchHHHHH
Q 042039          350 VIELLHKMKEKKVMPDASIVSM  371 (376)
Q Consensus       350 a~~~~~~~~~~~~~p~~~~~~~  371 (376)
                      ...+|++.++.  -|+...-..
T Consensus       641 TR~iYekaIe~--Lp~~~~r~m  660 (835)
T KOG2047|consen  641 TREIYEKAIES--LPDSKAREM  660 (835)
T ss_pred             cHHHHHHHHHh--CChHHHHHH
Confidence            55555555543  444444333

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

Probab=99.41  E-value=8.8e-11  Score=97.23  Aligned_cols=254  Identities=18%  Similarity=0.130  Sum_probs=194.1

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      ..-+.+.|++.+|.-.|+..++.+ +.+...|..|+......++-..|+..++++.+.. |.+..+...|.-.|...|.-
T Consensus       292 G~~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q  369 (579)
T KOG1125|consen  292 GCNLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQ  369 (579)
T ss_pred             HHHHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhH
Confidence            345678899999999999999875 4478899999999999999999999999999987 67888999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCC-------HhHHHHHHHHHHhccchHHHHHHHHHHHhc-CCCCCcchHHHHHHHHHhCCCHHH
Q 042039          173 EEALSLYREMVSKGIKPT-------VVTYNTLFLGLFEIHQVEHALKLFEEMQRD-DVAADTSTYNTFIDGLCKNGYIVE  244 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~  244 (376)
                      .+|+..++..+....+--       ...+.. -........+....++|-++... +..+++.+...|...|.-.|++++
T Consensus       370 ~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~-~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdr  448 (579)
T KOG1125|consen  370 NQALKMLDKWIRNKPKYVHLVSAGENEDFEN-TKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDR  448 (579)
T ss_pred             HHHHHHHHHHHHhCccchhccccCccccccC-CcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHH
Confidence            999999999876421100       000000 01112222334455555555444 434788899999999999999999


Q ss_pred             HHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC-HHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          245 AVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD-VVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       245 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      |++.|+.+.... +-|..+|+.|+..++...+.++|+..|+++++.  .|+ +.+.+.|+-.|...|.+++|.+.|-.++
T Consensus       449 aiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  449 AVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLEAL  525 (579)
T ss_pred             HHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHHHH
Confidence            999999998876 448899999999999999999999999999885  444 5677889999999999999999988776


Q ss_pred             Hc---------CCCCcHHHHHHHHHHHhhcCChhhHHH
Q 042039          324 EN---------AVAPNVIIFVTLIHGFVRINKPSKVIE  352 (376)
Q Consensus       324 ~~---------~~~~~~~~~~~l~~~~~~~g~~~~a~~  352 (376)
                      ..         ...++..+|..|=.++.-.++.|-+..
T Consensus       526 ~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~  563 (579)
T KOG1125|consen  526 SMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQE  563 (579)
T ss_pred             HhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHH
Confidence            42         112234577777777777777765444

>PF13041 PPR_2: PPR repeat family

Probab=99.40  E-value=1e-12  Score=74.84  Aligned_cols=50  Identities=54%  Similarity=0.950  Sum_probs=42.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH   63 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   63 (376)
                      ||+.+||.+|++|++.|++++|.++|++|.+.|++||..+|+.++.+|++
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            78888888888888888888888888888888888888888888888764

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

Probab=99.40  E-value=5.1e-11  Score=103.30  Aligned_cols=268  Identities=15%  Similarity=0.138  Sum_probs=164.7

Q ss_pred             cccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhH
Q 042039           10 VVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTF   89 (376)
Q Consensus        10 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   89 (376)
                      .|+.||.++|..+|..|+..|+.+.|- +|..|.-...+.+...++.++......++.+.+.           .|...+|
T Consensus        19 ~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-----------ep~aDty   86 (1088)
T KOG4318|consen   19 SGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-----------EPLADTY   86 (1088)
T ss_pred             hcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-----------CCchhHH
Confidence            466777777777777777777777777 7777776666667777777777777777666554           4567777


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      ..+..+|...|+...    |+...+        ....+...+...|--.....++..+.-.  +.....-.+.+....-.
T Consensus        87 t~Ll~ayr~hGDli~----fe~veq--------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~--p~~lpda~n~illlv~e  152 (1088)
T KOG4318|consen   87 TNLLKAYRIHGDLIL----FEVVEQ--------DLESINQSFSDHGVGSPERWFLMKIHCC--PHSLPDAENAILLLVLE  152 (1088)
T ss_pred             HHHHHHHHhccchHH----HHHHHH--------HHHHHHhhhhhhccCcHHHHHHhhcccC--cccchhHHHHHHHHHHH
Confidence            777777777777655    222221        1122233344444444444444443221  12222233344445556


Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELF  249 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  249 (376)
                      |-++.+++++..+...... .+...  +++-...  ++....++........-.+++.++..++.+-...|+.+.|..++
T Consensus       153 glwaqllkll~~~Pvsa~~-~p~~v--fLrqnv~--~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll  227 (1088)
T KOG4318|consen  153 GLWAQLLKLLAKVPVSAWN-APFQV--FLRQNVV--DNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLL  227 (1088)
T ss_pred             HHHHHHHHHHhhCCccccc-chHHH--HHHHhcc--CCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHH
Confidence            6677776666554332110 11111  2332222  22223333333322222578888888888888889999999999


Q ss_pred             HHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCC
Q 042039          250 RTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQ  311 (376)
Q Consensus       250 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  311 (376)
                      ..|.+.|.+.++.-|..++-.   .++..-+..++..|...|+.|+..|+...+..+..+|.
T Consensus       228 ~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  228 YEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             HHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            999888887776666666544   77777888888888888888888888888877777555

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

Probab=99.40  E-value=9.5e-11  Score=101.67  Aligned_cols=274  Identities=14%  Similarity=0.161  Sum_probs=169.6

Q ss_pred             HHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcC
Q 042039           37 ALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD  116 (376)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  116 (376)
                      .++-.+...|+.|+..+|..++.-|+..|+.+.|- +|.-|.-...+.+...++.++......++.+.+.          
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk----------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK----------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC----------
Confidence            34455566677777777777777777777777766 6666665555556666666666666666655544          


Q ss_pred             CCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH-CCCCCCHhHHH
Q 042039          117 VRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS-KGIKPTVVTYN  195 (376)
Q Consensus       117 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~  195 (376)
                       .|-+.+|..+..+|...||...    |+...+        ....+...+...|.-.....++..+.- .+.-|+.   .
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~----fe~veq--------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda---~  143 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLIL----FEVVEQ--------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDA---E  143 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHH----HHHHHH--------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhH---H
Confidence             4566677777777777777655    222221        111223333344443443344433221 1122333   2


Q ss_pred             HHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC-CHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhC
Q 042039          196 TLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG-YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKS  274 (376)
Q Consensus       196 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  274 (376)
                      ..+......|-++.+.+++..+..... ..+...  +++-+.... .+++-..+.+....   .|++.++..++.+-...
T Consensus       144 n~illlv~eglwaqllkll~~~Pvsa~-~~p~~v--fLrqnv~~ntpvekLl~~cksl~e---~~~s~~l~a~l~~alaa  217 (1088)
T KOG4318|consen  144 NAILLLVLEGLWAQLLKLLAKVPVSAW-NAPFQV--FLRQNVVDNTPVEKLLNMCKSLVE---APTSETLHAVLKRALAA  217 (1088)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCCcccc-cchHHH--HHHHhccCCchHHHHHHHHHHhhc---CCChHHHHHHHHHHHhc
Confidence            334444556677777777665533321 111111  233333322 34444444444443   46888899999888889


Q ss_pred             CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCC
Q 042039          275 GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINK  346 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  346 (376)
                      |+.+.|..++.+|.+.|++.+.+.|..++.+   .++...++.+++.|.+.|+.|+..|+...+-.+..+|.
T Consensus       218 g~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  218 GDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             CchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            9999999999999999988888888887765   78888888889999999999999998888777777554

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.38  E-value=8e-09  Score=80.56  Aligned_cols=305  Identities=11%  Similarity=0.051  Sum_probs=229.0

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChh-hHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAF-TYST  126 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~  126 (376)
                      +.++.-..-+...+...|++.+|+.-|...++.++. +-.++..-...|...|+-..|+.-+.++++.  +||-. .-..
T Consensus        35 ~advekhlElGk~lla~~Q~sDALt~yHaAve~dp~-~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQ  111 (504)
T KOG0624|consen   35 PADVEKHLELGKELLARGQLSDALTHYHAAVEGDPN-NYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQ  111 (504)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCch-hHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHH
Confidence            345666777888999999999999999999875322 3334445566889999999999999999885  67733 3334


Q ss_pred             HHHHHHhcCcHHHHHHHHHHHHhcCCCCC--hhh------------HHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHh
Q 042039          127 LMDGFCLTGKINRAEELFGSMESMGCKHD--DVS------------YNILINGYCKNKEVEEALSLYREMVSKGIKPTVV  192 (376)
Q Consensus       127 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  192 (376)
                      -...+.++|.++.|..-|+.+.+......  ..+            ....+..+...|+...|+..+..+++. .+-+..
T Consensus       112 Rg~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi-~~Wda~  190 (504)
T KOG0624|consen  112 RGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEI-QPWDAS  190 (504)
T ss_pred             hchhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhc-CcchhH
Confidence            56678899999999999999988752111  111            122344566789999999999999986 344788


Q ss_pred             HHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHH----HHHH-
Q 042039          193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQA----YNCL-  267 (376)
Q Consensus       193 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~~~l-  267 (376)
                      .+..-..+|...|++..|+.-+..+.+.. ..+...+..+...+...|+.+.++...++..+.+  |+...    |-.+ 
T Consensus       191 l~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKld--pdHK~Cf~~YKklk  267 (504)
T KOG0624|consen  191 LRQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLKLD--PDHKLCFPFYKKLK  267 (504)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccC--cchhhHHHHHHHHH
Confidence            88888999999999999999988887764 5577788888899999999999999999887764  33221    1111 


Q ss_pred             --------HHHHHhCCChHHHHHHHhcccccCCC---CCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCC-cHHHHH
Q 042039          268 --------IDGLCKSGRLEIALELFRSLPRRVLV---ADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP-NVIIFV  335 (376)
Q Consensus       268 --------~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~  335 (376)
                              +......++|.+++...+...+....   .....+..+-.++...+++.+|+....++++.  .| |..++.
T Consensus       268 Kv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~--d~~dv~~l~  345 (504)
T KOG0624|consen  268 KVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI--DPDDVQVLC  345 (504)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc--CchHHHHHH
Confidence                    22334567788888887776664221   11234566677888899999999999999885  44 488888


Q ss_pred             HHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          336 TLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       336 ~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      .-..+|.-...++.|+.-|++..+.+
T Consensus       346 dRAeA~l~dE~YD~AI~dye~A~e~n  371 (504)
T KOG0624|consen  346 DRAEAYLGDEMYDDAIHDYEKALELN  371 (504)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHhcC
Confidence            88899999999999999999988653

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

Probab=99.36  E-value=7.3e-09  Score=85.44  Aligned_cols=330  Identities=13%  Similarity=0.072  Sum_probs=224.3

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc-hHhHHHHHHHHHhCCC
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS-VVTFNVIMDELCKNGK  101 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~  101 (376)
                      ..+.+..|+++.|+.+|.+.+... |+|...|..-..+|...|++++|++--.+-++.  .|+ ..-|.....++.-.|+
T Consensus         9 gnaa~s~~d~~~ai~~~t~ai~l~-p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l--~p~w~kgy~r~Gaa~~~lg~   85 (539)
T KOG0548|consen    9 GNAAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRRL--NPDWAKGYSRKGAALFGLGD   85 (539)
T ss_pred             HHhhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHhc--CCchhhHHHHhHHHHHhccc
Confidence            345678899999999999988887 668888989999999999999998877776665  444 4578888888888999


Q ss_pred             hHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhc---C-------------------------c-----------------
Q 042039          102 MDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT---G-------------------------K-----------------  136 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~-------------------------~-----------------  136 (376)
                      +++|...|.+-++.. +.|...+..+..++...   +                         .                 
T Consensus        86 ~~eA~~ay~~GL~~d-~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~  164 (539)
T KOG0548|consen   86 YEEAILAYSEGLEKD-PSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKL  164 (539)
T ss_pred             HHHHHHHHHHHhhcC-CchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhc
Confidence            999999999888764 33455555555544111   0                         0                 


Q ss_pred             ------HHHHHHHHHHHH-----hc-------CCCC---------C-------------hhhHHHHHHHHHccCcHHHHH
Q 042039          137 ------INRAEELFGSME-----SM-------GCKH---------D-------------DVSYNILINGYCKNKEVEEAL  176 (376)
Q Consensus       137 ------~~~a~~~~~~~~-----~~-------~~~~---------~-------------~~~~~~l~~~~~~~~~~~~a~  176 (376)
                            +..+...+....     ..       ...|         .             ..-...+++...+..+++.|+
T Consensus       165 ~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~  244 (539)
T KOG0548|consen  165 YLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAI  244 (539)
T ss_pred             ccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHH
Confidence                  000100000000     00       0001         0             012345667777777888888


Q ss_pred             HHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcc-------hHHHHHHHHHhCCCHHHHHHHH
Q 042039          177 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTS-------TYNTFIDGLCKNGYIVEAVELF  249 (376)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~l~~~~~~~~~~~~a~~~~  249 (376)
                      +.+.......  .+..-++....++...|.+..+........+.|. ....       .+..+..+|.+.++++.++..|
T Consensus       245 q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gr-e~rad~klIak~~~r~g~a~~k~~~~~~ai~~~  321 (539)
T KOG0548|consen  245 QHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGR-ELRADYKLIAKALARLGNAYTKREDYEGAIKYY  321 (539)
T ss_pred             HHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhH-HHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHH
Confidence            8888887753  4555666677778888887777777666655541 1112       2233444666778888899888


Q ss_pred             HHhcccCCCchHHH-------------------------HHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHH
Q 042039          250 RTLGILKCELDIQA-------------------------YNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIH  304 (376)
Q Consensus       250 ~~~~~~~~~~~~~~-------------------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  304 (376)
                      .+.......|+...                         ...-+..+.+.|++..|...|.+++.+ .|.|...|....-
T Consensus       322 ~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr-~P~Da~lYsNRAa  400 (539)
T KOG0548|consen  322 QKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKR-DPEDARLYSNRAA  400 (539)
T ss_pred             HHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhc-CCchhHHHHHHHH
Confidence            88765444433211                         112245567789999999999998887 4778899999999


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          305 GLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       305 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      +|.+.|.+..|+.-.+..++.+ ++....|..=..++....++++|++.|++..+..
T Consensus       401 c~~kL~~~~~aL~Da~~~ieL~-p~~~kgy~RKg~al~~mk~ydkAleay~eale~d  456 (539)
T KOG0548|consen  401 CYLKLGEYPEALKDAKKCIELD-PNFIKAYLRKGAALRAMKEYDKALEAYQEALELD  456 (539)
T ss_pred             HHHHHhhHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999888888863 2234455555666777788999999999888654

>PF13041 PPR_2: PPR repeat family

Probab=99.32  E-value=5.2e-12  Score=71.86  Aligned_cols=47  Identities=26%  Similarity=0.593  Sum_probs=27.6

Q ss_pred             CcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHHhh
Q 042039          329 PNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVVDL  375 (376)
Q Consensus       329 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  375 (376)
                      ||..+|+.++.+|++.|++++|.++|++|.+.|+.||..||+.+|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~   47 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILING   47 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            45555555555555555555566666655555555665555555554

>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=99.31  E-value=6.4e-10  Score=88.72  Aligned_cols=251  Identities=13%  Similarity=0.045  Sum_probs=141.8

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChH
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMD  103 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  103 (376)
                      +.+.-.|++..++.-.+ ......+.+......+.+++...|+++.++.   ++... ..|.......+...+...++-+
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl~---ei~~~-~~~~l~av~~la~y~~~~~~~e   83 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVLS---EIKKS-SSPELQAVRLLAEYLSSPSDKE   83 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHHH---HS-TT-SSCCCHHHHHHHHHHCTSTTHH
T ss_pred             HHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHHH---HhccC-CChhHHHHHHHHHHHhCccchH
Confidence            44556788888776555 3333222334455566777777777665443   22222 2555555555544443334444


Q ss_pred             HHHHHHHHHHhcCCC-CChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          104 EASRLLDLMVQRDVR-PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      .+..-+++....... .+.......+.++...|++++|++++...      .+.......+.+|.+.++++.|.+.++.|
T Consensus        84 ~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~  157 (290)
T PF04733_consen   84 SALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNM  157 (290)
T ss_dssp             CHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444444443333222 12233333445556667788777776542      34566666777777788888888888777


Q ss_pred             HHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC
Q 042039          183 VSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE  258 (376)
Q Consensus       183 ~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  258 (376)
                      .+.  . +..+...+..++..    .+.+..|..+|+++... .++++.+.+.++.++...|++++|.+++.++...+. 
T Consensus       158 ~~~--~-eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-  232 (290)
T PF04733_consen  158 QQI--D-EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-  232 (290)
T ss_dssp             HCC--S-CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-
T ss_pred             Hhc--C-CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-
Confidence            764  2 23344445444433    23577777777776554 355666777777777777777777777777766553 


Q ss_pred             chHHHHHHHHHHHHhCCCh-HHHHHHHhccccc
Q 042039          259 LDIQAYNCLIDGLCKSGRL-EIALELFRSLPRR  290 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~  290 (376)
                      -++.++..++.+....|+. +.+.+++.++...
T Consensus       233 ~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  233 NDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             CHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             CCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            3666666777766666766 5566677766653

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.

>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=99.31  E-value=4.4e-10  Score=89.67  Aligned_cols=252  Identities=13%  Similarity=0.076  Sum_probs=153.4

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                      ++-+.-.|++..++.-.+ ........+......+.+++...|+++.++   .++.... .|.......+...+...++-
T Consensus         8 vrn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~   82 (290)
T PF04733_consen    8 VRNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDK   82 (290)
T ss_dssp             HHHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTH
T ss_pred             HHHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccch
Confidence            344556788888886665 223222223445666778888888876543   3333332 55655555555555443445


Q ss_pred             HHHHHHHHHHHhcCCC-CChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHH
Q 042039          138 NRAEELFGSMESMGCK-HDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEE  216 (376)
Q Consensus       138 ~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  216 (376)
                      +.+..-++........ .+.........++...|++++|++++...      .+.......+.++.+.++++.|.+.++.
T Consensus        83 e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~  156 (290)
T PF04733_consen   83 ESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKN  156 (290)
T ss_dssp             HCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            5555555444333222 22333344456667788888888877652      3556666777888888888888888888


Q ss_pred             HHhcCCCCCcchHHHHHHHHHh----CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCC
Q 042039          217 MQRDDVAADTSTYNTFIDGLCK----NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVL  292 (376)
Q Consensus       217 ~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  292 (376)
                      |.+.+   +..+...++.++..    .+.+.+|..+|+++... ..+++.+.+.++.+....|++++|.+++.+.... .
T Consensus       157 ~~~~~---eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~-~  231 (290)
T PF04733_consen  157 MQQID---EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEK-D  231 (290)
T ss_dssp             HHCCS---CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--
T ss_pred             HHhcC---CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh-c
Confidence            87653   34555556555543    23578888888887654 3457777788888888888888888888887665 3


Q ss_pred             CCCHHHHHHHHHHHHccCCh-hHHHHHHHHHHHc
Q 042039          293 VADVVTYNIMIHGLCNDGQM-DKAHDLFLDMEEN  325 (376)
Q Consensus       293 ~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~  325 (376)
                      +.++.+...++.+....|+. +.+.+++.++...
T Consensus       232 ~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  232 PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            45667777777777777776 5566677776654

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.

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

Probab=99.31  E-value=1.7e-09  Score=89.85  Aligned_cols=222  Identities=14%  Similarity=0.110  Sum_probs=142.8

Q ss_pred             HHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHH
Q 042039           25 GLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDE  104 (376)
Q Consensus        25 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  104 (376)
                      .+.+.|++.+|.-.|+...+.+ |.+..+|..|+......++-..|+..+++..+..+. +......|.-.|...|.-..
T Consensus       294 ~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhHHH
Confidence            4567777888888888777765 667778888888877777777788887777776433 56677777777777777777


Q ss_pred             HHHHHHHHHhcCCC--------CChhhHHHHHHHHHhcCcHHHHHHHHHHH-HhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039          105 ASRLLDLMVQRDVR--------PNAFTYSTLMDGFCLTGKINRAEELFGSM-ESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus       105 a~~~~~~~~~~~~~--------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      |+..++.-+...++        ++...-..  ..+.....+....++|-++ ...+...|+.+...|+-.|.-.|++++|
T Consensus       372 Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdra  449 (579)
T KOG1125|consen  372 ALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRA  449 (579)
T ss_pred             HHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHH
Confidence            77777776553211        00000000  1111122233444444443 3333346677777777777777777777


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      +..|+.++... +-|...|+.|...+....+.++|+..|.++++.. |.-.++...++..|...|.+.+|...|-.+
T Consensus       450 iDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLq-P~yVR~RyNlgIS~mNlG~ykEA~~hlL~A  524 (579)
T KOG1125|consen  450 VDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQLQ-PGYVRVRYNLGISCMNLGAYKEAVKHLLEA  524 (579)
T ss_pred             HHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcC-CCeeeeehhhhhhhhhhhhHHHHHHHHHHH
Confidence            77777777742 3356677777777777777777777777777653 334556667777777777777777766554

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.29  E-value=7.5e-08  Score=91.44  Aligned_cols=336  Identities=13%  Similarity=0.035  Sum_probs=210.9

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC------CCc--hHhHHHHHHHHH
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV------QPS--VVTFNVIMDELC   97 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~--~~~~~~l~~~~~   97 (376)
                      ....|+++.+...++.+.......++.........+...|++++|...+......-.      .+.  ......+...+.
T Consensus       384 l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~  463 (903)
T PRK04841        384 LFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAI  463 (903)
T ss_pred             HHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHH
Confidence            344566666666655542211112233334455666778899999999887754311      111  112223345567


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCCh----hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC---CC--ChhhHHHHHHHHHc
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNA----FTYSTLMDGFCLTGKINRAEELFGSMESMGC---KH--DDVSYNILINGYCK  168 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~  168 (376)
                      ..|++++|...+++........+.    .....+...+...|++++|...+++......   .+  ...+...+...+..
T Consensus       464 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~  543 (903)
T PRK04841        464 NDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFA  543 (903)
T ss_pred             hCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHH
Confidence            889999999999988763211121    2345566677889999999999988764311   11  12345567778888


Q ss_pred             cCcHHHHHHHHHHHHHC----CCC--C-CHhHHHHHHHHHHhccchHHHHHHHHHHHhcC--CCC--CcchHHHHHHHHH
Q 042039          169 NKEVEEALSLYREMVSK----GIK--P-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD--VAA--DTSTYNTFIDGLC  237 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~~l~~~~~  237 (376)
                      .|++++|...+++....    +..  + ....+..+...+...|++++|...+.+.....  ..+  ....+..+...+.
T Consensus       544 ~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~  623 (903)
T PRK04841        544 QGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISL  623 (903)
T ss_pred             CCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHH
Confidence            99999999998887652    211  1 12334455667778899999999988875531  111  2234455667788


Q ss_pred             hCCCHHHHHHHHHHhcccCC--CchHH--HH--HHHHHHHHhCCChHHHHHHHhcccccCCCCC---HHHHHHHHHHHHc
Q 042039          238 KNGYIVEAVELFRTLGILKC--ELDIQ--AY--NCLIDGLCKSGRLEIALELFRSLPRRVLVAD---VVTYNIMIHGLCN  308 (376)
Q Consensus       238 ~~~~~~~a~~~~~~~~~~~~--~~~~~--~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~  308 (376)
                      ..|++++|...+..+.....  .....  ..  ...+..+...|+.+.|...+...........   ...+..+..++..
T Consensus       624 ~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~  703 (903)
T PRK04841        624 ARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQIL  703 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHH
Confidence            89999999998888743211  10110  10  1122444568899999999877554211111   1123467778889


Q ss_pred             cCChhHHHHHHHHHHHc----CCCC-cHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          309 DGQMDKAHDLFLDMEEN----AVAP-NVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       309 ~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      .|++++|...++++...    +..+ ...+...+..++.+.|+.++|...+.+..+..
T Consensus       704 ~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        704 LGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            99999999999988753    2222 23456667788899999999999999988653

>PLN02789 farnesyltranstransferase

Probab=99.26  E-value=2.1e-08  Score=81.15  Aligned_cols=215  Identities=10%  Similarity=0.002  Sum_probs=140.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC-ChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN-DWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ++..+-..+...++.++|+.+.+++++.+ |.+..+|+....++...| ++++++..++++++.+.+ +..+|+....++
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~l  116 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWLA  116 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHHH
Confidence            44455555666788888888888888775 556677777777777777 578888888888877554 556677665555


Q ss_pred             HhCCCh--HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc---Cc
Q 042039           97 CKNGKM--DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN---KE  171 (376)
Q Consensus        97 ~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~  171 (376)
                      .+.|+.  +++..+++++++.+ +-|..+|.....++...|+++++++.++++++.+ +.+..+|+....++.+.   |.
T Consensus       117 ~~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d-~~N~sAW~~R~~vl~~~~~l~~  194 (320)
T PLN02789        117 EKLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEED-VRNNSAWNQRYFVITRSPLLGG  194 (320)
T ss_pred             HHcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHC-CCchhHHHHHHHHHHhcccccc
Confidence            566653  56777787887765 3467778777777778888888888888888776 55666777666555443   22


Q ss_pred             ----HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc----cchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          172 ----VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI----HQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       172 ----~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                          .++.+....+++.. .+-+...|..+...+...    +...+|.+.+.+....+ +.+...+..++..|+.
T Consensus       195 ~~~~~e~el~y~~~aI~~-~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        195 LEAMRDSELKYTIDAILA-NPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             ccccHHHHHHHHHHHHHh-CCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence                23556666566654 233556666666555552    23345666666655543 3344555566666553

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.25  E-value=4.3e-08  Score=82.84  Aligned_cols=307  Identities=16%  Similarity=0.081  Sum_probs=197.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .|...+. |...+++...++..+.+.+. .+...++....+-.+...|+-++|........+..+. +...|+.+.-.+.
T Consensus        10 lF~~~lk-~yE~kQYkkgLK~~~~iL~k-~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~-S~vCwHv~gl~~R   86 (700)
T KOG1156|consen   10 LFRRALK-CYETKQYKKGLKLIKQILKK-FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLK-SHVCWHVLGLLQR   86 (700)
T ss_pred             HHHHHHH-HHHHHHHHhHHHHHHHHHHh-CCccchhHHhccchhhcccchHHHHHHHHHHhccCcc-cchhHHHHHHHHh
Confidence            3444444 44678888888888888874 3556677777777778888889998888887776544 7778888888888


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      ...++++|+..|..++..+ +.|...+..+.-.-++.++++..........+.. +.....|..++.++.-.|+...|..
T Consensus        87 ~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~~L~g~y~~A~~  164 (700)
T KOG1156|consen   87 SDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQHLLGEYKMALE  164 (700)
T ss_pred             hhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888999999999988875 4567788888888888888888888877777764 4455677777888888888999998


Q ss_pred             HHHHHHHCC-CCCCHhHHHHHHHHH------HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          178 LYREMVSKG-IKPTVVTYNTLFLGL------FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       178 ~~~~~~~~~-~~~~~~~~~~l~~~~------~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      +++...+.. ..|+...+......+      ...|..+.|.+.+..-... +......-..-...+.+.+++++|..++.
T Consensus       165 il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~~y~  243 (700)
T KOG1156|consen  165 ILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ-IVDKLAFEETKADLLMKLGQLEEAVKVYR  243 (700)
T ss_pred             HHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH-HHHHHHHhhhHHHHHHHHhhHHhHHHHHH
Confidence            888887753 246666655544332      3456666666666554433 22223334445566778888888888888


Q ss_pred             HhcccCCCchHH-HHHHHHHHHHhCCChHHHH-HHHhcccccCCCCCHHHHHHHHHHHHccCCh-hHHHHHHHHHHHcCC
Q 042039          251 TLGILKCELDIQ-AYNCLIDGLCKSGRLEIAL-ELFRSLPRRVLVADVVTYNIMIHGLCNDGQM-DKAHDLFLDMEENAV  327 (376)
Q Consensus       251 ~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~  327 (376)
                      .+....  ||.. .|..+..++.+..+..++. .+|....+.  .|....-..+........++ +..-+++....+.|+
T Consensus       244 ~Ll~rn--Pdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~--y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~  319 (700)
T KOG1156|consen  244 RLLERN--PDNLDYYEGLEKALGKIKDMLEALKALYAILSEK--YPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGV  319 (700)
T ss_pred             HHHhhC--chhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhc--CcccccchhccHHHhCcchhHHHHHHHHHHHhhcCC
Confidence            887764  3433 3444444443333333333 556555443  22222222222222222333 333455666666666


Q ss_pred             CCcHHHH
Q 042039          328 APNVIIF  334 (376)
Q Consensus       328 ~~~~~~~  334 (376)
                      ++-...+
T Consensus       320 p~vf~dl  326 (700)
T KOG1156|consen  320 PSVFKDL  326 (700)
T ss_pred             Cchhhhh
Confidence            5443333

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.23  E-value=1.1e-08  Score=87.97  Aligned_cols=289  Identities=13%  Similarity=-0.004  Sum_probs=198.5

Q ss_pred             hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHH
Q 042039           32 VDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDL  111 (376)
Q Consensus        32 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  111 (376)
                      ..++++.+++..+.+ +.|+.+...+..-|+..++.+.|.+...+..+.+...+...|..++..+...+++.+|+.+.+.
T Consensus       460 h~kslqale~av~~d-~~dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~  538 (799)
T KOG4162|consen  460 HKKSLQALEEAVQFD-PTDPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDA  538 (799)
T ss_pred             HHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHH
Confidence            457888889888876 5566666777778888999999999999999987777899999999999999999999999998


Q ss_pred             HHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCCh-------hhHHHHHHHHHccCcHHHHHHHHHHH-
Q 042039          112 MVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-KHDD-------VSYNILINGYCKNKEVEEALSLYREM-  182 (376)
Q Consensus       112 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~-  182 (376)
                      ....- ..|-.....-+..-...++.+++......+...-- .+..       .....-........+..+|.+....+ 
T Consensus       539 al~E~-~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls  617 (799)
T KOG4162|consen  539 ALEEF-GDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLS  617 (799)
T ss_pred             HHHHh-hhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHH
Confidence            87642 11222222222223334555555544433322100 0000       00000000000011112222211111 


Q ss_pred             ----------------HHCCCCC--C------HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          183 ----------------VSKGIKP--T------VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       183 ----------------~~~~~~~--~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                                      ......|  +      ...|......+...+..+++...+.+..... +.....|...+..+..
T Consensus       618 ~l~a~~~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~~~~  696 (799)
T KOG4162|consen  618 SLVASQLKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLLLEV  696 (799)
T ss_pred             HHHHhhhhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHHHHH
Confidence                            1111111  2      2234455666778888899998888887764 5677788888889999


Q ss_pred             CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHH--HHhcccccCCCCCHHHHHHHHHHHHccCChhHHH
Q 042039          239 NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALE--LFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAH  316 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  316 (376)
                      .|..++|.+.|..+...++ .++.....++.++.+.|+..-|..  ++..+.+. .+.+...|..++..+.+.|+.++|.
T Consensus       697 ~~~~~EA~~af~~Al~ldP-~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~-dp~n~eaW~~LG~v~k~~Gd~~~Aa  774 (799)
T KOG4162|consen  697 KGQLEEAKEAFLVALALDP-DHVPSMTALAELLLELGSPRLAEKRSLLSDALRL-DPLNHEAWYYLGEVFKKLGDSKQAA  774 (799)
T ss_pred             HHhhHHHHHHHHHHHhcCC-CCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhh-CCCCHHHHHHHHHHHHHccchHHHH
Confidence            9999999999999887763 367889999999999998888877  99999887 4678999999999999999999999


Q ss_pred             HHHHHHHHc
Q 042039          317 DLFLDMEEN  325 (376)
Q Consensus       317 ~~~~~~~~~  325 (376)
                      +.|+...+.
T Consensus       775 ecf~aa~qL  783 (799)
T KOG4162|consen  775 ECFQAALQL  783 (799)
T ss_pred             HHHHHHHhh
Confidence            999988764

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.23  E-value=1.6e-08  Score=77.41  Aligned_cols=294  Identities=12%  Similarity=0.044  Sum_probs=204.5

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHH-HHHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYS-TLMDGF  131 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~  131 (376)
                      -+...+..+++..++++|++++..-.+...+ +......+..+|....++..|...|+++-..  .|...-|. .-...+
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~p~-~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSL   88 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERSPR-SRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSL   88 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHH
Confidence            3566677778889999999999988877443 7778888999999999999999999999876  44444443 346677


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHH
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      .+.+.+..|..+...+.+.. .....+...-.......+++..+..+.++....   .+..+.....-...+.|+++.|.
T Consensus        89 Y~A~i~ADALrV~~~~~D~~-~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~e---n~Ad~~in~gCllykegqyEaAv  164 (459)
T KOG4340|consen   89 YKACIYADALRVAFLLLDNP-ALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSE---NEADGQINLGCLLYKEGQYEAAV  164 (459)
T ss_pred             HHhcccHHHHHHHHHhcCCH-HHHHHHHHHHHHHhcccccCcchHHHHHhccCC---CccchhccchheeeccccHHHHH
Confidence            78899999999998886531 111122222233445678888888888876543   24556666667778999999999


Q ss_pred             HHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc-------------hH---------------HH
Q 042039          212 KLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCEL-------------DI---------------QA  263 (376)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-------------~~---------------~~  263 (376)
                      +-|+...+-+.-.....| .++-+..+.++++.|.+...++++.|++.             |.               ..
T Consensus       165 qkFqaAlqvsGyqpllAY-niALaHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eA  243 (459)
T KOG4340|consen  165 QKFQAALQVSGYQPLLAY-NLALAHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEA  243 (459)
T ss_pred             HHHHHHHhhcCCCchhHH-HHHHHHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHH
Confidence            999999887533333344 45556778899999999998886665431             11               12


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhcccccC-CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHh
Q 042039          264 YNCLIDGLCKSGRLEIALELFRSLPRRV-LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFV  342 (376)
Q Consensus       264 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  342 (376)
                      ++.-...+.+.|+++.|.+.+..|..+. ...|+.|...+.-.-. .+++.+..+-++-+.+.++ -...||..++-.|+
T Consensus       244 fNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~nP-fP~ETFANlLllyC  321 (459)
T KOG4340|consen  244 FNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQNP-FPPETFANLLLLYC  321 (459)
T ss_pred             hhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcCC-CChHHHHHHHHHHh
Confidence            2333444567899999999999886432 3456777666554332 3445555555555555543 35678888888899


Q ss_pred             hcCChhhHHHHHHH
Q 042039          343 RINKPSKVIELLHK  356 (376)
Q Consensus       343 ~~g~~~~a~~~~~~  356 (376)
                      +..-++-|-+++-+
T Consensus       322 KNeyf~lAADvLAE  335 (459)
T KOG4340|consen  322 KNEYFDLAADVLAE  335 (459)
T ss_pred             hhHHHhHHHHHHhh
Confidence            98888877776643

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.23  E-value=4.2e-07  Score=76.25  Aligned_cols=335  Identities=13%  Similarity=0.073  Sum_probs=198.9

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +-|...+..-+-++.+.++|++|+.+.+.-...  ..+...+..-+.+..+.+..++|+..++-..    +.+..+...-
T Consensus        43 pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~~fEKAYc~Yrlnk~Dealk~~~~~~----~~~~~ll~L~  116 (652)
T KOG2376|consen   43 PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSFFFEKAYCEYRLNKLDEALKTLKGLD----RLDDKLLELR  116 (652)
T ss_pred             CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchhhHHHHHHHHHcccHHHHHHHHhccc----ccchHHHHHH
Confidence            455667778888888999999998655433211  1111122344566677788888888877221    1133356666


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCC-------------------------C--ChhhH---HHHHHHHHhcCcHHHHHH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVR-------------------------P--NAFTY---STLMDGFCLTGKINRAEE  142 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~-------------------------~--~~~~~---~~l~~~~~~~~~~~~a~~  142 (376)
                      ...+.+.+++++|..+|+.+.+.+.+                         |  ...+|   ....-.+...|++.+|++
T Consensus       117 AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~e  196 (652)
T KOG2376|consen  117 AQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACILIENGKYNQAIE  196 (652)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHHHHhcccHHHHHH
Confidence            67778888888888888887654210                         0  01122   223344556788888888


Q ss_pred             HHHHHHhcC-------CCCCh-------hhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhH---------------
Q 042039          143 LFGSMESMG-------CKHDD-------VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT---------------  193 (376)
Q Consensus       143 ~~~~~~~~~-------~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---------------  193 (376)
                      +++.....+       -..+.       ..-..+.-++...|+.++|..+|...++.... |...               
T Consensus       197 lL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~~~~~-D~~~~Av~~NNLva~~~d~  275 (652)
T KOG2376|consen  197 LLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIKRNPA-DEPSLAVAVNNLVALSKDQ  275 (652)
T ss_pred             HHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhcCC-CchHHHHHhcchhhhcccc
Confidence            888772211       00000       12234455666788888888888877765321 1100               


Q ss_pred             ------------------------------------------------------------------HHHHHHHHH--hcc
Q 042039          194 ------------------------------------------------------------------YNTLFLGLF--EIH  205 (376)
Q Consensus       194 ------------------------------------------------------------------~~~l~~~~~--~~~  205 (376)
                                                                                        +..++....  +..
T Consensus       276 ~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~tnk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~  355 (652)
T KOG2376|consen  276 NYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFTNKMDQVRELSASLPGMSPESLFPILLQEATKVREK  355 (652)
T ss_pred             ccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHH
Confidence                                                                              000000000  001


Q ss_pred             chHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH--------HhcccCCCchHHHHHHHHHHHHhCCCh
Q 042039          206 QVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR--------TLGILKCELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       206 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~--------~~~~~~~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      .+..+..++....+........+....+......|+++.|.+++.        .+...+.  .+.+...+...+.+.++-
T Consensus       356 ~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~--~P~~V~aiv~l~~~~~~~  433 (652)
T KOG2376|consen  356 KHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKH--LPGTVGAIVALYYKIKDN  433 (652)
T ss_pred             HHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhcc--ChhHHHHHHHHHHhccCC
Confidence            122333333333333211123355566777889999999999998        5544443  345666777778888877


Q ss_pred             HHHHHHHhcccccC--CCCC----HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHH
Q 042039          278 EIALELFRSLPRRV--LVAD----VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVI  351 (376)
Q Consensus       278 ~~a~~~~~~~~~~~--~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  351 (376)
                      +.|..++.++...-  ..+.    ..++..++..-.+.|+-++|..+++++.+.+ +++..+...++.+|++. +++.|.
T Consensus       434 ~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~-d~eka~  511 (652)
T KOG2376|consen  434 DSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL-DPEKAE  511 (652)
T ss_pred             ccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc-CHHHHH
Confidence            77777776654320  0111    2234444445557799999999999999864 46888899999999876 788888


Q ss_pred             HHHHHHH
Q 042039          352 ELLHKMK  358 (376)
Q Consensus       352 ~~~~~~~  358 (376)
                      .+-+.+.
T Consensus       512 ~l~k~L~  518 (652)
T KOG2376|consen  512 SLSKKLP  518 (652)
T ss_pred             HHhhcCC
Confidence            8766653

>PLN02789 farnesyltranstransferase

Probab=99.21  E-value=7.1e-08  Score=78.17  Aligned_cols=214  Identities=10%  Similarity=0.027  Sum_probs=145.5

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCC-ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG-KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC  132 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  132 (376)
                      +..+-..+...++.++|+.+..++++.++. +..+|+....++...| ++++++..++++++.+ +.+..+|+....++.
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~lnP~-~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~l~  117 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLNPG-NYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHHHH
Confidence            334444455567888999999998886433 5566776666777777 5789999999988875 335566776666666


Q ss_pred             hcCcH--HHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc---cch
Q 042039          133 LTGKI--NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI---HQV  207 (376)
Q Consensus       133 ~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~  207 (376)
                      +.|+.  +++..+++++.+.. +.+..+|.....++...|+++++++.++++++.+.. +..+|......+.+.   +..
T Consensus       118 ~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~  195 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGL  195 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhccccccc
Confidence            66653  67788888888776 677888888888888889999999999999887543 566666666555443   222


Q ss_pred             ----HHHHHHHHHHHhcCCCCCcchHHHHHHHHHhC----CCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHh
Q 042039          208 ----EHALKLFEEMQRDDVAADTSTYNTFIDGLCKN----GYIVEAVELFRTLGILKCELDIQAYNCLIDGLCK  273 (376)
Q Consensus       208 ----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  273 (376)
                          +.......+++... +.+...++.+...+...    +...+|...+..+...+ +.++..+..++..|..
T Consensus       196 ~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        196 EAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             cccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence                35566666666654 56677777777777652    33455666666655544 2255566666666654

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

Probab=99.20  E-value=8.9e-09  Score=88.04  Aligned_cols=220  Identities=14%  Similarity=0.064  Sum_probs=175.2

Q ss_pred             CChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHH
Q 042039          119 PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLF  198 (376)
Q Consensus       119 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  198 (376)
                      |--..-..+...+...|-...|..++++...         |...+.+|...|+..+|..+..+..+  -+|++..|..++
T Consensus       396 p~Wq~q~~laell~slGitksAl~I~Erlem---------w~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LG  464 (777)
T KOG1128|consen  396 PIWQLQRLLAELLLSLGITKSALVIFERLEM---------WDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLG  464 (777)
T ss_pred             CcchHHHHHHHHHHHcchHHHHHHHHHhHHH---------HHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhh
Confidence            3333445677888889999999999987653         56678899999999999999988887  367888888888


Q ss_pred             HHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChH
Q 042039          199 LGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLE  278 (376)
Q Consensus       199 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  278 (376)
                      .......-+++|.++.+.....       +-..+.....+.++++++.+.++...+.+ +....+|..++.+..+.+++.
T Consensus       465 Dv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q  536 (777)
T KOG1128|consen  465 DVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQ  536 (777)
T ss_pred             hhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhH
Confidence            8777777788888887665332       22223333445789999999999887766 447789999999999999999


Q ss_pred             HHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          279 IALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       279 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      .|.+.|...... -|.+...|+.+..+|.+.++-.+|...+.++.+.+ ..+..+|...+......|.+++|.+.+.++.
T Consensus       537 ~av~aF~rcvtL-~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll  614 (777)
T KOG1128|consen  537 AAVKAFHRCVTL-EPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLL  614 (777)
T ss_pred             HHHHHHHHHhhc-CCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHH
Confidence            999999988765 45567899999999999999999999999999887 4466778777778889999999999999887


Q ss_pred             h
Q 042039          359 E  359 (376)
Q Consensus       359 ~  359 (376)
                      +
T Consensus       615 ~  615 (777)
T KOG1128|consen  615 D  615 (777)
T ss_pred             H
Confidence            4

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

Probab=99.18  E-value=4e-08  Score=89.92  Aligned_cols=234  Identities=14%  Similarity=0.088  Sum_probs=150.0

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-----hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-----AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSY  159 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  159 (376)
                      +...|-..+......++.++|.++.++++.. +.+.     ...|..+++.-...|.-+...++|+++.+..  ..-..|
T Consensus      1457 SSi~WI~YMaf~LelsEiekAR~iaerAL~t-IN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V~ 1533 (1710)
T KOG1070|consen 1457 SSILWIRYMAFHLELSEIEKARKIAERALKT-INFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTVH 1533 (1710)
T ss_pred             cchHHHHHHHHHhhhhhhHHHHHHHHHHhhh-CCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHHH
Confidence            4456666777777777777777777777653 2111     3456666666666677777777777776652  234566


Q ss_pred             HHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCC-CCcchHHHHHHHHHh
Q 042039          160 NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVA-ADTSTYNTFIDGLCK  238 (376)
Q Consensus       160 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~  238 (376)
                      ..|...|.+.+.+++|.++++.|.++ ..-....|...+..+.+.++-+.|..++.++++.-.+ .........+..-.+
T Consensus      1534 ~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk 1612 (1710)
T KOG1070|consen 1534 LKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFK 1612 (1710)
T ss_pred             HHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhh
Confidence            77777777777777777777777775 3345667777777777777777777777777665211 133445556666677


Q ss_pred             CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCH--HHHHHHHHHHHccCChhHHH
Q 042039          239 NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV--VTYNIMIHGLCNDGQMDKAH  316 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~  316 (376)
                      .|+.+.+..+|+......++ ....|+..++.-.+.|+.+.++.+|+++...++++-.  ..|...+..=-..|+-..++
T Consensus      1613 ~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~vE 1691 (1710)
T KOG1070|consen 1613 YGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEKNVE 1691 (1710)
T ss_pred             cCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchhhHH
Confidence            77777777777777665432 5667777777777777777777777777766655432  23344444334455555444


Q ss_pred             HHHHHHH
Q 042039          317 DLFLDME  323 (376)
Q Consensus       317 ~~~~~~~  323 (376)
                      .+=.++.
T Consensus      1692 ~VKarA~ 1698 (1710)
T KOG1070|consen 1692 YVKARAK 1698 (1710)
T ss_pred             HHHHHHH
Confidence            4444443

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.18  E-value=4.3e-08  Score=76.98  Aligned_cols=327  Identities=12%  Similarity=0.123  Sum_probs=183.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH-H
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV-I   92 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l   92 (376)
                      .++-.-..+.....+.++-++-....+.+...     .+--.+|.......-.+++|+++|.+.+..  .|.-...+. +
T Consensus       119 k~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----~EdqLSLAsvhYmR~HYQeAIdvYkrvL~d--n~ey~alNVy~  191 (557)
T KOG3785|consen  119 KTPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----LEDQLSLASVHYMRMHYQEAIDVYKRVLQD--NPEYIALNVYM  191 (557)
T ss_pred             CChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----HHHHHhHHHHHHHHHHHHHHHHHHHHHHhc--ChhhhhhHHHH
Confidence            33344444455556667766666665555432     233445566666666788999999888775  334444443 3


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHh--cCcHH-------------------------------
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFCL--TGKIN-------------------------------  138 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~--~~~~~-------------------------------  138 (376)
                      .-+|.+..-++-+.+++.-.++.  .|| ....+..+....+  .|+..                               
T Consensus       192 ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~~~l~rHNLVvFrn  269 (557)
T KOG3785|consen  192 ALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFIEYLCRHNLVVFRN  269 (557)
T ss_pred             HHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhHHHHHHcCeEEEeC
Confidence            44667777788888888777765  233 3333322222221  12211                               


Q ss_pred             --HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhcc-------chHH
Q 042039          139 --RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH-------QVEH  209 (376)
Q Consensus       139 --~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------~~~~  209 (376)
                        .|++++-.+.+    .-+.+...|+-.|.+.++.++|..+.+++..  .  ++.-|..-.-.....|       ...-
T Consensus       270 gEgALqVLP~L~~----~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~P--t--tP~EyilKgvv~aalGQe~gSreHlKi  341 (557)
T KOG3785|consen  270 GEGALQVLPSLMK----HIPEARLNLIIYYLNQNDVQEAISLCKDLDP--T--TPYEYILKGVVFAALGQETGSREHLKI  341 (557)
T ss_pred             CccHHHhchHHHh----hChHhhhhheeeecccccHHHHHHHHhhcCC--C--ChHHHHHHHHHHHHhhhhcCcHHHHHH
Confidence              11111111111    1233455677778889999999888776432  1  2222222222222223       3445


Q ss_pred             HHHHHHHHHhcCCCCC-cchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          210 ALKLFEEMQRDDVAAD-TSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       210 a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      |.+.|+.+-.++..-| ..--..++.++.-..++++.+..+..+..--.. |......++++++..|++.+|.++|-++.
T Consensus       342 AqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~N-dD~Fn~N~AQAk~atgny~eaEelf~~is  420 (557)
T KOG3785|consen  342 AQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTN-DDDFNLNLAQAKLATGNYVEAEELFIRIS  420 (557)
T ss_pred             HHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-cchhhhHHHHHHHHhcChHHHHHHHhhhc
Confidence            6666655544432222 223344555555566778877777776543322 33444567788888888888888887776


Q ss_pred             ccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHH-HHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          289 RRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVII-FVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       289 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      ...++.+..-...+.++|.+.+.++.|.+++-++..   +.+..+ ...+..-|.+.+++--|-+.|+.+....
T Consensus       421 ~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t---~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lD  491 (557)
T KOG3785|consen  421 GPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKTNT---PSERFSLLQLIANDCYKANEFYYAAKAFDELEILD  491 (557)
T ss_pred             ChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhcCC---chhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccC
Confidence            554443344445567788888888888777655432   223333 3333456777777777777777776543

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

Probab=99.17  E-value=1.6e-07  Score=77.75  Aligned_cols=321  Identities=14%  Similarity=0.049  Sum_probs=219.3

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      ++|...|..-..+|...|++++|++=-.+-.+.+ |.=+..|...+.++.-.|++++|+..|.+-++.... +...+..+
T Consensus        33 p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~-p~w~kgy~r~Gaa~~~lg~~~eA~~ay~~GL~~d~~-n~~L~~gl  110 (539)
T KOG0548|consen   33 PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLN-PDWAKGYSRKGAALFGLGDYEEAILAYSEGLEKDPS-NKQLKTGL  110 (539)
T ss_pred             CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcC-CchhhHHHHhHHHHHhcccHHHHHHHHHHHhhcCCc-hHHHHHhH
Confidence            4577888888889999999999988777666653 333678889999999999999999999888775322 44444444


Q ss_pred             HHHHHhC---C---------------------------------------------ChHHHHHHHHHHHh--------c-
Q 042039           93 MDELCKN---G---------------------------------------------KMDEASRLLDLMVQ--------R-  115 (376)
Q Consensus        93 ~~~~~~~---~---------------------------------------------~~~~a~~~~~~~~~--------~-  115 (376)
                      ..++...   +                                             +........-.+..        . 
T Consensus       111 ~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~l~d~r~m~a~~~l~~~~~~~~~~~~  190 (539)
T KOG0548|consen  111 AQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLYLNDPRLMKADGQLKGVDELLFYASG  190 (539)
T ss_pred             HHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhcccccHHHHHHHHHHhcCccccccccc
Confidence            4443111   0                                             00000000000000        0 


Q ss_pred             ------CCCCC---------h-------------hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039          116 ------DVRPN---------A-------------FTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYC  167 (376)
Q Consensus       116 ------~~~~~---------~-------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  167 (376)
                            +..|.         .             .-...+++...+..++..|.+.+.......  .+..-++....+|.
T Consensus       191 ~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~  268 (539)
T KOG0548|consen  191 IEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYL  268 (539)
T ss_pred             cccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHH
Confidence                  01110         0             113456677777888999999999988875  56667788888999


Q ss_pred             ccCcHHHHHHHHHHHHHCCCCCCHhH-------HHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcch------------
Q 042039          168 KNKEVEEALSLYREMVSKGIKPTVVT-------YNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTST------------  228 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~~~~~~~~~-------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~------------  228 (376)
                      ..|.+.+.........+.|.. ...-       +..+..++.+.++++.++..|.+.+.....|+...            
T Consensus       269 e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~  347 (539)
T KOG0548|consen  269 ERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEA  347 (539)
T ss_pred             hccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHH
Confidence            999988888888777665422 2222       23344566677888888888887765543332211            


Q ss_pred             -------------HHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC
Q 042039          229 -------------YNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD  295 (376)
Q Consensus       229 -------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  295 (376)
                                   ...-+..+.+.|++..|+..|.+++... +-|...|...+.+|.+.|.+..|++-.+...+. .++.
T Consensus       348 e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL-~p~~  425 (539)
T KOG0548|consen  348 ERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIEL-DPNF  425 (539)
T ss_pred             HHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-CchH
Confidence                         1222455778999999999999999887 448999999999999999999999988887776 4556


Q ss_pred             HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcH-HHHHHHHHHHh
Q 042039          296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV-IIFVTLIHGFV  342 (376)
Q Consensus       296 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~  342 (376)
                      ...|..=+.++....+|++|.+.|++.++.+  |+. .....+.++..
T Consensus       426 ~kgy~RKg~al~~mk~ydkAleay~eale~d--p~~~e~~~~~~rc~~  471 (539)
T KOG0548|consen  426 IKAYLRKGAALRAMKEYDKALEAYQEALELD--PSNAEAIDGYRRCVE  471 (539)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--chhHHHHHHHHHHHH
Confidence            6777777888888899999999999999864  443 33344444333

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

Probab=99.16  E-value=4.8e-08  Score=89.41  Aligned_cols=251  Identities=12%  Similarity=0.042  Sum_probs=186.3

Q ss_pred             hHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc-CCCC---ChhhHHHHHHHHHccCcHHHHHH
Q 042039          102 MDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM-GCKH---DDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      .+.|.++-+.++..  +.....|...+..+...++.++|.++.+++... ++.-   -...|.++++.-..-|.-+...+
T Consensus      1441 pesaeDferlvrss--PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~k 1518 (1710)
T KOG1070|consen 1441 PESAEDFERLVRSS--PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKK 1518 (1710)
T ss_pred             CcCHHHHHHHHhcC--CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHH
Confidence            33444444444332  334677888899999999999999999988653 1111   12356677777777777788889


Q ss_pred             HHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC
Q 042039          178 LYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC  257 (376)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  257 (376)
                      +|+++.+.  ......|..|...|.+.+.+++|.++++.|.+.- ......|...+..+.++++-+.|..++.++...-+
T Consensus      1519 VFeRAcqy--cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF-~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lP 1595 (1710)
T KOG1070|consen 1519 VFERACQY--CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKF-GQTRKVWIMYADFLLRQNEAEAARELLKRALKSLP 1595 (1710)
T ss_pred             HHHHHHHh--cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHh-cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcc
Confidence            99998884  3345678889999999999999999999998873 35678899999999999999999999999876432


Q ss_pred             C-chHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcH--HHH
Q 042039          258 E-LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV--IIF  334 (376)
Q Consensus       258 ~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~  334 (376)
                      . -........+..-.+.|+.+.+..+|+..+.. .|--...|+.++..-.+.|+.+.++.+|+++.+.++.|-.  ..|
T Consensus      1596 k~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~a-yPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfff 1674 (1710)
T KOG1070|consen 1596 KQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSA-YPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFF 1674 (1710)
T ss_pred             hhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhh-CccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHH
Confidence            2 13445555666778899999999999988876 5556788999999999999999999999999988777643  456


Q ss_pred             HHHHHHHhhcCChhhHHHHHHHHH
Q 042039          335 VTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       335 ~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      ...+..--+.|+-..+..+=.++.
T Consensus      1675 KkwLeyEk~~Gde~~vE~VKarA~ 1698 (1710)
T KOG1070|consen 1675 KKWLEYEKSHGDEKNVEYVKARAK 1698 (1710)
T ss_pred             HHHHHHHHhcCchhhHHHHHHHHH
Confidence            666665556677665554444433

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=99.15  E-value=1.4e-08  Score=79.91  Aligned_cols=187  Identities=9%  Similarity=-0.019  Sum_probs=115.3

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCCh---hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCch--Hh
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDV---VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV--VT   88 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~   88 (376)
                      .....+..+...+...|++++|...|+++.... |.+.   .++..++.++...|++++|...++++.+..+....  .+
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  109 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA  109 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH
Confidence            345566777777777788888888887776653 2222   45667777777778888888888877765332111  13


Q ss_pred             HHHHHHHHHhC--------CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHH
Q 042039           89 FNVIMDELCKN--------GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYN  160 (376)
Q Consensus        89 ~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  160 (376)
                      +..+..++...        |+.++|.+.++.+.+... .+......+.....    ...      ..        .....
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~a~~~~~~----~~~------~~--------~~~~~  170 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYP-NSEYAPDAKKRMDY----LRN------RL--------AGKEL  170 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCC-CChhHHHHHHHHHH----HHH------HH--------HHHHH
Confidence            44445555543        567777777777776531 12222211111100    000      00        01123


Q ss_pred             HHHHHHHccCcHHHHHHHHHHHHHCCC--CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          161 ILINGYCKNKEVEEALSLYREMVSKGI--KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      .+...+.+.|++++|+..++.+.+...  +.....+..++.++...|++++|..+++.+...
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            566778888999999999988887521  123567888888899999999999888877654

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).

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.13  E-value=5.2e-07  Score=85.79  Aligned_cols=338  Identities=12%  Similarity=-0.044  Sum_probs=204.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCC
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG  100 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  100 (376)
                      .....+...|++.+|...+......  ..-..............|+++.+..+++.+.......+..........+...|
T Consensus       346 raa~~~~~~g~~~~Al~~a~~a~d~--~~~~~ll~~~a~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g  423 (903)
T PRK04841        346 AAAEAWLAQGFPSEAIHHALAAGDA--QLLRDILLQHGWSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQH  423 (903)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHCCCH--HHHHHHHHHhHHHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCC
Confidence            3344455566666555544333211  00011222233445566787777777766522111112223344455667889


Q ss_pred             ChHHHHHHHHHHHhcCC------CCC--hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCCh----hhHHHHHHHHHc
Q 042039          101 KMDEASRLLDLMVQRDV------RPN--AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDD----VSYNILINGYCK  168 (376)
Q Consensus       101 ~~~~a~~~~~~~~~~~~------~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~  168 (376)
                      +++++..++......-.      .+.  ......+...+...|+++.|...++.........+.    .....+...+..
T Consensus       424 ~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~  503 (903)
T PRK04841        424 RYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHC  503 (903)
T ss_pred             CHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHH
Confidence            99999999988765311      111  122233445567889999999999998763211121    244567777888


Q ss_pred             cCcHHHHHHHHHHHHHCCC---CC--CHhHHHHHHHHHHhccchHHHHHHHHHHHhc----CCCC---CcchHHHHHHHH
Q 042039          169 NKEVEEALSLYREMVSKGI---KP--TVVTYNTLFLGLFEIHQVEHALKLFEEMQRD----DVAA---DTSTYNTFIDGL  236 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~---~~~~~~~l~~~~  236 (376)
                      .|++++|...+++......   .+  ...+...+...+...|+++.|...+++....    +...   ....+..+...+
T Consensus       504 ~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~  583 (903)
T PRK04841        504 KGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLL  583 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHH
Confidence            9999999999998875311   11  1234556677888999999999998876553    2111   122344556667


Q ss_pred             HhCCCHHHHHHHHHHhccc----CCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC--CCCCHH--HH--HHHHHHH
Q 042039          237 CKNGYIVEAVELFRTLGIL----KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV--LVADVV--TY--NIMIHGL  306 (376)
Q Consensus       237 ~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~--~~--~~l~~~~  306 (376)
                      ...|++++|...+......    +.......+..++..+...|+++.|...+..+....  ......  ..  ...+..+
T Consensus       584 ~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~  663 (903)
T PRK04841        584 WEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYW  663 (903)
T ss_pred             HHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHH
Confidence            7889999999998887442    111123455567778889999999999988764321  111111  00  1122344


Q ss_pred             HccCChhHHHHHHHHHHHcCCCCc---HHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          307 CNDGQMDKAHDLFLDMEENAVAPN---VIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       307 ~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      ...|+.+.|...+...........   ...+..+..++...|++++|...+++..+.
T Consensus       664 ~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~  720 (903)
T PRK04841        664 QMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNEN  720 (903)
T ss_pred             HHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            568899999998877654221111   112445677888999999999999988753

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

Probab=99.11  E-value=1.2e-07  Score=85.70  Aligned_cols=242  Identities=10%  Similarity=0.115  Sum_probs=136.8

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV   91 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   91 (376)
                      -+.+...|..|+..+...+++++|.++.+...+.. |.....|..++..+.+.++..++.-+  .+              
T Consensus        27 ~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~-P~~i~~yy~~G~l~~q~~~~~~~~lv--~~--------------   89 (906)
T PRK14720         27 SLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEH-KKSISALYISGILSLSRRPLNDSNLL--NL--------------   89 (906)
T ss_pred             CcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CcceehHHHHHHHHHhhcchhhhhhh--hh--------------
Confidence            34556677777777777777777777777665553 43445555555566666665544433  22              


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  171 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  171 (376)
                       +.......++.-...++..+...  .-+..++..++.+|-+.|+.++|..+|+++.+.. +.++.+.+.++..|... +
T Consensus        90 -l~~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-d  164 (906)
T PRK14720         90 -IDSFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-D  164 (906)
T ss_pred             -hhhcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-h
Confidence             22222233333333344444442  2244567777777777888888888888887776 66777777777777777 7


Q ss_pred             HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHH
Q 042039          172 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRT  251 (376)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  251 (376)
                      .++|.+++.++...               +...+++..+..+|.++.... +.+...+..+.+.....-           
T Consensus       165 L~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~-~~d~d~f~~i~~ki~~~~-----------  217 (906)
T PRK14720        165 KEKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYN-SDDFDFFLRIERKVLGHR-----------  217 (906)
T ss_pred             HHHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcC-cccchHHHHHHHHHHhhh-----------
Confidence            77777777776653               444556666666666666553 222222222222111110           


Q ss_pred             hcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHH
Q 042039          252 LGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLC  307 (376)
Q Consensus       252 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  307 (376)
                          +..--..++..+-..|...++++++..+++.+.+. .+.|......++.+|.
T Consensus       218 ----~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~-~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        218 ----EFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEH-DNKNNKAREELIRFYK  268 (906)
T ss_pred             ----ccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhc-CCcchhhHHHHHHHHH
Confidence                11112334444555556666666666666666655 2334445555555554

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

Probab=99.10  E-value=1.5e-08  Score=86.67  Aligned_cols=221  Identities=11%  Similarity=0.109  Sum_probs=169.5

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +|--..=..+.+.+...|-...|+.+|++..         .|..++.+|...|+..+|..+..+.++.  +|+...|..+
T Consensus       395 pp~Wq~q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~L  463 (777)
T KOG1128|consen  395 PPIWQLQRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLL  463 (777)
T ss_pred             CCcchHHHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHh
Confidence            3333444556778888899999999988765         4666788888899889998888887773  6677777777


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      +......--+++|.++.+..-.       .+-..+.......++++++.+.|+.-...+ +....+|..++.+..+.+++
T Consensus       464 GDv~~d~s~yEkawElsn~~sa-------rA~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~  535 (777)
T KOG1128|consen  464 GDVLHDPSLYEKAWELSNYISA-------RAQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKE  535 (777)
T ss_pred             hhhccChHHHHHHHHHhhhhhH-------HHHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhh
Confidence            7766555556777776655432       233344444555788999999998888776 66778888889999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      +.|.+.|...... -+.+...|+++..+|.+.++..+|...+.+..+.+ ..+...+...+....+.|.+++|++.+.++
T Consensus       536 q~av~aF~rcvtL-~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rl  613 (777)
T KOG1128|consen  536 QAAVKAFHRCVTL-EPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRL  613 (777)
T ss_pred             HHHHHHHHHHhhc-CCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHH
Confidence            9999999888874 23357789999999999999999999999998887 566777777788888899999999988887


Q ss_pred             cc
Q 042039          253 GI  254 (376)
Q Consensus       253 ~~  254 (376)
                      ..
T Consensus       614 l~  615 (777)
T KOG1128|consen  614 LD  615 (777)
T ss_pred             HH
Confidence            54

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

Probab=99.08  E-value=8.6e-08  Score=72.39  Aligned_cols=152  Identities=11%  Similarity=0.125  Sum_probs=103.5

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChH
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMD  103 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  103 (376)
                      -.|...|+++......+.+...   ..         .+...++.+++...+++.++.++. +...|..+...+...|+++
T Consensus        24 ~~Y~~~g~~~~v~~~~~~~~~~---~~---------~~~~~~~~~~~i~~l~~~L~~~P~-~~~~w~~Lg~~~~~~g~~~   90 (198)
T PRK10370         24 GSYLLSPKWQAVRAEYQRLADP---LH---------QFASQQTPEAQLQALQDKIRANPQ-NSEQWALLGEYYLWRNDYD   90 (198)
T ss_pred             HHHHHcchHHHHHHHHHHHhCc---cc---------cccCchhHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHCCCHH
Confidence            3577778877765444322211   00         111255667777777777776433 6777888888888888888


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHH-HhcCc--HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHH
Q 042039          104 EASRLLDLMVQRDVRPNAFTYSTLMDGF-CLTGK--INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR  180 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  180 (376)
                      +|...|++..+.. +.+...+..+..++ ...|+  .++|.+++++..+.+ +.+..++..++..+.+.|++++|+..|+
T Consensus        91 ~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~  168 (198)
T PRK10370         91 NALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQ  168 (198)
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHH
Confidence            8888888888764 33566777777653 56666  478888888888776 5677778888888888888888888888


Q ss_pred             HHHHCCCCCCH
Q 042039          181 EMVSKGIKPTV  191 (376)
Q Consensus       181 ~~~~~~~~~~~  191 (376)
                      ++++. .+|+.
T Consensus       169 ~aL~l-~~~~~  178 (198)
T PRK10370        169 KVLDL-NSPRV  178 (198)
T ss_pred             HHHhh-CCCCc
Confidence            88775 33443

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

Probab=99.07  E-value=1e-07  Score=71.90  Aligned_cols=158  Identities=15%  Similarity=0.095  Sum_probs=77.4

Q ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc
Q 042039          125 STLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       125 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  204 (376)
                      ..+...+...|+-+....+........ +.+......++....+.|++..|+..++++... -++|...|+.+.-+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~-~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAY-PKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccC-cccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHc
Confidence            344444444455444444444433221 333334444555555555555555555555443 234455555555555555


Q ss_pred             cchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHH
Q 042039          205 HQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELF  284 (376)
Q Consensus       205 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  284 (376)
                      |+++.|..-|.+..+.. +.++..++.++..+.-.|+.+.|..++........ -+..+-..+..+....|++++|.++.
T Consensus       148 Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         148 GRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             cChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHhhc
Confidence            55555555555554442 33444455555555555555555555555444331 24444455555555555555555544


Q ss_pred             hc
Q 042039          285 RS  286 (376)
Q Consensus       285 ~~  286 (376)
                      ..
T Consensus       226 ~~  227 (257)
T COG5010         226 VQ  227 (257)
T ss_pred             cc
Confidence            33

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

Probab=99.07  E-value=1.7e-07  Score=84.74  Aligned_cols=241  Identities=14%  Similarity=0.111  Sum_probs=173.2

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      +.+...+..|+..+...+++++|.++.+..++..+. ....|..++..+.+.++...+..+                 .+
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~-~i~~yy~~G~l~~q~~~~~~~~lv-----------------~~   89 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKK-SISALYISGILSLSRRPLNDSNLL-----------------NL   89 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCc-ceehHHHHHHHHHhhcchhhhhhh-----------------hh
Confidence            446788999999999999999999999987776322 344555555567777775554444                 23


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccch
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV  207 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  207 (376)
                      +.......++....-++..+...  +.+..++..++.+|-+.|+.++|..+|+++++.. +-++.+.+.+...|... +.
T Consensus        90 l~~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL  165 (906)
T PRK14720         90 IDSFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DK  165 (906)
T ss_pred             hhhcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hH
Confidence            33333344454444444455543  3455688899999999999999999999999975 55788999999999988 99


Q ss_pred             HHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcc
Q 042039          208 EHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSL  287 (376)
Q Consensus       208 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  287 (376)
                      ++|.+++.++...               +...+++.++.++|..+....+. +...+..+.+.....-.+          
T Consensus       166 ~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~~~-d~d~f~~i~~ki~~~~~~----------  219 (906)
T PRK14720        166 EKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYNSD-DFDFFLRIERKVLGHREF----------  219 (906)
T ss_pred             HHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcCcc-cchHHHHHHHHHHhhhcc----------
Confidence            9999999888664               66677899999999999877533 444444444433222111          


Q ss_pred             cccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHh
Q 042039          288 PRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFV  342 (376)
Q Consensus       288 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  342 (376)
                           .--..++..+...|...++++++..+++.+++.... |......++.+|.
T Consensus       220 -----~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~-n~~a~~~l~~~y~  268 (906)
T PRK14720        220 -----TRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNK-NNKAREELIRFYK  268 (906)
T ss_pred             -----chhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCc-chhhHHHHHHHHH
Confidence                 113445667778888999999999999999987544 6667777888776

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=99.07  E-value=8.9e-08  Score=75.38  Aligned_cols=187  Identities=12%  Similarity=0.018  Sum_probs=131.8

Q ss_pred             CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC-C-chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh---hh
Q 042039           49 PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ-P-SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA---FT  123 (376)
Q Consensus        49 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~  123 (376)
                      .....+..++..+...|++++|...|++++...+. | ...++..+..++...|++++|...++++++.... +.   .+
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~a  109 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN-HPDADYA  109 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-CCchHHH
Confidence            45677888889999999999999999999876332 1 1246677888999999999999999999876421 22   24


Q ss_pred             HHHHHHHHHhc--------CcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHH
Q 042039          124 YSTLMDGFCLT--------GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYN  195 (376)
Q Consensus       124 ~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  195 (376)
                      +..+..++...        |+++.|.+.++.+.... |.+...+..+.....    ....       .       .....
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~~~~----~~~~-------~-------~~~~~  170 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY-PNSEYAPDAKKRMDY----LRNR-------L-------AGKEL  170 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC-CCChhHHHHHHHHHH----HHHH-------H-------HHHHH
Confidence            55666666554        67888888888887764 333223322211111    0000       0       01123


Q ss_pred             HHHHHHHhccchHHHHHHHHHHHhcCC--CCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          196 TLFLGLFEIHQVEHALKLFEEMQRDDV--AADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       196 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      .+...+.+.|++++|...+..+.....  +.....+..++.++...|++++|..+++.+...
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            566778999999999999999987631  223568899999999999999999999887654

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).

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

Probab=99.05  E-value=5.9e-06  Score=68.95  Aligned_cols=151  Identities=11%  Similarity=0.129  Sum_probs=117.2

Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc-hHHHHHHHHHHHHhCCChHHHHHHHh
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCEL-DIQAYNCLIDGLCKSGRLEIALELFR  285 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~  285 (376)
                      .+....++++++......-.-+|..++..-.+..-...|..+|.++.+.+..+ +..+..+++..++ .++.+-|.++|+
T Consensus       347 ~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFe  425 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFE  425 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHH
Confidence            45556666666554333344567778888888888999999999998877666 5666777777665 688999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc--HHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          286 SLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN--VIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       286 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .-.+. ...++......+.-+...++-..|..+|++....++.|+  ..+|..++..-..-|+...+.++-+++..
T Consensus       426 LGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  426 LGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            86665 455566667788888899999999999999998865554  57899999988889999999999888764

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

Probab=99.04  E-value=1.8e-07  Score=70.59  Aligned_cols=164  Identities=15%  Similarity=0.082  Sum_probs=122.3

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      |... ..+...+...|+-+....+........ +.+.......+....+.|++..|...+++..... |+|...|+.+.-
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~-~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lga  142 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAY-PKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGA  142 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccC-cccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHH
Confidence            3444 556667777777777777777655432 3345555667888888888888888888887776 778888888888


Q ss_pred             HHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHH
Q 042039          165 GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVE  244 (376)
Q Consensus       165 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  244 (376)
                      +|.+.|++++|..-|.+..+. .+-++...+.+...+.-.|+.+.|..++....... +-+..+-..+.......|++++
T Consensus       143 aldq~Gr~~~Ar~ay~qAl~L-~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~  220 (257)
T COG5010         143 ALDQLGRFDEARRAYRQALEL-APNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFRE  220 (257)
T ss_pred             HHHHccChhHHHHHHHHHHHh-ccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHH
Confidence            888888888888888888875 23356677888888888888888888888877664 4467777888888888888888


Q ss_pred             HHHHHHHhc
Q 042039          245 AVELFRTLG  253 (376)
Q Consensus       245 a~~~~~~~~  253 (376)
                      |.++...-.
T Consensus       221 A~~i~~~e~  229 (257)
T COG5010         221 AEDIAVQEL  229 (257)
T ss_pred             HHhhccccc
Confidence            888766543

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.04  E-value=1.7e-07  Score=81.69  Aligned_cols=309  Identities=15%  Similarity=0.101  Sum_probs=175.0

Q ss_pred             ChhhHHHHHH--HHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc-C--------CC
Q 042039           15 NTVTYNTIID--GLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ-G--------VQ   83 (376)
Q Consensus        15 ~~~~~~~l~~--~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~--------~~   83 (376)
                      |..+-.++++  .|...|+.+.|.+-.+.++      +...|..+...|.+..+++-|.-.+-.|... |        ..
T Consensus       725 d~~TRkaml~FSfyvtiG~MD~AfksI~~Ik------S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~  798 (1416)
T KOG3617|consen  725 DESTRKAMLDFSFYVTIGSMDAAFKSIQFIK------SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQN  798 (1416)
T ss_pred             CHHHHHhhhceeEEEEeccHHHHHHHHHHHh------hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhC
Confidence            4445555553  4667899999988877666      4468899999999998888777666555331 0        11


Q ss_pred             CchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           84 PSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILI  163 (376)
Q Consensus        84 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  163 (376)
                      |+ .+-....-.....|.+++|..+|++..+.         ..+-..|...|.+++|.++-+.-....   -..+|....
T Consensus       799 ~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~---------DLlNKlyQs~g~w~eA~eiAE~~DRiH---Lr~Tyy~yA  865 (1416)
T KOG3617|consen  799 GE-EDEAKVAVLAIELGMLEEALILYRQCKRY---------DLLNKLYQSQGMWSEAFEIAETKDRIH---LRNTYYNYA  865 (1416)
T ss_pred             Cc-chhhHHHHHHHHHhhHHHHHHHHHHHHHH---------HHHHHHHHhcccHHHHHHHHhhcccee---hhhhHHHHH
Confidence            21 22233344556788899999999887654         234455667788888888766543322   123566666


Q ss_pred             HHHHccCcHHHHHHHHHHHH----------HCC---------CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC
Q 042039          164 NGYCKNKEVEEALSLYREMV----------SKG---------IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA  224 (376)
Q Consensus       164 ~~~~~~~~~~~a~~~~~~~~----------~~~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  224 (376)
                      ..+...+|.+.|++.|++..          ...         -..+...|......+...|+.+.|+.+|.....     
T Consensus       866 ~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D-----  940 (1416)
T KOG3617|consen  866 KYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD-----  940 (1416)
T ss_pred             HHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh-----
Confidence            66677778888887776431          110         112344555556666667777777777766543     


Q ss_pred             CcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc----------CC--
Q 042039          225 DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR----------VL--  292 (376)
Q Consensus       225 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----------~~--  292 (376)
                          |..+++..+-.|+.++|-++-++-      .|......+++.|...|++.+|..+|.++...          +.  
T Consensus       941 ----~fs~VrI~C~qGk~~kAa~iA~es------gd~AAcYhlaR~YEn~g~v~~Av~FfTrAqafsnAIRlcKEnd~~d 1010 (1416)
T KOG3617|consen  941 ----YFSMVRIKCIQGKTDKAARIAEES------GDKAACYHLARMYENDGDVVKAVKFFTRAQAFSNAIRLCKENDMKD 1010 (1416)
T ss_pred             ----hhhheeeEeeccCchHHHHHHHhc------ccHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCHHH
Confidence                233333444445555555444431      13344445555555555555555555443210          00  


Q ss_pred             ----------CCC-----------HHHHHHHHHHHHccCChhHHHHHHHH--------HHHc--CCCCcHHHHHHHHHHH
Q 042039          293 ----------VAD-----------VVTYNIMIHGLCNDGQMDKAHDLFLD--------MEEN--AVAPNVIIFVTLIHGF  341 (376)
Q Consensus       293 ----------~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~--------~~~~--~~~~~~~~~~~l~~~~  341 (376)
                                +.|           ..-+...+..|-+.|.+.+|+++.=+        ++..  ....|+...+.-...+
T Consensus      1011 ~L~nlal~s~~~d~v~aArYyEe~g~~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF 1090 (1416)
T KOG3617|consen 1011 RLANLALMSGGSDLVSAARYYEELGGYAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFF 1090 (1416)
T ss_pred             HHHHHHhhcCchhHHHHHHHHHHcchhhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence                      000           00112233345566666666554211        1111  2234566666666777


Q ss_pred             hhcCChhhHHHHHHHH
Q 042039          342 VRINKPSKVIELLHKM  357 (376)
Q Consensus       342 ~~~g~~~~a~~~~~~~  357 (376)
                      ....++++|..++-..
T Consensus      1091 ~~~~qyekAV~lL~~a 1106 (1416)
T KOG3617|consen 1091 ENNQQYEKAVNLLCLA 1106 (1416)
T ss_pred             HhHHHHHHHHHHHHHH
Confidence            7777777777665444

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

Probab=99.03  E-value=3.3e-08  Score=74.60  Aligned_cols=126  Identities=10%  Similarity=0.104  Sum_probs=107.8

Q ss_pred             cCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH-HhCCC--hHHH
Q 042039           29 EGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL-CKNGK--MDEA  105 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~--~~~a  105 (376)
                      .++.++++..++...+.+ |.+...|..++..|...|++++|...|++..+.... +...+..+..++ ...|+  .++|
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-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGE-NAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCCCCcHHH
Confidence            566788888888888776 889999999999999999999999999999997544 778888888864 67777  5999


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhh
Q 042039          106 SRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVS  158 (376)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  158 (376)
                      ..++++.++.+ +.+..++..++..+...|++++|...|+++.+.. +|+..-
T Consensus       130 ~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~-~~~~~r  180 (198)
T PRK10370        130 REMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQKVLDLN-SPRVNR  180 (198)
T ss_pred             HHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCccH
Confidence            99999999985 4478899999999999999999999999999886 454433

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.02  E-value=9e-07  Score=77.36  Aligned_cols=192  Identities=16%  Similarity=0.056  Sum_probs=121.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCC--------CCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGEN--------INPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS   85 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~   85 (376)
                      .+...|..+.+.|.+..+++-|.-.+-.|....        ...+...=..........|-+++|..+|.+-.+      
T Consensus       755 kS~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~e~eakvAvLAieLgMlEeA~~lYr~ckR------  828 (1416)
T KOG3617|consen  755 KSDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGEEDEAKVAVLAIELGMLEEALILYRQCKR------  828 (1416)
T ss_pred             hhhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCcchhhHHHHHHHHHhhHHHHHHHHHHHHH------
Confidence            345689999999999999888876666654321        011112223344445677889999999988755      


Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHh----------cC----
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMES----------MG----  151 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----------~~----  151 (376)
                         |..+=..|-..|.+++|.++-+.--+.  . =..||...+..+-..++.+.|++.|++...          ..    
T Consensus       829 ---~DLlNKlyQs~g~w~eA~eiAE~~DRi--H-Lr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~  902 (1416)
T KOG3617|consen  829 ---YDLLNKLYQSQGMWSEAFEIAETKDRI--H-LRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQI  902 (1416)
T ss_pred             ---HHHHHHHHHhcccHHHHHHHHhhccce--e-hhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHH
Confidence               234445677788888888776533221  1 135677777777778888888888776321          11    


Q ss_pred             -----CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC--------------------CCCCHhHHHHHHHHHHhccc
Q 042039          152 -----CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG--------------------IKPTVVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       152 -----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------------------~~~~~~~~~~l~~~~~~~~~  206 (376)
                           ...+...|.-.+...-..|+.+.|+.+|..+.+.-                    -..|......+.+.|...|+
T Consensus       903 e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D~fs~VrI~C~qGk~~kAa~iA~esgd~AAcYhlaR~YEn~g~  982 (1416)
T KOG3617|consen  903 EQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKDYFSMVRIKCIQGKTDKAARIAEESGDKAACYHLARMYENDGD  982 (1416)
T ss_pred             HHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhhhhhheeeEeeccCchHHHHHHHhcccHHHHHHHHHHhhhhHH
Confidence                 12345566667777778888899988888776520                    01133444556666666667


Q ss_pred             hHHHHHHHHHH
Q 042039          207 VEHALKLFEEM  217 (376)
Q Consensus       207 ~~~a~~~~~~~  217 (376)
                      +.+|..+|.+.
T Consensus       983 v~~Av~FfTrA  993 (1416)
T KOG3617|consen  983 VVKAVKFFTRA  993 (1416)
T ss_pred             HHHHHHHHHHH
Confidence            77776666554

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

Probab=99.00  E-value=1.5e-07  Score=83.56  Aligned_cols=165  Identities=11%  Similarity=0.068  Sum_probs=109.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC-CCchHhHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV-QPSVVTFNVIMDE   95 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~   95 (376)
                      ..|..|...|....+...|...|+..-+.+ +.+..........|++..+++.|..+.-..-+... ..-...|....-.
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~y  571 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPY  571 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhcccc
Confidence            357777777777777778888888777765 55677777788888888888888777333222110 0012233344445


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      |.+.++...+..-|+...+.+ +.|...|..++.+|..+|++..|.++|.++.... |.+...-.......+..|.+.+|
T Consensus       572 yLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr-P~s~y~~fk~A~~ecd~GkYkea  649 (1238)
T KOG1127|consen  572 YLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLLR-PLSKYGRFKEAVMECDNGKYKEA  649 (1238)
T ss_pred             ccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhcC-cHhHHHHHHHHHHHHHhhhHHHH
Confidence            667777777887777777664 3467788888888888888888888888877664 33333333344455667777777


Q ss_pred             HHHHHHHHH
Q 042039          176 LSLYREMVS  184 (376)
Q Consensus       176 ~~~~~~~~~  184 (376)
                      +..+...+.
T Consensus       650 ld~l~~ii~  658 (1238)
T KOG1127|consen  650 LDALGLIIY  658 (1238)
T ss_pred             HHHHHHHHH
Confidence            777766543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=99.00  E-value=7.9e-08  Score=68.68  Aligned_cols=94  Identities=9%  Similarity=-0.047  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  168 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  168 (376)
                      +..+...+...|++++|...|+.++... +.+...+..++.++...|++++|...|+++.... |.+...+..++.++..
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~  104 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKM  104 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHH
Confidence            3344555555566666666666655543 3345555556666666666666666666665554 4455555566666666


Q ss_pred             cCcHHHHHHHHHHHHH
Q 042039          169 NKEVEEALSLYREMVS  184 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~  184 (376)
                      .|++++|+..|+..++
T Consensus       105 ~g~~~eAi~~~~~Al~  120 (144)
T PRK15359        105 MGEPGLAREAFQTAIK  120 (144)
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            6666666666666555

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=99.00  E-value=7.6e-08  Score=68.75  Aligned_cols=122  Identities=14%  Similarity=0.011  Sum_probs=87.3

Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           36 KALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      ..++++..+.+  |  ..+..+...+...|++++|...|+.+....+. +...|..+..++...|++++|...|+.....
T Consensus        13 ~~~~~~al~~~--p--~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l   87 (144)
T PRK15359         13 EDILKQLLSVD--P--ETVYASGYASWQEGDYSRAVIDFSWLVMAQPW-SWRAHIALAGTWMMLKEYTTAINFYGHALML   87 (144)
T ss_pred             HHHHHHHHHcC--H--HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            34556665542  2  23556677778888888888888888776433 6777788888888888888888888888876


Q ss_pred             CCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039          116 DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus       116 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      + +.+...+..++.++...|++++|...|+...... |.++..+.....
T Consensus        88 ~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~-p~~~~~~~~~~~  134 (144)
T PRK15359         88 D-ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMS-YADASWSEIRQN  134 (144)
T ss_pred             C-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            4 4467778888888888888888888888887765 445555544443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.99  E-value=1.7e-07  Score=83.81  Aligned_cols=146  Identities=9%  Similarity=0.050  Sum_probs=119.4

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      +.++..+..|.....+.|++++|..+++.+.+..+. +......++..+.+.+++++|...+++.+... +-+......+
T Consensus        83 ~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd-~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~  160 (694)
T PRK15179         83 PHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPD-SSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLE  160 (694)
T ss_pred             cccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCC-cHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHH
Confidence            556888889999999999999999999999886433 56678888889999999999999999999875 3357778888


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHH
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTL  197 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  197 (376)
                      ..++.+.|++++|..+|+++...+ +.+..++..+..++...|+.++|...|++..+. ..+....|+.+
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~-~~~~~~~~~~~  228 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLDA-IGDGARKLTRR  228 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-hCcchHHHHHH
Confidence            889999999999999999998843 566888999999999999999999999998875 23334444433

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.99  E-value=3.4e-07  Score=81.91  Aligned_cols=135  Identities=12%  Similarity=0.097  Sum_probs=81.2

Q ss_pred             CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHH
Q 042039          153 KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTF  232 (376)
Q Consensus       153 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  232 (376)
                      +.++..+..|..+..+.|.+++|..+++.+.+. .+-+......++..+.+.+++++|...+++..... +.+......+
T Consensus        83 ~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~-~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~  160 (694)
T PRK15179         83 PHTELFQVLVARALEAAHRSDEGLAVWRGIHQR-FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLE  160 (694)
T ss_pred             cccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh-CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHH
Confidence            344566666666666666666666666666663 12234555556666666666666666666666554 4455556666


Q ss_pred             HHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          233 IDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       233 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      +.++.+.|++++|..+|+++...+ +-+..++..++.++...|+.++|...|+.+.+.
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            666666666666666666666533 224556666666666666666666666665544

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.95  E-value=1.9e-06  Score=64.75  Aligned_cols=161  Identities=15%  Similarity=0.063  Sum_probs=75.0

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      .++-+....|+.+-|...++++...- +-+..+-..-+-.+-..|++++|.++++.+.+.+ |.+..++-.-+.+.-..|
T Consensus        57 qV~IAAld~~~~~lAq~C~~~L~~~f-p~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~G  134 (289)
T KOG3060|consen   57 QVFIAALDTGRDDLAQKCINQLRDRF-PGSKRVGKLKAMLLEATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQG  134 (289)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHhhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcC
Confidence            33444445555555555555554442 2222222222223334455555555555555544 334444444444444444


Q ss_pred             cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC---CHHHHHH
Q 042039          171 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG---YIVEAVE  247 (376)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~  247 (376)
                      +.-+|++-+....+. +..|...|..+...|...|++++|.-.+++++-.. |.++..+..+...+.-.|   +...+.+
T Consensus       135 K~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~ark  212 (289)
T KOG3060|consen  135 KNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQ-PFNPLYFQRLAEVLYTQGGAENLELARK  212 (289)
T ss_pred             CcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            444555555555544 34455555555555555555555555555554442 333334444444333222   3344455


Q ss_pred             HHHHhccc
Q 042039          248 LFRTLGIL  255 (376)
Q Consensus       248 ~~~~~~~~  255 (376)
                      +|.+..+.
T Consensus       213 yy~~alkl  220 (289)
T KOG3060|consen  213 YYERALKL  220 (289)
T ss_pred             HHHHHHHh
Confidence            55554443

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

Probab=98.94  E-value=1.1e-06  Score=66.47  Aligned_cols=235  Identities=12%  Similarity=0.033  Sum_probs=99.7

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChH
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMD  103 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  103 (376)
                      +-+.-.|++..++..-+.....  +.+...-..+.++|...|++.....-.   ... -.|.......+......-++.+
T Consensus        16 Rn~fY~Gnyq~~ine~~~~~~~--~~~~e~d~y~~raylAlg~~~~~~~eI---~~~-~~~~lqAvr~~a~~~~~e~~~~   89 (299)
T KOG3081|consen   16 RNYFYLGNYQQCINEAEKFSSS--KTDVELDVYMYRAYLALGQYQIVISEI---KEG-KATPLQAVRLLAEYLELESNKK   89 (299)
T ss_pred             HHHHHhhHHHHHHHHHHhhccc--cchhHHHHHHHHHHHHccccccccccc---ccc-cCChHHHHHHHHHHhhCcchhH
Confidence            3444456666665554444332  123334444555555555544433222   111 1223333333333222233333


Q ss_pred             HHHH-HHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          104 EASR-LLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       104 ~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      +... +.+.+.......+......-+..|++.|++++|++......      +..+...=..++.+..+++-|.+.+++|
T Consensus        90 ~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~~lk~m  163 (299)
T KOG3081|consen   90 SILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEKELKKM  163 (299)
T ss_pred             HHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2222 22223222222222222333444555555555555554411      2222222233444455555555555555


Q ss_pred             HHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC
Q 042039          183 VSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE  258 (376)
Q Consensus       183 ~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  258 (376)
                      .+.   .+..+.+.|..++.+    .+....|.-+|+++.+. .+|++.+.+..+.++...|++++|..+++.+......
T Consensus       164 q~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~  239 (299)
T KOG3081|consen  164 QQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK  239 (299)
T ss_pred             Hcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC
Confidence            542   133444444444432    23344555555555443 2445555555555555555555555555555444322


Q ss_pred             chHHHHHHHHHHHHhCC
Q 042039          259 LDIQAYNCLIDGLCKSG  275 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~  275 (376)
                       ++.+...++..-...|
T Consensus       240 -dpetL~Nliv~a~~~G  255 (299)
T KOG3081|consen  240 -DPETLANLIVLALHLG  255 (299)
T ss_pred             -CHHHHHHHHHHHHHhC
Confidence             3444444443333333

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

Probab=98.93  E-value=1.9e-06  Score=65.23  Aligned_cols=251  Identities=13%  Similarity=0.051  Sum_probs=174.6

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                      ++-+.-.|.+..++..-.......  .+...-..+.++|...|++.....-   +... -.|....+..+......-++.
T Consensus        15 iRn~fY~Gnyq~~ine~~~~~~~~--~~~e~d~y~~raylAlg~~~~~~~e---I~~~-~~~~lqAvr~~a~~~~~e~~~   88 (299)
T KOG3081|consen   15 IRNYFYLGNYQQCINEAEKFSSSK--TDVELDVYMYRAYLALGQYQIVISE---IKEG-KATPLQAVRLLAEYLELESNK   88 (299)
T ss_pred             HHHHHHhhHHHHHHHHHHhhcccc--chhHHHHHHHHHHHHcccccccccc---cccc-cCChHHHHHHHHHHhhCcchh
Confidence            455556788888877766654432  3555566677888888887654332   2222 234444555555544444554


Q ss_pred             HHHH-HHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHH
Q 042039          138 NRAE-ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEE  216 (376)
Q Consensus       138 ~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  216 (376)
                      +.-. ++.+.+.......+......-+..|.+.+++++|++......      +......-...+.+..+.+.|.+.+++
T Consensus        89 ~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~~lk~  162 (299)
T KOG3081|consen   89 KSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEKELKK  162 (299)
T ss_pred             HHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444 444445444333444455556678999999999999988722      344445556677788999999999999


Q ss_pred             HHhcCCCCCcchHHHHHHHHHh----CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCC
Q 042039          217 MQRDDVAADTSTYNTFIDGLCK----NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVL  292 (376)
Q Consensus       217 ~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  292 (376)
                      |...+   +..+.+.++.++.+    .+....|.-+|+++.+.- +|++.+.+..+.++...|++++|..+++.+... .
T Consensus       163 mq~id---ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k~-~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k-d  237 (299)
T KOG3081|consen  163 MQQID---EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEKT-PPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK-D  237 (299)
T ss_pred             HHccc---hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhccc-CCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc-c
Confidence            98754   66778878888765    456899999999998744 679999999999999999999999999999877 4


Q ss_pred             CCCHHHHHHHHHHHHccCChhH-HHHHHHHHHHc
Q 042039          293 VADVVTYNIMIHGLCNDGQMDK-AHDLFLDMEEN  325 (376)
Q Consensus       293 ~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~  325 (376)
                      ..++.+...++.+-...|...+ ..+.+.++...
T Consensus       238 ~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  238 AKDPETLANLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             CCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            5577888777777777776654 45666666654

>PF12854 PPR_1: PPR repeat

Probab=98.92  E-value=1.8e-09  Score=55.03  Aligned_cols=34  Identities=59%  Similarity=0.960  Sum_probs=29.1

Q ss_pred             cccCCChhhHHHHHHHHHhcCChhHHHHHHHHhh
Q 042039           10 VVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMK   43 (376)
Q Consensus        10 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~   43 (376)
                      .|++||..+|+.+|.+|++.|++++|.++|++|.
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3678999999999999999999999999988874

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

Probab=98.90  E-value=9.3e-07  Score=78.74  Aligned_cols=183  Identities=12%  Similarity=0.037  Sum_probs=137.4

Q ss_pred             ChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHH
Q 042039           31 FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLD  110 (376)
Q Consensus        31 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  110 (376)
                      +...|+..|-+..+.. +.=...|..|+..|....+...|.+.|+++.+.... +...+......|++..+++.|..+.-
T Consensus       473 ~~~~al~ali~alrld-~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDat-daeaaaa~adtyae~~~we~a~~I~l  550 (1238)
T KOG1127|consen  473 NSALALHALIRALRLD-VSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDAT-DAEAAAASADTYAEESTWEEAFEICL  550 (1238)
T ss_pred             hHHHHHHHHHHHHhcc-cchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCch-hhhhHHHHHHHhhccccHHHHHHHHH
Confidence            3777777777777664 334568899999999888999999999999886433 67788889999999999999999954


Q ss_pred             HHHhcCC-CCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCC
Q 042039          111 LMVQRDV-RPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP  189 (376)
Q Consensus       111 ~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  189 (376)
                      ..-+... ......|....-.|...++...|...|+...... |.|...|..++.+|.+.|.+..|+++|.++...  .|
T Consensus       551 ~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L--rP  627 (1238)
T KOG1127|consen  551 RAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLL--RP  627 (1238)
T ss_pred             HHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhc--Cc
Confidence            4433211 1113344456667788899999999999998876 778899999999999999999999999998874  44


Q ss_pred             CHhHHHHH--HHHHHhccchHHHHHHHHHHHh
Q 042039          190 TVVTYNTL--FLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       190 ~~~~~~~l--~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      + .+|...  ....+..|.+.++...+..+..
T Consensus       628 ~-s~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  628 L-SKYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             H-hHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3 223222  2334566777777777766544

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.89  E-value=3e-06  Score=63.69  Aligned_cols=189  Identities=13%  Similarity=0.068  Sum_probs=138.0

Q ss_pred             cCcHHHHHHHHHHHHhc---C-CCCChh-hHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchH
Q 042039          134 TGKINRAEELFGSMESM---G-CKHDDV-SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVE  208 (376)
Q Consensus       134 ~~~~~~a~~~~~~~~~~---~-~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  208 (376)
                      ..+.++..+++..+...   + ..++.. .|..++-+....|+.+.|...++++... ++-+..+-..-...+-..|+++
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~-fp~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDR-FPGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhchh
Confidence            45678888888887543   2 223332 4556666777788889999999998876 3444444444444456678899


Q ss_pred             HHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          209 HALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       209 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      +|+++++.++..+ |.+..++-.-+...-..|+.-+|++-+....+.- ..|...|..+...|...|++++|.-.++++.
T Consensus       104 ~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F-~~D~EAW~eLaeiY~~~~~f~kA~fClEE~l  181 (289)
T KOG3060|consen  104 EAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKF-MNDQEAWHELAEIYLSEGDFEKAAFCLEELL  181 (289)
T ss_pred             hHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHh-cCcHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            9999999998887 6667777777777777888888888877776654 4488999999999999999999999999887


Q ss_pred             ccCCCCCHHHHHHHHHHHHccC---ChhHHHHHHHHHHHcC
Q 042039          289 RRVLVADVVTYNIMIHGLCNDG---QMDKAHDLFLDMEENA  326 (376)
Q Consensus       289 ~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~  326 (376)
                      -. .|.++..+..+...+.-.|   +.+.|.++|.+.++..
T Consensus       182 l~-~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~  221 (289)
T KOG3060|consen  182 LI-QPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLN  221 (289)
T ss_pred             Hc-CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhC
Confidence            65 4556677777777765554   5667888888888753

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

Probab=98.85  E-value=1.2e-05  Score=66.36  Aligned_cols=144  Identities=16%  Similarity=0.136  Sum_probs=107.1

Q ss_pred             HHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCC
Q 042039          196 TLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSG  275 (376)
Q Consensus       196 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  275 (376)
                      -....+...|+++.|+..+..+++.. |.++.........+.+.++.++|.+.++++....+. .......++.++.+.|
T Consensus       311 G~A~~~~~~~~~d~A~~~l~~L~~~~-P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~-~~~l~~~~a~all~~g  388 (484)
T COG4783         311 GRALQTYLAGQYDEALKLLQPLIAAQ-PDNPYYLELAGDILLEANKAKEAIERLKKALALDPN-SPLLQLNLAQALLKGG  388 (484)
T ss_pred             HHHHHHHHhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCC-ccHHHHHHHHHHHhcC
Confidence            33445567788888888888877763 566777777778888888888888888888776532 3667778888888888


Q ss_pred             ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHH
Q 042039          276 RLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLH  355 (376)
Q Consensus       276 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  355 (376)
                      ++.+|+.+++..... .+.|+..|..|.++|...|+..++.....+                  .|...|++++|...+.
T Consensus       389 ~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~AE------------------~~~~~G~~~~A~~~l~  449 (484)
T COG4783         389 KPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARAE------------------GYALAGRLEQAIIFLM  449 (484)
T ss_pred             ChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHHH------------------HHHhCCCHHHHHHHHH
Confidence            888888888887765 567888888888888888887777655443                  3445667777777666


Q ss_pred             HHHhC
Q 042039          356 KMKEK  360 (376)
Q Consensus       356 ~~~~~  360 (376)
                      ...+.
T Consensus       450 ~A~~~  454 (484)
T COG4783         450 RASQQ  454 (484)
T ss_pred             HHHHh
Confidence            66554

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

Probab=98.85  E-value=3.2e-07  Score=65.28  Aligned_cols=94  Identities=18%  Similarity=0.191  Sum_probs=45.5

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  168 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  168 (376)
                      ...+...+...|++++|...++.+...+ +.+...+..+..++...|++++|..+++.....+ +.+...+..+..++..
T Consensus        20 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~   97 (135)
T TIGR02552        20 IYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLA   97 (135)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHH
Confidence            3344444444555555555555544432 2234444445555555555555555555544443 3344444445555555


Q ss_pred             cCcHHHHHHHHHHHHH
Q 042039          169 NKEVEEALSLYREMVS  184 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~  184 (376)
                      .|++++|...++...+
T Consensus        98 ~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        98 LGEPESALKALDLAIE  113 (135)
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            5555555555555444

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

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

Probab=98.83  E-value=3.4e-07  Score=65.12  Aligned_cols=111  Identities=13%  Similarity=0.075  Sum_probs=69.6

Q ss_pred             HHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCC
Q 042039           38 LFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDV  117 (376)
Q Consensus        38 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  117 (376)
                      .++++...+ +.+......++..+...|++++|.+.++.+...+.. +...+..+..++...|++++|...+++..+.+ 
T Consensus         5 ~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-   81 (135)
T TIGR02552         5 TLKDLLGLD-SEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPY-NSRYWLGLAACCQMLKEYEEAIDAYALAAALD-   81 (135)
T ss_pred             hHHHHHcCC-hhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-
Confidence            344444443 334455566666666777777777777776665322 55666666667777777777777777666653 


Q ss_pred             CCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Q 042039          118 RPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus       118 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      +.+...+..+..++...|++++|...|+...+..
T Consensus        82 p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  115 (135)
T TIGR02552        82 PDDPRPYFHAAECLLALGEPESALKALDLAIEIC  115 (135)
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            3345666666667777777777777777666653

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

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

Probab=98.81  E-value=2.2e-05  Score=70.60  Aligned_cols=253  Identities=13%  Similarity=0.174  Sum_probs=129.4

Q ss_pred             CChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHH
Q 042039           30 GFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLL  109 (376)
Q Consensus        30 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  109 (376)
                      ++.++|.+.-++..      .+..|..+..+-.+.|...+|++-|-+.      .|+..|..++....+.|.+++-.+++
T Consensus      1089 ~~ldRA~efAe~~n------~p~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL 1156 (1666)
T KOG0985|consen 1089 GSLDRAYEFAERCN------EPAVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYL 1156 (1666)
T ss_pred             hhHHHHHHHHHhhC------ChHHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHH
Confidence            44455544444332      2344555555555555555555544221      14445555555555555555555555


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChh--------------------------hHHHHH
Q 042039          110 DLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDV--------------------------SYNILI  163 (376)
Q Consensus       110 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--------------------------~~~~l~  163 (376)
                      ....+..-+|...  ..++-+|++.++..+.++++.       .|+..                          -|..|.
T Consensus      1157 ~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi~-------gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La 1227 (1666)
T KOG0985|consen 1157 LMARKKVREPYID--SELIFAYAKTNRLTELEEFIA-------GPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLA 1227 (1666)
T ss_pred             HHHHHhhcCccch--HHHHHHHHHhchHHHHHHHhc-------CCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHH
Confidence            5554443333322  244555555555544444331       12222                          344455


Q ss_pred             HHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHH
Q 042039          164 NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIV  243 (376)
Q Consensus       164 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  243 (376)
                      ..+...|++..|...-+++      .+..+|..+..+|...+.+..|     +|-..++.....-+..++..|...|.++
T Consensus      1228 ~TLV~LgeyQ~AVD~aRKA------ns~ktWK~VcfaCvd~~EFrlA-----QiCGL~iivhadeLeeli~~Yq~rGyFe 1296 (1666)
T KOG0985|consen 1228 STLVYLGEYQGAVDAARKA------NSTKTWKEVCFACVDKEEFRLA-----QICGLNIIVHADELEELIEYYQDRGYFE 1296 (1666)
T ss_pred             HHHHHHHHHHHHHHHhhhc------cchhHHHHHHHHHhchhhhhHH-----HhcCceEEEehHhHHHHHHHHHhcCcHH
Confidence            5555555555555444332      2445666666666555444332     2222233344555677888888888888


Q ss_pred             HHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc-CCC------CCHHHHHHHHHHHHccCChhHHH
Q 042039          244 EAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR-VLV------ADVVTYNIMIHGLCNDGQMDKAH  316 (376)
Q Consensus       244 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~------~~~~~~~~l~~~~~~~~~~~~a~  316 (376)
                      +.+.+++...... ......|..++-.|.+- ++++..+.++-.-.+ +++      .....|..+...|.+-..++.|.
T Consensus      1297 ElIsl~Ea~LGLE-RAHMgmfTELaiLYsky-kp~km~EHl~LFwsRvNipKviRA~eqahlW~ElvfLY~~y~eyDNAa 1374 (1666)
T KOG0985|consen 1297 ELISLLEAGLGLE-RAHMGMFTELAILYSKY-KPEKMMEHLKLFWSRVNIPKVIRAAEQAHLWSELVFLYDKYEEYDNAA 1374 (1666)
T ss_pred             HHHHHHHhhhchh-HHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHhhhhhhHHH
Confidence            8888888765443 23455666676666543 233333333222111 011      12456777777777766666553

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

Probab=98.77  E-value=1.8e-05  Score=65.50  Aligned_cols=239  Identities=13%  Similarity=0.118  Sum_probs=144.1

Q ss_pred             HHHHHhcCC-hhHHHHHHHHhhh---CCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcC--CCCchHhHHHHHHHH
Q 042039           23 IDGLCKEGF-VDKAKALFLQMKG---ENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQG--VQPSVVTFNVIMDEL   96 (376)
Q Consensus        23 ~~~~~~~g~-~~~a~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~   96 (376)
                      +..+.+.|. ...-.+.|+++..   .+-.|...    +...=.-..++.++...-+++...+  ..|+...+...+...
T Consensus       209 i~~L~raGydp~gM~~ff~rl~~~~~~~~~~p~y----l~THPlp~~RIa~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~  284 (484)
T COG4783         209 ITTLVRAGYDPQGMPEFFERLADQLRYGGQPPEY----LLTHPLPEERIADLRNRAEQSPPYNKLDSPDFQLARARIRAK  284 (484)
T ss_pred             HHHHHHcCCCchhHHHHHHHHHHHHhcCCCCChH----HhcCCCchhHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHH
Confidence            344556663 4445677777763   22222221    1111122334555555555554332  133444445445444


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHH
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL  176 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  176 (376)
                      .....-..+..++.+..+   +.-..........+...|+++.|+..++.+.... |.++..+......+.+.++.++|.
T Consensus       285 ~~~~~~~~~~~~~~~~~~---~~~~aa~YG~A~~~~~~~~~d~A~~~l~~L~~~~-P~N~~~~~~~~~i~~~~nk~~~A~  360 (484)
T COG4783         285 YEALPNQQAADLLAKRSK---RGGLAAQYGRALQTYLAGQYDEALKLLQPLIAAQ-PDNPYYLELAGDILLEANKAKEAI  360 (484)
T ss_pred             hccccccchHHHHHHHhC---ccchHHHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHH
Confidence            433333333333332222   1123344455556667788888888888877654 566666777778888888888888


Q ss_pred             HHHHHHHHCCCCCC-HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          177 SLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       177 ~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      +.++++...  .|+ ......+..++.+.|++.+|+.+++...... +.++..|..+.++|...|+..++..-..+..  
T Consensus       361 e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~--  435 (484)
T COG4783         361 ERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARAEGY--  435 (484)
T ss_pred             HHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHHHHH--
Confidence            888888875  333 5666777788888888888888888877765 6778888888888888888777776655432  


Q ss_pred             CCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          256 KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                                      ...|++++|...+....+.
T Consensus       436 ----------------~~~G~~~~A~~~l~~A~~~  454 (484)
T COG4783         436 ----------------ALAGRLEQAIIFLMRASQQ  454 (484)
T ss_pred             ----------------HhCCCHHHHHHHHHHHHHh
Confidence                            2356777777776666554

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.76  E-value=1.7e-05  Score=68.99  Aligned_cols=108  Identities=21%  Similarity=0.213  Sum_probs=46.9

Q ss_pred             HHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHH
Q 042039          164 NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIV  243 (376)
Q Consensus       164 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  243 (376)
                      .+.....+|.+|+.+++.+....  .-..-|..+...|...|+++.|.++|.+.         ..+...+.+|.+.|+++
T Consensus       740 eaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw~  808 (1636)
T KOG3616|consen  740 EAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWE  808 (1636)
T ss_pred             HHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHH
Confidence            33344455555555555444431  12223444445555555555555554432         11233344555555555


Q ss_pred             HHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHH
Q 042039          244 EAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELF  284 (376)
Q Consensus       244 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  284 (376)
                      .|.++-.+..  ++......|..-..-+-..|++.+|.++|
T Consensus       809 da~kla~e~~--~~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  809 DAFKLAEECH--GPEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             HHHHHHHHhc--CchhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            5555544432  11222333333333344444444444433

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

Probab=98.75  E-value=8.3e-05  Score=67.16  Aligned_cols=183  Identities=12%  Similarity=0.065  Sum_probs=95.6

Q ss_pred             hhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHH
Q 042039          156 DVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDG  235 (376)
Q Consensus       156 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  235 (376)
                      +.+|..+..+-.+.|...+|++-|-+.      .|+..|..++....+.|.|++-.+++....+....|  ..-..++-+
T Consensus      1104 p~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~--~id~eLi~A 1175 (1666)
T KOG0985|consen 1104 PAVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREP--YIDSELIFA 1175 (1666)
T ss_pred             hHHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCc--cchHHHHHH
Confidence            345666666666666666666555331      245556666666666666666666665555543222  223455556


Q ss_pred             HHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc--------------------CCCCC
Q 042039          236 LCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR--------------------VLVAD  295 (376)
Q Consensus       236 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--------------------~~~~~  295 (376)
                      |.+.++..+-++.+.       .|+......++.-|...|.++.|.-+|......                    ....+
T Consensus      1176 yAkt~rl~elE~fi~-------gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAns 1248 (1666)
T KOG0985|consen 1176 YAKTNRLTELEEFIA-------GPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKANS 1248 (1666)
T ss_pred             HHHhchHHHHHHHhc-------CCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence            666666555444321       234444444455555555555554444321110                    00113


Q ss_pred             HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       296 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      ..+|..+..+|...+.+.-|     ++...++-....-...++..|...|-+++.+.+++...
T Consensus      1249 ~ktWK~VcfaCvd~~EFrlA-----QiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1249 TKTWKEVCFACVDKEEFRLA-----QICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             hhHHHHHHHHHhchhhhhHH-----HhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence            34444444444444433322     22222233345567778888888888888888777654

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

Probab=98.71  E-value=1.6e-06  Score=62.30  Aligned_cols=116  Identities=15%  Similarity=0.168  Sum_probs=55.2

Q ss_pred             CCChHHHHHHHHHHHhcCCCC--chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC--hhhHHHHHHHHHhcCcHHH
Q 042039           64 ANDWNEAKRLFFEMMDQGVQP--SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN--AFTYSTLMDGFCLTGKINR  139 (376)
Q Consensus        64 ~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~  139 (376)
                      .++...+...++.+.+.....  .......+...+...|++++|...|+.+......++  ......+..++...|++++
T Consensus        24 ~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~  103 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDE  103 (145)
T ss_pred             CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHH
Confidence            445555555555555542211  012223344455555555555555555555431111  1233344555555555555


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHH
Q 042039          140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       140 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                      |...++.....  +..+..+...+.++.+.|++++|...|+.
T Consensus       104 Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  104 ALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            55555443222  23334445555566666666666655554

>PF12854 PPR_1: PPR repeat

Probab=98.68  E-value=2.9e-08  Score=50.58  Aligned_cols=32  Identities=28%  Similarity=0.659  Sum_probs=21.1

Q ss_pred             CCCCcHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          326 AVAPNVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       326 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      |+.||..+|+.++.+|++.|+.++|.++|++|
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            45666666666666666666666666666665

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.68  E-value=2.5e-05  Score=67.98  Aligned_cols=171  Identities=20%  Similarity=0.206  Sum_probs=107.1

Q ss_pred             HHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccc
Q 042039          127 LMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       127 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  206 (376)
                      .+.+.....+|.+|+.+++.+....  .....|..+..-|...|+++.|.++|.+.-         .+...+..|.+.|+
T Consensus       738 aieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~k  806 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGK  806 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhcccc
Confidence            3445556677888888888777653  344566777788888888888888876532         23445677888888


Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhc
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  286 (376)
                      |+.|.++-.+...  .......|..-..-.-++|++.+|.++|-.+.    .|+     ..+.+|-+.|..+..+++..+
T Consensus       807 w~da~kla~e~~~--~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~-----~aiqmydk~~~~ddmirlv~k  875 (1636)
T KOG3616|consen  807 WEDAFKLAEECHG--PEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPD-----KAIQMYDKHGLDDDMIRLVEK  875 (1636)
T ss_pred             HHHHHHHHHHhcC--chhHHHHHHHhHHhHHhhcchhhhhheeEEcc----Cch-----HHHHHHHhhCcchHHHHHHHH
Confidence            8888877666532  23344455555556667778877777765443    333     235667777777777776665


Q ss_pred             ccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHH
Q 042039          287 LPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDM  322 (376)
Q Consensus       287 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  322 (376)
                      -...   .-..|...+..-+-..|+.+.|...|-++
T Consensus       876 ~h~d---~l~dt~~~f~~e~e~~g~lkaae~~flea  908 (1636)
T KOG3616|consen  876 HHGD---HLHDTHKHFAKELEAEGDLKAAEEHFLEA  908 (1636)
T ss_pred             hChh---hhhHHHHHHHHHHHhccChhHHHHHHHhh
Confidence            3221   11234445555666666666666555443

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

Probab=98.66  E-value=2.7e-06  Score=61.10  Aligned_cols=127  Identities=19%  Similarity=0.232  Sum_probs=72.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCch--HhHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD---VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV--VTFNV   91 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~   91 (376)
                      ..|..++..+ ..++...+...++.+.... +.+   ......+...+...|++++|...|+.+......|+.  .....
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~   90 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLR   90 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            3455555555 3666666666666666553 222   233444556666667777777777776665422221  23344


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHH
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSM  147 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  147 (376)
                      +...+...|++++|+..++.....  ......+...+.++...|++++|...|+..
T Consensus        91 LA~~~~~~~~~d~Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   91 LARILLQQGQYDEALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHcCCHHHHHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            566666677777777776553322  223445556666677777777777766653

>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=98.65  E-value=2.9e-06  Score=70.44  Aligned_cols=127  Identities=15%  Similarity=0.129  Sum_probs=101.2

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ..-..|+..+...++++.|+.+|+++.+..  |+  ....+++.+...++..+|.+++++.++.. +.+.......+..+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            344556677777889999999999988763  33  44557788888888889999999888763 44667777778888


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      ...++++.|.++.+++.... |.+..+|..|+.+|...|+++.|+..++.+.-
T Consensus       245 l~k~~~~lAL~iAk~av~ls-P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELS-PSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            89999999999999998875 56667999999999999999999988887653

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

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

Probab=98.65  E-value=0.00017  Score=60.62  Aligned_cols=356  Identities=12%  Similarity=0.136  Sum_probs=207.4

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +-|..+|+.||+-+..+ .++++.+.++++...- +..+..|..-+..-...++++....+|.+.+..-  .+...|...
T Consensus        17 P~di~sw~~lire~qt~-~~~~~R~~YEq~~~~F-P~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkv--LnlDLW~lY   92 (656)
T KOG1914|consen   17 PYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNVF-PSSPRAWKLYIERELASKDFESVEKLFSRCLVKV--LNLDLWKLY   92 (656)
T ss_pred             CccHHHHHHHHHHHccC-CHHHHHHHHHHHhccC-CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH--hhHhHHHHH
Confidence            45788999999988766 9999999999998663 6678899999999999999999999999988763  345566655


Q ss_pred             HHHHHh-CCChHH----HHHHHHHHHh-cCCCCC-hhhHHHHHHHH---------HhcCcHHHHHHHHHHHHhcCCCCCh
Q 042039           93 MDELCK-NGKMDE----ASRLLDLMVQ-RDVRPN-AFTYSTLMDGF---------CLTGKINRAEELFGSMESMGCKHDD  156 (376)
Q Consensus        93 ~~~~~~-~~~~~~----a~~~~~~~~~-~~~~~~-~~~~~~l~~~~---------~~~~~~~~a~~~~~~~~~~~~~~~~  156 (376)
                      +.--.+ .++...    ..+.|+-.+. .|+.+- ...|...+..+         ....+++...++|+++....+..-.
T Consensus        93 l~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~nlE  172 (656)
T KOG1914|consen   93 LSYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHNLE  172 (656)
T ss_pred             HHHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccccHH
Confidence            553322 233332    2333333332 343332 33455555433         3344677788888888764322111


Q ss_pred             hhHHHH------HHH-------HHccCcHHHHHHHHHHHHH--CCC-------CCC--------HhHHHHHHHH------
Q 042039          157 VSYNIL------ING-------YCKNKEVEEALSLYREMVS--KGI-------KPT--------VVTYNTLFLG------  200 (376)
Q Consensus       157 ~~~~~l------~~~-------~~~~~~~~~a~~~~~~~~~--~~~-------~~~--------~~~~~~l~~~------  200 (376)
                      ..|+-.      ++.       --+...+..|.++++++..  .|.       +|.        ...|..++.-      
T Consensus       173 kLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wEksNpL  252 (656)
T KOG1914|consen  173 KLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWEKSNPL  252 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHHhcCCc
Confidence            222211      111       1123456667777766643  121       111        0112222111      


Q ss_pred             -------------------------------------------HHhccc-------hHHHHHHHHHHHhcCCCCCcchHH
Q 042039          201 -------------------------------------------LFEIHQ-------VEHALKLFEEMQRDDVAADTSTYN  230 (376)
Q Consensus       201 -------------------------------------------~~~~~~-------~~~a~~~~~~~~~~~~~~~~~~~~  230 (376)
                                                                 +...|+       .+++..+++..+..-...+..+|.
T Consensus       253 ~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~Ly~  332 (656)
T KOG1914|consen  253 RTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKLLYF  332 (656)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                                       011111       223333333333221111222222


Q ss_pred             HHHHHHHhCC---CHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCC-CHHHHHHHHHHH
Q 042039          231 TFIDGLCKNG---YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA-DVVTYNIMIHGL  306 (376)
Q Consensus       231 ~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~  306 (376)
                      .+...--..-   ..+....++.++......--.-+|..++....+..-.+.|..+|.++.+.+..+ ++.+..+++.-+
T Consensus       333 ~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~  412 (656)
T KOG1914|consen  333 ALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYY  412 (656)
T ss_pred             HHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHH
Confidence            2222111111   234444455554432222123467777777778888999999999998776655 566667777665


Q ss_pred             HccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCch--HHHHHHHh
Q 042039          307 CNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA--SIVSMVVD  374 (376)
Q Consensus       307 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~--~~~~~ll~  374 (376)
                      + .++..-|.++|+--+.. ...++......+..+...|+-..+..+|++....++.||.  .+|..+|+
T Consensus       413 c-skD~~~AfrIFeLGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~  480 (656)
T KOG1914|consen  413 C-SKDKETAFRIFELGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLE  480 (656)
T ss_pred             h-cCChhHHHHHHHHHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHH
Confidence            5 57889999999877664 2234455566677778889999999999999988666654  46666553

>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=98.62  E-value=2.8e-06  Score=70.49  Aligned_cols=127  Identities=20%  Similarity=0.199  Sum_probs=106.5

Q ss_pred             HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           87 VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGY  166 (376)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  166 (376)
                      .....++..+...++++.|..+++++.+..  |+  ....+++.+...++-.+|.+++.+..... |.+..........+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            344556777778899999999999999874  44  45568888888999999999999998764 66777888888999


Q ss_pred             HccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          167 CKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       167 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      .+.++++.|+.+.+++... .+.+-.+|..|..+|...|+++.|+..++.+.-
T Consensus       245 l~k~~~~lAL~iAk~av~l-sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVEL-SPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHh-CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            9999999999999999986 344567999999999999999999999987643

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

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.61  E-value=3.3e-05  Score=62.48  Aligned_cols=265  Identities=11%  Similarity=0.001  Sum_probs=174.5

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC
Q 042039           20 NTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN   99 (376)
Q Consensus        20 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   99 (376)
                      ......+.+..++..|+..+...++.. +.++..|..-+..+...|++++|.--.++-++.... .........+++...
T Consensus        53 k~~gn~~yk~k~Y~nal~~yt~Ai~~~-pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~-~~k~~~r~~~c~~a~  130 (486)
T KOG0550|consen   53 KEEGNAFYKQKTYGNALKNYTFAIDMC-PDNASYYSNRAATLMMLGRFEEALGDARQSVRLKDG-FSKGQLREGQCHLAL  130 (486)
T ss_pred             HhhcchHHHHhhHHHHHHHHHHHHHhC-ccchhhhchhHHHHHHHHhHhhcccchhhheecCCC-ccccccchhhhhhhh
Confidence            334456777788999999999988876 556777777778888888888887777665553211 122333334444444


Q ss_pred             CChHHHHHHHHHH---------------HhcC-CCCChhhHHHH-HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039          100 GKMDEASRLLDLM---------------VQRD-VRPNAFTYSTL-MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNIL  162 (376)
Q Consensus       100 ~~~~~a~~~~~~~---------------~~~~-~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  162 (376)
                      ++..+|.+.++.-               .... -+|....+..+ ..++.-.|++++|.+.--.+.+.+ +.+......-
T Consensus       131 ~~~i~A~~~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld-~~n~~al~vr  209 (486)
T KOG0550|consen  131 SDLIEAEEKLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD-ATNAEALYVR  209 (486)
T ss_pred             HHHHHHHHHhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc-cchhHHHHhc
Confidence            4444444433321               1111 12333333333 345667789999998888877765 3444444444


Q ss_pred             HHHHHccCcHHHHHHHHHHHHHCCCCCCHh-------------HHHHHHHHHHhccchHHHHHHHHHHHhcC---CCCCc
Q 042039          163 INGYCKNKEVEEALSLYREMVSKGIKPTVV-------------TYNTLFLGLFEIHQVEHALKLFEEMQRDD---VAADT  226 (376)
Q Consensus       163 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~  226 (376)
                      ..++.-.++.+.+...|++.+..  .|+..             .+..-..-..+.|.+..|.+.+.+.+..+   ..++.
T Consensus       210 g~~~yy~~~~~ka~~hf~qal~l--dpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~na  287 (486)
T KOG0550|consen  210 GLCLYYNDNADKAINHFQQALRL--DPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNA  287 (486)
T ss_pred             ccccccccchHHHHHHHhhhhcc--ChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhH
Confidence            55666788899999999998875  34322             22233445678899999999999988764   34455


Q ss_pred             chHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          227 STYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       227 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      ..|........+.|+..+|+.--+.+...+.. -...+..-+.++...++|++|.+-+++..+.
T Consensus       288 klY~nra~v~~rLgrl~eaisdc~~Al~iD~s-yikall~ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  288 KLYGNRALVNIRLGRLREAISDCNEALKIDSS-YIKALLRRANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             HHHHHhHhhhcccCCchhhhhhhhhhhhcCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            56777778888999999999988887765411 2344555566777789999999999887654

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

Probab=98.61  E-value=0.00036  Score=62.30  Aligned_cols=225  Identities=14%  Similarity=0.036  Sum_probs=139.0

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHH
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEAS  106 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  106 (376)
                      ...+++.+|++..+++.+.. |....+-..-.-.+.+.|+.++|..+++.....+.. |..+...+-.+|...++.++|.
T Consensus        20 ld~~qfkkal~~~~kllkk~-Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~   97 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKKH-PNALYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAV   97 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHH
Confidence            45678888888888887663 222323333344567788888888888777665544 7778888888888888888888


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc----------HHHHH
Q 042039          107 RLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE----------VEEAL  176 (376)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~  176 (376)
                      .+|+...+.  .|+......+..+|.+-+.+.+-.+.--++-+. .|..+..+-.+++.....-.          ..-|.
T Consensus        98 ~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~  174 (932)
T KOG2053|consen   98 HLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAE  174 (932)
T ss_pred             HHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHH
Confidence            888888875  455667777777888877776655544444332 34555555556665544211          12344


Q ss_pred             HHHHHHHHCC-CCCCHhHHHHHHHHHHhccchHHHHHHHHH-HHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcc
Q 042039          177 SLYREMVSKG-IKPTVVTYNTLFLGLFEIHQVEHALKLFEE-MQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI  254 (376)
Q Consensus       177 ~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  254 (376)
                      +.++.+.+.+ .--+..-.......+...+.+++|..++.. ....-...+...-+.-+..+...+++.+..++-.++..
T Consensus       175 ~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~  254 (932)
T KOG2053|consen  175 KMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLE  254 (932)
T ss_pred             HHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHH
Confidence            4555555543 111222233333445566778888877733 33322233333444556667777788887777777776


Q ss_pred             cC
Q 042039          255 LK  256 (376)
Q Consensus       255 ~~  256 (376)
                      .+
T Consensus       255 k~  256 (932)
T KOG2053|consen  255 KG  256 (932)
T ss_pred             hC
Confidence            65

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.47  E-value=1e-05  Score=56.01  Aligned_cols=99  Identities=13%  Similarity=0.071  Sum_probs=60.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCC--CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--CchHhHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENI--NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PSVVTFNVI   92 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l   92 (376)
                      .++..++..+.+.|++++|.+.|+.+.+...  +.....+..++.++...|++++|.+.|+.+....+.  .....+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            3455666666777777777777777665431  111345556667777777777777777776654222  123455566


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhc
Q 042039           93 MDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      ..++...|++++|...++++++.
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHHH
Confidence            66666677777777777766665

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.

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.47  E-value=4.6e-06  Score=58.73  Aligned_cols=99  Identities=11%  Similarity=-0.011  Sum_probs=76.0

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      +......+...+...|++++|.++|+-+....+. +..-|..|..++-..|++++|+..|......+ +.++..+..+..
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~-~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~  111 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAW-SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAE  111 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHH
Confidence            4556667777778888888888888888776433 56667777778888888888888888888775 346778888888


Q ss_pred             HHHhcCcHHHHHHHHHHHHhc
Q 042039          130 GFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      ++...|+.+.|.+.|+..+..
T Consensus       112 c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        112 CYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            888888888888888877665

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.44  E-value=6.7e-05  Score=60.79  Aligned_cols=263  Identities=13%  Similarity=0.028  Sum_probs=122.2

Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC
Q 042039           56 SLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG  135 (376)
Q Consensus        56 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  135 (376)
                      .....+.+..++..|+..+...++..+. +..-|..-+..+...++++++..-.+.-++.. +-.........+++...+
T Consensus        54 ~~gn~~yk~k~Y~nal~~yt~Ai~~~pd-~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~k-d~~~k~~~r~~~c~~a~~  131 (486)
T KOG0550|consen   54 EEGNAFYKQKTYGNALKNYTFAIDMCPD-NASYYSNRAATLMMLGRFEEALGDARQSVRLK-DGFSKGQLREGQCHLALS  131 (486)
T ss_pred             hhcchHHHHhhHHHHHHHHHHHHHhCcc-chhhhchhHHHHHHHHhHhhcccchhhheecC-CCccccccchhhhhhhhH
Confidence            3444566677888888888888887544 45566666667777788888777776665532 112334444455555555


Q ss_pred             cHHHHHHHHHHHH---------------hcCC-CCChhhHHHH-HHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHH
Q 042039          136 KINRAEELFGSME---------------SMGC-KHDDVSYNIL-INGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLF  198 (376)
Q Consensus       136 ~~~~a~~~~~~~~---------------~~~~-~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  198 (376)
                      +..+|.+.++...               .... +|.-..+..+ ..++...|++++|.+.--..++.+ ..+......-.
T Consensus       132 ~~i~A~~~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld-~~n~~al~vrg  210 (486)
T KOG0550|consen  132 DLIEAEEKLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD-ATNAEALYVRG  210 (486)
T ss_pred             HHHHHHHHhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc-cchhHHHHhcc
Confidence            5555555444211               0000 0111112111 234444555555555555554431 11222222222


Q ss_pred             HHHHhccchHHHHHHHHHHHhcCCCCCcchH---HHHHH----------HHHhCCCHHHHHHHHHHhcccC---CCchHH
Q 042039          199 LGLFEIHQVEHALKLFEEMQRDDVAADTSTY---NTFID----------GLCKNGYIVEAVELFRTLGILK---CELDIQ  262 (376)
Q Consensus       199 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---~~l~~----------~~~~~~~~~~a~~~~~~~~~~~---~~~~~~  262 (376)
                      .++...++.+.+...|++.++.+  |+....   .....          -..+.|++..|.+.|...+..+   ..++..
T Consensus       211 ~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~nak  288 (486)
T KOG0550|consen  211 LCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAK  288 (486)
T ss_pred             cccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHH
Confidence            33344555556666665555543  221111   11111          1223455555555555544322   122333


Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          263 AYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       263 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      .|.....+..+.|+.++|+.--+.+.... +.-...+..-..++...++|++|.+-++++.+
T Consensus       289 lY~nra~v~~rLgrl~eaisdc~~Al~iD-~syikall~ra~c~l~le~~e~AV~d~~~a~q  349 (486)
T KOG0550|consen  289 LYGNRALVNIRLGRLREAISDCNEALKID-SSYIKALLRRANCHLALEKWEEAVEDYEKAMQ  349 (486)
T ss_pred             HHHHhHhhhcccCCchhhhhhhhhhhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44444444555555555555444444320 00011222223344444555555555555544

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

Probab=98.42  E-value=5.8e-06  Score=54.61  Aligned_cols=94  Identities=14%  Similarity=0.123  Sum_probs=52.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      |..+...+...|++++|...++++.+.. +.+...+..+..++...+++++|.+.++........ +...+..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD-NAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc-chhHHHHHHHHHHH
Confidence            4445555556666666666666665543 333455555566666666666666666665554322 33445555555555


Q ss_pred             CCChHHHHHHHHHHHh
Q 042039           99 NGKMDEASRLLDLMVQ  114 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~  114 (376)
                      .|+++.|...+....+
T Consensus        81 ~~~~~~a~~~~~~~~~   96 (100)
T cd00189          81 LGKYEEALEAYEKALE   96 (100)
T ss_pred             HHhHHHHHHHHHHHHc
Confidence            5666666555555543

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.42  E-value=1.6e-05  Score=56.10  Aligned_cols=98  Identities=14%  Similarity=0.049  Sum_probs=67.4

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILING  165 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  165 (376)
                      ......+...+...|++++|.++|+.+...+ +-+..-|..|..++-..|++.+|+..|....... +.++..+..+..+
T Consensus        35 l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c  112 (157)
T PRK15363         35 LNTLYRYAMQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAEC  112 (157)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHH
Confidence            3344455556667777777777777776654 3355666677777777777777777777777766 5666777777777


Q ss_pred             HHccCcHHHHHHHHHHHHHC
Q 042039          166 YCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       166 ~~~~~~~~~a~~~~~~~~~~  185 (376)
                      +...|+.+.|.+.|+..+..
T Consensus       113 ~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        113 YLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHcCCHHHHHHHHHHHHHH
Confidence            77777777777777776664

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=98.41  E-value=4.1e-06  Score=67.59  Aligned_cols=132  Identities=11%  Similarity=0.007  Sum_probs=74.0

Q ss_pred             hHHHHHHHHHHhccchHHHHHHHHHHHhc----C-CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhc----ccCC-CchH
Q 042039          192 VTYNTLFLGLFEIHQVEHALKLFEEMQRD----D-VAADTSTYNTFIDGLCKNGYIVEAVELFRTLG----ILKC-ELDI  261 (376)
Q Consensus       192 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~----~~~~-~~~~  261 (376)
                      ..|..+...|.-.|+++.|+...+.-+..    | -......+..+..+++-.|+++.|.+.|+...    +.+- ....
T Consensus       196 Ra~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEA  275 (639)
T KOG1130|consen  196 RAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEA  275 (639)
T ss_pred             chhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHH
Confidence            34555555566666777666555432221    1 11123455666667777777777777666542    1221 1234


Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhccccc----C-CCCCHHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPRR----V-LVADVVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      .+..+++..|.-..++++|+.++.+-+..    + ..-....+..|..+|...|..++|+.+.+...
T Consensus       276 QscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  276 QSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            45566677777777777777776552211    0 11234566777777777777777776665544

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

Probab=98.39  E-value=2.3e-05  Score=63.28  Aligned_cols=141  Identities=13%  Similarity=0.125  Sum_probs=77.6

Q ss_pred             hHHHHHHHHHhC-CCHHHHHHHHHHhccc----CCC-chHHHHHHHHHHHHhCCChHHHHHHHhcccccCCC-----CCH
Q 042039          228 TYNTFIDGLCKN-GYIVEAVELFRTLGIL----KCE-LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLV-----ADV  296 (376)
Q Consensus       228 ~~~~l~~~~~~~-~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~  296 (376)
                      .+..++..|... |++++|++.|+++...    +.+ .-...+..++..+.+.|++++|.++|+++......     .+.
T Consensus       116 ~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~  195 (282)
T PF14938_consen  116 CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSA  195 (282)
T ss_dssp             HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhH
Confidence            344455566666 7888888888776432    211 11345667788888888999999988876543221     122


Q ss_pred             -HHHHHHHHHHHccCChhHHHHHHHHHHHcC--CC--CcHHHHHHHHHHHhhcCChh---hHHHHHHHHHhCCCCCchHH
Q 042039          297 -VTYNIMIHGLCNDGQMDKAHDLFLDMEENA--VA--PNVIIFVTLIHGFVRINKPS---KVIELLHKMKEKKVMPDASI  368 (376)
Q Consensus       297 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~--~~~~~~~~l~~~~~~~g~~~---~a~~~~~~~~~~~~~p~~~~  368 (376)
                       ..+...+-++...|++..|.+.+++.....  ..  ........|+.++- .|+.+   .++.-|+.+    .+.|.--
T Consensus       196 ~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~-~~D~e~f~~av~~~d~~----~~ld~w~  270 (282)
T PF14938_consen  196 KEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYE-EGDVEAFTEAVAEYDSI----SRLDNWK  270 (282)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHH-TT-CCCHHHHCHHHTTS----S---HHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHH-hCCHHHHHHHHHHHccc----CccHHHH
Confidence             233445556777888888888888887542  21  12445666777664 34444   444444433    2344444


Q ss_pred             HHHHH
Q 042039          369 VSMVV  373 (376)
Q Consensus       369 ~~~ll  373 (376)
                      ...|+
T Consensus       271 ~~~l~  275 (282)
T PF14938_consen  271 TKMLL  275 (282)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.38  E-value=2.8e-05  Score=53.79  Aligned_cols=98  Identities=12%  Similarity=0.107  Sum_probs=49.7

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--CchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC--CChhhHHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR--PNAFTYSTLM  128 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~  128 (376)
                      ++..++..+.+.|++++|.+.|+++......  .....+..+..++...|+++.|...++.+......  .....+..++
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            3445555555566666666666665543211  01234444555555556666666666655543211  1123444555


Q ss_pred             HHHHhcCcHHHHHHHHHHHHhc
Q 042039          129 DGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      .++...|+.++|...++++...
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHH
Confidence            5555555555555555555554

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.

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=98.38  E-value=5e-06  Score=67.08  Aligned_cols=278  Identities=14%  Similarity=0.084  Sum_probs=179.0

Q ss_pred             ccCCChhhHHHHH--HHHHhcCChhHHHHHHHHhhhCCCCCC----hhhHHHHHHHHhcCCChHHHHHHHHHHHh----c
Q 042039           11 VCKPNTVTYNTII--DGLCKEGFVDKAKALFLQMKGENINPD----VVTYNSLIHGLCHANDWNEAKRLFFEMMD----Q   80 (376)
Q Consensus        11 ~~~p~~~~~~~l~--~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~   80 (376)
                      +...+...+...+  +-+++.|+....+.+|+..++.| ..|    ..+|..|..+|.-.+++++|+++...=+.    .
T Consensus        10 ~~~q~~SCleLalEGERLck~gdcraGv~ff~aA~qvG-TeDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~l   88 (639)
T KOG1130|consen   10 RYMQDRSCLELALEGERLCKMGDCRAGVDFFKAALQVG-TEDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLL   88 (639)
T ss_pred             hhhhhhHHHHHHHHHHHHHhccchhhhHHHHHHHHHhc-chHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHh
Confidence            3344445555554  45899999999999999999988 334    34577788888888999999887543211    1


Q ss_pred             CCCC-chHhHHHHHHHHHhCCChHHHHHHHHHHH----hcCC-CCChhhHHHHHHHHHhcCc------------------
Q 042039           81 GVQP-SVVTFNVIMDELCKNGKMDEASRLLDLMV----QRDV-RPNAFTYSTLMDGFCLTGK------------------  136 (376)
Q Consensus        81 ~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~----~~~~-~~~~~~~~~l~~~~~~~~~------------------  136 (376)
                      |-+. ...+-..|...+--.|.+++|.....+-+    +.|. ......+..+...|...|+                  
T Consensus        89 gdklGEAKssgNLGNtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~  168 (639)
T KOG1130|consen   89 GDKLGEAKSSGNLGNTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVT  168 (639)
T ss_pred             cchhccccccccccchhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHH
Confidence            1110 11222344555556677888766544332    2221 1234566677777765553                  


Q ss_pred             --HHHHHHHHHHHHh----cCC-CCChhhHHHHHHHHHccCcHHHHHHHHHHHHH----CCC-CCCHhHHHHHHHHHHhc
Q 042039          137 --INRAEELFGSMES----MGC-KHDDVSYNILINGYCKNKEVEEALSLYREMVS----KGI-KPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       137 --~~~a~~~~~~~~~----~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~-~~~~~~~~~l~~~~~~~  204 (376)
                        ++.|.++|..-.+    .|- -.-..+|..|.+.|.-.|+++.|+..-+.-+.    -|- ......+..+..++.-.
T Consensus       169 ~al~~Av~fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hifl  248 (639)
T KOG1130|consen  169 SALENAVKFYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFL  248 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhh
Confidence              3444555543222    110 11234677888888889999999987654332    221 12356778889999999


Q ss_pred             cchHHHHHHHHHHHhc----C-CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcc----cC-CCchHHHHHHHHHHHHhC
Q 042039          205 HQVEHALKLFEEMQRD----D-VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI----LK-CELDIQAYNCLIDGLCKS  274 (376)
Q Consensus       205 ~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~-~~~~~~~~~~l~~~~~~~  274 (376)
                      |+++.|.+.|......    + -.........+...|.-..++++|+.++.+-..    .+ ..-....+.+++.++...
T Consensus       249 g~fe~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~al  328 (639)
T KOG1130|consen  249 GNFELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNAL  328 (639)
T ss_pred             cccHhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence            9999999998765432    2 123455677788888888899999988876422    11 112456788999999999


Q ss_pred             CChHHHHHHHhcccc
Q 042039          275 GRLEIALELFRSLPR  289 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~  289 (376)
                      |..++|+.+.+..++
T Consensus       329 g~h~kAl~fae~hl~  343 (639)
T KOG1130|consen  329 GEHRKALYFAELHLR  343 (639)
T ss_pred             hhHHHHHHHHHHHHH
Confidence            999999988876543

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.37  E-value=0.00023  Score=55.80  Aligned_cols=183  Identities=9%  Similarity=-0.010  Sum_probs=102.0

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHh---HHHHHHHHHhCCChHHHHHHHHHHHhcCCCC-C-hhhH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVT---FNVIMDELCKNGKMDEASRLLDLMVQRDVRP-N-AFTY  124 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~-~~~~  124 (376)
                      +...+...+..+...|++++|.+.|+++....+.+ ...   ...++.++.+.+++++|...++++++..... + ..++
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~  109 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVL  109 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHH
Confidence            44445556666677888888888888887763332 222   2456677788888888888888888753221 1 2222


Q ss_pred             HHHHHHHHhcC---------------c---HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC
Q 042039          125 STLMDGFCLTG---------------K---INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG  186 (376)
Q Consensus       125 ~~l~~~~~~~~---------------~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  186 (376)
                      ..++.++...+               +   ...|...|+.+++.-  |+             ..-..+|...+..+... 
T Consensus       110 Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~y--P~-------------S~ya~~A~~rl~~l~~~-  173 (243)
T PRK10866        110 YMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGY--PN-------------SQYTTDATKRLVFLKDR-  173 (243)
T ss_pred             HHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHC--cC-------------ChhHHHHHHHHHHHHHH-
Confidence            22222211111               1   234445555555441  22             22234444444333321 


Q ss_pred             CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc--CCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          187 IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD--DVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       187 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                         -...-..+.+.|.+.|.+..|..-++.+++.  +.+........+..+|...|..++|..+...+
T Consensus       174 ---la~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l  238 (243)
T PRK10866        174 ---LAKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKII  238 (243)
T ss_pred             ---HHHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence               0111124556677777777777777777765  22334455666777777777777777766554

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.36  E-value=0.00035  Score=54.78  Aligned_cols=58  Identities=3%  Similarity=-0.000  Sum_probs=42.5

Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHc--CCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          301 IMIHGLCNDGQMDKAHDLFLDMEEN--AVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       301 ~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      .++..|.+.|.+..|..-++.+++.  +.+........+..+|...|..++|..+...+.
T Consensus       180 ~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        180 SVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            5666788888888888888888865  223345566777788888888888888776654

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

Probab=98.34  E-value=1.3e-06  Score=56.01  Aligned_cols=81  Identities=17%  Similarity=0.218  Sum_probs=39.0

Q ss_pred             cCChhHHHHHHHHhhhCCCC-CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHH
Q 042039           29 EGFVDKAKALFLQMKGENIN-PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASR  107 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  107 (376)
                      .|+++.|+.+++++.+.... ++...+..++.++.+.|++++|..++++ .+.+.. +......++.++.+.|++++|+.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~-~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPS-NPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHC-HHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCC-CHHHHHHHHHHHHHhCCHHHHHH
Confidence            35556666666665554311 1333444455666666666666666655 222111 22333344555556666666655


Q ss_pred             HHHH
Q 042039          108 LLDL  111 (376)
Q Consensus       108 ~~~~  111 (376)
                      ++++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            5543

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

Probab=98.34  E-value=2.1e-06  Score=55.09  Aligned_cols=20  Identities=30%  Similarity=0.494  Sum_probs=8.8

Q ss_pred             HHHHHHhCCChHHHHHHHhc
Q 042039          267 LIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       267 l~~~~~~~~~~~~a~~~~~~  286 (376)
                      ++.++.+.|++++|..++++
T Consensus        31 la~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen   31 LAQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             HHHHHHHTTHHHHHHHHHHC
T ss_pred             HHHHHHHCCCHHHHHHHHHH
Confidence            44444444444444444444

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

Probab=98.33  E-value=2.5e-05  Score=65.15  Aligned_cols=93  Identities=10%  Similarity=-0.035  Sum_probs=74.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  101 (376)
                      -...+...|++++|++.|+++++.+ +.+...|..+..+|...|++++|+..+++++..... +...|..+..++...|+
T Consensus         8 ~a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~-~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          8 KAKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDPS-LAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhCC
Confidence            3456777888888888888888776 667788888888888888888888888888886433 56678888888888888


Q ss_pred             hHHHHHHHHHHHhcC
Q 042039          102 MDEASRLLDLMVQRD  116 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~  116 (376)
                      +++|...|++.++.+
T Consensus        86 ~~eA~~~~~~al~l~  100 (356)
T PLN03088         86 YQTAKAALEKGASLA  100 (356)
T ss_pred             HHHHHHHHHHHHHhC
Confidence            888888888888763

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.32  E-value=1.1e-06  Score=45.51  Aligned_cols=33  Identities=58%  Similarity=0.953  Sum_probs=23.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPD   50 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~   50 (376)
                      +||.+|.+|++.|++++|.++|++|.+.|++||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            577777777777777777777777777776665

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.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.31  E-value=1.3e-06  Score=45.22  Aligned_cols=33  Identities=30%  Similarity=0.622  Sum_probs=26.0

Q ss_pred             HHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCc
Q 042039          333 IFVTLIHGFVRINKPSKVIELLHKMKEKKVMPD  365 (376)
Q Consensus       333 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~  365 (376)
                      +|+.++.+|.+.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            577777888888888888888888887777776

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

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.29  E-value=1.4e-06  Score=44.79  Aligned_cols=33  Identities=36%  Similarity=0.550  Sum_probs=22.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCC
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINP   49 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~   49 (376)
                      .+|+.++.+|++.|+++.|.++|+.|.+.|++|
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            466677777777777777777777776666554

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

Probab=98.29  E-value=4.2e-05  Score=63.82  Aligned_cols=93  Identities=14%  Similarity=0.070  Sum_probs=60.2

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCc
Q 042039           57 LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGK  136 (376)
Q Consensus        57 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  136 (376)
                      .+..+...|++++|++.|+++++.... +...|..+..++...|++++|+..++++++.. +.+...|..++.+|...|+
T Consensus         8 ~a~~a~~~~~~~~Ai~~~~~Al~~~P~-~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          8 KAKEAFVDDDFALAVDLYTQAIDLDPN-NAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCC
Confidence            345555667777777777777665433 45566666666777777777777777776653 2345566666666777777


Q ss_pred             HHHHHHHHHHHHhcC
Q 042039          137 INRAEELFGSMESMG  151 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~  151 (376)
                      +++|...|+++....
T Consensus        86 ~~eA~~~~~~al~l~  100 (356)
T PLN03088         86 YQTAKAALEKGASLA  100 (356)
T ss_pred             HHHHHHHHHHHHHhC
Confidence            777777777766654

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

Probab=98.29  E-value=0.0026  Score=57.09  Aligned_cols=199  Identities=13%  Similarity=0.107  Sum_probs=132.3

Q ss_pred             HHHHHHH--HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           19 YNTIIDG--LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        19 ~~~l~~~--~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      |..++.+  +.+.|+.++|..+++.....+ +.|..+...+-.+|...++.++|..+|++....  .|+......++.+|
T Consensus        44 ~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~-~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFmay  120 (932)
T KOG2053|consen   44 YAKVLKALSLFRLGKGDEALKLLEALYGLK-GTDDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMAY  120 (932)
T ss_pred             HHHHHHHHHHHHhcCchhHHHHHhhhccCC-CCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHHH
Confidence            4444444  457789999998888777665 347788888888999999999999999988875  56677777888888


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCc----------HHHHHHHHHHHHhcC-CCCChhhHHHHHHH
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGK----------INRAEELFGSMESMG-CKHDDVSYNILING  165 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~  165 (376)
                      .+.+++.+-.+.--++.+. .+-+...+-.++....+.-.          ..-|...++.+...+ .-.+..-.......
T Consensus       121 vR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~i  199 (932)
T KOG2053|consen  121 VREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLI  199 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHH
Confidence            8888877666655555553 34455666666666554321          234555666665543 11122222333455


Q ss_pred             HHccCcHHHHHHHHH-HHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          166 YCKNKEVEEALSLYR-EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       166 ~~~~~~~~~a~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                      +...|++++|+.++. ...+.-.+.+...-+.-+..+...++|.+..++..++...+
T Consensus       200 L~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~  256 (932)
T KOG2053|consen  200 LELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKG  256 (932)
T ss_pred             HHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhC
Confidence            567888999998884 33333233344444566677788888998888888888776

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

Probab=98.28  E-value=2.5e-05  Score=51.47  Aligned_cols=87  Identities=26%  Similarity=0.281  Sum_probs=32.8

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      +..+...|++++|...++++.+.. +.+...+..++.++...+++++|.+.++...... +.+..++..++.++...|++
T Consensus         7 a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   84 (100)
T cd00189           7 GNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGKY   84 (100)
T ss_pred             HHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHhH
Confidence            333334444444444444443321 1122333333334444444444444444433332 22223333333344444444


Q ss_pred             HHHHHHHHH
Q 042039          173 EEALSLYRE  181 (376)
Q Consensus       173 ~~a~~~~~~  181 (376)
                      ++|...+..
T Consensus        85 ~~a~~~~~~   93 (100)
T cd00189          85 EEALEAYEK   93 (100)
T ss_pred             HHHHHHHHH
Confidence            444444333

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=98.27  E-value=8.8e-05  Score=50.52  Aligned_cols=108  Identities=18%  Similarity=0.112  Sum_probs=70.5

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhcccCCCch--HHHHHHHHHHHHhCCChHHHHHHHhcccccCCCC---CHHHHHHHH
Q 042039          229 YNTFIDGLCKNGYIVEAVELFRTLGILKCELD--IQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA---DVVTYNIMI  303 (376)
Q Consensus       229 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~  303 (376)
                      ......++-..|+.++|+.+|++....+....  ...+..++..+...|++++|..++++.... .+.   +......+.
T Consensus         4 ~~~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~-~p~~~~~~~l~~f~A   82 (120)
T PF12688_consen    4 LYELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEE-FPDDELNAALRVFLA   82 (120)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-CCCccccHHHHHHHH
Confidence            44566677778888888888888877664433  456677778888888888888888877654 222   223333445


Q ss_pred             HHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 042039          304 HGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGF  341 (376)
Q Consensus       304 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  341 (376)
                      .++...|+.++|+..+-....    ++...|..-+..|
T Consensus        83 l~L~~~gr~~eAl~~~l~~la----~~~~~y~ra~~~y  116 (120)
T PF12688_consen   83 LALYNLGRPKEALEWLLEALA----ETLPRYRRAIRFY  116 (120)
T ss_pred             HHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            567778888888887766554    2333455555444

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

Probab=98.26  E-value=0.00037  Score=56.33  Aligned_cols=126  Identities=14%  Similarity=0.155  Sum_probs=50.5

Q ss_pred             HHHHHcc-CcHHHHHHHHHHHHHC----CCCC--CHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC-----Cc-chH
Q 042039          163 INGYCKN-KEVEEALSLYREMVSK----GIKP--TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA-----DT-STY  229 (376)
Q Consensus       163 ~~~~~~~-~~~~~a~~~~~~~~~~----~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~-~~~  229 (376)
                      +..|... |++++|++.|++..+.    + .+  -...+..+...+.+.|++++|.++|+++.......     +. ..+
T Consensus       121 A~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~  199 (282)
T PF14938_consen  121 AEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYF  199 (282)
T ss_dssp             HHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHH
Confidence            3344444 4555555555544431    1 10  12334444455555555555555555554431110     01 112


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHhcccCC----CchHHHHHHHHHHHHh--CCChHHHHHHHhcccc
Q 042039          230 NTFIDGLCKNGYIVEAVELFRTLGILKC----ELDIQAYNCLIDGLCK--SGRLEIALELFRSLPR  289 (376)
Q Consensus       230 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~  289 (376)
                      ...+.++...||+..|...+++.....+    .........++.++-.  ...+..+..-|+.+.+
T Consensus       200 l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~  265 (282)
T PF14938_consen  200 LKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISR  265 (282)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS-
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCc
Confidence            2333344455555555555555543321    1112334444444432  2234555555555443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=98.26  E-value=4.1e-05  Score=56.66  Aligned_cols=100  Identities=13%  Similarity=0.086  Sum_probs=53.4

Q ss_pred             hhHHHHHHHHhh-hCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCC--chHhHHHHHHHHHhCCChHHHHHH
Q 042039           32 VDKAKALFLQMK-GENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQP--SVVTFNVIMDELCKNGKMDEASRL  108 (376)
Q Consensus        32 ~~~a~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~  108 (376)
                      +..+...+..+. ..+.......|..++..+...|++++|+..|++.+.....+  ...++..+..++...|++++|...
T Consensus        15 ~~~~~~~l~~~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~   94 (168)
T CHL00033         15 FTIVADILLRILPTTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEY   94 (168)
T ss_pred             cccchhhhhHhccCCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            444444444443 22212234455666666666777777777777766543222  123566666666667777777777


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHH
Q 042039          109 LDLMVQRDVRPNAFTYSTLMDGFC  132 (376)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~l~~~~~  132 (376)
                      +++..... +.....+..+...+.
T Consensus        95 ~~~Al~~~-~~~~~~~~~la~i~~  117 (168)
T CHL00033         95 YFQALERN-PFLPQALNNMAVICH  117 (168)
T ss_pred             HHHHHHhC-cCcHHHHHHHHHHHH
Confidence            76666542 222334444444444

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

Probab=98.23  E-value=6.3e-05  Score=60.51  Aligned_cols=131  Identities=10%  Similarity=0.132  Sum_probs=73.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc-CCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH-ANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      .+|..++...-+.+..+.|..+|.++.+.+ ..+..+|...+..-.. .++.+.|.++|+...+. ...+...|...+..
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            356666666666666777777777766443 3344455544444222 44555577777766665 33355566666666


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCCh---hhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNA---FTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      +...++.+.|..+|++.+.. +.++.   ..|...+..=.+.|+.+.+.++.+++.+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            66666667777777666654 22221   25555555555566666666666555543

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.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.23  E-value=0.00014  Score=53.97  Aligned_cols=93  Identities=11%  Similarity=0.070  Sum_probs=66.1

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc--hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS--VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      ....+..++..+...|++++|...|++.++....+.  ...+..+..++.+.|++++|...+++.++.. +.+...+..+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l  112 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNI  112 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHH
Confidence            355677788888888888888888888876543322  3567778888888888888888888888753 3345666677


Q ss_pred             HHHHHhcCcHHHHHHH
Q 042039          128 MDGFCLTGKINRAEEL  143 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~  143 (376)
                      +.++...|+...+..-
T Consensus       113 g~~~~~~g~~~~a~~~  128 (172)
T PRK02603        113 AVIYHKRGEKAEEAGD  128 (172)
T ss_pred             HHHHHHcCChHhHhhC
Confidence            7777777765554433

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=98.23  E-value=5.4e-05  Score=56.02  Aligned_cols=95  Identities=12%  Similarity=0.032  Sum_probs=60.7

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCC--ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRP--NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILI  163 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  163 (376)
                      ...+..++..+...|++++|...+++.+.....+  ...++..+..++...|++++|...+++..... +.....+..++
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            4456666777777788888888888777653222  23467777777778888888888887777653 34445555666


Q ss_pred             HHHH-------ccCcHHHHHHHHHH
Q 042039          164 NGYC-------KNKEVEEALSLYRE  181 (376)
Q Consensus       164 ~~~~-------~~~~~~~a~~~~~~  181 (376)
                      .++.       ..|+++.|...+++
T Consensus       114 ~i~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033        114 VICHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             HHHHHhhHHHHHcccHHHHHHHHHH
Confidence            6655       55555544444433

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.22  E-value=2.8e-06  Score=43.60  Aligned_cols=33  Identities=24%  Similarity=0.523  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCC
Q 042039          332 IIFVTLIHGFVRINKPSKVIELLHKMKEKKVMP  364 (376)
Q Consensus       332 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p  364 (376)
                      .+|+.++.+|.+.|+++.|.++|+.|.+.|+.|
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            356777777777777777777777777777665

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

Probab=98.22  E-value=3.4e-05  Score=59.90  Aligned_cols=90  Identities=18%  Similarity=0.208  Sum_probs=61.1

Q ss_pred             HHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHH
Q 042039           60 GLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINR  139 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  139 (376)
                      -+.+.+++++|+..|.+++...+. |...|..-..+|.+.|.++.|++-.+..+..+ +--..+|..|..+|...|++.+
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~P~-nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-p~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELDPT-NAVYYCNRAAAYSKLGEYEDAVKDCESALSID-PHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCCC-cchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHccCcHHH
Confidence            345667777777777777775333 56666667777777777777777777776653 2235677777777777777777


Q ss_pred             HHHHHHHHHhcC
Q 042039          140 AEELFGSMESMG  151 (376)
Q Consensus       140 a~~~~~~~~~~~  151 (376)
                      |.+.|++..+..
T Consensus       168 A~~aykKaLeld  179 (304)
T KOG0553|consen  168 AIEAYKKALELD  179 (304)
T ss_pred             HHHHHHhhhccC
Confidence            777777777663

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

Probab=98.21  E-value=3.2e-05  Score=60.04  Aligned_cols=98  Identities=23%  Similarity=0.295  Sum_probs=67.5

Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  174 (376)
                      -..+.+++++|+..|.+.++.. +-|...|..-..+|++.|.++.|++-.+..+..+ +....+|..|..+|...|++++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-p~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID-PHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHccCcHHH
Confidence            3456677777777777777763 3356666677777777777777777777777665 4556677777777777777777


Q ss_pred             HHHHHHHHHHCCCCCCHhHHHH
Q 042039          175 ALSLYREMVSKGIKPTVVTYNT  196 (376)
Q Consensus       175 a~~~~~~~~~~~~~~~~~~~~~  196 (376)
                      |++.|++.++  +.|+..+|..
T Consensus       168 A~~aykKaLe--ldP~Ne~~K~  187 (304)
T KOG0553|consen  168 AIEAYKKALE--LDPDNESYKS  187 (304)
T ss_pred             HHHHHHhhhc--cCCCcHHHHH
Confidence            7777777776  4566555543

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.20  E-value=0.00014  Score=54.00  Aligned_cols=91  Identities=14%  Similarity=0.140  Sum_probs=69.1

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC--hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN--AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILI  163 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  163 (376)
                      ...+..+...+...|++++|...+++.++....+.  ...+..++.++.+.|++++|...+++..... +.+...+..++
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg  113 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNIA  113 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence            44577778888889999999999999887543222  4577888888999999999999999988765 45667777788


Q ss_pred             HHHHccCcHHHHHH
Q 042039          164 NGYCKNKEVEEALS  177 (376)
Q Consensus       164 ~~~~~~~~~~~a~~  177 (376)
                      .++...|+...+..
T Consensus       114 ~~~~~~g~~~~a~~  127 (172)
T PRK02603        114 VIYHKRGEKAEEAG  127 (172)
T ss_pred             HHHHHcCChHhHhh
Confidence            88877777544443

>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=98.20  E-value=7.2e-06  Score=50.32  Aligned_cols=64  Identities=16%  Similarity=0.161  Sum_probs=40.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC-ChHHHHHHHHHHHh
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN-DWNEAKRLFFEMMD   79 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~   79 (376)
                      ++.+|..+...+...|++++|+..|++..+.+ +.+...|..+..++...| ++++|++.+++.++
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            34556666666666666666666666666654 445566666666666666 56666666666554

...

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=98.18  E-value=0.0002  Score=62.54  Aligned_cols=142  Identities=14%  Similarity=0.068  Sum_probs=91.9

Q ss_pred             CCChhhHHHHHHHHhcC-----CChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC--------CChHHHHHHHHHHHh
Q 042039           48 NPDVVTYNSLIHGLCHA-----NDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN--------GKMDEASRLLDLMVQ  114 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~~~a~~~~~~~~~  114 (376)
                      +.+..+|...+++....     ++...|..+|+++++..+. ....+..+..++...        .+...+.+...+...
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~-~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPD-FTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            66777777776654332     2366788888888776322 233444433333221        123344444444433


Q ss_pred             c-CCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhH
Q 042039          115 R-DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT  193 (376)
Q Consensus       115 ~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  193 (376)
                      . ..+.++..+..+...+...|++++|...++++...+  |+...|..++.++...|+.++|.+.++++...  .|...+
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~P~~pt  488 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--RPGENT  488 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCCch
Confidence            2 123345677777777777899999999999998875  57788888999999999999999999988874  444444


Q ss_pred             H
Q 042039          194 Y  194 (376)
Q Consensus       194 ~  194 (376)
                      |
T Consensus       489 ~  489 (517)
T PRK10153        489 L  489 (517)
T ss_pred             H
Confidence            3

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

Probab=98.17  E-value=5.3e-05  Score=49.61  Aligned_cols=77  Identities=16%  Similarity=0.359  Sum_probs=49.6

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCC-CCChhhHHHHHHHHhcCC--------ChHHHHHHHHHHHhcCCCCchHhHHH
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENI-NPDVVTYNSLIHGLCHAN--------DWNEAKRLFFEMMDQGVQPSVVTFNV   91 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~~~   91 (376)
                      ..|..+...+++...-.+|+.+++.|+ .|+..+|+.++.+..+..        +.-+.+.+|+.++..+++|+..+|+.
T Consensus        30 ~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYni  109 (120)
T PF08579_consen   30 DNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNI  109 (120)
T ss_pred             HHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHH
Confidence            345556666777777777777777777 677777777776665542        23345666666666666666666666


Q ss_pred             HHHHHH
Q 042039           92 IMDELC   97 (376)
Q Consensus        92 l~~~~~   97 (376)
                      ++..+.
T Consensus       110 vl~~Ll  115 (120)
T PF08579_consen  110 VLGSLL  115 (120)
T ss_pred             HHHHHH
Confidence            665544

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 [, , ].

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

Probab=98.16  E-value=4.5e-05  Score=61.35  Aligned_cols=145  Identities=15%  Similarity=0.087  Sum_probs=100.2

Q ss_pred             hHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh-CCCHHHHHHHHHHhcccCCCchHHHHHHHHHH
Q 042039          192 VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK-NGYIVEAVELFRTLGILKCELDIQAYNCLIDG  270 (376)
Q Consensus       192 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  270 (376)
                      .+|..+++...+.+..+.|..+|.++.+.+ ..+..+|...+..-.. .++.+.|..+|+...+.- +.+...|...+..
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f-~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKF-PSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHH-TT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            467788888888888888999998887543 4456677777666444 566666888888887653 4467778888888


Q ss_pred             HHhCCChHHHHHHHhcccccCCCCCH---HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 042039          271 LCKSGRLEIALELFRSLPRRVLVADV---VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGF  341 (376)
Q Consensus       271 ~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  341 (376)
                      +...++.+.|..+|++.... .+++.   ..|..++..=.+.|+.+.+.++.+++.+.  .|+...+..++.-|
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            88888888888888888765 33332   47777888778888888888888888774  34444444444333

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.

>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=6.1e-05  Score=63.06  Aligned_cols=123  Identities=11%  Similarity=0.055  Sum_probs=76.6

Q ss_pred             CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc--CCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHH
Q 042039          187 IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD--DVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAY  264 (376)
Q Consensus       187 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  264 (376)
                      .+.+......++..+....+.+.+..++.+....  ....-+.+...+++.|.+.|..++++.+++.=...|+-||..++
T Consensus        62 ~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   62 KPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            3445555666666666666666677766666554  22223445556777777777777777777776666777777777


Q ss_pred             HHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc
Q 042039          265 NCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND  309 (376)
Q Consensus       265 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  309 (376)
                      +.++..+.+.|++..|.++...|.......+..++...+.+|.+.
T Consensus       142 n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  142 NLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            777777777777777777776665554445555554444444443

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 [].

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=98.13  E-value=0.00037  Score=60.92  Aligned_cols=137  Identities=10%  Similarity=0.068  Sum_probs=98.9

Q ss_pred             CCCCchHhHHHHHHHHHhC-----CChHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHhc--------CcHHHHHHHHHH
Q 042039           81 GVQPSVVTFNVIMDELCKN-----GKMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFCLT--------GKINRAEELFGS  146 (376)
Q Consensus        81 ~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~--------~~~~~a~~~~~~  146 (376)
                      ..+.+...|...+++....     ++...|..+|++.++.+  |+ ...+..+..++...        .+...+.+..++
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ld--P~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSE--PDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            3456778888887765432     23778999999999874  44 45555544444322        234455555555


Q ss_pred             HHhcC-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          147 MESMG-CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       147 ~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                      ..... .+.++..+..+.......|++++|...+++++..  .|+...|..+...+...|+.++|...+++..+.+
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L--~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~  483 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL--EMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLR  483 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            44431 2445677888877777889999999999999985  4688899999999999999999999999998764

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

Probab=98.11  E-value=0.00012  Score=61.41  Aligned_cols=122  Identities=16%  Similarity=0.166  Sum_probs=74.0

Q ss_pred             CCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc--CCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHH
Q 042039           83 QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR--DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYN  160 (376)
Q Consensus        83 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  160 (376)
                      +.+......++..+....+.+.+..++.++...  ....-+.|...+++.|...|..+.+..++..-...|+-||..+++
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            334445555555555555666666666666543  111223455566777777777777777777666667667777777


Q ss_pred             HHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc
Q 042039          161 ILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  204 (376)
                      .|+..+.+.|++..|.++...|...+...+..++...+.++.+.
T Consensus       143 ~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  143 LLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            77777777777777777666666555555555555555444443

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 [].

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=98.10  E-value=0.00072  Score=51.64  Aligned_cols=64  Identities=13%  Similarity=0.038  Sum_probs=41.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCC--CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENI--NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      ..+......+...|++.+|+..|+.+.....  +-...+...++.++.+.|++++|...+++.++.
T Consensus         6 ~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen    6 EALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3444455566778888888888888776521  222445666777788888888888888887775

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=98.10  E-value=0.0034  Score=51.02  Aligned_cols=297  Identities=14%  Similarity=0.096  Sum_probs=190.5

Q ss_pred             HHHHHHHHhc--CCChHHHHHHHHHHHhcCCCCchHhHHHHHH--HHHhCCChHHHHHHHHHHHhcCCCCChh--hHHHH
Q 042039           54 YNSLIHGLCH--ANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD--ELCKNGKMDEASRLLDLMVQRDVRPNAF--TYSTL  127 (376)
Q Consensus        54 ~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l  127 (376)
                      |..|-.+++.  .|+-..|.++-.+..+. +..|......++.  +-.-.|+++.|.+-|+.|...   |...  -...|
T Consensus        85 yqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRgL  160 (531)
T COG3898          85 YQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRGL  160 (531)
T ss_pred             HHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHHH
Confidence            4455444443  46777777776665432 2334444444444  445679999999999999863   2222  23334


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC-CCCCHhH--HHHHHHHHH--
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG-IKPTVVT--YNTLFLGLF--  202 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~--~~~l~~~~~--  202 (376)
                      .-...+.|+.+.|..+-+..-... +.-...+...+...+..|+|+.|+++.+.-+... +.++..-  -..|+.+-.  
T Consensus       161 yleAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s  239 (531)
T COG3898         161 YLEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMS  239 (531)
T ss_pred             HHHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHH
Confidence            444457799999999988887764 4556678888999999999999999999876642 3333221  122222211  


Q ss_pred             -hccchHHHHHHHHHHHhcCCCCCc-chHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHH
Q 042039          203 -EIHQVEHALKLFEEMQRDDVAADT-STYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIA  280 (376)
Q Consensus       203 -~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  280 (376)
                       -..+...|...-.+..+.  .|+. ..-.....++.+.|+..++-.+++.+=+..  |.+..+...  .+.+.|+  .+
T Consensus       240 ~ldadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~e--PHP~ia~lY--~~ar~gd--ta  311 (531)
T COG3898         240 LLDADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAE--PHPDIALLY--VRARSGD--TA  311 (531)
T ss_pred             HhcCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcC--CChHHHHHH--HHhcCCC--cH
Confidence             123455666665555554  3332 234455678899999999999999987664  444443322  2344554  33


Q ss_pred             HHHHhccc--ccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh-cCChhhHHHHHHHH
Q 042039          281 LELFRSLP--RRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR-INKPSKVIELLHKM  357 (376)
Q Consensus       281 ~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~a~~~~~~~  357 (376)
                      +.-+++..  ..-.+.+..+...+..+-...|++..|..--+....  ..|....|..+...-.. .|+-.++..++-+.
T Consensus       312 ~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r--~~pres~~lLlAdIeeAetGDqg~vR~wlAqa  389 (531)
T COG3898         312 LDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAAR--EAPRESAYLLLADIEEAETGDQGKVRQWLAQA  389 (531)
T ss_pred             HHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhh--hCchhhHHHHHHHHHhhccCchHHHHHHHHHH
Confidence            33333322  111334677778888899999999998887777665  46788888888776544 59999999999998


Q ss_pred             HhCCCCCc
Q 042039          358 KEKKVMPD  365 (376)
Q Consensus       358 ~~~~~~p~  365 (376)
                      .+..-.|+
T Consensus       390 v~APrdPa  397 (531)
T COG3898         390 VKAPRDPA  397 (531)
T ss_pred             hcCCCCCc
Confidence            87654543

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

Probab=98.09  E-value=2.2e-05  Score=47.45  Aligned_cols=58  Identities=19%  Similarity=0.214  Sum_probs=37.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      +...+.+.|++++|++.|+++.+.. |.+...+..+..++...|++++|...|+++++.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3455666677777777777766665 445666666666777777777777777666654

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

Probab=98.08  E-value=0.00049  Score=53.89  Aligned_cols=110  Identities=9%  Similarity=0.084  Sum_probs=87.3

Q ss_pred             HHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC---cHHHHHHHHHHHHh
Q 042039           73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG---KINRAEELFGSMES  149 (376)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~  149 (376)
                      -++.-+..++. |...|..|...|...|++..|...|.+..+.. ++++..+..+..++..+.   ...++..+|+++..
T Consensus       144 ~Le~~L~~nP~-d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~  221 (287)
T COG4235         144 RLETHLQQNPG-DAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALA  221 (287)
T ss_pred             HHHHHHHhCCC-CchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Confidence            33343444333 78889999999999999999999999998874 556777777777766543   46688899999988


Q ss_pred             cCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          150 MGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       150 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      .+ +.++.+...|...+...|++.+|...|+.|++.
T Consensus       222 ~D-~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         222 LD-PANIRALSLLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             cC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc
Confidence            76 678888888889999999999999999999986

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=98.08  E-value=0.00041  Score=47.28  Aligned_cols=90  Identities=22%  Similarity=0.175  Sum_probs=41.7

Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCC--HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCC--CCcchHHHHHHHHH
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPT--VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVA--ADTSTYNTFIDGLC  237 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~  237 (376)
                      +..++-..|+.++|+.+|++.+..|....  ...+..+...+...|++++|..+++........  .+......+..++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            34444555555555555555555444332  233444455555555555555555555443210  01122222333444


Q ss_pred             hCCCHHHHHHHHHH
Q 042039          238 KNGYIVEAVELFRT  251 (376)
Q Consensus       238 ~~~~~~~a~~~~~~  251 (376)
                      ..|+.++|+..+-.
T Consensus        87 ~~gr~~eAl~~~l~  100 (120)
T PF12688_consen   87 NLGRPKEALEWLLE  100 (120)
T ss_pred             HCCCHHHHHHHHHH
Confidence            55555555555444

>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=98.07  E-value=1.3e-05  Score=48.97  Aligned_cols=53  Identities=21%  Similarity=0.216  Sum_probs=35.0

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      .+.|++++|+++|+++.... |.+..++..++.+|.+.|++++|.++++++...
T Consensus         2 l~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hhccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            45667777777777766654 446666666777777777777777777766665

...

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

Probab=98.07  E-value=0.0005  Score=53.85  Aligned_cols=111  Identities=13%  Similarity=0.101  Sum_probs=92.1

Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC---cHHHHHHHHHHHHH
Q 042039          108 LLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK---EVEEALSLYREMVS  184 (376)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~  184 (376)
                      -++.-+..+ +.|...|..|...|...|+++.|...|.+..+.. ++++..+..+..++....   ...++..++++++.
T Consensus       144 ~Le~~L~~n-P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~  221 (287)
T COG4235         144 RLETHLQQN-PGDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALA  221 (287)
T ss_pred             HHHHHHHhC-CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Confidence            334444443 5588999999999999999999999999999886 678888888887776543   45789999999998


Q ss_pred             CCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          185 KGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       185 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                      .+ +.+..+...+...+...|++.+|...|+.|++..
T Consensus       222 ~D-~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~l  257 (287)
T COG4235         222 LD-PANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLL  257 (287)
T ss_pred             cC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC
Confidence            73 4478888889999999999999999999999985

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=98.06  E-value=0.0018  Score=49.42  Aligned_cols=65  Identities=15%  Similarity=0.167  Sum_probs=42.2

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--CchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      ...+...+..+...|++.+|.+.|+.+....+.  --......++.++.+.|+++.|...++++++.
T Consensus         5 ~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen    5 AEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344555666677778888888888888765222  12334556677777888888888888887765

>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=98.03  E-value=3.6e-05  Score=47.19  Aligned_cols=63  Identities=21%  Similarity=0.239  Sum_probs=34.4

Q ss_pred             hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC-cHHHHHHHHHHHHH
Q 042039          121 AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK-EVEEALSLYREMVS  184 (376)
Q Consensus       121 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~  184 (376)
                      ..+|..++..+...|++++|+..|++..+.. |.+...+..++.++...| ++++|++.+++.++
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            3445555555555555555555555555554 344555555555555555 45555555555544

...

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=98.02  E-value=0.0023  Score=46.31  Aligned_cols=126  Identities=12%  Similarity=0.041  Sum_probs=68.1

Q ss_pred             CCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCChhhHHH
Q 042039           83 QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-KHDDVSYNI  161 (376)
Q Consensus        83 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~  161 (376)
                      .|+...-..+..+..+.|+..+|...|++....-..-|......+.++....+++..|...++++.+.+. ..++.....
T Consensus        86 ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll  165 (251)
T COG4700          86 APTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLL  165 (251)
T ss_pred             chhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHH
Confidence            4455555556666666666666666666665543344455555566666666666666666666554421 012233444


Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHH
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  210 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  210 (376)
                      +.+.+...|.+.+|...|+...+.  -|+..........+.+.|+.+++
T Consensus       166 ~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea  212 (251)
T COG4700         166 FARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREA  212 (251)
T ss_pred             HHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHH
Confidence            556666666666666666666653  34444444444444555544433

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

Probab=98.00  E-value=8.3e-05  Score=48.71  Aligned_cols=76  Identities=13%  Similarity=0.336  Sum_probs=48.6

Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHcCC-CCcHHHHHHHHHHHhhcC--------ChhhHHHHHHHHHhCCCCCchHHHHH
Q 042039          301 IMIHGLCNDGQMDKAHDLFLDMEENAV-APNVIIFVTLIHGFVRIN--------KPSKVIELLHKMKEKKVMPDASIVSM  371 (376)
Q Consensus       301 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g--------~~~~a~~~~~~~~~~~~~p~~~~~~~  371 (376)
                      ..+..+...+++...-.+|+.+...|+ -|+..+|+.++.+..+..        +.-+.+.+|+.|...++.|+..||+.
T Consensus        30 ~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYni  109 (120)
T PF08579_consen   30 DNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNI  109 (120)
T ss_pred             HHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHH
Confidence            344445555666666666666666666 666666666666554421        23346677777777778888888887


Q ss_pred             HHhhC
Q 042039          372 VVDLL  376 (376)
Q Consensus       372 ll~~l  376 (376)
                      ++..|
T Consensus       110 vl~~L  114 (120)
T PF08579_consen  110 VLGSL  114 (120)
T ss_pred             HHHHH
Confidence            77643

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

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

Probab=98.00  E-value=9.4e-06  Score=40.54  Aligned_cols=29  Identities=38%  Similarity=0.736  Sum_probs=20.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCC
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGEN   46 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~   46 (376)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            57777777777777777777777776654

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.

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.99  E-value=0.0013  Score=50.38  Aligned_cols=178  Identities=16%  Similarity=0.096  Sum_probs=89.7

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHH
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEAS  106 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  106 (376)
                      ...|+..+.+.-+..+...        -...+.........+..++.|++-.       ....+.++.++.-.+.+.-..
T Consensus       133 ~~lgnpqesLdRl~~L~~~--------V~~ii~~~e~~~~~ESsv~lW~KRl-------~~Vmy~~~~~llG~kEy~iS~  197 (366)
T KOG2796|consen  133 QYLGNPQESLDRLHKLKTV--------VSKILANLEQGLAEESSIRLWRKRL-------GRVMYSMANCLLGMKEYVLSV  197 (366)
T ss_pred             HhcCCcHHHHHHHHHHHHH--------HHHHHHHHHhccchhhHHHHHHHHH-------HHHHHHHHHHHhcchhhhhhH
Confidence            3456666665554444321        1122233333333344555554432       223344555555556666666


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChh-----hHHHHHHHHHccCcHHHHHHHHHH
Q 042039          107 RLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDV-----SYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                      ..+.++++...+.++.....+++...+.||.+.|...|++..+..-..+..     +..+....|.-.+++..|...+.+
T Consensus       198 d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~  277 (366)
T KOG2796|consen  198 DAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTE  277 (366)
T ss_pred             HHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhh
Confidence            666666665544455556666666666666666666666554332222222     222333445555666666666666


Q ss_pred             HHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          182 MVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       182 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      +...+ +.++...+.-.-+..-.|+...|.+.++.+.+.
T Consensus       278 i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  278 ILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             ccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            55542 223333344444444456666666666666654

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.96  E-value=0.005  Score=53.97  Aligned_cols=241  Identities=17%  Similarity=0.119  Sum_probs=149.8

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc-CCCCchH--hH----HHHHHHHHhCCChHHHHHHHHHHHhcCCCCC
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ-GVQPSVV--TF----NVIMDELCKNGKMDEASRLLDLMVQRDVRPN  120 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~--~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  120 (376)
                      .|.+..|..+.......-.++-|...|-+.... |++.-..  +.    ..-.....--|++++|+++|-++-+++    
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~drrD----  764 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDADRRD----  764 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhccchhh----
Confidence            577888888888877777788888777655432 2211000  00    001122233478888888887775542    


Q ss_pred             hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 042039          121 AFTYSTLMDGFCLTGKINRAEELFGSMESMG-CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL  199 (376)
Q Consensus       121 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  199 (376)
                           ..+..+.+.|++-...++++.--... -..-..+|+.+...+.....|++|.+.|......         ...+.
T Consensus       765 -----LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~~---------e~~~e  830 (1189)
T KOG2041|consen  765 -----LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGDT---------ENQIE  830 (1189)
T ss_pred             -----hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccch---------HhHHH
Confidence                 24566677788877777765421110 0112347888888888888899999888764331         34567


Q ss_pred             HHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHH
Q 042039          200 GLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEI  279 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  279 (376)
                      ++.+..++++...+...+     +.+...+-.++.++...|.-++|.+.+-+..    .|.     ..+..|...++|.+
T Consensus       831 cly~le~f~~LE~la~~L-----pe~s~llp~~a~mf~svGMC~qAV~a~Lr~s----~pk-----aAv~tCv~LnQW~~  896 (1189)
T KOG2041|consen  831 CLYRLELFGELEVLARTL-----PEDSELLPVMADMFTSVGMCDQAVEAYLRRS----LPK-----AAVHTCVELNQWGE  896 (1189)
T ss_pred             HHHHHHhhhhHHHHHHhc-----CcccchHHHHHHHHHhhchHHHHHHHHHhcc----CcH-----HHHHHHHHHHHHHH
Confidence            777777777665554443     5667788889999999999999988776533    222     34566778888888


Q ss_pred             HHHHHhcccccCCCCCHHHH--------------HHHHHHHHccCChhHHHHHHHHHHH
Q 042039          280 ALELFRSLPRRVLVADVVTY--------------NIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       280 a~~~~~~~~~~~~~~~~~~~--------------~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      |.++-+...-    |...+.              ..-+..+.+.|++=.|.+++.+|.+
T Consensus       897 avelaq~~~l----~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae  951 (1189)
T KOG2041|consen  897 AVELAQRFQL----PQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAE  951 (1189)
T ss_pred             HHHHHHhccc----hhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhH
Confidence            8888776432    122111              1223345556666666666666643

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.95  E-value=0.0025  Score=55.25  Aligned_cols=88  Identities=18%  Similarity=0.172  Sum_probs=50.1

Q ss_pred             cchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHH--------
Q 042039          226 TSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVV--------  297 (376)
Q Consensus       226 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--------  297 (376)
                      ..+...+...+.+...+.-|.++|..+...         ..++......++|++|..+-++..+.  .|+..        
T Consensus       747 re~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLA  815 (1081)
T KOG1538|consen  747 REPLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLA  815 (1081)
T ss_pred             hhHHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhh
Confidence            344455555555566666777777666432         24555666777777777777765543  22221        


Q ss_pred             ---HHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          298 ---TYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       298 ---~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                         -|...-.+|.+.|+-.+|..+++++..
T Consensus       816 E~DrFeEAqkAfhkAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  816 ENDRFEEAQKAFHKAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             hhhhHHHHHHHHHHhcchHHHHHHHHHhhh
Confidence               122333455566666666666666654

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

Probab=97.95  E-value=6.3e-05  Score=45.40  Aligned_cols=56  Identities=14%  Similarity=0.204  Sum_probs=27.6

Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      +..+...|++++|...|+.+.... |.+...+..++.++...|++++|...|+++++
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344445555555555555555443 33444555555555555555555555555444

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

Probab=97.89  E-value=2e-05  Score=39.32  Aligned_cols=30  Identities=20%  Similarity=0.614  Sum_probs=20.5

Q ss_pred             HHHHHHHHHhhcCChhhHHHHHHHHHhCCC
Q 042039          333 IFVTLIHGFVRINKPSKVIELLHKMKEKKV  362 (376)
Q Consensus       333 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  362 (376)
                      +|+.++.+|.+.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            566677777777777777777777766653

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.

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.85  E-value=0.0051  Score=44.61  Aligned_cols=134  Identities=14%  Similarity=0.052  Sum_probs=101.2

Q ss_pred             CCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCC-CCCHhHHH
Q 042039          117 VRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGI-KPTVVTYN  195 (376)
Q Consensus       117 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~  195 (376)
                      ..|+...-..+..+....|+..+|...|++...--+-.|......+.++....+++..|...++++.+... .-++.+..
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            35677777788889999999999999999988765666777888888888889999999999998887531 11244556


Q ss_pred             HHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          196 TLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       196 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      .+.+.+...|.+.+|..-|+.....  -|+..........+.+.|+.+++..-+..+
T Consensus       165 l~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~aq~~~v  219 (251)
T COG4700         165 LFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANAQYVAV  219 (251)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHHHHHHH
Confidence            6778888899999999999988875  456665555666777888777665544333

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.84  E-value=0.00066  Score=53.73  Aligned_cols=88  Identities=13%  Similarity=0.073  Sum_probs=51.1

Q ss_pred             HhCCChHHHHHHHhcccccCCCCC---HHHHHHHHHHHHccCChhHHHHHHHHHHHcCC--CCcHHHHHHHHHHHhhcCC
Q 042039          272 CKSGRLEIALELFRSLPRRVLVAD---VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV--APNVIIFVTLIHGFVRINK  346 (376)
Q Consensus       272 ~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~  346 (376)
                      .+.|++++|...|+.+.+. .|.+   +..+..++.+|...|++++|...|+.+.+...  ......+..+...+...|+
T Consensus       154 ~~~~~y~~Ai~af~~fl~~-yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~  232 (263)
T PRK10803        154 QDKSRQDDAIVAFQNFVKK-YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGD  232 (263)
T ss_pred             HhcCCHHHHHHHHHHHHHH-CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCC
Confidence            4456666666666666654 2212   24556666666667777777777666665311  1123444445555666677


Q ss_pred             hhhHHHHHHHHHhC
Q 042039          347 PSKVIELLHKMKEK  360 (376)
Q Consensus       347 ~~~a~~~~~~~~~~  360 (376)
                      +++|...|+++.+.
T Consensus       233 ~~~A~~~~~~vi~~  246 (263)
T PRK10803        233 TAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHHHHHH
Confidence            77777777666654

>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=97.82  E-value=0.0001  Score=44.98  Aligned_cols=50  Identities=20%  Similarity=0.260  Sum_probs=23.9

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          134 TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       134 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      .|++++|.+.|+++.... |.+...+..++.+|.+.|++++|..+++++..
T Consensus         4 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             ccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            444555555555544443 33444444455555555555555555555444

...

>PRK15331 chaperone protein SicA; Provisional

Probab=97.81  E-value=0.0049  Score=44.06  Aligned_cols=91  Identities=15%  Similarity=0.093  Sum_probs=63.7

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  171 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  171 (376)
                      ...-+...|++++|..+|+-+...+ .-+..-+..|+.++-..+++++|...|......+ +.|+..+...+.++...|+
T Consensus        43 ~Ay~~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-~~dp~p~f~agqC~l~l~~  120 (165)
T PRK15331         43 HAYEFYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-KNDYRPVFFTGQCQLLMRK  120 (165)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-cCCCCccchHHHHHHHhCC
Confidence            3444566778888888777776654 3355566677777777777888888777776655 3555666667777777888


Q ss_pred             HHHHHHHHHHHHH
Q 042039          172 VEEALSLYREMVS  184 (376)
Q Consensus       172 ~~~a~~~~~~~~~  184 (376)
                      .+.|...|+....
T Consensus       121 ~~~A~~~f~~a~~  133 (165)
T PRK15331        121 AAKARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHHHHh
Confidence            8888887777776

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.81  E-value=0.00067  Score=53.68  Aligned_cols=96  Identities=11%  Similarity=0.062  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--CchHhHHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPD---VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PSVVTFNVIM   93 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~   93 (376)
                      |...+....+.|++++|+..|+.+.+.. |.+   ..++..++.+|...|++++|...|+.+.+..+.  .....+..++
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~y-P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg  224 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKY-PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG  224 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHC-cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence            3333333344566666666666665542 111   234555556666666666666666666543111  1233344444


Q ss_pred             HHHHhCCChHHHHHHHHHHHhc
Q 042039           94 DELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .++...|+.++|..+|+.+++.
T Consensus       225 ~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        225 VIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            4555556666666666655554

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

Probab=97.78  E-value=0.016  Score=48.29  Aligned_cols=201  Identities=13%  Similarity=0.092  Sum_probs=127.0

Q ss_pred             CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh----------c--
Q 042039          153 KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR----------D--  220 (376)
Q Consensus       153 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----------~--  220 (376)
                      +..+..|.-....+...++-+.|+...+.....  .|+...  .+...+.-..+-+.....|+...+          .  
T Consensus       299 ~~~~evw~dys~Y~~~isd~q~al~tv~rg~~~--spsL~~--~lse~yel~nd~e~v~~~fdk~~q~L~r~ys~~~s~~  374 (660)
T COG5107         299 YYAEEVWFDYSEYLIGISDKQKALKTVERGIEM--SPSLTM--FLSEYYELVNDEEAVYGCFDKCTQDLKRKYSMGESES  374 (660)
T ss_pred             hhhHHHHHHHHHHHhhccHHHHHHHHHHhcccC--CCchhe--eHHHHHhhcccHHHHhhhHHHHHHHHHHHHhhhhhhh
Confidence            345667776677777788888888887765542  333111  122222222232222222222110          0  


Q ss_pred             --CCC---------------CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC-CCchHHHHHHHHHHHHhCCChHHHHH
Q 042039          221 --DVA---------------ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK-CELDIQAYNCLIDGLCKSGRLEIALE  282 (376)
Q Consensus       221 --~~~---------------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~  282 (376)
                        +..               .-..++...+.+..+..-.+.|..+|-++.+.+ ..++...+++++..++ .|+..-|..
T Consensus       375 ~s~~D~N~e~~~Ell~kr~~k~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~  453 (660)
T COG5107         375 ASKVDNNFEYSKELLLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYN  453 (660)
T ss_pred             hccccCCccccHHHHHHHHhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHH
Confidence              110               011234445555566677899999999998877 4556677777777654 788899999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc--HHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          283 LFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN--VIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       283 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      +|+.-... .+.+....+..+..+...++-..|..+|+..++. +..+  ..+|..++..-...|+...+..+-++|.+.
T Consensus       454 ifelGl~~-f~d~~~y~~kyl~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~  531 (660)
T COG5107         454 IFELGLLK-FPDSTLYKEKYLLFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL  531 (660)
T ss_pred             HHHHHHHh-CCCchHHHHHHHHHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH
Confidence            99876654 3444444566777788889999999999977654 2223  567888888778888888888877777653

>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=97.76  E-value=0.0013  Score=47.33  Aligned_cols=74  Identities=9%  Similarity=0.183  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH-----hCCCCCchHHHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK-----EKKVMPDASIVSMV  372 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-----~~~~~p~~~~~~~l  372 (376)
                      ....++..+...|++++|..+++.+....+ .+...|..++.+|...|+..+|.+.|+++.     +.|+.|+..+-...
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP-~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~l~  142 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDP-YDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRALY  142 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHST-T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHHHH
Confidence            455677778889999999999999988643 377889999999999999999999998885     34899988876543

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

>PRK15331 chaperone protein SicA; Provisional

Probab=97.76  E-value=0.0016  Score=46.42  Aligned_cols=93  Identities=16%  Similarity=0.034  Sum_probs=70.8

Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccC
Q 042039          231 TFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDG  310 (376)
Q Consensus       231 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  310 (376)
                      ..+.-+...|++++|..+|+-+...++. ++.-+..|+.++-..+++++|+..|....... ..|+..+...+.++...|
T Consensus        42 ~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~-n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-~~dp~p~f~agqC~l~l~  119 (165)
T PRK15331         42 AHAYEFYNQGRLDEAETFFRFLCIYDFY-NPDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-KNDYRPVFFTGQCQLLMR  119 (165)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-cCCCCccchHHHHHHHhC
Confidence            3344456788888998888888776633 66777888888888888999988887765442 345666777888888889


Q ss_pred             ChhHHHHHHHHHHHc
Q 042039          311 QMDKAHDLFLDMEEN  325 (376)
Q Consensus       311 ~~~~a~~~~~~~~~~  325 (376)
                      +.+.|...|+.+.+.
T Consensus       120 ~~~~A~~~f~~a~~~  134 (165)
T PRK15331        120 KAAKARQCFELVNER  134 (165)
T ss_pred             CHHHHHHHHHHHHhC
Confidence            999998888888773

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.75  E-value=0.00023  Score=44.13  Aligned_cols=57  Identities=9%  Similarity=0.002  Sum_probs=39.8

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcC
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQG   81 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   81 (376)
                      ..|.+.+++++|+++++.+...+ |.++..+...+.++...|++++|.+.|++..+.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            45666777777777777777665 5566677777777777777777777777777653

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.73  E-value=0.017  Score=47.15  Aligned_cols=290  Identities=14%  Similarity=0.157  Sum_probs=176.5

Q ss_pred             hHHHHHHHHHh--cCChhHHHHHHHHhhhCCCCCChhhHHHHH--HHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH--
Q 042039           18 TYNTIIDGLCK--EGFVDKAKALFLQMKGENINPDVVTYNSLI--HGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV--   91 (376)
Q Consensus        18 ~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--   91 (376)
                      .|.+|-.++..  .|+-..|.++-.+..+. +..|...+..++  +.-.-.|+++.|.+-|+.|..     ++.+-..  
T Consensus        84 gyqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~-----dPEtRllGL  157 (531)
T COG3898          84 GYQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLD-----DPETRLLGL  157 (531)
T ss_pred             HHHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhc-----ChHHHHHhH
Confidence            35555555443  47777887777665432 233444444444  344456899999999999876     3333222  


Q ss_pred             --HHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CCCChh--hHHHHHHHH
Q 042039           92 --IMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG-CKHDDV--SYNILINGY  166 (376)
Q Consensus        92 --l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~--~~~~l~~~~  166 (376)
                        |.-..-+.|+.+.|.++-+..-..- +.-...+...+...+..|+++.|+++.+.-.... +.++..  .-..|+.+-
T Consensus       158 RgLyleAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAk  236 (531)
T COG3898         158 RGLYLEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAK  236 (531)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHH
Confidence              2223346788888888888776653 3346778888888999999999999988765432 222221  111122111


Q ss_pred             ---HccCcHHHHHHHHHHHHHCCCCCCH-hHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCH
Q 042039          167 ---CKNKEVEEALSLYREMVSKGIKPTV-VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYI  242 (376)
Q Consensus       167 ---~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  242 (376)
                         .-..+...|...-.+..+  +.|+. ..-..-..++.+.|+..++-.+++.+-+....|  ....  +..+.+.|+ 
T Consensus       237 A~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP--~ia~--lY~~ar~gd-  309 (531)
T COG3898         237 AMSLLDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHP--DIAL--LYVRARSGD-  309 (531)
T ss_pred             HHHHhcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCCh--HHHH--HHHHhcCCC-
Confidence               113356666666666655  34442 223344577888899999999999888774333  3222  222334454 


Q ss_pred             HHHHHHHHHhc---ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHc-cCChhHHHHH
Q 042039          243 VEAVELFRTLG---ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN-DGQMDKAHDL  318 (376)
Q Consensus       243 ~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~  318 (376)
                       .+.+-++++.   ... +.+......+.++-...|++..|..--+...+  ..|....|..|...-.. .|+-.++...
T Consensus       310 -ta~dRlkRa~~L~slk-~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r--~~pres~~lLlAdIeeAetGDqg~vR~w  385 (531)
T COG3898         310 -TALDRLKRAKKLESLK-PNNAESSLAVAEAALDAGEFSAARAKAEAAAR--EAPRESAYLLLADIEEAETGDQGKVRQW  385 (531)
T ss_pred             -cHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHhccchHHHHHHHHHHhh--hCchhhHHHHHHHHHhhccCchHHHHHH
Confidence             3333333332   222 22556667777788888888888877776655  35677777777766544 4888888888


Q ss_pred             HHHHHHc
Q 042039          319 FLDMEEN  325 (376)
Q Consensus       319 ~~~~~~~  325 (376)
                      +.+....
T Consensus       386 lAqav~A  392 (531)
T COG3898         386 LAQAVKA  392 (531)
T ss_pred             HHHHhcC
Confidence            8888764

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.68  E-value=0.021  Score=47.25  Aligned_cols=82  Identities=11%  Similarity=0.002  Sum_probs=55.1

Q ss_pred             hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC---CCCChhhHHHHHHHHHc---cCcHHHHHHHHHHHHHCCCCCCHhHH
Q 042039          121 AFTYSTLMDGFCLTGKINRAEELFGSMESMG---CKHDDVSYNILINGYCK---NKEVEEALSLYREMVSKGIKPTVVTY  194 (376)
Q Consensus       121 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~  194 (376)
                      ..+...++-+|....+++...++.+.+....   +......-...+-++.+   .|+.++|++++..+......+++.++
T Consensus       141 ~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~  220 (374)
T PF13281_consen  141 PDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTL  220 (374)
T ss_pred             hhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHH
Confidence            3445566667888888888888888887652   12223333445556666   78888888888886665566777788


Q ss_pred             HHHHHHHH
Q 042039          195 NTLFLGLF  202 (376)
Q Consensus       195 ~~l~~~~~  202 (376)
                      ..+++.|-
T Consensus       221 gL~GRIyK  228 (374)
T PF13281_consen  221 GLLGRIYK  228 (374)
T ss_pred             HHHHHHHH
Confidence            77776654

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.64  E-value=0.021  Score=47.34  Aligned_cols=100  Identities=11%  Similarity=0.052  Sum_probs=70.2

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcC---CCCChhhHHHHHHHHHh---cCcHHHHHHHHHHHHhcCCCCChhhH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRD---VRPNAFTYSTLMDGFCL---TGKINRAEELFGSMESMGCKHDDVSY  159 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~  159 (376)
                      ..+...++-+|....+++...++.+.+....   +.....+-...+-++.+   .|+.++|.+++..+......+++.++
T Consensus       141 ~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~  220 (374)
T PF13281_consen  141 PDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTL  220 (374)
T ss_pred             hhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHH
Confidence            3444566667888999999999999998641   11123333455666667   89999999999996665557888899


Q ss_pred             HHHHHHHHc---------cCcHHHHHHHHHHHHHC
Q 042039          160 NILINGYCK---------NKEVEEALSLYREMVSK  185 (376)
Q Consensus       160 ~~l~~~~~~---------~~~~~~a~~~~~~~~~~  185 (376)
                      ..++..|-.         ....++|+..|.+.-+.
T Consensus       221 gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~  255 (374)
T PF13281_consen  221 GLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI  255 (374)
T ss_pred             HHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC
Confidence            888887743         22356777777776653

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.60  E-value=0.00069  Score=41.95  Aligned_cols=54  Identities=13%  Similarity=0.036  Sum_probs=26.4

Q ss_pred             HHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          130 GFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      .|.+.++++.|.++++.+...+ |.++..+...+.++...|++++|...++...+
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3444455555555555554443 33444444455555555555555555555544

>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=97.55  E-value=0.00098  Score=47.97  Aligned_cols=72  Identities=22%  Similarity=0.315  Sum_probs=46.3

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHh-----cCCCCChhhH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQ-----RDVRPNAFTY  124 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  124 (376)
                      .+...++..+...|++++|..+++.+....+- +...|..++.++...|+..+|.+.|+.+.+     .|+.|+..+-
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            45566677777788888888888887776433 667777888888888888888888777653     4677766543

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

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.53  E-value=0.023  Score=43.37  Aligned_cols=25  Identities=16%  Similarity=0.201  Sum_probs=12.4

Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHH
Q 042039          124 YSTLMDGFCLTGKINRAEELFGSME  148 (376)
Q Consensus       124 ~~~l~~~~~~~~~~~~a~~~~~~~~  148 (376)
                      |.....+|....++++|...+.+..
T Consensus        34 yekAAvafRnAk~feKakdcLlkA~   58 (308)
T KOG1585|consen   34 YEKAAVAFRNAKKFEKAKDCLLKAS   58 (308)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHH
Confidence            3334444555555555555555443

>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=97.53  E-value=0.00041  Score=43.65  Aligned_cols=62  Identities=18%  Similarity=0.215  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHHHc----CC-CCc-HHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          297 VTYNIMIHGLCNDGQMDKAHDLFLDMEEN----AV-APN-VIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       297 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      .+++.++.+|...|++++|+..|+++.+.    |. .|+ ..++..+..+|...|++++|++++++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45556666666666666666666665532    11 111 3456666666677777777777766654

...

>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=97.53  E-value=0.0035  Score=46.85  Aligned_cols=86  Identities=21%  Similarity=0.259  Sum_probs=52.6

Q ss_pred             hHHHHHHHHHHHHh-----CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc----------------CChhHHHHH
Q 042039          260 DIQAYNCLIDGLCK-----SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND----------------GQMDKAHDL  318 (376)
Q Consensus       260 ~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------------~~~~~a~~~  318 (376)
                      +..+|..++..+.+     .|..+=....+..|.+.|+.-|..+|+.|+.++=+.                .+-+-|+++
T Consensus        46 ~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~l  125 (228)
T PF06239_consen   46 DKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDL  125 (228)
T ss_pred             cHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHH
Confidence            34444444444432     234444444555555555555556666555554331                233558888


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHhhcC
Q 042039          319 FLDMEENAVAPNVIIFVTLIHGFVRIN  345 (376)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~l~~~~~~~g  345 (376)
                      +++|...|+-||..++..++..+.+.+
T Consensus       126 L~qME~~gV~Pd~Et~~~ll~iFG~~s  152 (228)
T PF06239_consen  126 LEQMENNGVMPDKETEQMLLNIFGRKS  152 (228)
T ss_pred             HHHHHHcCCCCcHHHHHHHHHHhcccc
Confidence            999999999999999998888885544

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

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.51  E-value=0.043  Score=45.91  Aligned_cols=59  Identities=17%  Similarity=0.199  Sum_probs=45.7

Q ss_pred             HHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHH
Q 042039          306 LCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSM  371 (376)
Q Consensus       306 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~  371 (376)
                      +..+|++.++.-.-.-+.+  +.|++.+|..+.-+.....++++|..++.++     +|+..+++.
T Consensus       472 Lysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~L-----P~n~~~~ds  530 (549)
T PF07079_consen  472 LYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQKL-----PPNERMRDS  530 (549)
T ss_pred             HHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHHhC-----CCchhhHHH
Confidence            4567888887665555544  6789999999999999999999999999876     566666553

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>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=97.46  E-value=0.00033  Score=44.11  Aligned_cols=61  Identities=21%  Similarity=0.254  Sum_probs=31.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhC----CC-CCC-hhhHHHHHHHHhcCCChHHHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGE----NI-NPD-VVTYNSLIHGLCHANDWNEAKRLFFEMM   78 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~-~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~   78 (376)
                      +|+.+...|...|++++|++.|++..+.    |. .|+ ..++..++.++...|++++|++.+++..
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4555555666666666666666555432    10 011 3345555555555555555555555543

...

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.41  E-value=0.086  Score=47.04  Aligned_cols=325  Identities=12%  Similarity=0.099  Sum_probs=178.9

Q ss_pred             ccccCCChhhHHH-----HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC--hHHHHHHHHHHHhcC
Q 042039            9 GVVCKPNTVTYNT-----IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND--WNEAKRLFFEMMDQG   81 (376)
Q Consensus         9 ~~~~~p~~~~~~~-----l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~   81 (376)
                      ..|++-+..-|..     +++-+...+.|..|+++-..+...-.. +...|......+.+..+  -+++.+.+++=++..
T Consensus       425 ~~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~-~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~  503 (829)
T KOG2280|consen  425 RIGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQ-GDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAK  503 (829)
T ss_pred             ccCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCcccc-ccHHHHHHHHHHHhccCccchHHHHHHHHHhccc
Confidence            3455555555544     456677778888888887766533212 25666667777766632  223344333333322


Q ss_pred             CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC----CChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC------
Q 042039           82 VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR----PNAFTYSTLMDGFCLTGKINRAEELFGSMESMG------  151 (376)
Q Consensus        82 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------  151 (376)
                      . .....|..+++-....|+++-|..+++.=...+..    .+..-+...+.-+...|+.+-...++-.+...-      
T Consensus       504 ~-~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~  582 (829)
T KOG2280|consen  504 L-TPGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLF  582 (829)
T ss_pred             C-CCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence            2 23456777777777888888888776532221100    011223344455566666666666555543321      


Q ss_pred             -----CCCChhhHHHHHH---------HHHccCcHHHHHHHHH--HHHHCC-CCCCHhHHHHHHHHHHhccchH------
Q 042039          152 -----CKHDDVSYNILIN---------GYCKNKEVEEALSLYR--EMVSKG-IKPTVVTYNTLFLGLFEIHQVE------  208 (376)
Q Consensus       152 -----~~~~~~~~~~l~~---------~~~~~~~~~~a~~~~~--~~~~~~-~~~~~~~~~~l~~~~~~~~~~~------  208 (376)
                           .|.....|..+++         .|. .++-.+++..+.  ...... +.+-..........+.+.....      
T Consensus       583 ~~l~~~p~a~~lY~~~~r~~~~~~l~d~y~-q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~  661 (829)
T KOG2280|consen  583 MTLRNQPLALSLYRQFMRHQDRATLYDFYN-QDDNHQALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKAL  661 (829)
T ss_pred             HHHHhchhhhHHHHHHHHhhchhhhhhhhh-cccchhhhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHH
Confidence                 1111122222211         111 111112221111  100000 1111112222333333333211      


Q ss_pred             ----HHHHHHHHHHhc-CCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHH
Q 042039          209 ----HALKLFEEMQRD-DVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALEL  283 (376)
Q Consensus       209 ----~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  283 (376)
                          +-.++.+.+... +......+.+.-+.-+...|+..+|.++-.+..    -|+...|..-+.+++..+++++-.++
T Consensus       662 ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekf  737 (829)
T KOG2280|consen  662 EDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKF  737 (829)
T ss_pred             HHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHH
Confidence                112222222221 223444566667777888999999999988875    56888888889999999999998887


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHH
Q 042039          284 FRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLH  355 (376)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  355 (376)
                      -+...      ++.-|...+.+|.+.|+.++|.+++-+....     .    ..+.+|.+.|++.+|.++--
T Consensus       738 Akskk------sPIGy~PFVe~c~~~~n~~EA~KYiprv~~l-----~----ekv~ay~~~~~~~eAad~A~  794 (829)
T KOG2280|consen  738 AKSKK------SPIGYLPFVEACLKQGNKDEAKKYIPRVGGL-----Q----EKVKAYLRVGDVKEAADLAA  794 (829)
T ss_pred             HhccC------CCCCchhHHHHHHhcccHHHHhhhhhccCCh-----H----HHHHHHHHhccHHHHHHHHH
Confidence            76543      2455777889999999999999998765321     1    46677888888888876543

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.38  E-value=0.09  Score=46.66  Aligned_cols=309  Identities=15%  Similarity=0.133  Sum_probs=155.0

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHH----------HHHHhcCCChHHHHHHHHHHHhcC
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSL----------IHGLCHANDWNEAKRLFFEMMDQG   81 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l----------~~~~~~~~~~~~a~~~~~~~~~~~   81 (376)
                      -.|.+..|..+.+.....-.++.|...|-+...-   +.......|          ...-.--|++++|.++|-.+-++.
T Consensus       688 dnPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY---~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~drrD  764 (1189)
T KOG2041|consen  688 DNPHPRLWRLLAEYALFKLALDTAEHAFVRCGDY---AGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDADRRD  764 (1189)
T ss_pred             cCCchHHHHHHHHHHHHHHhhhhHhhhhhhhccc---cchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhccchhh
Confidence            3688999999999888888889998888776543   111111111          122223478999999987775542


Q ss_pred             CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcC-CCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHh-----------
Q 042039           82 VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD-VRPNAFTYSTLMDGFCLTGKINRAEELFGSMES-----------  149 (376)
Q Consensus        82 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----------  149 (376)
                               ..+..+.+.|++-...++++.--... ...-...++.+...++....|++|.+.|.....           
T Consensus       765 ---------LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~~e~~~ecly~l  835 (1189)
T KOG2041|consen  765 ---------LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGDTENQIECLYRL  835 (1189)
T ss_pred             ---------hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchHhHHHHHHHH
Confidence                     22445556666665555544311100 001134455555555555555555555543211           


Q ss_pred             ----------cCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          150 ----------MGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       150 ----------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                                ..+|.+....-.+..++.+.|.-++|.+.+-+...    |     ...+..|...++|.+|.++-+...-
T Consensus       836 e~f~~LE~la~~Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~----p-----kaAv~tCv~LnQW~~avelaq~~~l  906 (1189)
T KOG2041|consen  836 ELFGELEVLARTLPEDSELLPVMADMFTSVGMCDQAVEAYLRRSL----P-----KAAVHTCVELNQWGEAVELAQRFQL  906 (1189)
T ss_pred             HhhhhHHHHHHhcCcccchHHHHHHHHHhhchHHHHHHHHHhccC----c-----HHHHHHHHHHHHHHHHHHHHHhccc
Confidence                      12344555566666677777777766666543211    1     1234455566666666665543211


Q ss_pred             cCCCCCcch--------------HHHHHHHHHhCCCHHHHHHHHHHhcc----cCCCchH-HHHHHHHHHH---------
Q 042039          220 DDVAADTST--------------YNTFIDGLCKNGYIVEAVELFRTLGI----LKCELDI-QAYNCLIDGL---------  271 (376)
Q Consensus       220 ~~~~~~~~~--------------~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~~-~~~~~l~~~~---------  271 (376)
                          |...+              ....+..+.+.|+.-.|.+++.+|.+    .+.++-. .-...|...+         
T Consensus       907 ----~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~e~~K~~p~lr~KklYVL~AlLvE~h~~~ik  982 (1189)
T KOG2041|consen  907 ----PQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAEREQEKYVPYLRLKKLYVLGALLVENHRQTIK  982 (1189)
T ss_pred             ----hhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence                11111              11223344556665555566555533    2222211 1111111111         


Q ss_pred             -----HhCCChHHHHHHHhcccccC---CC------CCHHHHHHHHHHHHccCChhHHHHHHHHHHHc-CCCCcHHHHHH
Q 042039          272 -----CKSGRLEIALELFRSLPRRV---LV------ADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN-AVAPNVIIFVT  336 (376)
Q Consensus       272 -----~~~~~~~~a~~~~~~~~~~~---~~------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~  336 (376)
                           ...|..++|..+++...-..   +.      .....|..|.+--...|..+.|+..--.+.+. .+-|....|..
T Consensus       983 ~~~~~~~~g~~~dat~lles~~l~~~~ri~~n~WrgAEAyHFmilAQrql~eg~v~~Al~Tal~L~DYEd~lpP~eiySl 1062 (1189)
T KOG2041|consen  983 ELRKIDKHGFLEDATDLLESGLLAEQSRILENTWRGAEAYHFMILAQRQLFEGRVKDALQTALILSDYEDFLPPAEIYSL 1062 (1189)
T ss_pred             HhhhhhhcCcchhhhhhhhhhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHhchHHHHHHHHhhhccHhhcCCHHHHHHH
Confidence                 23466666666554432110   00      01233444555556677888777654444332 34566667776


Q ss_pred             HHHHHhhcC
Q 042039          337 LIHGFVRIN  345 (376)
Q Consensus       337 l~~~~~~~g  345 (376)
                      +.-+-+...
T Consensus      1063 lALaaca~r 1071 (1189)
T KOG2041|consen 1063 LALAACAVR 1071 (1189)
T ss_pred             HHHHHhhhh
Confidence            654444433

>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=97.37  E-value=0.0059  Score=45.70  Aligned_cols=84  Identities=23%  Similarity=0.296  Sum_probs=48.7

Q ss_pred             ChhhHHHHHHHHHh-----cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC----------------cHHHHHHH
Q 042039          120 NAFTYSTLMDGFCL-----TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK----------------EVEEALSL  178 (376)
Q Consensus       120 ~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----------------~~~~a~~~  178 (376)
                      +..+|..++..|.+     .|+.+-....+..|.+.|+..|..+|+.|++++=+..                +-+-|+++
T Consensus        46 ~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~l  125 (228)
T PF06239_consen   46 DKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDL  125 (228)
T ss_pred             cHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHH
Confidence            45555555555543     3666667777777777777777777777777765411                22334455


Q ss_pred             HHHHHHCCCCCCHhHHHHHHHHHHh
Q 042039          179 YREMVSKGIKPTVVTYNTLFLGLFE  203 (376)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~l~~~~~~  203 (376)
                      +++|...|+-||..++..++..+.+
T Consensus       126 L~qME~~gV~Pd~Et~~~ll~iFG~  150 (228)
T PF06239_consen  126 LEQMENNGVMPDKETEQMLLNIFGR  150 (228)
T ss_pred             HHHHHHcCCCCcHHHHHHHHHHhcc
Confidence            5555555555555555555544443

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

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=97.35  E-value=0.0042  Score=52.08  Aligned_cols=67  Identities=13%  Similarity=-0.007  Sum_probs=53.9

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCCh---hhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDV---VTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      +.+...|+.+..+|.+.|++++|+..|++.++.+ |.+.   .+|..+..+|...|++++|++.++++++.
T Consensus        72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~-Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALELN-PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4456788888888888999999999998888775 3333   35888888899999999999998888875

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.31  E-value=0.0079  Score=49.35  Aligned_cols=92  Identities=12%  Similarity=0.057  Sum_probs=46.1

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhc-----CCCC---------chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhh
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQ-----GVQP---------SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFT  123 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~-----~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  123 (376)
                      ...+.+.|++..|...|++++..     +..+         -..++..+..++.+.+++.+|+...+..+..+ ++|+..
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KA  293 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKA  293 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhH
Confidence            45677888888888888876553     0010         11233344444444444444444444444443 334444


Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039          124 YSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       124 ~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      ...-..++...|+++.|...|+++.+.
T Consensus       294 LyRrG~A~l~~~e~~~A~~df~ka~k~  320 (397)
T KOG0543|consen  294 LYRRGQALLALGEYDLARDDFQKALKL  320 (397)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            444444444444444444444444444

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

Probab=97.30  E-value=0.08  Score=44.39  Aligned_cols=339  Identities=13%  Similarity=0.122  Sum_probs=185.8

Q ss_pred             ccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHH
Q 042039           11 VCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFN   90 (376)
Q Consensus        11 ~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   90 (376)
                      .-+.|..+|..|+.-+..+|..++..++++++..- .|--+.+|...+.+-...++++....+|.+.+....  +...|.
T Consensus        37 dNPtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~p-fp~~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~l--~ldLW~  113 (660)
T COG5107          37 DNPTNILSYFQLIQYLETQESMDAEREMYEQLSSP-FPIMEHAWRLYMSGELARKDFRSVESLFGRCLKKSL--NLDLWM  113 (660)
T ss_pred             cCchhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCC-CccccHHHHHHhcchhhhhhHHHHHHHHHHHHhhhc--cHhHHH
Confidence            34567889999999999999999999999999854 244567888888888888899999999998887644  455555


Q ss_pred             HHHHHHHhCCC------hHHHHHHHHHHHh-cCCCCC-hhhHHHHHHHHH---h------cCcHHHHHHHHHHHHhcCCC
Q 042039           91 VIMDELCKNGK------MDEASRLLDLMVQ-RDVRPN-AFTYSTLMDGFC---L------TGKINRAEELFGSMESMGCK  153 (376)
Q Consensus        91 ~l~~~~~~~~~------~~~a~~~~~~~~~-~~~~~~-~~~~~~l~~~~~---~------~~~~~~a~~~~~~~~~~~~~  153 (376)
                      ..+.-..+.+.      -....+.|+-... .++.|- ...|...+...-   .      +.+++.....+.++....+.
T Consensus       114 lYl~YIRr~n~~~tGq~r~~i~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR~~Y~ral~tP~~  193 (660)
T COG5107         114 LYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIRNGYMRALQTPMG  193 (660)
T ss_pred             HHHHHHHhhCcccccchhhhhHHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHcCccc
Confidence            55543333321      1122223333332 233443 334444444322   2      23455666777777764321


Q ss_pred             CChhhHHHH------HHH-----HH--ccCcHHHHHHHHHHHHH--CCCCC----CHhH-----------HHHHH-----
Q 042039          154 HDDVSYNIL------ING-----YC--KNKEVEEALSLYREMVS--KGIKP----TVVT-----------YNTLF-----  198 (376)
Q Consensus       154 ~~~~~~~~l------~~~-----~~--~~~~~~~a~~~~~~~~~--~~~~~----~~~~-----------~~~l~-----  198 (376)
                      .-...|.-.      ++-     +.  ..--+-.|...++++..  .|...    +..+           |...+     
T Consensus       194 nleklW~dy~~fE~e~N~~TarKfvge~sp~ym~ar~~yqe~~nlt~Gl~v~~~~~~Rt~nK~~r~s~S~WlNwIkwE~e  273 (660)
T COG5107         194 NLEKLWKDYENFELELNKITARKFVGETSPIYMSARQRYQEIQNLTRGLSVKNPINLRTANKAARTSDSNWLNWIKWEME  273 (660)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHhccccccCchhhhhhccccccccchhhhHhhHhhc
Confidence            111122111      100     00  01123445555554432  11110    0111           11111     


Q ss_pred             ------------------------------------HHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCH
Q 042039          199 ------------------------------------LGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYI  242 (376)
Q Consensus       199 ------------------------------------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  242 (376)
                                                          ..+...++-+.|......    |.+..+.....+...|.-..+.
T Consensus       274 n~l~L~~~~~~qRi~y~~~q~~~y~~~~~evw~dys~Y~~~isd~q~al~tv~r----g~~~spsL~~~lse~yel~nd~  349 (660)
T COG5107         274 NGLKLGGRPHEQRIHYIHNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVER----GIEMSPSLTMFLSEYYELVNDE  349 (660)
T ss_pred             CCcccCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhccHHHHHHHHHHh----cccCCCchheeHHHHHhhcccH
Confidence                                                111223334444443333    2233333333333444444444


Q ss_pred             HHHHHHHHHhc--------------ccCC--Cc-------------hHHHHHHHHHHHHhCCChHHHHHHHhcccccC-C
Q 042039          243 VEAVELFRTLG--------------ILKC--EL-------------DIQAYNCLIDGLCKSGRLEIALELFRSLPRRV-L  292 (376)
Q Consensus       243 ~~a~~~~~~~~--------------~~~~--~~-------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~  292 (376)
                      +.....|+...              ..+.  .|             -..+|...+....+..-.+.|..+|-++.+.+ .
T Consensus       350 e~v~~~fdk~~q~L~r~ys~~~s~~~s~~D~N~e~~~Ell~kr~~k~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~  429 (660)
T COG5107         350 EAVYGCFDKCTQDLKRKYSMGESESASKVDNNFEYSKELLLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIV  429 (660)
T ss_pred             HHHhhhHHHHHHHHHHHHhhhhhhhhccccCCccccHHHHHHHHhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCC
Confidence            44433333320              0010  01             12345556666667777899999999998877 5


Q ss_pred             CCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcH-HHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          293 VADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNV-IIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       293 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .+++..+.+++..++ .|++..|..+|+--...  -||. ......+..+...++-+.|..+|+...+
T Consensus       430 ~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl~fLi~inde~naraLFetsv~  494 (660)
T COG5107         430 GHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYLLFLIRINDEENARALFETSVE  494 (660)
T ss_pred             CcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCcHHHHHHHHHHhHH
Confidence            667778888887655 67888999999876654  2343 3334555667788888888888886554

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=97.26  E-value=0.016  Score=48.83  Aligned_cols=64  Identities=11%  Similarity=0.095  Sum_probs=40.3

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-h---hhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-A---FTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      +...++.+..+|...|++++|+..|++.++.+  |+ .   .+|..+..+|...|+.++|.+.++++.+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~--Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELN--PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            34556666666666677777777776666643  33 2   24666666666667777776666666654

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.25  E-value=0.0084  Score=49.21  Aligned_cols=95  Identities=14%  Similarity=0.054  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHH
Q 042039          228 TYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLC  307 (376)
Q Consensus       228 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  307 (376)
                      ++..++.++.+.+++.+|+..-......+ +++...+..-+.++...|+++.|+..|+++++. -|.|...-..++.+-.
T Consensus       259 ~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~-~P~Nka~~~el~~l~~  336 (397)
T KOG0543|consen  259 CHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKL-EPSNKAARAELIKLKQ  336 (397)
T ss_pred             HhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHH
Confidence            45566667777777777777777776665 346666667777777777777777777777664 2334444444444444


Q ss_pred             ccCChh-HHHHHHHHHHH
Q 042039          308 NDGQMD-KAHDLFLDMEE  324 (376)
Q Consensus       308 ~~~~~~-~a~~~~~~~~~  324 (376)
                      +..++. ...++|..|..
T Consensus       337 k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  337 KIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            443333 33566666654

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.23  E-value=0.0091  Score=46.42  Aligned_cols=96  Identities=18%  Similarity=0.277  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhcccccCCCC---CHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC-CC-cHHHHHHH
Q 042039          263 AYNCLIDGLCKSGRLEIALELFRSLPRRVLVA---DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV-AP-NVIIFVTL  337 (376)
Q Consensus       263 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~-~~~~~~~l  337 (376)
                      .|+..+ .+.+.|++..|...|...++. .|.   ....+.+|+.++...|++++|...|..+.+.-. .| -+..+..|
T Consensus       144 ~Y~~A~-~~~ksgdy~~A~~~F~~fi~~-YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl  221 (262)
T COG1729         144 LYNAAL-DLYKSGDYAEAEQAFQAFIKK-YPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL  221 (262)
T ss_pred             HHHHHH-HHHHcCCHHHHHHHHHHHHHc-CCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH
Confidence            344433 344567788888877777665 222   245667778888888888888888877765421 11 24566677


Q ss_pred             HHHHhhcCChhhHHHHHHHHHhC
Q 042039          338 IHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       338 ~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      ..+..+.|+.++|...|+++.+.
T Consensus       222 g~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         222 GVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHH
Confidence            77777788888888888887754

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

Probab=97.21  E-value=0.09  Score=43.19  Aligned_cols=281  Identities=14%  Similarity=0.188  Sum_probs=149.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      +|..+.......|+.+-|..+++.      .|++.-   -+..+...|+.+.|   +.+..+.| .|| -+|..++..--
T Consensus         2 S~a~IA~~A~~~GR~~LA~~LL~~------Ep~~~~---qVplLL~m~e~e~A---L~kAi~Sg-D~D-Li~~vLl~L~~   67 (319)
T PF04840_consen    2 SYAEIARKAYEEGRPKLATKLLEL------EPRASK---QVPLLLKMGEDELA---LNKAIESG-DTD-LIYLVLLHLKR   67 (319)
T ss_pred             CHHHHHHHHHHcChHHHHHHHHHc------CCChHH---HHHHHhcCCchHHH---HHHHHHcC-Ccc-HHHHHHHHHHH
Confidence            577788888889999999888753      233221   24456667777766   44555553 223 23444444332


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      ... ..   +++ .++..  .|..   ..+...|++..+.+....+|.+-.+    ........+-.++.. .+.+.-..
T Consensus        68 ~l~-~s---~f~-~il~~--~p~a---~~l~~~~~r~~~~~~L~~~y~q~d~----~~~~a~~~l~~~~~~-~~~~~~~~  132 (319)
T PF04840_consen   68 KLS-LS---QFF-KILNQ--NPVA---SNLYKKYCREQDRELLKDFYYQEDR----FQELANLHLQEALSQ-KDVEEKIS  132 (319)
T ss_pred             hCC-HH---HHH-HHHHh--Ccch---HHHHHHHHHhccHHHHHHHHHhcch----HHHHHHHHHHHHHhC-CChHHHHH
Confidence            221 11   233 23322  2221   2334455555555555555543211    111122222222222 33333333


Q ss_pred             HHHHHHHCC-CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc-CCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          178 LYREMVSKG-IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD-DVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       178 ~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      .+..+.+.- -..+......++.-..+.      .++-..+.+. +......+.+..+.-+...|+...|.++-++..  
T Consensus       133 ~L~~a~~~y~~~k~~~f~~~~~e~q~~L------l~~Q~~Le~~~~~~f~~~Sl~~Ti~~li~~~~~k~A~kl~k~Fk--  204 (319)
T PF04840_consen  133 FLKQAQKLYSKSKNDAFEAKLIEEQIKL------LEYQKELEEKYNTNFVGLSLNDTIRKLIEMGQEKQAEKLKKEFK--  204 (319)
T ss_pred             HHHHHHHHHHhcchhHHHHHHHHHHHHH------HHHHHHHHHHhccchhcCCHHHHHHHHHHCCCHHHHHHHHHHcC--
Confidence            333333210 001111111111111111      1111111111 112223456666777788899988888877764  


Q ss_pred             CCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHH
Q 042039          256 KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFV  335 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  335 (376)
                        -|+...|...+.+++..++|++-.++...  +    -++.-|..++.+|.+.|+..+|..+..++     + +    .
T Consensus       205 --v~dkrfw~lki~aLa~~~~w~eL~~fa~s--k----KsPIGyepFv~~~~~~~~~~eA~~yI~k~-----~-~----~  266 (319)
T PF04840_consen  205 --VPDKRFWWLKIKALAENKDWDELEKFAKS--K----KSPIGYEPFVEACLKYGNKKEASKYIPKI-----P-D----E  266 (319)
T ss_pred             --CcHHHHHHHHHHHHHhcCCHHHHHHHHhC--C----CCCCChHHHHHHHHHCCCHHHHHHHHHhC-----C-h----H
Confidence              46888999999999999999988876543  1    14567888999999999999999888772     2 1    3


Q ss_pred             HHHHHHhhcCChhhHHHH
Q 042039          336 TLIHGFVRINKPSKVIEL  353 (376)
Q Consensus       336 ~l~~~~~~~g~~~~a~~~  353 (376)
                      .-+..|.+.|++.+|.+.
T Consensus       267 ~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  267 ERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             HHHHHHHHCCCHHHHHHH
Confidence            345566777777777654

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

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=97.21  E-value=0.13  Score=44.85  Aligned_cols=331  Identities=12%  Similarity=0.071  Sum_probs=181.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      -..|..++.---...+.+.+..++..++..- |.--.-|......=.+.|..+.+.++|++.+.. ++.+...|......
T Consensus        45 f~~wt~li~~~~~~~~~~~~r~~y~~fL~ky-Pl~~gyW~kfA~~E~klg~~~~s~~Vfergv~a-ip~SvdlW~~Y~~f  122 (577)
T KOG1258|consen   45 FDAWTTLIQENDSIEDVDALREVYDIFLSKY-PLCYGYWKKFADYEYKLGNAENSVKVFERGVQA-IPLSVDLWLSYLAF  122 (577)
T ss_pred             ccchHHHHhccCchhHHHHHHHHHHHHHhhC-ccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-hhhHHHHHHHHHHH
Confidence            3456666655445555566777777777542 333345666666667788899999999988764 55667777666554


Q ss_pred             HH-hCCChHHHHHHHHHHHhc-CCC-CChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc----
Q 042039           96 LC-KNGKMDEASRLLDLMVQR-DVR-PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK----  168 (376)
Q Consensus        96 ~~-~~~~~~~a~~~~~~~~~~-~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----  168 (376)
                      +. ..|+.+.....|+..... |.. .....|...+..-..++++.....+++++.+.....-...|.........    
T Consensus       123 ~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRileiP~~~~~~~f~~f~~~l~~~~~~  202 (577)
T KOG1258|consen  123 LKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEIPLHQLNRHFDRFKQLLNQNEEK  202 (577)
T ss_pred             HhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhhhhhHhHHHHHHHHHHHhcCChh
Confidence            43 457777888888877763 111 12446677777777888899999999888765211111111111111111    


Q ss_pred             -cCcHHHHHHHHHHHHHC---------------C----CCCC---HhHHHHHHHH-------HHhccchHHHHHHHHHHH
Q 042039          169 -NKEVEEALSLYREMVSK---------------G----IKPT---VVTYNTLFLG-------LFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       169 -~~~~~~a~~~~~~~~~~---------------~----~~~~---~~~~~~l~~~-------~~~~~~~~~a~~~~~~~~  218 (376)
                       ....+++.++-......               +    ..|.   ......+...       +............++..+
T Consensus       203 ~l~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~I  282 (577)
T KOG1258|consen  203 ILLSIDELIQLRSDVAERSKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGI  282 (577)
T ss_pred             hhcCHHHHHHHhhhHHhhhhcccccChhHHHHHHHhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhc
Confidence             12233333322222110               0    0000   0001111111       111111222222223222


Q ss_pred             hc---CCC----CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC
Q 042039          219 RD---DVA----ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV  291 (376)
Q Consensus       219 ~~---~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  291 (376)
                      +.   .+.    ++..+|...+..-...|+++.+.-++++....- ..-...|...+......|+.+-|..++....+..
T Consensus       283 krpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~c-A~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~  361 (577)
T KOG1258|consen  283 KRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIPC-ALYDEFWIKYARWMESSGDVSLANNVLARACKIH  361 (577)
T ss_pred             cccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhHH-hhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhc
Confidence            22   111    123456666677778888888888888875322 2234566666666667788888888887766553


Q ss_pred             CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHH-HHHHHHHHHhhcCChhhHH
Q 042039          292 LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVI-IFVTLIHGFVRINKPSKVI  351 (376)
Q Consensus       292 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~a~  351 (376)
                      .+..+.+...-....-..|+++.|..+++.+.+.-  |+.. .-..-+....+.|+.+.+.
T Consensus       362 ~k~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e~--pg~v~~~l~~~~~e~r~~~~~~~~  420 (577)
T KOG1258|consen  362 VKKTPIIHLLEARFEESNGNFDDAKVILQRIESEY--PGLVEVVLRKINWERRKGNLEDAN  420 (577)
T ss_pred             CCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHhhC--CchhhhHHHHHhHHHHhcchhhhh
Confidence            33333333333333445678999999999888753  4432 2222233455677777777

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.21  E-value=0.016  Score=46.40  Aligned_cols=113  Identities=15%  Similarity=0.037  Sum_probs=46.8

Q ss_pred             CcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC----HhHHHHHHHHHHhccchHHH
Q 042039          135 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT----VVTYNTLFLGLFEIHQVEHA  210 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a  210 (376)
                      |++.+|-..++++.+.- |.|..++...-.+|...|+.+.-...+++++.. ..++    ...-..+.-++...|-+++|
T Consensus       117 g~~h~a~~~wdklL~d~-PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  117 GKHHEAAIEWDKLLDDY-PTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             ccccHHHHHHHHHHHhC-chhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            44444444444444332 344444444444444444444444444444432 1111    11122222333344444444


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          211 LKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      .+.-++..+.+ +.+..........+...|+..++.+...
T Consensus       195 Ek~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~  233 (491)
T KOG2610|consen  195 EKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMY  233 (491)
T ss_pred             HHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHH
Confidence            44444444443 3333344444444444444444444433

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=97.21  E-value=0.016  Score=46.92  Aligned_cols=228  Identities=12%  Similarity=0.074  Sum_probs=144.7

Q ss_pred             HHhcCChhHHHHHHHHhhhCC--CCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc--CCC---CchHhHHHHHHHHHh
Q 042039           26 LCKEGFVDKAKALFLQMKGEN--INPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ--GVQ---PSVVTFNVIMDELCK   98 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~---~~~~~~~~l~~~~~~   98 (376)
                      +....+.++|+..|.+....-  ...--.++..+..+....|.+++++..--..+..  ...   .-...|..+.+++-+
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~   95 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEK   95 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456778889998888776541  1112345666777788888887765543222211  011   123456666677766


Q ss_pred             CCChHHHHHHHHHHHhc-CCCC---ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC-----CChhhHHHHHHHHHcc
Q 042039           99 NGKMDEASRLLDLMVQR-DVRP---NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCK-----HDDVSYNILINGYCKN  169 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~  169 (376)
                      ..++.+++.+-..-... |..|   .-.....+..++.-.+.++++++.|+.+......     ....++..|...|.+.
T Consensus        96 l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l  175 (518)
T KOG1941|consen   96 LCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQL  175 (518)
T ss_pred             HHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHH
Confidence            66777777766655542 2222   1234456778888888999999999988654311     1234788999999999


Q ss_pred             CcHHHHHHHHHHHHHC----CCCCC-----HhHHHHHHHHHHhccchHHHHHHHHHHHhc----CC-CCCcchHHHHHHH
Q 042039          170 KEVEEALSLYREMVSK----GIKPT-----VVTYNTLFLGLFEIHQVEHALKLFEEMQRD----DV-AADTSTYNTFIDG  235 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~----~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l~~~  235 (376)
                      .|+++|.-+..++.+.    ++..-     ......+.-++...|....|.+.-++..+.    |- .........++..
T Consensus       176 ~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDI  255 (518)
T KOG1941|consen  176 KDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADI  255 (518)
T ss_pred             HhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            9999999887776542    22211     122233445666778888888777766443    31 2234456677888


Q ss_pred             HHhCCCHHHHHHHHHHhc
Q 042039          236 LCKNGYIVEAVELFRTLG  253 (376)
Q Consensus       236 ~~~~~~~~~a~~~~~~~~  253 (376)
                      |...|+.+.|+.-|+++.
T Consensus       256 yR~~gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  256 YRSRGDLERAFRRYEQAM  273 (518)
T ss_pred             HHhcccHhHHHHHHHHHH
Confidence            999999999988887753

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=97.20  E-value=0.018  Score=40.26  Aligned_cols=81  Identities=11%  Similarity=0.044  Sum_probs=57.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCC--CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENI--NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      .+..-.....+.|++++|++.|+.+..+-.  +-...+...++.+|.+.+++++|...+++.++..+......|...+.+
T Consensus        12 ~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~g   91 (142)
T PF13512_consen   12 ELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRG   91 (142)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHH
Confidence            344445556689999999999999987731  224566778899999999999999999999987544233345444554


Q ss_pred             HHh
Q 042039           96 LCK   98 (376)
Q Consensus        96 ~~~   98 (376)
                      ++.
T Consensus        92 L~~   94 (142)
T PF13512_consen   92 LSY   94 (142)
T ss_pred             HHH
Confidence            443

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.20  E-value=0.025  Score=44.09  Aligned_cols=97  Identities=22%  Similarity=0.251  Sum_probs=66.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCC--CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC-C-chHhHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENI--NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ-P-SVVTFNVIM   93 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~l~   93 (376)
                      .|+.-+..+ +.|++..|...|...++...  +-...++.-|+.++...|++++|...|..+.+.-++ | -+..+..+.
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            566666544 66678888888887776631  112445556778888888888888888877775221 1 245666677


Q ss_pred             HHHHhCCChHHHHHHHHHHHhc
Q 042039           94 DELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .+..+.|+.++|..+|+++.+.
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHH
Confidence            7777788888888888888776

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=97.20  E-value=0.075  Score=42.01  Aligned_cols=142  Identities=18%  Similarity=0.155  Sum_probs=58.8

Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      ....|++.+|..+|....... +-+......++.+|...|+.+.|..++..+..............-+..+.+.....+.
T Consensus       144 ~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~~  222 (304)
T COG3118         144 LIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPEI  222 (304)
T ss_pred             hhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCCH
Confidence            344455555555555555442 1123344445555555555555555555543321111111111223333333333333


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHhCC
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD-VAADTSTYNTFIDGLCKNG  240 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~  240 (376)
                      ..+-.++-..  +.|...-..+...+...|+.+.|.+.+-.+.+.+ -..+...-..++..+.-.|
T Consensus       223 ~~l~~~~aad--Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g  286 (304)
T COG3118         223 QDLQRRLAAD--PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFG  286 (304)
T ss_pred             HHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcC
Confidence            3333333321  2244444445555555555555555444443331 1223334444444444444

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=97.16  E-value=0.074  Score=41.18  Aligned_cols=55  Identities=15%  Similarity=0.159  Sum_probs=29.2

Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCC---HhHHHHHHHHHHhccchHHHHHHHHHH
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPT---VVTYNTLFLGLFEIHQVEHALKLFEEM  217 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~  217 (376)
                      +.+.|.+.|.+..|..-++.+++. .+-.   ...+..+..+|...|-.++|.+.-.-+
T Consensus       173 IaryY~kr~~~~AA~nR~~~v~e~-y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl  230 (254)
T COG4105         173 IARYYLKRGAYVAAINRFEEVLEN-YPDTSAVREALARLEEAYYALGLTDEAKKTAKVL  230 (254)
T ss_pred             HHHHHHHhcChHHHHHHHHHHHhc-cccccchHHHHHHHHHHHHHhCChHHHHHHHHHH
Confidence            445566666666666666666654 2111   233444455555666655555544433

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=97.14  E-value=0.056  Score=47.24  Aligned_cols=178  Identities=15%  Similarity=0.102  Sum_probs=109.2

Q ss_pred             HHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcc------hHHHHHHHHH----hCCCHHH
Q 042039          175 ALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTS------TYNTFIDGLC----KNGYIVE  244 (376)
Q Consensus       175 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------~~~~l~~~~~----~~~~~~~  244 (376)
                      ..-+|.-++.. +||   .+..++....-.|+-+.+++.+....+.+--..+.      .|...+..+.    ...+.+.
T Consensus       176 G~G~f~L~lSl-LPp---~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~  251 (468)
T PF10300_consen  176 GFGLFNLVLSL-LPP---KVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEE  251 (468)
T ss_pred             HHHHHHHHHHh-CCH---HHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHH
Confidence            34455555553 333   34556666666788888888887766542111111      1222222222    2446778


Q ss_pred             HHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC---CCCCHHHHHHHHHHHHccCChhHHHHHHHH
Q 042039          245 AVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV---LVADVVTYNIMIHGLCNDGQMDKAHDLFLD  321 (376)
Q Consensus       245 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  321 (376)
                      |.+++..+...-+. +......-++.+...|+.++|++.|+......   .+.....+..++..+.-..+|++|.+.|..
T Consensus       252 a~~lL~~~~~~yP~-s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~  330 (468)
T PF10300_consen  252 AEELLEEMLKRYPN-SALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLR  330 (468)
T ss_pred             HHHHHHHHHHhCCC-cHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHH
Confidence            88888888765322 33334445677788899999999998755321   112234566777888888999999999999


Q ss_pred             HHHcCCCCcHHHHHHHHH-HHhhcCCh-------hhHHHHHHHHH
Q 042039          322 MEENAVAPNVIIFVTLIH-GFVRINKP-------SKVIELLHKMK  358 (376)
Q Consensus       322 ~~~~~~~~~~~~~~~l~~-~~~~~g~~-------~~a~~~~~~~~  358 (376)
                      +.+.+ ..+..+|..+.. ++...|+.       ++|.+++++..
T Consensus       331 L~~~s-~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  331 LLKES-KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHhcc-ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            88754 234555554443 44567777       78888888765

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.

>PRK11906 transcriptional regulator; Provisional

Probab=97.14  E-value=0.061  Score=45.56  Aligned_cols=149  Identities=13%  Similarity=0.079  Sum_probs=102.1

Q ss_pred             chHHHHHHHHHHH---hcCCCCCcchHHHHHHHHHh---------CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHh
Q 042039          206 QVEHALKLFEEMQ---RDDVAADTSTYNTFIDGLCK---------NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCK  273 (376)
Q Consensus       206 ~~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  273 (376)
                      ..+.|..+|.+..   ..+ +.....|..+..++..         ..+..+|.++.+++.+.+ +.|+.....++.+...
T Consensus       273 ~~~~Al~lf~ra~~~~~ld-p~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~  350 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQ-TLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-TVDGKILAIMGLITGL  350 (458)
T ss_pred             HHHHHHHHHHHHhhcccCC-cccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHh
Confidence            3567888888887   332 2234455555544432         234566778888888887 4488888888888888


Q ss_pred             CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc-HHHHHHHHHHHhhcCChhhHHH
Q 042039          274 SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN-VIIFVTLIHGFVRINKPSKVIE  352 (376)
Q Consensus       274 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~  352 (376)
                      .++++.|...|+++... .|....+|......+.-.|+.++|.+.+++..+..+.-- .......+..|+.. ..++|.+
T Consensus       351 ~~~~~~a~~~f~rA~~L-~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~~-~~~~~~~  428 (458)
T PRK11906        351 SGQAKVSHILFEQAKIH-STDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVVIKECVDMYVPN-PLKNNIK  428 (458)
T ss_pred             hcchhhHHHHHHHHhhc-CCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHHHHHHHHHHcCC-chhhhHH
Confidence            88999999999998876 344567788888888889999999999999877532211 22333344466554 5677777


Q ss_pred             HHHHHH
Q 042039          353 LLHKMK  358 (376)
Q Consensus       353 ~~~~~~  358 (376)
                      ++-+-.
T Consensus       429 ~~~~~~  434 (458)
T PRK11906        429 LYYKET  434 (458)
T ss_pred             HHhhcc
Confidence            765543

>PRK11906 transcriptional regulator; Provisional

Probab=97.12  E-value=0.077  Score=44.96  Aligned_cols=118  Identities=14%  Similarity=0.079  Sum_probs=78.5

Q ss_pred             ChHHHHHHHHHHHhc-CCCCc-hHhHHHHHHHHHh---------CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhc
Q 042039           66 DWNEAKRLFFEMMDQ-GVQPS-VVTFNVIMDELCK---------NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT  134 (376)
Q Consensus        66 ~~~~a~~~~~~~~~~-~~~~~-~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  134 (376)
                      ..+.|+.+|.+.... ...|+ ...|..+..++..         ..+..+|.++-+..++.+ +.|+.+...++.+....
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~  351 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-TVDGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhh
Confidence            456788888888822 23443 3344444333321         223456666777777765 44677777777777777


Q ss_pred             CcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          135 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      ++++.|...|++....+ |....+|........-.|+.++|.+.+++..+.
T Consensus       352 ~~~~~a~~~f~rA~~L~-Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrL  401 (458)
T PRK11906        352 GQAKVSHILFEQAKIHS-TDIASLYYYRALVHFHNEKIEEARICIDKSLQL  401 (458)
T ss_pred             cchhhHHHHHHHHhhcC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHhcc
Confidence            77888888888887776 556667777777777788888888888887664

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.10  E-value=0.085  Score=40.90  Aligned_cols=132  Identities=15%  Similarity=0.061  Sum_probs=74.4

Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcc-----hHHHH
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTS-----TYNTF  232 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-----~~~~l  232 (376)
                      +.+.++.++.-.+.+.-....+.+.++...+.++.....+++...+.|+.+.|...|+++.+..-..+..     +....
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            3445555555666666666666666665444455556666666666666666666666555432222222     22233


Q ss_pred             HHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          233 IDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       233 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      ...|.-.+++..|...+.++...+.. ++...+.-+-+..-.|+...|++.++.+...
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~-~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPR-NAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCC-chhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            33445556666666666666555422 4444454444455566777777777766654

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.07  E-value=0.085  Score=40.40  Aligned_cols=207  Identities=14%  Similarity=0.148  Sum_probs=94.9

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...|.....+|....++++|...+.+..+. ...+...|+ ..      ..++.|.-+.+++.+.  +--...+......
T Consensus        31 as~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfh-AA------KayEqaamLake~~kl--sEvvdl~eKAs~l  100 (308)
T KOG1585|consen   31 ASLYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFH-AA------KAYEQAAMLAKELSKL--SEVVDLYEKASEL  100 (308)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHH-HH------HHHHHHHHHHHHHHHh--HHHHHHHHHHHHH
Confidence            345556666777777777777776666532 111211111 11      1234444444444432  1112334444555


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC---C--CCCCHhHHHHHHHHHHhcc
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK---G--IKPTVVTYNTLFLGLFEIH  205 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~--~~~~~~~~~~l~~~~~~~~  205 (376)
                      |..+|..+.|-..+++.-+.                ...-++++|+++|++....   +  ...-...+..+.+.+.+..
T Consensus       101 Y~E~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~  164 (308)
T KOG1585|consen  101 YVECGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLE  164 (308)
T ss_pred             HHHhCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhH
Confidence            55566655555555544321                1234556666666655432   0  0011223344445555555


Q ss_pred             chHHHHHHHHHHHhc----C-CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC---CCchHHHHHHHHHHHHhCCCh
Q 042039          206 QVEHALKLFEEMQRD----D-VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK---CELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       206 ~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      .+++|...+.+-...    . .......+...+..+.-..++..|..+++.-...+   -.-+..+...|+.+| ..|+.
T Consensus       165 kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~  243 (308)
T KOG1585|consen  165 KFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDI  243 (308)
T ss_pred             HhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCH
Confidence            555554444322111    0 11111224444444555566666666666632211   122445556666555 35666


Q ss_pred             HHHHHHH
Q 042039          278 EIALELF  284 (376)
Q Consensus       278 ~~a~~~~  284 (376)
                      +++.+++
T Consensus       244 E~~~kvl  250 (308)
T KOG1585|consen  244 EEIKKVL  250 (308)
T ss_pred             HHHHHHH
Confidence            6655554

>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=97.07  E-value=0.012  Score=40.65  Aligned_cols=84  Identities=15%  Similarity=0.123  Sum_probs=65.4

Q ss_pred             hHHHHHHHHHHHHhCCChHHHHHHHhccc---------------ccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          260 DIQAYNCLIDGLCKSGRLEIALELFRSLP---------------RRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       260 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~---------------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      |..++..++.++++.|+.+....+++..-               .....|+..+..+++.+|+..+++..|.++++...+
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            45678889999999999999999887531               122457788888999999999999999999888875


Q ss_pred             c-CCCCcHHHHHHHHHHHhh
Q 042039          325 N-AVAPNVIIFVTLIHGFVR  343 (376)
Q Consensus       325 ~-~~~~~~~~~~~l~~~~~~  343 (376)
                      . +++-+..+|..|++-...
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v  100 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYV  100 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHH
Confidence            4 666678888888864433

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

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=97.05  E-value=0.092  Score=45.94  Aligned_cols=177  Identities=18%  Similarity=0.213  Sum_probs=110.9

Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcC-CCCch-----HhHHHHHHHHHh----CCChHHH
Q 042039           36 KALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQG-VQPSV-----VTFNVIMDELCK----NGKMDEA  105 (376)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~-----~~~~~l~~~~~~----~~~~~~a  105 (376)
                      .-+|.-+... +||.   +..++....-.|+-+.+++.+.+..+.+ +.-..     -.|+..+..++.    ....+.|
T Consensus       177 ~G~f~L~lSl-LPp~---~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a  252 (468)
T PF10300_consen  177 FGLFNLVLSL-LPPK---VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEA  252 (468)
T ss_pred             HHHHHHHHHh-CCHH---HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHH
Confidence            3444444433 2443   4556777777788888888888876642 22111     223444433332    4567888


Q ss_pred             HHHHHHHHhcCCCCChhhH-HHHHHHHHhcCcHHHHHHHHHHHHhcC---CCCChhhHHHHHHHHHccCcHHHHHHHHHH
Q 042039          106 SRLLDLMVQRDVRPNAFTY-STLMDGFCLTGKINRAEELFGSMESMG---CKHDDVSYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                      .++++.+.++  -|+...| ..-.+.+...|++++|.+.|++.....   .......+.-++-++.-..+|++|...+..
T Consensus       253 ~~lL~~~~~~--yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~  330 (468)
T PF10300_consen  253 EELLEEMLKR--YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLR  330 (468)
T ss_pred             HHHHHHHHHh--CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHH
Confidence            8999988886  4554444 345677778899999999998765321   112334566677788888999999999999


Q ss_pred             HHHCCCCCCHhHHHHHH-HHHHhccch-------HHHHHHHHHHHh
Q 042039          182 MVSKGIKPTVVTYNTLF-LGLFEIHQV-------EHALKLFEEMQR  219 (376)
Q Consensus       182 ~~~~~~~~~~~~~~~l~-~~~~~~~~~-------~~a~~~~~~~~~  219 (376)
                      +.+..-. +...|.-+. .++...++.       ++|.+++.++..
T Consensus       331 L~~~s~W-Ska~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  331 LLKESKW-SKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHhcccc-HHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            8885322 344443333 334456666       788888887644

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.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.96  E-value=0.0023  Score=34.79  Aligned_cols=39  Identities=15%  Similarity=0.217  Sum_probs=21.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSL   57 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l   57 (376)
                      +|..+...|.+.|++++|+++|+++.+.. |.|...+..+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~-P~~~~a~~~L   41 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALD-PDDPEAWRAL   41 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCCHHHHHHh
Confidence            45555555556666666666666555553 4444444443

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.96  E-value=0.12  Score=40.11  Aligned_cols=62  Identities=16%  Similarity=0.075  Sum_probs=35.2

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCC--CCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGV--QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +..-+..-.+.|++++|.+.|+.+..+.+  +-...+...++.++.+.++++.|....++.++.
T Consensus        37 LY~~g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~l  100 (254)
T COG4105          37 LYNEGLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRL  100 (254)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            33334444566677777777776665421  112334445555666666777777666666654

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.88  E-value=0.053  Score=44.01  Aligned_cols=230  Identities=10%  Similarity=0.053  Sum_probs=124.9

Q ss_pred             HHhcCCChHHHHHHHHHHHhcC--CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc--CCCCC---hhhHHHHHHHHH
Q 042039           60 GLCHANDWNEAKRLFFEMMDQG--VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR--DVRPN---AFTYSTLMDGFC  132 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~---~~~~~~l~~~~~  132 (376)
                      -+....+.++|+..|.+.+..-  ...-..++..+..+..+.|.+++++..--.-++.  .....   ...|..+.+++-
T Consensus        15 ~Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e   94 (518)
T KOG1941|consen   15 QLYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNE   94 (518)
T ss_pred             hHhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456677888888887776541  1112234556666777777777665543222221  01111   223445555555


Q ss_pred             hcCcHHHHHHHHHHHHhcC-CCC---ChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC-----CCCCHhHHHHHHHHHHh
Q 042039          133 LTGKINRAEELFGSMESMG-CKH---DDVSYNILINGYCKNKEVEEALSLYREMVSKG-----IKPTVVTYNTLFLGLFE  203 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~~-~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~  203 (376)
                      +..++.+++.+-..-.... ..+   .-.....+..++...+.++++++.|+.+.+--     ......++..+...+.+
T Consensus        95 ~l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~  174 (518)
T KOG1941|consen   95 KLCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQ  174 (518)
T ss_pred             HHHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHH
Confidence            5555556655554443321 111   11234456667777777888888887776521     11224566777777777


Q ss_pred             ccchHHHHHHHHHHHhc----CCCCC-----cchHHHHHHHHHhCCCHHHHHHHHHHhcc----cCCCc-hHHHHHHHHH
Q 042039          204 IHQVEHALKLFEEMQRD----DVAAD-----TSTYNTFIDGLCKNGYIVEAVELFRTLGI----LKCEL-DIQAYNCLID  269 (376)
Q Consensus       204 ~~~~~~a~~~~~~~~~~----~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~-~~~~~~~l~~  269 (376)
                      ..|+++|.-+..+..+.    ++..-     ......+..++...|....|.+.-++..+    .|..+ .......++.
T Consensus       175 l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aD  254 (518)
T KOG1941|consen  175 LKDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFAD  254 (518)
T ss_pred             HHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHH
Confidence            78888877666555432    11111     11223344556666777777666666532    23221 2334455667


Q ss_pred             HHHhCCChHHHHHHHhcccc
Q 042039          270 GLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       270 ~~~~~~~~~~a~~~~~~~~~  289 (376)
                      .|...|+.+.|..-|+++..
T Consensus       255 IyR~~gd~e~af~rYe~Am~  274 (518)
T KOG1941|consen  255 IYRSRGDLERAFRRYEQAMG  274 (518)
T ss_pred             HHHhcccHhHHHHHHHHHHH
Confidence            77777777777766665443

>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=96.86  E-value=0.098  Score=45.14  Aligned_cols=156  Identities=17%  Similarity=0.169  Sum_probs=83.5

Q ss_pred             HHccCcHHHHHHHHHH--HHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHH
Q 042039          166 YCKNKEVEEALSLYRE--MVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIV  243 (376)
Q Consensus       166 ~~~~~~~~~a~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  243 (376)
                      ..-.++++++.+....  +... +  +......++.-+.+.|-++.|.++..+         +.   .-.....+.|+.+
T Consensus       271 av~~~d~~~v~~~i~~~~ll~~-i--~~~~~~~i~~fL~~~G~~e~AL~~~~D---------~~---~rFeLAl~lg~L~  335 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLPN-I--PKDQGQSIARFLEKKGYPELALQFVTD---------PD---HRFELALQLGNLD  335 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGGG-----HHHHHHHHHHHHHTT-HHHHHHHSS----------HH---HHHHHHHHCT-HH
T ss_pred             HHHcCChhhhhhhhhhhhhccc-C--ChhHHHHHHHHHHHCCCHHHHHhhcCC---------hH---HHhHHHHhcCCHH
Confidence            3445666666555541  1111 1  133456666666677777777665332         21   1233445677777


Q ss_pred             HHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          244 EAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       244 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      .|.++.+..      .++..|..|+......|+++-|.+.|++...         +..|+-.|.-.|+.+.-.++.+...
T Consensus       336 ~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~  400 (443)
T PF04053_consen  336 IALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAE  400 (443)
T ss_dssp             HHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHH
Confidence            777665442      2566777788777778888888877776553         3456666677777766666666665


Q ss_pred             HcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          324 ENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       324 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      ..|-      ++....++.-.|+.++..+++.+-
T Consensus       401 ~~~~------~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  401 ERGD------INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             HTT-------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             HccC------HHHHHHHHHHcCCHHHHHHHHHHc
Confidence            5431      333344455567777766665543

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.

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.85  E-value=0.3  Score=43.15  Aligned_cols=251  Identities=14%  Similarity=0.106  Sum_probs=125.5

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC-----------hhhHHHHHHHHhcCCC--hHHHHHHHHHHHh
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD-----------VVTYNSLIHGLCHAND--WNEAKRLFFEMMD   79 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~-----------~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~   79 (376)
                      .|....+.+-+-.|...|.+++|..+--    .|+..+           .-.++..=.+|.+..+  +-+-+.-++++.+
T Consensus       553 ~~~evp~~~~m~q~Ieag~f~ea~~iac----lgVv~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~  628 (1081)
T KOG1538|consen  553 SAVEVPQSAPMYQYIERGLFKEAYQIAC----LGVTDTDWRELAMEALEALDFETARKAYIRVRDLRYLELISELEERKK  628 (1081)
T ss_pred             ecccccccccchhhhhccchhhhhcccc----cceecchHHHHHHHHHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            4455566666667788888888765411    111111           1112222233433332  2333444455566


Q ss_pred             cCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC----CChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCC
Q 042039           80 QGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR----PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHD  155 (376)
Q Consensus        80 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  155 (376)
                      .|-.|+...   +...++-.|.+.+|.++|.+--..+-.    .|... ...+.-+...|.-++-..+.++-.+-.  .+
T Consensus       629 rge~P~~iL---lA~~~Ay~gKF~EAAklFk~~G~enRAlEmyTDlRM-FD~aQE~~~~g~~~eKKmL~RKRA~WA--r~  702 (1081)
T KOG1538|consen  629 RGETPNDLL---LADVFAYQGKFHEAAKLFKRSGHENRALEMYTDLRM-FDYAQEFLGSGDPKEKKMLIRKRADWA--RN  702 (1081)
T ss_pred             cCCCchHHH---HHHHHHhhhhHHHHHHHHHHcCchhhHHHHHHHHHH-HHHHHHHhhcCChHHHHHHHHHHHHHh--hh
Confidence            666666443   345566777888887777543211100    00000 112233334444433333333221110  11


Q ss_pred             hhhHHHHHHHHHccCcHHHHHHHHH------HHHHCC---CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCc
Q 042039          156 DVSYNILINGYCKNKEVEEALSLYR------EMVSKG---IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT  226 (376)
Q Consensus       156 ~~~~~~l~~~~~~~~~~~~a~~~~~------~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  226 (376)
                      ..--......+...|+.++|..+.-      .+.+-+   ...+..+...+...+.+...+..|.++|..|-.       
T Consensus       703 ~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD-------  775 (1081)
T KOG1538|consen  703 IKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGD-------  775 (1081)
T ss_pred             cCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhcc-------
Confidence            1111233455556777777766532      111111   122455556666666677778888888887743       


Q ss_pred             chHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhc
Q 042039          227 STYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       227 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  286 (376)
                        ...+++.....+++++|..+-++..+..    +..|...++.++...++++|.+.|.+
T Consensus       776 --~ksiVqlHve~~~W~eAFalAe~hPe~~----~dVy~pyaqwLAE~DrFeEAqkAfhk  829 (1081)
T KOG1538|consen  776 --LKSLVQLHVETQRWDEAFALAEKHPEFK----DDVYMPYAQWLAENDRFEEAQKAFHK  829 (1081)
T ss_pred             --HHHHhhheeecccchHhHhhhhhCcccc----ccccchHHHHhhhhhhHHHHHHHHHH
Confidence              2456777888999999999988865432    22333444444444444444444443

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.85  E-value=0.17  Score=40.16  Aligned_cols=150  Identities=15%  Similarity=0.100  Sum_probs=90.2

Q ss_pred             HHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCCh
Q 042039          198 FLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       198 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      .......|+...|...|....... +.+......++.+|...|+.+.|..++..+..............-+..+.+....
T Consensus       141 ~~~~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~  219 (304)
T COG3118         141 AKELIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAAT  219 (304)
T ss_pred             hhhhhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcC
Confidence            344566778888888888877764 4456677778888888888888888888765432221122222223344444444


Q ss_pred             HHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC-CCcHHHHHHHHHHHhhcCChhhH
Q 042039          278 EIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV-APNVIIFVTLIHGFVRINKPSKV  350 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~a  350 (376)
                      .+...+-++...  .+.|...-..+...+...|+.+.|.+.+-.++..+. .-|...-..++..+.-.|..+.+
T Consensus       220 ~~~~~l~~~~aa--dPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~  291 (304)
T COG3118         220 PEIQDLQRRLAA--DPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPADPL  291 (304)
T ss_pred             CCHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCCHH
Confidence            443343333333  244677777888888888888888887776665421 12444555666666555543333

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

Probab=96.81  E-value=0.043  Score=37.94  Aligned_cols=86  Identities=10%  Similarity=0.051  Sum_probs=64.6

Q ss_pred             CcchHHHHHHHHHhCCCHHHHHHHHHHhc---------------ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          225 DTSTYNTFIDGLCKNGYIVEAVELFRTLG---------------ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       225 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~---------------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                      |..++..++.++++.|+.+....+++..=               .....|+..++.+++.+|+..|++..|.++.+.+.+
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            34677888889999999999988887751               112347788899999999999999999999988764


Q ss_pred             -cCCCCCHHHHHHHHHHHHccC
Q 042039          290 -RVLVADVVTYNIMIHGLCNDG  310 (376)
Q Consensus       290 -~~~~~~~~~~~~l~~~~~~~~  310 (376)
                       .+++.+..+|..|+.-....-
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v~s  102 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYVLS  102 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHHhc
Confidence             345556778887776655433

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

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.80  E-value=0.059  Score=43.29  Aligned_cols=154  Identities=13%  Similarity=0.101  Sum_probs=107.2

Q ss_pred             HhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh----hhHHHHHHHHHhcCc
Q 042039           61 LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA----FTYSTLMDGFCLTGK  136 (376)
Q Consensus        61 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~  136 (376)
                      ..-.|++.+|-..++++++. .+.|...+...=.++...|+.......+++++.. -.++.    .....+.-++...|-
T Consensus       113 ~~~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~  190 (491)
T KOG2610|consen  113 LWGRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGI  190 (491)
T ss_pred             hhccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhcc
Confidence            34567788888888888876 3447777777777888889888888888888754 12232    233344455667899


Q ss_pred             HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC---CCCCCHhHHHHHHHHHHhccchHHHHHH
Q 042039          137 INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK---GIKPTVVTYNTLFLGLFEIHQVEHALKL  213 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~~a~~~  213 (376)
                      +++|++.-++..+.+ +.|..+...+...+...+++.++.++..+-...   +--.-..-|-...-.+...+.++.|+.+
T Consensus       191 y~dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleI  269 (491)
T KOG2610|consen  191 YDDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEI  269 (491)
T ss_pred             chhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHH
Confidence            999999999998887 667777788888888899999998887664332   0001122333344455666889999999


Q ss_pred             HHHH
Q 042039          214 FEEM  217 (376)
Q Consensus       214 ~~~~  217 (376)
                      |+.-
T Consensus       270 yD~e  273 (491)
T KOG2610|consen  270 YDRE  273 (491)
T ss_pred             HHHH
Confidence            8753

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=96.79  E-value=0.075  Score=36.28  Aligned_cols=53  Identities=25%  Similarity=0.185  Sum_probs=24.9

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      +...|+.+.|++.|.+.+..- |....+|+.-..++.-+|+.++|++-+++..+
T Consensus        53 laE~g~Ld~AlE~F~qal~l~-P~raSayNNRAQa~RLq~~~e~ALdDLn~Ale  105 (175)
T KOG4555|consen   53 LAEAGDLDGALELFGQALCLA-PERASAYNNRAQALRLQGDDEEALDDLNKALE  105 (175)
T ss_pred             HHhccchHHHHHHHHHHHHhc-ccchHhhccHHHHHHHcCChHHHHHHHHHHHH
Confidence            334445555555554444332 33444455555555545555555544444444

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.69  E-value=0.006  Score=33.16  Aligned_cols=38  Identities=13%  Similarity=0.166  Sum_probs=21.3

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV   91 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   91 (376)
                      ++..+...|...|++++|.++|+++++..+. |...+..
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~-~~~a~~~   40 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPD-DPEAWRA   40 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-CHHHHHH
Confidence            4555666666666666666666666665322 3444433

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=96.69  E-value=0.31  Score=41.12  Aligned_cols=88  Identities=15%  Similarity=0.124  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHhcccCCCch----HHHHHHHHH--HHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHH
Q 042039          242 IVEAVELFRTLGILKCELD----IQAYNCLID--GLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKA  315 (376)
Q Consensus       242 ~~~a~~~~~~~~~~~~~~~----~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  315 (376)
                      +..-..+-+-+.+.|++|-    ...-+.+..  .+...|++.++.-.-.-+.+  +.|++.+|..++-+.....++++|
T Consensus       437 ~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA  514 (549)
T PF07079_consen  437 IPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEA  514 (549)
T ss_pred             HHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHH
Confidence            3444444444455555542    333444443  35668899888765544444  678999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCcHHHHHH
Q 042039          316 HDLFLDMEENAVAPNVIIFVT  336 (376)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~  336 (376)
                      ..++..+     +|+..+++.
T Consensus       515 ~~~l~~L-----P~n~~~~ds  530 (549)
T PF07079_consen  515 WEYLQKL-----PPNERMRDS  530 (549)
T ss_pred             HHHHHhC-----CCchhhHHH
Confidence            9999874     566666654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>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=96.68  E-value=0.26  Score=39.96  Aligned_cols=62  Identities=13%  Similarity=0.085  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHhcCcHH---HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          123 TYSTLMDGFCLTGKIN---RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      ++..++.++...+..+   +|..+++.+.... +..+.++..-+..+.+.++.+++.+.+.+|...
T Consensus        86 iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~  150 (278)
T PF08631_consen   86 ILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRS  150 (278)
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHh
Confidence            4455566666655543   3444444443332 333455555566666667777777777777765

It is also involved in sporulation [].

>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=96.62  E-value=0.094  Score=45.24  Aligned_cols=154  Identities=17%  Similarity=0.131  Sum_probs=72.0

Q ss_pred             HHhcCChhHHHHHHH--HhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChH
Q 042039           26 LCKEGFVDKAKALFL--QMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMD  103 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  103 (376)
                      ..-.++++++.++.+  ++.. .+  +......++..+.+.|-.+.|+++..         |+.   .-+....+.|+++
T Consensus       271 av~~~d~~~v~~~i~~~~ll~-~i--~~~~~~~i~~fL~~~G~~e~AL~~~~---------D~~---~rFeLAl~lg~L~  335 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLP-NI--PKDQGQSIARFLEKKGYPELALQFVT---------DPD---HRFELALQLGNLD  335 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGG-G----HHHHHHHHHHHHHTT-HHHHHHHSS----------HH---HHHHHHHHCT-HH
T ss_pred             HHHcCChhhhhhhhhhhhhcc-cC--ChhHHHHHHHHHHHCCCHHHHHhhcC---------ChH---HHhHHHHhcCCHH
Confidence            344566666555554  1111 11  13345556666666666666665532         111   2234445666666


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHH
Q 042039          104 EASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMV  183 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  183 (376)
                      .|.++.++.      .+...|..|.......|+++-|+++|.+..+         +..|+-.|.-.|+.+.-.++.+...
T Consensus       336 ~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~  400 (443)
T PF04053_consen  336 IALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAE  400 (443)
T ss_dssp             HHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHH
Confidence            665543322      2455666666666666666666666665432         3445555555666655555555555


Q ss_pred             HCCCCCCHhHHHHHHHHHHhccchHHHHHHHH
Q 042039          184 SKGIKPTVVTYNTLFLGLFEIHQVEHALKLFE  215 (376)
Q Consensus       184 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  215 (376)
                      ..|.      ++....++.-.|+.++..+++.
T Consensus       401 ~~~~------~n~af~~~~~lgd~~~cv~lL~  426 (443)
T PF04053_consen  401 ERGD------INIAFQAALLLGDVEECVDLLI  426 (443)
T ss_dssp             HTT-------HHHHHHHHHHHT-HHHHHHHHH
T ss_pred             HccC------HHHHHHHHHHcCCHHHHHHHHH
Confidence            4421      2333344444555555555544

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.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=96.60  E-value=0.088  Score=35.94  Aligned_cols=93  Identities=18%  Similarity=0.147  Sum_probs=56.8

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC---hhhHHHHHHHHHhc
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN---AFTYSTLMDGFCLT  134 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~  134 (376)
                      ..++...|+.+.|++.|.+.+..-+ .....|+.-..++.-+|+.++|+.-+++.++..-..+   ...|..-...|...
T Consensus        50 ~valaE~g~Ld~AlE~F~qal~l~P-~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~  128 (175)
T KOG4555|consen   50 AIALAEAGDLDGALELFGQALCLAP-ERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLL  128 (175)
T ss_pred             HHHHHhccchHHHHHHHHHHHHhcc-cchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHh
Confidence            4455666777777777777766522 2566777777777777777777777777666421112   12233444555666


Q ss_pred             CcHHHHHHHHHHHHhcC
Q 042039          135 GKINRAEELFGSMESMG  151 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~~  151 (376)
                      |+-+.|..-|+...+.|
T Consensus       129 g~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  129 GNDDAARADFEAAAQLG  145 (175)
T ss_pred             CchHHHHHhHHHHHHhC
Confidence            66666666666666555

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=96.55  E-value=0.26  Score=38.51  Aligned_cols=202  Identities=21%  Similarity=0.084  Sum_probs=94.4

Q ss_pred             hhHHHHHHHHHhcCcHHHHHHHHHHHHhc-CCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHH-
Q 042039          122 FTYSTLMDGFCLTGKINRAEELFGSMESM-GCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL-  199 (376)
Q Consensus       122 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~-  199 (376)
                      .........+...+.+..+...+...... ..+.....+......+...+++..+...+.........+ ......... 
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  138 (291)
T COG0457          60 GLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDP-DLAEALLALG  138 (291)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCc-chHHHHHHHH
Confidence            34444444555555555555555554431 112333444444555555555555555555555432221 111111122 


Q ss_pred             HHHhccchHHHHHHHHHHHhcCC--CCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCCh
Q 042039          200 GLFEIHQVEHALKLFEEMQRDDV--AADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      .+...++++.+...+........  ......+......+...++.+.+...+..............+..+...+...+++
T Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (291)
T COG0457         139 ALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKY  218 (291)
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHHcccH
Confidence            45555555555555555533210  0112222222223445556666666666655443111244555555666666666


Q ss_pred             HHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          278 EIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      +.|...+....... +.....+..+...+...+..+.+...+.+....
T Consensus       219 ~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         219 EEALEYYEKALELD-PDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHHHHHHHHHhhC-cccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66666666655431 112333344444444555566666666666553

>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=96.49  E-value=0.35  Score=39.18  Aligned_cols=165  Identities=14%  Similarity=0.166  Sum_probs=102.9

Q ss_pred             HHhcCChhHHHHHHHHhhhCC--CCCC-----hhhHHHHHHHHhcCC-ChHHHHHHHHHHHhc--------CCCCc----
Q 042039           26 LCKEGFVDKAKALFLQMKGEN--INPD-----VVTYNSLIHGLCHAN-DWNEAKRLFFEMMDQ--------GVQPS----   85 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~--~~~~-----~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~--------~~~~~----   85 (376)
                      ..+.|+.+.|..++.++....  ..|+     ...+...+......+ +++.|..++++..+.        ...|+    
T Consensus         3 A~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~el   82 (278)
T PF08631_consen    3 AWKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSEL   82 (278)
T ss_pred             chhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHH
Confidence            357899999999999987643  1222     122334445555666 888888888776553        12222    


Q ss_pred             -hHhHHHHHHHHHhCCChH---HHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHH
Q 042039           86 -VVTFNVIMDELCKNGKMD---EASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNI  161 (376)
Q Consensus        86 -~~~~~~l~~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  161 (376)
                       ..++..++.++...+..+   +|..+++.+.... +-.+.++..-+..+.+.++.+.+.+.+.+|...- ......+..
T Consensus        83 r~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~-~~~e~~~~~  160 (278)
T PF08631_consen   83 RLSILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSV-DHSESNFDS  160 (278)
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhc-ccccchHHH
Confidence             235667778888877654   5566666665542 2235566667777777899999999999998763 223445555


Q ss_pred             HHHHHHc--cCcHHHHHHHHHHHHHCCCCCCHh
Q 042039          162 LINGYCK--NKEVEEALSLYREMVSKGIKPTVV  192 (376)
Q Consensus       162 l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~  192 (376)
                      .+..+..  ......+...+..++...+.|...
T Consensus       161 ~l~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~~  193 (278)
T PF08631_consen  161 ILHHIKQLAEKSPELAAFCLDYLLLNRFKSSED  193 (278)
T ss_pred             HHHHHHHHHhhCcHHHHHHHHHHHHHHhCCChh
Confidence            5544422  233456666666666554555543

It is also involved in sporulation [].

>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=96.48  E-value=0.15  Score=34.95  Aligned_cols=66  Identities=17%  Similarity=0.319  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCC
Q 042039          296 VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKV  362 (376)
Q Consensus       296 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  362 (376)
                      ...+...+.....+|+-+.-.+++..+.+. -.+++.....+..+|.+.|+..++.++++++-++|+
T Consensus        86 se~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   86 SEYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             -HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            334445555566666666666666665542 245566666666666666666666666666666654

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

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=96.45  E-value=0.31  Score=38.11  Aligned_cols=224  Identities=21%  Similarity=0.099  Sum_probs=160.9

Q ss_pred             cCcHHHHHHHHHHHHhcCCC-CChhhHHHHHHHHHccCcHHHHHHHHHHHHHC-CCCCCHhHHHHHHHHHHhccchHHHH
Q 042039          134 TGKINRAEELFGSMESMGCK-HDDVSYNILINGYCKNKEVEEALSLYREMVSK-GIKPTVVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       134 ~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      .+....+...+......... ............+...+++..+...+...... ........+..........+++..+.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEAL  115 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHH
Confidence            34555666666666554311 13567778888889999999999999888752 23456677777888888888999999


Q ss_pred             HHHHHHHhcCCCCCcchHHHHHH-HHHhCCCHHHHHHHHHHhcccCC--CchHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          212 KLFEEMQRDDVAADTSTYNTFID-GLCKNGYIVEAVELFRTLGILKC--ELDIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      ..+.........+ ......... .+...|+++.|...+........  ......+......+...++.+.+...+....
T Consensus       116 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  194 (291)
T COG0457         116 ELLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKAL  194 (291)
T ss_pred             HHHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHH
Confidence            9999988764222 233333334 78899999999999999855321  1234445555555778899999999999988


Q ss_pred             ccCCCC-CHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          289 RRVLVA-DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       289 ~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      .. .+. ....+..+...+...++++.|...+......... ....+..+...+...+..+++...+.+..+.
T Consensus       195 ~~-~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         195 KL-NPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPD-NAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             hh-CcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcc-cHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            76 333 4677888899999999999999999999875322 2444555555555777889999888887754

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=96.43  E-value=0.26  Score=37.14  Aligned_cols=181  Identities=14%  Similarity=0.034  Sum_probs=102.5

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHH
Q 042039          134 TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKL  213 (376)
Q Consensus       134 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  213 (376)
                      .|-+.-|.--|.+..... |.-+.+||.++-.+...|+++.|.+.|+...+.+.. ...+...-.-++.-.|+++.|.+-
T Consensus        78 lGL~~LAR~DftQaLai~-P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~-y~Ya~lNRgi~~YY~gR~~LAq~d  155 (297)
T COG4785          78 LGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT-YNYAHLNRGIALYYGGRYKLAQDD  155 (297)
T ss_pred             hhHHHHHhhhhhhhhhcC-CCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCc-chHHHhccceeeeecCchHhhHHH
Confidence            344455555555555554 555678888888888999999999999998886322 223333333444556888888887


Q ss_pred             HHHHHhcCCCCCcchHHHHHHHH-HhCCCHHHHHHH-HHHhcccCCCchHHHHHH-HHHHHHhCCChHHHHHHHhccccc
Q 042039          214 FEEMQRDDVAADTSTYNTFIDGL-CKNGYIVEAVEL-FRTLGILKCELDIQAYNC-LIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      +...-+.+ +.|+  |..+--.. ...-++.+|..- .++....    +..-|.. ++..|...=..+.   +++++...
T Consensus       156 ~~~fYQ~D-~~DP--fR~LWLYl~E~k~dP~~A~tnL~qR~~~~----d~e~WG~~iV~~yLgkiS~e~---l~~~~~a~  225 (297)
T COG4785         156 LLAFYQDD-PNDP--FRSLWLYLNEQKLDPKQAKTNLKQRAEKS----DKEQWGWNIVEFYLGKISEET---LMERLKAD  225 (297)
T ss_pred             HHHHHhcC-CCCh--HHHHHHHHHHhhCCHHHHHHHHHHHHHhc----cHhhhhHHHHHHHHhhccHHH---HHHHHHhh
Confidence            77776654 2222  22222211 123355666543 3444322    2222322 2222322112222   22222211


Q ss_pred             CCCC-------CHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC
Q 042039          291 VLVA-------DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV  327 (376)
Q Consensus       291 ~~~~-------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  327 (376)
                       ...       -..+|..++..+...|+.++|..+|+-.+..++
T Consensus       226 -a~~n~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaiannV  268 (297)
T COG4785         226 -ATDNTSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAVANNV  268 (297)
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhH
Confidence             111       135788888999999999999999998887643

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=96.39  E-value=0.7  Score=41.64  Aligned_cols=175  Identities=15%  Similarity=0.092  Sum_probs=91.2

Q ss_pred             hhHHHHHHHHhhhCCCCCChhhHHHHHHHHh-----cCCChHHHHHHHHHHHh-------cCCCCchHhHHHHHHHHHhC
Q 042039           32 VDKAKALFLQMKGENINPDVVTYNSLIHGLC-----HANDWNEAKRLFFEMMD-------QGVQPSVVTFNVIMDELCKN   99 (376)
Q Consensus        32 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~   99 (376)
                      ...|.+.++.....|   +......++.++.     ...+++.|+.+|+.+.+       .+   .......+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcC
Confidence            356777777777665   3444444443333     33577788888877766       33   233445556666553


Q ss_pred             C-----ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhc---CcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc---
Q 042039          100 G-----KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT---GKINRAEELFGSMESMGCKHDDVSYNILINGYCK---  168 (376)
Q Consensus       100 ~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---  168 (376)
                      .     +.+.|..++...-+.| .|+.  ...+..++...   .+...|.++|..+...|   ...++..+..+|..   
T Consensus       302 ~~~~~~d~~~A~~~~~~aA~~g-~~~a--~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G---~~~A~~~la~~y~~G~g  375 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAAELG-NPDA--QYLLGVLYETGTKERDYRRAFEYYSLAAKAG---HILAIYRLALCYELGLG  375 (552)
T ss_pred             CCCccccHHHHHHHHHHHHhcC-CchH--HHHHHHHHHcCCccccHHHHHHHHHHHHHcC---ChHHHHHHHHHHHhCCC
Confidence            2     4566777777776665 2232  22333333332   24567777777777665   23333333333332   


Q ss_pred             -cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          169 -NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       169 -~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                       ..+.+.|..++.+..+.| .|....-...+..+.. +.++.+.-.+..+...
T Consensus       376 v~r~~~~A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~  426 (552)
T KOG1550|consen  376 VERNLELAFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAEL  426 (552)
T ss_pred             cCCCHHHHHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHh
Confidence             335677777777777665 2222222222222222 5555555554444443

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

Probab=96.35  E-value=0.57  Score=40.21  Aligned_cols=148  Identities=16%  Similarity=0.178  Sum_probs=78.4

Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCC-HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG  240 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  240 (376)
                      ++.-.-+..+++.-++.-+++++.  .|+ ...|..|.+  -......++.+++++..+.+-.    .+..- ......|
T Consensus       174 IMq~AWRERnp~aRIkaA~eALei--~pdCAdAYILLAE--EeA~Ti~Eae~l~rqAvkAgE~----~lg~s-~~~~~~g  244 (539)
T PF04184_consen  174 IMQKAWRERNPQARIKAAKEALEI--NPDCADAYILLAE--EEASTIVEAEELLRQAVKAGEA----SLGKS-QFLQHHG  244 (539)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHh--hhhhhHHHhhccc--ccccCHHHHHHHHHHHHHHHHH----hhchh-hhhhccc
Confidence            344444556666666666666663  343 233332221  2344567777777777665310    00000 0000111


Q ss_pred             CHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCC-CCHHHHHHHHHHHHccCChhHHHHHH
Q 042039          241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLV-ADVVTYNIMIHGLCNDGQMDKAHDLF  319 (376)
Q Consensus       241 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~  319 (376)
                      .      .++........+-..+-..++.++.+.|+.++|++.++++.+.... .+......|+.++...+.+.++..++
T Consensus       245 ~------~~e~~~~Rdt~~~~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL  318 (539)
T PF04184_consen  245 H------FWEAWHRRDTNVLVYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALL  318 (539)
T ss_pred             c------hhhhhhccccchhhhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHH
Confidence            1      1111112222223334455666777788888888888887654211 23446677888888888888888888


Q ss_pred             HHHHH
Q 042039          320 LDMEE  324 (376)
Q Consensus       320 ~~~~~  324 (376)
                      .+-.+
T Consensus       319 ~kYdD  323 (539)
T PF04184_consen  319 AKYDD  323 (539)
T ss_pred             HHhcc
Confidence            77654

The molecular function of this protein is uncertain.

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=96.17  E-value=0.81  Score=40.15  Aligned_cols=294  Identities=12%  Similarity=0.043  Sum_probs=174.8

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHh-cCCChHHHHHHHHHHHhc-CCC-CchHhHHHHHHHH
Q 042039           20 NTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLC-HANDWNEAKRLFFEMMDQ-GVQ-PSVVTFNVIMDEL   96 (376)
Q Consensus        20 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~-~~~-~~~~~~~~l~~~~   96 (376)
                      -.....=.+.|..+.+.++|++..+ +++.+...|......+. ..|+.+...+.|+.+... |.. .+...|...+..-
T Consensus        83 ~kfA~~E~klg~~~~s~~Vfergv~-aip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~e  161 (577)
T KOG1258|consen   83 KKFADYEYKLGNAENSVKVFERGVQ-AIPLSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFE  161 (577)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHH-hhhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHH
Confidence            3344444577899999999999985 45777788877765554 457888888999888775 322 2455678888877


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhc------CcHHHHHHHHHHHHh--------------------c
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT------GKINRAEELFGSMES--------------------M  150 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~------~~~~~a~~~~~~~~~--------------------~  150 (376)
                      ..++++.....++++.++.-.. ....+.....-+...      ...+++.++-.....                    .
T Consensus       162 n~qks~k~v~~iyeRileiP~~-~~~~~f~~f~~~l~~~~~~~l~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~  240 (577)
T KOG1258|consen  162 NGQKSWKRVANIYERILEIPLH-QLNRHFDRFKQLLNQNEEKILLSIDELIQLRSDVAERSKITHSQEPLEELEIGVKDS  240 (577)
T ss_pred             hccccHHHHHHHHHHHHhhhhh-HhHHHHHHHHHHHhcCChhhhcCHHHHHHHhhhHHhhhhcccccChhHHHHHHHhhc
Confidence            8888999999999999874111 111111111111111      122222222222111                    0


Q ss_pred             CCCCCh--hhHHHHHH-------HHHccCcHHHHHHHHHHHHHC---CCC----CCHhHHHHHHHHHHhccchHHHHHHH
Q 042039          151 GCKHDD--VSYNILIN-------GYCKNKEVEEALSLYREMVSK---GIK----PTVVTYNTLFLGLFEIHQVEHALKLF  214 (376)
Q Consensus       151 ~~~~~~--~~~~~l~~-------~~~~~~~~~~a~~~~~~~~~~---~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~  214 (376)
                      +.+.+.  .....+..       ++.......+....++.-++.   .+.    ++..+|...+.--...|+.+.+.-++
T Consensus       241 ~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~  320 (577)
T KOG1258|consen  241 TDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILF  320 (577)
T ss_pred             cCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHH
Confidence            100000  01111111       111222223333333333332   122    23567777788888899999999999


Q ss_pred             HHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCC
Q 042039          215 EEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA  294 (376)
Q Consensus       215 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  294 (376)
                      ++..-. ...-...|-..+.-....|+.+-|..++....+...+..+.+...-.......|++..|..+++.+... .+.
T Consensus       321 ercli~-cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e-~pg  398 (577)
T KOG1258|consen  321 ERCLIP-CALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEARFEESNGNFDDAKVILQRIESE-YPG  398 (577)
T ss_pred             HHHHhH-HhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHhh-CCc
Confidence            987643 123345566666666677999999998888776665544444444444556678999999999999887 333


Q ss_pred             CHHHHHHHHHHHHccCChhHHHH
Q 042039          295 DVVTYNIMIHGLCNDGQMDKAHD  317 (376)
Q Consensus       295 ~~~~~~~l~~~~~~~~~~~~a~~  317 (376)
                      -...-..-+....+.|+.+.+..
T Consensus       399 ~v~~~l~~~~~e~r~~~~~~~~~  421 (577)
T KOG1258|consen  399 LVEVVLRKINWERRKGNLEDANY  421 (577)
T ss_pred             hhhhHHHHHhHHHHhcchhhhhH
Confidence            33444444556667888888773

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

Probab=96.06  E-value=0.094  Score=41.65  Aligned_cols=79  Identities=10%  Similarity=0.107  Sum_probs=58.6

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHh-----cCCCCChhhHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQ-----RDVRPNAFTYS  125 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~  125 (376)
                      ..++..++..+...|+++.+...+++++...+. +...|..++.+|.+.|+...|+..|+++.+     .|+.|...+..
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~-~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~  231 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPY-DEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRA  231 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHH
Confidence            456777788888888888888888888776433 677788888888888888888888877765     46777766665


Q ss_pred             HHHHH
Q 042039          126 TLMDG  130 (376)
Q Consensus       126 ~l~~~  130 (376)
                      .....
T Consensus       232 ~y~~~  236 (280)
T COG3629         232 LYEEI  236 (280)
T ss_pred             HHHHH
Confidence            55555

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

Probab=96.03  E-value=0.86  Score=39.21  Aligned_cols=63  Identities=11%  Similarity=0.049  Sum_probs=40.9

Q ss_pred             hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC-CChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          122 FTYSTLMDGFCLTGKINRAEELFGSMESMGCK-HDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       122 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      .+-..+..++.+.|+.++|.+.++++.+.... .......+|+.++...+.+.++..++.+..+
T Consensus       260 y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdD  323 (539)
T PF04184_consen  260 YAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDD  323 (539)
T ss_pred             hhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcc
Confidence            33445666666777777777777777654311 2334666777777777777777777777644

The molecular function of this protein is uncertain.

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

Probab=95.97  E-value=0.11  Score=41.20  Aligned_cols=79  Identities=16%  Similarity=0.185  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH-----cCCCCcHHHHH
Q 042039          261 IQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE-----NAVAPNVIIFV  335 (376)
Q Consensus       261 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~  335 (376)
                      ..++..++..+...|+++.+...++++... -+-+...|..++.+|.+.|+...|+..|+++.+     .|+.|...+..
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~-dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~  231 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIEL-DPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRA  231 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhc-CccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHH
Confidence            345556666666666666666666666655 344666666666777777777776666666543     35666555555


Q ss_pred             HHHHH
Q 042039          336 TLIHG  340 (376)
Q Consensus       336 ~l~~~  340 (376)
                      .....
T Consensus       232 ~y~~~  236 (280)
T COG3629         232 LYEEI  236 (280)
T ss_pred             HHHHH
Confidence            44443

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.92  E-value=0.42  Score=34.69  Aligned_cols=124  Identities=13%  Similarity=0.090  Sum_probs=62.7

Q ss_pred             hcCCChHHHHHHHHHHHhcCCCCc-hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChh-h--HHHHHHHHHhcCcH
Q 042039           62 CHANDWNEAKRLFFEMMDQGVQPS-VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAF-T--YSTLMDGFCLTGKI  137 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~--~~~l~~~~~~~~~~  137 (376)
                      .+.+..++|+.-|..+.+.|...- +.............|+...|...|+++-.....|-.. -  -..-...+...|.+
T Consensus        69 A~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gsy  148 (221)
T COG4649          69 AQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGSY  148 (221)
T ss_pred             HHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhccccH
Confidence            344556666666666665544311 1112223334455566666666666665443222211 0  01112234455666


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          138 NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       138 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      +....-.+.+...+-+.....-..|.-+-.+.|++.+|.+.|.++...
T Consensus       149 ~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~D  196 (221)
T COG4649         149 DDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAND  196 (221)
T ss_pred             HHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHcc
Confidence            666666665554443444445555666666666666666666666553

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

Probab=95.81  E-value=0.21  Score=37.09  Aligned_cols=98  Identities=12%  Similarity=0.086  Sum_probs=62.9

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCC--chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHH--
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQP--SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYST--  126 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--  126 (376)
                      ...+..++..|.+.|+.+.|.+.|.++......+  -...+..+++.....+++..+...+.+....-..+.......  
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrl  115 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRL  115 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHH
Confidence            3567788888888888888888888887764333  244567777888888888888888777665321211111111  


Q ss_pred             ---HHHHHHhcCcHHHHHHHHHHHH
Q 042039          127 ---LMDGFCLTGKINRAEELFGSME  148 (376)
Q Consensus       127 ---l~~~~~~~~~~~~a~~~~~~~~  148 (376)
                         -+-.+...+++..|-+.|-...
T Consensus       116 k~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  116 KVYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHHhchHHHHHHHHHccC
Confidence               1222345678888887776654

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.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=95.69  E-value=2.1  Score=41.07  Aligned_cols=81  Identities=19%  Similarity=0.224  Sum_probs=44.1

Q ss_pred             HHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCH--HHHHHHHHHHHcc
Q 042039          232 FIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV--VTYNIMIHGLCND  309 (376)
Q Consensus       232 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~  309 (376)
                      .+..+.....+++|.-.|+.....         ...+.+|..+|+|.+|+.+..++...   .+.  .+-..|+.-+...
T Consensus       945 ya~hL~~~~~~~~Aal~Ye~~Gkl---------ekAl~a~~~~~dWr~~l~~a~ql~~~---~de~~~~a~~L~s~L~e~ 1012 (1265)
T KOG1920|consen  945 YADHLREELMSDEAALMYERCGKL---------EKALKAYKECGDWREALSLAAQLSEG---KDELVILAEELVSRLVEQ 1012 (1265)
T ss_pred             HHHHHHHhccccHHHHHHHHhccH---------HHHHHHHHHhccHHHHHHHHHhhcCC---HHHHHHHHHHHHHHHHHc
Confidence            334444555566666555554321         23345566667777776666654321   111  1224566666777


Q ss_pred             CChhHHHHHHHHHHH
Q 042039          310 GQMDKAHDLFLDMEE  324 (376)
Q Consensus       310 ~~~~~a~~~~~~~~~  324 (376)
                      +++-+|-++..+...
T Consensus      1013 ~kh~eAa~il~e~~s 1027 (1265)
T KOG1920|consen 1013 RKHYEAAKILLEYLS 1027 (1265)
T ss_pred             ccchhHHHHHHHHhc
Confidence            777777776666544

>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=95.69  E-value=0.51  Score=33.95  Aligned_cols=54  Identities=20%  Similarity=0.076  Sum_probs=31.2

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      -.+.++.+++..+++-+.-.. |.....-..-...+...|+|.+|..+|+++...
T Consensus        20 al~~~~~~D~e~lL~ALrvLR-P~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   20 ALRLGDPDDAEALLDALRVLR-PEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HHccCChHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            345566777777776665442 222333333445566677777777777776554

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=95.69  E-value=0.012  Score=29.83  Aligned_cols=30  Identities=23%  Similarity=0.269  Sum_probs=16.8

Q ss_pred             HhhhCCCCCChhhHHHHHHHHhcCCChHHHH
Q 042039           41 QMKGENINPDVVTYNSLIHGLCHANDWNEAK   71 (376)
Q Consensus        41 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   71 (376)
                      +.++.+ |.+..+|+.+...|...|++++|+
T Consensus         4 kAie~~-P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    4 KAIELN-PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHC-CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            334333 455666666666666666666554

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=95.68  E-value=3.2  Score=43.10  Aligned_cols=321  Identities=10%  Similarity=0.063  Sum_probs=163.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCC--CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENIN--PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      .+..+-.+.+.+.+|...+++-.....+  .....+..+...|...++++....+......   .|+  . ...+.....
T Consensus      1388 tLa~aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a---~~s--l-~~qil~~e~ 1461 (2382)
T KOG0890|consen 1388 TLARASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFA---DPS--L-YQQILEHEA 1461 (2382)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhc---Ccc--H-HHHHHHHHh
Confidence            4555667888899999999984221111  1233344445589999999988777654111   222  2 233445567


Q ss_pred             CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHH-HHHHHHccCcHHHHHH
Q 042039           99 NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNI-LINGYCKNKEVEEALS  177 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~  177 (376)
                      .|++..|...|+.+.+.+ ++....+..++......|.++......+-..... ++...-++. -..+-.+.++++....
T Consensus      1462 ~g~~~da~~Cye~~~q~~-p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~~-se~~~~~~s~~~eaaW~l~qwD~~e~ 1539 (2382)
T KOG0890|consen 1462 SGNWADAAACYERLIQKD-PDKEKHHSGVLKSMLAIQHLSTEILHLDGLIINR-SEEVDELNSLGVEAAWRLSQWDLLES 1539 (2382)
T ss_pred             hccHHHHHHHHHHhhcCC-CccccchhhHHHhhhcccchhHHHhhhcchhhcc-CHHHHHHHHHHHHHHhhhcchhhhhh
Confidence            899999999999999875 3346677777777777888888877666655442 222233332 3344466777776666


Q ss_pred             HHHHHHHCCCCCCHhHHHH--HHHHHHhccchH--HHHHHHHHHHhc--------CCC-CCcchHHHHHHHHHhCCCHHH
Q 042039          178 LYREMVSKGIKPTVVTYNT--LFLGLFEIHQVE--HALKLFEEMQRD--------DVA-ADTSTYNTFIDGLCKNGYIVE  244 (376)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~--l~~~~~~~~~~~--~a~~~~~~~~~~--------~~~-~~~~~~~~l~~~~~~~~~~~~  244 (376)
                      ...   ..    +..+|..  ++....+...-+  .-.+..+.+.+.        ... .-...|..+++...-.. .+.
T Consensus      1540 ~l~---~~----n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~e-l~~ 1611 (2382)
T KOG0890|consen 1540 YLS---DR----NIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLLE-LEN 1611 (2382)
T ss_pred             hhh---cc----cccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHHH-HHH
Confidence            554   11    1112221  222222221111  111122222111        000 11123333333332211 111


Q ss_pred             HHHHHHHhc-ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcc-c----ccC-CCCCHHHHHHHHHHHHccCChhHHHH
Q 042039          245 AVELFRTLG-ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSL-P----RRV-LVADVVTYNIMIHGLCNDGQMDKAHD  317 (376)
Q Consensus       245 a~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~-~----~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~  317 (376)
                      -.+.+.... ......+..-|..-+..-....+..+-+-.+++. .    +.+ ...-..+|...++.....|+++.|..
T Consensus      1612 ~~~~l~~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A~n 1691 (2382)
T KOG0890|consen 1612 SIEELKKVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRAQN 1691 (2382)
T ss_pred             HHHHhhccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHHHH
Confidence            111111111 0000111112222211111111111111111111 1    101 12235678888888888999999888


Q ss_pred             HHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          318 LFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      .+-++.+.+   -+..+...++-....|+...|+.++++-.+.
T Consensus      1692 all~A~e~r---~~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~ 1731 (2382)
T KOG0890|consen 1692 ALLNAKESR---LPEIVLERAKLLWQTGDELNALSVLQEILSK 1731 (2382)
T ss_pred             HHHhhhhcc---cchHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            877777654   3344555667778889999999988888754

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=95.66  E-value=0.67  Score=35.11  Aligned_cols=28  Identities=25%  Similarity=0.221  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                      .+|..++..+...|+.++|..+|+-...
T Consensus       238 EtyFYL~K~~l~~G~~~~A~~LfKLaia  265 (297)
T COG4785         238 ETYFYLGKYYLSLGDLDEATALFKLAVA  265 (297)
T ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            4455555555555555555555555443

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

Probab=95.65  E-value=0.26  Score=36.63  Aligned_cols=63  Identities=17%  Similarity=0.239  Sum_probs=41.7

Q ss_pred             HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC--hhhHHHHHHHHHhcCcHHHHHHHHHHHHh
Q 042039           87 VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN--AFTYSTLMDGFCLTGKINRAEELFGSMES  149 (376)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  149 (376)
                      ..+..++..|.+.|+.++|.+.|.++.+....+.  ...+..+++.....+++..+...+.++..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~  101 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES  101 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            3566677777777777777777777766543332  34556667777777777777777666644

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.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=95.63  E-value=0.014  Score=29.53  Aligned_cols=31  Identities=26%  Similarity=0.354  Sum_probs=16.9

Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHccCcHHHHH
Q 042039          145 GSMESMGCKHDDVSYNILINGYCKNKEVEEAL  176 (376)
Q Consensus       145 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  176 (376)
                      ++.++.. |.+..+|+.++.+|...|++++|+
T Consensus         3 ~kAie~~-P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELN-PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHC-CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            3344443 455556666666666666665554

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.63  E-value=0.51  Score=33.54  Aligned_cols=44  Identities=9%  Similarity=0.085  Sum_probs=24.6

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcC
Q 042039           20 NTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHA   64 (376)
Q Consensus        20 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   64 (376)
                      ..++..+.+.+.......+++.+...+ +.+...++.++..|++.
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~   54 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKY   54 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHH
Confidence            345555555556666666666655554 34555555566655543

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=95.50  E-value=1.4  Score=37.75  Aligned_cols=130  Identities=9%  Similarity=0.059  Sum_probs=88.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      -..-|.-....|+...|-+-+....++. +.++.............|+++.+.+.+....+. +.....+...+++....
T Consensus       292 ~~~si~k~~~~gd~~aas~~~~~~lr~~-~~~p~~i~l~~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~  369 (831)
T PRK15180        292 ITLSITKQLADGDIIAASQQLFAALRNQ-QQDPVLIQLRSVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHG  369 (831)
T ss_pred             HHHHHHHHhhccCHHHHHHHHHHHHHhC-CCCchhhHHHHHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhc
Confidence            3344445556788877765555444432 334444444455566789999999988776543 33456677888899999


Q ss_pred             CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Q 042039           99 NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      .|++++|..+-.-|+...++ ++..........-..|-++++.-.|+++...+
T Consensus       370 l~r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~  421 (831)
T PRK15180        370 LARWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLN  421 (831)
T ss_pred             hhhHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccC
Confidence            99999999999998877654 44444444444556678899999999987766

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.47  E-value=0.59  Score=33.22  Aligned_cols=40  Identities=15%  Similarity=0.131  Sum_probs=16.5

Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  168 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  168 (376)
                      +..+...+.......+++.+...+ +.+...++.++..|++
T Consensus        14 v~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~   53 (140)
T smart00299       14 VELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAK   53 (140)
T ss_pred             HHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHH
Confidence            333333344444444444444433 2333344444444443

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.45  E-value=0.66  Score=33.71  Aligned_cols=122  Identities=14%  Similarity=0.107  Sum_probs=56.6

Q ss_pred             hccchHHHHHHHHHHHhcCCCCCcc-hHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHH---HHHHHHHHHHhCCChH
Q 042039          203 EIHQVEHALKLFEEMQRDDVAADTS-TYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQ---AYNCLIDGLCKSGRLE  278 (376)
Q Consensus       203 ~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~  278 (376)
                      +.+..++|+.-|..+.+.|...-+. ............|+...|...|.++......|-..   .-..-...+...|.++
T Consensus        70 ~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gsy~  149 (221)
T COG4649          70 QENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGSYD  149 (221)
T ss_pred             HcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhccccHH
Confidence            3445555555555555544221111 11222333445556666666666554332222111   1111122344556666


Q ss_pred             HHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          279 IALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       279 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      ....-.+.+...+.+.-...-..|..+-.+.|++..|...|..+.+
T Consensus       150 dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         150 DVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            6655555554433333333444555555566666666666666654

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

Probab=95.42  E-value=0.035  Score=28.50  Aligned_cols=23  Identities=22%  Similarity=0.161  Sum_probs=10.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQ   41 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~   41 (376)
                      |+.|...|.+.|++++|+++|++
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            44444455555555555555544

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

Probab=95.38  E-value=0.043  Score=28.16  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=15.3

Q ss_pred             HHHHHHHHHccCcHHHHHHHHHHHH
Q 042039          159 YNILINGYCKNKEVEEALSLYREMV  183 (376)
Q Consensus       159 ~~~l~~~~~~~~~~~~a~~~~~~~~  183 (376)
                      +..|+.+|.+.|++++|+++|++.+
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4556666666666666666666643

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

Probab=95.26  E-value=1.4  Score=36.36  Aligned_cols=108  Identities=19%  Similarity=0.166  Sum_probs=66.3

Q ss_pred             HHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHh
Q 042039          194 YNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCK  273 (376)
Q Consensus       194 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  273 (376)
                      ...-+.-+...|+...|.++-.+..    .|+...|...+.+++..++|++-..+...   .   -+|.-|...+.+|.+
T Consensus       180 l~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s---k---KsPIGyepFv~~~~~  249 (319)
T PF04840_consen  180 LNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS---K---KSPIGYEPFVEACLK  249 (319)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC---C---CCCCChHHHHHHHHH
Confidence            3444455556677666666655442    45666777777777777777776665432   1   133456667777777


Q ss_pred             CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHH
Q 042039          274 SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLD  321 (376)
Q Consensus       274 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  321 (376)
                      .|+..+|..+..++.          +..-+..|.+.|++.+|.+..-+
T Consensus       250 ~~~~~eA~~yI~k~~----------~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  250 YGNKKEASKYIPKIP----------DEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             CCCHHHHHHHHHhCC----------hHHHHHHHHHCCCHHHHHHHHHH
Confidence            777777777776621          13455666777777777665443

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

>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=95.26  E-value=0.61  Score=32.14  Aligned_cols=65  Identities=14%  Similarity=0.179  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV  327 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  327 (376)
                      ......+..+...|+-++-.+++..+.+. -.+++.....+..+|.+.|+..++-+++.++-+.|+
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            33444455566666666666666665532 345666666677777777777777777776666654

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

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

Probab=95.16  E-value=0.25  Score=38.89  Aligned_cols=94  Identities=13%  Similarity=0.155  Sum_probs=54.0

Q ss_pred             hHHHHHHHHHHHHhC-----CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCC----------------hhHHHHH
Q 042039          260 DIQAYNCLIDGLCKS-----GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQ----------------MDKAHDL  318 (376)
Q Consensus       260 ~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------------~~~a~~~  318 (376)
                      |..+|...+..+...     +..+-....++.|.+.|+.-|..+|..|+..+-+..-                -+=++++
T Consensus        66 dK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~v  145 (406)
T KOG3941|consen   66 DKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKV  145 (406)
T ss_pred             cHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHH
Confidence            556666666666432     4455556666777777777788888877777654321                1124555


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHH
Q 042039          319 FLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHK  356 (376)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  356 (376)
                      +++|...|+-||..+-..|+.++   |++.-...-+.+
T Consensus       146 LeqME~hGVmPdkE~e~~lvn~F---Gr~~~p~~K~~R  180 (406)
T KOG3941|consen  146 LEQMEWHGVMPDKEIEDILVNAF---GRWNFPTKKVKR  180 (406)
T ss_pred             HHHHHHcCCCCchHHHHHHHHHh---ccccccHHHHHH
Confidence            55555555555555555555544   555444433333

>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=95.07  E-value=0.86  Score=32.82  Aligned_cols=53  Identities=25%  Similarity=0.090  Sum_probs=27.4

Q ss_pred             HhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          237 CKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       237 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      .+.++.+++..++..+....+. .+..-..-+..+...|++.+|..+|+.+...
T Consensus        21 l~~~~~~D~e~lL~ALrvLRP~-~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVLRPE-FPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HccCChHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            3455666666666665444322 2222333344455566666666666665543

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.04  E-value=1  Score=33.51  Aligned_cols=93  Identities=11%  Similarity=0.054  Sum_probs=59.8

Q ss_pred             HHHHHHhCCCHHHHHHHHHHhcccCCC--chHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc
Q 042039          232 FIDGLCKNGYIVEAVELFRTLGILKCE--LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND  309 (376)
Q Consensus       232 l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  309 (376)
                      +...+...+++++|...++........  .....-..+.+.....|.+++|+..++.....+.  .......-+..+...
T Consensus        95 lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w--~~~~~elrGDill~k  172 (207)
T COG2976          95 LAKAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKEESW--AAIVAELRGDILLAK  172 (207)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccH--HHHHHHHhhhHHHHc
Confidence            345667788888888888776543211  1122334566677778888888888877665432  233344556777778


Q ss_pred             CChhHHHHHHHHHHHcC
Q 042039          310 GQMDKAHDLFLDMEENA  326 (376)
Q Consensus       310 ~~~~~a~~~~~~~~~~~  326 (376)
                      |+-++|+.-|++..+.+
T Consensus       173 g~k~~Ar~ay~kAl~~~  189 (207)
T COG2976         173 GDKQEARAAYEKALESD  189 (207)
T ss_pred             CchHHHHHHHHHHHHcc
Confidence            88888888888777764

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.03  E-value=0.8  Score=32.26  Aligned_cols=57  Identities=16%  Similarity=0.195  Sum_probs=24.5

Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCC--CCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGC--KHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      +....+.|++++|.+.|+.+...-.  +-...+-..++.+|.+.+++++|...+++.++
T Consensus        17 a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFir   75 (142)
T PF13512_consen   17 AQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIR   75 (142)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            3333444445555554444443310  11222333444444444555555554444444

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.03  E-value=2.7  Score=38.25  Aligned_cols=303  Identities=11%  Similarity=0.111  Sum_probs=164.0

Q ss_pred             hCCCCCChhhHHH-----HHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC--hHHHHHHHHHHHhcC
Q 042039           44 GENINPDVVTYNS-----LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK--MDEASRLLDLMVQRD  116 (376)
Q Consensus        44 ~~~~~~~~~~~~~-----l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~  116 (376)
                      ..|++.+..-|..     ++.-+...+.+..|+++-..+...-.. ....|.....-+.+..+  -+++.+.+.+=+...
T Consensus       425 ~~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~-~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~  503 (829)
T KOG2280|consen  425 RIGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQ-GDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAK  503 (829)
T ss_pred             ccCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCcccc-ccHHHHHHHHHHHhccCccchHHHHHHHHHhccc
Confidence            4466666665554     455666778899999988776432212 25666666666666532  223333333222221


Q ss_pred             CCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC----CChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC------
Q 042039          117 VRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCK----HDDVSYNILINGYCKNKEVEEALSLYREMVSKG------  186 (376)
Q Consensus       117 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------  186 (376)
                      .. ....|..+++-....|+.+-|..+++.-...+..    .+..-+...+.-+...|+.+-...++-.+..+-      
T Consensus       504 ~~-~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~  582 (829)
T KOG2280|consen  504 LT-PGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLF  582 (829)
T ss_pred             CC-CceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence            22 3456777888888899999998887653222100    011122333444455666666655555544320      


Q ss_pred             -----CCCCHhHHHHHHH--------HHHhccchHHHHHHHH--HHHhc-CCCCCcchHHHHHHHHHhCCCHH---HH--
Q 042039          187 -----IKPTVVTYNTLFL--------GLFEIHQVEHALKLFE--EMQRD-DVAADTSTYNTFIDGLCKNGYIV---EA--  245 (376)
Q Consensus       187 -----~~~~~~~~~~l~~--------~~~~~~~~~~a~~~~~--~~~~~-~~~~~~~~~~~l~~~~~~~~~~~---~a--  245 (376)
                           .+.....|..+++        .+.+.++-..+...+.  ..... .+.+-..........+.+.....   +|  
T Consensus       583 ~~l~~~p~a~~lY~~~~r~~~~~~l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~e  662 (829)
T KOG2280|consen  583 MTLRNQPLALSLYRQFMRHQDRATLYDFYNQDDNHQALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKALE  662 (829)
T ss_pred             HHHHhchhhhHHHHHHHHhhchhhhhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHHH
Confidence                 1112222222222        1111222222222221  10000 01122223344444454443311   11  


Q ss_pred             -----HHHHHHhc-ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHH
Q 042039          246 -----VELFRTLG-ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLF  319 (376)
Q Consensus       246 -----~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  319 (376)
                           ..+.+.+. +.+.....-+.+.-+.-+...|+..+|.++-+++.    -||...|..-+.+++..+++++-+++-
T Consensus       663 d~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfA  738 (829)
T KOG2280|consen  663 DQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFA  738 (829)
T ss_pred             HHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHH
Confidence                 11111111 11111222345556667778899999999888765    368888988999999999998877765


Q ss_pred             HHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          320 LDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       320 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      +...      .+.-|...+.+|.+.|+.++|.+++.+..
T Consensus       739 kskk------sPIGy~PFVe~c~~~~n~~EA~KYiprv~  771 (829)
T KOG2280|consen  739 KSKK------SPIGYLPFVEACLKQGNKDEAKKYIPRVG  771 (829)
T ss_pred             hccC------CCCCchhHHHHHHhcccHHHHhhhhhccC
Confidence            5432      35567888999999999999999887763

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=94.82  E-value=3  Score=37.75  Aligned_cols=272  Identities=14%  Similarity=0.064  Sum_probs=160.9

Q ss_pred             hHHHHHHHHHHHhcCCCCchHhHHHHHHH-----HHhCCChHHHHHHHHHHHh-------cCCCCChhhHHHHHHHHHhc
Q 042039           67 WNEAKRLFFEMMDQGVQPSVVTFNVIMDE-----LCKNGKMDEASRLLDLMVQ-------RDVRPNAFTYSTLMDGFCLT  134 (376)
Q Consensus        67 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-----~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~  134 (376)
                      ...|.++++...+.|   +......+..+     +....+.+.|..+++.+.+       .+   .+.....+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcC
Confidence            467888888887765   33333333333     3355789999999999877       44   344666778888775


Q ss_pred             C-----cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc---CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHH----
Q 042039          135 G-----KINRAEELFGSMESMGCKHDDVSYNILINGYCKN---KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLF----  202 (376)
Q Consensus       135 ~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~----  202 (376)
                      .     +.+.|..++....+.| .|+..  ..++.++...   .+...|.++|..+...|..   ..+..+..++.    
T Consensus       302 ~~~~~~d~~~A~~~~~~aA~~g-~~~a~--~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~---~A~~~la~~y~~G~g  375 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAAELG-NPDAQ--YLLGVLYETGTKERDYRRAFEYYSLAAKAGHI---LAIYRLALCYELGLG  375 (552)
T ss_pred             CCCccccHHHHHHHHHHHHhcC-CchHH--HHHHHHHHcCCccccHHHHHHHHHHHHHcCCh---HHHHHHHHHHHhCCC
Confidence            3     6788999999998887 34433  3344444433   4678999999999988643   33334443333    


Q ss_pred             hccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHH-HH---Hh----C
Q 042039          203 EIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLID-GL---CK----S  274 (376)
Q Consensus       203 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~-~~---~~----~  274 (376)
                      ...+...|..++.+..+.+ .|........+..+.. ++++.+.-.+..+...+.+ ...+-...+. ..   ..    .
T Consensus       376 v~r~~~~A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g~~-~~q~~a~~l~~~~~~~~~~~~~~  452 (552)
T KOG1550|consen  376 VERNLELAFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELGYE-VAQSNAAYLLDQSEEDLFSRGVI  452 (552)
T ss_pred             cCCCHHHHHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhhhh-HHhhHHHHHHHhccccccccccc
Confidence            2347888999999998887 3333333333334444 7777777766666655533 2221111111 11   11    1


Q ss_pred             CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc----CChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh----cCC
Q 042039          275 GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND----GQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR----INK  346 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~  346 (376)
                      .+.+.+...+.+....|   +......+...|...    .+++.|...+......+   ....|+ +...+..    .. 
T Consensus       453 ~~~~~~~~~~~~a~~~g---~~~a~~~lgd~y~~g~g~~~d~~~a~~~y~~a~~~~---~~~~~n-lg~~~e~g~g~~~-  524 (552)
T KOG1550|consen  453 STLERAFSLYSRAAAQG---NADAILKLGDYYYYGLGTGRDPEKAAAQYARASEQG---AQALFN-LGYMHEHGEGIKV-  524 (552)
T ss_pred             cchhHHHHHHHHHHhcc---CHHHHhhhcceeeecCCCCCChHHHHHHHHHHHHhh---hHHHhh-hhhHHhcCcCcch-
Confidence            24556666666655443   455555566555443    35777888887777654   222222 3322211    22 


Q ss_pred             hhhHHHHHHHHHhCC
Q 042039          347 PSKVIELLHKMKEKK  361 (376)
Q Consensus       347 ~~~a~~~~~~~~~~~  361 (376)
                      ...|.+++++..+.+
T Consensus       525 ~~~a~~~~~~~~~~~  539 (552)
T KOG1550|consen  525 LHLAKRYYDQASEED  539 (552)
T ss_pred             hHHHHHHHHHHHhcC
Confidence            577777777776544

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.69  E-value=1.5  Score=40.21  Aligned_cols=119  Identities=18%  Similarity=0.216  Sum_probs=72.0

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc--hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS--VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ...-+..+.+..-++-|+.+-+.   .+..++  .........-+...|++++|...|-+.+.. +.|.     .++.-|
T Consensus       337 le~kL~iL~kK~ly~~Ai~LAk~---~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kf  407 (933)
T KOG2114|consen  337 LETKLDILFKKNLYKVAINLAKS---QHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEPS-----EVIKKF  407 (933)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHh---cCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CChH-----HHHHHh
Confidence            34455666666667777666433   222222  123334445556778888888877776653 2322     244455


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      ....+..+-..+++.+.+.|. .+...-..|+.+|.+.++.++-.++.+..
T Consensus       408 Ldaq~IknLt~YLe~L~~~gl-a~~dhttlLLncYiKlkd~~kL~efI~~~  457 (933)
T KOG2114|consen  408 LDAQRIKNLTSYLEALHKKGL-ANSDHTTLLLNCYIKLKDVEKLTEFISKC  457 (933)
T ss_pred             cCHHHHHHHHHHHHHHHHccc-ccchhHHHHHHHHHHhcchHHHHHHHhcC
Confidence            566667777777777777773 45566667788888888777766655543

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=94.67  E-value=1.2  Score=33.42  Aligned_cols=91  Identities=20%  Similarity=0.178  Sum_probs=51.2

Q ss_pred             HHHHccCcHHHHHHHHHHHHHCCCCCC-----HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          164 NGYCKNKEVEEALSLYREMVSKGIKPT-----VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       164 ~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                      .-+...|++++|..-|..++.. +++.     ...|..-..++.+.+.++.|+.-..+.++.+ +.....+..-+.+|.+
T Consensus       103 N~~F~ngdyeeA~skY~~Ale~-cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~-pty~kAl~RRAeayek  180 (271)
T KOG4234|consen  103 NELFKNGDYEEANSKYQEALES-CPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELN-PTYEKALERRAEAYEK  180 (271)
T ss_pred             HHhhhcccHHHHHHHHHHHHHh-CccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcC-chhHHHHHHHHHHHHh
Confidence            3345566777777777766664 2222     2233344455556666666666666666554 2233344444556666


Q ss_pred             CCCHHHHHHHHHHhcccC
Q 042039          239 NGYIVEAVELFRTLGILK  256 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~  256 (376)
                      ...+++|+.-|+.+.+..
T Consensus       181 ~ek~eealeDyKki~E~d  198 (271)
T KOG4234|consen  181 MEKYEEALEDYKKILESD  198 (271)
T ss_pred             hhhHHHHHHHHHHHHHhC
Confidence            666677766666666553

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

Probab=94.53  E-value=0.1  Score=26.14  Aligned_cols=27  Identities=15%  Similarity=0.222  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      +|..++.++...|++++|+..|+++++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            444555555555555555555555554

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 ....

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=94.51  E-value=0.091  Score=28.33  Aligned_cols=23  Identities=17%  Similarity=0.377  Sum_probs=12.2

Q ss_pred             HHHHHHccCChhHHHHHHHHHHH
Q 042039          302 MIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       302 l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      +..+|...|+.+.|.++++++..
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~   27 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIE   27 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Confidence            44555555555555555555554

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.

>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=94.42  E-value=0.63  Score=34.88  Aligned_cols=79  Identities=14%  Similarity=0.057  Sum_probs=59.1

Q ss_pred             HhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc---CCCCChhhHHHHHHHHHhcCcH
Q 042039           61 LCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR---DVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        61 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                      ..+.|+ ++|.+.|-++...+.--++.....++..|. ..+.+++..++...++.   +..+|+..+..|+..+.+.|++
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~  194 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNY  194 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcch
Confidence            344454 678888888877765546666665555554 67889999999888764   3366789999999999999999


Q ss_pred             HHHH
Q 042039          138 NRAE  141 (376)
Q Consensus       138 ~~a~  141 (376)
                      +.|-
T Consensus       195 e~AY  198 (203)
T PF11207_consen  195 EQAY  198 (203)
T ss_pred             hhhh
Confidence            8874

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

Probab=94.36  E-value=0.56  Score=37.04  Aligned_cols=69  Identities=16%  Similarity=0.155  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC----------------CChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           68 NEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN----------------GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        68 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      +-....++.|.+.|+..|..+|+.|+..+-+.                .+-+-++.++++|...|+.||..+-..++.++
T Consensus        89 eFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~F  168 (406)
T KOG3941|consen   89 EFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAF  168 (406)
T ss_pred             HHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHh
Confidence            33333444455555555555555555443221                23456788899999899999988888888888


Q ss_pred             HhcCc
Q 042039          132 CLTGK  136 (376)
Q Consensus       132 ~~~~~  136 (376)
                      .+.+.
T Consensus       169 Gr~~~  173 (406)
T KOG3941|consen  169 GRWNF  173 (406)
T ss_pred             ccccc
Confidence            87764

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=94.35  E-value=0.89  Score=33.98  Aligned_cols=91  Identities=14%  Similarity=0.124  Sum_probs=66.2

Q ss_pred             HHhcCCChHHHHHHHHHHHhcCCCCc----hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC
Q 042039           60 GLCHANDWNEAKRLFFEMMDQGVQPS----VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG  135 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  135 (376)
                      -+...|++++|..-|..++..-+...    ...|..-..+..+.+.++.|+.-..+.++.+ +........-+.+|.+..
T Consensus       104 ~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~-pty~kAl~RRAeayek~e  182 (271)
T KOG4234|consen  104 ELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELN-PTYEKALERRAEAYEKME  182 (271)
T ss_pred             HhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcC-chhHHHHHHHHHHHHhhh
Confidence            35678889999988888887622211    2345555667888889999988888888865 223445555577888888


Q ss_pred             cHHHHHHHHHHHHhcC
Q 042039          136 KINRAEELFGSMESMG  151 (376)
Q Consensus       136 ~~~~a~~~~~~~~~~~  151 (376)
                      .++.|+.-|.++....
T Consensus       183 k~eealeDyKki~E~d  198 (271)
T KOG4234|consen  183 KYEEALEDYKKILESD  198 (271)
T ss_pred             hHHHHHHHHHHHHHhC
Confidence            8999999999888774

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

Probab=94.32  E-value=0.14  Score=25.66  Aligned_cols=26  Identities=19%  Similarity=0.383  Sum_probs=11.3

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      |..++.++...|++++|+..|++.++
T Consensus         4 ~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    4 YYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            44444444444444444444444443

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

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

Probab=94.30  E-value=0.12  Score=25.77  Aligned_cols=27  Identities=15%  Similarity=0.218  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      .+..++.++...|++++|++.|+++.+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            344455555555555555555555544

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 ....

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.30  E-value=4.4  Score=37.50  Aligned_cols=252  Identities=15%  Similarity=0.123  Sum_probs=148.1

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC--hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPN--AFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGY  166 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  166 (376)
                      ...-+..+.+...++-|..+-+.   .+..++  .......+..+.+.|++++|...|-+....- .|+     .++.-|
T Consensus       337 le~kL~iL~kK~ly~~Ai~LAk~---~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~l-e~s-----~Vi~kf  407 (933)
T KOG2114|consen  337 LETKLDILFKKNLYKVAINLAKS---QHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFL-EPS-----EVIKKF  407 (933)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHh---cCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccC-ChH-----HHHHHh
Confidence            34456666777777777766543   222322  2344455666678899999998887765432 221     246666


Q ss_pred             HccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHH
Q 042039          167 CKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAV  246 (376)
Q Consensus       167 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  246 (376)
                      .......+-..+++.+.+.|+. +...-..|+.+|.+.++.++..++.+... .|..  ..-....+..+.+.+-.++|.
T Consensus       408 Ldaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl~~a~  483 (933)
T KOG2114|consen  408 LDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNYLDEAE  483 (933)
T ss_pred             cCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChHHHHH
Confidence            7777788888888888888765 56666788999999999998877766544 2211  223566677777888888888


Q ss_pred             HHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc-
Q 042039          247 ELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN-  325 (376)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-  325 (376)
                      .+-.....     +......+   +...+++++|+++++.+.-..   -..+....+..+.. ..+++-..++-+.... 
T Consensus       484 ~LA~k~~~-----he~vl~il---le~~~ny~eAl~yi~slp~~e---~l~~l~kyGk~Ll~-h~P~~t~~ili~~~t~~  551 (933)
T KOG2114|consen  484 LLATKFKK-----HEWVLDIL---LEDLHNYEEALRYISSLPISE---LLRTLNKYGKILLE-HDPEETMKILIELITEL  551 (933)
T ss_pred             HHHHHhcc-----CHHHHHHH---HHHhcCHHHHHHHHhcCCHHH---HHHHHHHHHHHHHh-hChHHHHHHHHHHHhhc
Confidence            77666542     23333333   456789999999998764221   12233333333333 2344444444444332 


Q ss_pred             CCCCcHHHH----HHHHHHHhhcCChhhHHHHHHHHHhCCCCCchH
Q 042039          326 AVAPNVIIF----VTLIHGFVRINKPSKVIELLHKMKEKKVMPDAS  367 (376)
Q Consensus       326 ~~~~~~~~~----~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~  367 (376)
                      +..+.....    ..+-....-.++++.....++.|.+.  .|+..
T Consensus       552 ~~~~~~~~~s~~~~~~~~i~if~~~~~~~~~Fl~~~~E~--s~~s~  595 (933)
T KOG2114|consen  552 NSQGKGKSLSNIPDSIEFIGIFSQNYQILLNFLESMSEI--SPDSE  595 (933)
T ss_pred             CCCCCCchhhcCccchhheeeeccCHHHHHHHHHHHHhc--CCCch
Confidence            212111111    11122234466777777777776654  44443

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=94.22  E-value=0.21  Score=40.43  Aligned_cols=90  Identities=11%  Similarity=0.022  Sum_probs=61.7

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChH
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMD  103 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  103 (376)
                      ..|+++|++++|++.|....... +.|+.++..-..+|.+..++..|..-.+..+..+ ..-...|..-+.+-...|...
T Consensus       105 N~yFKQgKy~EAIDCYs~~ia~~-P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg~~~  182 (536)
T KOG4648|consen  105 NTYFKQGKYEEAIDCYSTAIAVY-PHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLGNNM  182 (536)
T ss_pred             hhhhhccchhHHHHHhhhhhccC-CCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHhhHH
Confidence            34778888888888888777653 4477888888888888888887777777666542 112334555555555667777


Q ss_pred             HHHHHHHHHHhc
Q 042039          104 EASRLLDLMVQR  115 (376)
Q Consensus       104 ~a~~~~~~~~~~  115 (376)
                      +|.+-++..+..
T Consensus       183 EAKkD~E~vL~L  194 (536)
T KOG4648|consen  183 EAKKDCETVLAL  194 (536)
T ss_pred             HHHHhHHHHHhh
Confidence            777777777664

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.22  E-value=1.7  Score=32.42  Aligned_cols=56  Identities=9%  Similarity=0.041  Sum_probs=23.1

Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      .+.....|.+++|...++.....+  ........-++++...|+-++|..-|.+.+..
T Consensus       133 Arvq~q~~k~D~AL~~L~t~~~~~--w~~~~~elrGDill~kg~k~~Ar~ay~kAl~~  188 (207)
T COG2976         133 ARVQLQQKKADAALKTLDTIKEES--WAAIVAELRGDILLAKGDKQEARAAYEKALES  188 (207)
T ss_pred             HHHHHHhhhHHHHHHHHhcccccc--HHHHHHHHhhhHHHHcCchHHHHHHHHHHHHc
Confidence            334444444444444444433321  11122223334444444444444444444443

>KOG2471 consensus TPR repeat-containing protein [General function prediction only]

Probab=94.20  E-value=3.4  Score=35.72  Aligned_cols=109  Identities=15%  Similarity=-0.015  Sum_probs=63.9

Q ss_pred             HHHHhCCCHHHHHHHHHHhccc---CCCchH-----HHHHHHHHHHHhCCChHHHHHHHhcccc-------cCCCCC---
Q 042039          234 DGLCKNGYIVEAVELFRTLGIL---KCELDI-----QAYNCLIDGLCKSGRLEIALELFRSLPR-------RVLVAD---  295 (376)
Q Consensus       234 ~~~~~~~~~~~a~~~~~~~~~~---~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~-------~~~~~~---  295 (376)
                      ..+.-.|++.+|.+++-...-.   |...++     ..|+.++-.+.+.|.+.-+..+|.++.+       .|..|.   
T Consensus       248 q~eY~~gn~~kA~KlL~~sni~~~~g~~~T~q~~~cif~NNlGcIh~~~~~y~~~~~~F~kAL~N~c~qL~~g~~~~~~~  327 (696)
T KOG2471|consen  248 QLEYAHGNHPKAMKLLLVSNIHKEAGGTITPQLSSCIFNNNLGCIHYQLGCYQASSVLFLKALRNSCSQLRNGLKPAKTF  327 (696)
T ss_pred             HHHHHhcchHHHHHHHHhcccccccCccccchhhhheeecCcceEeeehhhHHHHHHHHHHHHHHHHHHHhccCCCCcce
Confidence            3455667777777776554211   111111     1234555555556666666655555442       232221   


Q ss_pred             -------HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh
Q 042039          296 -------VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR  343 (376)
Q Consensus       296 -------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  343 (376)
                             ....+..+-.|...|++-.|.+.|.+.... ...++..|..+..+|..
T Consensus       328 tls~nks~eilYNcG~~~Lh~grPl~AfqCf~~av~v-fh~nPrlWLRlAEcCim  381 (696)
T KOG2471|consen  328 TLSQNKSMEILYNCGLLYLHSGRPLLAFQCFQKAVHV-FHRNPRLWLRLAECCIM  381 (696)
T ss_pred             ehhcccchhhHHhhhHHHHhcCCcHHHHHHHHHHHHH-HhcCcHHHHHHHHHHHH
Confidence                   233445666778888888888888887764 34578888888888765

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=94.16  E-value=4.6  Score=37.17  Aligned_cols=66  Identities=12%  Similarity=0.074  Sum_probs=41.1

Q ss_pred             HHccCChhHHHHHHHHHHHcCC-CCc-------HHHHHHHHHHHhhcCChhhHHHHHH--------HHHhCCCCCchHHH
Q 042039          306 LCNDGQMDKAHDLFLDMEENAV-APN-------VIIFVTLIHGFVRINKPSKVIELLH--------KMKEKKVMPDASIV  369 (376)
Q Consensus       306 ~~~~~~~~~a~~~~~~~~~~~~-~~~-------~~~~~~l~~~~~~~g~~~~a~~~~~--------~~~~~~~~p~~~~~  369 (376)
                      .+-.+++..|...++.+.+..- .|+       +..+....-.+...|+.+.|...|.        .....+...+..++
T Consensus       371 ~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~yL~gl~~q~~g~l~~A~~~y~~~~~~~~~~~~~~~~~~El~il  450 (608)
T PF10345_consen  371 NFIRGDWSKATQELEFMRQLCQRSPSKLYESLYPLLHYLLGLYYQSTGDLEAALYQYQKPRFLLCEAANRKSKFRELYIL  450 (608)
T ss_pred             HHHCcCHHHHHHHHHHHHHHHhcCccchhhhhhHHHHHHHHHHHHHcCCHHHHHHHHhhhHHhhhhhhccCCcchHHHHH
Confidence            3457889999999998875421 111       2223333334556799999999997        45455555555554


Q ss_pred             HH
Q 042039          370 SM  371 (376)
Q Consensus       370 ~~  371 (376)
                      ..
T Consensus       451 a~  452 (608)
T PF10345_consen  451 AA  452 (608)
T ss_pred             HH
Confidence            43

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=94.10  E-value=3.1  Score=35.05  Aligned_cols=66  Identities=14%  Similarity=0.062  Sum_probs=49.8

Q ss_pred             CCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC---CcchHHHHHHHHHhCCCHHHHHHHHHHhcc
Q 042039          189 PTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA---DTSTYNTFIDGLCKNGYIVEAVELFRTLGI  254 (376)
Q Consensus       189 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  254 (376)
                      ....++..++..+.+.|.++.|...+..+...+...   .+.....-++..-..|+..+|+..++....
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345678888888899999999999888887653221   455566667777788888999988888765

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF07575 Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR011502 This is a family of nucleoporins conserved from yeast to human

Probab=94.06  E-value=4.6  Score=36.78  Aligned_cols=32  Identities=13%  Similarity=0.153  Sum_probs=0.0

Q ss_pred             hcCChhhHHHHHHHHHhCCCCCchHHHHHHHh
Q 042039          343 RINKPSKVIELLHKMKEKKVMPDASIVSMVVD  374 (376)
Q Consensus       343 ~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  374 (376)
                      +.|++.+|.+.+-.+.+.++.|...-...+.+
T Consensus       507 ~~~~~~~Aa~~Lv~Ll~~~~~Pk~f~~~LL~d  538 (566)
T PF07575_consen  507 DEGDFREAASLLVSLLKSPIAPKSFWPLLLCD  538 (566)
T ss_dssp             --------------------------------
T ss_pred             hhhhHHHHHHHHHHHHCCCCCcHHHHHHHHHH
Confidence            35777777777777777777776655554444

Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. ; PDB: 3F3F_D 3F3P_G 3F3G_G 3EWE_B.

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=93.84  E-value=3.5  Score=34.74  Aligned_cols=193  Identities=14%  Similarity=0.122  Sum_probs=102.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC---C-CchHhHHHHHHHHH
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV---Q-PSVVTFNVIMDELC   97 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~-~~~~~~~~l~~~~~   97 (376)
                      ..++.-+.|+|+...+........  .++...+..+...  ..++++++...++++...-.   . .....|........
T Consensus         4 ~~eaaWrl~~Wd~l~~~~~~~~~~--~~~~~~~~al~~l--~~~~~~~~~~~i~~~r~~~~~~l~~~~~~s~~~~y~~l~   79 (352)
T PF02259_consen    4 AAEAAWRLGDWDLLEEYLSQSNED--SPEYSFYRALLAL--RQGDYDEAKKYIEKARQLLLDELSALSSESYQRAYPSLV   79 (352)
T ss_pred             HHHHHHhcCChhhHHHHHhhccCC--ChhHHHHHHHHHH--hCccHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            356777889999865555554432  2344444444433  78899999888888765310   0 01122222222222


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh-----cCcHHHHHHHH---HHHHh--cCCCCChhhHHHHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL-----TGKINRAEELF---GSMES--MGCKHDDVSYNILINGYC  167 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~a~~~~---~~~~~--~~~~~~~~~~~~l~~~~~  167 (376)
                      ....+.+..++.+-.....  .+......++.....     .++++.-..++   ..+..  ........++..++..+.
T Consensus        80 ~lq~L~Elee~~~~~~~~~--~~~~~~~~l~~~W~~Rl~~~~~~~~~~~~il~~R~~~l~~~~~~~~~~~~~l~~a~~aR  157 (352)
T PF02259_consen   80 KLQQLVELEEIIELKSNLS--QNPQDLKSLLKRWRSRLPNMQDDFSVWEPILSLRRLVLSLILLPEELAETWLKFAKLAR  157 (352)
T ss_pred             HHhHHHHHHHHHHHHHhhc--ccHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHH
Confidence            2222233222222221110  001111111111110     12222111111   11111  112345567888999999


Q ss_pred             ccCcHHHHHHHHHHHHHCCCCC---CHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          168 KNKEVEEALSLYREMVSKGIKP---TVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      +.|.++.|...+..+...+...   .+.....-++.+-..|+..+|+..++.....
T Consensus       158 k~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~  213 (352)
T PF02259_consen  158 KAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKC  213 (352)
T ss_pred             HCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            9999999999999988753221   3455566677788889999999999888873

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=93.75  E-value=1.7  Score=30.80  Aligned_cols=53  Identities=13%  Similarity=0.002  Sum_probs=32.4

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      ...++.+++..+++.+.-.. |.....-..-...+...|+|.+|..+|+++.+.
T Consensus        21 L~~~d~~D~e~lLdALrvLr-P~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~   73 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVLR-PNLKELDMFDGWLLIARGNYDEAARILRELLSS   73 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHhC-CCccccchhHHHHHHHcCCHHHHHHHHHhhhcc
Confidence            34677777777777665442 222333333445566777777777777777665

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

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

Probab=93.73  E-value=0.21  Score=24.90  Aligned_cols=26  Identities=15%  Similarity=0.290  Sum_probs=11.2

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      +..+..++...|++++|++.|++.++
T Consensus         4 ~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    4 WYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            33444444444444444444444443

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 ....

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

Probab=93.66  E-value=1.3  Score=28.99  Aligned_cols=44  Identities=14%  Similarity=0.221  Sum_probs=19.3

Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          316 HDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .+-+..+...++.|++.+....+++|.+.+++.-|.++|+-...
T Consensus        30 rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~   73 (108)
T PF02284_consen   30 RRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKD   73 (108)
T ss_dssp             HHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            33344444444445555555555555555555555555554443

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 ....

>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=93.62  E-value=2.1  Score=31.33  Aligned_cols=100  Identities=18%  Similarity=0.224  Sum_probs=43.7

Q ss_pred             HHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC
Q 042039           73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC  152 (376)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  152 (376)
                      +++.+.+.+++|+...+..++..+.+.|++..    +.++++.++-+|.......+-.+.  +.+..+.++--+|...  
T Consensus        16 YirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkR--   87 (167)
T PF07035_consen   16 YIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKR--   87 (167)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHH--
Confidence            34444455556666666666666666665443    333333334444333222221111  1222222222222211  


Q ss_pred             CCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          153 KHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       153 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                        -...+..+++.+...|++-+|+++.+..
T Consensus        88 --L~~~~~~iievLL~~g~vl~ALr~ar~~  115 (167)
T PF07035_consen   88 --LGTAYEEIIEVLLSKGQVLEALRYARQY  115 (167)
T ss_pred             --hhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence              0012344555566666666666666554

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=93.38  E-value=3.7  Score=33.55  Aligned_cols=137  Identities=12%  Similarity=0.186  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh--c----cchHHHHHHHHHHHhcCCCC---CcchHHHHHHHHHhCCC--
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFE--I----HQVEHALKLFEEMQRDDVAA---DTSTYNTFIDGLCKNGY--  241 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~----~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~--  241 (376)
                      ++.+.+++.+.+.|..-+..+|.........  .    ....++..+++.|.+...-.   +...+..++..  ..++  
T Consensus        79 ~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e  156 (297)
T PF13170_consen   79 KEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVE  156 (297)
T ss_pred             HHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHH
Confidence            3444566666666666555554443332222  1    12446677777776664221   12222222211  2222  


Q ss_pred             --HHHHHHHHHHhcccCCCch--HHHHHHHHHHHHhCCC--hHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCC
Q 042039          242 --IVEAVELFRTLGILKCELD--IQAYNCLIDGLCKSGR--LEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQ  311 (376)
Q Consensus       242 --~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  311 (376)
                        .+.++.+|+.+...+...+  ......++........  ..++..+++.+.+.+++.....|..++-...-.+.
T Consensus       157 ~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall~~~  232 (297)
T PF13170_consen  157 ELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALLEDP  232 (297)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhcCCc
Confidence              2445566666666554432  2223333322222211  34667777777777777766666555544433333

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=93.18  E-value=0.99  Score=34.27  Aligned_cols=77  Identities=17%  Similarity=0.164  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC--CCchHhHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV--QPSVVTFNVIMDE   95 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~   95 (376)
                      +.+..++.+.+.++.++++...+.-.+.. |.+...-..++..++-.|+|++|..-++-.-....  .+-...|..++++
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            34556778888888999988888777665 66777778888888889999998887777655422  2234455555543

>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=93.10  E-value=2  Score=32.35  Aligned_cols=73  Identities=15%  Similarity=0.063  Sum_probs=43.8

Q ss_pred             HHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc---CCCCcHHHHHHHHHHHhhcCChhhHH
Q 042039          278 EIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN---AVAPNVIIFVTLIHGFVRINKPSKVI  351 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~a~  351 (376)
                      +.|.+.|-.+...+.-.++.....++..|. ..+.++++.++-++.+.   +-.+|+..+..|+..|.+.|+++.|-
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            555555555555544445555555554444 55666777776666543   22456677777777777777776653

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=93.00  E-value=1  Score=36.70  Aligned_cols=90  Identities=14%  Similarity=0.028  Sum_probs=57.7

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      ..-|.++|.+++|+..|...+... +-|++++..-+.+|.+...+..|+.-...+...+ ..-..+|..-+.+-...|..
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia~~-P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg~~  181 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIAVY-PHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLGNN  181 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhccC-CCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHhhH
Confidence            345677788888888887777652 2377777777788888888877777666666543 22233444444444455666


Q ss_pred             HHHHHHHHHHHH
Q 042039          173 EEALSLYREMVS  184 (376)
Q Consensus       173 ~~a~~~~~~~~~  184 (376)
                      .+|-+-++..++
T Consensus       182 ~EAKkD~E~vL~  193 (536)
T KOG4648|consen  182 MEAKKDCETVLA  193 (536)
T ss_pred             HHHHHhHHHHHh
Confidence            666666666655

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.86  E-value=2.6  Score=34.08  Aligned_cols=104  Identities=15%  Similarity=0.200  Sum_probs=73.6

Q ss_pred             CCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcC---CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChh
Q 042039           46 NINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQG---VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAF  122 (376)
Q Consensus        46 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  122 (376)
                      |.+.++.+...++..-....+++.+...+-+++...   ..|+. +-...++.+. .-++++++.++..-++-|+-||..
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~-~~~~~irlll-ky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNW-TIHTWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccc-cHHHHHHHHH-ccChHHHHHHHhCcchhccccchh
Confidence            445555556666666666788999998888876541   11121 1122333333 336778999998888999999999


Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      ++..++..+.+.+++.+|.++.-.+....
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            99999999999999999998887776543

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=92.85  E-value=1.2  Score=32.66  Aligned_cols=31  Identities=13%  Similarity=0.011  Sum_probs=16.6

Q ss_pred             hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 042039           32 VDKAKALFLQMKGENINPDVVTYNSLIHGLCH   63 (376)
Q Consensus        32 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   63 (376)
                      ++.|.+.++.....+ |.|...++.-..++..
T Consensus         7 FE~ark~aea~y~~n-P~DadnL~~WG~ALLE   37 (186)
T PF06552_consen    7 FEHARKKAEAAYAKN-PLDADNLTNWGGALLE   37 (186)
T ss_dssp             HHHHHHHHHHHHHH--TT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-cHhHHHHHHHHHHHHH
Confidence            456666666655444 6666666555544443

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.80  E-value=4.6  Score=33.04  Aligned_cols=133  Identities=14%  Similarity=0.203  Sum_probs=67.8

Q ss_pred             hHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh--c----CcHHHHHHHHHHHHhcCC---CCChhhHHHHHHHHHccCc-
Q 042039          102 MDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL--T----GKINRAEELFGSMESMGC---KHDDVSYNILINGYCKNKE-  171 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~----~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~-  171 (376)
                      +++...+++.+.+.|+.-+..++.........  .    .....|..+|+.|.+...   .++...+..++..  ..++ 
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            34556677777777776666555443333322  1    235567777777776541   1222233333222  2333 


Q ss_pred             ---HHHHHHHHHHHHHCCCCCCHh--HHHHHHHHHHhccc--hHHHHHHHHHHHhcCCCCCcchHHHHHHHH
Q 042039          172 ---VEEALSLYREMVSKGIKPTVV--TYNTLFLGLFEIHQ--VEHALKLFEEMQRDDVAADTSTYNTFIDGL  236 (376)
Q Consensus       172 ---~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  236 (376)
                         .+.+..+|+.+.+.|...+..  ....++.......+  ..++.++++.+.+.++++....|..++-..
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLa  227 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLA  227 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHH
Confidence               245566666666666554322  22222222221111  346677777777777776666666555443

>PRK11619 lytic murein transglycosylase; Provisional

Probab=92.77  E-value=8  Score=35.72  Aligned_cols=250  Identities=9%  Similarity=-0.026  Sum_probs=114.7

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  171 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  171 (376)
                      .+..+.+.+++.....++.    . .+.+...-...+.+....|+.++|......+-..| ...+.....+...+.+.|.
T Consensus       105 ~l~~La~~~~w~~~~~~~~----~-~p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW~~g-~~~p~~cd~l~~~~~~~g~  178 (644)
T PRK11619        105 FVNELARREDWRGLLAFSP----E-KPKPVEARCNYYYAKWATGQQQEAWQGAKELWLTG-KSLPNACDKLFSVWQQSGK  178 (644)
T ss_pred             HHHHHHHccCHHHHHHhcC----C-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-CCCChHHHHHHHHHHHcCC
Confidence            3344555666666555221    1 13344444566677777888777777777665555 3445566666666664443


Q ss_pred             HHH--HHHHHHHHHHCCCCCCHhHHHHHHHHH-----------Hh-ccchHHHHHHHHHHHhcCCCCCcc--hHHHHHHH
Q 042039          172 VEE--ALSLYREMVSKGIKPTVVTYNTLFLGL-----------FE-IHQVEHALKLFEEMQRDDVAADTS--TYNTFIDG  235 (376)
Q Consensus       172 ~~~--a~~~~~~~~~~~~~~~~~~~~~l~~~~-----------~~-~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~  235 (376)
                      ...  ..+-++.+...|   +...-..+...+           .. ..+...+...+..     ++++..  .+..+...
T Consensus       179 lt~~d~w~R~~~al~~~---~~~lA~~l~~~l~~~~~~~a~a~~al~~~p~~~~~~~~~-----~~~~~~~~~~~~~~l~  250 (644)
T PRK11619        179 QDPLAYLERIRLAMKAG---NTGLVTYLAKQLPADYQTIASALIKLQNDPNTVETFART-----TGPTDFTRQMAAVAFA  250 (644)
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHhcChhHHHHHHHHHHHHHCHHHHHHHhhc-----cCCChhhHHHHHHHHH
Confidence            322  222222222221   111111111111           00 0111111111110     111211  11111111


Q ss_pred             HHhCCCHHHHHHHHHHhcccC-CCch--HHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCCh
Q 042039          236 LCKNGYIVEAVELFRTLGILK-CELD--IQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQM  312 (376)
Q Consensus       236 ~~~~~~~~~a~~~~~~~~~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  312 (376)
                      -....+.+.|..++....... ..+.  ..+...++......+..++|...+......  ..+......-+..-...+++
T Consensus       251 Rlar~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~--~~~~~~~e~r~r~Al~~~dw  328 (644)
T PRK11619        251 SVARQDAENARLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMR--SQSTSLLERRVRMALGTGDR  328 (644)
T ss_pred             HHHHhCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcccc--cCCcHHHHHHHHHHHHccCH
Confidence            223445677777777653322 1111  122333333333332255666666554432  12444444555555577777


Q ss_pred             hHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          313 DKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       313 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      +.+...+..|.... .-...-...+.+++...|+.++|...|+++.
T Consensus       329 ~~~~~~i~~L~~~~-~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~a  373 (644)
T PRK11619        329 RGLNTWLARLPMEA-KEKDEWRYWQADLLLEQGRKAEAEEILRQLM  373 (644)
T ss_pred             HHHHHHHHhcCHhh-ccCHhhHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            77777777664321 1233344445666666777777777777763

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

Probab=92.66  E-value=0.32  Score=25.60  Aligned_cols=26  Identities=23%  Similarity=0.312  Sum_probs=13.3

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMM   78 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~   78 (376)
                      +++.+...|...|++++|..++++..
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            44555555555555555555555544

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=92.44  E-value=2.6  Score=31.10  Aligned_cols=41  Identities=20%  Similarity=0.251  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          172 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      +++|...|+++.+  ..|+...|..-+....      +|-.+..++.+.
T Consensus        96 F~kA~~~FqkAv~--~~P~ne~Y~ksLe~~~------kap~lh~e~~~~  136 (186)
T PF06552_consen   96 FEKATEYFQKAVD--EDPNNELYRKSLEMAA------KAPELHMEIHKQ  136 (186)
T ss_dssp             HHHHHHHHHHHHH--H-TT-HHHHHHHHHHH------THHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHh--cCCCcHHHHHHHHHHH------hhHHHHHHHHHH
Confidence            4455555555555  3566666666655542      345555555544

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

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

Probab=92.40  E-value=0.39  Score=25.27  Aligned_cols=26  Identities=15%  Similarity=0.272  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      +++.++..|...|++++|..+++++.
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            44555555555555555555555544

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=92.37  E-value=11  Score=36.54  Aligned_cols=56  Identities=18%  Similarity=0.057  Sum_probs=28.4

Q ss_pred             HHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          232 FIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       232 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      .+.+|..+|++.+|..+..++...... -..+-..|+.-+...+++-+|-++..+..
T Consensus       971 Al~a~~~~~dWr~~l~~a~ql~~~~de-~~~~a~~L~s~L~e~~kh~eAa~il~e~~ 1026 (1265)
T KOG1920|consen  971 ALKAYKECGDWREALSLAAQLSEGKDE-LVILAEELVSRLVEQRKHYEAAKILLEYL 1026 (1265)
T ss_pred             HHHHHHHhccHHHHHHHHHhhcCCHHH-HHHHHHHHHHHHHHcccchhHHHHHHHHh
Confidence            345556666666666666554321100 11112445555666666666666655544

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=92.26  E-value=7.2  Score=33.93  Aligned_cols=92  Identities=10%  Similarity=0.156  Sum_probs=69.7

Q ss_pred             HHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHc--cCChhHHHHHHHHHHHc-CCCCcHHHHHHHHHHH
Q 042039          265 NCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN--DGQMDKAHDLFLDMEEN-AVAPNVIIFVTLIHGF  341 (376)
Q Consensus       265 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~  341 (376)
                      +.++..+.+.|-..+|...+..+... .||+...|..+++.=..  .-+..-+..+++.+... |  .++..|...+.--
T Consensus       464 s~~l~~~~e~~~~~~ark~y~~l~~l-pp~sl~l~r~miq~e~~~~sc~l~~~r~~yd~a~~~fg--~d~~lw~~y~~~e  540 (568)
T KOG2396|consen  464 SKYLDWAYESGGYKKARKVYKSLQEL-PPFSLDLFRKMIQFEKEQESCNLANIREYYDRALREFG--ADSDLWMDYMKEE  540 (568)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHhC-CCccHHHHHHHHHHHhhHhhcCchHHHHHHHHHHHHhC--CChHHHHHHHHhh
Confidence            45667777888899999999998876 67788888877764322  22377888899888754 5  5778888887777


Q ss_pred             hhcCChhhHHHHHHHHHh
Q 042039          342 VRINKPSKVIELLHKMKE  359 (376)
Q Consensus       342 ~~~g~~~~a~~~~~~~~~  359 (376)
                      ...|.++.+-.++.++.+
T Consensus       541 ~~~g~~en~~~~~~ra~k  558 (568)
T KOG2396|consen  541 LPLGRPENCGQIYWRAMK  558 (568)
T ss_pred             ccCCCcccccHHHHHHHH
Confidence            789999998888777654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=92.20  E-value=2.1  Score=27.69  Aligned_cols=44  Identities=11%  Similarity=0.190  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          315 AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       315 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      +.+-+..+...++.|++.+....+++|.+.+++.-|.++++-..
T Consensus        26 ~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          26 LRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             HHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            33334444444444444444445555555555555555444443

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.

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=92.20  E-value=7.1  Score=33.77  Aligned_cols=121  Identities=10%  Similarity=0.043  Sum_probs=72.5

Q ss_pred             hcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHH
Q 042039           62 CHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAE  141 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  141 (376)
                      ...|+...|-+-+...++.. +.++.............|+++.+...+....+. +.....+...+++.....|+++.|.
T Consensus       300 ~~~gd~~aas~~~~~~lr~~-~~~p~~i~l~~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~l~r~~~a~  377 (831)
T PRK15180        300 LADGDIIAASQQLFAALRNQ-QQDPVLIQLRSVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHGLARWREAL  377 (831)
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCCchhhHHHHHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhchhhHHHHH
Confidence            34566665544444433331 112333333344556778888888877766543 2334567777888888888888888


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          142 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      ..-+-|....+. ++.............|-++++.-.|+++...
T Consensus       378 s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~  420 (831)
T PRK15180        378 STAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLL  420 (831)
T ss_pred             HHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhcc
Confidence            888777765533 3333333333334456678888888887764

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=91.86  E-value=5.5  Score=31.74  Aligned_cols=125  Identities=14%  Similarity=0.077  Sum_probs=58.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhhhCC-----C-CCCh-------hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCch
Q 042039           20 NTIIDGLCKEGFVDKAKALFLQMKGEN-----I-NPDV-------VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV   86 (376)
Q Consensus        20 ~~l~~~~~~~g~~~~a~~~~~~~~~~~-----~-~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~   86 (376)
                      ..-.+.+.-..|+..|++..++-.+.=     . .++.       .....=|.+++..++|.+++...-+--+..-+...
T Consensus        39 e~Aad~LvV~rdF~aal~tCerglqsL~~~a~~ee~~~~~~evK~sLcvvGIQALAEmnrWreVLsWvlqyYq~pEklPp  118 (309)
T PF07163_consen   39 EEAADLLVVHRDFQAALETCERGLQSLASDADAEEPAGSSLEVKCSLCVVGIQALAEMNRWREVLSWVLQYYQVPEKLPP  118 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhhhhhhhhhhhHHHHHHHhhHHHHHHHHHHHhcCcccCCH
Confidence            333344555567777777766654321     0 1110       01122245666666666665555444332222223


Q ss_pred             HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHH-----hcCcHHHHHHHH
Q 042039           87 VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC-----LTGKINRAEELF  144 (376)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~~~~~~a~~~~  144 (376)
                      .+...-+-.|.+.+++..+.++-..-++..-..+..-|..++..|.     -.|.+++|+++.
T Consensus       119 kIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLlPLG~~~eAeelv  181 (309)
T PF07163_consen  119 KILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLLPLGHFSEAEELV  181 (309)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHhccccHHHHHHHH
Confidence            3444444556666666666665555554311112223444444333     335556555554

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

>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]

Probab=91.84  E-value=3.3  Score=32.07  Aligned_cols=85  Identities=15%  Similarity=0.004  Sum_probs=51.2

Q ss_pred             HHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHH
Q 042039          201 LFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIA  280 (376)
Q Consensus       201 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  280 (376)
                      |.....++.|+..+.+.+..+ |....-|..-+.++.+..+++.+..--+++.+.... .......++.+......+++|
T Consensus        20 ~f~~k~y~~ai~~y~raI~~n-P~~~~Y~tnralchlk~~~~~~v~~dcrralql~~N-~vk~h~flg~~~l~s~~~~ea   97 (284)
T KOG4642|consen   20 CFIPKRYDDAIDCYSRAICIN-PTVASYYTNRALCHLKLKHWEPVEEDCRRALQLDPN-LVKAHYFLGQWLLQSKGYDEA   97 (284)
T ss_pred             ccchhhhchHHHHHHHHHhcC-CCcchhhhhHHHHHHHhhhhhhhhhhHHHHHhcChH-HHHHHHHHHHHHHhhccccHH
Confidence            445556677777666666543 222344555666667777777776666665554311 234445566666677777777


Q ss_pred             HHHHhcc
Q 042039          281 LELFRSL  287 (376)
Q Consensus       281 ~~~~~~~  287 (376)
                      +..+++.
T Consensus        98 I~~Lqra  104 (284)
T KOG4642|consen   98 IKVLQRA  104 (284)
T ss_pred             HHHHHHH
Confidence            7777765

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=91.80  E-value=8.4  Score=33.71  Aligned_cols=178  Identities=11%  Similarity=0.110  Sum_probs=116.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      |-...-+++..+..+.+++-...+..+|...|  .+...|..++.+|... ..++-..+|+++.+.... |...-..|+.
T Consensus        65 ~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~~ReLa~  140 (711)
T COG1747          65 DDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVIGRELAD  140 (711)
T ss_pred             cchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHHHHHHHH
Confidence            45566778888888888888888888888875  4677888899999888 668888899988876444 4444444444


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCC--C---hhhHHHHHHHHHhcCcHHHHHHHHHHHHhc-CCCCChhhHHHHHHHHHc
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRP--N---AFTYSTLMDGFCLTGKINRAEELFGSMESM-GCKHDDVSYNILINGYCK  168 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~--~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~  168 (376)
                      . ...++.+.+..+|.++..+-++.  +   ...|..+...  -..+.+....+..++... |...-...+.-+-.-|..
T Consensus       141 ~-yEkik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~--i~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~  217 (711)
T COG1747         141 K-YEKIKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPEL--IGDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSE  217 (711)
T ss_pred             H-HHHhchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHh--ccccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhcc
Confidence            4 44488888888888887653221  1   1233333321  145666666666666443 333344455566677888


Q ss_pred             cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHH
Q 042039          169 NKEVEEALSLYREMVSKGIKPTVVTYNTLFLG  200 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  200 (376)
                      ..++++|++++...++.+ ..|..+...++..
T Consensus       218 ~eN~~eai~Ilk~il~~d-~k~~~ar~~~i~~  248 (711)
T COG1747         218 NENWTEAIRILKHILEHD-EKDVWARKEIIEN  248 (711)
T ss_pred             ccCHHHHHHHHHHHhhhc-chhhhHHHHHHHH
Confidence            899999999999877763 2244444444433

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=91.55  E-value=12  Score=35.12  Aligned_cols=227  Identities=17%  Similarity=0.091  Sum_probs=115.1

Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChh-------hHHHH-HHHHHhcCcHHHHHHHHHHHHhcC----CCCChhhHHHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAF-------TYSTL-MDGFCLTGKINRAEELFGSMESMG----CKHDDVSYNIL  162 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l  162 (376)
                      ......++.+|..++.++...-..|+..       .+..+ .......|+++.|.++.+.....-    ..+....+..+
T Consensus       424 ~~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~  503 (894)
T COG2909         424 LLASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVL  503 (894)
T ss_pred             HHHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhh
Confidence            4456788999999988887642222211       12222 223345688899888888776541    12334456677


Q ss_pred             HHHHHccCcHHHHHHHHHHHHHCCCCCCHh---HHHHH--HHHHHhccchHHH--HHHHHHHHhcC---CC---CCcchH
Q 042039          163 INGYCKNKEVEEALSLYREMVSKGIKPTVV---TYNTL--FLGLFEIHQVEHA--LKLFEEMQRDD---VA---ADTSTY  229 (376)
Q Consensus       163 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l--~~~~~~~~~~~~a--~~~~~~~~~~~---~~---~~~~~~  229 (376)
                      +.+..-.|++++|..+..+..+..-.-+..   .|..+  ...+...|+...+  ...+.......   .+   +-..+.
T Consensus       504 ~~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r  583 (894)
T COG2909         504 GEAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIR  583 (894)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHH
Confidence            778888899999998888766531122222   22222  2334455633222  22232222221   01   112234


Q ss_pred             HHHHHHHHhC-CCHHHHHHHHHHhcccCCCchH--HHHHHHHHHHHhCCChHHHHHHHhcccccCCCC----CHHHHHHH
Q 042039          230 NTFIDGLCKN-GYIVEAVELFRTLGILKCELDI--QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA----DVVTYNIM  302 (376)
Q Consensus       230 ~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~l  302 (376)
                      ..+..++.+. +...++..-++-.......|-.  ..+..++......|+.++|...+.++......+    +...-...
T Consensus       584 ~~ll~~~~r~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~~~~  663 (894)
T COG2909         584 AQLLRAWLRLDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAAAYK  663 (894)
T ss_pred             HHHHHHHHHHhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHHHHH
Confidence            4444444441 1222222222222222112111  122367777888999999998888765432222    22222222


Q ss_pred             HHH--HHccCChhHHHHHHHH
Q 042039          303 IHG--LCNDGQMDKAHDLFLD  321 (376)
Q Consensus       303 ~~~--~~~~~~~~~a~~~~~~  321 (376)
                      +..  -...|+...+.....+
T Consensus       664 v~~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         664 VKLILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             hhHHHhcccCCHHHHHHHHHh
Confidence            222  2356777777666555

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=91.31  E-value=2.3  Score=27.52  Aligned_cols=38  Identities=11%  Similarity=0.137  Sum_probs=15.0

Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHH
Q 042039          109 LDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGS  146 (376)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  146 (376)
                      ++.+...+..|++.+....+++|.+.+++..|.++|+.
T Consensus        30 mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~   67 (103)
T cd00923          30 LNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEA   67 (103)
T ss_pred             HHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            33333333333333344444444444444444444433

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.

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

Probab=91.30  E-value=0.66  Score=23.04  Aligned_cols=27  Identities=22%  Similarity=0.298  Sum_probs=15.0

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      +|..+...+...|++++|.+.|++.++
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            345555555555555555555555544

...

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

Probab=91.26  E-value=0.7  Score=22.95  Aligned_cols=27  Identities=19%  Similarity=0.144  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      +|..++..|...|++++|...|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            445555556666666666666665554

...

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=91.23  E-value=13  Score=34.92  Aligned_cols=225  Identities=15%  Similarity=0.102  Sum_probs=121.8

Q ss_pred             HHHHhcCcHHHHHHHHHHHHhcCCCCChh-------hHHHH-HHHHHccCcHHHHHHHHHHHHHC----CCCCCHhHHHH
Q 042039          129 DGFCLTGKINRAEELFGSMESMGCKHDDV-------SYNIL-INGYCKNKEVEEALSLYREMVSK----GIKPTVVTYNT  196 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~l-~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~  196 (376)
                      .......++++|..++.++...-..|+..       .+..+ .......|++++|.++.+.....    -..+....+..
T Consensus       423 W~~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv  502 (894)
T COG2909         423 WLLASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSV  502 (894)
T ss_pred             HHHHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhh
Confidence            34456788999999998886543222221       22222 23345578999999999888774    12233555667


Q ss_pred             HHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHH---H--HHHHHhCCCH--HHHHHHHHHhccc----CC--CchHHH
Q 042039          197 LFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNT---F--IDGLCKNGYI--VEAVELFRTLGIL----KC--ELDIQA  263 (376)
Q Consensus       197 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---l--~~~~~~~~~~--~~a~~~~~~~~~~----~~--~~~~~~  263 (376)
                      +..+..-.|++++|..+.....+..-..+...+..   +  ...+...|..  .+....+......    ..  .+-..+
T Consensus       503 ~~~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~  582 (894)
T COG2909         503 LGEAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRI  582 (894)
T ss_pred             hhHHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHH
Confidence            77788888999999998877665522223222222   2  2234556632  2222222222111    00  112234


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhcccccC--CCCCH--H--HHHHHHHHHHccCChhHHHHHHHHHHHcCCC----CcHHH
Q 042039          264 YNCLIDGLCKSGRLEIALELFRSLPRRV--LVADV--V--TYNIMIHGLCNDGQMDKAHDLFLDMEENAVA----PNVII  333 (376)
Q Consensus       264 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~--~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~  333 (376)
                      ...+..++.+   .+.+..-.....+.+  ..|..  .  .+..|+......|++++|...++++......    ++...
T Consensus       583 r~~ll~~~~r---~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a  659 (894)
T COG2909         583 RAQLLRAWLR---LDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLA  659 (894)
T ss_pred             HHHHHHHHHH---HhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHH
Confidence            4455555544   333333222222111  11222  1  2236778888999999999999988754222    22222


Q ss_pred             HHHHHH--HHhhcCChhhHHHHHHH
Q 042039          334 FVTLIH--GFVRINKPSKVIELLHK  356 (376)
Q Consensus       334 ~~~l~~--~~~~~g~~~~a~~~~~~  356 (376)
                      -...+.  .-...|+.+++.....+
T Consensus       660 ~~~~v~~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         660 AAYKVKLILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             HHHHhhHHHhcccCCHHHHHHHHHh
Confidence            222332  22457888887777665

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

Probab=91.23  E-value=0.35  Score=23.79  Aligned_cols=23  Identities=22%  Similarity=0.393  Sum_probs=9.7

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHh
Q 042039           57 LIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        57 l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      ++.++.+.|++++|.+.|+++++
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~   28 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIK   28 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH
Confidence            33344444444444444444433

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

Probab=91.23  E-value=2  Score=28.15  Aligned_cols=40  Identities=10%  Similarity=0.104  Sum_probs=15.1

Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHH
Q 042039          108 LLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSM  147 (376)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  147 (376)
                      -++.+...+..|++.+....+++|.+.+++..|.++|+.+
T Consensus        32 glN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~i   71 (108)
T PF02284_consen   32 GLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGI   71 (108)
T ss_dssp             HHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            3333333334444444444444444444444444444443

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 ....

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.17  E-value=4.1  Score=28.99  Aligned_cols=51  Identities=16%  Similarity=0.045  Sum_probs=23.9

Q ss_pred             CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          239 NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      .++++++..++..+....+. .+..-..-+..+...|++++|..+|+++.+.
T Consensus        23 ~~d~~D~e~lLdALrvLrP~-~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~   73 (153)
T TIGR02561        23 SADPYDAQAMLDALRVLRPN-LKELDMFDGWLLIARGNYDEAARILRELLSS   73 (153)
T ss_pred             cCCHHHHHHHHHHHHHhCCC-ccccchhHHHHHHHcCCHHHHHHHHHhhhcc
Confidence            45555555555555433221 1222222233345556666666666555543

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=90.96  E-value=0.77  Score=24.78  Aligned_cols=28  Identities=18%  Similarity=0.271  Sum_probs=17.3

Q ss_pred             HHHHHhhcCChhhHHHHHHHHHhCCCCC
Q 042039          337 LIHGFVRINKPSKVIELLHKMKEKKVMP  364 (376)
Q Consensus       337 l~~~~~~~g~~~~a~~~~~~~~~~~~~p  364 (376)
                      |.++|...|+.+.|.+++++..+.|-.|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~~~~   32 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEGDEA   32 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcCCHH
Confidence            5566666666666666666666554433

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.

>COG0790 FOG: TPR repeat, SEL1 subfamily [General function prediction only]

Probab=90.90  E-value=7.8  Score=31.70  Aligned_cols=83  Identities=18%  Similarity=0.232  Sum_probs=42.5

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----c
Q 042039          133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE----I  204 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~  204 (376)
                      ..+++..+...+......+   +......+...|..    ..+..+|...|....+.|..   .....+...+..    .
T Consensus        53 ~~~~~~~a~~~~~~a~~~~---~~~a~~~l~~~y~~g~gv~~~~~~A~~~~~~~a~~g~~---~a~~~lg~~~~~G~gv~  126 (292)
T COG0790          53 YPPDYAKALKSYEKAAELG---DAAALALLGQMYGAGKGVSRDKTKAADWYRCAAADGLA---EALFNLGLMYANGRGVP  126 (292)
T ss_pred             ccccHHHHHHHHHHhhhcC---ChHHHHHHHHHHHhccCccccHHHHHHHHHHHhhcccH---HHHHhHHHHHhcCCCcc
Confidence            4456777777777766543   22333344444433    33456677777655554322   223334444433    2


Q ss_pred             cchHHHHHHHHHHHhcC
Q 042039          205 HQVEHALKLFEEMQRDD  221 (376)
Q Consensus       205 ~~~~~a~~~~~~~~~~~  221 (376)
                      .+..+|...+.++.+.|
T Consensus       127 ~d~~~A~~~~~~Aa~~g  143 (292)
T COG0790         127 LDLVKALKYYEKAAKLG  143 (292)
T ss_pred             cCHHHHHHHHHHHHHcC
Confidence            25555666666665554

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.68  E-value=11  Score=33.77  Aligned_cols=163  Identities=18%  Similarity=0.159  Sum_probs=105.9

Q ss_pred             ChhhHHHHHHH-----HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhH
Q 042039           15 NTVTYNTIIDG-----LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTF   89 (376)
Q Consensus        15 ~~~~~~~l~~~-----~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   89 (376)
                      |+..|..+++.     ..-.|+++.|..++..+.       ....+.++..+..+|-.++|+++-         +|+.  
T Consensus       580 nVi~y~l~l~vleyqt~vmrrd~~~a~~vLp~I~-------k~~rt~va~Fle~~g~~e~AL~~s---------~D~d--  641 (794)
T KOG0276|consen  580 NVISYKILLEVLEYQTLVLRRDLEVADGVLPTIP-------KEIRTKVAHFLESQGMKEQALELS---------TDPD--  641 (794)
T ss_pred             ceEeEeeehHHHHHHHHhhhccccccccccccCc-------hhhhhhHHhHhhhccchHhhhhcC---------CChh--
Confidence            45555554443     344577777777554443       234455667777777777776542         2222  


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                       .-.....+.|+++.|.++..+..      +..-|..|.++....+++..|.++|.+..+         |..|+-.+...
T Consensus       642 -~rFelal~lgrl~iA~~la~e~~------s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~  705 (794)
T KOG0276|consen  642 -QRFELALKLGRLDIAFDLAVEAN------SEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSS  705 (794)
T ss_pred             -hhhhhhhhcCcHHHHHHHHHhhc------chHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhc
Confidence             12345567888888888765542      457788999999999999999999987654         34566667777


Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEM  217 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  217 (376)
                      |+-+....+-....+.|.. +.     ...++...|+++++.+++..-
T Consensus       706 g~~~~l~~la~~~~~~g~~-N~-----AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  706 GNAEGLAVLASLAKKQGKN-NL-----AFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             CChhHHHHHHHHHHhhccc-ch-----HHHHHHHcCCHHHHHHHHHhc
Confidence            7776666666666665432 32     234566778888888877654

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

Probab=90.59  E-value=0.49  Score=23.25  Aligned_cols=23  Identities=17%  Similarity=0.283  Sum_probs=10.5

Q ss_pred             HHHHHHccCChhHHHHHHHHHHH
Q 042039          302 MIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       302 l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      ++.++.+.|++++|.+.|+++++
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~   28 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIK   28 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH
Confidence            34444444444444444444443

>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=90.43  E-value=0.61  Score=21.67  Aligned_cols=16  Identities=25%  Similarity=0.204  Sum_probs=6.2

Q ss_pred             HHHHHhCCChHHHHHH
Q 042039          268 IDGLCKSGRLEIALEL  283 (376)
Q Consensus       268 ~~~~~~~~~~~~a~~~  283 (376)
                      +.++...|++++|..+
T Consensus         8 a~~~~~~G~~~eA~~~   23 (26)
T PF07721_consen    8 ARALLAQGDPDEAERL   23 (26)
T ss_pred             HHHHHHcCCHHHHHHH
Confidence            3333333444433333

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

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.25  E-value=15  Score=33.97  Aligned_cols=150  Identities=15%  Similarity=0.202  Sum_probs=87.8

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCC---ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhC
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINP---DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKN   99 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   99 (376)
                      ++.+.+.+.+++|+++.+.....  .|   -......++..+...|++++|-...-.|...    +..-|..-...+...
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~~~--~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn----~~~eWe~~V~~f~e~  436 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASIGN--EERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN----NAAEWELWVFKFAEL  436 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhccCC--ccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc----hHHHHHHHHHHhccc
Confidence            56778889999999988766544  33   3456777888888899999998888887653    555566555555555


Q ss_pred             CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHH------------------HhcCCCCChhhHHH
Q 042039          100 GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSM------------------ESMGCKHDDVSYNI  161 (376)
Q Consensus       100 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~------------------~~~~~~~~~~~~~~  161 (376)
                      ++......++   .......++..|..++..+.. .+...-.++....                  .+.  ..+......
T Consensus       437 ~~l~~Ia~~l---Pt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~--Se~~~L~e~  510 (846)
T KOG2066|consen  437 DQLTDIAPYL---PTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQN--SESTALLEV  510 (846)
T ss_pred             cccchhhccC---CCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhh--ccchhHHHH
Confidence            5544332221   111111234455555555544 2222111111110                  010  122234455


Q ss_pred             HHHHHHccCcHHHHHHHHHHHHH
Q 042039          162 LINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      |+..|...++++.|++.+-.+.+
T Consensus       511 La~LYl~d~~Y~~Al~~ylklk~  533 (846)
T KOG2066|consen  511 LAHLYLYDNKYEKALPIYLKLQD  533 (846)
T ss_pred             HHHHHHHccChHHHHHHHHhccC
Confidence            88888888899998888876554

>KOG4507 consensus Uncharacterized conserved protein, contains TPR repeats [Function unknown]

Probab=90.15  E-value=2.4  Score=37.40  Aligned_cols=88  Identities=16%  Similarity=0.121  Sum_probs=50.6

Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHH
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL  176 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  176 (376)
                      ...|+...|...+.................++....+.|....|..++.+..... ...+-++..+++++....+.++|+
T Consensus       618 r~~gn~~~a~~cl~~a~~~~p~~~~v~~v~la~~~~~~~~~~da~~~l~q~l~~~-~sepl~~~~~g~~~l~l~~i~~a~  696 (886)
T KOG4507|consen  618 RAVGNSTFAIACLQRALNLAPLQQDVPLVNLANLLIHYGLHLDATKLLLQALAIN-SSEPLTFLSLGNAYLALKNISGAL  696 (886)
T ss_pred             eecCCcHHHHHHHHHHhccChhhhcccHHHHHHHHHHhhhhccHHHHHHHHHhhc-ccCchHHHhcchhHHHHhhhHHHH
Confidence            3456666666666655543222223344455556666666666666666665554 334445556666666666677777


Q ss_pred             HHHHHHHHC
Q 042039          177 SLYREMVSK  185 (376)
Q Consensus       177 ~~~~~~~~~  185 (376)
                      +.|+++.+.
T Consensus       697 ~~~~~a~~~  705 (886)
T KOG4507|consen  697 EAFRQALKL  705 (886)
T ss_pred             HHHHHHHhc
Confidence            776666664

>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=90.04  E-value=0.15  Score=36.39  Aligned_cols=52  Identities=8%  Similarity=0.052  Sum_probs=23.6

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHH
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLF   74 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~   74 (376)
                      +..+.+.+.......+++.+...+...+....+.++..|++.++.++..+++
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L   65 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFL   65 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTT
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHc
Confidence            3344444455555555555544433334444555555555554444444444

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.

>KOG4507 consensus Uncharacterized conserved protein, contains TPR repeats [Function unknown]

Probab=89.89  E-value=1.6  Score=38.38  Aligned_cols=102  Identities=12%  Similarity=-0.126  Sum_probs=70.6

Q ss_pred             CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHH
Q 042039          224 ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMI  303 (376)
Q Consensus       224 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  303 (376)
                      |-...++.....+...|+...|...+..+....+.-.......++....+.|-...|..++.+.+... ...+-++..++
T Consensus       605 p~w~~ln~aglywr~~gn~~~a~~cl~~a~~~~p~~~~v~~v~la~~~~~~~~~~da~~~l~q~l~~~-~sepl~~~~~g  683 (886)
T KOG4507|consen  605 PIWLILNEAGLYWRAVGNSTFAIACLQRALNLAPLQQDVPLVNLANLLIHYGLHLDATKLLLQALAIN-SSEPLTFLSLG  683 (886)
T ss_pred             CeEEEeecccceeeecCCcHHHHHHHHHHhccChhhhcccHHHHHHHHHHhhhhccHHHHHHHHHhhc-ccCchHHHhcc
Confidence            33334444444455678888888888877654433333455667777777777788888887766553 34566777888


Q ss_pred             HHHHccCChhHHHHHHHHHHHcC
Q 042039          304 HGLCNDGQMDKAHDLFLDMEENA  326 (376)
Q Consensus       304 ~~~~~~~~~~~a~~~~~~~~~~~  326 (376)
                      .++....+.+.|++.|+++.+..
T Consensus       684 ~~~l~l~~i~~a~~~~~~a~~~~  706 (886)
T KOG4507|consen  684 NAYLALKNISGALEAFRQALKLT  706 (886)
T ss_pred             hhHHHHhhhHHHHHHHHHHHhcC
Confidence            88888888999999888888754

>KOG1308 consensus Hsp70-interacting protein Hip/Transient component of progesterone receptor complexes and an Hsp70-binding protein [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=89.42  E-value=0.33  Score=39.37  Aligned_cols=87  Identities=17%  Similarity=0.188  Sum_probs=47.1

Q ss_pred             cCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHhcCcHHHHH
Q 042039           63 HANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFCLTGKINRAE  141 (376)
Q Consensus        63 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~  141 (376)
                      ..|.++.|++.|...+..+ ++....|..-..++.+.+.+..|++-+...+..+  || ..-|-.-..+....|++.+|.
T Consensus       126 n~G~~~~ai~~~t~ai~ln-p~~a~l~~kr~sv~lkl~kp~~airD~d~A~ein--~Dsa~~ykfrg~A~rllg~~e~aa  202 (377)
T KOG1308|consen  126 NDGEFDTAIELFTSAIELN-PPLAILYAKRASVFLKLKKPNAAIRDCDFAIEIN--PDSAKGYKFRGYAERLLGNWEEAA  202 (377)
T ss_pred             cCcchhhhhcccccccccC-CchhhhcccccceeeeccCCchhhhhhhhhhccC--cccccccchhhHHHHHhhchHHHH
Confidence            4555666666666666543 2244445555556666666666666666655542  22 222333333444456666666


Q ss_pred             HHHHHHHhcCC
Q 042039          142 ELFGSMESMGC  152 (376)
Q Consensus       142 ~~~~~~~~~~~  152 (376)
                      ..++...+.+.
T Consensus       203 ~dl~~a~kld~  213 (377)
T KOG1308|consen  203 HDLALACKLDY  213 (377)
T ss_pred             HHHHHHHhccc
Confidence            66666666543

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.35  E-value=8.1  Score=34.51  Aligned_cols=99  Identities=16%  Similarity=0.150  Sum_probs=48.0

Q ss_pred             HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHH
Q 042039          202 FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIAL  281 (376)
Q Consensus       202 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  281 (376)
                      .+.|+++.|.++..+.      .+..-|..|..+....+++..|.+.|.+...         |..|+-.+...|+-+-..
T Consensus       648 l~lgrl~iA~~la~e~------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~  712 (794)
T KOG0276|consen  648 LKLGRLDIAFDLAVEA------NSEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLA  712 (794)
T ss_pred             hhcCcHHHHHHHHHhh------cchHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHH
Confidence            3455555555544332      2444556666666666666666666655432         223344444455544433


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHH
Q 042039          282 ELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLD  321 (376)
Q Consensus       282 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  321 (376)
                      .+-....+.|.      .+....+|...|+++++.+++.+
T Consensus       713 ~la~~~~~~g~------~N~AF~~~~l~g~~~~C~~lLi~  746 (794)
T KOG0276|consen  713 VLASLAKKQGK------NNLAFLAYFLSGDYEECLELLIS  746 (794)
T ss_pred             HHHHHHHhhcc------cchHHHHHHHcCCHHHHHHHHHh
Confidence            33333333321      12222345556666666666544

>PRK09687 putative lyase; Provisional

Probab=88.93  E-value=11  Score=30.61  Aligned_cols=235  Identities=14%  Similarity=0.061  Sum_probs=143.2

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCCh----HHHHHHHHHHHhcCCCCChhh
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKM----DEASRLLDLMVQRDVRPNAFT  123 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~  123 (376)
                      .+|.......+..+...|. +++...+..+...   ++...-...+.++...|+.    .++...+..+...  .++..+
T Consensus        34 d~d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~V  107 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACV  107 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHH
Confidence            4466677777777777775 3444444555442   3555555666677777763    4677777776443  345555


Q ss_pred             HHHHHHHHHhcCc-----HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHH
Q 042039          124 YSTLMDGFCLTGK-----INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLF  198 (376)
Q Consensus       124 ~~~l~~~~~~~~~-----~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  198 (376)
                      -...+.++...+.     ...+...+.....   .++..+-...+.++.+.++ ++++..+-.+.+.   ++..+-...+
T Consensus       108 R~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~d---~~~~VR~~A~  180 (280)
T PRK09687        108 RASAINATGHRCKKNPLYSPKIVEQSQITAF---DKSTNVRFAVAFALSVIND-EAAIPLLINLLKD---PNGDVRNWAA  180 (280)
T ss_pred             HHHHHHHHhcccccccccchHHHHHHHHHhh---CCCHHHHHHHHHHHhccCC-HHHHHHHHHHhcC---CCHHHHHHHH
Confidence            5555555554432     1233444433333   3466667777778877776 5677777777763   4555555556


Q ss_pred             HHHHhcc-chHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCCh
Q 042039          199 LGLFEIH-QVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       199 ~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      .++...+ +.+.+...+..+..   .++..+-...+.++.+.++. .++..+-.....+   +  .....+.++...|..
T Consensus       181 ~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~ALg~ig~~  251 (280)
T PRK09687        181 FALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAAGELGDK  251 (280)
T ss_pred             HHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHHHhcCCH
Confidence            6665543 24466666666664   34667777888888888884 5555555554432   2  234677888888885


Q ss_pred             HHHHHHHhcccccCCCCCHHHHHHHHHHHH
Q 042039          278 EIALELFRSLPRRVLVADVVTYNIMIHGLC  307 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  307 (376)
                       +|...+..+.+.  .+|..+-...+.++.
T Consensus       252 -~a~p~L~~l~~~--~~d~~v~~~a~~a~~  278 (280)
T PRK09687        252 -TLLPVLDTLLYK--FDDNEIITKAIDKLK  278 (280)
T ss_pred             -hHHHHHHHHHhh--CCChhHHHHHHHHHh
Confidence             688888887764  347766666666554

>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=88.64  E-value=0.28  Score=35.02  Aligned_cols=84  Identities=11%  Similarity=0.133  Sum_probs=51.2

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCc
Q 042039           57 LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGK  136 (376)
Q Consensus        57 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  136 (376)
                      ++..+.+.+.+.....+++.+...+...+....+.++..|++.+..++..++++..       +..-...++..|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~-------~~yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTS-------NNYDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS-------SSS-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccc-------cccCHHHHHHHHHhcch
Confidence            45556667777777777877776655556777778888888877767766666511       11222345555666666


Q ss_pred             HHHHHHHHHHH
Q 042039          137 INRAEELFGSM  147 (376)
Q Consensus       137 ~~~a~~~~~~~  147 (376)
                      ++++.-++.++
T Consensus        86 ~~~a~~Ly~~~   96 (143)
T PF00637_consen   86 YEEAVYLYSKL   96 (143)
T ss_dssp             HHHHHHHHHCC
T ss_pred             HHHHHHHHHHc
Confidence            66665555543

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.

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=88.52  E-value=6.9  Score=30.00  Aligned_cols=59  Identities=17%  Similarity=0.223  Sum_probs=34.2

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      ..+..+.+.+.+.+++...++-++.. +.|...-..++..++-.|++++|..-++-.-..
T Consensus         6 ~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l   64 (273)
T COG4455           6 DTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATL   64 (273)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhc
Confidence            34445556666666666666655543 334455556666666666666666655555443

>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=88.18  E-value=8.5  Score=28.27  Aligned_cols=135  Identities=13%  Similarity=0.156  Sum_probs=83.2

Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           36 KALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .+++..+.+.+++|+...+..++..+.+.|++.....+    +..++-+|.......+-.  ..+....+.++--+|.++
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~ql----lq~~Vi~DSk~lA~~LLs--~~~~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQL----LQYHVIPDSKPLACQLLS--LGNQYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHH----HhhcccCCcHHHHHHHHH--hHccChHHHHHHHHHHHH
Confidence            34556667778899999999999999999987765554    444555555444333322  223344455555555543


Q ss_pred             CCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          116 DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       116 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      = .   ..+..+++.+...|++-+|.++.+......    ......++.+..+.+|...-..+++-...
T Consensus        88 L-~---~~~~~iievLL~~g~vl~ALr~ar~~~~~~----~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   88 L-G---TAYEEIIEVLLSKGQVLEALRYARQYHKVD----SVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             h-h---hhHHHHHHHHHhCCCHHHHHHHHHHcCCcc----cCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1 1   244567778888999999999887764322    22234456666666776655555555444

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=88.13  E-value=22  Score=32.91  Aligned_cols=155  Identities=10%  Similarity=0.051  Sum_probs=65.7

Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHh--
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD-VAADTSTYNTFIDGLCK--  238 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~--  238 (376)
                      ....+.-.|+++.|++.+-.  ..+...+...+...+..+.-.+-.+...   ..+.... ..+.+--+..++..|.+  
T Consensus       264 Yf~~LlLtgqFE~AI~~L~~--~~~~~~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~arLI~~Y~~~F  338 (613)
T PF04097_consen  264 YFQVLLLTGQFEAAIEFLYR--NEFNRVDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNFARLIGQYTRSF  338 (613)
T ss_dssp             HHHHHHHTT-HHHHHHHHHT----T-HHHHHHHHHHHHHTT---------------------------HHHHHHHHHHTT
T ss_pred             HHHHHHHHhhHHHHHHHHHh--hccCcccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCHHHHHHHHHHHH
Confidence            34455668999999998877  1122334444433333322222111111   2222211 01122456777777765  


Q ss_pred             -CCCHHHHHHHHHHhcccCCCchHHHHHH-HHHHHHhCCChHHHHHHHhcccccC---------------CCC-CH---H
Q 042039          239 -NGYIVEAVELFRTLGILKCELDIQAYNC-LIDGLCKSGRLEIALELFRSLPRRV---------------LVA-DV---V  297 (376)
Q Consensus       239 -~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~---------------~~~-~~---~  297 (376)
                       ..++.+|.+++--+.....+.....+.. +.......++++   .++..+...|               ... +.   .
T Consensus       339 ~~td~~~Al~Y~~li~~~~~~~~~~l~~~~l~eLvletref~---~LLG~i~~dG~r~~G~i~~~~~Li~~~~~~~~~~~  415 (613)
T PF04097_consen  339 EITDPREALQYLYLICLFKDPEQRNLFHECLRELVLETREFD---LLLGDINPDGSRTPGLIERRLSLIKFDDDEDFLRE  415 (613)
T ss_dssp             TTT-HHHHHHHHHGGGGS-SCCHHHHHHHHHHHHHHHH--HH---HHHEEE-TTS-EEE-HHHHTGGGGT-SSSSHHHHH
T ss_pred             hccCHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHccCCHH---HHCCCCCCCCccccceeeccccccCCCCcHHHHHH
Confidence             5678899998887765543222333322 222233333222   2222211111               111 11   2


Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      .....+.-+...|++++|+.+|+-+.+
T Consensus       416 i~~~~A~~~e~~g~~~dAi~Ly~La~~  442 (613)
T PF04097_consen  416 IIEQAAREAEERGRFEDAILLYHLAEE  442 (613)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhh
Confidence            233445557778899999888887654

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

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

Probab=88.08  E-value=3.7  Score=28.10  Aligned_cols=46  Identities=9%  Similarity=0.019  Sum_probs=29.9

Q ss_pred             HHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          279 IALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       279 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      +..+-+..+....+.|++.....-+++|.+.+++..|.++|+-+..
T Consensus        67 EvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~  112 (149)
T KOG4077|consen   67 EVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKD  112 (149)
T ss_pred             HHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            4445555555555667777777777777777777777777766654

>PRK11619 lytic murein transglycosylase; Provisional

Probab=87.97  E-value=23  Score=32.95  Aligned_cols=115  Identities=12%  Similarity=0.063  Sum_probs=58.7

Q ss_pred             CcHHHHHHHHHHHHhcC-CCCC--hhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHH
Q 042039          135 GKINRAEELFGSMESMG-CKHD--DVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      .+.+.|...+....... ..+.  ...+..++......+..+++...+......  ..+......-+......++++.+.
T Consensus       255 ~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~--~~~~~~~e~r~r~Al~~~dw~~~~  332 (644)
T PRK11619        255 QDAENARLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMR--SQSTSLLERRVRMALGTGDRRGLN  332 (644)
T ss_pred             hCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcccc--cCCcHHHHHHHHHHHHccCHHHHH
Confidence            34566666666653322 1111  112223332222222234455555443322  123333444455555677777777


Q ss_pred             HHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          212 KLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      ..+..|.... .....-...+++++...|+.++|...|+.+
T Consensus       333 ~~i~~L~~~~-~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~  372 (644)
T PRK11619        333 TWLARLPMEA-KEKDEWRYWQADLLLEQGRKAEAEEILRQL  372 (644)
T ss_pred             HHHHhcCHhh-ccCHhhHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            7777664432 334455666777766777777777777776

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.93  E-value=11  Score=29.31  Aligned_cols=14  Identities=29%  Similarity=0.437  Sum_probs=7.9

Q ss_pred             CCChHHHHHHHHHH
Q 042039           99 NGKMDEASRLLDLM  112 (376)
Q Consensus        99 ~~~~~~a~~~~~~~  112 (376)
                      .+.+++|.+++.+.
T Consensus        27 ~~k~eeAadl~~~A   40 (288)
T KOG1586|consen   27 SNKYEEAAELYERA   40 (288)
T ss_pred             CcchHHHHHHHHHH
Confidence            34566666666544

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=87.80  E-value=42  Score=35.84  Aligned_cols=288  Identities=10%  Similarity=0.056  Sum_probs=147.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      |..+...|..-++++...-+...-..   .|+   ...-+......|+|..|...|+.+.+.+.. ...+++.++.....
T Consensus      1423 ~fllq~lY~~i~dpDgV~Gv~~~r~a---~~s---l~~qil~~e~~g~~~da~~Cye~~~q~~p~-~~~~~~g~l~sml~ 1495 (2382)
T KOG0890|consen 1423 YFLLQNLYGSIHDPDGVEGVSARRFA---DPS---LYQQILEHEASGNWADAAACYERLIQKDPD-KEKHHSGVLKSMLA 1495 (2382)
T ss_pred             HHHHHHHHHhcCCcchhhhHHHHhhc---Ccc---HHHHHHHHHhhccHHHHHHHHHHhhcCCCc-cccchhhHHHhhhc
Confidence            33344467777777766666553111   122   333455567789999999999999987422 46778888888888


Q ss_pred             CCChHHHHHHHHHHHhcCCCCChhhHH-HHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHH--HHHHHHc--cCcHH
Q 042039           99 NGKMDEASRLLDLMVQRDVRPNAFTYS-TLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNI--LINGYCK--NKEVE  173 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--l~~~~~~--~~~~~  173 (376)
                      .|.+.......+-..... .+....++ .-..+--+.++++.....+.   ..    +...|..  ++....+  ..|.-
T Consensus      1496 ~~~l~t~i~~~dg~~~~~-se~~~~~~s~~~eaaW~l~qwD~~e~~l~---~~----n~e~w~~~~~g~~ll~~~~kD~~ 1567 (2382)
T KOG0890|consen 1496 IQHLSTEILHLDGLIINR-SEEVDELNSLGVEAAWRLSQWDLLESYLS---DR----NIEYWSVESIGKLLLRNKKKDEI 1567 (2382)
T ss_pred             ccchhHHHhhhcchhhcc-CHHHHHHHHHHHHHHhhhcchhhhhhhhh---cc----cccchhHHHHHHHHHhhcccchh
Confidence            888888887666665442 22333333 33444467788887777765   11    1222222  2333322  22222


Q ss_pred             HHHHHHHHHHHCCCCC---------CHhHHHHHHHHHHhccchHHHHHHHHHHHhc-CCCCCcchHHHHHHHHHhCCCHH
Q 042039          174 EALSLYREMVSKGIKP---------TVVTYNTLFLGLFEIHQVEHALKLFEEMQRD-DVAADTSTYNTFIDGLCKNGYIV  243 (376)
Q Consensus       174 ~a~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~  243 (376)
                      .-.+.++.+.+.-+.|         -...|..++..+.-.. .+...+.+...... ....+..-|..-+..-....+..
T Consensus      1568 ~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~e-l~~~~~~l~~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~ 1646 (2382)
T KOG0890|consen 1568 ATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLLE-LENSIEELKKVSYDEDSANNSDNWKNRLERTQPSFRIK 1646 (2382)
T ss_pred             hHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHHH-HHHHHHHhhccCccccccccchhHHHHHHHhchhHHHH
Confidence            2223333333221111         0122222222221111 11111111111000 00111111111221111111122


Q ss_pred             HHHHHHHHhc----cc-CC-CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHH
Q 042039          244 EAVELFRTLG----IL-KC-ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHD  317 (376)
Q Consensus       244 ~a~~~~~~~~----~~-~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  317 (376)
                      +-+--+++..    .. +. .--...|...++.....|.++.|...+-.+.+.+   -+..+...+......|+...|+.
T Consensus      1647 epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A~nall~A~e~r---~~~i~~E~AK~lW~~gd~~~Al~ 1723 (2382)
T KOG0890|consen 1647 EPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRAQNALLNAKESR---LPEIVLERAKLLWQTGDELNALS 1723 (2382)
T ss_pred             hHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHHHHHHHhhhhcc---cchHHHHHHHHHHhhccHHHHHH
Confidence            2222222211    11 11 1235678888888888999999998887777653   34556677788888999999999


Q ss_pred             HHHHHHHc
Q 042039          318 LFLDMEEN  325 (376)
Q Consensus       318 ~~~~~~~~  325 (376)
                      ++++..+.
T Consensus      1724 ~Lq~~l~~ 1731 (2382)
T KOG0890|consen 1724 VLQEILSK 1731 (2382)
T ss_pred             HHHHHHHh
Confidence            99988754

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=87.73  E-value=19  Score=31.73  Aligned_cols=61  Identities=13%  Similarity=0.087  Sum_probs=26.7

Q ss_pred             hhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          157 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       157 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      ....+++..+..+-.+.-...+..+++.-  ..+...+..++++|... ..++-..+|+++.+.
T Consensus        67 ~~l~~~~~~f~~n~k~~~veh~c~~~l~~--~e~kmal~el~q~y~en-~n~~l~~lWer~ve~  127 (711)
T COG1747          67 SCLVTLLTIFGDNHKNQIVEHLCTRVLEY--GESKMALLELLQCYKEN-GNEQLYSLWERLVEY  127 (711)
T ss_pred             hHHHHHHHHhccchHHHHHHHHHHHHHHh--cchHHHHHHHHHHHHhc-CchhhHHHHHHHHHh
Confidence            33444444444444444444444444442  22334444444444444 334444444444443

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.35  E-value=15  Score=30.08  Aligned_cols=48  Identities=8%  Similarity=0.136  Sum_probs=28.5

Q ss_pred             ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          276 RLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       276 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      +.++++.++..=+..|+-||..++..++..+.+.+++.+|..+.-.|+
T Consensus       115 ~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             ChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            455666666555566666666666666666666666666655554444

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=87.35  E-value=24  Score=32.62  Aligned_cols=168  Identities=11%  Similarity=0.056  Sum_probs=96.8

Q ss_pred             ChhhHHHHHHHHH-hcCChhHHHHHHHHhhhCCCCCChh-----hHHHHHHHHhcCCChHHHHHHHHHHHhcCCC----C
Q 042039           15 NTVTYNTIIDGLC-KEGFVDKAKALFLQMKGENINPDVV-----TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ----P   84 (376)
Q Consensus        15 ~~~~~~~l~~~~~-~~g~~~~a~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~   84 (376)
                      +..++..+...+. ...+++.|...+++.......++..     ....++..+.+.+... |...+++.++.--.    +
T Consensus        58 ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~  136 (608)
T PF10345_consen   58 EARVRLRLASILLEETENLDLAETYLEKAILLCERHRLTDLKFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSA  136 (608)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchh
Confidence            3456667777776 5689999999999875543233221     2335567777776655 88888887764211    2


Q ss_pred             chHhHHHH-HHHHHhCCChHHHHHHHHHHHhcC---CCCChhhHHHHHHHHH--hcCcHHHHHHHHHHHHhcC-------
Q 042039           85 SVVTFNVI-MDELCKNGKMDEASRLLDLMVQRD---VRPNAFTYSTLMDGFC--LTGKINRAEELFGSMESMG-------  151 (376)
Q Consensus        85 ~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~--~~~~~~~a~~~~~~~~~~~-------  151 (376)
                      -...+..+ +..+...++...|.+.++.+....   ..|...++..+..+..  +.+..+++.+.++.+....       
T Consensus       137 w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~~~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~  216 (608)
T PF10345_consen  137 WYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPAVFVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDP  216 (608)
T ss_pred             HHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCC
Confidence            22233333 223333478999999998887642   2333444444444433  4455666777666663221       


Q ss_pred             --CCCChhhHHHHHHHH--HccCcHHHHHHHHHHHH
Q 042039          152 --CKHDDVSYNILINGY--CKNKEVEEALSLYREMV  183 (376)
Q Consensus       152 --~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~  183 (376)
                        .+|...+|..++..+  ...|+++.+...++++.
T Consensus       217 ~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq  252 (608)
T PF10345_consen  217 SVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQ  252 (608)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence              123444566665544  45677666666655543

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=87.26  E-value=14  Score=29.81  Aligned_cols=59  Identities=15%  Similarity=0.163  Sum_probs=38.8

Q ss_pred             HHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHH
Q 042039          159 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       159 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  218 (376)
                      ++.....|...|.+.+|.++.++.+.. -+.+...+..++..+...|+--.+.+.++++.
T Consensus       282 lgkva~~yle~g~~neAi~l~qr~ltl-dpL~e~~nk~lm~~la~~gD~is~~khyerya  340 (361)
T COG3947         282 LGKVARAYLEAGKPNEAIQLHQRALTL-DPLSEQDNKGLMASLATLGDEISAIKHYERYA  340 (361)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHhhc-ChhhhHHHHHHHHHHHHhccchhhhhHHHHHH
Confidence            344556677777777777777777665 24456666677777777777666666665553

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=86.67  E-value=15  Score=29.62  Aligned_cols=72  Identities=13%  Similarity=0.057  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh-----CCCCCchHHHH
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE-----KKVMPDASIVS  370 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~~~  370 (376)
                      ++......|..+|.+.+|.++.++.+..+ +.+...+..|+..+...|+--.+.+.++++.+     .|+..|..+..
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyerya~vleaelgi~vddsiee  357 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDDSIEE  357 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhCCCcchhHHH
Confidence            45566778899999999999999998764 33677788888999999998888888887753     47777776654

>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]

Probab=86.59  E-value=14  Score=28.94  Aligned_cols=79  Identities=11%  Similarity=0.025  Sum_probs=31.5

Q ss_pred             CChHHHHHHHHHHHhcCCCCch-HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHhcCcHHHHHH
Q 042039           65 NDWNEAKRLFFEMMDQGVQPSV-VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFCLTGKINRAEE  142 (376)
Q Consensus        65 ~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~  142 (376)
                      .++..|+..|.+.+..  .|+. .-|..-+.++.+..+++.+..--.+.++.  .|| +.....+.........++.|+.
T Consensus        24 k~y~~ai~~y~raI~~--nP~~~~Y~tnralchlk~~~~~~v~~dcrralql--~~N~vk~h~flg~~~l~s~~~~eaI~   99 (284)
T KOG4642|consen   24 KRYDDAIDCYSRAICI--NPTVASYYTNRALCHLKLKHWEPVEEDCRRALQL--DPNLVKAHYFLGQWLLQSKGYDEAIK   99 (284)
T ss_pred             hhhchHHHHHHHHHhc--CCCcchhhhhHHHHHHHhhhhhhhhhhHHHHHhc--ChHHHHHHHHHHHHHHhhccccHHHH
Confidence            3444444444444432  2222 22233333444444444444444444432  222 2233333444444444444444


Q ss_pred             HHHHH
Q 042039          143 LFGSM  147 (376)
Q Consensus       143 ~~~~~  147 (376)
                      .+.+.
T Consensus       100 ~Lqra  104 (284)
T KOG4642|consen  100 VLQRA  104 (284)
T ss_pred             HHHHH
Confidence            44444

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=86.55  E-value=18  Score=30.23  Aligned_cols=82  Identities=9%  Similarity=-0.034  Sum_probs=43.7

Q ss_pred             CCChhhHHHHHHHHhcCC------------ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           48 NPDVVTYNSLIHGLCHAN------------DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~------------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      |.|+.+|..++..--..-            -.+.-+.+++++++.++ .+...+..++..+.+..+.++..+-+++++..
T Consensus        16 P~di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~np-~~~~L~l~~l~~~~~~~~~~~l~~~we~~l~~   94 (321)
T PF08424_consen   16 PHDIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHNP-DSERLLLGYLEEGEKVWDSEKLAKKWEELLFK   94 (321)
T ss_pred             cccHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            556667666654322211            13344566666666533 24555555666666666666666666666665


Q ss_pred             CCCCChhhHHHHHHHH
Q 042039          116 DVRPNAFTYSTLMDGF  131 (376)
Q Consensus       116 ~~~~~~~~~~~l~~~~  131 (376)
                      . +-+...|...+...
T Consensus        95 ~-~~~~~LW~~yL~~~  109 (321)
T PF08424_consen   95 N-PGSPELWREYLDFR  109 (321)
T ss_pred             C-CCChHHHHHHHHHH
Confidence            2 22445555554443

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=86.49  E-value=15  Score=29.28  Aligned_cols=50  Identities=10%  Similarity=0.078  Sum_probs=25.5

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCh---hhHHHHHHHHhcCCChHHHHHHHHHHH
Q 042039           29 EGFVDKAKALFLQMKGENINPDV---VTYNSLIHGLCHANDWNEAKRLFFEMM   78 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~   78 (376)
                      ....++|+.-|++..+.......   .+...++....+.+++++....|.+++
T Consensus        40 e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlL   92 (440)
T KOG1464|consen   40 EDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLL   92 (440)
T ss_pred             ccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence            34566666666665544212222   233444555556666666655555554

>PRK12798 chemotaxis protein; Reviewed

Probab=85.60  E-value=22  Score=30.44  Aligned_cols=152  Identities=14%  Similarity=0.119  Sum_probs=80.4

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHH-HccCcHHHHHHHHHHHHHCCCCCC----HhHHHHHHHHHHhccch
Q 042039          133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGY-CKNKEVEEALSLYREMVSKGIKPT----VVTYNTLFLGLFEIHQV  207 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~  207 (376)
                      -.|+-.++.+.+..+.....++....+..|+.+- ....++.+|+.+|+...-.  .|.    ......-+......|+.
T Consensus       124 ~~Gr~~~a~~~La~i~~~~l~~~lg~~laLv~a~l~~~~dP~~Al~~lD~aRLl--aPGTLvEEAALRRsi~la~~~g~~  201 (421)
T PRK12798        124 LSGRGREARKLLAGVAPEYLPAELGAYLALVQGNLMVATDPATALKLLDQARLL--APGTLVEEAALRRSLFIAAQLGDA  201 (421)
T ss_pred             HcCCHHHHHHHhhcCChhhcCchhhhHHHHHHHHHhcccCHHHHHHHHHHHHHh--CCchHHHHHHHHHhhHHHHhcCcH
Confidence            3677777777777776655566666666665543 3355677777777776542  232    23333444455666777


Q ss_pred             HHHHHHHHHHHhc-CCCCC-cchHHHHHHHHHhCCC---HHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHH
Q 042039          208 EHALKLFEEMQRD-DVAAD-TSTYNTFIDGLCKNGY---IVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALE  282 (376)
Q Consensus       208 ~~a~~~~~~~~~~-~~~~~-~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  282 (376)
                      +++..+-....+. ...|- ......+...+.+..+   .+.-..++..|   ...--...|..+.+.-.-.|+.+-|.-
T Consensus       202 ~rf~~la~~Y~rRF~~S~YA~~F~~~F~~~~~~~~d~~~~~~l~~~ls~~---d~~~q~~lYL~iAR~Ali~Gk~~lA~~  278 (421)
T PRK12798        202 DKFEALARNYLRRFRHSPYASQFAQRFVDLVVRLDDEIRDARLVEILSFM---DPERQRELYLRIARAALIDGKTELARF  278 (421)
T ss_pred             HHHHHHHHHHHHHhccCchHHHHHHHHHHHHHhccccccHHHHHHHHHhc---CchhHHHHHHHHHHHHHHcCcHHHHHH
Confidence            7665555444333 11111 1222233333333332   22222233222   212234567777777777777777766


Q ss_pred             HHhcccc
Q 042039          283 LFRSLPR  289 (376)
Q Consensus       283 ~~~~~~~  289 (376)
                      .-++...
T Consensus       279 As~~A~~  285 (421)
T PRK12798        279 ASERALK  285 (421)
T ss_pred             HHHHHHH
Confidence            6665544

>PRK09687 putative lyase; Provisional

Probab=85.46  E-value=18  Score=29.41  Aligned_cols=58  Identities=9%  Similarity=0.084  Sum_probs=24.4

Q ss_pred             CHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          295 DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       295 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      +..+-...+.++.+.++ ..|+..+-+..+.+   +  .....+.++...|.. +|...+..+.+
T Consensus       205 ~~~VR~~A~~aLg~~~~-~~av~~Li~~L~~~---~--~~~~a~~ALg~ig~~-~a~p~L~~l~~  262 (280)
T PRK09687        205 NEEIRIEAIIGLALRKD-KRVLSVLIKELKKG---T--VGDLIIEAAGELGDK-TLLPVLDTLLY  262 (280)
T ss_pred             ChHHHHHHHHHHHccCC-hhHHHHHHHHHcCC---c--hHHHHHHHHHhcCCH-hHHHHHHHHHh
Confidence            34444444444444444 23444333333321   1  122344444445543 35555555543

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=85.34  E-value=21  Score=29.86  Aligned_cols=135  Identities=7%  Similarity=0.015  Sum_probs=79.4

Q ss_pred             chHhHHHHHHHHHhCC------------ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC
Q 042039           85 SVVTFNVIMDELCKNG------------KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC  152 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~------------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  152 (376)
                      |+.+|..++..--..-            -.+.-+.+++++++.+ +.+......++..+.+..+.+...+-++++.... 
T Consensus        18 di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~n-p~~~~L~l~~l~~~~~~~~~~~l~~~we~~l~~~-   95 (321)
T PF08424_consen   18 DIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHN-PDSERLLLGYLEEGEKVWDSEKLAKKWEELLFKN-   95 (321)
T ss_pred             cHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHC-
Confidence            6777777765433221            1345567778877774 3456677777888888888888888888887764 


Q ss_pred             CCChhhHHHHHHHHHc---cCcHHHHHHHHHHHHHC------CC----CCC-------HhHHHHHHHHHHhccchHHHHH
Q 042039          153 KHDDVSYNILINGYCK---NKEVEEALSLYREMVSK------GI----KPT-------VVTYNTLFLGLFEIHQVEHALK  212 (376)
Q Consensus       153 ~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~------~~----~~~-------~~~~~~l~~~~~~~~~~~~a~~  212 (376)
                      +.+...|...+.....   .-.++....+|.+.++.      +.    .+.       ...+..+.......|..+.|..
T Consensus        96 ~~~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~l~~L~~~~~~~~~~~~~~~~~e~~~l~v~~r~~~fl~~aG~~E~Ava  175 (321)
T PF08424_consen   96 PGSPELWREYLDFRQSNFASFTVSDVRDVYEKCLRALSRRRSGRMTSHPDLPELEEFMLYVFLRLCRFLRQAGYTERAVA  175 (321)
T ss_pred             CCChHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHHCCchHHHHH
Confidence            4466677766665544   23456666666655442      11    000       1222333333445566666666


Q ss_pred             HHHHHHhcC
Q 042039          213 LFEEMQRDD  221 (376)
Q Consensus       213 ~~~~~~~~~  221 (376)
                      +++.+.+.+
T Consensus       176 ~~Qa~lE~n  184 (321)
T PF08424_consen  176 LWQALLEFN  184 (321)
T ss_pred             HHHHHHHHH
Confidence            666665543

>smart00028 TPR Tetratricopeptide repeats

Probab=84.95  E-value=1.9  Score=20.29  Aligned_cols=22  Identities=18%  Similarity=0.265  Sum_probs=9.1

Q ss_pred             HHHHHHhcCCChHHHHHHHHHH
Q 042039           56 SLIHGLCHANDWNEAKRLFFEM   77 (376)
Q Consensus        56 ~l~~~~~~~~~~~~a~~~~~~~   77 (376)
                      .+..++...+++++|...++..
T Consensus         6 ~~a~~~~~~~~~~~a~~~~~~~   27 (34)
T smart00028        6 NLGNAYLKLGDYDEALEYYEKA   27 (34)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHH
Confidence            3333444444444444444433

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

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

Probab=84.92  E-value=4.1  Score=22.52  Aligned_cols=34  Identities=15%  Similarity=0.190  Sum_probs=25.4

Q ss_pred             HhhcCChhhHHHHHHHHHhCCCCCchHHHHHHHh
Q 042039          341 FVRINKPSKVIELLHKMKEKKVMPDASIVSMVVD  374 (376)
Q Consensus       341 ~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  374 (376)
                      ..+.|-.+++..++++|.+.|+..+...+..+++
T Consensus        12 Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen   12 AKRRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            3456777778888888888888888887777765

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

>COG0790 FOG: TPR repeat, SEL1 subfamily [General function prediction only]

Probab=84.90  E-value=20  Score=29.33  Aligned_cols=25  Identities=16%  Similarity=0.065  Sum_probs=14.8

Q ss_pred             CHHHHHHHHHHhcccCCCchHHHHH
Q 042039          241 YIVEAVELFRTLGILKCELDIQAYN  265 (376)
Q Consensus       241 ~~~~a~~~~~~~~~~~~~~~~~~~~  265 (376)
                      +...|...+......+.........
T Consensus       252 ~~~~a~~~~~~~~~~~~~~~~~~~~  276 (292)
T COG0790         252 DKKQALEWLQKACELGFDNACEALR  276 (292)
T ss_pred             CHHHHHHHHHHHHHcCChhHHHHHH
Confidence            6667777777766665544444333

>PRK10941 hypothetical protein; Provisional

Probab=84.59  E-value=15  Score=29.68  Aligned_cols=60  Identities=15%  Similarity=-0.047  Sum_probs=32.2

Q ss_pred             HHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          265 NCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       265 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      ..+-.+|.+.++++.|+.+.+.+... .|.++.-+..-+-.|.+.|.+..|..=++..++.
T Consensus       185 ~nLK~~~~~~~~~~~AL~~~e~ll~l-~P~dp~e~RDRGll~~qL~c~~~A~~DL~~fl~~  244 (269)
T PRK10941        185 DTLKAALMEEKQMELALRASEALLQF-DPEDPYEIRDRGLIYAQLDCEHVALSDLSYFVEQ  244 (269)
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHh
Confidence            34444455556666666665555544 3334444555555555566666655555555543

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=84.32  E-value=19  Score=28.68  Aligned_cols=203  Identities=12%  Similarity=0.089  Sum_probs=126.8

Q ss_pred             CCCCchHhHHHHHHH-HHhCCChHHHHHHHHHHHhcCCCCChh---hHHHHHHHHHhcCcHHHHHHHHHHHHhc---CC-
Q 042039           81 GVQPSVVTFNVIMDE-LCKNGKMDEASRLLDLMVQRDVRPNAF---TYSTLMDGFCLTGKINRAEELFGSMESM---GC-  152 (376)
Q Consensus        81 ~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~-  152 (376)
                      +..||+..-+..-.+ -.+..++++|+.-|++.++.......+   +...++....+.+++++..+.|.++...   .+ 
T Consensus        21 ~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVT  100 (440)
T KOG1464|consen   21 NSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVT  100 (440)
T ss_pred             CCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHh
Confidence            445666554433222 124458999999999998864333333   4456788899999999999999887532   11 


Q ss_pred             -CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC-----CCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC--
Q 042039          153 -KHDDVSYNILINGYCKNKEVEEALSLYREMVSK-----GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA--  224 (376)
Q Consensus       153 -~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--  224 (376)
                       ..+..+.+.++..-....+.+--..+|+.-++.     +-+.=-.|-..+...|...+.+.+..+++.++..+--..  
T Consensus       101 rNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edG  180 (440)
T KOG1464|consen  101 RNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDG  180 (440)
T ss_pred             ccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccC
Confidence             234556777777777677776666666654331     111112233567888899999999999988886542111  


Q ss_pred             ---------CcchHHHHHHHHHhCCCHHHHHHHHHHhcccC-CCchHHHHHHHHHH-----HHhCCChHHHHHHH
Q 042039          225 ---------DTSTYNTFIDGLCKNGYIVEAVELFRTLGILK-CELDIQAYNCLIDG-----LCKSGRLEIALELF  284 (376)
Q Consensus       225 ---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~-----~~~~~~~~~a~~~~  284 (376)
                               -...|..=++.|....+-.+...++++..... .-|.+... .+++-     ..+.|++++|..-|
T Consensus       181 edD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlIm-GvIRECGGKMHlreg~fe~AhTDF  254 (440)
T KOG1464|consen  181 EDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIM-GVIRECGGKMHLREGEFEKAHTDF  254 (440)
T ss_pred             chhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHHH-hHHHHcCCccccccchHHHHHhHH
Confidence                     12356666778888888777788888765432 23444433 33333     35678888876543

>PRK10941 hypothetical protein; Provisional

Probab=83.47  E-value=22  Score=28.70  Aligned_cols=76  Identities=11%  Similarity=-0.037  Sum_probs=52.7

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcC-CCCChhhHHHHHHH
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD-VRPNAFTYSTLMDG  130 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~  130 (376)
                      .+.+-.+|.+.++++.|+.+.+.+....+. ++.-+..-.-.|.+.|.+..|..-++..++.. -.|+.......+..
T Consensus       184 l~nLK~~~~~~~~~~~AL~~~e~ll~l~P~-dp~e~RDRGll~~qL~c~~~A~~DL~~fl~~~P~dp~a~~ik~ql~~  260 (269)
T PRK10941        184 LDTLKAALMEEKQMELALRASEALLQFDPE-DPYEIRDRGLIYAQLDCEHVALSDLSYFVEQCPEDPISEMIRAQIHS  260 (269)
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCcHHHHHHHHHHHHhCCCchhHHHHHHHHHH
Confidence            455667788888999999988888886433 55666667777888888888888888887653 22334444444433

>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane

Probab=83.35  E-value=5.7  Score=24.68  Aligned_cols=46  Identities=11%  Similarity=0.164  Sum_probs=26.6

Q ss_pred             ccCChhHHHHHHHHHHHcCCCCc--HHHHHHHHHHHhhcCChhhHHHH
Q 042039          308 NDGQMDKAHDLFLDMEENAVAPN--VIIFVTLIHGFVRINKPSKVIEL  353 (376)
Q Consensus       308 ~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~  353 (376)
                      ...+.++|+..|..+++....+.  -.++..++.+|...|++.++++.
T Consensus        18 ~~~~~~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~~L~f   65 (80)
T PF10579_consen   18 HQNETQQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYREMLAF   65 (80)
T ss_pred             ccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55566667777766665432222  23455556667777777666554

Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=83.10  E-value=23  Score=28.66  Aligned_cols=185  Identities=9%  Similarity=0.071  Sum_probs=110.6

Q ss_pred             CCChhhHHHHHHHHHhc----CC---hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHh-cCCCC
Q 042039           13 KPNTVTYNTIIDGLCKE----GF---VDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMD-QGVQP   84 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~----g~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~   84 (376)
                      .|....+..++.-|...    |.   -++-+..++-....-......-|..|+.   ......+|+++|+..-. ..+--
T Consensus        86 ~p~~y~~~~~~~DYf~lK~s~g~~Lt~~Dli~FL~~~i~~~~~~k~~~Y~~LVk---~N~~Vv~aL~L~~~~~~~~~Ii~  162 (292)
T PF13929_consen   86 DPQNYSVRRFINDYFLLKKSMGCELTKEDLISFLKLVIINLSSNKSFNYWDLVK---RNKIVVEALKLYDGLNPDESIIF  162 (292)
T ss_pred             CcccCCHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhccccccchHHHHHHH---hhHHHHHHHHHhhccCcccceee
Confidence            45555555555544432    21   1334444444333211111122555442   23456778888873221 22444


Q ss_pred             chHhHHHHHHHHHh-CC-ChHHHHHHHHHHHh-cCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc-CCCCChhhHH
Q 042039           85 SVVTFNVIMDELCK-NG-KMDEASRLLDLMVQ-RDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM-GCKHDDVSYN  160 (376)
Q Consensus        85 ~~~~~~~l~~~~~~-~~-~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~  160 (376)
                      |..+...+++.... .+ ....-.++.+-+.. .+..++..+...++..++..+++..-.++++..... +...|...|.
T Consensus       163 d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~  242 (292)
T PF13929_consen  163 DEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWA  242 (292)
T ss_pred             ChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHH
Confidence            77788888887766 22 22222233333332 234667788889999999999999999999988765 4567888999


Q ss_pred             HHHHHHHccCcHHHHHHHHHHH-----HHCCCCCCHhHHHHHHHH
Q 042039          161 ILINGYCKNKEVEEALSLYREM-----VSKGIKPTVVTYNTLFLG  200 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~-----~~~~~~~~~~~~~~l~~~  200 (376)
                      .++..-...|+..-..++.++-     .+.++..+...-..+-+.
T Consensus       243 ~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~L~~~L~~L  287 (292)
T PF13929_consen  243 EFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDELRSQLSEL  287 (292)
T ss_pred             HHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHHHHHHHHHH
Confidence            9999999999988777777642     334555555554444443

>PF09670 Cas_Cas02710: CRISPR-associated protein (Cas_Cas02710)

Probab=82.89  E-value=17  Score=31.09  Aligned_cols=57  Identities=14%  Similarity=0.112  Sum_probs=39.7

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCCChh--hHHHHHHHHhcC--CChHHHHHHHHHHHhc
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINPDVV--TYNSLIHGLCHA--NDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~--~~~~~a~~~~~~~~~~   80 (376)
                      +..+.+.+++..|.++++.+... ++++..  .+..+..+|...  -++.+|.+.++.....
T Consensus       138 a~~l~n~~~y~aA~~~l~~l~~r-l~~~~~~~~~~~l~~~y~~WD~fd~~~A~~~l~~~~~~  198 (379)
T PF09670_consen  138 AKELFNRYDYGAAARILEELLRR-LPGREEYQRYKDLCEGYDAWDRFDHKEALEYLEKLLKR  198 (379)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHh-CCchhhHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            34456888999999999998876 555544  455555555544  4677888888887654

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

Probab=82.72  E-value=5.5  Score=23.50  Aligned_cols=30  Identities=13%  Similarity=0.384  Sum_probs=18.9

Q ss_pred             cHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          330 NVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       330 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      |..-.-.++.+|.+.|++++|.++++++.+
T Consensus        22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~~   51 (62)
T PF14689_consen   22 DFLNHLQVIYGLLQLGKYEEAKEYIKELSK   51 (62)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            444445566777777777777777777653

>COG4259 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.70  E-value=11  Score=24.62  Aligned_cols=59  Identities=10%  Similarity=0.032  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHH
Q 042039          137 INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTL  197 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  197 (376)
                      ....++.++++...+....+.....|.-.|.+.|+.+.|.+-|+.-..  .-|.+.+|...
T Consensus        53 ~~~le~~~ek~~ak~~~vpPG~HAhLGlLys~~G~~e~a~~eFetEKa--lFPES~~fmDF  111 (121)
T COG4259          53 TAALEKYLEKIGAKNGAVPPGYHAHLGLLYSNSGKDEQAVREFETEKA--LFPESGVFMDF  111 (121)
T ss_pred             HHHHHHHHHHHhhcCCCCCCcHHHHHHHHHhhcCChHHHHHHHHHhhh--hCccchhHHHH
Confidence            344455666666666555556666777778888888888887776554  34555555433

>KOG3364 consensus Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis]

Probab=82.22  E-value=15  Score=25.82  Aligned_cols=68  Identities=12%  Similarity=0.052  Sum_probs=40.7

Q ss_pred             CchHHHHHHHHHHHHhCCC---hHHHHHHHhcccccC-CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          258 ELDIQAYNCLIDGLCKSGR---LEIALELFRSLPRRV-LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       258 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      .++..+-..+..++.+..+   ..+.+.+++.+.+.. ..........+.-++.+.+++++++++.+.+.+.
T Consensus        29 ~~s~~s~f~lAwaLV~S~~~~dv~~GI~iLe~l~~~~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~  100 (149)
T KOG3364|consen   29 DVSKQSQFNLAWALVRSRDTEDVQEGIVILEDLLKSAHPERRRECLYYLAVGHYRLKEYSKSLRYVDALLET  100 (149)
T ss_pred             cchHHHHHHHHHHHHcccchHHHHHhHHHHHHHhhhcCcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhh
Confidence            4455666666777766554   445556666666421 1122334455666777777777777777777664

>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function

Probab=82.21  E-value=24  Score=28.33  Aligned_cols=28  Identities=25%  Similarity=0.112  Sum_probs=18.1

Q ss_pred             chHHHHHHHHHHHHhCCChHHHHHHHhc
Q 042039          259 LDIQAYNCLIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~  286 (376)
                      .++.....++..|.+.|++.+|...|-.
T Consensus        88 Gdp~LH~~~a~~~~~e~~~~~A~~Hfl~  115 (260)
T PF04190_consen   88 GDPELHHLLAEKLWKEGNYYEAERHFLL  115 (260)
T ss_dssp             --HHHHHHHHHHHHHTT-HHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHhhccHHHHHHHHHh
Confidence            3667777777777777777777766643

; PDB: 3LKU_E 2WPV_G.

>KOG3364 consensus Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis]

Probab=82.16  E-value=15  Score=25.80  Aligned_cols=67  Identities=9%  Similarity=0.100  Sum_probs=32.5

Q ss_pred             CChhhHHHHHHHHhcCC---ChHHHHHHHHHHHhc-CCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           49 PDVVTYNSLIHGLCHAN---DWNEAKRLFFEMMDQ-GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        49 ~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      ++..+-..+..++.+..   +..+.+.+++.+.+. ...........+.-++.+.++++++.++.+.+++.
T Consensus        30 ~s~~s~f~lAwaLV~S~~~~dv~~GI~iLe~l~~~~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~  100 (149)
T KOG3364|consen   30 VSKQSQFNLAWALVRSRDTEDVQEGIVILEDLLKSAHPERRRECLYYLAVGHYRLKEYSKSLRYVDALLET  100 (149)
T ss_pred             chHHHHHHHHHHHHcccchHHHHHhHHHHHHHhhhcCcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhh
Confidence            34444445555555443   334455555555541 11112233334444555666666666666666554

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=82.09  E-value=25  Score=28.31  Aligned_cols=21  Identities=14%  Similarity=0.031  Sum_probs=10.6

Q ss_pred             HHHhcCCChHHHHHHHHHHHh
Q 042039           59 HGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      ..+.-..||..|++..++..+
T Consensus        43 d~LvV~rdF~aal~tCerglq   63 (309)
T PF07163_consen   43 DLLVVHRDFQAALETCERGLQ   63 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555443

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

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=80.86  E-value=34  Score=29.17  Aligned_cols=62  Identities=8%  Similarity=0.003  Sum_probs=35.0

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhc--CCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHh
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQ--GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQ  114 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  114 (376)
                      .+.-+...|...|+++.|++.|-+.+..  ..+..+..|..++......|+|.....+..+..+
T Consensus       152 a~~Dl~dhy~~cG~l~~Alr~YsR~RdYCTs~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~s  215 (466)
T KOG0686|consen  152 ALEDLGDHYLDCGQLDNALRCYSRARDYCTSAKHVINMCLNLILVSIYMGNWGHVLSYISKAES  215 (466)
T ss_pred             HHHHHHHHHHHhccHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHh
Confidence            4555666666677777777776664432  1112334455556666666666666555555544

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.71  E-value=25  Score=27.48  Aligned_cols=54  Identities=7%  Similarity=0.180  Sum_probs=30.2

Q ss_pred             CcHHHHHHHHHHHHhc--C---CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCC
Q 042039          135 GKINRAEELFGSMESM--G---CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK  188 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~--~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  188 (376)
                      .+++.|+..|+..-+.  +   .......+..+...-...+++.+|+++|++.....+.
T Consensus       128 ~d~ekaI~~YE~Aae~yk~ees~ssANKC~lKvA~yaa~leqY~~Ai~iyeqva~~s~~  186 (288)
T KOG1586|consen  128 QDFEKAIAHYEQAAEYYKGEESVSSANKCLLKVAQYAAQLEQYSKAIDIYEQVARSSLD  186 (288)
T ss_pred             HHHHHHHHHHHHHHHHHcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4556666666655332  1   0111223444455556677888888888887765433

>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]

Probab=80.20  E-value=25  Score=27.68  Aligned_cols=62  Identities=15%  Similarity=-0.025  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          263 AYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       263 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      .+.....++...|++-++++.-.++++. .+.|...|..-+.+.+..=+.++|..-|..+++.
T Consensus       232 LllNy~QC~L~~~e~yevleh~seiL~~-~~~nvKA~frRakAhaa~Wn~~eA~~D~~~vL~l  293 (329)
T KOG0545|consen  232 LLLNYCQCLLKKEEYYEVLEHCSEILRH-HPGNVKAYFRRAKAHAAVWNEAEAKADLQKVLEL  293 (329)
T ss_pred             HHHhHHHHHhhHHHHHHHHHHHHHHHhc-CCchHHHHHHHHHHHHhhcCHHHHHHHHHHHHhc
Confidence            3445556667778888888888887776 5667888888888888888888888888888875

>KOG1308 consensus Hsp70-interacting protein Hip/Transient component of progesterone receptor complexes and an Hsp70-binding protein [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=80.19  E-value=1.8  Score=35.31  Aligned_cols=119  Identities=13%  Similarity=-0.027  Sum_probs=80.7

Q ss_pred             HHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC-HHHHHHHHHHHHccCChhH
Q 042039          236 LCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD-VVTYNIMIHGLCNDGQMDK  314 (376)
Q Consensus       236 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~  314 (376)
                      ....|.++.|++.+...+..+ ++....|..-..++.+.+++..|++=+......  .|| ..-|-.-..+-.-.|++.+
T Consensus       124 Aln~G~~~~ai~~~t~ai~ln-p~~a~l~~kr~sv~lkl~kp~~airD~d~A~ei--n~Dsa~~ykfrg~A~rllg~~e~  200 (377)
T KOG1308|consen  124 ALNDGEFDTAIELFTSAIELN-PPLAILYAKRASVFLKLKKPNAAIRDCDFAIEI--NPDSAKGYKFRGYAERLLGNWEE  200 (377)
T ss_pred             HhcCcchhhhhcccccccccC-CchhhhcccccceeeeccCCchhhhhhhhhhcc--CcccccccchhhHHHHHhhchHH
Confidence            456788999999998888776 446677777788888888888888888777764  333 3344444555666788999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          315 AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       315 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      |...++.+.+.+..+....|..  ...-..+..++-...+++.++
T Consensus       201 aa~dl~~a~kld~dE~~~a~lK--eV~p~a~ki~e~~~k~er~~~  243 (377)
T KOG1308|consen  201 AAHDLALACKLDYDEANSATLK--EVFPNAGKIEEHRRKYERARE  243 (377)
T ss_pred             HHHHHHHHHhccccHHHHHHHH--HhccchhhhhhchhHHHHHHH
Confidence            9999998888776655544433  333444555555555555443

>KOG0376 consensus Serine-threonine phosphatase 2A, catalytic subunit [General function prediction only]

Probab=80.14  E-value=5.9  Score=34.18  Aligned_cols=106  Identities=10%  Similarity=0.061  Sum_probs=74.7

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCC
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG  100 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  100 (376)
                      .-+..+.+.+.++.|+.++.++++.+ +..+..|..-..++.+.+++..|+.=+.++++..+. -...|..-..++.+.+
T Consensus         9 ~ean~~l~~~~fd~avdlysKaI~ld-pnca~~~anRa~a~lK~e~~~~Al~Da~kaie~dP~-~~K~Y~rrg~a~m~l~   86 (476)
T KOG0376|consen    9 NEANEALKDKVFDVAVDLYSKAIELD-PNCAIYFANRALAHLKVESFGGALHDALKAIELDPT-YIKAYVRRGTAVMALG   86 (476)
T ss_pred             hHHhhhcccchHHHHHHHHHHHHhcC-CcceeeechhhhhheeechhhhHHHHHHhhhhcCch-hhheeeeccHHHHhHH
Confidence            34556677888999999999998875 445556666668888999999998888888876422 3345555556677777


Q ss_pred             ChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039          101 KMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus       101 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      .+.+|...|+.....  .|+..-....+.-
T Consensus        87 ~~~~A~~~l~~~~~l--~Pnd~~~~r~~~E  114 (476)
T KOG0376|consen   87 EFKKALLDLEKVKKL--APNDPDATRKIDE  114 (476)
T ss_pred             HHHHHHHHHHHhhhc--CcCcHHHHHHHHH
Confidence            888888888887764  5665444444443

>PF12862 Apc5: Anaphase-promoting complex subunit 5

Probab=80.06  E-value=12  Score=24.25  Aligned_cols=54  Identities=13%  Similarity=0.011  Sum_probs=29.7

Q ss_pred             HHhcCChhHHHHHHHHhh----hCCCCC----ChhhHHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           26 LCKEGFVDKAKALFLQMK----GENINP----DVVTYNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~----~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      ..+.|++.+|.+.+.+.-    ..+...    -..+...+...+...|++++|.+.+++.++
T Consensus         8 ~~~~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~   69 (94)
T PF12862_consen    8 ALRSGDYSEALDALHRYFDYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIR   69 (94)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            446778887765555443    222111    022333445556666777777777766654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	376
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-19
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-19
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-17
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	5e-15
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	5e-08
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
3v6t_A	499	DHAX3; tandem repeats, DNA specific binding protei	6e-06
3v6t_A	499	DHAX3; tandem repeats, DNA specific binding protei	3e-05
3v6t_A	499	DHAX3; tandem repeats, DNA specific binding protei	6e-04
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	3e-05
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	3e-04
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	8e-05
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	1e-04
3ugm_A	1047	TAL effector avrbs3/PTHA; TAL effector; 3.00A {Xan	1e-04
3ugm_A	1047	TAL effector avrbs3/PTHA; TAL effector; 3.00A {Xan	1e-04
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	3e-04

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 89.9 bits (221), Expect = 1e-19
 Identities = 23/211 (10%), Positives = 61/211 (28%), Gaps = 5/211 (2%)

Query: 13  KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENIN---PDVVTYNSLIHGLCHANDWNE 69
                              +  A  L +   G+        +  YN+++ G      + E
Sbjct: 124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKE 183

Query: 70  AKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEA-SRLLDLMVQRDVRPNAFTYSTLM 128
              + F + D G+ P ++++   +  + +  +      R L+ M Q  ++  A   + L+
Sbjct: 184 LVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLL 243

Query: 129 DGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK 188
                   +    ++  +          V+ + L+              L+   +     
Sbjct: 244 SEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLH-LPLKTLQC 302

Query: 189 PTVVTYNTLFLGLFEIHQVEHALKLFEEMQR 219
                 +        +  VE      +E++ 
Sbjct: 303 LFEKQLHMELASRVCVVSVEKPTLPSKEVKH 333

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 88.3 bits (217), Expect = 4e-19
 Identities = 27/232 (11%), Positives = 62/232 (26%), Gaps = 4/232 (1%)

Query: 35  AKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD 94
           A  L    +    +P       L+         +  +    +     +            
Sbjct: 76  AGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFK 135

Query: 95  ELCKNGKMDEASRLLDL---MVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG 151
                 ++  A  LL +     Q+        Y+ +M G+   G       +   ++  G
Sbjct: 136 CCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAG 195

Query: 152 CKHDDVSYNILINGYCKNKEVEEALSLY-REMVSKGIKPTVVTYNTLFLGLFEIHQVEHA 210
              D +SY   +    +  +    +     +M  +G+K   +    L         ++  
Sbjct: 196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV 255

Query: 211 LKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQ 262
            K+                +  +  +      V   +L   L  L+C  + Q
Sbjct: 256 HKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQ 307

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 84.1 bits (206), Expect = 1e-17
 Identities = 31/224 (13%), Positives = 78/224 (34%), Gaps = 9/224 (4%)

Query: 14  PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEA-KR 72
                YN ++ G  ++G   +   +   +K   + PD+++Y + +  +   +      +R
Sbjct: 163 LTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIER 222

Query: 73  LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC 132
              +M  +G++   +   V++ E  +   +    ++          P     S L+    
Sbjct: 223 CLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVY 282

Query: 133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV 192
                    +L   ++++ C  +    ++ +        VE+       + SK +K    
Sbjct: 283 AKDGRVSYPKLHLPLKTLQCLFEK-QLHMELASRVCVVSVEK-----PTLPSKEVKHARK 336

Query: 193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGL 236
           T  TL     +   +  AL+  +     +V     +   F+  L
Sbjct: 337 TLKTLRDQWEK--ALCRALRETKNRLEREVYEGRFSLYPFLCLL 378

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 75.6 bits (184), Expect = 5e-15
 Identities = 18/194 (9%), Positives = 56/194 (28%), Gaps = 1/194 (0%)

Query: 173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTF 232
           +     + +    G +  ++ +    L   ++    H L +    ++         YN  
Sbjct: 112 QAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAV 171

Query: 233 IDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGR-LEIALELFRSLPRRV 291
           + G  + G   E V +   +       D+ +Y   +  + +  +           + +  
Sbjct: 172 MLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEG 231

Query: 292 LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVI 351
           L    +   +++        +   H +          P  +    L+      +      
Sbjct: 232 LKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYP 291

Query: 352 ELLHKMKEKKVMPD 365
           +L   +K  + + +
Sbjct: 292 KLHLPLKTLQCLFE 305

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 54.1 bits (128), Expect = 5e-08
 Identities = 12/97 (12%), Positives = 31/97 (31%), Gaps = 3/97 (3%)

Query: 273 KSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFL---DMEENAVAP 329
               L++         +  L                  Q+  AH L +      +     
Sbjct: 104 GKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLL 163

Query: 330 NVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA 366
            + ++  ++ G+ R     +++ +L  +K+  + PD 
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDL 200

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 45.6 bits (106), Expect = 2e-05
 Identities = 10/110 (9%), Positives = 30/110 (27%), Gaps = 1/110 (0%)

Query: 12  CKPNTVTYNTIIDGLCKEG-FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEA 70
             P+ ++Y   +  + ++       +    QM  E +    +    L+     A      
Sbjct: 196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV 255

Query: 71  KRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN 120
            ++          P  V  + ++ ++          +L   +        
Sbjct: 256 HKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFE 305

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 64.5 bits (156), Expect = 2e-11
 Identities = 65/431 (15%), Positives = 135/431 (31%), Gaps = 120/431 (27%)

Query: 12  CK-----PNTVTYNTIIDGLCKEG-FVDKAKALF--LQMKGENINPDVVTYNSLIHGLCH 63
           CK     P ++     ID +      V     LF  L  K E +          +  +  
Sbjct: 35  CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM------VQKFVEEVLR 88

Query: 64  AN-DWNEAKRLFFEMMDQGVQPSVVT--FNVIMDELCKNGKM---DEASRLLDLMVQRD- 116
            N  +     L   +  +  QPS++T  +    D L  + ++      SRL   +  R  
Sbjct: 89  INYKF-----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA 143

Query: 117 ---VRPNAFTYSTL--MDGF---CLTGKINRAEELFGSMESMGCKHDDVSYNIL-IN-GY 166
              +RP       +  + G     +   +  + ++   M+          + I  +N   
Sbjct: 144 LLELRPA--KNVLIDGVLGSGKTWVALDVCLSYKVQCKMD----------FKIFWLNLKN 191

Query: 167 CKNKE--VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALK-LFEEMQR---- 219
           C + E  +E    L  ++       +  + N        IH ++  L+ L +        
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL----RIHSIQAELRRLLKSKPYENCL 247

Query: 220 ---DDVAADTSTYNTFIDGLCK------NGYIVEAVELFRT---------LGILKCE-LD 260
               +V  +   +N F +  CK         + + +    T         + +   E   
Sbjct: 248 LVLLNVQ-NAKAWNAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305

Query: 261 IQA--YNCLIDGL----CKSGRLEIAL--ELFRSLPRRVLVADVVTYNIMIHGLCNDGQM 312
           +     +C    L      +    +++  E  R             ++   H  C+  ++
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT--------WDNWKHVNCD--KL 355

Query: 313 DKAHDLFLDMEENAVAPNVI--IFVTL-IHGF---VRINKPSKVIELL-HKMKEKKVMPD 365
               +  L++ E    P     +F  L +  F     I  P+ ++ L+   + +  VM  
Sbjct: 356 TTIIESSLNVLE----PAEYRKMFDRLSV--FPPSAHI--PTILLSLIWFDVIKSDVM-- 405

Query: 366 ASIVSMVVDLL 376
                +VV+ L
Sbjct: 406 -----VVVNKL 411

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 58.3 bits (140), Expect = 2e-09
 Identities = 51/364 (14%), Positives = 114/364 (31%), Gaps = 74/364 (20%)

Query: 1   MANGNGEIGVVCKPNTVT----YNTIIDGLCKEGFVDKAKALFLQ-MKG----------- 44
           + N N     V     V+    Y  +   L +   +  AK + +  + G           
Sbjct: 119 LYNDN----QVFAKYNVSRLQPYLKLRQALLE---LRPAKNVLIDGVLGSGKTWVALDVC 171

Query: 45  -----ENINPDVVTYNSLIHGLCHANDW--NEAKRLFFEMMDQGVQPSVVTFNVIMDELC 97
                +      + + +L    C++ +      ++L +++       S  + N+ +    
Sbjct: 172 LSYKVQCKMDFKIFWLNL--KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR--- 226

Query: 98  KNGKMDEASRLL-------DLMVQRDVRP----NAFTYSTLMDGFCLTGKINRAEELFGS 146
            +    E  RLL        L+V  +V+     NAF      +  C      R +++   
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF------NLSCKILLTTRFKQVTDF 280

Query: 147 MESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLF--EI 204
           + +    H  +S +          EV+  L  Y +   + +   V+T N   L +    I
Sbjct: 281 LSAATTTH--ISLDHHSMTLTP-DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337

Query: 205 HQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDI--Q 262
                    ++ +  D +   T+   + ++ L       E  ++F  L +      I   
Sbjct: 338 RDGLATWDNWKHVNCDKL---TTIIESSLNVLEPA----EYRKMFDRLSVFPPSAHIPTI 390

Query: 263 AYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGL-----CNDGQMDKAHD 317
             + +   + KS  + +  +L +     ++        I I  +              H 
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHK---YSLVEKQPKESTISIPSIYLELKVKLENEYALHR 447

Query: 318 LFLD 321
             +D
Sbjct: 448 SIVD 451

>3v6t_A DHAX3; tandem repeats, DNA specific binding protein, DNA binding DNA complex; HET: DNA; 1.85A {Xanthomonas} PDB: 3v6p_A 2kq5_A Length = 499

 Score = 47.1 bits (112), Expect = 6e-06
 Identities = 21/168 (12%), Positives = 46/168 (27%), Gaps = 18/168 (10%)

Query: 155 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHALKL 213
             V+      G    + V+  L +  +  + G+ P  VV   +   G   +  V+  L +
Sbjct: 105 QVVAIASHDGGKQALETVQRLLPVLCQ--AHGLTPEQVVAIASHDGGKQALETVQALLPV 162

Query: 214 FE---EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG 270
                 +  + V A      +   G      +   + +      L  +  + A      G
Sbjct: 163 LCQAHGLTPEQVVA----IASNGGGKQALETVQRLLPVLCQAHGLTPQ-QVVAIASNGGG 217

Query: 271 LCKSGRLEIALELFRSLPRRVLV---ADVVTYNIMIHGLCNDGQMDKA 315
                 ++  L +      +        VV       G      + + 
Sbjct: 218 KQALETVQRLLPVL----CQAHGLTPQQVVAIASNGGGKQALETVQRL 261

>3v6t_A DHAX3; tandem repeats, DNA specific binding protein, DNA binding DNA complex; HET: DNA; 1.85A {Xanthomonas} PDB: 3v6p_A 2kq5_A Length = 499

 Score = 44.7 bits (106), Expect = 3e-05
 Identities = 40/315 (12%), Positives = 80/315 (25%), Gaps = 31/315 (9%)

Query: 13  KPNTV-TYNTIIDGLCKEGFVDKAKALFLQMKGENINPD-VVTYNSLIHGLCHANDWNEA 70
            P  V    +   G      V +   +  Q  G  + P+ VV   S   G          
Sbjct: 102 TPQQVVAIASHDGGKQALETVQRLLPVLCQAHG--LTPEQVVAIASHDGGKQALETVQAL 159

Query: 71  KRLFFEMMDQGVQPSVVTFNVIMDELCKN-GKMDEASRLLDLMVQRDVRPN-AFTYSTLM 128
             +  +    G+ P  V          +    +     +L         P      ++  
Sbjct: 160 LPVLCQ--AHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLT--PQQVVAIASNG 215

Query: 129 DGFCLTGKINRAEELFGSMESMGCKHDDV-SYNILINGYCKNKEVEEALSLYREMVSKGI 187
            G      + R   +    ++ G     V +      G    + V+  L +  +    G+
Sbjct: 216 GGKQALETVQRLLPVLC--QAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAH--GL 271

Query: 188 KPT-VVTYNTLFLGLFEIHQVEHALKLFE---EMQRDDVAADTSTYNTFIDGLCKNGYIV 243
            P  VV   +   G   +  V+  L +      +    V A      +   G      + 
Sbjct: 272 TPQQVVAIASNSGGKQALETVQRLLPVLCQAHGLTPQQVVA----IASNGGGKQALETVQ 327

Query: 244 EAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLV---ADVVTYN 300
             + +      L  +  + A      G      ++  L +      +        VV   
Sbjct: 328 RLLPVLCQAHGLTPQ-QVVAIASHDGGKQALETVQRLLPVL----CQAHGLTPEQVVAIA 382

Query: 301 IMIHGLCNDGQMDKA 315
               G      + + 
Sbjct: 383 SNGGGKQALETVQRL 397

>3v6t_A DHAX3; tandem repeats, DNA specific binding protein, DNA binding DNA complex; HET: DNA; 1.85A {Xanthomonas} PDB: 3v6p_A 2kq5_A Length = 499

 Score = 40.9 bits (96), Expect = 6e-04
 Identities = 22/173 (12%), Positives = 44/173 (25%), Gaps = 18/173 (10%)

Query: 154 HDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHALK 212
              V+      G    + V+  L +  +    G+ P  VV   +   G   +  V+  L 
Sbjct: 308 QQVVAIASNGGGKQALETVQRLLPVLCQAH--GLTPQQVVAIASHDGGKQALETVQRLLP 365

Query: 213 LFE---EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLID 269
           +      +  + V A      +   G      +   + +      L  E  + A      
Sbjct: 366 VLCQAHGLTPEQVVA----IASNGGGKQALETVQRLLPVLCQAHGLTPE-QVVAIASHDG 420

Query: 270 GLCKSGRLEIALELFRSLPRRVLV---ADVVTYNIMIHGLCNDGQMDKAHDLF 319
           G      ++  L +      +        VV       G      +       
Sbjct: 421 GKQALETVQRLLPVL----CQAHGLTPQQVVAIASNGGGRPALESIVAQLSRP 469

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe} Length = 597

 Score = 44.8 bits (106), Expect = 3e-05
 Identities = 47/290 (16%), Positives = 87/290 (30%), Gaps = 37/290 (12%)

Query: 37  ALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL 96
           A F+  K  +I  +      L    C   D+  AK L  +        S     +    L
Sbjct: 103 AAFVGEKVLDITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDL--YNRSSACRYLAAFCL 160

Query: 97  CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDD 156
            K      A     L +  +  P                    A +L   M+  G K + 
Sbjct: 161 VKLYDWQGA-----LNLLGETNP-------------FRKDEKNANKLL--MQDGGIKLEA 200

Query: 157 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLG--LFEIHQVEHALKL 213
               +    Y      + A   Y+E +   +       ++ L     L    + +  LKL
Sbjct: 201 SMCYLRGQVYTNLSNFDRAKECYKEALM--VDAKCYEAFDQLVSNHLLTADEEWDLVLKL 258

Query: 214 -FEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLC 272
            +    ++D A   S Y   ++       +  A +   ++  L+         C  D L 
Sbjct: 259 NYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLE--KSSDLLLCKADTLF 316

Query: 273 KSGRLEIALELFRSLPRRVLVAD---VVTYNIMIHGLCNDGQMDKAHDLF 319
              R    L +      ++L  D   +  Y + +  L   G+ +K + + 
Sbjct: 317 VRSRFIDVLAIT----TKILEIDPYNLDVYPLHLASLHESGEKNKLYLIS 362

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe} Length = 597

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 39/342 (11%), Positives = 98/342 (28%), Gaps = 60/342 (17%)

Query: 26  LCKEGFVDKAKALFLQMKGENINPD-VVTYNSLIHGLCHAND--WNEAKRLFFEMMDQGV 82
                  D+AK  +   +   ++      ++ L+       D  W+   +L +    +  
Sbjct: 210 YTNLSNFDRAKECY--KEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKED 267

Query: 83  QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEE 142
              + +  ++      +      +      +      ++       D   +  +      
Sbjct: 268 AAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL-EKSSDLLLCKADTLFVRSRFIDVLA 326

Query: 143 LFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGL 201
           +   +  +   + DV Y + +    ++ E  +   +  ++V     P   VT+  + +  
Sbjct: 327 ITTKILEIDPYNLDV-YPLHLASLHESGEKNKLYLISNDLVD--RHPEKAVTWLAVGIYY 383

Query: 202 FEIHQVEHALKLFE---EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRT------- 251
             ++++  A + F     M      A    +  F       G   +A+  + T       
Sbjct: 384 LCVNKISEARRYFSKSSTMDPQFGPA----WIGFAHSFAIEGEHDQAISAYTTAARLFQG 439

Query: 252 -------LGILKCEL-------------------DIQAYNCLIDGLC--KSGRLEIALEL 283
                  LG+   +L                   D    N L  G+       ++ A+  
Sbjct: 440 THLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNEL--GVVAFNKSDMQTAINH 497

Query: 284 FR---SLPRRVLVAD---VVTYNIMIHGLCNDGQMDKAHDLF 319
           F+    L ++    +     T+  + H        D A D  
Sbjct: 498 FQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDAL 539

>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 Length = 537

 Score = 43.6 bits (103), Expect = 8e-05
 Identities = 41/293 (13%), Positives = 89/293 (30%), Gaps = 34/293 (11%)

Query: 15  NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD-VVTYNSLIHGLCHANDWNEAKRL 73
            T     + + L  +        L      + +  +  +            N+  +A+ L
Sbjct: 206 ATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVL 265

Query: 74  FFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFC 132
             E ++  + P+  ++  +   L       E  +     V  +  P    TY      + 
Sbjct: 266 LQESIN--LHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN--PEYPPTYYHRGQMYF 321

Query: 133 LTGKINRAEELFGSMESMGCKHDDV-SYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 191
           +      A+E F   ++     ++V  Y  L     K  +  E+ + + E       PT+
Sbjct: 322 ILQDYKNAKEDF--QKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKL--KFPTL 377

Query: 192 V-TYNTLFLGLFEIHQVEHALKLFE---EMQRDDVAA------------DTSTYNTFIDG 235
                     L +    + A+K ++    ++                    +  ++    
Sbjct: 378 PEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPT 437

Query: 236 LCKNGYIVEAVELFRTLGILKCELD---IQAYNCLIDGLCKSGRLEIALELFR 285
                    A++L        CELD    QA   L     +  +++ A+ELF 
Sbjct: 438 QLDEEKFNAAIKLLTKA----CELDPRSEQAKIGLAQLKLQMEKIDEAIELFE 486

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus} Length = 291

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 29/208 (13%), Positives = 64/208 (30%), Gaps = 10/208 (4%)

Query: 45  ENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE-LCKNGKMD 103
            +  P++         L   +  +         M + V  +  TF ++       +   D
Sbjct: 59  PSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPD 118

Query: 104 EASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNI-L 162
            A R L       +   A T   L+       +++ A +    M+               
Sbjct: 119 AALRTLH--QGDSLECMAMTVQILL----KLDRLDLARKELKKMQDQDEDATLTQLATAW 172

Query: 163 INGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDV 222
           ++     +++++A  +++EM  K   PT++  N          + E A  + +E    D 
Sbjct: 173 VSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD- 230

Query: 223 AADTSTYNTFIDGLCKNGYIVEAVELFR 250
           +    T    +      G   E    + 
Sbjct: 231 SGHPETLINLVVLSQHLGKPPEVTNRYL 258

>3ugm_A TAL effector avrbs3/PTHA; TAL effector; 3.00A {Xanthomonas oryzae} Length = 1047

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 21/171 (12%), Positives = 46/171 (26%), Gaps = 19/171 (11%)

Query: 153 KHDDV-SYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHA 210
               V +      G    + ++  L +  +  + G+ P  VV   +   G   +  V+  
Sbjct: 222 TPAQVVAIASHDGGKQALETMQRLLPVLCQ--AHGLPPDQVVAIASNIGGKQALETVQRL 279

Query: 211 LKLFE---EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCL 267
           L +      +  D V A      +   G      +   + +      L  +  + A    
Sbjct: 280 LPVLCQAHGLTPDQVVA----IASHGGGKQALETVQRLLPVLCQAHGLTPD-QVVAIASH 334

Query: 268 IDGLCKSGRLEIALELFRSLPRRVLV---ADVVTYNIMIHGLCNDGQMDKA 315
             G      ++  L +      +        VV       G      + + 
Sbjct: 335 DGGKQALETVQRLLPVL----CQAHGLTPDQVVAIASNGGGKQALETVQRL 381

>3ugm_A TAL effector avrbs3/PTHA; TAL effector; 3.00A {Xanthomonas oryzae} Length = 1047

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 17/135 (12%), Positives = 38/135 (28%), Gaps = 11/135 (8%)

Query: 155 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGLFEIHQVEHALKL 213
             V+      G    + V+  L +  +  + G+    VV   +   G   +  V+  L +
Sbjct: 564 QVVAIASNGGGKQALETVQRLLPVLCQ--AHGLTQVQVVAIASNIGGKQALETVQRLLPV 621

Query: 214 FE---EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG 270
                 +    V A      +   G      +   + +      L  +  + A      G
Sbjct: 622 LCQAHGLTPAQVVA----IASHDGGKQALETVQRLLPVLCQAHGLTPD-QVVAIASNGGG 676

Query: 271 LCKSGRLEIALELFR 285
                 ++  L +  
Sbjct: 677 KQALETVQRLLPVLC 691

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens} Length = 311

 Score = 41.0 bits (97), Expect = 3e-04
 Identities = 37/197 (18%), Positives = 65/197 (32%), Gaps = 30/197 (15%)

Query: 14  PNT-VTYNTIIDGLCKEGFVDKAKALF---LQMK----GENINPDV-VTYNSLIHGLCHA 64
           P    T N +     K G   +A+ L    L+++    G++ +PDV    N+L     + 
Sbjct: 108 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKD-HPDVAKQLNNLALLCQNQ 166

Query: 65  NDWNEAKRLF---FEMMDQ--GVQ-PSV-VTFNVIMDELCKNGKMDEASRL----LDLMV 113
             + E +  +    E+     G   P+V  T N +     K GK  +A  L    L    
Sbjct: 167 GKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAH 226

Query: 114 QRDVRPN----AFTYSTLMDGFCLTGKINRAEELF---GSMESMGCKHDDV--SYNILIN 164
           +R+           +    +     GK           G  ++       V  +   L  
Sbjct: 227 EREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGA 286

Query: 165 GYCKNKEVEEALSLYRE 181
            Y +  + E A +L   
Sbjct: 287 LYRRQGKFEAAETLEEA 303

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	376
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.97
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.97
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.96
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.96
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.96
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.95
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.95
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.95
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.94
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.93
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.92
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.92
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.91
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.91
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.91
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.91
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.91
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.9
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.89
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.88
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.88
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.87
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.86
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.85
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.85
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.84
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.84
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.84
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.84
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.84
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.84
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.83
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.82
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.81
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.81
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.8
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.8
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.8
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.8
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.8
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.79
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.78
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.78
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.78
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.78
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.78
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.78
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.77
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.77
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.77
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.76
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.76
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.75
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.75
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.74
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.74
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.73
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.73
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.72
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.72
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.72
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.71
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.7
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.7
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.69
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.68
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.67
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.66
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.65
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.64
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.63
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.63
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.63
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.61
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.61
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.6
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.57
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.57
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.53
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.52
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.51
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.51
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.48
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.48
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.47
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.46
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.44
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.43
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.43
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.43
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.42
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.41
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.4
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.39
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.39
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.38
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.38
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.38
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.37
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.37
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.37
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.36
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.35
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.34
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.34
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.34
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.3
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.29
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.25
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	99.23
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	99.21
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	99.2
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	99.19
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.18
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.17
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.16
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.15
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	99.15
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	99.14
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.14
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	99.14
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	99.14
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	99.13
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	99.12
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.11
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.11
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.11
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.1
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	99.1
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	99.1
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	99.1
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	99.1
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	99.09
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	99.08
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	99.08
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	99.07
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	99.07
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	99.06
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	99.05
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	99.04
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	99.04
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	99.04
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	99.01
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	99.01
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	99.0
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.98
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.97
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.97
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.96
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.95
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.92
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.91
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.91
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.89
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.88
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.87
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.87
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.87
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.86
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.85
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.85
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.84
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.83
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.83
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.82
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.8
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.78
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.77
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.76
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.73
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.71
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.71
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.7
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.69
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.68
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.67
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.65
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.65
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.64
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.64
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.63
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.63
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.59
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.58
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.57
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.53
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.52
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.49
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.43
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.4
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.39
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.39
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.38
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.36
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.35
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	98.32
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	98.28
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	98.26
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	98.25
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.24
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	98.16
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	98.05
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.9
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.8
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.69
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.64
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.63
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.62
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.62
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	97.61
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.57
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.55
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.52
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.51
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.46
1pc2_A	152	Mitochondria fission protein; unknown function; NM	97.46
1pc2_A	152	Mitochondria fission protein; unknown function; NM	97.33
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.24
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	97.22
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	97.16
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	97.12
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	97.12
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.04
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.91
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.89
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.86
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	96.83
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	96.69
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	96.24
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.18
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	96.14
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	96.11
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.06
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	95.59
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	95.44
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	95.35
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	95.25
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	95.12
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	95.11
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	94.85
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.75
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.54
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	93.99
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	93.85
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	93.84
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	93.8
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	93.34
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	92.3
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	92.17
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	92.14
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	91.7
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	91.44
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	91.17
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	90.52
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	90.44
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	90.17
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	87.75
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	87.52
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	87.49
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	87.0
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	86.79
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	86.39
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	84.78
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	84.32
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	83.93
2p58_C	116	Putative type III secretion protein YSCG; type III	83.46
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	83.19
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	82.26
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	80.46

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

Probab=100.00  E-value=5.3e-35  Score=261.57  Aligned_cols=347  Identities=12%  Similarity=0.039  Sum_probs=306.5

Q ss_pred             cccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHH--------------------------------
Q 042039           10 VVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSL--------------------------------   57 (376)
Q Consensus        10 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l--------------------------------   57 (376)
                      .+.++++.+|+.++..|.+.|++++|+++|+++.+.+ +.+...+..+                                
T Consensus       194 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  272 (597)
T 2xpi_A          194 GGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVD-AKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLR  272 (597)
T ss_dssp             SSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHH
T ss_pred             cccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-chhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHH
Confidence            3456678999999999999999999999999998875 4455554444                                


Q ss_pred             ------HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           58 ------IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        58 ------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                            +..|.+.|++++|.++|+++.+.  +++..++..++..+.+.|++++|..+|+++.+.+ +.+..++..++.++
T Consensus       273 ~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~  349 (597)
T 2xpi_A          273 SLYMLKLNKTSHEDELRRAEDYLSSINGL--EKSSDLLLCKADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASL  349 (597)
T ss_dssp             HHHHTTSCTTTTHHHHHHHHHHHHTSTTG--GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHH
T ss_pred             HHHHHHHHHHcCcchHHHHHHHHHHhhcC--CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHH
Confidence                  44556778999999999998875  5789999999999999999999999999999875 44788999999999


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHH
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      ...|++++|.++++++.... +.+..++..++.+|.+.|++++|.++|+++.+. .+.+..+|..++..+.+.|++++|.
T Consensus       350 ~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~  427 (597)
T 2xpi_A          350 HESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTM-DPQFGPAWIGFAHSFAIEGEHDQAI  427 (597)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999998765 678889999999999999999999999999885 2446889999999999999999999


Q ss_pred             HHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc-
Q 042039          212 KLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR-  290 (376)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-  290 (376)
                      ++|+++.+.+ +.+..++..++.+|.+.|++++|.++|+++.... +.++.+|..++..|.+.|++++|.++|+++.+. 
T Consensus       428 ~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  505 (597)
T 2xpi_A          428 SAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLV  505 (597)
T ss_dssp             HHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhh
Confidence            9999999875 5688899999999999999999999999998776 347899999999999999999999999998765 


Q ss_pred             ---CCCCC--HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCc
Q 042039          291 ---VLVAD--VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPD  365 (376)
Q Consensus       291 ---~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~  365 (376)
                         +..|+  ..+|..++.+|.+.|++++|.+.++++.+.+ +.+..+|..+..+|.+.|++++|.+.++++.+.  .|+
T Consensus       506 ~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~p~  582 (597)
T 2xpi_A          506 KKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIALVYLHKKIPGLAITHLHESLAI--SPN  582 (597)
T ss_dssp             HHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             hccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCC
Confidence               45666  7899999999999999999999999999875 347899999999999999999999999999975  444


Q ss_pred             hH
Q 042039          366 AS  367 (376)
Q Consensus       366 ~~  367 (376)
                      ..
T Consensus       583 ~~  584 (597)
T 2xpi_A          583 EI  584 (597)
T ss_dssp             CH
T ss_pred             Ch
Confidence            43

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

Probab=100.00  E-value=1.6e-34  Score=258.37  Aligned_cols=248  Identities=13%  Similarity=0.106  Sum_probs=156.1

Q ss_pred             ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 042039          120 NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL  199 (376)
Q Consensus       120 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  199 (376)
                      +..++..++..|.+.|++++|.++|+++...+ +.+..++..++.++.+.|++++|..+++++.+. .+.+..++..++.
T Consensus       304 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~  381 (597)
T 2xpi_A          304 SSDLLLCKADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDR-HPEKAVTWLAVGI  381 (597)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHH-CTTSHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhh-CcccHHHHHHHHH
Confidence            34445555555555555555555555555443 334455555555555555555555555555543 2335666666777


Q ss_pred             HHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHH
Q 042039          200 GLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEI  279 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  279 (376)
                      .|.+.|++++|.++|+++.+.. +.+..++..++..|.+.|++++|+++|+++.... +.+..++..++.+|.+.|++++
T Consensus       382 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~  459 (597)
T 2xpi_A          382 YYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILL  459 (597)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHH
Confidence            7777777777777777766653 3455567777777777777777777777766554 2356667777777777777777


Q ss_pred             HHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc----CCCCc--HHHHHHHHHHHhhcCChhhHHHH
Q 042039          280 ALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN----AVAPN--VIIFVTLIHGFVRINKPSKVIEL  353 (376)
Q Consensus       280 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~g~~~~a~~~  353 (376)
                      |.++|+++.+. .+.+..+|..++..|.+.|++++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.+.
T Consensus       460 A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~  538 (597)
T 2xpi_A          460 ANEYLQSSYAL-FQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDA  538 (597)
T ss_dssp             HHHHHHHHHHH-CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHh-CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            77777776654 3446667777777777777777777777777654    44555  56777777777777777777777


Q ss_pred             HHHHHhCCCCCchHHHHHHH
Q 042039          354 LHKMKEKKVMPDASIVSMVV  373 (376)
Q Consensus       354 ~~~~~~~~~~p~~~~~~~ll  373 (376)
                      ++++.+.+ +.+..++..+.
T Consensus       539 ~~~~~~~~-p~~~~~~~~l~  557 (597)
T 2xpi_A          539 LNQGLLLS-TNDANVHTAIA  557 (597)
T ss_dssp             HHHHHHHS-SCCHHHHHHHH
T ss_pred             HHHHHHhC-CCChHHHHHHH
Confidence            77776654 22444554443

>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=100.00  E-value=3.1e-31  Score=224.44  Aligned_cols=342  Identities=14%  Similarity=0.056  Sum_probs=302.6

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      .+...+..+...+...|++++|...++...+.. |.+..+|..++.++...|++++|.+.|+++.+..+. +..+|..++
T Consensus        31 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~  108 (388)
T 1w3b_A           31 DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPD-FIDGYINLA  108 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCcc-hHHHHHHHH
Confidence            345667778888999999999999999998775 778899999999999999999999999999987433 567899999


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHH
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  173 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  173 (376)
                      .++...|++++|...++++++.+ +.+...+..+...+...|++++|.+.|+++.... |.+..++..++.++...|+++
T Consensus       109 ~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~  186 (388)
T 1w3b_A          109 AALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIW  186 (388)
T ss_dssp             HHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence            99999999999999999999874 3346678889999999999999999999998875 667889999999999999999


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhc
Q 042039          174 EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLG  253 (376)
Q Consensus       174 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  253 (376)
                      +|...|+++.+.+ +.+...+..+...+...|++++|...+.+..... +.+..++..++.++...|++++|+..++++.
T Consensus       187 ~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  264 (388)
T 1w3b_A          187 LAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAI  264 (388)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999863 3467889999999999999999999999998875 5567889999999999999999999999998


Q ss_pred             ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHH
Q 042039          254 ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVII  333 (376)
Q Consensus       254 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  333 (376)
                      ...+ .++.++..++.++.+.|++++|...++++.+. .+.+..++..++..+...|++++|...++++.+.. +.+..+
T Consensus       265 ~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~  341 (388)
T 1w3b_A          265 ELQP-HFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAA  341 (388)
T ss_dssp             HTCS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHH
T ss_pred             hhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHH
Confidence            8763 36788999999999999999999999999877 56788999999999999999999999999998863 336788


Q ss_pred             HHHHHHHHhhcCChhhHHHHHHHHHhCCCCCch
Q 042039          334 FVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA  366 (376)
Q Consensus       334 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  366 (376)
                      +..+...|.+.|++++|...++++.+.  .|+.
T Consensus       342 ~~~l~~~~~~~g~~~~A~~~~~~a~~~--~p~~  372 (388)
T 1w3b_A          342 HSNLASVLQQQGKLQEALMHYKEAIRI--SPTF  372 (388)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCC
Confidence            999999999999999999999999864  4543

>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=100.00  E-value=3.3e-30  Score=218.20  Aligned_cols=330  Identities=13%  Similarity=0.049  Sum_probs=295.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  101 (376)
                      +...+.+.|++++|++.++++.+.. |.+...+..+...+...|++++|...++..++.. +.+..+|..+...+...|+
T Consensus         5 ~a~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~   82 (388)
T 1w3b_A            5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCC
Confidence            4567889999999999999998775 6678888899999999999999999999998874 3478899999999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHH
Q 042039          102 MDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                      +++|...|+++++.. +.+..++..++.++...|++++|.+.|+++.... |.+...+..+..++...|++++|.+.|++
T Consensus        83 ~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  160 (388)
T 1w3b_A           83 LQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACYLK  160 (388)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            999999999999864 3456789999999999999999999999999876 56677888999999999999999999999


Q ss_pred             HHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchH
Q 042039          182 MVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDI  261 (376)
Q Consensus       182 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  261 (376)
                      +.+.. +.+..++..+...+...|++++|...|+++.+.+ +.+...+..++..+...|++++|...++++....+ .+.
T Consensus       161 al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~  237 (388)
T 1w3b_A          161 AIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NHA  237 (388)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TCH
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-CCH
Confidence            99863 4467889999999999999999999999999876 55678899999999999999999999999987763 368


Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGF  341 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  341 (376)
                      .++..++.++...|++++|...++++.+. .+.+..++..++.++.+.|++++|...++++.+.. +.+..++..+...+
T Consensus       238 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  315 (388)
T 1w3b_A          238 VVHGNLACVYYEQGLIDLAIDTYRRAIEL-QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIK  315 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT-CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHH
Confidence            88999999999999999999999999876 45568899999999999999999999999999874 44788999999999


Q ss_pred             hhcCChhhHHHHHHHHHhC
Q 042039          342 VRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       342 ~~~g~~~~a~~~~~~~~~~  360 (376)
                      .+.|++++|.+.++++.+.
T Consensus       316 ~~~g~~~~A~~~~~~al~~  334 (388)
T 1w3b_A          316 REQGNIEEAVRLYRKALEV  334 (388)
T ss_dssp             HTTTCHHHHHHHHHHHTTS
T ss_pred             HHcCCHHHHHHHHHHHHhc
Confidence            9999999999999999865

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

Probab=99.98  E-value=5.8e-31  Score=226.32  Aligned_cols=188  Identities=16%  Similarity=0.172  Sum_probs=174.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC---------hHHHHHHHHHHHhcCCCCchH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND---------WNEAKRLFFEMMDQGVQPSVV   87 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------~~~a~~~~~~~~~~~~~~~~~   87 (376)
                      ..++.+|+.|++.|++++|+++|++|.+.|++||..+|+.|+.+|...+.         +++|.++|++|...|+.||..
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~  106 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA  106 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHH
Confidence            35788899999999999999999999999999999999999999987654         678999999999999999999


Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYC  167 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  167 (376)
                      +|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.|+.+|+
T Consensus       107 tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~  186 (501)
T 4g26_A          107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSM  186 (501)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc
Q 042039          168 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  204 (376)
                      +.|++++|.+++++|.+.+..|+..||..++..+...
T Consensus       187 ~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          187 DTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             hCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999998887754

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

Probab=99.98  E-value=1.5e-30  Score=223.77  Aligned_cols=206  Identities=17%  Similarity=0.214  Sum_probs=180.9

Q ss_pred             hHHHHHHHHhhhCCCCCCh-hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC---------h
Q 042039           33 DKAKALFLQMKGENINPDV-VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK---------M  102 (376)
Q Consensus        33 ~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------~  102 (376)
                      ..+..+.+++.+.+..+.+ ..++.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|.+.+.         +
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l   86 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL   86 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHH
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchH
Confidence            3455666677777665554 46888999999999999999999999999999999999999999987664         6


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          103 DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      ++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+|++.|++++|.++|++|
T Consensus        87 ~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M  166 (501)
T 4g26_A           87 SRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM  166 (501)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHH
Confidence            88999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          183 VSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       183 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                      .+.|+.|+..+|+.++.+|++.|++++|.+++++|.+.+..|+..+++.++..+..
T Consensus       167 ~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          167 VESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             HhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999988865

>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=99.97  E-value=7.2e-28  Score=207.98  Aligned_cols=336  Identities=12%  Similarity=0.089  Sum_probs=282.6

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +.++..|..++..+.+.|++++|+.+|+++.+.. +.+..++..++.++...|++++|...|+++++.++. +..++..+
T Consensus        23 p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l  100 (450)
T 2y4t_A           23 MADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMD-FTAARLQR  100 (450)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-cHHHHHHH
Confidence            4467789999999999999999999999998775 668999999999999999999999999999987544 67889999


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCCh---hhHHHH------------HHHHHhcCcHHHHHHHHHHHHhcCCCCChh
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNA---FTYSTL------------MDGFCLTGKINRAEELFGSMESMGCKHDDV  157 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  157 (376)
                      +.++...|++++|...|+++.+.. +.+.   ..+..+            +..+...|++++|...|+++.... +.+..
T Consensus       101 ~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~  178 (450)
T 2y4t_A          101 GHLLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAE  178 (450)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChH
Confidence            999999999999999999999864 2234   455444            455889999999999999998875 67888


Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHH-----
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTF-----  232 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-----  232 (376)
                      ++..++.+|...|++++|+..++++.+. .+.+..++..++..+...|++++|...++++.... +.+...+..+     
T Consensus       179 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~~~~~~  256 (450)
T 2y4t_A          179 LRELRAECFIKEGEPRKAISDLKAASKL-KNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKK  256 (450)
T ss_dssp             HHHHHHHHHHHTTCGGGGHHHHHHHHHH-HCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHHHHHHH
Confidence            9999999999999999999999999886 34578899999999999999999999999998764 3344444444     


Q ss_pred             -------HHHHHhCCCHHHHHHHHHHhcccCCCch----HHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHH
Q 042039          233 -------IDGLCKNGYIVEAVELFRTLGILKCELD----IQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNI  301 (376)
Q Consensus       233 -------~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  301 (376)
                             +..+...|++++|...++.+....+. +    ...+..++.++.+.|++++|...++++.+. .+.+...+..
T Consensus       257 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~-~p~~~~~~~~  334 (450)
T 2y4t_A          257 LNKLIESAEELIRDGRYTDATSKYESVMKTEPS-IAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQM-EPDNVNALKD  334 (450)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CcccHHHHHH
Confidence                   78899999999999999999876433 2    457888999999999999999999998876 4557899999


Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHH------------HHhhcC-----ChhhHHHHHHHH
Q 042039          302 MIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIH------------GFVRIN-----KPSKVIELLHKM  357 (376)
Q Consensus       302 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~------------~~~~~g-----~~~~a~~~~~~~  357 (376)
                      ++.+|...|++++|...++++.+.... +...+..+..            .|...|     +.+++.+.++++
T Consensus       335 l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~~~~~~~~~y~~~  406 (450)
T 2y4t_A          335 RAEAYLIEEMYDEAIQDYETAQEHNEN-DQQIREGLEKAQRLLKQSQKRDYYKILGVKRNAKKQEIIKAYRKL  406 (450)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTSSS-CHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTCCTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhCcc-hHHHHHHHHHHHHHhhcccchhHHHHhCCCccCCHHHHHHHHHHH
Confidence            999999999999999999999985322 4566666653            344445     566778888873

>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=99.97  E-value=1.3e-26  Score=200.03  Aligned_cols=325  Identities=12%  Similarity=0.045  Sum_probs=266.7

Q ss_pred             hHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHH
Q 042039           33 DKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLM  112 (376)
Q Consensus        33 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  112 (376)
                      ..+...+.++.... |.+...+..++..+.+.|++++|+.+|+++++..+ .+..++..++.++...|++++|...++++
T Consensus         9 ~~~~~~~~~~~~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a   86 (450)
T 2y4t_A            9 SGVDLGTENLYFQS-MADVEKHLELGKKLLAAGQLADALSQFHAAVDGDP-DNYIAYYRRATVFLAMGKSKAALPDLTKV   86 (450)
T ss_dssp             ---------------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cccccccccccccc-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            33444555555444 66788999999999999999999999999998743 37889999999999999999999999999


Q ss_pred             HhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCCh---hhHHHH------------HHHHHccCcHHHHHH
Q 042039          113 VQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDD---VSYNIL------------INGYCKNKEVEEALS  177 (376)
Q Consensus       113 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~~a~~  177 (376)
                      ++.+ +.+..++..++.++...|++++|...|+++.... +.+.   ..+..+            +..+...|++++|+.
T Consensus        87 l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~  164 (450)
T 2y4t_A           87 IQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIA  164 (450)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            9875 4468889999999999999999999999999875 4444   555555            455899999999999


Q ss_pred             HHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC
Q 042039          178 LYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC  257 (376)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  257 (376)
                      .++++.+. .+.+..++..++.++...|++++|...++++.+.. +.+..++..++.++...|++++|...++++....+
T Consensus       165 ~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p  242 (450)
T 2y4t_A          165 FLDKILEV-CVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQ  242 (450)
T ss_dssp             HHHHHHHH-CTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHh-CCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            99999986 34578889999999999999999999999998875 56788999999999999999999999999987653


Q ss_pred             CchHHHHHHH------------HHHHHhCCChHHHHHHHhcccccCCCCC----HHHHHHHHHHHHccCChhHHHHHHHH
Q 042039          258 ELDIQAYNCL------------IDGLCKSGRLEIALELFRSLPRRVLVAD----VVTYNIMIHGLCNDGQMDKAHDLFLD  321 (376)
Q Consensus       258 ~~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~  321 (376)
                      . +...+..+            +..+...|++++|...|+++.+.. +.+    ...+..++.++.+.|++++|+..+++
T Consensus       243 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  320 (450)
T 2y4t_A          243 D-HKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE-PSIAEYTVRSKERICHCFSKDEKPVEAIRVCSE  320 (450)
T ss_dssp             T-CHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             C-hHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            3 44555444            888999999999999999998752 223    44788899999999999999999999


Q ss_pred             HHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHH
Q 042039          322 MEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASI  368 (376)
Q Consensus       322 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~  368 (376)
                      +.+.. +.+...|..+..+|...|++++|...++++.+.  .|+...
T Consensus       321 a~~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~  364 (450)
T 2y4t_A          321 VLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYETAQEH--NENDQQ  364 (450)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--SSSCHH
T ss_pred             HHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CcchHH
Confidence            98864 336889999999999999999999999999874  555443

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

Probab=99.96  E-value=7.4e-27  Score=205.05  Aligned_cols=342  Identities=11%  Similarity=-0.036  Sum_probs=265.7

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCC--------
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQP--------   84 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--------   84 (376)
                      .||+.+|..+..++.+.|++++|+..++++.+.+ |.+..++..++.++...|++++|...|+++...+...        
T Consensus        36 ~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  114 (514)
T 2gw1_A           36 KEDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPML  114 (514)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHH
T ss_pred             CccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHH
Confidence            3778888888888888888888888888888765 6677788888888888888888888888887654211        


Q ss_pred             ----------------------------------------------------------------------chHhHHHHHH
Q 042039           85 ----------------------------------------------------------------------SVVTFNVIMD   94 (376)
Q Consensus        85 ----------------------------------------------------------------------~~~~~~~l~~   94 (376)
                                                                                            +...+.....
T Consensus       115 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (514)
T 2gw1_A          115 ERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGL  194 (514)
T ss_dssp             HHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHH
Confidence                                                                                  1222333333


Q ss_pred             HHHh---CCChHHHHHHHHHHHh-----cCC--------CCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhh
Q 042039           95 ELCK---NGKMDEASRLLDLMVQ-----RDV--------RPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVS  158 (376)
Q Consensus        95 ~~~~---~~~~~~a~~~~~~~~~-----~~~--------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  158 (376)
                      .+..   .|++++|..+++++.+     ...        +.+..++..++..+...|++++|...++++.... +. ..+
T Consensus       195 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-~~-~~~  272 (514)
T 2gw1_A          195 SNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF-PR-VNS  272 (514)
T ss_dssp             HHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC-CC-HHH
T ss_pred             HHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-cc-HHH
Confidence            3443   7888888888888877     311        1224567778888888899999999998888775 23 778


Q ss_pred             HHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 042039          159 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK  238 (376)
Q Consensus       159 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  238 (376)
                      +..++.++...|++++|...++++.... +.+...+..+...+...|++++|...++++.+.. +.+...+..++..+..
T Consensus       273 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  350 (514)
T 2gw1_A          273 YIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYR  350 (514)
T ss_dssp             HHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHH
Confidence            8888888899999999999998888763 3467788888888999999999999999988775 4567788888888999


Q ss_pred             CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCC-CC----HHHHHHHHHHHHc---cC
Q 042039          239 NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLV-AD----VVTYNIMIHGLCN---DG  310 (376)
Q Consensus       239 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~---~~  310 (376)
                      .|++++|...++.+.... +.+...+..++..+...|++++|...++++.+.... ++    ...+..++.++..   .|
T Consensus       351 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  429 (514)
T 2gw1_A          351 ENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVE  429 (514)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTT
T ss_pred             cCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcC
Confidence            999999999999887765 335678888899999999999999999887654211 11    3378888899999   89


Q ss_pred             ChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          311 QMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       311 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      ++++|...++++.+.. +.+..++..+...|.+.|++++|...++++.+..
T Consensus       430 ~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  479 (514)
T 2gw1_A          430 NFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAITLFEESADLA  479 (514)
T ss_dssp             HHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhc
Confidence            9999999999988764 2357778888899999999999999999988653

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

Probab=99.96  E-value=2.1e-26  Score=202.24  Aligned_cols=339  Identities=14%  Similarity=0.030  Sum_probs=287.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +...|......+.+.|++++|+..|+++.+.+  |+..+|..++.++...|++++|.+.++++++.++. +..++..++.
T Consensus         5 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~   81 (514)
T 2gw1_A            5 YALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPD-YSKVLLRRAS   81 (514)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSC-CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChH-HHHHHHHHHH
Confidence            35678888999999999999999999999875  68999999999999999999999999999987543 6788999999


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCC-------------------------------------------------------
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRP-------------------------------------------------------  119 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~-------------------------------------------------------  119 (376)
                      ++...|++++|...|+++.+.+...                                                       
T Consensus        82 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (514)
T 2gw1_A           82 ANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSV  161 (514)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCH
T ss_pred             HHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchh
Confidence            9999999999999999998764211                                                       


Q ss_pred             -----------------------ChhhHHHHHHHHHh---cCcHHHHHHHHHHHHh-----cCC--------CCChhhHH
Q 042039          120 -----------------------NAFTYSTLMDGFCL---TGKINRAEELFGSMES-----MGC--------KHDDVSYN  160 (376)
Q Consensus       120 -----------------------~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~-----~~~--------~~~~~~~~  160 (376)
                                             +...+...+..+..   .|++++|..+++++..     ...        +.+..++.
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (514)
T 2gw1_A          162 TSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLE  241 (514)
T ss_dssp             HHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHH
Confidence                                   12233334444443   8999999999999987     311        23456788


Q ss_pred             HHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC
Q 042039          161 ILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG  240 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  240 (376)
                      .++.++...|++++|...++++.+..  |+...+..++.++...|++++|...++.+.... +.+...+..++..+...|
T Consensus       242 ~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  318 (514)
T 2gw1_A          242 HTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQ  318 (514)
T ss_dssp             HHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhC
Confidence            89999999999999999999999864  338889999999999999999999999998875 567788999999999999


Q ss_pred             CHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHH
Q 042039          241 YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFL  320 (376)
Q Consensus       241 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  320 (376)
                      ++++|...++.+...... +...+..++..+...|++++|...++++.+. .+.+...+..++..+...|++++|...++
T Consensus       319 ~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~la~~~~~~~~~~~A~~~~~  396 (514)
T 2gw1_A          319 NYDQAGKDFDKAKELDPE-NIFPYIQLACLAYRENKFDDCETLFSEAKRK-FPEAPEVPNFFAEILTDKNDFDKALKQYD  396 (514)
T ss_dssp             CTTHHHHHHHHHHHTCSS-CSHHHHHHHHHTTTTTCHHHHHHHHHHHHHH-STTCSHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhChh-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-cccCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            999999999999877633 6778999999999999999999999998876 45577889999999999999999999999


Q ss_pred             HHHHcCCC-Cc----HHHHHHHHHHHhh---cCChhhHHHHHHHHHhCC
Q 042039          321 DMEENAVA-PN----VIIFVTLIHGFVR---INKPSKVIELLHKMKEKK  361 (376)
Q Consensus       321 ~~~~~~~~-~~----~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~~  361 (376)
                      ++.+.... ++    ...+..+...+..   .|++++|...++++.+..
T Consensus       397 ~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~  445 (514)
T 2gw1_A          397 LAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD  445 (514)
T ss_dssp             HHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC
T ss_pred             HHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC
Confidence            99865322 11    3388889999999   999999999999998753

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

Probab=99.96  E-value=1.6e-25  Score=187.33  Aligned_cols=319  Identities=11%  Similarity=0.049  Sum_probs=238.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      |+..+..+...+...|++++|+..|+++.+.. |.+..++..++.++...|++++|...++++.+..+. +...+..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMD-FTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-cchHHHHHHH
Confidence            46778889999999999999999999998875 667889999999999999999999999999987433 6788899999


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCC--CChhhHHHH------------HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVR--PNAFTYSTL------------MDGFCLTGKINRAEELFGSMESMGCKHDDVSYN  160 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  160 (376)
                      ++...|++++|...++++.+....  .+...+..+            +..+...|++++|...++++.... |.+...+.
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  158 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRE  158 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHH
Confidence            999999999999999999886320  244445444            577788888888888888888775 56777888


Q ss_pred             HHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHH----------
Q 042039          161 ILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYN----------  230 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----------  230 (376)
                      .++.++...|++++|...++++.+. .+.+..++..+...+...|++++|...++.+.+.. +.+...+.          
T Consensus       159 ~~~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~  236 (359)
T 3ieg_A          159 LRAECFIKEGEPRKAISDLKAASKL-KSDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNK  236 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTT-CSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHHH
Confidence            8888888888888888888888876 34467788888888888888888888888887764 33333222          


Q ss_pred             --HHHHHHHhCCCHHHHHHHHHHhcccCCCchH----HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHH
Q 042039          231 --TFIDGLCKNGYIVEAVELFRTLGILKCELDI----QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIH  304 (376)
Q Consensus       231 --~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  304 (376)
                        .++..+.+.|++++|...++++...... ++    ..+..++.++...|++++|...++++.+. .+.+..++..++.
T Consensus       237 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~  314 (359)
T 3ieg_A          237 LIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQM-EPDNVNALKDRAE  314 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CcccHHHHHHHHH
Confidence              2255567777777777777777655432 22    23445667777777777777777777665 3446667777777


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 042039          305 GLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGF  341 (376)
Q Consensus       305 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  341 (376)
                      ++...|++++|...|+++.+..+. +...+..+..+.
T Consensus       315 ~~~~~g~~~~A~~~~~~a~~~~p~-~~~~~~~l~~~~  350 (359)
T 3ieg_A          315 AYLIEEMYDEAIQDYEAAQEHNEN-DQQIREGLEKAQ  350 (359)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCC-ChHHHHHHHHHH
Confidence            777777777777777777765321 344445444443

>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=99.95  E-value=6.9e-25  Score=193.61  Aligned_cols=336  Identities=13%  Similarity=0.071  Sum_probs=255.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...|..+...+.+.|++++|+..|+++.+.+ |.++.++..++.++...|++++|++.|+++++.++. +..++..++.+
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~  102 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPD-HSKALLRRASA  102 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-hHHHHHHHHHH
Confidence            4567788888888888888888888888775 667888888888888888888888888888887533 67778888888


Q ss_pred             HHhCCChHHHHHHHHHH---------------------------------------------------------------
Q 042039           96 LCKNGKMDEASRLLDLM---------------------------------------------------------------  112 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~---------------------------------------------------------------  112 (376)
                      +...|++++|...|+.+                                                               
T Consensus       103 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (537)
T 3fp2_A          103 NESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSS  182 (537)
T ss_dssp             HHHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHH
Confidence            88888888887766422                                                               


Q ss_pred             ----------------------------------------------HhcCCCCC--------hhhHHHHHHHHHhcCcHH
Q 042039          113 ----------------------------------------------VQRDVRPN--------AFTYSTLMDGFCLTGKIN  138 (376)
Q Consensus       113 ----------------------------------------------~~~~~~~~--------~~~~~~l~~~~~~~~~~~  138 (376)
                                                                    ++.  .|+        ..++..+...+...|+++
T Consensus       183 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~  260 (537)
T 3fp2_A          183 VNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSA--NTVDDPLRENAALALCYTGIFHFLKNNLL  260 (537)
T ss_dssp             SCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH--CCCcchhhHHHHHHHHHHHHHHHhcccHH
Confidence                                                          111  111        123455566677778888


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHH
Q 042039          139 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       139 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  218 (376)
                      +|...++++....  |+..++..++.++...|++++|...++++.+.. +.+..++..+...+...|++++|...++++.
T Consensus       261 ~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  337 (537)
T 3fp2_A          261 DAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQ  337 (537)
T ss_dssp             HHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            8888888888764  447778888888888888888888888888753 3457778888888888888888888888888


Q ss_pred             hcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC-----CC
Q 042039          219 RDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV-----LV  293 (376)
Q Consensus       219 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~  293 (376)
                      +.. +.+...+..++.++...|++++|...++.+.... +.+...+..++..+...|++++|...++++.+..     ..
T Consensus       338 ~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~  415 (537)
T 3fp2_A          338 SLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIH  415 (537)
T ss_dssp             HHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCS
T ss_pred             HhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhH
Confidence            765 4566778888888888888888888888887765 3356778888888888888888888888876432     11


Q ss_pred             CCHHHHHHHHHHHHcc----------CChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          294 ADVVTYNIMIHGLCND----------GQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       294 ~~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      .....+.....++...          |++++|...++++.+... .+...+..+...|.+.|++++|.+.|+++.+..
T Consensus       416 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  492 (537)
T 3fp2_A          416 VGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDP-RSEQAKIGLAQLKLQMEKIDEAIELFEDSAILA  492 (537)
T ss_dssp             STTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            1222344556667777          888899999988887643 356788889999999999999999999988754

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

Probab=99.95  E-value=3.8e-24  Score=178.94  Aligned_cols=309  Identities=12%  Similarity=0.055  Sum_probs=262.1

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      ++..+..++..+...|++++|+..|+++++..+. +..++..+..++...|++++|...++++++.. +.+...+..++.
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPD-NYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHH
Confidence            4677888999999999999999999999987543 67899999999999999999999999999874 446788999999


Q ss_pred             HHHhcCcHHHHHHHHHHHHhcCCC---CChhhHHHH------------HHHHHccCcHHHHHHHHHHHHHCCCCCCHhHH
Q 042039          130 GFCLTGKINRAEELFGSMESMGCK---HDDVSYNIL------------INGYCKNKEVEEALSLYREMVSKGIKPTVVTY  194 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  194 (376)
                      ++...|++++|...++++.... +   .+...+..+            +..+...|++++|+..++++.+. .+.+...+
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~  157 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSN-PSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEV-CVWDAELR  157 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHH
T ss_pred             HHHHcCChHHHHHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CCCchHHH
Confidence            9999999999999999999875 3   355555555            68889999999999999999986 34578889


Q ss_pred             HHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHH---------
Q 042039          195 NTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYN---------  265 (376)
Q Consensus       195 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---------  265 (376)
                      ..+...+...|++++|...++++.+.. +.+...+..++..+...|++++|...++.+....+. +...+.         
T Consensus       158 ~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~~~~~~~~  235 (359)
T 3ieg_A          158 ELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQD-HKRCFAHYKQVKKLN  235 (359)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcc-chHHHHHHHHHHHHH
Confidence            999999999999999999999999875 667889999999999999999999999999876533 333332         


Q ss_pred             ---HHHHHHHhCCChHHHHHHHhcccccCCCCCH----HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHH
Q 042039          266 ---CLIDGLCKSGRLEIALELFRSLPRRVLVADV----VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLI  338 (376)
Q Consensus       266 ---~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  338 (376)
                         .++..+...|++++|...++++.+.. +.+.    ..+..++.++...|++++|...++++.+.. +.+..++..+.
T Consensus       236 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~  313 (359)
T 3ieg_A          236 KLIESAEELIRDGRYTDATSKYESVMKTE-PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQME-PDNVNALKDRA  313 (359)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence               33777899999999999999988762 3333    335568889999999999999999999864 33788999999


Q ss_pred             HHHhhcCChhhHHHHHHHHHhCCCCCchHH
Q 042039          339 HGFVRINKPSKVIELLHKMKEKKVMPDASI  368 (376)
Q Consensus       339 ~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~  368 (376)
                      ..|...|++++|...++++.+.  .|+...
T Consensus       314 ~~~~~~g~~~~A~~~~~~a~~~--~p~~~~  341 (359)
T 3ieg_A          314 EAYLIEEMYDEAIQDYEAAQEH--NENDQQ  341 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTT--CTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc--CCCChH
Confidence            9999999999999999999965  455443

>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=99.95  E-value=6.1e-24  Score=175.61  Aligned_cols=288  Identities=14%  Similarity=0.051  Sum_probs=170.9

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH
Q 042039           12 CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV   91 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   91 (376)
                      .+.++..+..++..+...|++++|+++|+++.+.. +.+...+..++.++...|++++|...++++.+.... +...+..
T Consensus        18 ~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~   95 (330)
T 3hym_B           18 LQENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPS-NPVSWFA   95 (330)
T ss_dssp             --CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-STHHHHH
T ss_pred             chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHH
Confidence            34455566666666666677777777777666554 445556666666666667777777777766665322 4556666


Q ss_pred             HHHHHHhCC-ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC
Q 042039           92 IMDELCKNG-KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus        92 l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      +...+...| ++++|...++++.+.. +.+...+..++.++...|++++|...++++.... +.+...+..++.++...|
T Consensus        96 l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~  173 (330)
T 3hym_B           96 VGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTN  173 (330)
T ss_dssp             HHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHh
Confidence            666666666 6666777776666653 2345566666666666677777777776666654 334555666666666666


Q ss_pred             cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC--------CCCCcchHHHHHHHHHhCCCH
Q 042039          171 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD--------VAADTSTYNTFIDGLCKNGYI  242 (376)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~l~~~~~~~~~~  242 (376)
                      ++++|...++++.+.. +.+...+..++..+...|++++|...++++.+..        .+....++..++.++...|++
T Consensus       174 ~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~  252 (330)
T 3hym_B          174 NSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKY  252 (330)
T ss_dssp             CHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCH
Confidence            6777766666666642 3345566666666666666666666666665431        022234555555556666666


Q ss_pred             HHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHH
Q 042039          243 VEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGL  306 (376)
Q Consensus       243 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  306 (376)
                      ++|...++++..... .+...+..++.++...|++++|...++++.+. .+.+...+..+..++
T Consensus       253 ~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~  314 (330)
T 3hym_B          253 AEALDYHRQALVLIP-QNASTYSAIGYIHSLMGNFENAVDYFHTALGL-RRDDTFSVTMLGHCI  314 (330)
T ss_dssp             HHHHHHHHHHHHHST-TCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT-CSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCc-cchHHHHHHHHHHHHhccHHHHHHHHHHHHcc-CCCchHHHHHHHHHH
Confidence            666666655554432 24455555555555555565665555555544 233444555555544

>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=99.94  E-value=3.7e-24  Score=176.95  Aligned_cols=294  Identities=15%  Similarity=0.055  Sum_probs=245.9

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      +.+...+..++..+...|++++|.++|+++.+..+. +...+..++.++...|++++|..+++++.+.. +.+...+..+
T Consensus        19 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l   96 (330)
T 3hym_B           19 QENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPF-HASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAV   96 (330)
T ss_dssp             -CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-ChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHH
Confidence            556778888999999999999999999999887433 56677778888999999999999999999874 4467888999


Q ss_pred             HHHHHhcC-cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccc
Q 042039          128 MDGFCLTG-KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       128 ~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  206 (376)
                      +..+...| ++++|...|+++.... +.+...+..++.++...|++++|+..++++.+.. +.+...+..+...+...|+
T Consensus        97 ~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~  174 (330)
T 3hym_B           97 GCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNN  174 (330)
T ss_dssp             HHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhh
Confidence            99999999 9999999999998876 5677889999999999999999999999998863 3356777789999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC--------CCchHHHHHHHHHHHHhCCChH
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK--------CELDIQAYNCLIDGLCKSGRLE  278 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~l~~~~~~~~~~~  278 (376)
                      +++|...++++.+.. +.+...+..++..+...|++++|...++++....        .+.....+..++.++...|+++
T Consensus       175 ~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  253 (330)
T 3hym_B          175 SKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYA  253 (330)
T ss_dssp             HHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHH
Confidence            999999999998875 5667888999999999999999999999886532        1224578889999999999999


Q ss_pred             HHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHH-hhcCChh
Q 042039          279 IALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGF-VRINKPS  348 (376)
Q Consensus       279 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~~~  348 (376)
                      +|...++++.+. .+.+...+..++.++...|++++|.+.++++.+... .+...+..+..++ ...|+.+
T Consensus       254 ~A~~~~~~a~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          254 EALDYHRQALVL-IPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRR-DDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHHHHHHHHHH-STTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCS-CCHHHHHHHHHHHHTTTTC--
T ss_pred             HHHHHHHHHHhh-CccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCC-CchHHHHHHHHHHHHHhCchh
Confidence            999999998876 355778899999999999999999999999987642 2677778787777 4555544

>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=99.93  E-value=1.2e-23  Score=176.67  Aligned_cols=313  Identities=14%  Similarity=0.053  Sum_probs=220.8

Q ss_pred             cCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHH-HHHHHHhcCCC-C--chHhHHHHHHHHHhCCChHH
Q 042039           29 EGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKR-LFFEMMDQGVQ-P--SVVTFNVIMDELCKNGKMDE  104 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~-~~~~~~~~~~~-~--~~~~~~~l~~~~~~~~~~~~  104 (376)
                      .+.++.+...|+.+...+  |+         ++...|++++|.+ .+++....... |  +...+..+...+...|++++
T Consensus        14 ~~~~~~~~~~~~~~~~~~--~~---------~~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   82 (368)
T 1fch_A           14 VDFWDKLQAELEEMAKRD--AE---------AHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPN   82 (368)
T ss_dssp             -------------------------------------------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHH
T ss_pred             cccHHHHHHHHHHHHcCC--ch---------hhHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHH
Confidence            344555555555555442  11         2334577888887 77766544221 1  34567778888888888888


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          105 ASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       105 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      |...++++++.. +.+..++..++.++...|++++|...++++.... |.+..++..++.++...|++++|...++++..
T Consensus        83 A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  160 (368)
T 1fch_A           83 AVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLR  160 (368)
T ss_dssp             HHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            888888888764 4467778888888888888888888888887775 56777888888888888888888888888887


Q ss_pred             CCCCCCHhHHHH---------------HHHHHHhccchHHHHHHHHHHHhcCCCC-CcchHHHHHHHHHhCCCHHHHHHH
Q 042039          185 KGIKPTVVTYNT---------------LFLGLFEIHQVEHALKLFEEMQRDDVAA-DTSTYNTFIDGLCKNGYIVEAVEL  248 (376)
Q Consensus       185 ~~~~~~~~~~~~---------------l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~  248 (376)
                      .... +...+..               .+..+...|++++|...++++.+..... +..++..++..+...|++++|+..
T Consensus       161 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~  239 (368)
T 1fch_A          161 YTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDC  239 (368)
T ss_dssp             TSTT-TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            5322 2222211               1333348899999999999998875221 577889999999999999999999


Q ss_pred             HHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 042039          249 FRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVA  328 (376)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  328 (376)
                      ++++.... +.+...+..++..+...|++++|...++++.+. .+.+...+..++.++...|++++|...|+++.+....
T Consensus       240 ~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~  317 (368)
T 1fch_A          240 FTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL-QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRK  317 (368)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence            99988775 336789999999999999999999999998876 4567889999999999999999999999999865322


Q ss_pred             C----------cHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          329 P----------NVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       329 ~----------~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      .          ...+|..+..+|...|++++|..++++.
T Consensus       318 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          318 SRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             C------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             CCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHHH
Confidence            1          1678999999999999999999887743

>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=99.92  E-value=4.9e-23  Score=172.92  Aligned_cols=292  Identities=14%  Similarity=-0.030  Sum_probs=235.0

Q ss_pred             HHHhcCChhHHHH-HHHHhhhCCCC-C--ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCC
Q 042039           25 GLCKEGFVDKAKA-LFLQMKGENIN-P--DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG  100 (376)
Q Consensus        25 ~~~~~g~~~~a~~-~~~~~~~~~~~-~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  100 (376)
                      ++...|++++|++ .+++....... |  +...+..++..+...|++++|...|+++++..+. +..++..+..++...|
T Consensus        34 ~~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g  112 (368)
T 1fch_A           34 AHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPK-HMEAWQYLGTTQAENE  112 (368)
T ss_dssp             ------------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCc
Confidence            3445688999998 88877655311 1  3567889999999999999999999999987533 7788999999999999


Q ss_pred             ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHH----------------HHHH
Q 042039          101 KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYN----------------ILIN  164 (376)
Q Consensus       101 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----------------~l~~  164 (376)
                      ++++|...++++++.. +.+..++..++.++...|++++|...++++.... +.+...+.                .+..
T Consensus       113 ~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (368)
T 1fch_A          113 QELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYT-PAYAHLVTPAEEGAGGAGLGPSKRILGS  190 (368)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-TTTGGGCC---------------CTTHH
T ss_pred             CHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHhhhhcccHHHHHHHH
Confidence            9999999999999875 4578899999999999999999999999998875 33333332                2344


Q ss_pred             HHHccCcHHHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHH
Q 042039          165 GYCKNKEVEEALSLYREMVSKGIKP-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIV  243 (376)
Q Consensus       165 ~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  243 (376)
                      .+ ..|++++|...++++.+..... +..++..++..+...|++++|...++++.... +.+..++..++..+...|+++
T Consensus       191 ~~-~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~  268 (368)
T 1fch_A          191 LL-SDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSE  268 (368)
T ss_dssp             HH-HHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             Hh-hcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHH
Confidence            44 8999999999999999863221 57889999999999999999999999998875 556788999999999999999


Q ss_pred             HHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC-----------HHHHHHHHHHHHccCCh
Q 042039          244 EAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD-----------VVTYNIMIHGLCNDGQM  312 (376)
Q Consensus       244 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----------~~~~~~l~~~~~~~~~~  312 (376)
                      +|...++++.... +.+...+..++.++...|++++|...++++.+.. +.+           ..+|..++.++...|++
T Consensus       269 ~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  346 (368)
T 1fch_A          269 EAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQ-RKSRGPRGEGGAMSENIWSTLRLALSMLGQS  346 (368)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-HTC------CCCCCHHHHHHHHHHHHHHTCG
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCCCccccccchhhHHHHHHHHHHHHhCCh
Confidence            9999999998775 3468899999999999999999999999987642 222           68899999999999999


Q ss_pred             hHHHHHHHHHH
Q 042039          313 DKAHDLFLDME  323 (376)
Q Consensus       313 ~~a~~~~~~~~  323 (376)
                      ++|..++++..
T Consensus       347 ~~A~~~~~~~l  357 (368)
T 1fch_A          347 DAYGAADARDL  357 (368)
T ss_dssp             GGHHHHHTTCH
T ss_pred             HhHHHhHHHHH
Confidence            99999887543

>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=99.92  E-value=1.1e-21  Score=173.04  Aligned_cols=307  Identities=12%  Similarity=0.036  Sum_probs=256.8

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc------------
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ------------   80 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------------   80 (376)
                      +.++.+|..+..++.+.|++++|++.|+++.+.+ |.+..++..++.++...|++++|...|+.+...            
T Consensus        56 p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  134 (537)
T 3fp2_A           56 PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTDAMFDLSVLSLNGDFDGASIEPML  134 (537)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHC-----------CHH
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCChHHHHHHH
Confidence            3467889999999999999999999999998876 668889999999999999999888877422100            


Q ss_pred             --------------------------------------------------------------------------------
Q 042039           81 --------------------------------------------------------------------------------   80 (376)
Q Consensus        81 --------------------------------------------------------------------------------   80 (376)
                                                                                                      
T Consensus       135 ~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a  214 (537)
T 3fp2_A          135 ERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVA  214 (537)
T ss_dssp             HHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHH
Confidence                                                                                            


Q ss_pred             ---------------CCCCc--------hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH
Q 042039           81 ---------------GVQPS--------VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        81 ---------------~~~~~--------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                                     ...|+        ..++..+...+...|++++|...++++.+..  |+...+..++..+...|++
T Consensus       215 ~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~  292 (537)
T 3fp2_A          215 NDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENS  292 (537)
T ss_dssp             HHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCC
T ss_pred             HHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCH
Confidence                           01111        1235566677888999999999999999874  5578899999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHH
Q 042039          138 NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEM  217 (376)
Q Consensus       138 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  217 (376)
                      ++|...++++.... +.+..++..++.++...|++++|...++++.+.. +.+...+..+...+...|++++|...++++
T Consensus       293 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  370 (537)
T 3fp2_A          293 QEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNET  370 (537)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99999999998876 6678899999999999999999999999999863 335778999999999999999999999999


Q ss_pred             HhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC-----chHHHHHHHHHHHHhC----------CChHHHHH
Q 042039          218 QRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE-----LDIQAYNCLIDGLCKS----------GRLEIALE  282 (376)
Q Consensus       218 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~----------~~~~~a~~  282 (376)
                      .+.. +.+...+..++..+...|++++|...++.+......     .....+...+.++...          |++++|..
T Consensus       371 ~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~  449 (537)
T 3fp2_A          371 KLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIK  449 (537)
T ss_dssp             HHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHH
T ss_pred             HHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHH
Confidence            9875 566788999999999999999999999998654311     1223345566777777          99999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 042039          283 LFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA  326 (376)
Q Consensus       283 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  326 (376)
                      .++++.+. .+.+...+..++.++...|++++|.+.|+++.+..
T Consensus       450 ~~~~a~~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  492 (537)
T 3fp2_A          450 LLTKACEL-DPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILA  492 (537)
T ss_dssp             HHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHh-CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            99999876 45678899999999999999999999999999864

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.91  E-value=5.8e-20  Score=159.98  Aligned_cols=323  Identities=12%  Similarity=0.039  Sum_probs=175.9

Q ss_pred             ChhhHHHHHHHHHh----cCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----CCChHHHHHHHHHHHhcCCCCch
Q 042039           15 NTVTYNTIIDGLCK----EGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH----ANDWNEAKRLFFEMMDQGVQPSV   86 (376)
Q Consensus        15 ~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~   86 (376)
                      |+.++..+...|..    .+++++|+..|++..+.|   ++.++..|...|..    .+++++|.+.|++..+.|   +.
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  111 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LP  111 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            55666666666666    666666666666666543   45566666666666    666666666666666543   44


Q ss_pred             HhHHHHHHHHHh----CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCCCChhh
Q 042039           87 VTFNVIMDELCK----NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCKHDDVS  158 (376)
Q Consensus        87 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  158 (376)
                      ..+..+...|..    .+++++|...|++..+.+   +...+..+...|..    .+++++|.++|++..+.+   +..+
T Consensus       112 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a  185 (490)
T 2xm6_A          112 QAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWS  185 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHH
Confidence            455556666655    556666666666665543   34455555555554    456666666666655543   4455


Q ss_pred             HHHHHHHHHc----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCC--------
Q 042039          159 YNILINGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDV--------  222 (376)
Q Consensus       159 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~--------  222 (376)
                      +..+...|..    .+++++|+..|++..+.+   +...+..+...+..    .+++++|...+++..+.+.        
T Consensus       186 ~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg  262 (490)
T 2xm6_A          186 CNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLG  262 (490)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            5555555554    555555555555555432   33344444444443    4444555555544443320        


Q ss_pred             -------------------------CCCcchHHHHHHHHHhC-----CCHHHHHHHHHHhcccCCCchHHHHHHHHHHHH
Q 042039          223 -------------------------AADTSTYNTFIDGLCKN-----GYIVEAVELFRTLGILKCELDIQAYNCLIDGLC  272 (376)
Q Consensus       223 -------------------------~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  272 (376)
                                               ..+...+..+...|...     +++++|+.+++++.+.+   ++..+..++..|.
T Consensus       263 ~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~  339 (490)
T 2xm6_A          263 YILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYF  339 (490)
T ss_dssp             HHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHH
Confidence                                     01223344444444444     45555555555544432   2334444444444


Q ss_pred             hCC---ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHc----cCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh--
Q 042039          273 KSG---RLEIALELFRSLPRRVLVADVVTYNIMIHGLCN----DGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR--  343 (376)
Q Consensus       273 ~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--  343 (376)
                      ..|   ++++|...|++..+.   .++..+..+...|..    .+++++|...|++..+.+   +...+..+...|..  
T Consensus       340 ~~g~~~~~~~A~~~~~~a~~~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~  413 (490)
T 2xm6_A          340 RLGSEEEHKKAVEWFRKAAAK---GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGL  413 (490)
T ss_dssp             HSCCHHHHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTS
T ss_pred             hCCCcccHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCC
Confidence            433   455555555555543   244555556666655    566666666666666543   34455555555555  


Q ss_pred             --cCChhhHHHHHHHHHhCC
Q 042039          344 --INKPSKVIELLHKMKEKK  361 (376)
Q Consensus       344 --~g~~~~a~~~~~~~~~~~  361 (376)
                        .+++++|..+|++..+.+
T Consensus       414 g~~~d~~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          414 GVERDYVQAWAWFDTASTND  433 (490)
T ss_dssp             SSCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCC
Confidence              566666666666666554

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.91  E-value=1e-19  Score=158.36  Aligned_cols=302  Identities=13%  Similarity=0.043  Sum_probs=227.5

Q ss_pred             hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----CCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh----CCChH
Q 042039           32 VDKAKALFLQMKGENINPDVVTYNSLIHGLCH----ANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK----NGKMD  103 (376)
Q Consensus        32 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~  103 (376)
                      ...+...++...+.|   ++.++..+...|..    .+++++|...|++..+.|   +...+..+...|..    .++++
T Consensus        23 ~~~~~~~~~~~a~~g---~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~   96 (490)
T 2xm6_A           23 GNVNLEQLKQKAESG---EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYA   96 (490)
T ss_dssp             --CCHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             hhHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHH
Confidence            344567777776654   78889999999988    899999999999998863   67788889999998    89999


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc----cCcHHHH
Q 042039          104 EASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCKHDDVSYNILINGYCK----NKEVEEA  175 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a  175 (376)
                      +|...|++..+.+   +...+..+...|..    .+++++|..+|++..+.+   ++..+..+..+|..    .+++++|
T Consensus        97 ~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A  170 (490)
T 2xm6_A           97 QAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMA  170 (490)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            9999999999865   66778889999988    789999999999998865   67788889999987    8899999


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh----CCCHHHHHH
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK----NGYIVEAVE  247 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~  247 (376)
                      ++.|++..+.+   +...+..+...|..    .++.++|...+.+..+.+   +...+..+...|..    .+++++|..
T Consensus       171 ~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~  244 (490)
T 2xm6_A          171 REWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRV  244 (490)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            99999999864   67888889999888    899999999999998765   45667777777775    778888888


Q ss_pred             HHHHhcccCCCchHHHHHHHHHHHHh----CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc-----CChhHHHHH
Q 042039          248 LFRTLGILKCELDIQAYNCLIDGLCK----SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND-----GQMDKAHDL  318 (376)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~  318 (376)
                      +|++....+   ++..+..++..|..    .+++++|...|++..+.+   +...+..+...|...     +++++|...
T Consensus       245 ~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~  318 (490)
T 2xm6_A          245 LFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISW  318 (490)
T ss_dssp             HHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHH
Confidence            888877654   34556666666666    677777777777766542   445555666666555     666666666


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHhhcC---ChhhHHHHHHHHHhC
Q 042039          319 FLDMEENAVAPNVIIFVTLIHGFVRIN---KPSKVIELLHKMKEK  360 (376)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~  360 (376)
                      |+++.+.+   +...+..+...|...|   ++++|.++|++..+.
T Consensus       319 ~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~  360 (490)
T 2xm6_A          319 YTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK  360 (490)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC
Confidence            66665542   2334444444444433   445555555555444

>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=99.91  E-value=6.4e-22  Score=163.25  Aligned_cols=268  Identities=10%  Similarity=-0.051  Sum_probs=189.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +...|..+...+...|++++|+.+|+++.+.. +.+..++..++.++...|++++|.+.++++.+.... +..++..+..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~   97 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAV   97 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcC-CHHHHHHHHH
Confidence            45667888888999999999999999988765 567888888999999999999999999998887433 6778888888


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH--------------HH-HHHhcCcHHHHHHHHHHHHhcCCCCChhhH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL--------------MD-GFCLTGKINRAEELFGSMESMGCKHDDVSY  159 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  159 (376)
                      .+...|++++|...++++.+.. +.+...+..+              .. .+...|++++|...++++.... +.+..++
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  175 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQ-PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLH  175 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTS-TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHH
Confidence            9999999999999999988764 2233333333              22 3566677777777777776664 4466677


Q ss_pred             HHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhC
Q 042039          160 NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKN  239 (376)
Q Consensus       160 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  239 (376)
                      ..++.++...|++++|...++++.+.. +.+..++..+...+...|++++|...++++.+.. +.+...+..++.++...
T Consensus       176 ~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~  253 (327)
T 3cv0_A          176 ASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNM  253 (327)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHh
Confidence            777777777777777777777776652 3345666677777777777777777777766654 34556666677777777


Q ss_pred             CCHHHHHHHHHHhcccCCCc-----------hHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          240 GYIVEAVELFRTLGILKCEL-----------DIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       240 ~~~~~a~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      |++++|...++++.......           +...+..++.++...|++++|..++++..
T Consensus       254 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          254 SQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             TCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             ccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            77777777776665443221           35566666666667777777766666544

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

Probab=99.91  E-value=2e-22  Score=169.01  Aligned_cols=266  Identities=12%  Similarity=-0.036  Sum_probs=144.6

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..++..+.+.|++++|+..|+++++..+. +..++..+..++...|++++|...|+++++.. +.+..++..++.+
T Consensus        65 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  142 (365)
T 4eqf_A           65 WPGAFEEGLKRLKEGDLPVTILFMEAAILQDPG-DAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVS  142 (365)
T ss_dssp             CTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            344555555555556666666666555554322 45555555555556666666666665555543 2235555555555


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhh----------HHHHHHHHHccCcHHHHHHHHHHHHHCCCC-CCHhHHHHHHH
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVS----------YNILINGYCKNKEVEEALSLYREMVSKGIK-PTVVTYNTLFL  199 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~----------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~  199 (376)
                      +...|++++|...++++.... +.+...          +..++.++...|++++|+..++++.+.... ++..++..++.
T Consensus       143 ~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~  221 (365)
T 4eqf_A          143 YTNTSHQQDACEALKNWIKQN-PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGV  221 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHH
T ss_pred             HHccccHHHHHHHHHHHHHhC-ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHH
Confidence            666666666666665555442 111122          223355666666666666666666654211 14555666666


Q ss_pred             HHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHH
Q 042039          200 GLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEI  279 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  279 (376)
                      .+...|++++|...++++.+.. +.+..++..++.++...|++++|+..++++.... +.+..++..++.+|...|++++
T Consensus       222 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~  299 (365)
T 4eqf_A          222 LFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYRE  299 (365)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHH
Confidence            6666666666666666666553 3445566666666666666666666666665544 2245566666666666666666


Q ss_pred             HHHHHhcccccCC-----------CCCHHHHHHHHHHHHccCChhHHHHHHHH
Q 042039          280 ALELFRSLPRRVL-----------VADVVTYNIMIHGLCNDGQMDKAHDLFLD  321 (376)
Q Consensus       280 a~~~~~~~~~~~~-----------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  321 (376)
                      |...|+++.+...           ..+...|..+..++...|+.+.+..+.++
T Consensus       300 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          300 AVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            6666666543210           00245566666666666666666665544

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

Probab=99.91  E-value=3.3e-23  Score=173.77  Aligned_cols=265  Identities=12%  Similarity=0.036  Sum_probs=222.5

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      +...+..++..+...|++++|..+|+++++.. +.+..++..++.++...|++++|...|+++.... |.+..++..++.
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  141 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAV  141 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            45568889999999999999999999999875 4578899999999999999999999999999886 667889999999


Q ss_pred             HHHccCcHHHHHHHHHHHHHCCCCCC-----------HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC--CcchHHH
Q 042039          165 GYCKNKEVEEALSLYREMVSKGIKPT-----------VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA--DTSTYNT  231 (376)
Q Consensus       165 ~~~~~~~~~~a~~~~~~~~~~~~~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~  231 (376)
                      +|...|++++|+..++++.+..  |+           ...+..+...+...|++++|...++++.+.. +.  +..++..
T Consensus       142 ~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~  218 (365)
T 4eqf_A          142 SYTNTSHQQDACEALKNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQN-GDMIDPDLQTG  218 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC--HHHHCC-------------------CCHHHHHHHHHHHHHHHHS-CSSCCHHHHHH
T ss_pred             HHHccccHHHHHHHHHHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhC-cCccCHHHHHH
Confidence            9999999999999999998852  22           2223445788999999999999999999875 33  6788999


Q ss_pred             HHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCC
Q 042039          232 FIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQ  311 (376)
Q Consensus       232 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  311 (376)
                      ++..+...|++++|+..++++.... +.+..++..++.++...|++++|...|+++.+. .+.+..++..++.+|...|+
T Consensus       219 l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~  296 (365)
T 4eqf_A          219 LGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEI-QPGFIRSRYNLGISCINLGA  296 (365)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-CCCchHHHHHHHHHHHHCCC
Confidence            9999999999999999999998876 347889999999999999999999999999876 45568899999999999999


Q ss_pred             hhHHHHHHHHHHHcCCC-----------CcHHHHHHHHHHHhhcCChhhHHHHHHH
Q 042039          312 MDKAHDLFLDMEENAVA-----------PNVIIFVTLIHGFVRINKPSKVIELLHK  356 (376)
Q Consensus       312 ~~~a~~~~~~~~~~~~~-----------~~~~~~~~l~~~~~~~g~~~~a~~~~~~  356 (376)
                      +++|...|+++.+....           .+...|..+..++...|+.+.+....++
T Consensus       297 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          297 YREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             CHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            99999999999864211           1357899999999999999988887665

>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=99.90  E-value=9.2e-22  Score=162.31  Aligned_cols=280  Identities=13%  Similarity=-0.042  Sum_probs=179.8

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..++..+...|++++|..+|+++.+..+. +...+..+..++...|++++|...++++.+.. +.+..++..++..
T Consensus        21 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~   98 (327)
T 3cv0_A           21 HENPMEEGLSMLKLANLAEAALAFEAVCQAAPE-REEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVS   98 (327)
T ss_dssp             SSCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHH
Confidence            344555666666666666666666666655322 45555666666666666666666666666543 2345555566666


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHH-HH-HHHhccchH
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTL-FL-GLFEIHQVE  208 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-~~-~~~~~~~~~  208 (376)
                      +...|++++|.+.++++.... +.+...+..+....                      |+......+ .. .+...|+++
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~  155 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQ-PQYEQLGSVNLQAD----------------------VDIDDLNVQSEDFFFAAPNEYR  155 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTS-TTTTTC------------------------------------------CCTTSHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHhHHH----------------------HHHHHHHHHHHhHHHHHcccHH
Confidence            666666666666666665543 22222222220000                      000011111 22 356677777


Q ss_pred             HHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          209 HALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       209 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      +|...++++.+.. +.+...+..++..+...|++++|...++++.... +.+...+..++..+...|++++|...++++.
T Consensus       156 ~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  233 (327)
T 3cv0_A          156 ECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRAL  233 (327)
T ss_dssp             HHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            7777777777664 4466677777788888888888888888877665 3356778888888888888888888888877


Q ss_pred             ccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCC-----------cHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          289 RRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP-----------NVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       289 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      +. .+.+...+..++.++...|++++|...++++.+.....           +...+..+..++.+.|++++|..++++.
T Consensus       234 ~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  312 (327)
T 3cv0_A          234 DI-NPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQN  312 (327)
T ss_dssp             HH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCC
T ss_pred             Hc-CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            65 34567788888888888899999998888887653221           4677888888899999999998887754


Q ss_pred             H
Q 042039          358 K  358 (376)
Q Consensus       358 ~  358 (376)
                      .
T Consensus       313 l  313 (327)
T 3cv0_A          313 V  313 (327)
T ss_dssp             S
T ss_pred             H
Confidence            3

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.89  E-value=1.3e-20  Score=163.66  Aligned_cols=350  Identities=12%  Similarity=-0.043  Sum_probs=242.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhC--------CCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc-----
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGE--------NINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ-----   80 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----   80 (376)
                      .....||.+...+...|++++|++.|++..+.        ..+....+|..++.+|...|++++|...++++.+.     
T Consensus        49 ~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~  128 (472)
T 4g1t_A           49 FKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFS  128 (472)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcc
Confidence            34567999999999999999999999987542        12345678999999999999999999999988753     


Q ss_pred             C-CC-CchHhHHHHHHHHHh--CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH---HhcCcHHHHHHHHHHHHhcCCC
Q 042039           81 G-VQ-PSVVTFNVIMDELCK--NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF---CLTGKINRAEELFGSMESMGCK  153 (376)
Q Consensus        81 ~-~~-~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~~~~  153 (376)
                      + .. ....++.....++..  .+++++|...|++.++.. +.++..+..+..++   ...++.++|.+.+++..+.. |
T Consensus       129 ~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p  206 (472)
T 4g1t_A          129 SPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-P  206 (472)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-S
T ss_pred             cccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-C
Confidence            1 11 134566666655554  457999999999999874 33566666665554   34577788999999988876 5


Q ss_pred             CChhhHHHHHHHHHc----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchH
Q 042039          154 HDDVSYNILINGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTY  229 (376)
Q Consensus       154 ~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  229 (376)
                      .+..++..+...+..    .+++++|.+.+++.... .+.+..++..+...+...|++++|...+.++.+.. |.+..++
T Consensus       207 ~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~  284 (472)
T 4g1t_A          207 DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEK-APGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLH  284 (472)
T ss_dssp             SCHHHHHHHHHHHHHCC------CHHHHHHHHHHHH-CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHH
T ss_pred             cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh-CccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHH
Confidence            566677666655544    56788999999998886 34567888999999999999999999999998875 5566677


Q ss_pred             HHHHHHHHhC-------------------CCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          230 NTFIDGLCKN-------------------GYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       230 ~~l~~~~~~~-------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      ..++.+|...                   +..+.|...++.+.... +.+...+..++..+...|++++|...|+++.+.
T Consensus       285 ~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~  363 (472)
T 4g1t_A          285 CQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSK  363 (472)
T ss_dssp             HHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhc
Confidence            7777665432                   23567888888877665 335677888999999999999999999998875


Q ss_pred             CCCCCH--HHHHHHHH-HHHccCChhHHHHHHHHHHHcCC-----------------------CCcHHHHHHHHHHHhhc
Q 042039          291 VLVADV--VTYNIMIH-GLCNDGQMDKAHDLFLDMEENAV-----------------------APNVIIFVTLIHGFVRI  344 (376)
Q Consensus       291 ~~~~~~--~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~-----------------------~~~~~~~~~l~~~~~~~  344 (376)
                      ...+..  ..+..+.. .....|++++|+..|+++++...                       +.+..+|..+...|...
T Consensus       364 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~  443 (472)
T 4g1t_A          364 ELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELN  443 (472)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            332221  12333333 34578899999999888765421                       22467889999999999


Q ss_pred             CChhhHHHHHHHHHhCC-CCCchHH
Q 042039          345 NKPSKVIELLHKMKEKK-VMPDASI  368 (376)
Q Consensus       345 g~~~~a~~~~~~~~~~~-~~p~~~~  368 (376)
                      |++++|++.|++..+.+ ..|+..+
T Consensus       444 g~~~~A~~~y~kALe~~~~~p~a~~  468 (472)
T 4g1t_A          444 EKMQQADEDSERGLESGSLIPSASS  468 (472)
T ss_dssp             HHCC---------------------
T ss_pred             CCHHHHHHHHHHHHhcCCCCCcHhh
Confidence            99999999999998764 4455443

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

Probab=99.88  E-value=3.1e-20  Score=149.61  Aligned_cols=253  Identities=11%  Similarity=0.011  Sum_probs=165.5

Q ss_pred             HHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCCh
Q 042039           23 IDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKM  102 (376)
Q Consensus        23 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  102 (376)
                      ++.....|+++.|+..++........+.......+.++|...|+++.|+..++.    ..+|+..++..+...+...++.
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~   81 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRR   81 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcH
Confidence            345667788888888877765543111134556677788888888888776644    1345666777777777778888


Q ss_pred             HHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHH
Q 042039          103 DEASRLLDLMVQRDVRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                      ++|.+.+++++..+..| +...+..++.++...|++++|.+.+++      +.+..++..++.++.+.|++++|.+.+++
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~  155 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKK  155 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            88888888877665333 455666777778888888888888776      45667777777888888888888888888


Q ss_pred             HHHCCCCCCHhHHHHH----HHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC
Q 042039          182 MVSKGIKPTVVTYNTL----FLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC  257 (376)
Q Consensus       182 ~~~~~~~~~~~~~~~l----~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  257 (376)
                      +.+..  |+.. ...+    +..+...|++++|..+|+++.+.. +.+...++.++.++.+.|++++|...++++....+
T Consensus       156 ~~~~~--p~~~-~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p  231 (291)
T 3mkr_A          156 MQDQD--EDAT-LTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDS  231 (291)
T ss_dssp             HHHHC--TTCH-HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHhhC--cCcH-HHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            77752  3321 1222    222333466777777777766653 45566666666667777777777777776665542


Q ss_pred             CchHHHHHHHHHHHHhCCChHH-HHHHHhccccc
Q 042039          258 ELDIQAYNCLIDGLCKSGRLEI-ALELFRSLPRR  290 (376)
Q Consensus       258 ~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~  290 (376)
                       .++.++..++..+...|+.++ +.++++++.+.
T Consensus       232 -~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          232 -GHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             -TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence             256666666666666666654 45566665553

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

Probab=99.88  E-value=3.2e-20  Score=149.60  Aligned_cols=275  Identities=9%  Similarity=0.033  Sum_probs=212.3

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                      ++.....|++..|+..+++.....+.+.......+.++|...|+++.|...++.   . .+|+..++..++..+...++.
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~~~   81 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHSRR   81 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCCcH
Confidence            445667899999999988765542222234556778899999999999986654   2 356677888889999999999


Q ss_pred             HHHHHHHHHHHhcCC-CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHH
Q 042039          138 NRAEELFGSMESMGC-KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEE  216 (376)
Q Consensus       138 ~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  216 (376)
                      ++|.+.++++...+. |.+...+..++.++...|++++|++.+++      +.+...+..++..+.+.|++++|.+.+++
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~  155 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKK  155 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            999999999887653 55677888888999999999999999987      46788899999999999999999999999


Q ss_pred             HHhcCCCCCcchHHHHH----HHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCC
Q 042039          217 MQRDDVAADTSTYNTFI----DGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVL  292 (376)
Q Consensus       217 ~~~~~~~~~~~~~~~l~----~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  292 (376)
                      +.+..  |+.. ...+.    ..+...|++++|..+|+++.... +.++..++.++.++.+.|++++|...++++... .
T Consensus       156 ~~~~~--p~~~-~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~-~  230 (291)
T 3mkr_A          156 MQDQD--EDAT-LTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDK-D  230 (291)
T ss_dssp             HHHHC--TTCH-HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C
T ss_pred             HHhhC--cCcH-HHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-C
Confidence            98874  3332 22222    33445689999999999998875 458889999999999999999999999998876 4


Q ss_pred             CCCHHHHHHHHHHHHccCChhH-HHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHH
Q 042039          293 VADVVTYNIMIHGLCNDGQMDK-AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIE  352 (376)
Q Consensus       293 ~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  352 (376)
                      |.++.++..++..+...|+.++ +.++++++.+..  |+.....   ....+.+.++++..
T Consensus       231 p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~--P~~~~~~---d~~~~~~~fd~~~~  286 (291)
T 3mkr_A          231 SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAH--RSHPFIK---EYRAKENDFDRLVL  286 (291)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHH---HHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC--CCChHHH---HHHHHHHHHHHHHH
Confidence            6678899999999999999876 578889988753  4433222   22344455555544

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

Probab=99.87  E-value=2.7e-18  Score=150.98  Aligned_cols=340  Identities=8%  Similarity=0.053  Sum_probs=238.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      -|..+|..++. +.+.|++++|..+|+++.+.. |.+...|..++..+.+.|++++|..+|++++..  .|+...|..++
T Consensus        11 ~~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw~~~~   86 (530)
T 2ooe_A           11 YDLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLWKCYL   86 (530)
T ss_dssp             TCHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHHHHHH
T ss_pred             CCHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHHHHHH
Confidence            36778999998 478899999999999999875 778889999999999999999999999999886  35777777766


Q ss_pred             HHH-HhCCChHHHHH----HHHHHHhc-CCCC-ChhhHHHHHHHHHh---------cCcHHHHHHHHHHHHhcCCCCChh
Q 042039           94 DEL-CKNGKMDEASR----LLDLMVQR-DVRP-NAFTYSTLMDGFCL---------TGKINRAEELFGSMESMGCKHDDV  157 (376)
Q Consensus        94 ~~~-~~~~~~~~a~~----~~~~~~~~-~~~~-~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~  157 (376)
                      ... ...|+.++|.+    +|+..+.. |..| +...|...+.....         .|+++.|..+|++...........
T Consensus        87 ~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~  166 (530)
T 2ooe_A           87 SYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQ  166 (530)
T ss_dssp             HHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHH
T ss_pred             HHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHH
Confidence            533 35577666654    66666542 3333 35566666665544         677888888888877631111112


Q ss_pred             hHHHHHHHH-------------HccCcHH---------------------------------------------------
Q 042039          158 SYNILINGY-------------CKNKEVE---------------------------------------------------  173 (376)
Q Consensus       158 ~~~~l~~~~-------------~~~~~~~---------------------------------------------------  173 (376)
                      .|.......             .+.+++.                                                   
T Consensus       167 ~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~  246 (530)
T 2ooe_A          167 LWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLR  246 (530)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCcc
Confidence            222111100             0111122                                                   


Q ss_pred             ---------HHHHHHHHHHHCCCCCCHhHHHHHHHHHHh-------ccchH-------HHHHHHHHHHhcCCCCCcchHH
Q 042039          174 ---------EALSLYREMVSKGIKPTVVTYNTLFLGLFE-------IHQVE-------HALKLFEEMQRDDVAADTSTYN  230 (376)
Q Consensus       174 ---------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~  230 (376)
                               .+..+|++++.. .+.+...|..++..+.+       .|+++       +|..++++.++.-.+.+...+.
T Consensus       247 ~~~~~~~~~~a~~~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~  325 (530)
T 2ooe_A          247 TEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYF  325 (530)
T ss_dssp             CSCSHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHH
T ss_pred             CCcchhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHH
Confidence                     344455555553 23345666666666664       67776       8889998888632355677888


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhcccCCCchH-HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHH-HHc
Q 042039          231 TFIDGLCKNGYIVEAVELFRTLGILKCELDI-QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHG-LCN  308 (376)
Q Consensus       231 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~  308 (376)
                      .++..+.+.|++++|..+|+++....+. ++ ..|..++..+.+.|++++|..+|+++.+. .+.+...+...+.. +..
T Consensus       326 ~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~-~~~~~~~~~~~a~~~~~~  403 (530)
T 2ooe_A          326 AYADYEESRMKYEKVHSIYNRLLAIEDI-DPTLVYIQYMKFARRAEGIKSGRMIFKKARED-ARTRHHVYVTAALMEYYC  403 (530)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSSSS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC-TTCCTHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHhCcccc-CchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc-cCCchHHHHHHHHHHHHH
Confidence            8888888999999999999998876422 33 57888888888889999999999988775 23334444433333 335


Q ss_pred             cCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          309 DGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       309 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      .|++++|..+|+++++.. +.+...|..++..+.+.|+.++|..+|++....+
T Consensus       404 ~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          404 SKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             TCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             cCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            899999999999988763 2367888888988999999999999999998764

>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=99.86  E-value=7.8e-21  Score=156.47  Aligned_cols=268  Identities=13%  Similarity=0.174  Sum_probs=138.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      +++.+|..++.++.+.|++++|++.|.+.      +|..+|..++..+...|++++|+..++..++.  .+++.+.+.++
T Consensus        30 ~~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li  101 (449)
T 1b89_A           30 NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELI  101 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHH
Confidence            45569999999999999999999999653      47779999999999999999999988877764  44577888999


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHH
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  173 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  173 (376)
                      .+|.+.|+++++.++++       .|+..+|..++..|...|.+++|..+|..+         ..|..++.++.+.|+++
T Consensus       102 ~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq  165 (449)
T 1b89_A          102 FALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQ  165 (449)
T ss_dssp             -------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHH
T ss_pred             HHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccHH
Confidence            99999999999888774       367779999999999999999999999966         46999999999999999


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhc
Q 042039          174 EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLG  253 (376)
Q Consensus       174 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  253 (376)
                      +|.+.++++      .++.+|..++.+|...|+++.|......+     ...+.-...++..|.+.|.+++|+.+++...
T Consensus       166 ~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L-----~~~ad~l~~lv~~Yek~G~~eEai~lLe~aL  234 (449)
T 1b89_A          166 AAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI-----VVHADELEELINYYQDRGYFEELITMLEAAL  234 (449)
T ss_dssp             HHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTT-----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHH-----HhCHhhHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            999999988      27889999999999999999996655432     2344446678889999999999999999998


Q ss_pred             ccCCCchHHHHHHHHHHHHhC--CChHHHHHHHhcccccCCCC------CHHHHHHHHHHHHccCChhHHHHHH
Q 042039          254 ILKCELDIQAYNCLIDGLCKS--GRLEIALELFRSLPRRVLVA------DVVTYNIMIHGLCNDGQMDKAHDLF  319 (376)
Q Consensus       254 ~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~a~~~~  319 (376)
                      ... +.....|..+..+|++-  ++..+.++.|..-..  ++|      +...|..+...|...++++.|....
T Consensus       235 ~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~in--i~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~tm  305 (449)
T 1b89_A          235 GLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVN--IPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITM  305 (449)
T ss_dssp             TST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSC--HHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhc--CcHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH
Confidence            776 45678888888887764  455666666654332  333      4678899999999999999887643

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

Probab=99.85  E-value=2.7e-17  Score=144.65  Aligned_cols=342  Identities=11%  Similarity=0.036  Sum_probs=247.4

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHH-hcCCChHHHHH----HHHHHHhc-CCCC-c
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGL-CHANDWNEAKR----LFFEMMDQ-GVQP-S   85 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~a~~----~~~~~~~~-~~~~-~   85 (376)
                      +-+...|..++..+.+.|++++|..+|+++....  |+...|..++... ...|+.+.|.+    +|++.+.. |..| +
T Consensus        43 P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p~~~lw~~~~~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~  120 (530)
T 2ooe_A           43 PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--LHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMS  120 (530)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--CCHHHHHHHHHHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTC
T ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CChHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHCCCCccc
Confidence            4466789999999999999999999999999874  5777887777533 45577776655    67766553 4333 4


Q ss_pred             hHhHHHHHHHHHh---------CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH-------------HhcCcH------
Q 042039           86 VVTFNVIMDELCK---------NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF-------------CLTGKI------  137 (376)
Q Consensus        86 ~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-------------~~~~~~------  137 (376)
                      ...|...+.....         .|+++.|..+|++.++....+....|.......             ...+++      
T Consensus       121 ~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~  200 (530)
T 2ooe_A          121 YQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRV  200 (530)
T ss_dssp             HHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHH
Confidence            5566666665544         577888888888887631111012222111100             000111      


Q ss_pred             ------------------------------------------------------HHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039          138 ------------------------------------------------------NRAEELFGSMESMGCKHDDVSYNILI  163 (376)
Q Consensus       138 ------------------------------------------------------~~a~~~~~~~~~~~~~~~~~~~~~l~  163 (376)
                                                                            +.+..+|+++.... |.++..|..++
T Consensus       201 ~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~  279 (530)
T 2ooe_A          201 AKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAA  279 (530)
T ss_dssp             HHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence                                                                  24445666665543 55677788888


Q ss_pred             HHHHc-------cCcHH-------HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCc-ch
Q 042039          164 NGYCK-------NKEVE-------EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT-ST  228 (376)
Q Consensus       164 ~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~  228 (376)
                      ..+.+       .|+++       +|..++++.++.-.+.+...|..++..+.+.|++++|..+|+++++.. +.+. ..
T Consensus       280 ~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~  358 (530)
T 2ooe_A          280 QYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE-DIDPTLV  358 (530)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS-SSCHHHH
T ss_pred             HHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcc-ccCchHH
Confidence            87775       78877       899999999873234468889999999999999999999999999863 2232 47


Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHH-HHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHH
Q 042039          229 YNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG-LCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLC  307 (376)
Q Consensus       229 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  307 (376)
                      |..++..+.+.|+.++|..+|+++..... .+...+...+.. +...|+.++|..+|+++.+. .+.+...|..++..+.
T Consensus       359 ~~~~~~~~~~~~~~~~A~~~~~~Al~~~~-~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~-~p~~~~~~~~~~~~~~  436 (530)
T 2ooe_A          359 YIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLS  436 (530)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCTT-CCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhccC-CchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH-CCCCHHHHHHHHHHHH
Confidence            88888888899999999999999987642 233444333333 34689999999999998876 4557889999999999


Q ss_pred             ccCChhHHHHHHHHHHHcCC-CCc--HHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          308 NDGQMDKAHDLFLDMEENAV-APN--VIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       308 ~~~~~~~a~~~~~~~~~~~~-~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      +.|+.++|..+|+++...+. .|+  ...|...+......|+.+.+..+++++.+.
T Consensus       437 ~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          437 HLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             TTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             hCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            99999999999999998642 232  447888888888899999999999998764

>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=99.85  E-value=2.4e-20  Score=153.56  Aligned_cols=282  Identities=12%  Similarity=0.137  Sum_probs=136.4

Q ss_pred             hcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHH
Q 042039           28 KEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASR  107 (376)
Q Consensus        28 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  107 (376)
                      +.|++++|.+.++++.      ++.+|..++.++.+.|++++|++.|.+.      +|...|..++..+...|++++|..
T Consensus        15 ~~~~ld~A~~fae~~~------~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           15 HIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCC------ChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHH
Confidence            6688999999999883      2358999999999999999999999653      477799999999999999999999


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCC
Q 042039          108 LLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGI  187 (376)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  187 (376)
                      +++..++.  .+++.+...++.+|.+.|++.++.++++       .|+..+|..++..|...|.+++|...|..+     
T Consensus        83 yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-----  148 (449)
T 1b89_A           83 YLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----  148 (449)
T ss_dssp             ----------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT-----
T ss_pred             HHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh-----
Confidence            88887774  4457788899999999999999998884       366679999999999999999999999976     


Q ss_pred             CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHH
Q 042039          188 KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCL  267 (376)
Q Consensus       188 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  267 (376)
                          ..|..++.++.+.|+++.|.+.+.++      .++.+|..++.+|...|+++.|......+.     ..+.....+
T Consensus       149 ----~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-----~~ad~l~~l  213 (449)
T 1b89_A          149 ----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-----VHADELEEL  213 (449)
T ss_dssp             ----TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-----TCHHHHHHH
T ss_pred             ----hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-----hCHhhHHHH
Confidence                47899999999999999999999988      267899999999999999999976655432     244446678


Q ss_pred             HHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc--CChhHHHHHHHHHHHcCCCC------cHHHHHHHHH
Q 042039          268 IDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND--GQMDKAHDLFLDMEENAVAP------NVIIFVTLIH  339 (376)
Q Consensus       268 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~  339 (376)
                      +..|.+.|++++|..+++...... +-....|..+..+|++-  ++..+.++.|..-+  +++|      +...|..++.
T Consensus       214 v~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~i--ni~k~~~~~~~~~~w~e~~~  290 (449)
T 1b89_A          214 INYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRV--NIPKVLRAAEQAHLWAELVF  290 (449)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTS--CHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh--cCcHHHHHHHHHHHHHHHHH
Confidence            999999999999999999988663 55677888888888764  34444444443221  2333      4567999999


Q ss_pred             HHhhcCChhhHHHH
Q 042039          340 GFVRINKPSKVIEL  353 (376)
Q Consensus       340 ~~~~~g~~~~a~~~  353 (376)
                      .|...++++.|...
T Consensus       291 ly~~~~e~d~A~~t  304 (449)
T 1b89_A          291 LYDKYEEYDNAIIT  304 (449)
T ss_dssp             HHHHTTCHHHHHHH
T ss_pred             HHHhhchHHHHHHH
Confidence            99999999988764

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

Probab=99.84  E-value=4.9e-19  Score=136.56  Aligned_cols=210  Identities=13%  Similarity=0.005  Sum_probs=105.9

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      ++++..+..+...+.+.|++++|+..|++..+.+ |.+...+..+..++...|++++|+..++++++..+. +...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPR-YLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHH
Confidence            4556666666677777777777777777766654 556666667777777777777777777776665332 45556666


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      ..++...+             ..  ...         .....|++++|...+++..+.. |.+...+..++.++...|++
T Consensus        80 g~~~~~~~-------------~~--~~~---------~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~  134 (217)
T 2pl2_A           80 SEAYVALY-------------RQ--AED---------RERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGER  134 (217)
T ss_dssp             HHHHHHHH-------------HT--CSS---------HHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhh-------------hh--hhh---------hcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCh
Confidence            66665550             00  000         0001155555555555554443 33444555555555555555


Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      ++|+..|+++++..  .+...+..+..++...|++++|...++++.+.. |.+...+..++.++...|++++|+..+++.
T Consensus       135 ~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          135 DKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            55555555555543  344455555555555555555555555555443 334444555555555555555555555443

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

Probab=99.84  E-value=8.5e-19  Score=139.35  Aligned_cols=226  Identities=12%  Similarity=0.085  Sum_probs=147.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--Cc----hHhH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PS----VVTF   89 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~   89 (376)
                      ...|..+...+...|++++|+..|+++.+..  .+..++..++.++...|++++|.+.++++.+....  ++    ..++
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            4567777777777788888888877777665  56677777777777777777777777777664211  11    4566


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      ..+..++...|++++|...++++.+..  |+.       ..+...|++++|...++++.... +.+...+..++.++...
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  152 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSLTEH--RTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTK  152 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--CCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcC--chh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHh
Confidence            677777777777777777777777642  332       33445566777777777766654 34555666667777777


Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELF  249 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  249 (376)
                      |++++|+..++++.+.. +.+..++..+..++...|++++|...++++.+.. +.+...+..++.++...|++++|...+
T Consensus       153 ~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  230 (258)
T 3uq3_A          153 SDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETL  230 (258)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            77777777777766642 3345566666666666666666666666666553 334555666666666666666666666


Q ss_pred             HHhccc
Q 042039          250 RTLGIL  255 (376)
Q Consensus       250 ~~~~~~  255 (376)
                      +.+...
T Consensus       231 ~~a~~~  236 (258)
T 3uq3_A          231 DAARTK  236 (258)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            665443

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

Probab=99.84  E-value=6.3e-19  Score=135.94  Aligned_cols=200  Identities=14%  Similarity=0.014  Sum_probs=143.6

Q ss_pred             CchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           84 PSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILI  163 (376)
Q Consensus        84 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  163 (376)
                      ++...+..+...+...|++++|...+++.++.. +.+...+..++.++...|++++|...++++.+.. |.+...+..++
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            345556666666666666666666666666653 3345666666666666666666666666666654 45556666666


Q ss_pred             HHHHcc-----------CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHH
Q 042039          164 NGYCKN-----------KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTF  232 (376)
Q Consensus       164 ~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  232 (376)
                      .++...           |++++|+..+++.++.. +.+...+..+..++...|++++|+..++++++.+  .+...+..+
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~l  157 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSAL  157 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHH
Confidence            666666           99999999999999863 3467889999999999999999999999999887  678899999


Q ss_pred             HHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          233 IDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       233 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                      +.++...|++++|+..++++.... +.++..+..++.++...|++++|...+++...
T Consensus       158 a~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  213 (217)
T 2pl2_A          158 AELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAALEHH  213 (217)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC----------------
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHhh
Confidence            999999999999999999998876 34788899999999999999999999987653

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

Probab=99.84  E-value=1.2e-18  Score=138.42  Aligned_cols=223  Identities=13%  Similarity=0.052  Sum_probs=116.6

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC--CC----hhhHHH
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCK--HD----DVSYNI  161 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~~~  161 (376)
                      .+..+...+...|++++|...++++++..  .+..++..++.++...|++++|...++++......  ++    ..++..
T Consensus         7 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            7 KEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            34444444445555555555555544443  34444445555555555555555555544433200  00    345555


Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCC
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGY  241 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  241 (376)
                      ++.++...|++++|...++++.+.  .|+.       ..+...|++++|...++.+.... +.+...+..++..+...|+
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  154 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTKSD  154 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHhcC
Confidence            555555566666666666555553  2221       22344455555666555555543 2334455555555666666


Q ss_pred             HHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHH
Q 042039          242 IVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLD  321 (376)
Q Consensus       242 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  321 (376)
                      +++|...++++.... +.+...+..++..+...|++++|...++++.+. .+.+...+..++.++...|++++|...+++
T Consensus       155 ~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  232 (258)
T 3uq3_A          155 WPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEK-DPNFVRAYIRKATAQIAVKEYASALETLDA  232 (258)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh-CHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            666666666655443 224555556666666666666666666665544 233455566666666666666666666666


Q ss_pred             HHH
Q 042039          322 MEE  324 (376)
Q Consensus       322 ~~~  324 (376)
                      +.+
T Consensus       233 a~~  235 (258)
T 3uq3_A          233 ART  235 (258)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

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

Probab=99.84  E-value=3.4e-18  Score=137.07  Aligned_cols=250  Identities=15%  Similarity=0.054  Sum_probs=176.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc--hHhHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS--VVTFNVI   92 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l   92 (376)
                      |...+......+...|++++|+..|+++.+.. |.+..++..++.++...|++++|++.++++.+.+..++  ...|..+
T Consensus         2 n~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~l   80 (272)
T 3u4t_A            2 NDDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYY   80 (272)
T ss_dssp             ---CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHH
Confidence            34556777788888889999999998888775 55667888888888888999999988888887432222  2347788


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      ...+...|++++|...+++..+.. +.+..++..++.++...|++++|...++++.... +.+...+..++..+...+++
T Consensus        81 g~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~  158 (272)
T 3u4t_A           81 GKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEY  158 (272)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHH
Confidence            888888888888888888888764 3356788888888888888888888888887764 55667777777333344588


Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccc---hHHHHHHHHHHHhcC-CCCC------cchHHHHHHHHHhCCCH
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ---VEHALKLFEEMQRDD-VAAD------TSTYNTFIDGLCKNGYI  242 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~l~~~~~~~~~~  242 (376)
                      ++|...++++.+.. +.+...+..+..++...++   +++|...++++.+.. ..|+      ..++..++..|...|++
T Consensus       159 ~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  237 (272)
T 3u4t_A          159 VKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDK  237 (272)
T ss_dssp             HHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCH
Confidence            88888888888752 3346677777777777777   777777777766542 1122      13566666777777777


Q ss_pred             HHHHHHHHHhcccCCCchHHHHHHHHH
Q 042039          243 VEAVELFRTLGILKCELDIQAYNCLID  269 (376)
Q Consensus       243 ~~a~~~~~~~~~~~~~~~~~~~~~l~~  269 (376)
                      ++|...++++....+. ++.....+..
T Consensus       238 ~~A~~~~~~al~~~p~-~~~a~~~l~~  263 (272)
T 3u4t_A          238 VKADAAWKNILALDPT-NKKAIDGLKM  263 (272)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHC-
T ss_pred             HHHHHHHHHHHhcCcc-HHHHHHHhhh
Confidence            7777777777665422 4444444433

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.84  E-value=2.2e-17  Score=143.30  Aligned_cols=308  Identities=11%  Similarity=-0.045  Sum_probs=228.8

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc--------CCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcC---
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ--------GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD---  116 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---  116 (376)
                      +.....|+.++..+...|++++|++.|++.++.        ..+....+|..+..+|...|++++|...++++.+..   
T Consensus        48 ~~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~  127 (472)
T 4g1t_A           48 EFKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKF  127 (472)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHS
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhc
Confidence            445678999999999999999999999988652        112245689999999999999999999999887521   


Q ss_pred             ---CCC-ChhhHHHHHHHHHh--cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHH---HccCcHHHHHHHHHHHHHCCC
Q 042039          117 ---VRP-NAFTYSTLMDGFCL--TGKINRAEELFGSMESMGCKHDDVSYNILINGY---CKNKEVEEALSLYREMVSKGI  187 (376)
Q Consensus       117 ---~~~-~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~~~  187 (376)
                         ..+ ...++.....++..  .+++++|...|+++.... |.++..+..+..++   ...++.++|++.+++.++.. 
T Consensus       128 ~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-  205 (472)
T 4g1t_A          128 SSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-  205 (472)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-
T ss_pred             ccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-
Confidence               111 24556666655554  457999999999999886 55666776666554   44677788999999988853 


Q ss_pred             CCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHH
Q 042039          188 KPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQA  263 (376)
Q Consensus       188 ~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  263 (376)
                      +.+..++..+...+..    .+++++|.+.+++..... +....++..++..|...|++++|...++++....+. +..+
T Consensus       206 p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~  283 (472)
T 4g1t_A          206 PDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPN-NAYL  283 (472)
T ss_dssp             SSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHH
T ss_pred             CcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCC-hHHH
Confidence            3355666666555443    467889999999998875 667788999999999999999999999999887633 6777


Q ss_pred             HHHHHHHHHhC-------------------CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          264 YNCLIDGLCKS-------------------GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       264 ~~~l~~~~~~~-------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      +..++.+|...                   +.+++|...++++... .+.+...+..++..+...|++++|+..|+++++
T Consensus       284 ~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~  362 (472)
T 4g1t_A          284 HCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEA-NDNLFRVCSILASLHALADQYEEAEYYFQKEFS  362 (472)
T ss_dssp             HHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHH-CTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhc-CCchhhhhhhHHHHHHHhccHHHHHHHHHHHHh
Confidence            77777766432                   2366788888887765 355677888999999999999999999999998


Q ss_pred             cCCCCcHH--HHHHHHH-HHhhcCChhhHHHHHHHHHhC
Q 042039          325 NAVAPNVI--IFVTLIH-GFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       325 ~~~~~~~~--~~~~l~~-~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      ....+...  .+..+.. .+...|++++|+..|++..+.
T Consensus       363 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i  401 (472)
T 4g1t_A          363 KELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKI  401 (472)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHS
T ss_pred             cCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            65443321  2333332 345789999999999998764

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

Probab=99.83  E-value=7.6e-18  Score=135.01  Aligned_cols=235  Identities=11%  Similarity=-0.011  Sum_probs=151.7

Q ss_pred             hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC--HhHHHHHHH
Q 042039          122 FTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT--VVTYNTLFL  199 (376)
Q Consensus       122 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~  199 (376)
                      ..+...+..+...|++++|...|+++.+.. |.+...+..++.++...|++++|+..++++.+.+..++  ...+..+..
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGK   82 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHH
Confidence            344555666666677777777776666654 34455666666677777777777777776666321111  223666667


Q ss_pred             HHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHH
Q 042039          200 GLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEI  279 (376)
Q Consensus       200 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  279 (376)
                      .+...|++++|...++++.+.. +.+..++..++..+...|++++|+..++++.... +.+...+..++..+...+++++
T Consensus        83 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~  160 (272)
T 3u4t_A           83 ILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVK  160 (272)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHH
Confidence            7777777777777777776654 4455677777777777777777777777777664 3356666666633334457777


Q ss_pred             HHHHHhcccccCCCCCHHHHHHHHHHHHccCC---hhHHHHHHHHHHHcC-CCCc------HHHHHHHHHHHhhcCChhh
Q 042039          280 ALELFRSLPRRVLVADVVTYNIMIHGLCNDGQ---MDKAHDLFLDMEENA-VAPN------VIIFVTLIHGFVRINKPSK  349 (376)
Q Consensus       280 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~l~~~~~~~g~~~~  349 (376)
                      |...++++.+. .+.+...+..++.++...|+   +++|...++++.+.. ..|+      ...|..+...|...|++++
T Consensus       161 A~~~~~~a~~~-~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  239 (272)
T 3u4t_A          161 ADSSFVKVLEL-KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVK  239 (272)
T ss_dssp             HHHHHHHHHHH-STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHh-CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHH
Confidence            77777777665 34456666777777777776   777777777776531 1122      2456667777777788888


Q ss_pred             HHHHHHHHHhC
Q 042039          350 VIELLHKMKEK  360 (376)
Q Consensus       350 a~~~~~~~~~~  360 (376)
                      |.+.++++.+.
T Consensus       240 A~~~~~~al~~  250 (272)
T 3u4t_A          240 ADAAWKNILAL  250 (272)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            88888877754

>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=99.82  E-value=5.5e-18  Score=141.00  Aligned_cols=249  Identities=9%  Similarity=-0.007  Sum_probs=178.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC-hHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND-WNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      ..+|+.+...+.+.|++++|+..++++++.+ |.+..+|..+..++...|+ +++|+..|+++++.... +...|..+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~-~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCC-CHHHHHHHHH
Confidence            4567777778888888888888888888775 6677788888888888886 88888888888887544 6777888888


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc-cCcHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK-NKEVE  173 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~  173 (376)
                      ++...|++++|+..|+++++.+ +-+...|..+..++...|++++|+..++++.... +.+..+|+.++.++.. .|..+
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcch
Confidence            8888888888888888888764 3467778888888888888888888888888776 5677788888888877 55546


Q ss_pred             HH-----HHHHHHHHHCCCCCCHhHHHHHHHHHHhcc--chHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC------
Q 042039          174 EA-----LSLYREMVSKGIKPTVVTYNTLFLGLFEIH--QVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG------  240 (376)
Q Consensus       174 ~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~------  240 (376)
                      +|     +..+++++... +-+...|..+...+...|  ++++|.+.+.++ +.. +.+...+..++.+|.+.|      
T Consensus       253 eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~-p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          253 RAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPS-HSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTT-CCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccC-CCCHHHHHHHHHHHHHHhcccccc
Confidence            66     47777777642 335667777777777766  577777777776 332 445566677777776653      


Q ss_pred             ---CHHHHHHHHHHh-cccCCCchHHHHHHHHHHHH
Q 042039          241 ---YIVEAVELFRTL-GILKCELDIQAYNCLIDGLC  272 (376)
Q Consensus       241 ---~~~~a~~~~~~~-~~~~~~~~~~~~~~l~~~~~  272 (376)
                         ..++|+.+++++ .+.+ +.....|..++..+.
T Consensus       330 ~~~~~~~A~~~~~~l~~~~D-P~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          330 KEDILNKALELCEILAKEKD-TIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHTTC-GGGHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhC-chhHHHHHHHHHHHH
Confidence               247777777777 4443 224455555554443

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

Probab=99.81  E-value=9.9e-18  Score=134.56  Aligned_cols=247  Identities=9%  Similarity=-0.074  Sum_probs=151.3

Q ss_pred             cCCChHHHHHHHHHHHhcCCC---CchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHH
Q 042039           63 HANDWNEAKRLFFEMMDQGVQ---PSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINR  139 (376)
Q Consensus        63 ~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  139 (376)
                      ..|++++|++.|+++++....   .+..++..++..+...|++++|...++++++.. +.+..++..++.++...|++++
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            346677777777777665221   134566667777777777777777777777653 3356677777777777777777


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       140 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      |...|+++.... +.+..++..++.++...|++++|...++++.+.  .|+.......+..+...|++++|...+.....
T Consensus        96 A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  172 (275)
T 1xnf_A           96 AYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFE  172 (275)
T ss_dssp             HHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            777777777664 445667777777777778888888888777764  33333333344444566777888887777666


Q ss_pred             cCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc---hHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCH
Q 042039          220 DDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCEL---DIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV  296 (376)
Q Consensus       220 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  296 (376)
                      .. +++... ..++..+...++.++|...++.+.......   +...+..++..+...|++++|...|+++.... +.+ 
T Consensus       173 ~~-~~~~~~-~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~-  248 (275)
T 1xnf_A          173 KS-DKEQWG-WNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN-VHN-  248 (275)
T ss_dssp             HS-CCCSTH-HHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-CTT-
T ss_pred             cC-CcchHH-HHHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-chh-
Confidence            53 333333 345666667777777777777766543111   13556666666666666666666666665541 112 


Q ss_pred             HHHHHHHHHHHccCChhHHHHHH
Q 042039          297 VTYNIMIHGLCNDGQMDKAHDLF  319 (376)
Q Consensus       297 ~~~~~l~~~~~~~~~~~~a~~~~  319 (376)
                        +.....++...|++++|++.+
T Consensus       249 --~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          249 --FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             --CHHHHHHHHHHHHHHHC----
T ss_pred             --HHHHHHHHHHHHHHHhhHHHH
Confidence              222234455555555555544

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.81  E-value=4.8e-18  Score=145.70  Aligned_cols=314  Identities=15%  Similarity=0.077  Sum_probs=207.7

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCCh---HHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDW---NEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .+...+.+.|++++|+++|++..+.|   ++.++..+...|...|++   ++|...|++..+.    ++..+..+...+.
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~   80 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLA   80 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC--------------------------------CHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHH
Confidence            35667778888888888888887765   444555666677777777   7888888877753    5556666666555


Q ss_pred             hCC-----ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh-----------------------------------cCc-
Q 042039           98 KNG-----KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL-----------------------------------TGK-  136 (376)
Q Consensus        98 ~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----------------------------------~~~-  136 (376)
                      ..+     ++++|...|++..+.|.   ...+..+...|..                                   .+. 
T Consensus        81 ~~~~~~~~~~~~A~~~~~~Aa~~g~---~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~  157 (452)
T 3e4b_A           81 AKPGATEAEHHEAESLLKKAFANGE---GNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQGTY  157 (452)
T ss_dssp             TC--CCHHHHHHHHHHHHHHHHTTC---SSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHHTCG
T ss_pred             hCCCCCCcCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCc
Confidence            554     66788888888777542   1244444444443                                   332 


Q ss_pred             ---HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC---cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc----cc
Q 042039          137 ---INRAEELFGSMESMGCKHDDVSYNILINGYCKNK---EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI----HQ  206 (376)
Q Consensus       137 ---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~  206 (376)
                         .+.+..+++...    ..++.++..+..+|...|   +.++|+..|++..+.| +++...+..+...|...    ++
T Consensus       158 ~~~~~~a~~~~~~a~----~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d  232 (452)
T 3e4b_A          158 DQHLDDVERICKAAL----NTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPD  232 (452)
T ss_dssp             GGGHHHHHHHHHHHT----TTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCC
T ss_pred             ccCHHHHHHHHHHHH----cCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCC
Confidence               222333333332    234448888899998899   8999999999998875 34555556777777655    68


Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHH-H--HhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCC-----ChH
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDG-L--CKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSG-----RLE  278 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~  278 (376)
                      +++|...|++..    +.++..+..+... +  ...+++++|+.+|++....+   ++..+..++..|. .|     +++
T Consensus       233 ~~~A~~~~~~aa----~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~  304 (452)
T 3e4b_A          233 EKTAQALLEKIA----PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAK  304 (452)
T ss_dssp             HHHHHHHHHHHG----GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHH
T ss_pred             HHHHHHHHHHHc----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHH
Confidence            999999999987    3466777888877 4  56889999999999988766   6677888888887 45     999


Q ss_pred             HHHHHHhcccccCCCCCHHHHHHHHHHHHc----cCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh----cCChhhH
Q 042039          279 IALELFRSLPRRVLVADVVTYNIMIHGLCN----DGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR----INKPSKV  350 (376)
Q Consensus       279 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a  350 (376)
                      +|...|++..    +.++.....+...|..    ..++++|...|++..+.|   +......|...|..    ..++++|
T Consensus       305 ~A~~~~~~Aa----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~d~~~A  377 (452)
T 3e4b_A          305 AAEAHFEKAV----GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG---QNSADFAIAQLFSQGKGTKPDPLNA  377 (452)
T ss_dssp             HHHHHHHTTT----TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTHHHHHHHHHHSCTTBCCCHHHH
T ss_pred             HHHHHHHHHh----CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHHHHHHHHHHHhCCCCCCCHHHH
Confidence            9999999987    3467788888888876    448999999999998865   34555666666664    4589999


Q ss_pred             HHHHHHHHhCCCCC
Q 042039          351 IELLHKMKEKKVMP  364 (376)
Q Consensus       351 ~~~~~~~~~~~~~p  364 (376)
                      ..+|++..+.|...
T Consensus       378 ~~~~~~A~~~g~~~  391 (452)
T 3e4b_A          378 YVFSQLAKAQDTPE  391 (452)
T ss_dssp             HHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHCCCHH
Confidence            99999999887543

>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=99.80  E-value=2.4e-17  Score=137.17  Aligned_cols=248  Identities=11%  Similarity=0.069  Sum_probs=185.9

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCc-HHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGK-INRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      ...|..+..++...|++++|+..++++++.. +-+..+|..+..++...|+ +++|+..|+++.... |.+..+|..+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
Confidence            4567777777888888888888888888764 3357778888888888886 888888888888776 567778888888


Q ss_pred             HHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHh-CCCHH
Q 042039          165 GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCK-NGYIV  243 (376)
Q Consensus       165 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~  243 (376)
                      ++...|++++|+..|+++++.. +-+...|..+..++...|++++|+..++++++.+ +.+...+..++.++.. .|..+
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcch
Confidence            8888888888888888888763 3367788888888888888888888888888775 5567778888888887 55546


Q ss_pred             HH-----HHHHHHhcccCCCchHHHHHHHHHHHHhCC--ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccC------
Q 042039          244 EA-----VELFRTLGILKCELDIQAYNCLIDGLCKSG--RLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDG------  310 (376)
Q Consensus       244 ~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~------  310 (376)
                      +|     +..++++....+. +...|..+..++...|  ++++|.+.+.++ +. .+.+...+..++.+|.+.|      
T Consensus       253 eA~~~~el~~~~~Al~l~P~-~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          253 RAVLEREVQYTLEMIKLVPH-NESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHHhcccccc
Confidence            66     4778887776533 6778888888888877  688888888877 33 4556777888888887764      


Q ss_pred             ---ChhHHHHHHHHH-HHcCCCC-cHHHHHHHHHHHh
Q 042039          311 ---QMDKAHDLFLDM-EENAVAP-NVIIFVTLIHGFV  342 (376)
Q Consensus       311 ---~~~~a~~~~~~~-~~~~~~~-~~~~~~~l~~~~~  342 (376)
                         .+++|+++++++ .+.  .| ....|..+...+.
T Consensus       330 ~~~~~~~A~~~~~~l~~~~--DP~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          330 KEDILNKALELCEILAKEK--DTIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHTT--CGGGHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHh--CchhHHHHHHHHHHHH
Confidence               258888888888 554  34 3455666655543

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

Probab=99.80  E-value=8.1e-18  Score=132.43  Aligned_cols=203  Identities=12%  Similarity=0.094  Sum_probs=125.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      .+...|..+...+...|++++|+..|+++.+.. +.+..++..++.++...|++++|.+.++++.+.... +...+..+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la   98 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSS-AATAYYGAG   98 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCc-chHHHHHHH
Confidence            345667777777777788888888888777654 556777777777777778888888887777765332 566677777


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHH
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  173 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  173 (376)
                      ..+...|++++|...++++.+.. +.+...+..++..+...|++++|...++++.... +.+...+..++.++...|+++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~  176 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLD  176 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHH
Confidence            77777777777777777777653 3356666677777777777777777777776654 445666667777777777777


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          174 EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       174 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                      +|...++++.+.. +.+..++..+..++...|++++|...++++.+..
T Consensus       177 ~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          177 EALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            7777777766642 3345566666666666677777777776666553

>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=99.80  E-value=2.8e-16  Score=125.90  Aligned_cols=224  Identities=13%  Similarity=0.032  Sum_probs=156.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----CCChHHHHHHHHHHHhcCCCCchHhHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH----ANDWNEAKRLFFEMMDQGVQPSVVTFN   90 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~   90 (376)
                      ++.++..+...+...|++++|+..|++..+.   .+..++..+...+..    .+++++|...|++..+.+   +...+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            4566777777777777888888887777763   355667777777777    777777877777777754   566677


Q ss_pred             HHHHHHHh----CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           91 VIMDELCK----NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCKHDDVSYNIL  162 (376)
Q Consensus        91 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  162 (376)
                      .+...+..    .+++++|...+++..+.+   +...+..+...|..    .+++++|..+|++..+.+   +...+..+
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l  152 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTIL  152 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHH
Confidence            77777777    777777777777777654   55667777777777    777777777777777654   45566667


Q ss_pred             HHHHHc----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHHHH
Q 042039          163 INGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTFID  234 (376)
Q Consensus       163 ~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  234 (376)
                      ..+|..    .+++++|+..+++..+.+   +...+..+...+..    .+++++|...+++..+.+   +...+..+..
T Consensus       153 g~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l~~  226 (273)
T 1ouv_A          153 GSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGA  226 (273)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHHHHH
Confidence            777766    777777777777777653   44566666666666    677777777777766653   2455666666


Q ss_pred             HHHh----CCCHHHHHHHHHHhcccC
Q 042039          235 GLCK----NGYIVEAVELFRTLGILK  256 (376)
Q Consensus       235 ~~~~----~~~~~~a~~~~~~~~~~~  256 (376)
                      +|..    .+++++|...++++...+
T Consensus       227 ~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            6666    667777777776666554

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.80  E-value=5.5e-17  Score=139.14  Aligned_cols=307  Identities=10%  Similarity=-0.016  Sum_probs=211.7

Q ss_pred             ChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHH---HHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHH
Q 042039           31 FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNE---AKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASR  107 (376)
Q Consensus        31 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  107 (376)
                      ++++|+..|++..+.|   +..++..|...|...+..++   +.+.+......|   +......+...|...+.++++..
T Consensus        89 ~~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~~~~~~~~~~  162 (452)
T 3e4b_A           89 EHHEAESLLKKAFANG---EGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRTQGTYDQHLD  162 (452)
T ss_dssp             HHHHHHHHHHHHHHTT---CSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHHHTCGGGGHH
T ss_pred             CHHHHHHHHHHHHHCC---CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcccCHH
Confidence            4455555555555543   12244445555544443222   223333322222   23445555566666664444433


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHhcC---cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc----CcHHHHHHHHH
Q 042039          108 LLDLMVQRDVRPNAFTYSTLMDGFCLTG---KINRAEELFGSMESMGCKHDDVSYNILINGYCKN----KEVEEALSLYR  180 (376)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~  180 (376)
                      ....+.+.-...++..+..+...|...|   +.++|.+.|++..+.+ +++...+..+..+|...    +++++|+..|+
T Consensus       163 ~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~  241 (452)
T 3e4b_A          163 DVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDEKTAQALLE  241 (452)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence            3332322212334458889999999999   9999999999999988 56666668888888765    79999999999


Q ss_pred             HHHHCCCCCCHhHHHHHHHH-H--HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC-----CHHHHHHHHHHh
Q 042039          181 EMVSKGIKPTVVTYNTLFLG-L--FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG-----YIVEAVELFRTL  252 (376)
Q Consensus       181 ~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~a~~~~~~~  252 (376)
                      +.. .   .+...+..+... +  ...+++++|...|++..+.+   +...+..+...|. .|     ++++|+.+|++.
T Consensus       242 ~aa-~---g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~A  313 (452)
T 3e4b_A          242 KIA-P---GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKA  313 (452)
T ss_dssp             HHG-G---GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTT
T ss_pred             HHc-C---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHH
Confidence            987 3   356677777776 4  56899999999999998876   6678888888887 45     999999999998


Q ss_pred             cccCCCchHHHHHHHHHHHHh----CCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHc----cCChhHHHHHHHHHHH
Q 042039          253 GILKCELDIQAYNCLIDGLCK----SGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCN----DGQMDKAHDLFLDMEE  324 (376)
Q Consensus       253 ~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~  324 (376)
                      . .+   ++.....++..|..    ..++++|...|++..+.|   +......+...|..    ..++.+|...|+...+
T Consensus       314 a-~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~  386 (452)
T 3e4b_A          314 V-GR---EVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG---QNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKA  386 (452)
T ss_dssp             T-TT---CHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHT
T ss_pred             h-CC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Confidence            8 33   67788888888876    449999999999988865   45567778888774    5689999999999998


Q ss_pred             cCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          325 NAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       325 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      .|.. +.......+......++.++|..+.++..+.
T Consensus       387 ~g~~-~a~~~l~~l~~~~~~~~~~~a~~~~~~~~~~  421 (452)
T 3e4b_A          387 QDTP-EANDLATQLEAPLTPAQRAEGQRLVQQELAA  421 (452)
T ss_dssp             TCCH-HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCH-HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHh
Confidence            8733 3333333334444556777888888876653

>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=99.80  E-value=3e-16  Score=125.73  Aligned_cols=223  Identities=10%  Similarity=0.007  Sum_probs=125.1

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCCCChhhHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCKHDDVSYN  160 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  160 (376)
                      +..++..+...+...|++++|...|++..+.+   +...+..+...+..    .+++++|...|++..+.+   ++.++.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            44455556666666666666666666666522   34555556666666    666666666666666543   455566


Q ss_pred             HHHHHHHc----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHH
Q 042039          161 ILINGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTF  232 (376)
Q Consensus       161 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  232 (376)
                      .+..+|..    .+++++|+..|++..+.+   +...+..+...+..    .+++++|...+++..+.+   +...+..+
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l  152 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTIL  152 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHH
Confidence            66666666    666666666666666542   44555555555555    566666666666555543   33445555


Q ss_pred             HHHHHh----CCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHh----CCChHHHHHHHhcccccCCCCCHHHHHHHHH
Q 042039          233 IDGLCK----NGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCK----SGRLEIALELFRSLPRRVLVADVVTYNIMIH  304 (376)
Q Consensus       233 ~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  304 (376)
                      ...|..    .+++++|+..++++...+   ++..+..++..|..    .+++++|...+++..+.+   +...+..+..
T Consensus       153 g~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l~~  226 (273)
T 1ouv_A          153 GSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGA  226 (273)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHHHHH
Confidence            555555    555555555555555442   23445555555555    555555555555555432   2444455555


Q ss_pred             HHHc----cCChhHHHHHHHHHHHc
Q 042039          305 GLCN----DGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       305 ~~~~----~~~~~~a~~~~~~~~~~  325 (376)
                      .|..    .+++++|.+.|++..+.
T Consensus       227 ~~~~g~~~~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHHH
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHHc
Confidence            5555    55555555555555554

>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=99.79  E-value=1.2e-16  Score=126.52  Aligned_cols=200  Identities=10%  Similarity=-0.050  Sum_probs=95.7

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ..+..++..+...|++++|.+.|+++.+.... +...+..+...+...|++++|...++++.+.. +.+...+..++..+
T Consensus        38 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~  115 (252)
T 2ho1_A           38 DAYIQLGLGYLQRGNTEQAKVPLRKALEIDPS-SADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHH
Confidence            34444444555555555555555554443211 34444444555555555555555555554432 22344444455555


Q ss_pred             HhcCcHHHHHHHHHHHHhcCC-CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHH
Q 042039          132 CLTGKINRAEELFGSMESMGC-KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  210 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  210 (376)
                      ...|++++|.++++++...+. +.+...+..++.++...|++++|...++++.+.. +.+...+..+...+...|++++|
T Consensus       116 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHH
Confidence            555555555555555544111 2233344445555555555555555555554431 22344445555555555555555


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          211 LKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      ...++.+.+.. +.+...+..++..+...|++++|...++.+...
T Consensus       195 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          195 RQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            55555554432 233444445555555555555555555555443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.78  E-value=1.1e-17  Score=142.05  Aligned_cols=302  Identities=14%  Similarity=0.073  Sum_probs=163.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC----hhhHHHHHHHHhcCCChHHHHHHHHHHHhc----CCCC-
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD----VVTYNSLIHGLCHANDWNEAKRLFFEMMDQ----GVQP-   84 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-   84 (376)
                      +....+......+...|++++|+..|+++.+.+ +.+    ..++..++.++...|++++|...++++...    +..| 
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            444556666667777777777777777776653 223    245666677777777777777777765442    1111 


Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-CC----hhhHHHHHHHHHhcCc--------------------HHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR-PN----AFTYSTLMDGFCLTGK--------------------INR  139 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~--------------------~~~  139 (376)
                      ...++..+...+...|++++|...+++.++.... ++    ..++..++..+...|+                    +++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            1334555666666666666666666665543100 01    2244445555555555                    444


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCC-CCHhHHHHHHHHHHhccchHHHHHHHHHHH
Q 042039          140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK-PTVVTYNTLFLGLFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       140 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  218 (376)
                      |...+++.....                               ...+.. ....++..+...+...|++++|...+++..
T Consensus       166 A~~~~~~al~~~-------------------------------~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  214 (406)
T 3sf4_A          166 AVDFYEENLSLV-------------------------------TALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRL  214 (406)
T ss_dssp             HHHHHHHHHHHH-------------------------------HHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-------------------------------HhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            444444433210                               000000 012334444555555555555555555544


Q ss_pred             hcCCC-C----CcchHHHHHHHHHhCCCHHHHHHHHHHhcccC----CCc-hHHHHHHHHHHHHhCCChHHHHHHHhccc
Q 042039          219 RDDVA-A----DTSTYNTFIDGLCKNGYIVEAVELFRTLGILK----CEL-DIQAYNCLIDGLCKSGRLEIALELFRSLP  288 (376)
Q Consensus       219 ~~~~~-~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  288 (376)
                      +.... +    ...++..++..+...|++++|...++++....    ..+ ...++..++..+...|++++|...++++.
T Consensus       215 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  294 (406)
T 3sf4_A          215 LIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHL  294 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence            32100 0    11245556666666666666666666654321    010 14456667777777777777777777655


Q ss_pred             ccCC----C-CCHHHHHHHHHHHHccCChhHHHHHHHHHHHc----CC-CCcHHHHHHHHHHHhhcCCh
Q 042039          289 RRVL----V-ADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN----AV-APNVIIFVTLIHGFVRINKP  347 (376)
Q Consensus       289 ~~~~----~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~g~~  347 (376)
                      ....    . ....++..++.++...|++++|...++++.+.    +. .....++..+...+...|+.
T Consensus       295 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          295 AIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence            3210    0 11446667777788888888888888776543    11 11244566666777766665

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

Probab=99.78  E-value=1e-17  Score=134.43  Aligned_cols=249  Identities=10%  Similarity=-0.017  Sum_probs=196.4

Q ss_pred             HHhcCChhHHHHHHHHhhhCCC---CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCCh
Q 042039           26 LCKEGFVDKAKALFLQMKGENI---NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKM  102 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  102 (376)
                      ....|++++|+..|+++.+...   +.+..++..++.++...|++++|...|+++++..+. +..++..++.++...|++
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~   93 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNF   93 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHccCH
Confidence            3456889999999999998632   235678999999999999999999999999987543 688999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          103 DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      ++|...++++++.. +.+..++..++.++...|++++|...++++....  |+..........+...|++++|...+++.
T Consensus        94 ~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  170 (275)
T 1xnf_A           94 DAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLKQH  170 (275)
T ss_dssp             HHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            99999999999874 4467889999999999999999999999999875  34344444555667789999999999888


Q ss_pred             HHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCC---CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc
Q 042039          183 VSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVA---ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCEL  259 (376)
Q Consensus       183 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  259 (376)
                      .... +++...+ .++..+...++.++|...+.........   .+...+..++..+...|++++|...++++....+. 
T Consensus       171 ~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-  247 (275)
T 1xnf_A          171 FEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVH-  247 (275)
T ss_dssp             HHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCT-
T ss_pred             HhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCch-
Confidence            8752 3344444 4677778888889999999988765321   12577889999999999999999999999876522 


Q ss_pred             hHHHHHHHHHHHHhCCChHHHHHHH
Q 042039          260 DIQAYNCLIDGLCKSGRLEIALELF  284 (376)
Q Consensus       260 ~~~~~~~l~~~~~~~~~~~~a~~~~  284 (376)
                      +   +.....++...|++++|++.+
T Consensus       248 ~---~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          248 N---FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             T---CHHHHHHHHHHHHHHHC----
T ss_pred             h---HHHHHHHHHHHHHHHhhHHHH
Confidence            3   223355677788888888776

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

Probab=99.78  E-value=2.4e-16  Score=122.38  Aligned_cols=203  Identities=9%  Similarity=-0.040  Sum_probs=126.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      ++..|..+...+...|++++|+..++++.+.. +.+..++..++.++...|++++|.+.++++...... +..++..++.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPD-SAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-ChHHHHHHHH
Confidence            34566666777777777777777777766654 445666667777777777777777777776665322 4556666666


Q ss_pred             HHHhC-CChHHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           95 ELCKN-GKMDEASRLLDLMVQRDVRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        95 ~~~~~-~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      .+... |++++|...++++.+.+..| +...+..++.++...|++++|...++++.... +.+...+..++.++...|++
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCH
Confidence            66777 77777777777666621122 24556666666666666666666666666553 34455666666666666666


Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      ++|...++++.+.....+...+..+...+...|+.+.+..+++.+.+.
T Consensus       164 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          164 GDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence            666666666665421134455555555556666666666666665543

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

Probab=99.78  E-value=3.7e-17  Score=128.66  Aligned_cols=202  Identities=12%  Similarity=0.132  Sum_probs=137.3

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      ....|..++..+...|++++|...|+++++.... +...+..+...+...|++++|...++++.+.. +.+..++..++.
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   99 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKE-DAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGN   99 (243)
T ss_dssp             --------------------CCTTHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHH
Confidence            4566777788888888888888888888775333 57777788888888888888888888888764 345677778888


Q ss_pred             HHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHH
Q 042039          130 GFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH  209 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  209 (376)
                      .+...|++++|.+.++++.+.. +.+...+..++.++...|++++|...++++.+. .+.+...+..+...+...|++++
T Consensus       100 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A          100 VYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL-NENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHcCCHHH
Confidence            8888888888888888887765 556777778888888888888888888887775 23356677777777778888888


Q ss_pred             HHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC
Q 042039          210 ALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK  256 (376)
Q Consensus       210 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  256 (376)
                      |...++++.+.. +.+..++..++.++...|++++|...++++....
T Consensus       178 A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          178 ALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            888887777664 4456667777777777777777777777776654

>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=99.78  E-value=3e-15  Score=137.93  Aligned_cols=296  Identities=13%  Similarity=0.132  Sum_probs=169.9

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCC--CCChhhHHHHHHH---------------------------HhcC
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENI--NPDVVTYNSLIHG---------------------------LCHA   64 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~---------------------------~~~~   64 (376)
                      -|+.--...+.+|...|.+.+|+++++++.-.+.  ..+...-+.++.+                           +...
T Consensus       983 ~~PeeVs~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIkaD~~Rv~eyI~kLd~~d~~eIA~Iai~l 1062 (1630)
T 1xi4_A          983 QDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISN 1062 (1630)
T ss_pred             cCHHHhHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHhChhhHHHHHHHhhhccHHHHHHHHHhC
Confidence            3444456677888999999999999999984431  1223333434433                           3444


Q ss_pred             CChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHH
Q 042039           65 NDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELF  144 (376)
Q Consensus        65 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  144 (376)
                      |.+++|..+|++..    . .....+.+   +-..+++++|.++.++.      -++.+|..++.++...|++++|...|
T Consensus      1063 glyEEAf~IYkKa~----~-~~~A~~VL---ie~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~~kEAIdsY 1128 (1630)
T 1xi4_A         1063 ELFEEAFAIFRKFD----V-NTSAVQVL---IEHIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSY 1128 (1630)
T ss_pred             CCHHHHHHHHHHcC----C-HHHHHHHH---HHHHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            44555555554431    0 11111111   11344445554444433      13456666666666666666666666


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC
Q 042039          145 GSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA  224 (376)
Q Consensus       145 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  224 (376)
                      .+.      .+...|..++.++.+.|++++|++.+...++..  +++.....++.+|.+.++++....+.    .   .+
T Consensus      1129 iKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~---~~ 1193 (1630)
T 1xi4_A         1129 IKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N---GP 1193 (1630)
T ss_pred             Hhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h---CC
Confidence            443      345566666666666677767666666665542  22222334666666666655432221    1   23


Q ss_pred             CcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHH
Q 042039          225 DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIH  304 (376)
Q Consensus       225 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  304 (376)
                      +...+..++..|...|++++|..+|..+         ..|..++..+.+.|++++|.+.+++..      +..+|..+..
T Consensus      1194 n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~------n~~aWkev~~ 1258 (1630)
T 1xi4_A         1194 NNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVCF 1258 (1630)
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhC------CHHHHHHHHH
Confidence            3445555666666666666666666663         256666666666666666666666542      3456666666


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          305 GLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       305 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      +|...|++..|......+     ..++..+..++..|.+.|.+++|+.+++...
T Consensus      1259 acve~~Ef~LA~~cgl~I-----iv~~deLeeli~yYe~~G~feEAI~LlE~aL 1307 (1630)
T 1xi4_A         1259 ACVDGKEFRLAQMCGLHI-----VVHADELEELINYYQDRGYFEELITMLEAAL 1307 (1630)
T ss_pred             HHhhhhHHHHHHHHHHhh-----hcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            666666666655544332     2255566677778888888888888887765

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.78  E-value=6.5e-18  Score=143.54  Aligned_cols=266  Identities=12%  Similarity=0.015  Sum_probs=161.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhC----CCC-CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC-C----c
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGE----NIN-PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ-P----S   85 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~----~   85 (376)
                      ..+|..+...+...|++++|...++++...    +.+ ....++..++.++...|++++|...++++...... +    .
T Consensus        47 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  126 (406)
T 3sf4_A           47 SAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGE  126 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccch
Confidence            357889999999999999999999987543    211 23567888999999999999999999998764111 1    1


Q ss_pred             hHhHHHHHHHHHhCCC--------------------hHHHHHHHHHHHhc----CCCC-ChhhHHHHHHHHHhcCcHHHH
Q 042039           86 VVTFNVIMDELCKNGK--------------------MDEASRLLDLMVQR----DVRP-NAFTYSTLMDGFCLTGKINRA  140 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~--------------------~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a  140 (376)
                      ..++..+...+...|+                    +++|...+++..+.    +..+ ...++..++..+...|++++|
T Consensus       127 ~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  206 (406)
T 3sf4_A          127 ARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDA  206 (406)
T ss_dssp             HHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHH
T ss_pred             HHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHH
Confidence            4478888889999999                    88888888877652    1011 133566666777777777777


Q ss_pred             HHHHHHHHhcCCC-CC----hhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCC-CCHhHHHHHHHHHHhccchHHHHHHH
Q 042039          141 EELFGSMESMGCK-HD----DVSYNILINGYCKNKEVEEALSLYREMVSKGIK-PTVVTYNTLFLGLFEIHQVEHALKLF  214 (376)
Q Consensus       141 ~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~  214 (376)
                      ...+++....... ++    ..++..++.++...|++++|...+++....... ++.                       
T Consensus       207 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~-----------------------  263 (406)
T 3sf4_A          207 VIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDR-----------------------  263 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH-----------------------
T ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCc-----------------------
Confidence            7777766543210 11    115555666666666666666666665542100 000                       


Q ss_pred             HHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC-----CchHHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          215 EEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC-----ELDIQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       215 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                              .....++..++..+...|++++|...++.+.....     .....++..++.++...|++++|...+++..+
T Consensus       264 --------~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          264 --------AVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             --------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             --------hHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                    00022344445555555555555555555432110     11134556666667777777777777766543


Q ss_pred             c----CC-CCCHHHHHHHHHHHHccCCh
Q 042039          290 R----VL-VADVVTYNIMIHGLCNDGQM  312 (376)
Q Consensus       290 ~----~~-~~~~~~~~~l~~~~~~~~~~  312 (376)
                      .    +. +....++..+...+...|+.
T Consensus       336 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          336 ISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence            2    10 11234455566666655554

>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=99.77  E-value=5.2e-16  Score=122.80  Aligned_cols=200  Identities=13%  Similarity=0.011  Sum_probs=100.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ..|..+...+...|++++|+..|+++.+.. +.+..++..++.++...|++++|.+.++++.+.... +...+..+...+
T Consensus        38 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~  115 (252)
T 2ho1_A           38 DAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR-NARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHHH
Confidence            344555555555555555555555554443 334455555555555555555555555555544222 344455555555


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      ...|++++|..+++++.+.+..| +...+..++.++...|++++|...++++.... +.+...+..++.++...|++++|
T Consensus       116 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHH
Confidence            55555555555555555411122 23444455555555555555555555555443 33444555555555555555555


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      ...++++.+. .+.+...+..+...+...|++++|.+.++.+.+.
T Consensus       195 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          195 RQYYDLFAQG-GGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHHHTT-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-CcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            5555555543 1233444445555555555555555555555443

>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=99.77  E-value=5.9e-15  Score=136.09  Aligned_cols=290  Identities=13%  Similarity=0.184  Sum_probs=174.5

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      +.+|..+..++.+.|++++|++.|.+.      .|...|..++.++.+.|++++|.+.+...++..  +++.....++.+
T Consensus      1105 p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~Lafa 1176 (1630)
T 1xi4_A         1105 PAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFA 1176 (1630)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHH
Confidence            455666666666666666666666443      245555566666666666666666666555542  222222235555


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      |++.+++++...+    ++   .++...+..++..|...|++++|..+|..+         ..|..++.++.+.|++++|
T Consensus      1177 YAKl~rleele~f----I~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~A 1240 (1630)
T 1xi4_A         1177 LAKTNRLAELEEF----IN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAA 1240 (1630)
T ss_pred             HHhhcCHHHHHHH----Hh---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHH
Confidence            6666555543222    11   234444555666666666666666666653         2466666666666666666


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      ++.+++.      .+..+|..+..+|...|++..|......     +..++..+..++..|.+.|.+++|+.+++.....
T Consensus      1241 IEaarKA------~n~~aWkev~~acve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~L 1309 (1630)
T 1xi4_A         1241 VDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGL 1309 (1630)
T ss_pred             HHHHHHh------CCHHHHHHHHHHHhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhcc
Confidence            6666654      2445666666666666666666655443     2335556778888888889999999999888766


Q ss_pred             CCCchHHHHHHHHHHHHhC--CChHHHHHHHhcccccCCCC------CHHHHHHHHHHHHccCChhHHHHHH--------
Q 042039          256 KCELDIQAYNCLIDGLCKS--GRLEIALELFRSLPRRVLVA------DVVTYNIMIHGLCNDGQMDKAHDLF--------  319 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~a~~~~--------  319 (376)
                      . +-....|..++..+.+.  ++..++.++|..-..  +++      +...|..++..|.+.|+++.|....        
T Consensus      1310 e-raH~gmftELaiLyaKy~peklmEhlk~f~~rin--i~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~ 1386 (1630)
T 1xi4_A         1310 E-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVN--IPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAW 1386 (1630)
T ss_pred             C-hhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc--cchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhh
Confidence            5 44566776677666654  355566666654332  222      4667888888999999999887322        


Q ss_pred             -----HHHHHcCCCCcHHHHHHHHHHHhhcC
Q 042039          320 -----LDMEENAVAPNVIIFVTLIHGFVRIN  345 (376)
Q Consensus       320 -----~~~~~~~~~~~~~~~~~l~~~~~~~g  345 (376)
                           ...+.  ...++..|...+..|...+
T Consensus      1387 ~~~~Fk~~i~--kv~n~elyykai~Fyl~~~ 1415 (1630)
T 1xi4_A         1387 KEGQFKDIIT--KVANVELYYRAIQFYLEFK 1415 (1630)
T ss_pred             hhHHHHHHhc--ccccHHHHHHHHHHHHhhC
Confidence                 12121  2346777777777777655

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

Probab=99.77  E-value=3.6e-16  Score=121.34  Aligned_cols=211  Identities=10%  Similarity=0.008  Sum_probs=110.5

Q ss_pred             hhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHH
Q 042039          157 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGL  236 (376)
Q Consensus       157 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  236 (376)
                      ..+..++..+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.... +.+..++..++..+
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~   86 (225)
T 2vq2_A            9 NIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFL   86 (225)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHH
Confidence            344444444444444444444444444431 2233444444444444555555555554444432 23344455555555


Q ss_pred             HhC-CCHHHHHHHHHHhcccCC-CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhH
Q 042039          237 CKN-GYIVEAVELFRTLGILKC-ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDK  314 (376)
Q Consensus       237 ~~~-~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  314 (376)
                      ... |++++|...++++..... +.+...+..++..+...|++++|...++++.+. .+.+...+..++.++...|++++
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~la~~~~~~~~~~~  165 (225)
T 2vq2_A           87 CGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAA-QPQFPPAFKELARTKMLAGQLGD  165 (225)
T ss_dssp             HTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCchHHHHHHHHHHHcCCHHH
Confidence            555 555555555555544111 123455566666666666666666666665554 23345566666666666666666


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHH
Q 042039          315 AHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV  372 (376)
Q Consensus       315 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  372 (376)
                      |...++++.+.....+...+..+...+...|+.+++..+++.+.+.  .|+......+
T Consensus       166 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~~~  221 (225)
T 2vq2_A          166 ADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--FPYSEELQTV  221 (225)
T ss_dssp             HHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHHHH
Confidence            6666666665432134455555555666666666666666666543  3444444433

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.76  E-value=3.6e-17  Score=139.29  Aligned_cols=236  Identities=14%  Similarity=0.136  Sum_probs=121.4

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCch----HhHHHHHHHHHhCCChHHHHHHHHHHHhc----C-CCCCh
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV----VTFNVIMDELCKNGKMDEASRLLDLMVQR----D-VRPNA  121 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~  121 (376)
                      ...+..+...+...|++++|+..|+++++.... +.    ..+..+...+...|++++|...+++.++.    + .+...
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  126 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEA  126 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHH
Confidence            334555666777777777777777777765332 22    35666667777777777777777766542    1 01124


Q ss_pred             hhHHHHHHHHHhcCcHHHHHHHHHHHHhcC-----CCCChhhHHHHHHHHHccCc-----------------HHHHHHHH
Q 042039          122 FTYSTLMDGFCLTGKINRAEELFGSMESMG-----CKHDDVSYNILINGYCKNKE-----------------VEEALSLY  179 (376)
Q Consensus       122 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~  179 (376)
                      .++..+...+...|++++|...++++....     .+....++..++.+|...|+                 +++|+..+
T Consensus       127 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~  206 (411)
T 4a1s_A          127 KSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFY  206 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHH
Confidence            456666666777777777777776664431     11223355666666666666                 66666666


Q ss_pred             HHHHHC----CC-CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCC-CC----cchHHHHHHHHHhCCCHHHHHHHH
Q 042039          180 REMVSK----GI-KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVA-AD----TSTYNTFIDGLCKNGYIVEAVELF  249 (376)
Q Consensus       180 ~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~  249 (376)
                      ++..+.    +. .....++..+...+...|++++|...+++..+.... .+    ...+..++..+...|++++|...+
T Consensus       207 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  286 (411)
T 4a1s_A          207 QENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHY  286 (411)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            554431    00 011234444555555555555555555554443100 00    113444444445555555555555


Q ss_pred             HHhcccCCC-----chHHHHHHHHHHHHhCCChHHHHHHHhcc
Q 042039          250 RTLGILKCE-----LDIQAYNCLIDGLCKSGRLEIALELFRSL  287 (376)
Q Consensus       250 ~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  287 (376)
                      +++......     ....++..++..+...|++++|...++++
T Consensus       287 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  329 (411)
T 4a1s_A          287 KRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRH  329 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444322100     00233444444444444444444444443

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.76  E-value=5.2e-17  Score=138.30  Aligned_cols=270  Identities=13%  Similarity=0.060  Sum_probs=132.1

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh----hhHHHHHHHHHhcCcHHHHHHHHHHHHhcC-----CCCChhh
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA----FTYSTLMDGFCLTGKINRAEELFGSMESMG-----CKHDDVS  158 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~  158 (376)
                      .+..+...+...|++++|...++++++.+ +.+.    .++..++..+...|++++|...++++....     .+....+
T Consensus        50 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           50 ELALEGERLCNAGDCRAGVAFFQAAIQAG-TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHHHHHHhc-ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            34445555555566666666666555542 1122    345555555555666666666555554320     1122344


Q ss_pred             HHHHHHHHHccCcHHHHHHHHHHHHHC----C-CCCCHhHHHHHHHHHHhccc-----------------hHHHHHHHHH
Q 042039          159 YNILINGYCKNKEVEEALSLYREMVSK----G-IKPTVVTYNTLFLGLFEIHQ-----------------VEHALKLFEE  216 (376)
Q Consensus       159 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~~~  216 (376)
                      +..++.+|...|++++|...++++.+.    + .+....++..+...+...|+                 +++|...+.+
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~  208 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQE  208 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHH
Confidence            555555556666666666655554432    0 01123445555555555555                 5556555555


Q ss_pred             HHhc----C-CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC-----chHHHHHHHHHHHHhCCChHHHHHHHhc
Q 042039          217 MQRD----D-VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE-----LDIQAYNCLIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       217 ~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~  286 (376)
                      ..+.    + .+....++..++..+...|++++|...++++......     .....+..++..+...|++++|...+++
T Consensus       209 al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  288 (411)
T 4a1s_A          209 NLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKR  288 (411)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            4332    0 0112234555555555666666666555555332100     0112455555555666666666665555


Q ss_pred             ccccCCC-----CCHHHHHHHHHHHHccCChhHHHHHHHHHHHcC-----CCCcHHHHHHHHHHHhhcCChhhHHHHHHH
Q 042039          287 LPRRVLV-----ADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA-----VAPNVIIFVTLIHGFVRINKPSKVIELLHK  356 (376)
Q Consensus       287 ~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  356 (376)
                      +......     ....++..++..+...|++++|...++++.+..     ......++..+...|...|++++|...+++
T Consensus       289 al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  368 (411)
T 4a1s_A          289 TLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQ  368 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            4432100     013445555555566666666666655554320     000123455555555566666666665555


Q ss_pred             HH
Q 042039          357 MK  358 (376)
Q Consensus       357 ~~  358 (376)
                      ..
T Consensus       369 al  370 (411)
T 4a1s_A          369 HL  370 (411)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

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

Probab=99.75  E-value=4.9e-16  Score=116.62  Aligned_cols=167  Identities=16%  Similarity=0.084  Sum_probs=138.9

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      ++..|..+...+.+.|++++|++.|++..+.+ |.+..++..++.++...|++++|...+..+...... +...+..+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT-SAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch-hHHHHHHHHH
Confidence            56778888889999999999999999888776 667888888888999999999999998888876443 5667777888


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  174 (376)
                      .+...++++.+...+.+..+.. +.+...+..++.++...|++++|.+.|+++.+.. |.+..++..++.+|.+.|++++
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~  159 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDE  159 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHH
Confidence            8888888999998888888764 4467788888888888899999999888888876 6677888888888888899999


Q ss_pred             HHHHHHHHHHC
Q 042039          175 ALSLYREMVSK  185 (376)
Q Consensus       175 a~~~~~~~~~~  185 (376)
                      |++.|+++++.
T Consensus       160 A~~~~~~al~~  170 (184)
T 3vtx_A          160 AVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHhC
Confidence            99888888874

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.75  E-value=4.7e-16  Score=131.01  Aligned_cols=296  Identities=13%  Similarity=0.013  Sum_probs=150.1

Q ss_pred             HHhcCChhHHHHHHHHhhhC--CCCCC--hhhHHHHHHH--HhcCCChHHHH-----------HHHHHHHhcCCCCch--
Q 042039           26 LCKEGFVDKAKALFLQMKGE--NINPD--VVTYNSLIHG--LCHANDWNEAK-----------RLFFEMMDQGVQPSV--   86 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~--~~~~~--~~~~~~l~~~--~~~~~~~~~a~-----------~~~~~~~~~~~~~~~--   86 (376)
                      +.+.+++++|..+++++.+.  ....+  ...|..++..  ....++++.+.           +.++.+.......+.  
T Consensus        22 ~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~~~~~~~l  101 (383)
T 3ulq_A           22 YIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQARLTGLL  101 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcCCCchhHH
Confidence            45788999999999988654  22223  3333433322  11223333343           555555432111010  


Q ss_pred             --HhHHHHHHHHHhCCChHHHHHHHHHHHhc----CCCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC------C
Q 042039           87 --VTFNVIMDELCKNGKMDEASRLLDLMVQR----DVRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGC------K  153 (376)
Q Consensus        87 --~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~  153 (376)
                        ..+......+...|++++|...+++..+.    +..+ ...++..++..+...|+++.|...+++..+...      +
T Consensus       102 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~  181 (383)
T 3ulq_A          102 EYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNI  181 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchH
Confidence              11222455667777888888888777653    1111 234666777777777777777777777654311      1


Q ss_pred             CChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCC-CCC----HhHHHHHHHHHHhccchHHHHHHHHHHHhc-----CCC
Q 042039          154 HDDVSYNILINGYCKNKEVEEALSLYREMVSKGI-KPT----VVTYNTLFLGLFEIHQVEHALKLFEEMQRD-----DVA  223 (376)
Q Consensus       154 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~  223 (376)
                      ....++..++.+|...|++++|+..++++++... .++    ..++..++.++...|++++|...+++..+.     ..+
T Consensus       182 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~  261 (383)
T 3ulq_A          182 RLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILP  261 (383)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccch
Confidence            1123566677777777777777777776654210 011    234555666666666666666666655541     112


Q ss_pred             CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC----CCchHHHHHHHHHHHHhCCC---hHHHHHHHhcccccCCCCCH
Q 042039          224 ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK----CELDIQAYNCLIDGLCKSGR---LEIALELFRSLPRRVLVADV  296 (376)
Q Consensus       224 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~  296 (376)
                      ....++..++..+...|++++|...++++....    .+.....+..+...+...|+   +++|+.++++...  .+...
T Consensus       262 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~--~~~~~  339 (383)
T 3ulq_A          262 SLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKML--YADLE  339 (383)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTC--HHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcC--HHHHH
Confidence            223445555555555555555555555543221    01111223334444444444   4444444444311  11122


Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          297 VTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       297 ~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      ..+..++..|...|++++|...++++.
T Consensus       340 ~~~~~la~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          340 DFAIDVAKYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334444444445555555555444443

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.74  E-value=9.7e-17  Score=132.57  Aligned_cols=281  Identities=14%  Similarity=0.082  Sum_probs=157.1

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc---hHhHHHHHHHHHhCCChHHHHHHHHHHHhc----CCCC-Chhh
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS---VVTFNVIMDELCKNGKMDEASRLLDLMVQR----DVRP-NAFT  123 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~  123 (376)
                      ..+...+..+...|++++|...|+++++......   ...+..+...+...|++++|...+++..+.    +..+ ...+
T Consensus         6 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   85 (338)
T 3ro2_A            6 LELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKA   85 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHH
Confidence            3445556666666777777777777666532211   245556666666666666666666665432    1011 1334


Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHhcCCC-CC----hhhHHHHHHHHHccCc-------------HHHHHHHHHHHHHC
Q 042039          124 YSTLMDGFCLTGKINRAEELFGSMESMGCK-HD----DVSYNILINGYCKNKE-------------VEEALSLYREMVSK  185 (376)
Q Consensus       124 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~-------------~~~a~~~~~~~~~~  185 (376)
                      +..++..+...|++++|...+++....... ++    ..++..++..+...|+             .+++...       
T Consensus        86 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~-------  158 (338)
T 3ro2_A           86 SGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNA-------  158 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHH-------
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHH-------
Confidence            455555555566666666655555432100 01    1144444555555555             0000000       


Q ss_pred             CCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc----C-CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCC---
Q 042039          186 GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD----D-VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKC---  257 (376)
Q Consensus       186 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---  257 (376)
                                           +++|...+++....    + .+.....+..++..+...|++++|...++++.....   
T Consensus       159 ---------------------~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~  217 (338)
T 3ro2_A          159 ---------------------LQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFG  217 (338)
T ss_dssp             ---------------------HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHT
T ss_pred             ---------------------HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcC
Confidence                                 44444444333221    0 011123455556666666666666666666543210   


Q ss_pred             --CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCC-C----CHHHHHHHHHHHHccCChhHHHHHHHHHHHcC----
Q 042039          258 --ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLV-A----DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA----  326 (376)
Q Consensus       258 --~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----  326 (376)
                        ......+..++..+...|++++|...+++....... .    ...++..++..+...|++++|...++++.+..    
T Consensus       218 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~  297 (338)
T 3ro2_A          218 DKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELK  297 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcC
Confidence              111236677777778888888888888776532100 1    14567778888888888888888888876531    


Q ss_pred             C-CCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhC
Q 042039          327 V-APNVIIFVTLIHGFVRINKPSKVIELLHKMKEK  360 (376)
Q Consensus       327 ~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  360 (376)
                      . .....++..+...|...|++++|...+++..+.
T Consensus       298 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          298 DRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            1 112446777888888899999999999888764

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

Probab=99.74  E-value=4.7e-18  Score=151.49  Aligned_cols=150  Identities=13%  Similarity=0.181  Sum_probs=123.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhh---CCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKG---ENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      ..+||++|++|++.|++++|.++|++|.+   .|..||..+|+.||.+|++.|++++|.++|++|.+.|+.||..||+.+
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            46899999999999999999999988764   478999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCh-HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCC------hhhHHHHHHH
Q 042039           93 MDELCKNGKM-DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHD------DVSYNILING  165 (376)
Q Consensus        93 ~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~l~~~  165 (376)
                      +.++++.|+. ++|.++|++|.+.|+.||..+|+.++....+.    .+++..+++ .-+..|+      ..+...|.+.
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~----~vL~~Vrkv-~P~f~p~~~~~~~~~t~~LL~dl  281 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA----TVLKAVHKV-KPTFSLPPQLPPPVNTSKLLRDV  281 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH----HHHHHHGGG-CCCCCCCCCCCCCCCCCTTTHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH----HHHHHHHHh-CcccCCCCCCcccccchHHHHHH
Confidence            9999999985 78999999999999999999999887655433    333333333 1222222      3344556666


Q ss_pred             HHccC
Q 042039          166 YCKNK  170 (376)
Q Consensus       166 ~~~~~  170 (376)
                      |.+.+
T Consensus       282 ~s~d~  286 (1134)
T 3spa_A          282 YAKDG  286 (1134)
T ss_dssp             HCCCS
T ss_pred             HccCC
Confidence            66544

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.73  E-value=1.8e-16  Score=130.99  Aligned_cols=278  Identities=15%  Similarity=0.100  Sum_probs=180.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC----hhhHHHHHHHHhcCCChHHHHHHHHHHHhc----CCCC-ch
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD----VVTYNSLIHGLCHANDWNEAKRLFFEMMDQ----GVQP-SV   86 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~   86 (376)
                      ...+......+...|++++|+..|+++.+.. +.+    ...+..++..+...|++++|.+.++++...    +..| ..
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   83 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   83 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHH
Confidence            4456677788999999999999999998874 334    467889999999999999999999997653    1121 25


Q ss_pred             HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-CC----hhhHHHHHHHHHhcCc--------------------HHHHH
Q 042039           87 VTFNVIMDELCKNGKMDEASRLLDLMVQRDVR-PN----AFTYSTLMDGFCLTGK--------------------INRAE  141 (376)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~--------------------~~~a~  141 (376)
                      .++..+...+...|++++|...+++..+.... ++    ..++..+...+...|+                    +++|.
T Consensus        84 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~  163 (338)
T 3ro2_A           84 KASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAV  163 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHH
Confidence            57888899999999999999999998764211 12    3377788888999999                    88888


Q ss_pred             HHHHHHHhc----C-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCC-CCHhHHHHHHHHHHhccchHHHHHHHH
Q 042039          142 ELFGSMESM----G-CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK-PTVVTYNTLFLGLFEIHQVEHALKLFE  215 (376)
Q Consensus       142 ~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~  215 (376)
                      ..+++....    + .+....++..++..+...|++++|...+++..+.... ++.                        
T Consensus       164 ~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~------------------------  219 (338)
T 3ro2_A          164 DLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDK------------------------  219 (338)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCH------------------------
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCCh------------------------
Confidence            888776432    1 0112235566666677777777777777666542100 000                        


Q ss_pred             HHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC----C-CchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          216 EMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK----C-ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       216 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                             .....++..++..+...|++++|...++++....    . .....++..++..+...|++++|...++++...
T Consensus       220 -------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  292 (338)
T 3ro2_A          220 -------AAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAI  292 (338)
T ss_dssp             -------HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -------HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence                   0001133444444445555555555554443211    0 011345566666677777777777776665432


Q ss_pred             C----C-CCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          291 V----L-VADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       291 ~----~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      .    . .....++..++..+...|++++|...++++.+.
T Consensus       293 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          293 AQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             HHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            1    0 011345667777777788888888888777653

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.73  E-value=9.9e-16  Score=129.05  Aligned_cols=298  Identities=12%  Similarity=0.002  Sum_probs=213.5

Q ss_pred             HHhcCCChHHHHHHHHHHHhc--CC--CCchHhHHHHHHH--HHhCCChHHHH-----------HHHHHHHhcCCCCC--
Q 042039           60 GLCHANDWNEAKRLFFEMMDQ--GV--QPSVVTFNVIMDE--LCKNGKMDEAS-----------RLLDLMVQRDVRPN--  120 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~~~~~~~--~~--~~~~~~~~~l~~~--~~~~~~~~~a~-----------~~~~~~~~~~~~~~--  120 (376)
                      .+.+.+++++|..+++++.+.  ..  .++...|..++..  ....+.++.+.           ..++.+.....+.+  
T Consensus        21 ~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~~~~~~~  100 (383)
T 3ulq_A           21 MYIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQARLTGL  100 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcCCCchhH
Confidence            356789999999999998764  22  2333444444332  22223344444           66666544311111  


Q ss_pred             --hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC--CCC---ChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC--CC---
Q 042039          121 --AFTYSTLMDGFCLTGKINRAEELFGSMESMG--CKH---DDVSYNILINGYCKNKEVEEALSLYREMVSKG--IK---  188 (376)
Q Consensus       121 --~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~---  188 (376)
                        ...+...+..+...|++++|...++++...-  .+.   ...++..++.+|...|++++|+..+++..+..  ..   
T Consensus       101 l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~  180 (383)
T 3ulq_A          101 LEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYN  180 (383)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTH
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccch
Confidence              1122336777889999999999999997641  111   34578899999999999999999999987631  11   


Q ss_pred             -CCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC-----CcchHHHHHHHHHhCCCHHHHHHHHHHhccc----CC-
Q 042039          189 -PTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA-----DTSTYNTFIDGLCKNGYIVEAVELFRTLGIL----KC-  257 (376)
Q Consensus       189 -~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-  257 (376)
                       ....++..+..++...|++++|...+.+..+.....     ...++..++.+|...|++++|...++++...    +. 
T Consensus       181 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~  260 (383)
T 3ulq_A          181 IRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNIL  260 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccc
Confidence             124578888999999999999999999887652111     1247888999999999999999999998762    22 


Q ss_pred             CchHHHHHHHHHHHHhCCChHHHHHHHhcccccC----CCCCHHHHHHHHHHHHccCC---hhHHHHHHHHHHHcCCCCc
Q 042039          258 ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV----LVADVVTYNIMIHGLCNDGQ---MDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       258 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~  330 (376)
                      +....++..++.++...|++++|...+++..+..    .+.....+..+...+...|+   +++|+.++++...  ....
T Consensus       261 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~--~~~~  338 (383)
T 3ulq_A          261 PSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKML--YADL  338 (383)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTC--HHHH
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcC--HHHH
Confidence            4457789999999999999999999999876531    12223345678888999999   7777777776621  1223


Q ss_pred             HHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          331 VIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       331 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      ...+..+...|...|++++|...+++..+
T Consensus       339 ~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          339 EDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45677889999999999999999999875

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

Probab=99.72  E-value=1.5e-17  Score=148.42  Aligned_cols=114  Identities=12%  Similarity=0.169  Sum_probs=72.9

Q ss_pred             chHHHHHHHHHhCCCHHHHHHHHHHhc---ccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHH
Q 042039          227 STYNTFIDGLCKNGYIVEAVELFRTLG---ILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMI  303 (376)
Q Consensus       227 ~~~~~l~~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  303 (376)
                      .+|+.++.+|++.|+.++|.++|..|.   ..|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..||+.++
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            456666666666666666666665543   23556666666666666666666666666666666666666666666666


Q ss_pred             HHHHccCCh-hHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 042039          304 HGLCNDGQM-DKAHDLFLDMEENAVAPNVIIFVTLIHG  340 (376)
Q Consensus       304 ~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~  340 (376)
                      .++++.|+. ++|.++|++|.+.|+.||..+|+.++.+
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~  245 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSE  245 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCH
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccCh
Confidence            666666653 5566666666666666666666665543

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

Probab=99.72  E-value=8.6e-16  Score=132.61  Aligned_cols=217  Identities=14%  Similarity=0.045  Sum_probs=168.1

Q ss_pred             ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCCh-HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHH
Q 042039           66 DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKM-DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELF  144 (376)
Q Consensus        66 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  144 (376)
                      +++++++.+++..... +.+...+..+...+...|++ ++|...|++.++.. +.+...+..++.+|...|++++|.+.|
T Consensus        83 ~~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~  160 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCF  160 (474)
T ss_dssp             HHHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4677777777766542 23677778888888888888 88888888888764 335778888888888888888888888


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHcc---------CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc--------cch
Q 042039          145 GSMESMGCKHDDVSYNILINGYCKN---------KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI--------HQV  207 (376)
Q Consensus       145 ~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~  207 (376)
                      +++.+..  |+...+..+..++...         |++++|+..++++++.. +.+...|..+..++...        |++
T Consensus       161 ~~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~  237 (474)
T 4abn_A          161 SGALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKIS  237 (474)
T ss_dssp             HHHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchH
Confidence            8888764  4567788888888888         88888888888888752 34577788888888887        888


Q ss_pred             HHHHHHHHHHHhcCCC---CCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHH
Q 042039          208 EHALKLFEEMQRDDVA---ADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELF  284 (376)
Q Consensus       208 ~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  284 (376)
                      ++|...|+++.+.. +   .+...+..++.+|...|++++|...|+++....+. +...+..+..++...|++++|...+
T Consensus       238 ~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          238 QQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPA-WPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            88888888888764 3   56777888888888888888888888888776533 6677888888888888888888877


Q ss_pred             hcccc
Q 042039          285 RSLPR  289 (376)
Q Consensus       285 ~~~~~  289 (376)
                      .++..
T Consensus       316 ~~~~~  320 (474)
T 4abn_A          316 GKTKP  320 (474)
T ss_dssp             TTCCH
T ss_pred             ccccC
Confidence            77643

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

Probab=99.72  E-value=1e-14  Score=118.85  Aligned_cols=234  Identities=9%  Similarity=0.011  Sum_probs=131.1

Q ss_pred             hhhHHHHHHHHHhc----CCh----hHHHHHHHHhhhCCCCCChhhHHHHHHHHhc-------CCCh-------HHHHHH
Q 042039           16 TVTYNTIIDGLCKE----GFV----DKAKALFLQMKGENINPDVVTYNSLIHGLCH-------ANDW-------NEAKRL   73 (376)
Q Consensus        16 ~~~~~~l~~~~~~~----g~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~-------~~a~~~   73 (376)
                      ...|...+....+.    ++.    ++|+..|+++.... |.++..|..++..+..       .|++       ++|..+
T Consensus         8 ~~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~   86 (308)
T 2ond_A            8 VDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANI   86 (308)
T ss_dssp             HHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHH
Confidence            34566666654443    222    56667777776654 5566677666666543       3554       666666


Q ss_pred             HHHHHh-cCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-hh-hHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           74 FFEMMD-QGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN-AF-TYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        74 ~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      |++.++ ..+ .+...|..++..+...|++++|..+|+++++.  .|+ .. +|..++..+.+.|++++|..+|+++.+.
T Consensus        87 ~~rAl~~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  163 (308)
T 2ond_A           87 YERAISTLLK-KNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  163 (308)
T ss_dssp             HHHHHTTTTT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHhCc-ccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            666666 222 24456666666666666666666666666664  232 32 5666666666666666666666666655


Q ss_pred             CCCCChhhHHHHHHHHH-ccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC-CCC--Cc
Q 042039          151 GCKHDDVSYNILINGYC-KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD-VAA--DT  226 (376)
Q Consensus       151 ~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~  226 (376)
                      . +.+...|...+.... ..|++++|..+|+++++. .+.+...|..++..+.+.|++++|..+|++++... .+|  ..
T Consensus       164 ~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~-~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~  241 (308)
T 2ond_A          164 A-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSG  241 (308)
T ss_dssp             T-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCH
T ss_pred             C-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHH
Confidence            3 333334433332221 246666666666666554 22245555555566666666666666666665542 122  23


Q ss_pred             chHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          227 STYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       227 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      ..+..++....+.|+.+.|..+++++...
T Consensus       242 ~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          242 EIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34555555555566666666666555443

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

Probab=99.71  E-value=1.6e-14  Score=117.73  Aligned_cols=234  Identities=11%  Similarity=-0.018  Sum_probs=156.4

Q ss_pred             hHhHHHHHHHHHhC----CCh----HHHHHHHHHHHhcCCCCChhhHHHHHHHHHh-------cCcH-------HHHHHH
Q 042039           86 VVTFNVIMDELCKN----GKM----DEASRLLDLMVQRDVRPNAFTYSTLMDGFCL-------TGKI-------NRAEEL  143 (376)
Q Consensus        86 ~~~~~~l~~~~~~~----~~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~-------~~a~~~  143 (376)
                      ...|...+....+.    ++.    ++|...|++++... +.++..|..++..+..       .|++       ++|..+
T Consensus         8 ~~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~   86 (308)
T 2ond_A            8 VDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANI   86 (308)
T ss_dssp             HHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHH
Confidence            44566666654443    232    57777888887753 4456777777776653       4664       778888


Q ss_pred             HHHHHh-cCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC-Hh-HHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          144 FGSMES-MGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VV-TYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       144 ~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      |++... .. |.+...|..++..+.+.|++++|..+|+++++.  .|+ .. +|..++..+.+.|++++|..+|+++.+.
T Consensus        87 ~~rAl~~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  163 (308)
T 2ond_A           87 YERAISTLL-KKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  163 (308)
T ss_dssp             HHHHHTTTT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHhC-cccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            888877 33 455667777888888888888888888888774  343 33 6777777777778888888888887765


Q ss_pred             CCCCCcchHHHHHHHHH-hCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC-CCC--CH
Q 042039          221 DVAADTSTYNTFIDGLC-KNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV-LVA--DV  296 (376)
Q Consensus       221 ~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~  296 (376)
                      . +.+...+...+.... ..|++++|..+|+++....+ .++..|..++..+.+.|++++|..+|+++.... .+|  ..
T Consensus       164 ~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~  241 (308)
T 2ond_A          164 A-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSG  241 (308)
T ss_dssp             T-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCH
T ss_pred             C-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHH
Confidence            4 334444443333322 25777788877777766542 256777777777777777788877777777642 233  35


Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          297 VTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       297 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      ..|..++......|+.++|..+++++.+.
T Consensus       242 ~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          242 EIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            56667777777777777777777777765

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

Probab=99.70  E-value=2.3e-15  Score=129.94  Aligned_cols=216  Identities=12%  Similarity=0.001  Sum_probs=180.4

Q ss_pred             ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH-HHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHH
Q 042039          101 KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI-NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLY  179 (376)
Q Consensus       101 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  179 (376)
                      .++++...++...... +.+...+..++..+...|++ ++|.+.|+++.+.. +.+..+|..++.+|...|++++|...|
T Consensus        83 ~~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~  160 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCF  160 (474)
T ss_dssp             HHHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4567777777766653 44678888899999999999 99999999998876 567888999999999999999999999


Q ss_pred             HHHHHCCCCCCHhHHHHHHHHHHhc---------cchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhC--------CCH
Q 042039          180 REMVSKGIKPTVVTYNTLFLGLFEI---------HQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKN--------GYI  242 (376)
Q Consensus       180 ~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~  242 (376)
                      +++++.  .|+...+..+...+...         |++++|...++++++.. +.+...+..++.+|...        |++
T Consensus       161 ~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~  237 (474)
T 4abn_A          161 SGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKIS  237 (474)
T ss_dssp             HHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchH
Confidence            999885  46678888889999998         99999999999998875 55678888899999888        889


Q ss_pred             HHHHHHHHHhcccCCC--chHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHH
Q 042039          243 VEAVELFRTLGILKCE--LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFL  320 (376)
Q Consensus       243 ~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  320 (376)
                      ++|+..|+++....+.  .+...+..++.+|...|++++|...|+++.+. .+.+...+..+..++...|++++|++.+.
T Consensus       238 ~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l-~p~~~~a~~~l~~~~~~lg~~~eAi~~~~  316 (474)
T 4abn_A          238 QQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL-DPAWPEPQQREQQLLEFLSRLTSLLESKG  316 (474)
T ss_dssp             HHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999998876531  47888999999999999999999999998876 45567788888899999999999887765


Q ss_pred             HH
Q 042039          321 DM  322 (376)
Q Consensus       321 ~~  322 (376)
                      ++
T Consensus       317 ~~  318 (474)
T 4abn_A          317 KT  318 (474)
T ss_dssp             TC
T ss_pred             cc
Confidence            54

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

Probab=99.70  E-value=1.1e-14  Score=109.22  Aligned_cols=167  Identities=16%  Similarity=0.137  Sum_probs=106.7

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      ++.+|..++.++...|++++|++.|++.++..+. +..++..+..++...|++++|...+....... +.+...+..+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPN-NVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHH
Confidence            4556667777777777777777777777665433 55666666667777777777777776666653 334555666666


Q ss_pred             HHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHH
Q 042039          130 GFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH  209 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  209 (376)
                      .+...++++.+...+.+..... +.+..++..++.++.+.|++++|++.|++.++.. +.+..++..+..++...|++++
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~  159 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDE  159 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHH
Confidence            6666667777776666666654 4455666666666666666666666666666642 2345556666666666666666


Q ss_pred             HHHHHHHHHhc
Q 042039          210 ALKLFEEMQRD  220 (376)
Q Consensus       210 a~~~~~~~~~~  220 (376)
                      |.+.|+++++.
T Consensus       160 A~~~~~~al~~  170 (184)
T 3vtx_A          160 AVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHhC
Confidence            66666666554

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

Probab=99.69  E-value=1.9e-16  Score=129.47  Aligned_cols=251  Identities=16%  Similarity=0.100  Sum_probs=149.8

Q ss_pred             cccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhC-------CCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc--
Q 042039           10 VVCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGE-------NINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ--   80 (376)
Q Consensus        10 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--   80 (376)
                      ...+.+..++..+...+...|++++|+.+++++.+.       ..+....++..++.++...|++++|...+++++..  
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  100 (311)
T 3nf1_A           21 YEIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIRE  100 (311)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            333445677888888888889999988888888763       22445667888888888888888888888887764  


Q ss_pred             ----CCCC-chHhHHHHHHHHHhCCChHHHHHHHHHHHhc------CCCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHH
Q 042039           81 ----GVQP-SVVTFNVIMDELCKNGKMDEASRLLDLMVQR------DVRP-NAFTYSTLMDGFCLTGKINRAEELFGSME  148 (376)
Q Consensus        81 ----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  148 (376)
                          +..| ...++..+...+...|++++|...++++.+.      +..| ...++..++..+...|++++|..+++++.
T Consensus       101 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  180 (311)
T 3nf1_A          101 KTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRAL  180 (311)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence                1122 3456777778888888888888888877753      1112 24556677777777888888888777776


Q ss_pred             hc------C-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC-------CCCCHhHHHHHHHHHHhccchHHHHHHH
Q 042039          149 SM------G-CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG-------IKPTVVTYNTLFLGLFEIHQVEHALKLF  214 (376)
Q Consensus       149 ~~------~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~a~~~~  214 (376)
                      ..      + .+....++..++.++...|++++|...++++.+..       ..+........                 
T Consensus       181 ~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~-----------------  243 (311)
T 3nf1_A          181 EIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMH-----------------  243 (311)
T ss_dssp             HHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHH-----------------
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHH-----------------
Confidence            54      1 12233466677777777777777777777776520       01110000000                 


Q ss_pred             HHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          215 EEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       215 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                                 ...+......+...+.+.++...++...... +....++..++.+|...|++++|..+++++.+
T Consensus       244 -----------~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          244 -----------AEEREECKGKQKDGTSFGEYGGWYKACKVDS-PTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             -----------HHHHHHC-------CCSCCCC---------C-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             -----------HHHHHHhcCchhhHHHHHHHHHHHhhcCCCC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                       0111112222333444445555555554332 23455666677777777777777777766554

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.68  E-value=3.1e-14  Score=119.66  Aligned_cols=310  Identities=10%  Similarity=-0.022  Sum_probs=167.6

Q ss_pred             cCCChhhHHHHHHHH--HhcCChhHHHHHHHHhhhC--CC--CCChhhHHHHHHHH--hcCCChHHHH---------HHH
Q 042039           12 CKPNTVTYNTIIDGL--CKEGFVDKAKALFLQMKGE--NI--NPDVVTYNSLIHGL--CHANDWNEAK---------RLF   74 (376)
Q Consensus        12 ~~p~~~~~~~l~~~~--~~~g~~~~a~~~~~~~~~~--~~--~~~~~~~~~l~~~~--~~~~~~~~a~---------~~~   74 (376)
                      ..|+...-+.+-+.|  ...+++++|..+++++.+.  ..  ..+...|..++..-  ...+.+..+.         +.+
T Consensus         6 ~~~~~~v~~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l   85 (378)
T 3q15_A            6 AIPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELL   85 (378)
T ss_dssp             CBCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHH
Confidence            345666666666676  7889999999999887543  11  22233334443321  1112222222         555


Q ss_pred             HHHHhcCCCCch----HhHHHHHHHHHhCCChHHHHHHHHHHHhcCC-CCC----hhhHHHHHHHHHhcCcHHHHHHHHH
Q 042039           75 FEMMDQGVQPSV----VTFNVIMDELCKNGKMDEASRLLDLMVQRDV-RPN----AFTYSTLMDGFCLTGKINRAEELFG  145 (376)
Q Consensus        75 ~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~~~~a~~~~~  145 (376)
                      +.+.....+.+.    ..+......+...|++++|...+++..+... .++    ..++..++.+|...|+++.|...++
T Consensus        86 ~~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~  165 (378)
T 3q15_A           86 ETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHIL  165 (378)
T ss_dssp             HHHHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            554332111011    1223344556677888888888887765311 111    3456677777777788888777777


Q ss_pred             HHHhcCC--C----CChhhHHHHHHHHHccCcHHHHHHHHHHHHHC----CCC-CCHhHHHHHHHHHHhccchHHHHHHH
Q 042039          146 SMESMGC--K----HDDVSYNILINGYCKNKEVEEALSLYREMVSK----GIK-PTVVTYNTLFLGLFEIHQVEHALKLF  214 (376)
Q Consensus       146 ~~~~~~~--~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~  214 (376)
                      +......  +    ....++..++.+|...|++++|.+.+++.++.    +.+ ....++..+..++...|++++|...+
T Consensus       166 ~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~  245 (378)
T 3q15_A          166 QALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHF  245 (378)
T ss_dssp             HHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            7654310  0    12345667777777777777777777776652    111 11345566666666777777777777


Q ss_pred             HHHHh-----cCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC----CCchHHHHHHHHHHHHhCCC---hHHHHH
Q 042039          215 EEMQR-----DDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK----CELDIQAYNCLIDGLCKSGR---LEIALE  282 (376)
Q Consensus       215 ~~~~~-----~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~---~~~a~~  282 (376)
                      .+...     .. +....++..++..+.+.|++++|...++++....    .+.....+..+...+...++   +.+|+.
T Consensus       246 ~~al~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~  324 (378)
T 3q15_A          246 QKAAKVSREKVP-DLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLS  324 (378)
T ss_dssp             HHHHHHHHHHCG-GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHH
T ss_pred             HHHHHHHHhhCC-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHH
Confidence            66655     22 2224555666666666666666666666654321    11122334444445555555   555555


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          283 LFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       283 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      .+++...  .+.....+..++..|...|++++|...|+++.+
T Consensus       325 ~~~~~~~--~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          325 YFEKKNL--HAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHTTC--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhCCC--hhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5554221  111223444555555566666666655555543

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.67  E-value=2.1e-14  Score=120.65  Aligned_cols=309  Identities=10%  Similarity=-0.028  Sum_probs=216.3

Q ss_pred             CCChhhHHHHHHHH--hcCCChHHHHHHHHHHHhc--CC--CCchHhHHHHHHH--HHhCCChHHHH---------HHHH
Q 042039           48 NPDVVTYNSLIHGL--CHANDWNEAKRLFFEMMDQ--GV--QPSVVTFNVIMDE--LCKNGKMDEAS---------RLLD  110 (376)
Q Consensus        48 ~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~--~~--~~~~~~~~~l~~~--~~~~~~~~~a~---------~~~~  110 (376)
                      .|+..+-..+-..|  ...+++++|.++++++.+.  ..  .++...|..++..  ....+.+..+.         ..++
T Consensus         7 ~~~~~v~~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l~   86 (378)
T 3q15_A            7 IPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLE   86 (378)
T ss_dssp             BCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHHH
Confidence            44555555555555  7889999999999988653  12  2234444444432  11122322233         5666


Q ss_pred             HHHhcCCCCC----hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-----CCChhhHHHHHHHHHccCcHHHHHHHHHH
Q 042039          111 LMVQRDVRPN----AFTYSTLMDGFCLTGKINRAEELFGSMESMGC-----KHDDVSYNILINGYCKNKEVEEALSLYRE  181 (376)
Q Consensus       111 ~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  181 (376)
                      .+.....+.+    ...+...+..+...|++++|...++++.....     +....++..++.+|...|++++|...+++
T Consensus        87 ~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~  166 (378)
T 3q15_A           87 TIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQ  166 (378)
T ss_dssp             HHHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence            6543211111    11334456677889999999999999876421     11245788899999999999999999999


Q ss_pred             HHHCC--CC----CCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC-----CCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          182 MVSKG--IK----PTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD-----VAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       182 ~~~~~--~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      ..+..  ..    ....++..+..++...|++++|...+.+..+..     ......++..++.+|...|++++|...++
T Consensus       167 al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~  246 (378)
T 3q15_A          167 ALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQ  246 (378)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            87631  11    125577889999999999999999999887641     11123467889999999999999999999


Q ss_pred             Hhcc-----cCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC----CCCCHHHHHHHHHHHHccCC---hhHHHHH
Q 042039          251 TLGI-----LKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV----LVADVVTYNIMIHGLCNDGQ---MDKAHDL  318 (376)
Q Consensus       251 ~~~~-----~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~---~~~a~~~  318 (376)
                      ++..     .. +....++..++.++.+.|++++|...+++..+..    .+.....+..+...+...++   +.+|+..
T Consensus       247 ~al~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~  325 (378)
T 3q15_A          247 KAAKVSREKVP-DLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSY  325 (378)
T ss_dssp             HHHHHHHHHCG-GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHhhCC-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            9876     33 3347888999999999999999999999876532    22223456667777788888   7777777


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          319 FLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      +++...  .......+..+...|...|++++|...+++..+
T Consensus       326 ~~~~~~--~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          326 FEKKNL--HAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHTTC--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhCCC--hhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            776321  122345677888999999999999999998864

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

Probab=99.66  E-value=7.6e-16  Score=125.82  Aligned_cols=135  Identities=17%  Similarity=0.139  Sum_probs=72.6

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhc-------CCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc------C
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ-------GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR------D  116 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~  116 (376)
                      +..++..++..+...|++++|..+++++.+.       ..+....++..+...+...|++++|...++++++.      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            3556666667777777777777777766652       11223445556666666666666666666666543      1


Q ss_pred             CCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc------C-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          117 VRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESM------G-CKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       117 ~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      ..| ...++..++..+...|++++|...++++...      + .+....++..++.++...|++++|+..++++.+
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~  181 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALE  181 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            111 2344555555555556666666555555432      1 011223444455555555555555555555443

>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=99.65  E-value=9.8e-15  Score=130.99  Aligned_cols=167  Identities=13%  Similarity=0.035  Sum_probs=152.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      -++.+|+.+...+.+.|++++|++.|++.++.. +.+..+|..++.+|.+.|++++|++.|+++++.... +...|..+.
T Consensus         7 ~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~-~~~a~~nLg   84 (723)
T 4gyw_A            7 THADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT-FADAYSNMG   84 (723)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHH
Confidence            347889999999999999999999999999886 667899999999999999999999999999997544 688999999


Q ss_pred             HHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHH
Q 042039           94 DELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  173 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  173 (376)
                      .++...|++++|++.|++.++.. +-+...+..++.++...|++++|++.|+++.+.. |.+..++..++.++...|+++
T Consensus        85 ~~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~~~  162 (723)
T 4gyw_A           85 NTLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCDWT  162 (723)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCCT
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhcccHH
Confidence            99999999999999999999874 3468899999999999999999999999999986 677889999999999999999


Q ss_pred             HHHHHHHHHHH
Q 042039          174 EALSLYREMVS  184 (376)
Q Consensus       174 ~a~~~~~~~~~  184 (376)
                      +|.+.++++.+
T Consensus       163 ~A~~~~~kal~  173 (723)
T 4gyw_A          163 DYDERMKKLVS  173 (723)
T ss_dssp             THHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999988765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.64  E-value=5.9e-13  Score=111.67  Aligned_cols=302  Identities=13%  Similarity=0.045  Sum_probs=212.9

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchH----hHHHHHHHHHhCCChHHHHHHHHHHHhcCC-CCC----hh
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVV----TFNVIMDELCKNGKMDEASRLLDLMVQRDV-RPN----AF  122 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~  122 (376)
                      .........+...|++++|...+++........+..    ++..+...+...|++++|...+++...... ..+    ..
T Consensus        15 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~   94 (373)
T 1hz4_A           15 EFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALW   94 (373)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHH
Confidence            344556677888999999999999988764332222    456677788899999999999999876321 112    22


Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhc----CCC--C-ChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCC--C--CH
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESM----GCK--H-DDVSYNILINGYCKNKEVEEALSLYREMVSKGIK--P--TV  191 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~--~~  191 (376)
                      ++..+...+...|++++|...+++....    +.+  | ...++..+..++...|++++|...+++.......  +  ..
T Consensus        95 ~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  174 (373)
T 1hz4_A           95 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  174 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHH
Confidence            3567788889999999999999988653    211  1 2345677888999999999999999998874221  1  23


Q ss_pred             hHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCc-chHH-----HHHHHHHhCCCHHHHHHHHHHhcccCCCc---hHH
Q 042039          192 VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT-STYN-----TFIDGLCKNGYIVEAVELFRTLGILKCEL---DIQ  262 (376)
Q Consensus       192 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~  262 (376)
                      .++..+...+...|++++|...+++.......++. ..+.     ..+..+...|++++|...++........+   ...
T Consensus       175 ~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~  254 (373)
T 1hz4_A          175 QCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQG  254 (373)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHH
Confidence            46777888899999999999999988764212221 1121     23344778999999999999987654321   133


Q ss_pred             HHHHHHHHHHhCCChHHHHHHHhccccc----CCCCCH-HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHH
Q 042039          263 AYNCLIDGLCKSGRLEIALELFRSLPRR----VLVADV-VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTL  337 (376)
Q Consensus       263 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  337 (376)
                      .+..++..+...|++++|...++.+...    +.+++. ..+..+..++...|++++|...+++.....  +.    ...
T Consensus       255 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~--~~----~g~  328 (373)
T 1hz4_A          255 QWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLA--NR----TGF  328 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--HH----HCC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh--cc----ccH
Confidence            5677888899999999999999887543    111222 366677888899999999999999998752  11    112


Q ss_pred             HHHHhhcCChhhHHHHHHHHHhCC
Q 042039          338 IHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       338 ~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      +..+...|  +....+++.+....
T Consensus       329 ~~~~~~~g--~~~~~ll~~~~~~~  350 (373)
T 1hz4_A          329 ISHFVIEG--EAMAQQLRQLIQLN  350 (373)
T ss_dssp             CHHHHTTH--HHHHHHHHHHHHTT
T ss_pred             HHHHHHcc--HHHHHHHHHHHhCC
Confidence            23344445  67778888887654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.63  E-value=5.7e-13  Score=111.74  Aligned_cols=300  Identities=12%  Similarity=0.011  Sum_probs=210.6

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCCh----hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC-Cc----hHh
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDV----VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ-PS----VVT   88 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~   88 (376)
                      ........+...|++++|...+++........+.    .++..+...+...|++++|.+.+++....... .+    ..+
T Consensus        16 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   95 (373)
T 1hz4_A           16 FNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   95 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            3445556777899999999999998876422222    25677788899999999999999998764211 11    233


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhc----CCC--C-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCC----Chh
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQR----DVR--P-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKH----DDV  157 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~  157 (376)
                      +..+...+...|++++|...+++.++.    +..  | ....+..+...+...|++++|...+++........    ...
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  175 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  175 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHH
Confidence            567788899999999999999998763    211  2 23456678889999999999999999987653211    234


Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC-HhHHH-----HHHHHHHhccchHHHHHHHHHHHhcCCCCC---cch
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYN-----TLFLGLFEIHQVEHALKLFEEMQRDDVAAD---TST  228 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~  228 (376)
                      ++..+...+...|++++|...+++.......++ ...+.     ..+..+...|++++|...+.........+.   ...
T Consensus       176 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  255 (373)
T 1hz4_A          176 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  255 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHH
Confidence            677888999999999999999999876421111 11222     123447789999999999998876532111   124


Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhccc----CCCchH-HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHH
Q 042039          229 YNTFIDGLCKNGYIVEAVELFRTLGIL----KCELDI-QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMI  303 (376)
Q Consensus       229 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  303 (376)
                      +..+...+...|++++|...++.+...    +..++. ..+..+..++...|+.++|...+++......  .    ....
T Consensus       256 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~~--~----~g~~  329 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLAN--R----TGFI  329 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH--H----HCCC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhc--c----ccHH
Confidence            567788899999999999999987543    212222 3667778889999999999999998876511  1    1122


Q ss_pred             HHHHccCChhHHHHHHHHHHHc
Q 042039          304 HGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       304 ~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      ..+...|  +....+++.+...
T Consensus       330 ~~~~~~g--~~~~~ll~~~~~~  349 (373)
T 1hz4_A          330 SHFVIEG--EAMAQQLRQLIQL  349 (373)
T ss_dssp             HHHHTTH--HHHHHHHHHHHHT
T ss_pred             HHHHHcc--HHHHHHHHHHHhC
Confidence            3344444  4556666666654

>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=99.63  E-value=8.5e-14  Score=104.32  Aligned_cols=166  Identities=17%  Similarity=0.074  Sum_probs=121.7

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...|..+...+...|++++|+..++++.+.. +.+..++..++.++...|++++|.+.++++.+... .+...+..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAP-DNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHH
Confidence            3456677777888888888888888877664 55677777888888888888888888888777632 256677777777


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      +...|++++|...++++.+.. +.+...+..++..+...|++++|...++++.... +.+..++..++.++...|++++|
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHH
Confidence            777788888888887777653 3456667777777777777777777777777664 45566777777777777777777


Q ss_pred             HHHHHHHHHC
Q 042039          176 LSLYREMVSK  185 (376)
Q Consensus       176 ~~~~~~~~~~  185 (376)
                      ...++++.+.
T Consensus       164 ~~~~~~~~~~  173 (186)
T 3as5_A          164 LPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHc
Confidence            7777776653

>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=99.63  E-value=1.1e-13  Score=107.55  Aligned_cols=210  Identities=12%  Similarity=0.004  Sum_probs=163.4

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      +.|+..|......+...|++++|+..|++..+...+++...+..++.++...|++++|++.|++.++..+. +...+..+
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l   82 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYN-LANAYIGK   82 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCS-HHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcc-hHHHHHHH
Confidence            34678899999999999999999999999998863378888888999999999999999999999987544 67789999


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCCh-------hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCC--ChhhHHHHH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNA-------FTYSTLMDGFCLTGKINRAEELFGSMESMGCKH--DDVSYNILI  163 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~  163 (376)
                      ..++...|++++|...+++.++.. +.+.       ..+..+...+...|++++|...|+++.+.. |.  +..++..++
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~l~  160 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVT-SKKWKTDALYSLG  160 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSS-CHHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcC-CCcccHHHHHHHH
Confidence            999999999999999999999874 3344       458888899999999999999999999875 44  467888888


Q ss_pred             HHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHH
Q 042039          164 NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFID  234 (376)
Q Consensus       164 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  234 (376)
                      .+|...|+     ..++.+...+ ..+...+....  ....+.+++|...+++..+.. |.+..+...+..
T Consensus       161 ~~~~~~~~-----~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~-p~~~~~~~~l~~  222 (228)
T 4i17_A          161 VLFYNNGA-----DVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLS-PNRTEIKQMQDQ  222 (228)
T ss_dssp             HHHHHHHH-----HHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHH-----HHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcC-CCCHHHHHHHHH
Confidence            88865543     3445555442 22334443332  344567899999999998875 344444444433

>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=99.61  E-value=7e-14  Score=125.48  Aligned_cols=168  Identities=14%  Similarity=0.070  Sum_probs=151.0

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      |.+..+|+.++.++.+.|++++|++.|+++++.... +..++..+..++.+.|++++|+..|++.++.+ +-+...+..+
T Consensus         6 P~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~-~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nL   83 (723)
T 4gyw_A            6 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPE-FAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNM   83 (723)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence            456789999999999999999999999999997544 67899999999999999999999999999874 3458899999


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccch
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV  207 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  207 (376)
                      +.++...|++++|.+.|+++.+.. +.+..++..++.+|...|++++|+..|+++++.. +-+...+..++.++...|++
T Consensus        84 g~~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~~  161 (723)
T 4gyw_A           84 GNTLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCDW  161 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhcccH
Confidence            999999999999999999999886 6778899999999999999999999999999863 33588899999999999999


Q ss_pred             HHHHHHHHHHHh
Q 042039          208 EHALKLFEEMQR  219 (376)
Q Consensus       208 ~~a~~~~~~~~~  219 (376)
                      ++|.+.++++.+
T Consensus       162 ~~A~~~~~kal~  173 (723)
T 4gyw_A          162 TDYDERMKKLVS  173 (723)
T ss_dssp             TTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999887755

>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=99.61  E-value=2.7e-13  Score=105.36  Aligned_cols=210  Identities=10%  Similarity=0.010  Sum_probs=163.6

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      +.++..+...+..+...|++++|++.|++.++...+++...+..+..++...|++++|...+++.++.. +.+..++..+
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l   82 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGK   82 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHH
Confidence            346788999999999999999999999999998654677888889999999999999999999999874 3357889999


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCCh-------hhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC---HhHHHHH
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDD-------VSYNILINGYCKNKEVEEALSLYREMVSKGIKPT---VVTYNTL  197 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l  197 (376)
                      +.++...|++++|...+++..... |.+.       ..|..++.++...|++++|+..|+++++.  .|+   ...+..+
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l  159 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSL  159 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHH
Confidence            999999999999999999999875 4555       56888899999999999999999999985  444   5677777


Q ss_pred             HHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHH
Q 042039          198 FLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG  270 (376)
Q Consensus       198 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  270 (376)
                      ..++...|+     ..++.+.... ..+...+...  .....+.+++|...++++.+..+. +..+...+...
T Consensus       160 ~~~~~~~~~-----~~~~~a~~~~-~~~~~~~~~~--~~~~~~~~~~A~~~~~~a~~l~p~-~~~~~~~l~~i  223 (228)
T 4i17_A          160 GVLFYNNGA-----DVLRKATPLA-SSNKEKYASE--KAKADAAFKKAVDYLGEAVTLSPN-RTEIKQMQDQV  223 (228)
T ss_dssp             HHHHHHHHH-----HHHHHHGGGT-TTCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHH-----HHHHHHHhcc-cCCHHHHHHH--HHHHHHHHHHHHHHHHHHhhcCCC-CHHHHHHHHHH
Confidence            777765543     3445554443 2233333322  234456789999999999887633 55555555443

>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=99.60  E-value=2.4e-11  Score=108.04  Aligned_cols=344  Identities=8%  Similarity=-0.009  Sum_probs=214.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC---hHHHHHHHHHHHhcCC-CCchHhH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND---WNEAKRLFFEMMDQGV-QPSVVTF   89 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~-~~~~~~~   89 (376)
                      -|..+|..++..+.+.+.++.+..+|+++...- |.....|...+..-.+.+.   ++.+..+|++.+.... .|++..|
T Consensus        64 ~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~f-P~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW  142 (679)
T 4e6h_A           64 TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDRF-PLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLW  142 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHH
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            467889999999999999999999999998774 7788889988988888888   9999999999988631 3688888


Q ss_pred             HHHHHHHHhCCCh--------HHHHHHHHHHHh-cCC-CCC-hhhHHHHHHHHH---------hcCcHHHHHHHHHHHHh
Q 042039           90 NVIMDELCKNGKM--------DEASRLLDLMVQ-RDV-RPN-AFTYSTLMDGFC---------LTGKINRAEELFGSMES  149 (376)
Q Consensus        90 ~~l~~~~~~~~~~--------~~a~~~~~~~~~-~~~-~~~-~~~~~~l~~~~~---------~~~~~~~a~~~~~~~~~  149 (376)
                      ...+....+.++.        +...++|+..+. .|. .++ ...|...+....         ..++++.+..+|+++..
T Consensus       143 ~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~  222 (679)
T 4e6h_A          143 LSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLC  222 (679)
T ss_dssp             HHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHh
Confidence            8877765555443        334466766654 344 343 456666665433         23345667777777664


Q ss_pred             cCCCCChhhHH---------------------------------------------------------------------
Q 042039          150 MGCKHDDVSYN---------------------------------------------------------------------  160 (376)
Q Consensus       150 ~~~~~~~~~~~---------------------------------------------------------------------  160 (376)
                      ........+|.                                                                     
T Consensus       223 iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql  302 (679)
T 4e6h_A          223 QPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQQL  302 (679)
T ss_dssp             SCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHH
T ss_pred             CccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHHHH
Confidence            31111111111                                                                     


Q ss_pred             ----HHHHHHHccC-------cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHH-HHHHHHHhcCCCCCcch
Q 042039          161 ----ILINGYCKNK-------EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL-KLFEEMQRDDVAADTST  228 (376)
Q Consensus       161 ----~l~~~~~~~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~  228 (376)
                          ..+..--..+       ..+.+..+|++++.. .+-....|...+..+...|+.+.|. +++++..... |.+...
T Consensus       303 ~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~-P~s~~L  380 (679)
T 4e6h_A          303 LIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCI-PNSAVL  380 (679)
T ss_dssp             HHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhC-CCCHHH
Confidence                1111100000       011223344444443 2334555555555566677777775 8888877643 445555


Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhcccCC---------Cc------------hHHHHHHHHHHHHhCCChHHHHHHHhcc
Q 042039          229 YNTFIDGLCKNGYIVEAVELFRTLGILKC---------EL------------DIQAYNCLIDGLCKSGRLEIALELFRSL  287 (376)
Q Consensus       229 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---------~~------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~  287 (376)
                      +...+....+.|+++.|.++|+++.....         .|            ...+|...+....+.|..+.|..+|.++
T Consensus       381 wl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A  460 (679)
T 4e6h_A          381 AFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKC  460 (679)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            66677777788888888888888764310         02            2335777777777778888888888887


Q ss_pred             cccCCCCCHHHHHHHHHHHHcc-CChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          288 PRRVLVADVVTYNIMIHGLCND-GQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       288 ~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      .+.........|...+..-.+. ++.+.|..+|+..++. .+.+...|...+......|+.+.|..+|++..+..
T Consensus       461 ~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~  534 (679)
T 4e6h_A          461 RRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKI  534 (679)
T ss_dssp             HHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTS
T ss_pred             HHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence            6541112234444333333333 4478888888887765 23355566667776677788888888888877654

>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=99.57  E-value=6e-13  Score=99.64  Aligned_cols=166  Identities=14%  Similarity=0.060  Sum_probs=120.7

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..++..+...|++++|.+.++++.+... .+...+..+...+...|++++|...++++.+.. +.+...+..++..
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADA-FDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            44566677777788888888888877766532 256677777777888888888888888877763 3356677777777


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHH
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  210 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  210 (376)
                      +...|++++|.+.++++.... +.+...+..++.++...|++++|...++++.+.. +.+...+..+...+...|++++|
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHH
Confidence            778888888888888777664 4566677777777777888888888887777652 33566677777777777777777


Q ss_pred             HHHHHHHHhc
Q 042039          211 LKLFEEMQRD  220 (376)
Q Consensus       211 ~~~~~~~~~~  220 (376)
                      ...++.+.+.
T Consensus       164 ~~~~~~~~~~  173 (186)
T 3as5_A          164 LPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHc
Confidence            7777776654

>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=99.57  E-value=2e-11  Score=108.46  Aligned_cols=220  Identities=11%  Similarity=-0.019  Sum_probs=169.6

Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHH-HHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHH
Q 042039          139 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL-SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEM  217 (376)
Q Consensus       139 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  217 (376)
                      .+..+|+++.... +.....|...+..+...|+.++|. .+|++.... ++.+...|...+......|+++.|.++|+.+
T Consensus       327 Rv~~~Ye~aL~~~-p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~  404 (679)
T 4e6h_A          327 RMTYVYMQAAQHV-CFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSC  404 (679)
T ss_dssp             HHHHHHHHHHHHT-TTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            3455677666653 567778888888888889999997 999999875 5556777788888888999999999999998


Q ss_pred             HhcCC---------CCC------------cchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhC-C
Q 042039          218 QRDDV---------AAD------------TSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKS-G  275 (376)
Q Consensus       218 ~~~~~---------~~~------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~  275 (376)
                      +....         .|+            ..+|...+....+.|..+.|..+|.++...........|...+..-.+. +
T Consensus       405 l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~  484 (679)
T 4e6h_A          405 IDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISK  484 (679)
T ss_dssp             HHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCC
Confidence            76410         121            2357777777788899999999999997651122344555544444454 4


Q ss_pred             ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCC--cHHHHHHHHHHHhhcCChhhHHHH
Q 042039          276 RLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP--NVIIFVTLIHGFVRINKPSKVIEL  353 (376)
Q Consensus       276 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~  353 (376)
                      +.+.|.++|+..++. .+.+...+...+......|+.+.|..+|++++.....+  ....|...+..-.+.|+.+.+.++
T Consensus       485 d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v  563 (679)
T 4e6h_A          485 DTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTL  563 (679)
T ss_dssp             CCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHH
T ss_pred             CHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            599999999999887 56677777888888888999999999999999864322  456788888888889999999999


Q ss_pred             HHHHHhCC
Q 042039          354 LHKMKEKK  361 (376)
Q Consensus       354 ~~~~~~~~  361 (376)
                      .+++.+.-
T Consensus       564 ~~R~~~~~  571 (679)
T 4e6h_A          564 EKRFFEKF  571 (679)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHHhC
Confidence            99998763

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

Probab=99.53  E-value=5.7e-12  Score=101.68  Aligned_cols=209  Identities=12%  Similarity=-0.014  Sum_probs=124.0

Q ss_pred             ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc----CCCCC-hhhHHHHHHHHHhcCcHHHH
Q 042039           66 DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR----DVRPN-AFTYSTLMDGFCLTGKINRA  140 (376)
Q Consensus        66 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a  140 (376)
                      ++++|...|+++               +..+...|++++|...|.+..+.    +.++. ..++..++.+|...|++++|
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A   96 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNA   96 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            477777777665               33566778888888877777653    21111 45677777777778888888


Q ss_pred             HHHHHHHHhcCCC---C--ChhhHHHHHHHHHcc-CcHHHHHHHHHHHHHCCCCC-C----HhHHHHHHHHHHhccchHH
Q 042039          141 EELFGSMESMGCK---H--DDVSYNILINGYCKN-KEVEEALSLYREMVSKGIKP-T----VVTYNTLFLGLFEIHQVEH  209 (376)
Q Consensus       141 ~~~~~~~~~~~~~---~--~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~~~~~~  209 (376)
                      ...+++.......   +  ...++..++.+|... |++++|+..|++.++..... +    ..++..+...+...|++++
T Consensus        97 ~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~  176 (292)
T 1qqe_A           97 VDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIE  176 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHH
Confidence            7777776553210   0  134667777777775 88888888777776531100 1    3456666777777777777


Q ss_pred             HHHHHHHHHhcCCCCCcc------hHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc-h---HHHHHHHHHHHH--hCCCh
Q 042039          210 ALKLFEEMQRDDVAADTS------TYNTFIDGLCKNGYIVEAVELFRTLGILKCEL-D---IQAYNCLIDGLC--KSGRL  277 (376)
Q Consensus       210 a~~~~~~~~~~~~~~~~~------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~---~~~~~~l~~~~~--~~~~~  277 (376)
                      |...++++.+........      .+..++.++...|++++|...+++.....+.. +   ...+..++.++.  ..+++
T Consensus       177 A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~  256 (292)
T 1qqe_A          177 ASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQL  256 (292)
T ss_dssp             HHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTH
T ss_pred             HHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHH
Confidence            777777776653222111      35556666777777777777777765543210 0   112333444443  34556


Q ss_pred             HHHHHHHhcccc
Q 042039          278 EIALELFRSLPR  289 (376)
Q Consensus       278 ~~a~~~~~~~~~  289 (376)
                      ++|+..|+.+..
T Consensus       257 ~~A~~~~~~~~~  268 (292)
T 1qqe_A          257 SEHCKEFDNFMR  268 (292)
T ss_dssp             HHHHHHHTTSSC
T ss_pred             HHHHHHhccCCc
Confidence            666666666544

>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=99.52  E-value=1.9e-13  Score=109.85  Aligned_cols=229  Identities=16%  Similarity=0.077  Sum_probs=162.3

Q ss_pred             HHhcCChhHHHHHHHHhhhC-------CCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc------CCCC-chHhHHH
Q 042039           26 LCKEGFVDKAKALFLQMKGE-------NINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ------GVQP-SVVTFNV   91 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~   91 (376)
                      ....|++++|+..+++..+.       +.+....++..++.++...|++++|...++++++.      +..| ...++..
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            34567777777777776552       22345778999999999999999999999998865      2222 3567888


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhc------CC-CCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc------C-CCCChh
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQR------DV-RPNAFTYSTLMDGFCLTGKINRAEELFGSMESM------G-CKHDDV  157 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~  157 (376)
                      +..++...|++++|...++++++.      .. +....++..++..+...|++++|...++++...      + .+....
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            999999999999999999998864      11 223667888999999999999999999998765      1 133456


Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHC-------CCCCC-HhHHHHHHHHHHhccchHHHH------HHHHHHHhcCCC
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSK-------GIKPT-VVTYNTLFLGLFEIHQVEHAL------KLFEEMQRDDVA  223 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~-~~~~~~l~~~~~~~~~~~~a~------~~~~~~~~~~~~  223 (376)
                      ++..++.++...|++++|...++++.+.       ...+. ...+..+.......+....+.      ..+..... ..+
T Consensus       171 ~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  249 (283)
T 3edt_B          171 TKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV-DSP  249 (283)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC-CCH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC-CCH
Confidence            7889999999999999999999998763       11222 333333333333333322222      22221111 112


Q ss_pred             CCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          224 ADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       224 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      ....++..++.+|...|++++|..+++++.+.
T Consensus       250 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          250 TVNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            34557888999999999999999999987653

>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=99.51  E-value=1.1e-12  Score=105.36  Aligned_cols=159  Identities=19%  Similarity=0.130  Sum_probs=120.4

Q ss_pred             hcCCChHHHHHHHHHHHhc-------CCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc------CCCC-ChhhHHHH
Q 042039           62 CHANDWNEAKRLFFEMMDQ-------GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR------DVRP-NAFTYSTL  127 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~l  127 (376)
                      ...|++++|+..|++.++.       ..+....++..+...+...|++++|...++++++.      +..| ...++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            3567777777777777652       22224667888999999999999999999998864      2122 35678889


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcC-------CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC------CCCC-CHhH
Q 042039          128 MDGFCLTGKINRAEELFGSMESMG-------CKHDDVSYNILINGYCKNKEVEEALSLYREMVSK------GIKP-TVVT  193 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~  193 (376)
                      +.++...|++++|...++++....       .+....++..++.++...|++++|...++++.+.      +..| ...+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            999999999999999999887641       1334567888899999999999999999988764      1122 3566


Q ss_pred             HHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          194 YNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       194 ~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      +..+..++...|++++|...++++.+.
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            778888888889999888888887653

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

Probab=99.51  E-value=4e-12  Score=100.89  Aligned_cols=103  Identities=10%  Similarity=-0.021  Sum_probs=80.5

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--CchH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD---VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PSVV   87 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~   87 (376)
                      +.++..+..+...+.+.|++++|+..|+++.+.. |.+   ..++..++.++...|++++|+..|+++++..+.  ....
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~   90 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQ   90 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHH
Confidence            3456777888888888999999999999888764 334   677888888899999999999999998886331  1245


Q ss_pred             hHHHHHHHHHh--------CCChHHHHHHHHHHHhcC
Q 042039           88 TFNVIMDELCK--------NGKMDEASRLLDLMVQRD  116 (376)
Q Consensus        88 ~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~  116 (376)
                      .+..+..++..        .|++++|...|+++++..
T Consensus        91 a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~  127 (261)
T 3qky_A           91 AEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY  127 (261)
T ss_dssp             HHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC
Confidence            67777778888        888888888888888763

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

Probab=99.48  E-value=6.1e-12  Score=101.52  Aligned_cols=210  Identities=14%  Similarity=0.083  Sum_probs=151.7

Q ss_pred             ChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc----CCCCc-hHhHHHHHHHHHhCCChHHH
Q 042039           31 FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ----GVQPS-VVTFNVIMDELCKNGKMDEA  105 (376)
Q Consensus        31 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a  105 (376)
                      ++++|...|++.               +..|...|++++|.+.|++....    +.+++ ..+|+.+..+|...|++++|
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A   96 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNA   96 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            477777777665               45677889999999999888764    22222 45788899999999999999


Q ss_pred             HHHHHHHHhcCCC-CC----hhhHHHHHHHHHhc-CcHHHHHHHHHHHHhcCCCC-C----hhhHHHHHHHHHccCcHHH
Q 042039          106 SRLLDLMVQRDVR-PN----AFTYSTLMDGFCLT-GKINRAEELFGSMESMGCKH-D----DVSYNILINGYCKNKEVEE  174 (376)
Q Consensus       106 ~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~~~~~~  174 (376)
                      +..+++.++.... .+    ..++..++.+|... |++++|...|++........ +    ..++..++.++...|++++
T Consensus        97 ~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~  176 (292)
T 1qqe_A           97 VDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIE  176 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHH
Confidence            9999888764211 01    35778889999996 99999999999987653111 1    3568889999999999999


Q ss_pred             HHHHHHHHHHCCCCCCH------hHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC-C---cchHHHHHHHHH--hCCCH
Q 042039          175 ALSLYREMVSKGIKPTV------VTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA-D---TSTYNTFIDGLC--KNGYI  242 (376)
Q Consensus       175 a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~---~~~~~~l~~~~~--~~~~~  242 (376)
                      |+..|++..+.......      ..+..+..++...|+++.|...+++..+..... +   ...+..++.++.  ..+++
T Consensus       177 A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~  256 (292)
T 1qqe_A          177 ASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQL  256 (292)
T ss_dssp             HHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTH
T ss_pred             HHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHH
Confidence            99999999985322221      156778888999999999999999987653111 1   112444555554  45679


Q ss_pred             HHHHHHHHHhccc
Q 042039          243 VEAVELFRTLGIL  255 (376)
Q Consensus       243 ~~a~~~~~~~~~~  255 (376)
                      ++|+..|+.+...
T Consensus       257 ~~A~~~~~~~~~l  269 (292)
T 1qqe_A          257 SEHCKEFDNFMRL  269 (292)
T ss_dssp             HHHHHHHTTSSCC
T ss_pred             HHHHHHhccCCcc
Confidence            9999999887654

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

Probab=99.48  E-value=2.8e-12  Score=97.94  Aligned_cols=115  Identities=15%  Similarity=0.149  Sum_probs=61.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHH----------------HHHHHhcCCChHHHHHHHHHHHh
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNS----------------LIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~----------------l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      +..+......+...|++++|+..|++..+.+ |.+...|..                ++.++...|++++|+..|++.++
T Consensus         4 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A            4 VDEMLQKVSAAIEAGQNGQAVSYFRQTIALN-IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3344555566777788888888888777654 334455554                45555555555555555555554


Q ss_pred             cCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh
Q 042039           80 QGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL  133 (376)
Q Consensus        80 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  133 (376)
                      ..+. +...+..+..++...|++++|...|+++++.. +.+..++..++.+|..
T Consensus        83 ~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~  134 (208)
T 3urz_A           83 KAPN-NVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYL  134 (208)
T ss_dssp             HCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            4222 34444455555555555555555555555442 2234444444444433

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

Probab=99.47  E-value=7.5e-12  Score=99.32  Aligned_cols=171  Identities=9%  Similarity=0.004  Sum_probs=114.2

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc---hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCC-C-CChh
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS---VVTFNVIMDELCKNGKMDEASRLLDLMVQRDV-R-PNAF  122 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~-~~~~  122 (376)
                      +.+...+..++..+...|++++|+..|+++++..+. +   ...+..+..++...|++++|...|+++++... . ....
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~   90 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRT-HEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQ   90 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSC-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCC-CcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHH
Confidence            456778888899999999999999999999886433 3   56788888899999999999999999988632 1 1245


Q ss_pred             hHHHHHHHHHh--------cCcHHHHHHHHHHHHhcCCCCChhhH-----------------HHHHHHHHccCcHHHHHH
Q 042039          123 TYSTLMDGFCL--------TGKINRAEELFGSMESMGCKHDDVSY-----------------NILINGYCKNKEVEEALS  177 (376)
Q Consensus       123 ~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~-----------------~~l~~~~~~~~~~~~a~~  177 (376)
                      .+..++.++..        .|++++|...|+++.... |.+....                 ..++.+|...|++++|+.
T Consensus        91 a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  169 (261)
T 3qky_A           91 AEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY-PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAV  169 (261)
T ss_dssp             HHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC-TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC-cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            67778888888        899999999999988764 3333333                 334555555555555555


Q ss_pred             HHHHHHHCCCCC--CHhHHHHHHHHHHhc----------cchHHHHHHHHHHHhc
Q 042039          178 LYREMVSKGIKP--TVVTYNTLFLGLFEI----------HQVEHALKLFEEMQRD  220 (376)
Q Consensus       178 ~~~~~~~~~~~~--~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~  220 (376)
                      .|+++++.....  ....+..+..++...          |++++|...++++.+.
T Consensus       170 ~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          170 TYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            555555431110  123444444444433          4445555555554443

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

Probab=99.46  E-value=9.6e-11  Score=92.77  Aligned_cols=178  Identities=11%  Similarity=0.029  Sum_probs=86.8

Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCChhhHHHHHHHHHccCcHHHHHHHHHHHH
Q 042039          105 ASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-KHDDVSYNILINGYCKNKEVEEALSLYREMV  183 (376)
Q Consensus       105 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  183 (376)
                      +...+++.+..+ .++..++..++.++...|++++|++++.+....+. ..+...+..++.++.+.|+.+.|.+.++.|.
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            455555555443 33444445556666666666666666666544431 1344455556666666666666666666665


Q ss_pred             HCCCCC-----CHhHHHHHHHHHH--hcc--chHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcc
Q 042039          184 SKGIKP-----TVVTYNTLFLGLF--EIH--QVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGI  254 (376)
Q Consensus       184 ~~~~~~-----~~~~~~~l~~~~~--~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  254 (376)
                      +.  .|     +..+...++.++.  ..|  ++..|..+|+++...  .|+......+..++.+.|++++|...++.+..
T Consensus       164 ~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          164 NA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            53  33     2344444444422  122  556666666665443  22211222222255555666666665554433


Q ss_pred             cC---------CCchHHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          255 LK---------CELDIQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       255 ~~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                      ..         -+.++.++..++......|+  +|.++++++.+
T Consensus       240 ~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~  281 (310)
T 3mv2_B          240 DYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK  281 (310)
T ss_dssp             HHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH
T ss_pred             hcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH
Confidence            20         02244444444444444444  45555555544

>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=99.44  E-value=2.4e-12  Score=116.10  Aligned_cols=173  Identities=14%  Similarity=-0.044  Sum_probs=112.5

Q ss_pred             hcCCChHHHHHHHHHHH--------hcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh
Q 042039           62 CHANDWNEAKRLFFEMM--------DQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL  133 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  133 (376)
                      ...|++++|++.+++++        +.. +.+...+..+..++...|++++|...++++++.+ +.+...+..++.++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHH
Confidence            56677777777777776        332 2245566666777777777777777777777653 3356667777777777


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHH
Q 042039          134 TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKL  213 (376)
Q Consensus       134 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  213 (376)
                      .|++++|.+.|+++.+.. |.+...+..++.++.+.|++++ +..|+++++.+ +.+...+..+..++...|++++|.+.
T Consensus       480 ~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            777777777777776665 4556667777777777777777 77777776642 23456677777777777777777777


Q ss_pred             HHHHHhcCCCCCcchHHHHHHHHHhCC
Q 042039          214 FEEMQRDDVAADTSTYNTFIDGLCKNG  240 (376)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~l~~~~~~~~  240 (376)
                      |+++.+.+ +.+...+..++.++...+
T Consensus       557 ~~~al~l~-P~~~~a~~~~~~~~~~~~  582 (681)
T 2pzi_A          557 LDEVPPTS-RHFTTARLTSAVTLLSGR  582 (681)
T ss_dssp             HHTSCTTS-TTHHHHHHHHHHHTC---
T ss_pred             HHhhcccC-cccHHHHHHHHHHHHccC
Confidence            77766653 334555666666655543

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

Probab=99.43  E-value=1.6e-11  Score=93.71  Aligned_cols=58  Identities=22%  Similarity=0.281  Sum_probs=23.7

Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      ++.++.+.|++++|+..|++.++.. +.+...+..+..++...|++++|...|+++++.
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  117 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQL  117 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            3444444444444444444444431 113333444444444444444444444444433

>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=99.43  E-value=1.1e-12  Score=94.41  Aligned_cols=143  Identities=7%  Similarity=-0.034  Sum_probs=82.7

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChH
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMD  103 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  103 (376)
                      ..+...|++++|++.++...... +.+...+..+..+|.+.|++++|++.|++.++..+. +..+|..+..++...|+++
T Consensus         5 ~~~~~~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~   82 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER-DPKAHRFLGLLYELEENTD   82 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCchH
Confidence            34445566666666666665442 333445556666666666666666666666665333 5566666666666666666


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHH-HHHHHhcCCCCChhhHHHHHHHHHccC
Q 042039          104 EASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEEL-FGSMESMGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      +|...|++.++.+ +-+..++..++.++.+.|++++|.+. ++++.+.. |.++.+|......+...|
T Consensus        83 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~-P~~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A           83 KAVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLF-PGSPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhC
Confidence            6666666666653 22455666666666666666554433 45555554 445555555555555544

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.43  E-value=5.8e-10  Score=89.22  Aligned_cols=223  Identities=10%  Similarity=-0.015  Sum_probs=148.1

Q ss_pred             HhcCC-hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC--ChHHHHHHHHHHHhcCCCCchHhHHHHHHHH----HhC
Q 042039           27 CKEGF-VDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN--DWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL----CKN   99 (376)
Q Consensus        27 ~~~g~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~   99 (376)
                      .+.|. .++|+++++.++..+ |.+..+|+.-..++...+  ++++++++++.++..+++ +..+|+.-...+    ...
T Consensus        43 ~~~~e~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk-~y~aW~~R~~iL~~~~~~l  120 (306)
T 3dra_A           43 MKAEEYSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEK-NYQIWNYRQLIIGQIMELN  120 (306)
T ss_dssp             HHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHHHT
T ss_pred             HHcCCCCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcc-cHHHHHHHHHHHHHHHHhc
Confidence            34444 468999999988876 667788888888888888  899999999998887555 566666555544    444


Q ss_pred             ---CChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHH--HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc---
Q 042039          100 ---GKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKIN--RAEELFGSMESMGCKHDDVSYNILINGYCKNKE---  171 (376)
Q Consensus       100 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---  171 (376)
                         +++++++.+++.+++.. +-+..+|..-..++...|.++  ++.+.++++.+.+ +.+..+|+....+....+.   
T Consensus       121 ~~~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~  198 (306)
T 3dra_A          121 NNDFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLAT  198 (306)
T ss_dssp             TTCCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCC
T ss_pred             cccCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccch
Confidence               67888888888888765 446777777777777777777  7788888887766 5666777766666666665   


Q ss_pred             ---HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHH-HHHHHHHHHhcC--CCCCcchHHHHHHHHHhCCCHHHH
Q 042039          172 ---VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH-ALKLFEEMQRDD--VAADTSTYNTFIDGLCKNGYIVEA  245 (376)
Q Consensus       172 ---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a  245 (376)
                         ++++++.+++++... +-+...|..+...+.+.|+... +..+..++...+  .+.++..+..++.++.+.|+.++|
T Consensus       199 ~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A  277 (306)
T 3dra_A          199 DNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNES  277 (306)
T ss_dssp             HHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHH
Confidence               667777777766652 3356666666666655555333 333444443321  123444555556666666666666


Q ss_pred             HHHHHHhcc
Q 042039          246 VELFRTLGI  254 (376)
Q Consensus       246 ~~~~~~~~~  254 (376)
                      .++++.+..
T Consensus       278 ~~~~~~l~~  286 (306)
T 3dra_A          278 RTVYDLLKS  286 (306)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            666666553

>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=99.42  E-value=9.6e-12  Score=112.18  Aligned_cols=186  Identities=9%  Similarity=-0.071  Sum_probs=146.0

Q ss_pred             HhCCChHHHHHHHHHHH--------hcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc
Q 042039           97 CKNGKMDEASRLLDLMV--------QRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  168 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  168 (376)
                      ...|++++|++.+++.+        +.. +.+...+..++.++...|++++|...|+++.+.. +.+...+..++.++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHH
Confidence            67788999999999888        432 3456778888888999999999999999988775 6677888889999999


Q ss_pred             cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHH
Q 042039          169 NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVEL  248 (376)
Q Consensus       169 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  248 (376)
                      .|++++|+..|+++++.. +.+...+..+..++...|++++ ...|+++++.+ +.+...+..++.++.+.|++++|+..
T Consensus       480 ~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999999988863 3357778888888999999999 99999888875 55677888889999999999999999


Q ss_pred             HHHhcccCCCchHHHHHHHHHHHHhCCC--------hHHHHHHHhccc
Q 042039          249 FRTLGILKCELDIQAYNCLIDGLCKSGR--------LEIALELFRSLP  288 (376)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------~~~a~~~~~~~~  288 (376)
                      |+++...+.. +...+..++.++...++        +++|.+.+..+.
T Consensus       557 ~~~al~l~P~-~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~  603 (681)
T 2pzi_A          557 LDEVPPTSRH-FTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALP  603 (681)
T ss_dssp             HHTSCTTSTT-HHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSC
T ss_pred             HHhhcccCcc-cHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCC
Confidence            9998877532 56777777777765444        556666665553

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

Probab=99.41  E-value=1.3e-10  Score=92.01  Aligned_cols=244  Identities=9%  Similarity=-0.014  Sum_probs=157.3

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                      ++-..-.|++..++.-..   +............+.++++..|++...         ....|....+..+...+ ..+  
T Consensus        20 ikn~fy~G~yq~~i~e~~---~~~~~~~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~~~-~~~--   84 (310)
T 3mv2_B           20 IKQNYYTGNFVQCLQEIE---KFSKVTDNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQFL-DTK--   84 (310)
T ss_dssp             HHHHHTTTCHHHHTHHHH---TSSCCCCHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHHHH-TTT--
T ss_pred             HHHHHHhhHHHHHHHHHH---hcCccchHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHHHh-ccc--
Confidence            344555788877776332   222222233444456778877776641         11233333444333333 222  


Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCC-CCCHhHHHHHHHHHHhccchHHHHHHHHH
Q 042039          138 NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGI-KPTVVTYNTLFLGLFEIHQVEHALKLFEE  216 (376)
Q Consensus       138 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  216 (376)
                        |...|++....+ +++...+..++.++...|++++|++++.+.+..+. .-+...+...+..+.+.|+.+.|.+.++.
T Consensus        85 --a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~  161 (310)
T 3mv2_B           85 --NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDN  161 (310)
T ss_dssp             --CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             --HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence              677777776654 45566667888888889999999999998877543 23567778888889999999999999998


Q ss_pred             HHhcCCCC-----CcchHHHHHHHH--HhCC--CHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcc
Q 042039          217 MQRDDVAA-----DTSTYNTFIDGL--CKNG--YIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSL  287 (376)
Q Consensus       217 ~~~~~~~~-----~~~~~~~l~~~~--~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  287 (376)
                      |.+.  .|     +..+...++.++  ...|  ++.+|..+|+++...  .|+......+..++.+.|++++|.+.++.+
T Consensus       162 ~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l  237 (310)
T 3mv2_B          162 YTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELL  237 (310)
T ss_dssp             HHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            8775  34     355566666553  3334  888899999998655  333222223333788889999999988865


Q ss_pred             cccC---------CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          288 PRRV---------LVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       288 ~~~~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      .+..         .+.++.++..++......|+  +|.+++.++.+.
T Consensus       238 ~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          238 LSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             HSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             HHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence            5421         14466777666666666676  788888888875

>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=99.40  E-value=8e-11  Score=90.03  Aligned_cols=175  Identities=11%  Similarity=-0.022  Sum_probs=95.7

Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhcc----chHHHHHHHH
Q 042039          140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH----QVEHALKLFE  215 (376)
Q Consensus       140 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~  215 (376)
                      |.++|++..+.+   ++.++..+...|...+++++|+..|++..+.+   ++..+..+...|.. +    ++++|...|+
T Consensus         5 A~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            5 PGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAE   77 (212)
T ss_dssp             TTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHH
Confidence            444455544432   44455555555555555555555555555542   34444455555544 4    5555555555


Q ss_pred             HHHhcCCCCCcchHHHHHHHHHh----CCCHHHHHHHHHHhcccCCC-chHHHHHHHHHHHHh----CCChHHHHHHHhc
Q 042039          216 EMQRDDVAADTSTYNTFIDGLCK----NGYIVEAVELFRTLGILKCE-LDIQAYNCLIDGLCK----SGRLEIALELFRS  286 (376)
Q Consensus       216 ~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~~  286 (376)
                      +..+.+   ++..+..+...|..    .+++++|+.+|++....+.. ..+..+..++..|..    .+++++|...|++
T Consensus        78 ~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~  154 (212)
T 3rjv_A           78 KAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKG  154 (212)
T ss_dssp             HHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            554433   34445555555554    56666666666666655421 124566666666666    5666666666666


Q ss_pred             ccccCCCCCHHHHHHHHHHHHcc-C-----ChhHHHHHHHHHHHcC
Q 042039          287 LPRRVLVADVVTYNIMIHGLCND-G-----QMDKAHDLFLDMEENA  326 (376)
Q Consensus       287 ~~~~~~~~~~~~~~~l~~~~~~~-~-----~~~~a~~~~~~~~~~~  326 (376)
                      ..+.  +.+...+..+...|... |     ++++|...|++..+.|
T Consensus       155 A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          155 SSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            6554  22444555566655432 2     6666666666666654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.39  E-value=1.9e-09  Score=86.23  Aligned_cols=217  Identities=8%  Similarity=0.001  Sum_probs=123.0

Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC--cHHHHHHHHHHHHhcCCCCChhhHHHHHHHH----Hcc---CcHH
Q 042039          103 DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG--KINRAEELFGSMESMGCKHDDVSYNILINGY----CKN---KEVE  173 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~---~~~~  173 (376)
                      ++|+.+++.++..+ +-+..+|+.-..++...+  ++++++++++.+...+ |.+..+|+.-..++    ...   ++++
T Consensus        50 ~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l~~~~~~~  127 (306)
T 3dra_A           50 ERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELNNNDFDPY  127 (306)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHTTTCCCTH
T ss_pred             HHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhccccCCHH
Confidence            34555555555442 223444444444444444  5555555555555543 33444444433333    333   4555


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchH--HHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCC------HHHH
Q 042039          174 EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVE--HALKLFEEMQRDDVAADTSTYNTFIDGLCKNGY------IVEA  245 (376)
Q Consensus       174 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~------~~~a  245 (376)
                      +++.+++++++.. +-+..+|..-...+...+.++  ++++.++++++.+ +.+..+++.-...+...+.      ++++
T Consensus       128 ~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~~~~~eE  205 (306)
T 3dra_A          128 REFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATDNTIDEE  205 (306)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchhhhHHHH
Confidence            6666666665542 234555555555555555555  5666666666554 3445555544444444444      6777


Q ss_pred             HHHHHHhcccCCCchHHHHHHHHHHHHhCCChHH-HHHHHhcccccC--CCCCHHHHHHHHHHHHccCChhHHHHHHHHH
Q 042039          246 VELFRTLGILKCELDIQAYNCLIDGLCKSGRLEI-ALELFRSLPRRV--LVADVVTYNIMIHGLCNDGQMDKAHDLFLDM  322 (376)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  322 (376)
                      ++.++.+....+. +...|+.+...+.+.|+... +..+..++...+  .+.++..+..++.++.+.|+.++|.++++.+
T Consensus       206 l~~~~~aI~~~p~-n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l  284 (306)
T 3dra_A          206 LNYVKDKIVKCPQ-NPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLL  284 (306)
T ss_dssp             HHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCC-CccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            7777777666533 67777777777777776433 445666655432  2346677777778888888888888888887


Q ss_pred             HH
Q 042039          323 EE  324 (376)
Q Consensus       323 ~~  324 (376)
                      .+
T Consensus       285 ~~  286 (306)
T 3dra_A          285 KS  286 (306)
T ss_dssp             HH
T ss_pred             Hh
Confidence            75

>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=99.39  E-value=3.4e-11  Score=84.76  Aligned_cols=129  Identities=16%  Similarity=0.229  Sum_probs=71.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      +|..+...+...|++++|..+++++.+.+ +.+...+..++..+...|++++|...++++...+.. +...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCC-chHHHHHHHHHHH
Confidence            45555666666666666666666665543 334555555666666666666666666666554322 3445555555555


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHh
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMES  149 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  149 (376)
                      ..|++++|...++++.+.. +.+..++..++..+...|++++|...++++..
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            5555666655555555542 22344455555555555555555555555544

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.38  E-value=1.1e-10  Score=90.24  Aligned_cols=188  Identities=9%  Similarity=-0.056  Sum_probs=123.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCC-C-ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCch--HhHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENIN-P-DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV--VTFN   90 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~   90 (376)
                      +...+..+...+.+.|++++|+..|+++.+.... + ...++..++.++...|++++|+..|+++++..+....  ..+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            4566777888899999999999999999876311 1 2467888999999999999999999999886443111  2455


Q ss_pred             HHHHHHHh------------------CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC
Q 042039           91 VIMDELCK------------------NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC  152 (376)
Q Consensus        91 ~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  152 (376)
                      .+..++..                  .|++++|...|+++++.. +-+...........          .+....     
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-P~~~~a~~a~~~l~----------~~~~~~-----  146 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-PNSQYTTDATKRLV----------FLKDRL-----  146 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-TTCTTHHHHHHHHH----------HHHHHH-----
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-cCChhHHHHHHHHH----------HHHHHH-----
Confidence            55555544                  456666666666666642 11222221111000          000000     


Q ss_pred             CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCC--CHhHHHHHHHHHHhccchHHHHHHHHHHHhcC
Q 042039          153 KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP--TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD  221 (376)
Q Consensus       153 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  221 (376)
                         ......++..|.+.|++++|+..|+++++.....  ....+..+..++.+.|++++|.+.++.+...+
T Consensus       147 ---~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          147 ---AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             ---HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             ---HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence               0112356778888899999999999888752111  12567788888889999999999888887764

>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=99.38  E-value=4e-12  Score=91.45  Aligned_cols=146  Identities=10%  Similarity=-0.107  Sum_probs=89.2

Q ss_pred             HHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCC
Q 042039          197 LFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGR  276 (376)
Q Consensus       197 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  276 (376)
                      |...+...|++++|+..+....... +.+...+..++..|.+.|++++|+..|+++....+. ++.++..++.++...|+
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER-DPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCc
Confidence            3444555666677776666665542 334445566677777777777777777777666532 56677777777777777


Q ss_pred             hHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHH-HHHHHHcCCCCcHHHHHHHHHHHhhcCC
Q 042039          277 LEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDL-FLDMEENAVAPNVIIFVTLIHGFVRINK  346 (376)
Q Consensus       277 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~g~  346 (376)
                      +++|+..|+++.+. .|.+...+..++.+|.+.|++++|.+. ++++.+..+. ++.+|......+...|+
T Consensus        81 ~~~A~~~~~~al~~-~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~-~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           81 TDKAVECYRRSVEL-NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPG-SPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTCCC
T ss_pred             hHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhCc
Confidence            77777777776665 344566777777777777777665544 4666664322 45555555555555553

>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=99.38  E-value=9.9e-12  Score=92.17  Aligned_cols=164  Identities=12%  Similarity=0.037  Sum_probs=103.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH-
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE-   95 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-   95 (376)
                      ..+..+...+.+.|++++|+..|++..+.. |.+...+..+..++...|++++|+..++++....+  +...+...... 
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            345666677778888888888888777654 55677788888888888888888888877766532  33332222211 


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHccCcHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKH-DDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~  174 (376)
                      +...+...++...+++.++.. +.+...+..++.++...|++++|...|+++......+ +...+..++.++...|+.++
T Consensus        84 ~~~~~~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  162 (176)
T 2r5s_A           84 LHQQAAESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNA  162 (176)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCH
T ss_pred             HHhhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCc
Confidence            112223334566666666653 2346666667777777777777777777766654211 23466666677777777777


Q ss_pred             HHHHHHHHHH
Q 042039          175 ALSLYREMVS  184 (376)
Q Consensus       175 a~~~~~~~~~  184 (376)
                      |...|++.+.
T Consensus       163 A~~~y~~al~  172 (176)
T 2r5s_A          163 IASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            7776666543

>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=99.37  E-value=1.1e-10  Score=89.33  Aligned_cols=176  Identities=11%  Similarity=0.016  Sum_probs=94.6

Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCC----ChHHHHHHH
Q 042039           34 KAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG----KMDEASRLL  109 (376)
Q Consensus        34 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~  109 (376)
                      +|++.|++..+.|   ++.++..+...|...+++++|.+.|++..+.|   +...+..+...|.. +    ++++|..+|
T Consensus         4 eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~   76 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLA   76 (212)
T ss_dssp             CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHH
T ss_pred             hHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHH
Confidence            4555566555543   55566666666666666666666666666543   44455555555555 4    566666666


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCC-CChhhHHHHHHHHHc----cCcHHHHHHHHH
Q 042039          110 DLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCK-HDDVSYNILINGYCK----NKEVEEALSLYR  180 (376)
Q Consensus       110 ~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~  180 (376)
                      ++..+.+   ++..+..+...|..    .+++++|..+|++..+.+.. ..+.++..|..+|..    .+++++|+..|+
T Consensus        77 ~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~  153 (212)
T 3rjv_A           77 EKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFK  153 (212)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHH
T ss_pred             HHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            6665543   34455555555554    55666666666666554310 014555555555555    555666666666


Q ss_pred             HHHHCCCCCCHhHHHHHHHHHHhc-c-----chHHHHHHHHHHHhcC
Q 042039          181 EMVSKGIKPTVVTYNTLFLGLFEI-H-----QVEHALKLFEEMQRDD  221 (376)
Q Consensus       181 ~~~~~~~~~~~~~~~~l~~~~~~~-~-----~~~~a~~~~~~~~~~~  221 (376)
                      +..+.  +.+...+..+...|... |     ++++|...++...+.|
T Consensus       154 ~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          154 GSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            65553  12333444444444332 1     4555555555554443

>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=99.37  E-value=7.2e-11  Score=83.09  Aligned_cols=129  Identities=18%  Similarity=0.298  Sum_probs=80.6

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC  132 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  132 (376)
                      ++..++..+...|++++|..+++++.+.... +...+..++..+...|++++|..+++++.+.+ +.+...+..++..+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCc-chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            4555666666677777777777776655322 45556666666666667777777776666553 334555666666666


Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          133 LTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      ..|++++|.+.++++.... +.+...+..++.++...|++++|...++++..
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            6666666666666666553 34455566666666666666666666666655

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

Probab=99.37  E-value=2e-11  Score=98.12  Aligned_cols=168  Identities=11%  Similarity=0.005  Sum_probs=134.2

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhh-HHH
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFT-YST  126 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~  126 (376)
                      +.+...+..+...+...|++++|...|++++...+. +...+..+..++...|++++|...++++....  |+... ...
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~  190 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQ-NGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLV  190 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTS-CHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc-chhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHH
Confidence            556677888888999999999999999999887544 67788889999999999999999999887763  34332 333


Q ss_pred             HHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhcc
Q 042039          127 LMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP-TVVTYNTLFLGLFEIH  205 (376)
Q Consensus       127 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~  205 (376)
                      ....+...++.+.|...+++..... |.+...+..++..+...|++++|+..|+++++..... +...+..++..+...|
T Consensus       191 ~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g  269 (287)
T 3qou_A          191 AQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALG  269 (287)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHC
T ss_pred             HHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcC
Confidence            3344667778888889999888876 6778889999999999999999999999998863221 2667888999999999


Q ss_pred             chHHHHHHHHHHHh
Q 042039          206 QVEHALKLFEEMQR  219 (376)
Q Consensus       206 ~~~~a~~~~~~~~~  219 (376)
                      +.+.|...+++.+.
T Consensus       270 ~~~~a~~~~r~al~  283 (287)
T 3qou_A          270 TGDALASXYRRQLY  283 (287)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHH
Confidence            99999888887654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.36  E-value=5.7e-09  Score=90.08  Aligned_cols=320  Identities=9%  Similarity=-0.036  Sum_probs=176.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC-hHHHHHHHHHHHhc-CCCC-chHhHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND-WNEAKRLFFEMMDQ-GVQP-SVVTFNVIM   93 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~-~~~~-~~~~~~~l~   93 (376)
                      ..|...+..+-. |+++.+..+|++....  .|+...|...+....+.++ .+....+|+.++.. |..| +...|...+
T Consensus        16 ~vyer~l~~~P~-~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi   92 (493)
T 2uy1_A           16 AIMEHARRLYMS-KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYI   92 (493)
T ss_dssp             HHHHHHHHHHHT-TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCC-CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHH
Confidence            456666655544 6777777777777764  4577777776666655552 34556666666553 3222 445565555


Q ss_pred             HHHH----hCCChHHHHHHHHHHHhcCCCCC--hh---------------------------------------------
Q 042039           94 DELC----KNGKMDEASRLLDLMVQRDVRPN--AF---------------------------------------------  122 (376)
Q Consensus        94 ~~~~----~~~~~~~a~~~~~~~~~~~~~~~--~~---------------------------------------------  122 (376)
                      ..+.    ..++.+.+..+|++.+..  ++.  ..                                             
T Consensus        93 ~f~~~~~~~~~~~~~vR~iy~rAL~~--P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~  170 (493)
T 2uy1_A           93 EEEGKIEDEQTRIEKIRNGYMRALQT--PMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGW  170 (493)
T ss_dssp             HHTSSCSSHHHHHHHHHHHHHHHHTS--CCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHhchhhhHHHHHHHHHHHHHHhC--hhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhc
Confidence            5432    234566677777777652  111  11                                             


Q ss_pred             ---hHHHHHHHHHhc--C--c---HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHh
Q 042039          123 ---TYSTLMDGFCLT--G--K---INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV  192 (376)
Q Consensus       123 ---~~~~l~~~~~~~--~--~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  192 (376)
                         .|...+..-...  +  +   .+.+..+|+++.... +.++..|...+..+.+.|+.++|..+++++...  +.+..
T Consensus       171 s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~-p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~  247 (493)
T 2uy1_A          171 SVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSF-YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMF  247 (493)
T ss_dssp             SHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSH
T ss_pred             cHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHH
Confidence               111111111110  0  0   233455666665543 455666666666677777777777777777765  22322


Q ss_pred             HHHHHHHHHHhccchHHHHHHHHHHHhcC------------CCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCch
Q 042039          193 TYNTLFLGLFEIHQVEHALKLFEEMQRDD------------VAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELD  260 (376)
Q Consensus       193 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  260 (376)
                      .+..    +....+.+..   ++.+...-            ......+|...+....+.++.+.|..+|+++ ... ..+
T Consensus       248 l~~~----y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~  318 (493)
T 2uy1_A          248 LSLY----YGLVMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVG  318 (493)
T ss_dssp             HHHH----HHHHTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCC
T ss_pred             HHHH----HHhhcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCC
Confidence            2221    1111111111   11111110            0001233455555555667788888888888 321 224


Q ss_pred             HHHHHHHHHHHHhCC-ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHH
Q 042039          261 IQAYNCLIDGLCKSG-RLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIH  339 (376)
Q Consensus       261 ~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  339 (376)
                      ...|...+..-...+ +.+.|..+|+...+. .+.++..+...+......|+.+.|..+|+++.     .....|...+.
T Consensus       319 ~~v~i~~A~lE~~~~~d~~~ar~ife~al~~-~~~~~~~~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~  392 (493)
T 2uy1_A          319 PHVFIYCAFIEYYATGSRATPYNIFSSGLLK-HPDSTLLKEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIE  392 (493)
T ss_dssp             HHHHHHHHHHHHHHHCCSHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHH
Confidence            444543333333333 688888888887765 33345556666776777888888888888862     25667777777


Q ss_pred             HHhhcCChhhHHHHHHHHHh
Q 042039          340 GFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       340 ~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .-...|+.+.+.++++++.+
T Consensus       393 fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          393 YEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHH
Confidence            66777888888888887764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.35  E-value=4.5e-10  Score=86.81  Aligned_cols=186  Identities=9%  Similarity=-0.040  Sum_probs=125.3

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCC--chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh---hhH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQP--SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA---FTY  124 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~  124 (376)
                      +...+..++..+...|++++|+..|+++++..+..  ....+..++.++...|++++|...|+++++.... +.   ..+
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~-~~~~~~a~   81 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT-HPNIDYVM   81 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTTHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-CCcHHHHH
Confidence            45567778888999999999999999998864321  1357788889999999999999999999886422 22   245


Q ss_pred             HHHHHHHHh------------------cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC
Q 042039          125 STLMDGFCL------------------TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG  186 (376)
Q Consensus       125 ~~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  186 (376)
                      ..++.++..                  .|++++|...|+++.+.. |.+..++.......          .+...+    
T Consensus        82 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-P~~~~a~~a~~~l~----------~~~~~~----  146 (225)
T 2yhc_A           82 YMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-PNSQYTTDATKRLV----------FLKDRL----  146 (225)
T ss_dssp             HHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-TTCTTHHHHHHHHH----------HHHHHH----
T ss_pred             HHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-cCChhHHHHHHHHH----------HHHHHH----
Confidence            555555554                  345555555555555442 22222221111000          000000    


Q ss_pred             CCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCC---cchHHHHHHHHHhCCCHHHHHHHHHHhcccC
Q 042039          187 IKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAAD---TSTYNTFIDGLCKNGYIVEAVELFRTLGILK  256 (376)
Q Consensus       187 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  256 (376)
                          ......+...+...|++++|...|+.+++.. |.+   ...+..++.++.+.|++++|.+.++.+...+
T Consensus       147 ----~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          147 ----AKYEYSVAEYYTERGAWVAVVNRVEGMLRDY-PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             ----HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             ----HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHC-cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence                0112356778999999999999999999874 222   2568889999999999999999999887654

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

Probab=99.34  E-value=8.1e-11  Score=94.57  Aligned_cols=168  Identities=8%  Similarity=-0.005  Sum_probs=128.1

Q ss_pred             CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHH
Q 042039          188 KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCL  267 (376)
Q Consensus       188 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  267 (376)
                      +.+...+..+...+...|++++|...++++.+.. +.+...+..++..+...|++++|...++++....+. ........
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~-~~~~~~~~  191 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQD-TRYQGLVA  191 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCS-HHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcc-hHHHHHHH
Confidence            4456667777788888888888888888888775 556778888888888888999998888888766432 23333334


Q ss_pred             HHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCC-cHHHHHHHHHHHhhcCC
Q 042039          268 IDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP-NVIIFVTLIHGFVRINK  346 (376)
Q Consensus       268 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~  346 (376)
                      ...+...++.++|...++++... .|.+...+..++..+...|++++|+..|+++++..... +...+..++..+...|+
T Consensus       192 ~~~l~~~~~~~~a~~~l~~al~~-~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          192 QIELLXQAADTPEIQQLQQQVAE-NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCT
T ss_pred             HHHHHhhcccCccHHHHHHHHhc-CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCC
Confidence            44466777788888888887776 45677888888889999999999999999888764332 25678888888888898


Q ss_pred             hhhHHHHHHHHH
Q 042039          347 PSKVIELLHKMK  358 (376)
Q Consensus       347 ~~~a~~~~~~~~  358 (376)
                      .++|...+++..
T Consensus       271 ~~~a~~~~r~al  282 (287)
T 3qou_A          271 GDALASXYRRQL  282 (287)
T ss_dssp             TCHHHHHHHHHH
T ss_pred             CCcHHHHHHHHH
Confidence            888888887764

>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=99.34  E-value=4.9e-11  Score=105.74  Aligned_cols=154  Identities=10%  Similarity=-0.014  Sum_probs=109.8

Q ss_pred             cCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHH
Q 042039           29 EGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRL  108 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  108 (376)
                      .|++++|++.+++..+.. +.+...+..+...+...|++++|.+.|++..+.... +...+..+..++...|++++|...
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPG-HPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTT-CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHH
Confidence            467888888888887765 556788888888888888888888888888876433 577788888888888888888888


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc---CcHHHHHHHHHHHHHC
Q 042039          109 LDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN---KEVEEALSLYREMVSK  185 (376)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~  185 (376)
                      +++.++.. +.+...+..++.++...|++++|.+.++++.+.. +.+...+..++.++...   |++++|.+.++++.+.
T Consensus        80 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           80 LQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            88888764 3457788888888888888888888888888775 55677888888888888   8888888888888875


Q ss_pred             C
Q 042039          186 G  186 (376)
Q Consensus       186 ~  186 (376)
                      +
T Consensus       158 ~  158 (568)
T 2vsy_A          158 G  158 (568)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.34  E-value=2.3e-11  Score=90.17  Aligned_cols=162  Identities=10%  Similarity=0.024  Sum_probs=103.1

Q ss_pred             HHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHH-H
Q 042039          193 TYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG-L  271 (376)
Q Consensus       193 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~  271 (376)
                      .+......+...|++++|...++++.+.. +.+...+..++.++...|++++|+..++++....+  ++......... +
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~~~~~~~~~   84 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYKSLIAKLEL   84 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHHHHHHHHHH
Confidence            34455566666777777777777666553 44566677777777777777777777777665532  33333222211 1


Q ss_pred             HhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCC-cHHHHHHHHHHHhhcCChhhH
Q 042039          272 CKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP-NVIIFVTLIHGFVRINKPSKV  350 (376)
Q Consensus       272 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a  350 (376)
                      ...++..+|...++++.+. .|.+...+..++.++...|++++|...|+++.+..+.+ +...+..+...+...|+.++|
T Consensus        85 ~~~~~~~~a~~~~~~al~~-~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A  163 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAA-NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAI  163 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHH-STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHH
T ss_pred             HhhcccchHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcH
Confidence            1222333466777776654 34457777778888888888888888888877754332 245677777778888888888


Q ss_pred             HHHHHHHH
Q 042039          351 IELLHKMK  358 (376)
Q Consensus       351 ~~~~~~~~  358 (376)
                      ...|++..
T Consensus       164 ~~~y~~al  171 (176)
T 2r5s_A          164 ASKYRRQL  171 (176)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88777664

>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=99.30  E-value=8.6e-11  Score=95.50  Aligned_cols=200  Identities=8%  Similarity=-0.028  Sum_probs=114.7

Q ss_pred             hcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHH
Q 042039           28 KEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASR  107 (376)
Q Consensus        28 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  107 (376)
                      ..|++++|.+++++..+.. +..   +      +...+++++|...|+++               +..|...|++++|..
T Consensus         3 ~~~~~~eA~~~~~~a~k~~-~~~---~------~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~   57 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYL-KTS---F------MKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAKD   57 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHH-CCC---S------SSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHc-ccc---c------cCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHHH
Confidence            3567888888888776542 111   0      11146677777766654               345666777777777


Q ss_pred             HHHHHHhcCC---CC--ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC---CC--ChhhHHHHHHHHHccCcHHHHHH
Q 042039          108 LLDLMVQRDV---RP--NAFTYSTLMDGFCLTGKINRAEELFGSMESMGC---KH--DDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus       108 ~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      .+.+..+...   .+  -..++..++.+|...|++++|...|++......   .+  ...++..+..+|.. |++++|+.
T Consensus        58 ~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~  136 (307)
T 2ifu_A           58 AYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVH  136 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHH
Confidence            7776654311   00  134566667777777777777777776654310   11  13456667777766 77777777


Q ss_pred             HHHHHHHCCCC---C--CHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCC-----cchHHHHHHHHHhCCCHHHHHH
Q 042039          178 LYREMVSKGIK---P--TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAAD-----TSTYNTFIDGLCKNGYIVEAVE  247 (376)
Q Consensus       178 ~~~~~~~~~~~---~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~  247 (376)
                      .|++.+.....   +  ...++..+...+...|++++|+..+++.........     ...+..++.++...|++++|..
T Consensus       137 ~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~  216 (307)
T 2ifu_A          137 LYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQK  216 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            77776652100   0  134556666666666777777666666654311000     1234444555555666666666


Q ss_pred             HHHHhc
Q 042039          248 LFRTLG  253 (376)
Q Consensus       248 ~~~~~~  253 (376)
                      .|++..
T Consensus       217 ~~~~al  222 (307)
T 2ifu_A          217 CVRESY  222 (307)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            666665

>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=99.29  E-value=1.7e-10  Score=102.37  Aligned_cols=163  Identities=8%  Similarity=-0.051  Sum_probs=123.4

Q ss_pred             CCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHH
Q 042039           64 ANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEEL  143 (376)
Q Consensus        64 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  143 (376)
                      .|++++|.+.++++.+.... +...+..+...+...|++++|...+++.++.. +.+...+..++.++...|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQ-DFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             -------------------C-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            47889999999998876433 67889999999999999999999999999874 44678899999999999999999999


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc---cchHHHHHHHHHHHhc
Q 042039          144 FGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI---HQVEHALKLFEEMQRD  220 (376)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~  220 (376)
                      +++..+.. +.+...+..++.++...|++++|.+.++++.+.. +.+...+..+..++...   |+.++|.+.+++..+.
T Consensus        80 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           80 LQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            99998876 6678899999999999999999999999998863 34678888999999999   9999999999999887


Q ss_pred             CCCCCcchHHH
Q 042039          221 DVAADTSTYNT  231 (376)
Q Consensus       221 ~~~~~~~~~~~  231 (376)
                      + +.+...+..
T Consensus       158 ~-p~~~~~~~~  167 (568)
T 2vsy_A          158 G-VGAVEPFAF  167 (568)
T ss_dssp             T-CCCSCHHHH
T ss_pred             C-CcccChHHH
Confidence            5 333444433

>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=99.25  E-value=1.1e-10  Score=94.83  Aligned_cols=226  Identities=9%  Similarity=0.038  Sum_probs=158.1

Q ss_pred             CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh-cCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHH
Q 042039           99 NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL-TGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      .|++++|.+++++..+.. +.          .+.. .++++.|...|.++               +..|...|++++|..
T Consensus         4 ~~~~~eA~~~~~~a~k~~-~~----------~~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~   57 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYL-KT----------SFMKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAKD   57 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHH-CC----------CSSSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHc-cc----------cccCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHHH
Confidence            466777888877776542 11          0222 46777777777654               557788999999999


Q ss_pred             HHHHHHHCC----CC-CCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCC---CC--CcchHHHHHHHHHhCCCHHHHHH
Q 042039          178 LYREMVSKG----IK-PTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDV---AA--DTSTYNTFIDGLCKNGYIVEAVE  247 (376)
Q Consensus       178 ~~~~~~~~~----~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~a~~  247 (376)
                      .|.++....    .. .-..+|..+..++...|++++|...+++.+....   .+  ...++..+..+|.. |++++|+.
T Consensus        58 ~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~  136 (307)
T 2ifu_A           58 AYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVH  136 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHH
Confidence            999887631    11 1145788888999999999999999998765411   11  23567788888988 99999999


Q ss_pred             HHHHhcccCCCc-----hHHHHHHHHHHHHhCCChHHHHHHHhcccccC----CCCC-HHHHHHHHHHHHccCChhHHHH
Q 042039          248 LFRTLGILKCEL-----DIQAYNCLIDGLCKSGRLEIALELFRSLPRRV----LVAD-VVTYNIMIHGLCNDGQMDKAHD  317 (376)
Q Consensus       248 ~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~-~~~~~~l~~~~~~~~~~~~a~~  317 (376)
                      .++++.......     ...++..++..+...|++++|+..|+++....    ..+. ...+..++.++...|++++|..
T Consensus       137 ~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~  216 (307)
T 2ifu_A          137 LYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQK  216 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            999987542111     14678889999999999999999999987531    1111 2366677788888899999999


Q ss_pred             HHHHHHHcCCCC-cHH---HHHHHHHHHhhcCChhhHHHH
Q 042039          318 LFLDMEENAVAP-NVI---IFVTLIHGFVRINKPSKVIEL  353 (376)
Q Consensus       318 ~~~~~~~~~~~~-~~~---~~~~l~~~~~~~g~~~~a~~~  353 (376)
                      .|++.. ..... +..   ....++.++ ..|+.+.+.++
T Consensus       217 ~~~~al-~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          217 CVRESY-SIPGFSGSEDCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHHHHT-TSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             HHHHHh-CCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHHH
Confidence            999998 53221 221   244455555 56777666663

>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=99.23  E-value=1.6e-08  Score=81.81  Aligned_cols=183  Identities=13%  Similarity=0.018  Sum_probs=135.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC-ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN-DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      ++.+-....+.+..++|+++++.++..+ |.+..+|+.-..++...| .+++++++++.++...++ +..+|+.-..++.
T Consensus        57 ~~~~r~~~~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPK-ny~aW~hR~wlL~  134 (349)
T 3q7a_A           57 MDYFRAIAAKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLK-SYQVWHHRLLLLD  134 (349)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCC-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHH
Confidence            3333334445556678999999999887 667888888888888888 599999999999988655 7778887777776


Q ss_pred             hC-C-ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHH--------HHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           98 KN-G-KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKIN--------RAEELFGSMESMGCKHDDVSYNILINGYC  167 (376)
Q Consensus        98 ~~-~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  167 (376)
                      .. + ++++++.+++++++.+ +.|..+|.....++.+.|.++        ++.+.++++.+.. +.+..+|+....++.
T Consensus       135 ~l~~~~~~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~  212 (349)
T 3q7a_A          135 RISPQDPVSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRV  212 (349)
T ss_dssp             HHCCSCCHHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHT
T ss_pred             HhcCCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            66 6 8899999999999875 446777777666666666665        8888888888876 667788888888777


Q ss_pred             ccCc-------HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccc
Q 042039          168 KNKE-------VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       168 ~~~~-------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  206 (376)
                      +.+.       ++++++.+++++... +-|...|..+-..+.+.|.
T Consensus       213 ~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          213 SRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             TSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             hccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC
Confidence            7765       677888888877752 3356666655555554443

>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=99.21  E-value=7.1e-08  Score=78.07  Aligned_cols=218  Identities=10%  Similarity=0.053  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC-cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc-C-cHHHHHHHH
Q 042039          103 DEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG-KINRAEELFGSMESMGCKHDDVSYNILINGYCKN-K-EVEEALSLY  179 (376)
Q Consensus       103 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-~~~~a~~~~  179 (376)
                      ++|+.+++.++..+ +-+..+|+.-..++...| .+++++++++.+.... |.+..+|+.-..++... + +++++++++
T Consensus        71 e~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~~~~~~EL~~~  148 (349)
T 3q7a_A           71 ERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISPQDPVSEIEYI  148 (349)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCCSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcCCChHHHHHHH
Confidence            34444444444432 112333444334443444 2444444444444443 33444444433333333 3 444444444


Q ss_pred             HHHHHCCCCCCHhHHHHHHHHHHhccchH--------HHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCC-------HHH
Q 042039          180 REMVSKGIKPTVVTYNTLFLGLFEIHQVE--------HALKLFEEMQRDDVAADTSTYNTFIDGLCKNGY-------IVE  244 (376)
Q Consensus       180 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-------~~~  244 (376)
                      +++++.. +-+..+|..-...+.+.+.++        ++++.++++++.+ +.+..+++.....+.+.+.       +++
T Consensus       149 ~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~e  226 (349)
T 3q7a_A          149 HGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQD  226 (349)
T ss_dssp             HHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHH
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHHH
Confidence            4444432 223344433333333333333        4555555555543 3344445544444444443       455


Q ss_pred             HHHHHHHhcccCCCchHHHHHHHHHHHHhCCCh--------------------HHHHHHHhcccccC-----CCCCHHHH
Q 042039          245 AVELFRTLGILKCELDIQAYNCLIDGLCKSGRL--------------------EIALELFRSLPRRV-----LVADVVTY  299 (376)
Q Consensus       245 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------------------~~a~~~~~~~~~~~-----~~~~~~~~  299 (376)
                      +++.++++....+. |...|+.+-..+.+.|+.                    .....+...+....     ..+++..+
T Consensus       227 ELe~~~~aI~~~P~-n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al  305 (349)
T 3q7a_A          227 ELIYILKSIHLIPH-NVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLAL  305 (349)
T ss_dssp             HHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHH
T ss_pred             HHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHH
Confidence            66666665555422 555555555555544432                    23333333443321     13566777


Q ss_pred             HHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          300 NIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       300 ~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      ..++..|...|+.++|.++++.+.+.
T Consensus       306 ~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          306 EYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            77888888888888888888887643

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

Probab=99.20  E-value=4.1e-10  Score=78.07  Aligned_cols=96  Identities=10%  Similarity=0.019  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .+......+.+.|++++|++.|++.++.+ |.+..+|..++.++...|++++|++.|++.++.+.. +...|..+..++.
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~   92 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK-FIKGYIRKAACLV   92 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh-hhHHHHHHHHHHH
Confidence            34444444555555555555555444443 334444444455555555555555555544443222 3444444444444


Q ss_pred             hCCChHHHHHHHHHHHhc
Q 042039           98 KNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~  115 (376)
                      ..|++++|...|++.++.
T Consensus        93 ~~~~~~~A~~~~~~al~l  110 (126)
T 4gco_A           93 AMREWSKAQRAYEDALQV  110 (126)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            444444444444444443

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

Probab=99.19  E-value=6.2e-10  Score=77.15  Aligned_cols=109  Identities=10%  Similarity=0.063  Sum_probs=60.4

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+...+..+.+.|++++|++.|++.++..+. +...|..+..++...|++++|+..+++.++.+ +.+...|..++.+
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~   90 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPE-NAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAAC   90 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHH
Confidence            344555566666666666666666666554322 45555555666666666666666666665543 2245555555666


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNIL  162 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  162 (376)
                      +...|++++|.+.|+++.+.. |.+..++..+
T Consensus        91 ~~~~~~~~~A~~~~~~al~l~-P~~~~a~~~l  121 (126)
T 4gco_A           91 LVAMREWSKAQRAYEDALQVD-PSNEEAREGV  121 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-cCCHHHHHHH
Confidence            666666666666666655553 3344444433

>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=99.18  E-value=3.6e-09  Score=80.95  Aligned_cols=129  Identities=14%  Similarity=0.024  Sum_probs=103.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ..+..+...+...|++++|+..|++..    +|+..++..++.++...|++++|++.|++.++.... +...+..+..++
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~lg~~~   81 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLY   81 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHH
Confidence            446667778888999999999998774    457788889999999999999999999998887433 677888888899


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCCh----------------hhHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNA----------------FTYSTLMDGFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      ...|++++|...+++..+.. +.+.                ..+..++.++...|++++|...|+++....
T Consensus        82 ~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           82 YQTEKYDLAIKDLKEALIQL-RGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHHTT-TTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHcccHHHHHHHHHHHHHhC-CCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            99999999999999888753 2222                567778888888888888888888887764

>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=99.17  E-value=4.4e-09  Score=80.44  Aligned_cols=128  Identities=16%  Similarity=0.041  Sum_probs=107.9

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ..+..++..+...|++++|+..|+++.    .|+...+..+..++...|++++|...+++.++.. +.+...+..++.++
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~   81 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLY   81 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHH
Confidence            345667888889999999999998774    5578889999999999999999999999998874 44678888999999


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCCh----------------hhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDD----------------VSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      ...|++++|...|+++.... +.+.                .++..++.++...|++++|...++++.+.
T Consensus        82 ~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           82 YQTEKYDLAIKDLKEALIQL-RGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHHTT-TTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHcccHHHHHHHHHHHHHhC-CCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            99999999999999998764 3333                67888899999999999999999998885

>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=99.16  E-value=3.6e-09  Score=85.36  Aligned_cols=202  Identities=9%  Similarity=0.046  Sum_probs=135.0

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC-CCch----H
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV-QPSV----V   87 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~   87 (376)
                      .|+..+...+...+.-.-     ..++..-... .......+...+..+...|++++|...+++..+... .|+.    .
T Consensus        43 ~~~~~~l~~i~~~l~~~~-----~~~~~~~~~~-~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~  116 (293)
T 3u3w_A           43 YPSMDILQGIAAKLQIPI-----IHFYEVLIYS-DIERKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQ  116 (293)
T ss_dssp             CCCHHHHHHHHHHHTCCT-----HHHHHTTTSS-CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhCcCH-----HHHhCCCCCC-cchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHH
Confidence            577777777777654321     1122211111 012245666667788888999999999988877532 2221    1


Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-CC----hhhHHHHHHHHHhcCcHHHHHHHHHHHHh----c--CCCCCh
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVR-PN----AFTYSTLMDGFCLTGKINRAEELFGSMES----M--GCKHDD  156 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~--~~~~~~  156 (376)
                      .+..+...+...+++++|...++++++.... ++    ..++..++.+|...|++++|...|+++.+    .  ..+...
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            2334666777778889999999888874322 22    23678888889999999999998888863    1  111223


Q ss_pred             hhHHHHHHHHHccCcHHHHHHHHHHHHHC----CCCC-CHhHHHHHHHHHHhccc-hHHHHHHHHHHHhc
Q 042039          157 VSYNILINGYCKNKEVEEALSLYREMVSK----GIKP-TVVTYNTLFLGLFEIHQ-VEHALKLFEEMQRD  220 (376)
Q Consensus       157 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~  220 (376)
                      .++..++.+|.+.|++++|+..+++.++.    +..+ -..++..+..++...|+ +++|...+++....
T Consensus       197 ~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~i  266 (293)
T 3u3w_A          197 KVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASFF  266 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence            47788889999999999999988887753    1122 26678888888888884 58888888877653

>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=99.15  E-value=4.3e-10  Score=90.02  Aligned_cols=194  Identities=12%  Similarity=-0.023  Sum_probs=113.2

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +...+..+...+.+.|++++|+..|++..+.. +.+...|..++.++...|++++|+..++++++.... +...+..+..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            45667777788888888888888888887764 557777888888888888888888888888776433 5667777788


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  174 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  174 (376)
                      ++...|++++|...+++..+.+.. +...+...+....+   ...+... ........+.+......+....  .|++++
T Consensus        81 ~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~---~~~~~~~-~~~~~~~~~~~~~i~~~l~~l~--~~~~~~  153 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALR---IAKKKRW-NSIEERRIHQESELHSYLTRLI--AAERER  153 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHH---HHHHHHH-HHHHHTCCCCCCHHHHHHHHHH--HHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHH---HHHHHHH-HHHHHHHHhhhHHHHHHHHHHH--HHHHHH
Confidence            888888888888888877764211 11111111111111   1111111 1122222344444444443322  567777


Q ss_pred             HHHHHHHHHHCCCCCC-HhHHHHHHHHHHhc-cchHHHHHHHHHHHh
Q 042039          175 ALSLYREMVSKGIKPT-VVTYNTLFLGLFEI-HQVEHALKLFEEMQR  219 (376)
Q Consensus       175 a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~  219 (376)
                      |++.++...+.  .|+ ......+...+.+. +.++++.++|..+.+
T Consensus       154 A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          154 ELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            77777766653  333 22223333333333 456666777766544

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=99.15  E-value=3.9e-09  Score=82.50  Aligned_cols=199  Identities=10%  Similarity=0.024  Sum_probs=134.7

Q ss_pred             ccCcHHHHHHHHHHHHHCCCCCCHhHHHHH-------HHHHHhccchHHHHHHHHHHHhcC---C--CCC----------
Q 042039          168 KNKEVEEALSLYREMVSKGIKPTVVTYNTL-------FLGLFEIHQVEHALKLFEEMQRDD---V--AAD----------  225 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~~~~~~---~--~~~----------  225 (376)
                      ..++...|.+.|.++.+.. +-....|..+       ...+...++..+++..+.......   .  ..+          
T Consensus        18 ~~~d~~~A~~~F~~a~~~d-P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD-ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             cCCCHHHHHHHHHHHHHhC-hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            4677777777777777652 2245556555       445555555555555554444310   0  000          


Q ss_pred             -----cchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCC--HHH
Q 042039          226 -----TSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVAD--VVT  298 (376)
Q Consensus       226 -----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~  298 (376)
                           ......++..+...|++++|.++|..+...+  |+......++..+.+.+++++|+..|+...... .|.  ...
T Consensus        97 ~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a  173 (282)
T 4f3v_A           97 PVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAA  173 (282)
T ss_dssp             ECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHH
T ss_pred             ccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHH
Confidence                 1234456677888999999999999887754  333367777778899999999999998766542 121  346


Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCCC--cHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHH
Q 042039          299 YNIMIHGLCNDGQMDKAHDLFLDMEENAVAP--NVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMV  372 (376)
Q Consensus       299 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  372 (376)
                      +..+..++...|++++|+..|++.......|  ..........++.+.|+.++|..+|+++....  |+......|
T Consensus       174 ~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~--P~~~~~~aL  247 (282)
T 4f3v_A          174 GVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH--PEPKVAAAL  247 (282)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--CCHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHH
Confidence            7888999999999999999999988543224  34466677788899999999999999998764  444444333

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

Probab=99.14  E-value=2.5e-09  Score=74.89  Aligned_cols=122  Identities=8%  Similarity=-0.035  Sum_probs=88.3

Q ss_pred             ccCCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHH
Q 042039           11 VCKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFN   90 (376)
Q Consensus        11 ~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   90 (376)
                      ..+.+...|..+...+...|++++|+..|++..+.. +.+..++..++.++...|++++|.+.++++.+.... +...+.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~   88 (133)
T 2lni_A           11 MNPDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT-FIKGYT   88 (133)
T ss_dssp             SSSCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT-CHHHHH
T ss_pred             cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-chHHHH
Confidence            344556778888888888888888888888887764 556778888888888888888888888888776433 566777


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG  135 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  135 (376)
                      .+..++...|++++|...+++..+.. +.+...+..+..++...|
T Consensus        89 ~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           89 RKAAALEAMKDYTKAMDVYQKALDLD-SSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-GGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhc
Confidence            77778888888888888888777653 223455555555555443

>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=99.14  E-value=7.1e-10  Score=88.72  Aligned_cols=97  Identities=10%  Similarity=-0.081  Sum_probs=46.3

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..++..+...|++++|+..|+++++.... +...+..+..++...|++++|...+++.++.. +.+...+..++.+
T Consensus         4 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   81 (281)
T 2c2l_A            4 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQC   81 (281)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            344444555555555555555555555544221 34444445555555555555555555554432 2234444444444


Q ss_pred             HHhcCcHHHHHHHHHHHHh
Q 042039          131 FCLTGKINRAEELFGSMES  149 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~  149 (376)
                      +...|++++|...|+++..
T Consensus        82 ~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            4455555555554444433

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

Probab=99.14  E-value=9.7e-10  Score=78.50  Aligned_cols=98  Identities=13%  Similarity=0.136  Sum_probs=58.4

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILING  165 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  165 (376)
                      ...+..+...+...|++++|...|++++..+ +.+...|..++.++...|++++|...|+++.... |.++..+..++.+
T Consensus        36 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~  113 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQC  113 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHH
Confidence            3445555556666666666666666666553 3345556666666666666666666666666554 4455566666666


Q ss_pred             HHccCcHHHHHHHHHHHHHC
Q 042039          166 YCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       166 ~~~~~~~~~a~~~~~~~~~~  185 (376)
                      |...|++++|...|+++++.
T Consensus       114 ~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          114 QLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            66666666666666666653

>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=99.14  E-value=3.4e-09  Score=77.43  Aligned_cols=97  Identities=12%  Similarity=0.046  Sum_probs=50.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ..|..+...+...|++++|...|++..+.. +.+..++..++.++...|++++|...+++.++.... +...+..+..++
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHH
Confidence            344455555555555555555555555443 334555555555555555555555555555544221 344455555555


Q ss_pred             HhCCChHHHHHHHHHHHhc
Q 042039           97 CKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~  115 (376)
                      ...|++++|...++++.+.
T Consensus        92 ~~~~~~~~A~~~~~~a~~~  110 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKV  110 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHh
Confidence            5555555555555555543

>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=99.13  E-value=1.7e-10  Score=94.78  Aligned_cols=143  Identities=10%  Similarity=-0.040  Sum_probs=77.5

Q ss_pred             CChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc--------------hHhHHHHHHH
Q 042039           30 GFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS--------------VVTFNVIMDE   95 (376)
Q Consensus        30 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~   95 (376)
                      +++++|++.|+...... +.+...+..+...+...|++++|+..|++.+.......              ...|..+..+
T Consensus       127 ~~~~~A~~~~~~a~~~~-p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~  205 (336)
T 1p5q_A          127 KSFEKAKESWEMNSEEK-LEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMC  205 (336)
T ss_dssp             EEEECCCCGGGCCHHHH-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             eecccccchhcCCHHHH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHH
Confidence            44555555554443321 22455666677777777777777777777766533211              2455555555


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      +.+.|++++|+..++++++.. +.+...+..++.++...|++++|...|+++.+.. |.+..++..+..++...|+.++|
T Consensus       206 ~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          206 HLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555555555543 2244555555555555555555555555555543 33444555555555555555554

>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=99.12  E-value=5.2e-09  Score=76.41  Aligned_cols=128  Identities=13%  Similarity=0.080  Sum_probs=70.7

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ..+..++..+...|++++|...|++.++.... +...+..+..++...|++++|...+++.++.. +.+...+..++.++
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELNPS-NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            34555566666666666666666666654322 45555566666666666666666666666543 23455555566666


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCChhhHHH--HHHHHHccCcHHHHHHHHHHH
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDDVSYNI--LINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~~~~~~a~~~~~~~  182 (376)
                      ...|++++|...++++.... +.+...+..  .+..+...|++++|+..+...
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            66666666666666655543 233333322  222244555555555555544

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.11  E-value=1.8e-07  Score=80.76  Aligned_cols=296  Identities=11%  Similarity=-0.003  Sum_probs=187.4

Q ss_pred             ccCCChhhHHHHHHHHHhcCC-hhHHHHHHHHhhhC-CC-CCChhhHHHHHHHHhc----CCChHHHHHHHHHHHhcCCC
Q 042039           11 VCKPNTVTYNTIIDGLCKEGF-VDKAKALFLQMKGE-NI-NPDVVTYNSLIHGLCH----ANDWNEAKRLFFEMMDQGVQ   83 (376)
Q Consensus        11 ~~~p~~~~~~~l~~~~~~~g~-~~~a~~~~~~~~~~-~~-~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~   83 (376)
                      ...|++..|...+....+.+. .+....+|+..... |. +.+...|...+..+..    .++.+.+.++|++++.....
T Consensus        42 ~~~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~  121 (493)
T 2uy1_A           42 KKSYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMG  121 (493)
T ss_dssp             TTCCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCT
T ss_pred             ccCCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhh
Confidence            345788888888887777663 45567777776653 31 3466777777766542    35677788888888764211


Q ss_pred             CchH------------------------------------------------hHHHHHHHHHhC--CC-----hHHHHHH
Q 042039           84 PSVV------------------------------------------------TFNVIMDELCKN--GK-----MDEASRL  108 (376)
Q Consensus        84 ~~~~------------------------------------------------~~~~l~~~~~~~--~~-----~~~a~~~  108 (376)
                      .-..                                                .|...+..-...  +-     .+.+..+
T Consensus       122 ~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~  201 (493)
T 2uy1_A          122 SLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFI  201 (493)
T ss_dssp             THHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHH
Confidence            1111                                                111111111111  00     2345667


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCC--
Q 042039          109 LDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG--  186 (376)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--  186 (376)
                      |++++... +.++..|...+..+...|+.+.|..++++....  |.+...+...+.. ...+   +.   ++.+.+.-  
T Consensus       202 ye~al~~~-p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~~-~e~~---~~---~~~l~~~~~~  271 (493)
T 2uy1_A          202 HNYILDSF-YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGLV-MDEE---AV---YGDLKRKYSM  271 (493)
T ss_dssp             HHHHHHHT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHH-TTCT---HH---HHHHHHHTC-
T ss_pred             HHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHhh-cchh---HH---HHHHHHHHHh
Confidence            88877753 445778888888899999999999999999987  4554444332222 1111   11   22222210  


Q ss_pred             -------C---CCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCC-CHHHHHHHHHHhccc
Q 042039          187 -------I---KPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNG-YIVEAVELFRTLGIL  255 (376)
Q Consensus       187 -------~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~  255 (376)
                             .   ......|...+....+.++.+.|..+|+++ +.. ..+...|...+..-...+ +.+.|..+|+.+...
T Consensus       272 ~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~  349 (493)
T 2uy1_A          272 GEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLK  349 (493)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHH
T ss_pred             hccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHH
Confidence                   0   112345667777777788999999999999 322 233344443333333333 699999999998775


Q ss_pred             CCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          256 KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      . +.++..+...+......|+.+.|..+|+.+.+     ....|...+..-...|+.+.+..+++++.+
T Consensus       350 ~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~~k-----~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          350 H-PDSTLLKEEFFLFLLRIGDEENARALFKRLEK-----TSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             C-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSCC-----BHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4 22455666778878889999999999999842     567788888777788999999999988874

>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=99.11  E-value=6.6e-08  Score=77.91  Aligned_cols=161  Identities=13%  Similarity=0.055  Sum_probs=82.5

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCC-CCCh----hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCC-C----hhhHHH
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDV-RPNA----FTYSTLMDGFCLTGKINRAEELFGSMESMGCKH-D----DVSYNI  161 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~----~~~~~~  161 (376)
                      .+..+...|++++|..++++..+... .|+.    ..+..++..+...+++++|...++++....... +    ..+++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            35556667777777777777665321 1111    122234555555566777777776666532111 1    124666


Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHC-----CCCC-CHhHHHHHHHHHHhccchHHHHHHHHHHHhcC----C-CCCcchHH
Q 042039          162 LINGYCKNKEVEEALSLYREMVSK-----GIKP-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD----V-AADTSTYN  230 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~  230 (376)
                      ++.+|...|++++|+..++++++.     +..+ ...++..++..|...|++++|...+++.++..    . ..-..++.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            666666667777777666666531     1111 12345555555666666666666555544321    0 01123444


Q ss_pred             HHHHHHHhCCC-HHHHHHHHHHh
Q 042039          231 TFIDGLCKNGY-IVEAVELFRTL  252 (376)
Q Consensus       231 ~l~~~~~~~~~-~~~a~~~~~~~  252 (376)
                      .++.++.+.|+ +++|...++++
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~A  263 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHH
Confidence            55555555552 35555554443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.11  E-value=1.8e-08  Score=81.20  Aligned_cols=162  Identities=9%  Similarity=0.012  Sum_probs=86.6

Q ss_pred             HHHHHHhccchHHHHHHHHHHHhcCCCCC-----cchHHHHHHHHHhCCCHHHHHHHHHHhcccCC---Cc--hHHHHHH
Q 042039          197 LFLGLFEIHQVEHALKLFEEMQRDDVAAD-----TSTYNTFIDGLCKNGYIVEAVELFRTLGILKC---EL--DIQAYNC  266 (376)
Q Consensus       197 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~  266 (376)
                      .+..+...|++++|.+.+....+......     ...+..++..+...|++++|+..++++.....   .+  ...+++.
T Consensus        81 ~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 2qfc_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHH
Confidence            34444445555555555544444321100     01122344445556666666666666543211   11  1346666


Q ss_pred             HHHHHHhCCChHHHHHHHhccccc--CCCCC----HHHHHHHHHHHHccCChhHHHHHHHHHHHcC----CCC-cHHHHH
Q 042039          267 LIDGLCKSGRLEIALELFRSLPRR--VLVAD----VVTYNIMIHGLCNDGQMDKAHDLFLDMEENA----VAP-NVIIFV  335 (376)
Q Consensus       267 l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~~~~~  335 (376)
                      ++..|...|++++|...++++.+.  ..+.+    ..++..++.+|...|++++|+..+++..+..    ... -..+|.
T Consensus       161 lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~  240 (293)
T 2qfc_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            677777777777777777665521  01111    1466667777777777777777777665431    000 145666


Q ss_pred             HHHHHHhhcCChhhH-HHHHHHHH
Q 042039          336 TLIHGFVRINKPSKV-IELLHKMK  358 (376)
Q Consensus       336 ~l~~~~~~~g~~~~a-~~~~~~~~  358 (376)
                      .+..+|.+.|++++| ...+++..
T Consensus       241 ~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          241 QRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHH
Confidence            677777777777777 56566554

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.10  E-value=5.2e-09  Score=84.40  Aligned_cols=171  Identities=8%  Similarity=0.050  Sum_probs=126.2

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc-----hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC---CC-
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS-----VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR---PN-  120 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~-  120 (376)
                      ....+...+..+...|++++|.+.+++.++......     ...+..+...+...|++++|...+++.++....   +. 
T Consensus        74 ~~~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~  153 (293)
T 2qfc_A           74 RKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQ  153 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHH
Confidence            445666778888899999999999988887533211     123445667778888999999999998764211   11 


Q ss_pred             -hhhHHHHHHHHHhcCcHHHHHHHHHHHHhc--CCCCC----hhhHHHHHHHHHccCcHHHHHHHHHHHHHCC----CCC
Q 042039          121 -AFTYSTLMDGFCLTGKINRAEELFGSMESM--GCKHD----DVSYNILINGYCKNKEVEEALSLYREMVSKG----IKP  189 (376)
Q Consensus       121 -~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~  189 (376)
                       ..++..++..|...|++++|...++++...  ..+.+    ..++..++.+|...|++++|+..+++.++..    ...
T Consensus       154 ~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~  233 (293)
T 2qfc_A          154 NLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMA  233 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCS
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHH
Confidence             447888999999999999999999988632  01111    2578889999999999999999999887531    111


Q ss_pred             -CHhHHHHHHHHHHhccchHHH-HHHHHHHHhc
Q 042039          190 -TVVTYNTLFLGLFEIHQVEHA-LKLFEEMQRD  220 (376)
Q Consensus       190 -~~~~~~~l~~~~~~~~~~~~a-~~~~~~~~~~  220 (376)
                       -..++..+..++...|++++| ...+++....
T Consensus       234 ~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~  266 (293)
T 2qfc_A          234 LIGQLYYQRGECLRKLEYEEAEIEDAYKKASFF  266 (293)
T ss_dssp             SHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence             166788899999999999999 7777776543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=99.10  E-value=5.1e-09  Score=81.87  Aligned_cols=197  Identities=8%  Similarity=-0.070  Sum_probs=135.6

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCChhhHHHH-------HHHHHccCcHHHHHHHHHHHHHCCCCCC---------------
Q 042039          133 LTGKINRAEELFGSMESMGCKHDDVSYNIL-------INGYCKNKEVEEALSLYREMVSKGIKPT---------------  190 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------  190 (376)
                      ..++...|.+.|.++.... |.....|..+       ...+.+.++..+++..+.....  +.|+               
T Consensus        18 ~~~d~~~A~~~F~~a~~~d-P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~~   94 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD-ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGDI   94 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCCC
T ss_pred             cCCCHHHHHHHHHHHHHhC-hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCccccc
Confidence            4677888888888887775 5566677766       4555555555555555555443  1221               


Q ss_pred             -------HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCch--H
Q 042039          191 -------VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELD--I  261 (376)
Q Consensus       191 -------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~  261 (376)
                             ......+...+...|++++|.+.|+.+...+  |+......+...+.+.+++++|+..|+...... .|.  .
T Consensus        95 ~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~  171 (282)
T 4f3v_A           95 TYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAG  171 (282)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHH
T ss_pred             ccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHH
Confidence                   2334456677788889999998888877654  322266667778889999999999998665432 221  3


Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhcccccCCCC--CHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHH
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA--DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTL  337 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  337 (376)
                      ..+..++.++...|++++|+..|++.......|  ........+.++.+.|+.++|...|+++....  |+...+..|
T Consensus       172 ~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~--P~~~~~~aL  247 (282)
T 4f3v_A          172 AAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH--PEPKVAAAL  247 (282)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--CCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHH
Confidence            467888889999999999999999887543313  34567778888999999999999999998864  444444433

>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=99.10  E-value=4.7e-07  Score=72.93  Aligned_cols=199  Identities=12%  Similarity=-0.009  Sum_probs=129.5

Q ss_pred             hhHHHHHHHH---HhcCChh-HHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC----------hHHHHHHHHHHHhcCC
Q 042039           17 VTYNTIIDGL---CKEGFVD-KAKALFLQMKGENINPDVVTYNSLIHGLCHAND----------WNEAKRLFFEMMDQGV   82 (376)
Q Consensus        17 ~~~~~l~~~~---~~~g~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~   82 (376)
                      ..|..+.+.+   .+.|.+. +|+++++.++..+ |.+..+|+.-..++...++          +++++.+++.++...+
T Consensus        27 ~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~n-P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~P  105 (331)
T 3dss_A           27 KLYQSATQAVFQKRQAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNP  105 (331)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCC
Confidence            4455554433   3556655 7888888888776 5566777766555554443          5778888888887655


Q ss_pred             CCchHhHHHHHHHHHhCC--ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCc-HHHHHHHHHHHHhcCCCCChhhH
Q 042039           83 QPSVVTFNVIMDELCKNG--KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGK-INRAEELFGSMESMGCKHDDVSY  159 (376)
Q Consensus        83 ~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~  159 (376)
                      + +..+|+.-..++...+  .+++++.+++.+++.+ +-|..+|+.-..++...|. ++++.+.++++.... +.+..+|
T Consensus       106 K-ny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-p~N~SAW  182 (331)
T 3dss_A          106 K-SYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSW  182 (331)
T ss_dssp             T-CHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-SCCHHHH
T ss_pred             C-CHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-CCCHHHH
Confidence            4 6777777777777777  3788888888888875 4467777777777777777 578888888888776 5677777


Q ss_pred             HHHHHHHHcc--------------CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc-----------cchHHHHHHH
Q 042039          160 NILINGYCKN--------------KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI-----------HQVEHALKLF  214 (376)
Q Consensus       160 ~~l~~~~~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~  214 (376)
                      +....++...              +.++++++.+...+... +-|...|.-+-..+...           +.++++++.+
T Consensus       183 ~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~  261 (331)
T 3dss_A          183 HYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESC  261 (331)
T ss_dssp             HHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHH
Confidence            7666665544              44677777777777652 33555554333333332           2344555555


Q ss_pred             HHHHhc
Q 042039          215 EEMQRD  220 (376)
Q Consensus       215 ~~~~~~  220 (376)
                      .++.+.
T Consensus       262 ~elle~  267 (331)
T 3dss_A          262 KELQEL  267 (331)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            555544

>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=99.10  E-value=1.5e-09  Score=77.57  Aligned_cols=99  Identities=12%  Similarity=0.008  Sum_probs=50.4

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      +...+..+...+...|++++|+..|++++...+. +...|..+..++...|++++|...|++++..+ +.+...+..++.
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~   97 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHY-DSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAE   97 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHH
Confidence            3444555555555555555555555555544222 44445555555555555555555555555442 223444555555


Q ss_pred             HHHhcCcHHHHHHHHHHHHhc
Q 042039          130 GFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      ++...|++++|...|+++...
T Consensus        98 ~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           98 CLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            555555555555555555443

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

Probab=99.10  E-value=8.7e-10  Score=78.74  Aligned_cols=126  Identities=10%  Similarity=-0.017  Sum_probs=99.7

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ......+.+.+...+-+++++       +.. |.+...+..+...+.+.|++++|+..|++++...+. +...|..+..+
T Consensus         9 ~~~~~~l~~~~~~~~~l~~al-------~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~   79 (151)
T 3gyz_A            9 ESISTAVIDAINSGATLKDIN-------AIP-DDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY-NVDYIMGLAAI   79 (151)
T ss_dssp             CHHHHHHHHHHHTSCCTGGGC-------CSC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHh-------CCC-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            445566666666665555443       332 446778888889999999999999999999887544 67888889999


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      +...|++++|...|++.++.. +.++..+..++.++...|++++|...|+++....
T Consensus        80 ~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A           80 YQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            999999999999999998875 3467888889999999999999999999998874

>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=99.09  E-value=1.8e-09  Score=80.01  Aligned_cols=122  Identities=8%  Similarity=0.089  Sum_probs=82.5

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH-HHhCCCh--H
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE-LCKNGKM--D  103 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~  103 (376)
                      ...|++++|+..+++..+.. +.+...+..++.++...|++++|...|+++.+.... +...+..+..+ +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGE-NAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcCCcchH
Confidence            45677777777777776654 556677777777777788888888888777765332 55666666666 6677776  7


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Q 042039          104 EASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      +|...++++++.. +.+...+..++.++...|++++|...|+++....
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            7777777777653 3345666777777777777777777777777654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=99.08  E-value=2e-09  Score=81.60  Aligned_cols=157  Identities=12%  Similarity=-0.004  Sum_probs=99.8

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc----CCC-CchHhHHHHHHHHHhCCC
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ----GVQ-PSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~  101 (376)
                      ...|++++|.+.++.+... ......++..+...+...|++++|...+++.+..    +.. ....++..+...+...|+
T Consensus         3 ~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            4678888888855555432 1345677888888888888888888888887662    111 124466777778888888


Q ss_pred             hHHHHHHHHHHHhc----CCCC--ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCC----hhhHHHHHHHHHccC
Q 042039          102 MDEASRLLDLMVQR----DVRP--NAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-KHD----DVSYNILINGYCKNK  170 (376)
Q Consensus       102 ~~~a~~~~~~~~~~----~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~  170 (376)
                      +++|...+++.++.    +..+  ....+..+...+...|++++|...+++...... ..+    ..++..+..++...|
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  161 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEK  161 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCc
Confidence            88888888777653    1011  134566677777777888888777777653210 011    223466677777777


Q ss_pred             cHHHHHHHHHHHHH
Q 042039          171 EVEEALSLYREMVS  184 (376)
Q Consensus       171 ~~~~a~~~~~~~~~  184 (376)
                      ++++|...+++..+
T Consensus       162 ~~~~A~~~~~~al~  175 (203)
T 3gw4_A          162 NLLEAQQHWLRARD  175 (203)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            77777777776654

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

Probab=99.08  E-value=7.5e-09  Score=71.41  Aligned_cols=98  Identities=13%  Similarity=0.206  Sum_probs=56.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...|..+...+...|++++|++.++++.+.. +.+..++..++.++...|++++|...++++.+... .+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHH
Confidence            3455556666666666666666666665543 34455555666666666666666666666655422 244455555555


Q ss_pred             HHhCCChHHHHHHHHHHHhc
Q 042039           96 LCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +...|++++|...++++.+.
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHh
Confidence            55666666666666555554

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

Probab=99.07  E-value=3e-09  Score=74.14  Aligned_cols=117  Identities=12%  Similarity=-0.043  Sum_probs=58.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...|..+...+...|++++|+..+++..... +.+...+..++.++...|++++|.+.+++....... +...+..+..+
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~   89 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPA-YSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCcc-CHHHHHHHHHH
Confidence            4445555555555555555555555555443 334455555555555555555555555555544221 34444555555


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG  135 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  135 (376)
                      +...|++++|...+++..+.. +.+...+..+..++...|
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~  128 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLR  128 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHT
T ss_pred             HHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHh
Confidence            555555555555555555442 223344444444444433

>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=99.07  E-value=2.3e-09  Score=79.35  Aligned_cols=121  Identities=7%  Similarity=0.103  Sum_probs=97.5

Q ss_pred             hcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH-HHhcCcH--H
Q 042039           62 CHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG-FCLTGKI--N  138 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~  138 (376)
                      ...|++++|...+++.++.... +...+..+..++...|++++|...++++++.. +.+...+..++.+ +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANPQ-NSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCCS-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchH
Confidence            4568889999999998876433 67888889999999999999999999998864 3467778888888 7788988  9


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          139 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       139 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      +|...++++.... |.+...+..++.++...|++++|...++++.+.
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            9999999988875 566788888999999999999999999998885

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

Probab=99.06  E-value=6.4e-09  Score=72.76  Aligned_cols=118  Identities=7%  Similarity=-0.001  Sum_probs=69.3

Q ss_pred             CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           49 PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLM  128 (376)
Q Consensus        49 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  128 (376)
                      .+...+..++..+...|++++|...|+++.+.... +...+..+..++...|++++|...++++.+.. +.+...+..++
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la   91 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPK-DAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKA   91 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHH
Confidence            34556666666666666777777766666654322 45556666666666666666666666666543 23455566666


Q ss_pred             HHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039          129 DGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      .++...|++++|.+.|++..... +.+...+..+..++...
T Consensus        92 ~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~  131 (133)
T 2lni_A           92 AALEAMKDYTKAMDVYQKALDLD-SSCKEAADGYQRCMMAQ  131 (133)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-GGGTHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHh
Confidence            66666666666666666665543 33344455555444433

>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=99.05  E-value=1.7e-09  Score=77.32  Aligned_cols=110  Identities=10%  Similarity=-0.023  Sum_probs=85.2

Q ss_pred             HHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC
Q 042039           73 LFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC  152 (376)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  152 (376)
                      .|++++... +.+...+..+...+...|++++|...|++++..+ +.+...+..++.++...|++++|...|+++.... 
T Consensus         9 ~~~~al~~~-p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-   85 (148)
T 2vgx_A            9 TIAMLNEIS-SDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-   85 (148)
T ss_dssp             SHHHHTTCC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             hHHHHHcCC-HhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-
Confidence            445555432 1245567777888888888888888888888764 4467788888888888888888888888888775 


Q ss_pred             CCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          153 KHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       153 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      |.++..+..++.++...|++++|...|++.++.
T Consensus        86 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           86 IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            567778888888888888888888888888774

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

Probab=99.04  E-value=3.1e-09  Score=75.48  Aligned_cols=98  Identities=14%  Similarity=0.082  Sum_probs=46.7

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..+...+...|++++|...|++++...+. +...|..+..++...|++++|...|++.+..+ +.+...+..++.+
T Consensus        18 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   95 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDDAQKIFQALCMLDHY-DARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAEC   95 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHH
Confidence            334444444555555555555555555444222 34444444555555555555555555554442 2234444445555


Q ss_pred             HHhcCcHHHHHHHHHHHHhc
Q 042039          131 FCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~  150 (376)
                      +...|++++|...|+++...
T Consensus        96 ~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           96 HLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            55555555555555544443

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

Probab=99.04  E-value=5.6e-09  Score=72.76  Aligned_cols=119  Identities=11%  Similarity=0.058  Sum_probs=65.0

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      +...+..++..+...|++++|...++++...... +...+..+..++...|++++|...+++..+.. +.+...+..++.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~   88 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELNPA-NAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHH
Confidence            3445555566666666666666666666554222 44555555556666666666666666655542 223445555555


Q ss_pred             HHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc
Q 042039          130 GFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  171 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  171 (376)
                      ++...|++++|...+++..... +.+...+..+..++...|+
T Consensus        89 ~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           89 ALSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTT
T ss_pred             HHHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhc
Confidence            5556666666666665555543 3344445555555544443

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

Probab=99.04  E-value=1.7e-08  Score=69.51  Aligned_cols=113  Identities=16%  Similarity=0.218  Sum_probs=62.1

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..++..+...|++++|.+.++++.+... .+...+..+...+...|++++|..+++++.+.. +.+..++..++..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            44555566666666666666666666655432 244555555666666666666666666665542 2344555555555


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGY  166 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  166 (376)
                      +...|++++|...++++.... +.+...+..+..++
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~  121 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAK  121 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            666666666666666555543 33344444444433

>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=99.01  E-value=1e-08  Score=84.28  Aligned_cols=131  Identities=9%  Similarity=-0.035  Sum_probs=113.3

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC---------------hhhHHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD---------------VVTYNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      +...|..+...+.+.|++++|+..|++..+.. +.+               ..+|..+..++...|++++|+..|+++++
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~-p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  224 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWL-EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALE  224 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh-hccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            35678889999999999999999999998875 333               58999999999999999999999999999


Q ss_pred             cCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHH-HHHHHHHH
Q 042039           80 QGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRA-EELFGSME  148 (376)
Q Consensus        80 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a-~~~~~~~~  148 (376)
                      .... +...+..+..++...|++++|...|+++++.. +.+..++..+..++...|+.++| ...++.+.
T Consensus       225 ~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          225 LDSN-NEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7543 78899999999999999999999999999874 44678888999999999999988 44666554

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=99.01  E-value=4.4e-09  Score=79.70  Aligned_cols=156  Identities=11%  Similarity=-0.014  Sum_probs=74.0

Q ss_pred             ccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc-----CCCCCcchHHHHHHHHHhCCCH
Q 042039          168 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD-----DVAADTSTYNTFIDGLCKNGYI  242 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~  242 (376)
                      ..|++++|.+.++.+... ......++..+...+...|++++|...+++....     ..+....++..++..+...|++
T Consensus         4 ~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~   82 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNW   82 (203)
T ss_dssp             ---CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             ccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCH
Confidence            456666666644444331 2223455566666666666666666666665542     0111233455555555556666


Q ss_pred             HHHHHHHHHhccc----CCC--chHHHHHHHHHHHHhCCChHHHHHHHhcccccCC-CCC----HHHHHHHHHHHHccCC
Q 042039          243 VEAVELFRTLGIL----KCE--LDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVL-VAD----VVTYNIMIHGLCNDGQ  311 (376)
Q Consensus       243 ~~a~~~~~~~~~~----~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~  311 (376)
                      ++|...+++....    +..  .....+..++..+...|++++|...+++...... ..+    ..++..+..++...|+
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            6666555554332    101  1123445555555555555555555555432100 001    1223444555555555


Q ss_pred             hhHHHHHHHHHHH
Q 042039          312 MDKAHDLFLDMEE  324 (376)
Q Consensus       312 ~~~a~~~~~~~~~  324 (376)
                      +++|...+++..+
T Consensus       163 ~~~A~~~~~~al~  175 (203)
T 3gw4_A          163 LLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            5555555555444

>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=99.00  E-value=9.5e-10  Score=83.14  Aligned_cols=146  Identities=16%  Similarity=0.034  Sum_probs=66.8

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc---------------hHhHH
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS---------------VVTFN   90 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~~~   90 (376)
                      ....|+++++.+.|+.-.... ......+..++..+...|++++|+..|++.+.......               ...+.
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (198)
T 2fbn_A           14 RENLYFQGAKKSIYDYTDEEK-VQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNL   92 (198)
T ss_dssp             --------CCCSGGGCCHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhccccCchhhCCHHHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHH
Confidence            334455555555554322211 22344566666677777777777777777766422110               13444


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK  170 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  170 (376)
                      .+..++...|++++|...+++.++.. +.+...+..++.++...|++++|...|+++.... |.+..++..+..++...+
T Consensus        93 ~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~  170 (198)
T 2fbn_A           93 NLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLK  170 (198)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHH
Confidence            44445555555555555555554432 2234444444555555555555555555544443 233344444444444444


Q ss_pred             cHHH
Q 042039          171 EVEE  174 (376)
Q Consensus       171 ~~~~  174 (376)
                      +.++
T Consensus       171 ~~~~  174 (198)
T 2fbn_A          171 EARK  174 (198)
T ss_dssp             HHHC
T ss_pred             HHHH
Confidence            3333

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

Probab=98.98  E-value=7.1e-09  Score=73.59  Aligned_cols=100  Identities=10%  Similarity=-0.081  Sum_probs=89.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      +...+..+...+.+.|++++|+..|+++...+ |.+...|..+..++...|++++|+..|++++...+. +...+..+..
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~   94 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN-EPRFPFHAAE   94 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CcHHHHHHHH
Confidence            44567778889999999999999999998876 678899999999999999999999999999997544 6778889999


Q ss_pred             HHHhCCChHHHHHHHHHHHhcC
Q 042039           95 ELCKNGKMDEASRLLDLMVQRD  116 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~  116 (376)
                      ++...|++++|...|+..++..
T Consensus        95 ~~~~~g~~~~A~~~~~~al~~~  116 (142)
T 2xcb_A           95 CHLQLGDLDGAESGFYSARALA  116 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999998763

>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=98.97  E-value=1.6e-08  Score=70.11  Aligned_cols=98  Identities=11%  Similarity=-0.002  Sum_probs=66.5

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...|..+...+.+.|++++|+..|++..+.. +.+...|..++.++...|++++|+..+++.++..+. +...+..+..+
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~   81 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN-FVRAYIRKATA   81 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-cHHHHHHHHHH
Confidence            3456666667777777777777777776654 556667777777777777777777777777665433 45666666777


Q ss_pred             HHhCCChHHHHHHHHHHHhc
Q 042039           96 LCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +...|++++|...+++.++.
T Consensus        82 ~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           82 QIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhCHHHHHHHHHHHHHh
Confidence            77777777777777766654

>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=98.97  E-value=3.2e-08  Score=67.40  Aligned_cols=98  Identities=12%  Similarity=0.049  Sum_probs=59.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      +..+..+...+...|++++|...|++..... +.+...+..++.++...|++++|...+++..+.... +...+..+..+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~   81 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcc-cHHHHHHHHHH
Confidence            4455666666666666666666666665543 445556666666666666666666666666654322 45555556666


Q ss_pred             HHhCCChHHHHHHHHHHHhc
Q 042039           96 LCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +...|++++|...+++..+.
T Consensus        82 ~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHhhHHHHHHHHHHHHHc
Confidence            66666666666666666554

>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=98.96  E-value=1.2e-08  Score=70.68  Aligned_cols=98  Identities=9%  Similarity=0.123  Sum_probs=61.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--Cc----hHhHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PS----VVTFN   90 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~~   90 (376)
                      .++..+...+.+.|++++|++.|++.++.. |.+..+|..++.+|...|++++|++.+++.++....  ++    ..+|.
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~   87 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMS   87 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHH
Confidence            456666777777777777777777776654 556667777777777777777777777776654211  01    12455


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           91 VIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        91 ~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .+..++...|++++|+..|++.+..
T Consensus        88 ~lg~~~~~~~~~~~A~~~~~kal~~  112 (127)
T 4gcn_A           88 RAGNAFQKQNDLSLAVQWFHRSLSE  112 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5555666666666666666666553

>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=98.95  E-value=2.5e-09  Score=80.82  Aligned_cols=151  Identities=11%  Similarity=-0.022  Sum_probs=90.9

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh---------------
Q 042039           57 LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA---------------  121 (376)
Q Consensus        57 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---------------  121 (376)
                      .+......|+++++.+.|+...... ......+..+...+...|++++|...|++.++.... +.               
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~   87 (198)
T 2fbn_A           10 HSSGRENLYFQGAKKSIYDYTDEEK-VQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIH-TEEWDDQILLDKKKNIE   87 (198)
T ss_dssp             ------------CCCSGGGCCHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTT-CTTCCCHHHHHHHHHHH
T ss_pred             hhhhhhhhhhccccCchhhCCHHHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhc-ccccchhhHHHHHHHHH
Confidence            3444455566666666665332221 113456777788888999999999999998875321 22               


Q ss_pred             -hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHH
Q 042039          122 -FTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLG  200 (376)
Q Consensus       122 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  200 (376)
                       .++..++.++...|++++|...++++.... +.+..++..++.++...|++++|+..|++..+.. +.+...+..+..+
T Consensus        88 ~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  165 (198)
T 2fbn_A           88 ISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELC  165 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHH
Confidence             566677777777777777777777777664 4566677777777777777777777777777642 2345556666666


Q ss_pred             HHhccchHHHH
Q 042039          201 LFEIHQVEHAL  211 (376)
Q Consensus       201 ~~~~~~~~~a~  211 (376)
                      +...++.+++.
T Consensus       166 ~~~~~~~~~~~  176 (198)
T 2fbn_A          166 VNKLKEARKKD  176 (198)
T ss_dssp             HHHHHHHHC--
T ss_pred             HHHHHHHHHHH
Confidence            65555555544

>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=98.92  E-value=8.4e-08  Score=65.25  Aligned_cols=97  Identities=10%  Similarity=0.029  Sum_probs=50.3

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ..+..++..+...|++++|...|++....... +...+..+..++...|++++|...+++..+.. +.+...+..++.++
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLDPH-NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            34455555555555555555555555554222 44445555555555555555555555555442 22344455555555


Q ss_pred             HhcCcHHHHHHHHHHHHhc
Q 042039          132 CLTGKINRAEELFGSMESM  150 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~  150 (376)
                      ...|++++|...+++....
T Consensus        83 ~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTT
T ss_pred             HHHhhHHHHHHHHHHHHHc
Confidence            5555555555555555544

>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=98.91  E-value=6e-08  Score=67.13  Aligned_cols=95  Identities=14%  Similarity=0.011  Sum_probs=46.4

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYC  167 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  167 (376)
                      .+..+...+...|++++|...|++.++.. +.+...+..++.++...|++++|...++++.... |.+...+..++.++.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            34444444445555555555555544432 2234444455555555555555555555554443 334444555555555


Q ss_pred             ccCcHHHHHHHHHHHHH
Q 042039          168 KNKEVEEALSLYREMVS  184 (376)
Q Consensus       168 ~~~~~~~a~~~~~~~~~  184 (376)
                      ..|++++|...|+++.+
T Consensus        84 ~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           84 AVKEYASALETLDAART  100 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHH
Confidence            55555555555555444

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

Probab=98.91  E-value=2.8e-08  Score=72.42  Aligned_cols=100  Identities=7%  Similarity=-0.050  Sum_probs=70.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      .+...|..+...+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|+..|++.++.... +...|..+.
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg   86 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-YSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHH
Confidence            345567777777777777777777777777664 456677777777777777777777777777766433 566677777


Q ss_pred             HHHHhCCChHHHHHHHHHHHhc
Q 042039           94 DELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .++...|++++|...|++.++.
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHh
Confidence            7777777777777777777664

>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=98.89  E-value=6.2e-06  Score=66.49  Aligned_cols=138  Identities=9%  Similarity=0.023  Sum_probs=82.8

Q ss_pred             cCCChH-HHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC----------hHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           63 HANDWN-EAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK----------MDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        63 ~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      +.|.+. +|+++++.++..++. +..+|+.--.++...+.          +++++.+++.++... +-+..+|+.-..++
T Consensus        41 ~~~e~s~eaL~~t~~~L~~nP~-~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-PKny~aW~hR~wlL  118 (331)
T 3dss_A           41 QAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLL  118 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            444444 678888888776443 44555544433333322          466677777776654 33566666666666


Q ss_pred             HhcC--cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc-HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc
Q 042039          132 CLTG--KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE-VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  204 (376)
Q Consensus       132 ~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  204 (376)
                      ...+  .++++..+++++.+.. +.+..+|+.-..+....|. ++++++.++++++.. +.+..+|......+...
T Consensus       119 ~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-p~N~SAW~~R~~ll~~l  192 (331)
T 3dss_A          119 SRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQL  192 (331)
T ss_dssp             HHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHH
T ss_pred             hccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHh
Confidence            6666  3677777777777665 5566666666666666666 467777777777653 33555565555544443

>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=98.88  E-value=5.6e-08  Score=67.31  Aligned_cols=61  Identities=11%  Similarity=0.171  Sum_probs=33.2

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHh
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQ  114 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  114 (376)
                      ++..++..+.+.|++++|++.|++.++..+. +...|..+..++...|++++|+..+++.++
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~-~~~~~~nlg~~~~~~~~~~~A~~~~~~al~   70 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELDPS-NITFYNNKAAVYFEEKKFAECVQFCEKAVE   70 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4445555555555555555555555554322 444555555555555555555555555544

>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=98.87  E-value=5.9e-08  Score=68.25  Aligned_cols=98  Identities=14%  Similarity=-0.042  Sum_probs=56.7

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      ++..|..+...+...|++++|+..|++..... +.+...+..++.++...|++++|...+++.++.... +...+..+..
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~   85 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQ   85 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCch-hHHHHHHHHH
Confidence            44555666666666666666666666655543 444555666666666666666666666666554322 4455555555


Q ss_pred             HHHhCCChHHHHHHHHHHHh
Q 042039           95 ELCKNGKMDEASRLLDLMVQ  114 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~  114 (376)
                      ++...|++++|...++++++
T Consensus        86 ~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHH
Confidence            66666666666666655554

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

Probab=98.87  E-value=6.3e-08  Score=70.53  Aligned_cols=100  Identities=11%  Similarity=0.063  Sum_probs=64.8

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      +...+..+...+...|++++|++.|++.++.... +...|..+..++...|++++|+..+++.++.. +.+...+..+..
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPA-NPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            4556666666777777777777777777665332 55666666666677777777777777666653 334566666666


Q ss_pred             HHHhcCcHHHHHHHHHHHHhcC
Q 042039          130 GFCLTGKINRAEELFGSMESMG  151 (376)
Q Consensus       130 ~~~~~~~~~~a~~~~~~~~~~~  151 (376)
                      ++...|++++|...|+++....
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhC
Confidence            6666667777766666666553

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

Probab=98.87  E-value=4.1e-08  Score=66.14  Aligned_cols=98  Identities=13%  Similarity=-0.015  Sum_probs=49.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCC--chHhHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQP--SVVTFNVIM   93 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~   93 (376)
                      ...|..+...+...|++++|+..|++..+.. +.+..++..++.++...|++++|.+.+++..+.. +.  +...+..+.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~   83 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKA   83 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHH
Confidence            3444555555555555555555555554443 3344455555555555555555555555555432 11  234444455


Q ss_pred             HHHHhC-CChHHHHHHHHHHHhc
Q 042039           94 DELCKN-GKMDEASRLLDLMVQR  115 (376)
Q Consensus        94 ~~~~~~-~~~~~a~~~~~~~~~~  115 (376)
                      .++... |++++|.+.++.+...
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           84 DALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHHhCCHHHHHHHHHHHhhc
Confidence            555555 5555555555555443

>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=98.86  E-value=7.8e-08  Score=67.59  Aligned_cols=100  Identities=11%  Similarity=-0.042  Sum_probs=60.3

Q ss_pred             CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           49 PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLM  128 (376)
Q Consensus        49 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  128 (376)
                      .+...+..++..+...|++++|...|++.+..... +...+..+..++...|++++|...+++.++.+ +.+...+..++
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcC-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            34556666666666666666666666666665322 45556666666666666666666666666543 22455566666


Q ss_pred             HHHHhcCcHHHHHHHHHHHHhc
Q 042039          129 DGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      .++...|++++|...|+++...
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH
Confidence            6666666666666666665543

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

Probab=98.85  E-value=1.3e-07  Score=67.35  Aligned_cols=99  Identities=18%  Similarity=0.093  Sum_probs=56.2

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPD---VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV   91 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   91 (376)
                      +...+..+...+...|++++|+..|++..+.. +.+   ...+..+..++...|++++|+..+++..+.... +...+..
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~  104 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLD-ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG-DVKALYR  104 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC-CHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc-ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc-CHHHHHH
Confidence            34555666666666666666666666666543 212   455555566666666666666666665554222 3445555


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhc
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +..++...|++++|...+++.++.
T Consensus       105 ~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A          105 RSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHc
Confidence            555555666666666666655554

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

Probab=98.85  E-value=7.8e-08  Score=64.74  Aligned_cols=99  Identities=14%  Similarity=0.064  Sum_probs=58.4

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCC--ChhhHHHH
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRP--NAFTYSTL  127 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l  127 (376)
                      +...+..++..+...|++++|...++++.+.... +...+..+..++...|++++|...+++.++.. +.  +...+..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l   82 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPE-ESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAK   82 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHH
Confidence            4455566666666666666666666666655322 44555556666666666666666666666542 22  34555556


Q ss_pred             HHHHHhc-CcHHHHHHHHHHHHhc
Q 042039          128 MDGFCLT-GKINRAEELFGSMESM  150 (376)
Q Consensus       128 ~~~~~~~-~~~~~a~~~~~~~~~~  150 (376)
                      +.++... |++++|.+.++++...
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           83 ADALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhhc
Confidence            6666666 6666666666666554

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.84  E-value=6.2e-09  Score=89.32  Aligned_cols=157  Identities=8%  Similarity=-0.061  Sum_probs=69.8

Q ss_pred             ChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHH
Q 042039           31 FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLD  110 (376)
Q Consensus        31 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  110 (376)
                      ++++|++.|+...... +.....+..+...+.+.|++++|+..|+++++.......  +           ..+...    
T Consensus       249 ~~~~A~~~~~~~~~~~-~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~--~-----------~~~~~~----  310 (457)
T 1kt0_A          249 SFEKAKESWEMDTKEK-LEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYG--L-----------SEKESK----  310 (457)
T ss_dssp             EEECCCCGGGSCHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCS--C-----------CHHHHH----
T ss_pred             hcccCcchhhcCHHHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccccc--C-----------ChHHHH----
Confidence            3444444443333221 223445666666666667777777777666654222110  0           000000    


Q ss_pred             HHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC
Q 042039          111 LMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT  190 (376)
Q Consensus       111 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  190 (376)
                      +..    .....+|..+..++.+.|++++|...++++.... +.+..++..++.+|...|++++|+..|+++++.. +.+
T Consensus       311 ~~~----~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~  384 (457)
T 1kt0_A          311 ASE----SFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQN  384 (457)
T ss_dssp             HHH----HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----
T ss_pred             HHH----HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCC
Confidence            000    0002344445555555555555555555555443 3344455555555555555555555555555431 123


Q ss_pred             HhHHHHHHHHHHhccchHHHH
Q 042039          191 VVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       191 ~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      ...+..+..++...++.+++.
T Consensus       385 ~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          385 KAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            344444444555555444443

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

Probab=98.83  E-value=2.8e-07  Score=65.57  Aligned_cols=114  Identities=13%  Similarity=0.064  Sum_probs=80.9

Q ss_pred             CCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc----hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhh
Q 042039           48 NPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS----VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFT  123 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  123 (376)
                      +.+...+..++..+...|++++|.+.|++.++..  |+    ...+..+..++...|++++|...+++.++.. +.+...
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  101 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKA  101 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHH
Confidence            3456777888888888888888888888887753  33    5667777777888888888888888877753 335667


Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039          124 YSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILING  165 (376)
Q Consensus       124 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  165 (376)
                      +..++.++...|++++|...|++..... +.+...+..+..+
T Consensus       102 ~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  142 (148)
T 2dba_A          102 LYRRSQALEKLGRLDQAVLDLQRCVSLE-PKNKVFQEALRNI  142 (148)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHH
Confidence            7777777778888888888887777664 3444444444433

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

Probab=98.83  E-value=3.1e-08  Score=67.99  Aligned_cols=97  Identities=8%  Similarity=-0.102  Sum_probs=66.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      ..+..+...+.+.|++++|+..|++..+.. |.+...|..+..++...|++++|+..|++.++..+. +...+..+..++
T Consensus        18 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~~~~~la~~~   95 (121)
T 1hxi_A           18 ENPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSH   95 (121)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            345566666777777777777777777664 556677777777777777777777777777766433 556666677777


Q ss_pred             HhCCChHHHHHHHHHHHhc
Q 042039           97 CKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~  115 (376)
                      ...|++++|...+++.++.
T Consensus        96 ~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           96 TNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHC-
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            7777777777777777654

>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=98.82  E-value=4.1e-08  Score=68.28  Aligned_cols=99  Identities=12%  Similarity=0.151  Sum_probs=64.3

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC--Cc----hHhH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ--PS----VVTF   89 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~   89 (376)
                      ...|..+...+...|++++|+..|++..+.. +.+...+..++.++...|++++|...++++......  ++    ..++
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHH
Confidence            3456666777777777777777777776654 445666777777777777777777777776654211  11    4455


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      ..+..++...|++++|...++++.+.
T Consensus        83 ~~la~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           83 ARIGNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            66666666666666666666666664

>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=98.80  E-value=1.1e-07  Score=66.00  Aligned_cols=94  Identities=18%  Similarity=0.281  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCC-------hhhHHH
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHD-------DVSYNI  161 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-------~~~~~~  161 (376)
                      +..+...+...|++++|...+++..+.. +.+...+..++.++...|++++|...++++.... +.+       ..++..
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVG-RENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-HHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhc-cccchhHHHHHHHHHH
Confidence            3344444444444444444444444432 2233444444444444455555555444444332 111       334445


Q ss_pred             HHHHHHccCcHHHHHHHHHHHHH
Q 042039          162 LINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      ++.++...|++++|...++++.+
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHH
Confidence            55555555555555555555554

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

Probab=98.78  E-value=3.6e-07  Score=63.34  Aligned_cols=95  Identities=17%  Similarity=0.106  Sum_probs=61.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCCh---hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc---hHhHHHH
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDV---VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS---VVTFNVI   92 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l   92 (376)
                      +..+...+...|++++|+..|+++.+.. +.+.   .++..++.++...|++++|...|+++++..+. +   ...+..+
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~l   82 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELY-PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHHH
Confidence            4455566667777777777777776653 3333   46666777777777777777777777665322 2   4456666


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhc
Q 042039           93 MDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      ..++...|++++|...++++++.
T Consensus        83 a~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           83 GLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH
Confidence            66777777777777777777665

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.77  E-value=1.1e-06  Score=75.02  Aligned_cols=198  Identities=9%  Similarity=0.014  Sum_probs=120.0

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCCCCh----------------hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC-C
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQRDVRPNA----------------FTYSTLMDGFCLTGKINRAEELFGSMESMGCK-H  154 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~  154 (376)
                      -.+.+.+.|++++|.+.|..+++.......                ..+..++..|...|++++|.+.+..+...-.. +
T Consensus        10 ~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~   89 (434)
T 4b4t_Q           10 EARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFA   89 (434)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence            355667788888888888888875422111                12566777788888888888877776543111 1


Q ss_pred             Ch----hhHHHHHHHHHccCcHHHHHHHHHHHHHC----CCCC-CHhHHHHHHHHHHhccchHHHHHHHHHHHhcCC---
Q 042039          155 DD----VSYNILINGYCKNKEVEEALSLYREMVSK----GIKP-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDV---  222 (376)
Q Consensus       155 ~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---  222 (376)
                      +.    .+.+.+...+...|++++|..+++.....    +..+ -..++..++..+...|++++|..++..+...-.   
T Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           90 KSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             chHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            11    13344455555677777887777776542    2222 245566777777777777777777776654311   


Q ss_pred             --CCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc----CCCch--HHHHHHHHHHHHhCCChHHHHHHHhcccc
Q 042039          223 --AADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL----KCELD--IQAYNCLIDGLCKSGRLEIALELFRSLPR  289 (376)
Q Consensus       223 --~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  289 (376)
                        +....++...+..|...|++++|..+++++...    ..++.  ...+..++..+...|++++|...|.+..+
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence              112335666677777777777777777665431    11111  23455556666677777777777666544

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

Probab=98.76  E-value=1.2e-07  Score=64.90  Aligned_cols=60  Identities=13%  Similarity=0.022  Sum_probs=23.0

Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHH
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMV  183 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  183 (376)
                      .+..++.++...|++++|...|+++.... |.+...+..++.++...|++++|+..+++++
T Consensus        53 a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~al  112 (121)
T 1hxi_A           53 AWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33333333333344444444443333332 2233333333334444444444444443333

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.73  E-value=8.5e-07  Score=75.72  Aligned_cols=199  Identities=9%  Similarity=0.027  Sum_probs=146.4

Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHhcCCCCch----------------HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-
Q 042039           56 SLIHGLCHANDWNEAKRLFFEMMDQGVQPSV----------------VTFNVIMDELCKNGKMDEASRLLDLMVQRDVR-  118 (376)
Q Consensus        56 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-  118 (376)
                      .-+..+.+.|++++|++.|.++++.......                ..+..++..|...|++++|.+++..+...... 
T Consensus         9 ~~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~   88 (434)
T 4b4t_Q            9 EEARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQF   88 (434)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTS
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence            3466788899999999999999987433211                24678899999999999999999988763211 


Q ss_pred             CCh----hhHHHHHHHHHhcCcHHHHHHHHHHHHhc----C-CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC--CC
Q 042039          119 PNA----FTYSTLMDGFCLTGKINRAEELFGSMESM----G-CKHDDVSYNILINGYCKNKEVEEALSLYREMVSK--GI  187 (376)
Q Consensus       119 ~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~  187 (376)
                      ++.    .+...+...+...|+++.|..+++.....    + ...-..++..++..|...|++++|..+++++...  +.
T Consensus        89 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~  168 (434)
T 4b4t_Q           89 AKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKL  168 (434)
T ss_dssp             CHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTS
T ss_pred             cchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhc
Confidence            121    22334445555678999999999887543    1 1222457788999999999999999999988763  11


Q ss_pred             --C-CCHhHHHHHHHHHHhccchHHHHHHHHHHHhcC--CCCC----cchHHHHHHHHHhCCCHHHHHHHHHHhcc
Q 042039          188 --K-PTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDD--VAAD----TSTYNTFIDGLCKNGYIVEAVELFRTLGI  254 (376)
Q Consensus       188 --~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  254 (376)
                        . ....++..++..|...|++++|..++++.....  ...+    ...+..++..+...+++++|...+..+..
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          169 DDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             SCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence              1 125678888999999999999999999876541  1111    23456667778889999999999988753

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.71  E-value=2.3e-07  Score=79.60  Aligned_cols=138  Identities=13%  Similarity=-0.036  Sum_probs=69.9

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...|..+...+.+.|++++|+..|++..+.. +.+...           . .+...    +...    .....|..+..+
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~-p~~~~~-----------~-~~~~~----~~~~----~~~~~~~nla~~  326 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL-EMEYGL-----------S-EKESK----ASES----FLLAAFLNLAMC  326 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-TTCCSC-----------C-HHHHH----HHHH----HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh-cccccC-----------C-hHHHH----HHHH----HHHHHHHHHHHH
Confidence            4478888999999999999999999998753 222100           0 00000    0000    012334444444


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      +.+.|++++|+..++++++.. +.+...+..+..+|...|++++|...|+++.+.. |.+..++..+..++.+.++.+++
T Consensus       327 ~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a  404 (457)
T 1kt0_A          327 YLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQISMCQKKAKEHNER  404 (457)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555555554442 2234444455555555555555555555554443 33444445555555555544444


Q ss_pred             H
Q 042039          176 L  176 (376)
Q Consensus       176 ~  176 (376)
                      .
T Consensus       405 ~  405 (457)
T 1kt0_A          405 D  405 (457)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.71  E-value=1.1e-08  Score=88.21  Aligned_cols=125  Identities=11%  Similarity=0.006  Sum_probs=95.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .|..+...+.+.|++++|++.|++..+.. +.+..+|..++.++.+.|++++|++.++++++.... +...+..+..++.
T Consensus         8 ~~~~lg~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~lg~~~~   85 (477)
T 1wao_1            8 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNM   85 (477)
T ss_dssp             TSSSSSSSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHH
Confidence            34455566778899999999999988775 567888999999999999999999999999887433 6778888888999


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH--HHhcCcHHHHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG--FCLTGKINRAEELFG  145 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  145 (376)
                      ..|++++|...++++++.. +.+...+..+..+  +.+.|++++|.+.++
T Consensus        86 ~~g~~~eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           86 ALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHTCHHHHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999988864 2244555556555  777888899988888

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

Probab=98.70  E-value=8.7e-07  Score=61.35  Aligned_cols=94  Identities=13%  Similarity=0.119  Sum_probs=49.0

Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHhcCCCCch---HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC---hhhHHHHH
Q 042039           55 NSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV---VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN---AFTYSTLM  128 (376)
Q Consensus        55 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~  128 (376)
                      ..++..+...|++++|...|+++.+..+. +.   ..+..+..++...|++++|...++++++.. +.+   ...+..++
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~la   83 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYPN-GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY-PTHDKAAGGLLKLG   83 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSS-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTSTTHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC-CCCcccHHHHHHHH
Confidence            34455555566666666666665554222 22   344555555555566666666665555542 112   33445555


Q ss_pred             HHHHhcCcHHHHHHHHHHHHhc
Q 042039          129 DGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      .++...|++++|...|+++...
T Consensus        84 ~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           84 LSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            5555555555555555555544

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.69  E-value=2.2e-08  Score=86.30  Aligned_cols=125  Identities=12%  Similarity=0.084  Sum_probs=101.6

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFC  132 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  132 (376)
                      .+..++..+.+.|++++|++.|+++++.... +...+..+..++.+.|++++|...+++.++.. +.+...+..++.+|.
T Consensus         8 ~~~~lg~~~~~~g~~~~A~~~~~~Al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~   85 (477)
T 1wao_1            8 ELKTQANDYFKAKDYENAIKFYSQAIELNPS-NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNM   85 (477)
T ss_dssp             TSSSSSSSTTTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            3444556677889999999999999987433 68889999999999999999999999999874 446788999999999


Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHH--HHccCcHHHHHHHHH
Q 042039          133 LTGKINRAEELFGSMESMGCKHDDVSYNILING--YCKNKEVEEALSLYR  180 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  180 (376)
                      ..|++++|.+.|+++.+.. +.+...+..+..+  +.+.|++++|++.++
T Consensus        86 ~~g~~~eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           86 ALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHTCHHHHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999998875 4566677777766  888899999999988

>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=98.68  E-value=2.9e-07  Score=76.51  Aligned_cols=91  Identities=12%  Similarity=-0.030  Sum_probs=54.0

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      +...|..+..++.+.|++++|+..++++++.. +.+...+..+..+|...|++++|...|+++.+.. +.+...+..+..
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-P~~~~~~~~l~~  349 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLK  349 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            34455666666666666666666666666543 2245566666666666666666666666666554 345555556666


Q ss_pred             HHHccCcHHHHHH
Q 042039          165 GYCKNKEVEEALS  177 (376)
Q Consensus       165 ~~~~~~~~~~a~~  177 (376)
                      ++...++.+++.+
T Consensus       350 ~~~~~~~~~~a~k  362 (370)
T 1ihg_A          350 VKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            6665555555543

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.67  E-value=1.2e-07  Score=68.65  Aligned_cols=132  Identities=14%  Similarity=0.058  Sum_probs=81.6

Q ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHhcccCC---Cc--hHHHHHHHHHHHHhCCChHHHHHHHhcccccC----CCC-CHH
Q 042039          228 TYNTFIDGLCKNGYIVEAVELFRTLGILKC---EL--DIQAYNCLIDGLCKSGRLEIALELFRSLPRRV----LVA-DVV  297 (376)
Q Consensus       228 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~~  297 (376)
                      ++..++..+...|++++|...++++.....   .+  ...++..++..+...|++++|...+++..+..    .++ ...
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            345555556666666666666655543210   00  11356666777777777777777777654321    000 134


Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHHc----CCC-CcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEEN----AVA-PNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .+..++..+...|++++|...+++..+.    +.. .....+..+...+...|++++|.+.+++..+
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            5667777788888888888888777643    111 1234567777888888888888888888764

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

Probab=98.65  E-value=8.3e-08  Score=65.41  Aligned_cols=87  Identities=11%  Similarity=0.058  Sum_probs=58.7

Q ss_pred             hcCChhHHHHHHHHhhhCC--CCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHH
Q 042039           28 KEGFVDKAKALFLQMKGEN--INPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEA  105 (376)
Q Consensus        28 ~~g~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  105 (376)
                      ..|++++|+..|++..+.+  .+.+..++..++.++...|++++|+..|+++++..+. +...+..+..++...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHH
Confidence            3567777777777777653  2344567777777777777777777777777776433 566677777777777777777


Q ss_pred             HHHHHHHHhc
Q 042039          106 SRLLDLMVQR  115 (376)
Q Consensus       106 ~~~~~~~~~~  115 (376)
                      ...+++.+..
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            7777777665

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.65  E-value=2.9e-07  Score=66.61  Aligned_cols=131  Identities=10%  Similarity=0.075  Sum_probs=55.6

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCC-Cc----hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-CC----hh
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ-PS----VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR-PN----AF  122 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~  122 (376)
                      ++..+...+...|++++|...+++....... ++    ..++..+...+...|++++|...+++..+.... ++    ..
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            3444444444555555555555444432100 00    123444444555555555555555544432100 00    22


Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhcC----C-CCChhhHHHHHHHHHccCcHHHHHHHHHHHH
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESMG----C-KHDDVSYNILINGYCKNKEVEEALSLYREMV  183 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  183 (376)
                      .+..++..+...|++++|...+++.....    . +....++..+..++...|++++|.+.+++..
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  156 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  156 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            34444445555555555555554443221    0 0012234444555555555555555555444

>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=98.64  E-value=4.9e-07  Score=75.12  Aligned_cols=91  Identities=10%  Similarity=-0.051  Sum_probs=74.2

Q ss_pred             ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 042039          120 NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL  199 (376)
Q Consensus       120 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  199 (376)
                      +..++..++.++.+.|++++|...++++.+.. +.+..++..++.+|...|++++|+..|+++++.. +.+...+..+..
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-P~~~~~~~~l~~  349 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLK  349 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            46778888899999999999999999998875 5677888889999999999999999999988862 335677777777


Q ss_pred             HHHhccchHHHHH
Q 042039          200 GLFEIHQVEHALK  212 (376)
Q Consensus       200 ~~~~~~~~~~a~~  212 (376)
                      ++...++.+++.+
T Consensus       350 ~~~~~~~~~~a~k  362 (370)
T 1ihg_A          350 VKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777777654

>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=98.64  E-value=2.6e-06  Score=74.81  Aligned_cols=174  Identities=11%  Similarity=-0.045  Sum_probs=130.5

Q ss_pred             hcCC-hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC----------hHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           28 KEGF-VDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND----------WNEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        28 ~~g~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      +.|. .++|++.++++...+ |.+..+|+.-..++...|+          ++++++.++++++..++ +..+|+.-..++
T Consensus        40 ~~~~~~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l  117 (567)
T 1dce_A           40 QAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLL  117 (567)
T ss_dssp             HTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            3444 467789999988876 6677788877777777776          88899999998887655 777888888888


Q ss_pred             HhCC--ChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC-cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc----
Q 042039           97 CKNG--KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG-KINRAEELFGSMESMGCKHDDVSYNILINGYCKN----  169 (376)
Q Consensus        97 ~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----  169 (376)
                      .+.+  ++++++..++++++.+ +-+..+|.....++...| .++++.+.++++.+.. +.+..+|+....++.+.    
T Consensus       118 ~~l~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~~~  195 (567)
T 1dce_A          118 SRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQP  195 (567)
T ss_dssp             HTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCC
T ss_pred             HHcccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhcccc
Confidence            8888  6689999999998875 447778888777777888 7888888888888776 56777887777666553    


Q ss_pred             ----------CcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccc
Q 042039          170 ----------KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       170 ----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  206 (376)
                                +.++++++.+++++... +-+...|..+...+...+.
T Consensus       196 ~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          196 DSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             CSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCC
T ss_pred             cccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCC
Confidence                      45678888888877752 3356666666666655555

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

Probab=98.63  E-value=3.7e-07  Score=66.26  Aligned_cols=62  Identities=15%  Similarity=0.103  Sum_probs=27.5

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      .|..+..++.+.|++++|+..++++++.+ +.+...+..++.++...|++++|...|+++...
T Consensus        65 ~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           65 LYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            34444444444444444444444444432 223344444444444444444444444444443

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

Probab=98.63  E-value=5.3e-07  Score=65.43  Aligned_cols=100  Identities=13%  Similarity=0.082  Sum_probs=87.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhC--------C---------CCCChhhHHHHHHHHhcCCChHHHHHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGE--------N---------INPDVVTYNSLIHGLCHANDWNEAKRLFFEMM   78 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--------~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   78 (376)
                      ...+......+.+.|++++|+..|++....        .         .+.+..+|..+..++...|++++|+..+++++
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            567888899999999999999999998775        1         12345789999999999999999999999999


Q ss_pred             hcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcC
Q 042039           79 DQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRD  116 (376)
Q Consensus        79 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  116 (376)
                      +..+. +...|..+..++...|++++|...|++.++..
T Consensus        91 ~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  127 (162)
T 3rkv_A           91 KREET-NEKALFRRAKARIAAWKLDEAEEDLKLLLRNH  127 (162)
T ss_dssp             HHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hcCCc-chHHHHHHHHHHHHHhcHHHHHHHHHHHHhcC
Confidence            97543 68899999999999999999999999999873

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

Probab=98.59  E-value=1.6e-07  Score=63.92  Aligned_cols=87  Identities=14%  Similarity=0.072  Sum_probs=62.7

Q ss_pred             hCCCHHHHHHHHHHhcccC--CCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHH
Q 042039          238 KNGYIVEAVELFRTLGILK--CELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKA  315 (376)
Q Consensus       238 ~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  315 (376)
                      ..|++++|+..|+++...+  .+.+...+..++.++...|++++|+..++++.+. .|.+...+..++.++...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQ-FPNHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCchHHHHHHHHHHHHcCCHHHH
Confidence            3567778888888877653  1334667778888888888888888888887766 455677788888888888888888


Q ss_pred             HHHHHHHHHc
Q 042039          316 HDLFLDMEEN  325 (376)
Q Consensus       316 ~~~~~~~~~~  325 (376)
                      +..++++.+.
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            8888888765

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.58  E-value=9.4e-07  Score=62.44  Aligned_cols=97  Identities=14%  Similarity=-0.027  Sum_probs=55.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCC------Ch-----hhHHHHHHHHhcCCChHHHHHHHHHHHhc-----
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINP------DV-----VTYNSLIHGLCHANDWNEAKRLFFEMMDQ-----   80 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~------~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----   80 (376)
                      ..+......+.+.|++++|+..|++.++.....      +.     ..|..+..++...|++++|+..+++.++.     
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            445666677777888888888888777653110      11     25666666666666666666666666553     


Q ss_pred             --CCCCchHhH----HHHHHHHHhCCChHHHHHHHHHHHh
Q 042039           81 --GVQPSVVTF----NVIMDELCKNGKMDEASRLLDLMVQ  114 (376)
Q Consensus        81 --~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~  114 (376)
                        .+. +...|    .....++...|++++|+..|++.++
T Consensus        92 e~~pd-~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           92 ELNQD-EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             CTTST-HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCCCc-hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence              221 33344    5555555555555555555555544

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

Probab=98.57  E-value=3.9e-07  Score=74.88  Aligned_cols=149  Identities=7%  Similarity=-0.048  Sum_probs=64.3

Q ss_pred             hhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           51 VVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG  130 (376)
Q Consensus        51 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  130 (376)
                      ...+..+...+...|++++|+..|++.+..  .|+...       +...++.+++...+          ...++..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l----------~~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAV----------KNPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHH----------HTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHH----------HHHHHHHHHHH
Confidence            345666677777777777777777777664  233221       11112222221111          01245556666


Q ss_pred             HHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHH-HHhccchHH
Q 042039          131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLG-LFEIHQVEH  209 (376)
Q Consensus       131 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~  209 (376)
                      +.+.|++++|...++++.... +.+..++..++.+|...|++++|...|+++++.. +.+...+..+... ....+..+.
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~-p~~~~a~~~L~~l~~~~~~~~~~  317 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYA-PDDKAIRRELRALAEQEKALYQK  317 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666666554 4455566666666666666666666666665531 1123333333333 223344555


Q ss_pred             HHHHHHHHHhc
Q 042039          210 ALKLFEEMQRD  220 (376)
Q Consensus       210 a~~~~~~~~~~  220 (376)
                      +...|..+...
T Consensus       318 a~~~~~~~l~~  328 (338)
T 2if4_A          318 QKEMYKGIFKG  328 (338)
T ss_dssp             -----------
T ss_pred             HHHHHHHhhCC
Confidence            55666665543

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

Probab=98.53  E-value=3.8e-07  Score=74.95  Aligned_cols=149  Identities=12%  Similarity=0.034  Sum_probs=81.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      ...+..+...+.+.|++++|+..|++.....  |+..       .+...+++.++...+          ....|..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~-------~~~~~~~~~~~~~~l----------~~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYM--GDDF-------MFQLYGKYQDMALAV----------KNPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHS--CHHH-------HHTCCHHHHHHHHHH----------HTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHh--ccch-------hhhhcccHHHHHHHH----------HHHHHHHHHHH
Confidence            4567778888999999999999999988753  3322       122334444443322          12366777788


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHH-HHccCcHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILING-YCKNKEVEE  174 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~  174 (376)
                      +.+.|++++|+..+++.++.. +.+...+..++.+|...|++++|...|+++.... +.+..++..+..+ ....+..++
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~-p~~~~a~~~L~~l~~~~~~~~~~  317 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYA-PDDKAIRRELRALAEQEKALYQK  317 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            888888888888888887764 3457778888888888888888888888887664 4455566666555 334556677


Q ss_pred             HHHHHHHHHHC
Q 042039          175 ALSLYREMVSK  185 (376)
Q Consensus       175 a~~~~~~~~~~  185 (376)
                      +...|..+...
T Consensus       318 a~~~~~~~l~~  328 (338)
T 2if4_A          318 QKEMYKGIFKG  328 (338)
T ss_dssp             -----------
T ss_pred             HHHHHHHhhCC
Confidence            77788777664

>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=98.52  E-value=1.8e-05  Score=69.53  Aligned_cols=175  Identities=10%  Similarity=-0.012  Sum_probs=135.9

Q ss_pred             CChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC----------hHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhc
Q 042039           65 NDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK----------MDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT  134 (376)
Q Consensus        65 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  134 (376)
                      ...++|++.+++++..++. +..+|+.-..++...|+          +++++..++.+++.. +-+..+|..-..++.+.
T Consensus        43 ~~~eeal~~~~~~l~~nP~-~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l  120 (567)
T 1dce_A           43 ELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRL  120 (567)
T ss_dssp             CCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc
Confidence            3456789999999987554 66777777777777666          899999999999875 34778888888888888


Q ss_pred             C--cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC-cHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc-------
Q 042039          135 G--KINRAEELFGSMESMGCKHDDVSYNILINGYCKNK-EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI-------  204 (376)
Q Consensus       135 ~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------  204 (376)
                      +  +++++.+.++++.+.. +.+..+|+.-..++.+.| .++++++.++++++.. +-+..+|......+...       
T Consensus       121 ~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~~~~~~  198 (567)
T 1dce_A          121 PEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSG  198 (567)
T ss_dssp             SSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             ccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhccccccc
Confidence            8  7799999999999887 678888888888888888 8899999999988864 34677777777766653       


Q ss_pred             -------cchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHH
Q 042039          205 -------HQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVE  244 (376)
Q Consensus       205 -------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  244 (376)
                             +.++++.+.+..++... |.+..+|......+.+.++.++
T Consensus       199 ~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          199 PQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCCccc
Confidence                   55678888888887765 5677778777777777666433

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.49  E-value=2.7e-06  Score=60.11  Aligned_cols=61  Identities=8%  Similarity=0.009  Sum_probs=40.0

Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhc-------CCCCChhhH----HHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESM-------GCKHDDVSY----NILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      .|..+..++...|++++|+..+++.+..       . |.+...|    ...+.++...|++++|+..|++.++
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~-pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN-QDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTT-STHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCC-CchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            5666666666666666666666666654       4 3445566    6677777777777777777777665

>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=98.43  E-value=1.4e-05  Score=55.91  Aligned_cols=110  Identities=10%  Similarity=-0.058  Sum_probs=60.3

Q ss_pred             ChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh----CCChHHHH
Q 042039           31 FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK----NGKMDEAS  106 (376)
Q Consensus        31 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~  106 (376)
                      ++++|++.|++..+.+ .+..  .  +...|...+.+++|.++|++..+.|   +...+..+...|..    .+++++|.
T Consensus        10 d~~~A~~~~~~aa~~g-~~~a--~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELN-EMFG--C--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTT-CTTH--H--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCC-CHhh--h--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            4566666666666555 2222  2  5555555555666666666665542   44555555555555    55566666


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcC
Q 042039          107 RLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMG  151 (376)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  151 (376)
                      .+|++..+.|   ++..+..+...|..    .+++++|..+|++..+.|
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            6666655543   34445555555555    455555555555555543

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

Probab=98.40  E-value=1.6e-06  Score=74.35  Aligned_cols=62  Identities=8%  Similarity=-0.003  Sum_probs=28.4

Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhc-----C--CCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESM-----G--CKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      +++.++..|...|++++|+.+++++...     |  .|....+...+..++...+.+++|..+|..+++
T Consensus       395 ~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          395 AVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444455555555554444444221     1  111222334444555555555555555555544

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

Probab=98.39  E-value=3.2e-06  Score=72.48  Aligned_cols=126  Identities=9%  Similarity=-0.015  Sum_probs=91.9

Q ss_pred             HHHhCCChHHHHHHHHHHHhc---CCCC----ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc-----C--CCCChhhHH
Q 042039           95 ELCKNGKMDEASRLLDLMVQR---DVRP----NAFTYSTLMDGFCLTGKINRAEELFGSMESM-----G--CKHDDVSYN  160 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~---~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~  160 (376)
                      .+..+|++++|+.++++.++.   -..+    ...+++.++..|...|++++|..++++....     |  .|....+++
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            345678888888888777652   1112    2456788888888888888888888876542     2  233455789


Q ss_pred             HHHHHHHccCcHHHHHHHHHHHHHC-----CC-CCC-HhHHHHHHHHHHhccchHHHHHHHHHHHhc
Q 042039          161 ILINGYCKNKEVEEALSLYREMVSK-----GI-KPT-VVTYNTLFLGLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      .|+..|...|++++|..+++++++.     |. .|+ ..+...+..++...+.+++|..++..+.+.
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999988752     21 122 445566777888899999999999988764

>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=98.39  E-value=1.6e-05  Score=55.70  Aligned_cols=110  Identities=11%  Similarity=0.057  Sum_probs=67.5

Q ss_pred             ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHH
Q 042039           66 DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAE  141 (376)
Q Consensus        66 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~  141 (376)
                      ++++|.+.|++..+.|.. ...    +...|...+..++|..+|++..+.+   +...+..+...|..    .+++++|.
T Consensus        10 d~~~A~~~~~~aa~~g~~-~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELNEM-FGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTTCT-THH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCH-hhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            566677777776665522 222    5555555566666777776666653   45566666666665    56666777


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHc----cCcHHHHHHHHHHHHHCC
Q 042039          142 ELFGSMESMGCKHDDVSYNILINGYCK----NKEVEEALSLYREMVSKG  186 (376)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  186 (376)
                      .+|++..+.+   ++.++..|..+|..    .+++++|...|++..+.|
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            7766666653   45556666666666    566666666666666654

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

Probab=98.38  E-value=1.3e-06  Score=58.60  Aligned_cols=91  Identities=11%  Similarity=0.061  Sum_probs=57.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc------hH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS------VV   87 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~   87 (376)
                      ++...|..+...+...|++++|+..|++..+.. +.+..++..++.++...|++++|++.+++.++.... +      ..
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~   79 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTST-AEHVAIRSK   79 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSS-TTSHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ccHHHHHHH
Confidence            345567777777777777777777777777664 556677777777777777777777777777765322 2      33


Q ss_pred             hHHHHHHHHHhCCChHHHH
Q 042039           88 TFNVIMDELCKNGKMDEAS  106 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~  106 (376)
                      .+..+..++...|+++.+.
T Consensus        80 ~~~~~~~~~~~~~~~~~a~   98 (111)
T 2l6j_A           80 LQYRLELAQGAVGSVQIPV   98 (111)
T ss_dssp             HHHHHHHHHHHHHCCCCCS
T ss_pred             HHHHHHHHHHHHHhHhhhH
Confidence            4444444554444444433

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

Probab=98.36  E-value=4.3e-07  Score=61.00  Aligned_cols=95  Identities=12%  Similarity=0.033  Sum_probs=67.0

Q ss_pred             hHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc------HHH
Q 042039          260 DIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN------VII  333 (376)
Q Consensus       260 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~  333 (376)
                      +...+..++..+...|++++|...|+++.+. .+.+...+..++.++...|++++|+..++++++.... +      ...
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~-~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~   80 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITA-QPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTST-AEHVAIRSKL   80 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSS-TTSHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ccHHHHHHHH
Confidence            4566777778888888888888888887765 4456777788888888888888888888888775322 2      445


Q ss_pred             HHHHHHHHhhcCChhhHHHHHHH
Q 042039          334 FVTLIHGFVRINKPSKVIELLHK  356 (376)
Q Consensus       334 ~~~l~~~~~~~g~~~~a~~~~~~  356 (376)
                      +..+..++...|+++.|...+++
T Consensus        81 ~~~~~~~~~~~~~~~~a~~~~~~  103 (111)
T 2l6j_A           81 QYRLELAQGAVGSVQIPVVEVDE  103 (111)
T ss_dssp             HHHHHHHHHHHHCCCCCSSSSSS
T ss_pred             HHHHHHHHHHHHhHhhhHhHHHH
Confidence            56666666666766666554443

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

Probab=98.35  E-value=4.5e-06  Score=56.41  Aligned_cols=81  Identities=10%  Similarity=0.067  Sum_probs=62.1

Q ss_pred             hHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHH
Q 042039           33 DKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLM  112 (376)
Q Consensus        33 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  112 (376)
                      ++|+..|++..+.. +.+...+..++.++...|++++|+..|++.++.... +...|..+..++...|++++|...|++.
T Consensus         2 ~~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            2 QAITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPT-YSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CCHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45677777777665 567778888888888888888888888888876433 5667777888888888888888888887


Q ss_pred             Hhc
Q 042039          113 VQR  115 (376)
Q Consensus       113 ~~~  115 (376)
                      ++.
T Consensus        80 l~~   82 (115)
T 2kat_A           80 LAA   82 (115)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            764

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

Probab=98.32  E-value=4.9e-06  Score=53.36  Aligned_cols=64  Identities=13%  Similarity=0.223  Sum_probs=35.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      ...|..+...+...|++++|+..|++..+.. +.+..++..+..++...|++++|...+++..+.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            3445555555555556666665555555443 334455555555555555555555555555554

>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=98.28  E-value=2.7e-06  Score=59.96  Aligned_cols=59  Identities=17%  Similarity=0.208  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc-----------CcHHHHHHHHHHHHHCCCCCCHhHHHHHH
Q 042039          137 INRAEELFGSMESMGCKHDDVSYNILINGYCKN-----------KEVEEALSLYREMVSKGIKPTVVTYNTLF  198 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  198 (376)
                      +++|+..|++..+.. |....+|..++.+|...           |++++|++.|+++++  +.|+...|...+
T Consensus        62 ~~eAi~~le~AL~ld-P~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al  131 (158)
T 1zu2_A           62 IQEAITKFEEALLID-PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSL  131 (158)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHH
Confidence            346666666666654 44555666666666655           367777777777776  345554444333

>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=98.26  E-value=2.6e-06  Score=60.10  Aligned_cols=87  Identities=13%  Similarity=0.014  Sum_probs=60.7

Q ss_pred             HhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCCh----------HHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 042039           27 CKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDW----------NEAKRLFFEMMDQGVQPSVVTFNVIMDEL   96 (376)
Q Consensus        27 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----------~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   96 (376)
                      .+.+.+++|++.+++..+.+ |.+...|..+..++...+++          ++|+..|++.++..+. +..+|..+..+|
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~ay   90 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAY   90 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHHH
Confidence            35566888888888888776 66788888888888877765          4777777777776433 556677777777


Q ss_pred             HhCC-----------ChHHHHHHHHHHHhc
Q 042039           97 CKNG-----------KMDEASRLLDLMVQR  115 (376)
Q Consensus        97 ~~~~-----------~~~~a~~~~~~~~~~  115 (376)
                      ...|           ++++|...|++.++.
T Consensus        91 ~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l  120 (158)
T 1zu2_A           91 TSFAFLTPDETEAKHNFDLATQFFQQAVDE  120 (158)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcccCcchhhhhccHHHHHHHHHHHHHh
Confidence            6653           566666666666654

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

Probab=98.25  E-value=1.4e-05  Score=51.20  Aligned_cols=82  Identities=15%  Similarity=0.131  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHH
Q 042039          260 DIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIH  339 (376)
Q Consensus       260 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  339 (376)
                      +...+..++..+...|++++|...+++..+. .+.+...+..++.++...|++++|...++++.+... .+...+..+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALEL-DPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCHHHHHHHHH
Confidence            4456667777777777777777777777655 344566777777777777777777777777776532 24555555555


Q ss_pred             HHhh
Q 042039          340 GFVR  343 (376)
Q Consensus       340 ~~~~  343 (376)
                      .+.+
T Consensus        86 ~~~~   89 (91)
T 1na3_A           86 AKQK   89 (91)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5544

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

Probab=98.24  E-value=8.8e-06  Score=54.93  Aligned_cols=78  Identities=12%  Similarity=0.085  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          105 ASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       105 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      +...+++.++.. +.+...+..++..+...|++++|...|+++.... +.+...+..++.++...|++++|...|++..+
T Consensus         4 a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A            4 ITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444444432 2234455555555555555555555555555543 33444555555555555555555555555544

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

Probab=98.16  E-value=8e-06  Score=53.57  Aligned_cols=65  Identities=17%  Similarity=0.121  Sum_probs=44.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      +...|..+...+.+.|++++|+..|+++.+.+ +.+..+|..+..+|...|++++|.+.|++.++.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            45566677777777777777777777776654 445666777777777777777777777766543

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

Probab=98.05  E-value=3.1e-05  Score=50.67  Aligned_cols=64  Identities=19%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          120 NAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       120 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      +...+..++.++...|++++|...|+++.+.. |.+..+|..++.+|...|++++|+..+++.++
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            45556666666666666666666666666654 44555666666666666666666666666554

>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=97.90  E-value=0.00046  Score=56.01  Aligned_cols=144  Identities=12%  Similarity=0.051  Sum_probs=90.1

Q ss_pred             CCChhhHHHHHHHHh--cCC---ChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH----hCC-C---hHHHHHHHHHHHh
Q 042039           48 NPDVVTYNSLIHGLC--HAN---DWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC----KNG-K---MDEASRLLDLMVQ  114 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~--~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~-~---~~~a~~~~~~~~~  114 (376)
                      +.+..+|...+++..  ..+   +..+|..+|+++++..+. ....+..+..++.    ..+ .   .......++....
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~-~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a  269 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPE-FTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVT  269 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHh
Confidence            556666666654433  222   356788888888776322 2333333332221    111 1   1111122222211


Q ss_pred             -cCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhH
Q 042039          115 -RDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT  193 (376)
Q Consensus       115 -~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  193 (376)
                       ...+.++.++..+...+...|++++|...++++...+  |+...|..+...+...|++++|.+.|+++...  .|...+
T Consensus       270 ~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t  345 (372)
T 3ly7_A          270 LPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANT  345 (372)
T ss_dssp             CGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHH
T ss_pred             cccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcCh
Confidence             1124567788877777777899999999999999885  67777888889999999999999999998884  566666


Q ss_pred             HHH
Q 042039          194 YNT  196 (376)
Q Consensus       194 ~~~  196 (376)
                      |..
T Consensus       346 ~~~  348 (372)
T 3ly7_A          346 LYW  348 (372)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>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=97.80  E-value=0.00096  Score=54.19  Aligned_cols=143  Identities=10%  Similarity=0.027  Sum_probs=96.6

Q ss_pred             CCCchHhHHHHHHHHH--hCC---ChHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHhc---C-----cHHHHHHHHHHH
Q 042039           82 VQPSVVTFNVIMDELC--KNG---KMDEASRLLDLMVQRDVRPN-AFTYSTLMDGFCLT---G-----KINRAEELFGSM  147 (376)
Q Consensus        82 ~~~~~~~~~~l~~~~~--~~~---~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~---~-----~~~~a~~~~~~~  147 (376)
                      .+.+...|...+++..  ..+   +..+|..+|++.++..  |+ ...+..+..+|...   +     ........++..
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            3557777777776543  333   3578999999999874  44 45555444444311   1     111111222222


Q ss_pred             Hh-cCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCc
Q 042039          148 ES-MGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT  226 (376)
Q Consensus       148 ~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  226 (376)
                      .. ...+.++.++..+...+...|++++|...+++++..+  |+...|..+...+...|++++|.+.+++....+  |..
T Consensus       268 ~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~--P~~  343 (372)
T 3ly7_A          268 VTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLR--PGA  343 (372)
T ss_dssp             HTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CSH
T ss_pred             HhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCc
Confidence            11 1125677788888877777899999999999999964  788888888899999999999999999998874  455


Q ss_pred             chHH
Q 042039          227 STYN  230 (376)
Q Consensus       227 ~~~~  230 (376)
                      .+|.
T Consensus       344 ~t~~  347 (372)
T 3ly7_A          344 NTLY  347 (372)
T ss_dssp             HHHH
T ss_pred             ChHH
Confidence            5544

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.69  E-value=0.00033  Score=44.82  Aligned_cols=66  Identities=11%  Similarity=0.025  Sum_probs=35.1

Q ss_pred             CChhhHHHHHHHHHhcCC---hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           14 PNTVTYNTIIDGLCKEGF---VDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      +|+..+..+..++...++   .++|..++++.++.+ |.++.+...++..+.+.|++++|+..|+++.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            444555555555543333   455555555555554 445555555555555555555555555555554

>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=97.64  E-value=0.00013  Score=61.54  Aligned_cols=61  Identities=10%  Similarity=-0.051  Sum_probs=31.6

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhc-----C-CCCC-hhhHHHHHHHHHhcCcHHHHHHHHHHHH
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQR-----D-VRPN-AFTYSTLMDGFCLTGKINRAEELFGSME  148 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~  148 (376)
                      +++.++.+|...|++++|..++++.++.     | ..|+ ..+++.++..|...|++++|+.+++++.
T Consensus       342 ~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          342 MMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            4555555555555555555555555431     1 1111 3345555555666666666666555553

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

Probab=97.63  E-value=0.00048  Score=44.63  Aligned_cols=60  Identities=13%  Similarity=0.192  Sum_probs=49.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChh-hHHHHHHHHhcCCChHHHHHHHHHHHhcCC
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVV-TYNSLIHGLCHANDWNEAKRLFFEMMDQGV   82 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   82 (376)
                      ....+.+.|++++|+..|+++.+.. +.+.. .+..++.++...|++++|.+.|++.++..+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p   66 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNP   66 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence            4566778899999999999888765 55677 888888889999999999999999888643

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

Probab=97.62  E-value=0.00031  Score=59.34  Aligned_cols=88  Identities=11%  Similarity=0.084  Sum_probs=45.6

Q ss_pred             HhcCCChHHHHHHHHHHHhcC---CCC----chHhHHHHHHHHHhCCChHHHHHHHHHHHhc-----C-CCCC-hhhHHH
Q 042039           61 LCHANDWNEAKRLFFEMMDQG---VQP----SVVTFNVIMDELCKNGKMDEASRLLDLMVQR-----D-VRPN-AFTYST  126 (376)
Q Consensus        61 ~~~~~~~~~a~~~~~~~~~~~---~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~-~~~~~~  126 (376)
                      +...|++++|+.++++.++..   ..|    ...+++.++.+|...|++++|+.++++++..     | ..|+ ..+++.
T Consensus       297 ~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~n  376 (429)
T 3qwp_A          297 LKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMK  376 (429)
T ss_dssp             HHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHH
T ss_pred             HHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHH
Confidence            334556666666665555421   111    1234555566666666666666666555431     1 1111 334555


Q ss_pred             HHHHHHhcCcHHHHHHHHHHHH
Q 042039          127 LMDGFCLTGKINRAEELFGSME  148 (376)
Q Consensus       127 l~~~~~~~~~~~~a~~~~~~~~  148 (376)
                      ++..|...|++++|+.+++++.
T Consensus       377 La~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          377 VGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCHHHHHHHHHHHH
Confidence            6666666666666666666553

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

Probab=97.62  E-value=0.00021  Score=46.45  Aligned_cols=57  Identities=18%  Similarity=0.244  Sum_probs=29.5

Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCChh-hHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDDV-SYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      +..+...|++++|...++++.+.. +.+.. .+..++.++...|++++|...|+++++.
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            344445555555555555555443 33444 5555555555555555555555555543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=97.61  E-value=3.7e-08  Score=81.18  Aligned_cols=265  Identities=12%  Similarity=0.148  Sum_probs=186.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      +..|..|..+..+.|+..+|++.|-   +.   .|+..|..++....+.|.+++-++.+...++..-  ++..=+.|+-+
T Consensus        54 p~VWs~LgkAqL~~~~v~eAIdsyI---kA---~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~k--e~~IDteLi~a  125 (624)
T 3lvg_A           54 PAVWSQLAKAQLQKGMVKEAIDSYI---KA---DDPSSYMEVVQAANTSGNWEELVKYLQMARKKAR--ESYVETELIFA  125 (624)
T ss_dssp             CCCSSSHHHHTTTSSSCTTTTTSSC---CC---SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCC--STTTTHHHHHH
T ss_pred             ccHHHHHHHHHHccCchHHHHHHHH---hC---CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhc--ccccHHHHHHH
Confidence            4568888888888888888877653   22   2566778888888888888888888877665522  44444677888


Q ss_pred             HHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           96 LCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      |++.++..+..+++       ..||..-...++.-|...|.++.|.-+|..+.         -|..|..++.+.|++..|
T Consensus       126 yAk~~rL~elEefl-------~~~N~A~iq~VGDrcf~e~lYeAAKilys~is---------N~akLAstLV~L~~yq~A  189 (624)
T 3lvg_A          126 LAKTNRLAELEEFI-------NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS---------NFGRLASTLVHLGEYQAA  189 (624)
T ss_dssp             HHTSCSSSTTTSTT-------SCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSC---------CCTTTSSSSSSCSGGGSS
T ss_pred             HHhhCcHHHHHHHH-------cCCCcccHHHHHHHHHHccCHHHHHHHHHhCc---------cHHHHHHHHHHHHHHHHH
Confidence            88888876644433       24566666778888888888887777765433         244566777888888888


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      .+.-++      ..++.||..+..+|...+++..|.-.--.++-     .+.-+..++..|...|.+++-+.+++.....
T Consensus       190 VdaArK------Ans~ktWKeV~~ACvd~~EfrLAqicGLniIv-----hadeL~elv~~YE~~G~f~ELIsLlEaglgl  258 (624)
T 3lvg_A          190 VDGARK------ANSTRTWKEVCFACVDGKEFRLAQMCGLHIVV-----HADELEELINYYQDRGYFEELITMLEAALGL  258 (624)
T ss_dssp             TTTTTT------CCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHC-----CSSCCSGGGSSSSTTCCCTTSTTTHHHHTTS
T ss_pred             HHHHHh------cCChhHHHHHHHHHhCchHHHHHHHhcchhcc-----cHHHHHHHHHHHHhCCCHHHHHHHHHHHhCC
Confidence            765443      23678899999999999998877655444432     2233445677788999999999999998755


Q ss_pred             CCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCC-------CHHHHHHHHHHHHccCChhHHHH
Q 042039          256 KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA-------DVVTYNIMIHGLCNDGQMDKAHD  317 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-------~~~~~~~l~~~~~~~~~~~~a~~  317 (376)
                      . ......|+.|+-.|++- ++++..+.++..-.+-.-|       ....|..++-.|.+-.+++.|..
T Consensus       259 E-rAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~l  325 (624)
T 3lvg_A          259 E-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII  325 (624)
T ss_dssp             T-TCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHH
T ss_pred             C-chhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHH
Confidence            4 44788899998888764 5677777776654331112       24567777778887777776643

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

Probab=97.57  E-value=0.00035  Score=59.06  Aligned_cols=92  Identities=12%  Similarity=0.044  Sum_probs=62.6

Q ss_pred             HHHHHhCCChHHHHHHHhcccccC---CCC----CHHHHHHHHHHHHccCChhHHHHHHHHHHHc-----C-CCCc-HHH
Q 042039          268 IDGLCKSGRLEIALELFRSLPRRV---LVA----DVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN-----A-VAPN-VII  333 (376)
Q Consensus       268 ~~~~~~~~~~~~a~~~~~~~~~~~---~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~-~~~  333 (376)
                      +..+...|++++|+.++++.+...   ..|    ...+++.++.+|...|++++|+.+++++++.     | ..|+ ..+
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            444556778888888887665321   112    2456777888888888888888888877642     2 1222 356


Q ss_pred             HHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          334 FVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       334 ~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      ++.|...|...|++++|..++++..+
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            77788888888888888888887763

>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=97.55  E-value=0.00049  Score=58.09  Aligned_cols=61  Identities=8%  Similarity=-0.033  Sum_probs=30.4

Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHC-----C-CCCC-HhHHHHHHHHHHhccchHHHHHHHHHHH
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSK-----G-IKPT-VVTYNTLFLGLFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~  218 (376)
                      +++.++.+|...|++++|+.++++.+..     | ..|+ ..+++.+...|...|++++|..++++++
T Consensus       342 ~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          342 MMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            4555555555555555555555554431     1 1111 3345555555555555555555555543

>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=97.52  E-value=0.0026  Score=49.60  Aligned_cols=86  Identities=10%  Similarity=0.024  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHhcCCCC--ChhhHHHHHHHHHc-----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhc-cchH
Q 042039          137 INRAEELFGSMESMGCKH--DDVSYNILINGYCK-----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI-HQVE  208 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~  208 (376)
                      ...|...++++.+.. |.  +...|..++..|..     .|+.++|.+.|++.++.+..-+..++......++.. ++.+
T Consensus       179 l~~A~a~lerAleLD-P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~  257 (301)
T 3u64_A          179 VHAAVMMLERACDLW-PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRA  257 (301)
T ss_dssp             HHHHHHHHHHHHHHC-TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHH
T ss_pred             HHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHH
Confidence            567778888888774 22  35578888888888     488899999999888853222367777777877774 8888


Q ss_pred             HHHHHHHHHHhcCCC
Q 042039          209 HALKLFEEMQRDDVA  223 (376)
Q Consensus       209 ~a~~~~~~~~~~~~~  223 (376)
                      .+.+.+++.+.....
T Consensus       258 ~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          258 GFDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHcCCCC
Confidence            888888888887554

>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=97.51  E-value=0.021  Score=44.61  Aligned_cols=91  Identities=15%  Similarity=0.182  Sum_probs=47.5

Q ss_pred             HHHHHHHhcccccCCCCC---HHHHHHHHHHHHc-----cCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhh-cCChh
Q 042039          278 EIALELFRSLPRRVLVAD---VVTYNIMIHGLCN-----DGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVR-INKPS  348 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~  348 (376)
                      ..|...++++.+.  .|+   ...|..++..|..     -|+.++|.++|+++++.+..-+..++......+++ .|+.+
T Consensus       180 ~~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~  257 (301)
T 3u64_A          180 HAAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRA  257 (301)
T ss_dssp             HHHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHH
T ss_pred             HHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHH
Confidence            4455555555543  222   3455555555555     26666666666666654322124455555555555 36666


Q ss_pred             hHHHHHHHHHhCCCC--CchHHHH
Q 042039          349 KVIELLHKMKEKKVM--PDASIVS  370 (376)
Q Consensus       349 ~a~~~~~~~~~~~~~--p~~~~~~  370 (376)
                      ++.+.+++.......  |+....+
T Consensus       258 ~a~~~L~kAL~a~p~~~P~~~lan  281 (301)
T 3u64_A          258 GFDEALDRALAIDPESVPHNKLLV  281 (301)
T ss_dssp             HHHHHHHHHHHCCGGGCSSCHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCChhHHH
Confidence            666666666655544  5544443

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.46  E-value=0.0015  Score=41.71  Aligned_cols=67  Identities=10%  Similarity=0.074  Sum_probs=39.9

Q ss_pred             CCChhhHHHHHHHHhcCCC---hHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           48 NPDVVTYNSLIHGLCHAND---WNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +.++..+..+..++...++   .++|..++++.++..+. +......+...+...|++++|...|+.+++.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~-~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPY-NEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            4455566666655543333   56666666666665333 4555666666666666666666666666655

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=97.46  E-value=0.00098  Score=46.48  Aligned_cols=82  Identities=13%  Similarity=0.071  Sum_probs=52.4

Q ss_pred             hhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC---ChHHHHHHHHHHHhcCCCC--chHhHHHHHHHHHhCCChHHHH
Q 042039           32 VDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN---DWNEAKRLFFEMMDQGVQP--SVVTFNVIMDELCKNGKMDEAS  106 (376)
Q Consensus        32 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~  106 (376)
                      ...+.+.|.+..+.+ +++..+...+..++++.+   +.++++.+++.+.+.. .|  +...+..+.-++.+.|++++|.
T Consensus        14 l~~~~~~y~~e~~~~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHH
Confidence            445555566555555 466677777777777766   5557777777776653 12  3445556666667777777777


Q ss_pred             HHHHHHHhc
Q 042039          107 RLLDLMVQR  115 (376)
Q Consensus       107 ~~~~~~~~~  115 (376)
                      ++++.+++.
T Consensus        92 ~y~~~lL~i  100 (152)
T 1pc2_A           92 KYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            777777765

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=97.33  E-value=0.003  Score=44.07  Aligned_cols=80  Identities=16%  Similarity=0.090  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC---cHHHHHHHHHHHHhcCCC-CChhhHHHHHHHHHccCcHHHHHHHH
Q 042039          104 EASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG---KINRAEELFGSMESMGCK-HDDVSYNILINGYCKNKEVEEALSLY  179 (376)
Q Consensus       104 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~  179 (376)
                      .+.+-|.+..+.+ +++..+...+..++++++   +++++..+++.+.+...| .....+..+.-+|.+.|++++|.+.+
T Consensus        16 ~~~~~y~~e~~~~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~   94 (152)
T 1pc2_A           16 KFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYV   94 (152)
T ss_dssp             HHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHH
Confidence            3344444444443 245555555666666655   455666666665554311 13445555566666666666666666


Q ss_pred             HHHHH
Q 042039          180 REMVS  184 (376)
Q Consensus       180 ~~~~~  184 (376)
                      +.+++
T Consensus        95 ~~lL~   99 (152)
T 1pc2_A           95 RGLLQ   99 (152)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            66666

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.24  E-value=0.026  Score=52.25  Aligned_cols=75  Identities=12%  Similarity=0.106  Sum_probs=39.1

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHcc
Q 042039           90 NVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  169 (376)
Q Consensus        90 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  169 (376)
                      ..++..+.+.|.++.|.++.+         +..   .-.......|+++.|.++.+.+      .+...|..++..+.+.
T Consensus       633 ~~~~~~l~~~~~~~~a~~~~~---------~~~---~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~  694 (814)
T 3mkq_A          633 TKIARFLEGQEYYEEALNISP---------DQD---QKFELALKVGQLTLARDLLTDE------SAEMKWRALGDASLQR  694 (814)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCC---------CHH---HHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCChHHheecCC---------Ccc---hheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHc
Confidence            444555555566555554432         110   1122334556666666654321      3445666666666666


Q ss_pred             CcHHHHHHHHHHH
Q 042039          170 KEVEEALSLYREM  182 (376)
Q Consensus       170 ~~~~~a~~~~~~~  182 (376)
                      ++++.|.+.|.++
T Consensus       695 ~~~~~A~~~y~~~  707 (814)
T 3mkq_A          695 FNFKLAIEAFTNA  707 (814)
T ss_dssp             TCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHc
Confidence            6666666666654

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=97.22  E-value=0.0034  Score=41.12  Aligned_cols=66  Identities=11%  Similarity=-0.017  Sum_probs=35.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCC------CCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGEN------INPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      +...+..+...+.+.|++..|...|+...+..      ..+....+..+..++.+.|+++.|...++++.+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            34445556666666666666666666554421      1223445555555555666666666655555554

>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=97.16  E-value=0.0087  Score=41.18  Aligned_cols=51  Identities=12%  Similarity=0.049  Sum_probs=22.2

Q ss_pred             CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 042039          275 GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA  326 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  326 (376)
                      ++.++|.++|+.++...... ...|...++.-.++|+.+.|.+++.+.+..+
T Consensus        74 ~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~  124 (161)
T 4h7y_A           74 QEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERG  124 (161)
T ss_dssp             HCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccC
Confidence            44455555554443321111 3333333444444555555555555554443

>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=97.12  E-value=0.014  Score=40.21  Aligned_cols=104  Identities=12%  Similarity=0.089  Sum_probs=58.4

Q ss_pred             CChhhHHHHHHHHHccCcH------HHHHHHHHHHHHCCCCCCHh-HHHHHHH------HHHhccchHHHHHHHHHHHhc
Q 042039          154 HDDVSYNILINGYCKNKEV------EEALSLYREMVSKGIKPTVV-TYNTLFL------GLFEIHQVEHALKLFEEMQRD  220 (376)
Q Consensus       154 ~~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~~~~~-~~~~l~~------~~~~~~~~~~a~~~~~~~~~~  220 (376)
                      .+..+|-..+...-+.|++      ++..++|+++... ++|+.. .|...+.      .+...++.++|.++|+.++..
T Consensus        11 ~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           11 NNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            3445555555555555555      5666666666654 444311 1111110      112346777777777777654


Q ss_pred             CCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCc
Q 042039          221 DVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCEL  259 (376)
Q Consensus       221 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  259 (376)
                      + +.-...+...++.-.+.|+...|.+++.+....+..|
T Consensus        90 h-KkFAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~  127 (161)
T 4h7y_A           90 C-KKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP  127 (161)
T ss_dssp             C-TTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC
T ss_pred             h-HHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc
Confidence            2 2225555555666667788888888887777766553

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=97.12  E-value=0.0079  Score=39.29  Aligned_cols=66  Identities=12%  Similarity=0.102  Sum_probs=46.0

Q ss_pred             ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcC------CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           50 DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQG------VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        50 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +..-+..++..+...|++..|...|+.+.+..      ..+....+..+..++.+.|+++.|..+++++.+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            45556677778888888888888887776641      1224556677777777777777777777777765

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.04  E-value=0.035  Score=51.45  Aligned_cols=157  Identities=17%  Similarity=0.154  Sum_probs=98.3

Q ss_pred             HHHHHhcCcHHHHHH-HHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccc
Q 042039          128 MDGFCLTGKINRAEE-LFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ  206 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  206 (376)
                      .......+++++|.+ ++..+      ++......++..+.+.|.++.|+++.+...            .-.......|+
T Consensus       606 ~~~~~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~~~~~~a~~~~~~~~------------~~f~~~l~~~~  667 (814)
T 3mkq_A          606 FQTLTLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQEYYEEALNISPDQD------------QKFELALKVGQ  667 (814)
T ss_dssp             HHHHHHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHTTCHHHHHHHCCCHH------------HHHHHHHHHTC
T ss_pred             HhHHHHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhCCChHHheecCCCcc------------hheehhhhcCC
Confidence            344455777877766 44211      112233677777778888888876653211            11334456788


Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhc
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRS  286 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  286 (376)
                      ++.|.++.+.+      .+...|..++..+.+.++++.|++.|.++..         +..+...+...|+.+...++.+.
T Consensus       668 ~~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~  732 (814)
T 3mkq_A          668 LTLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKD  732 (814)
T ss_dssp             HHHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHH
Confidence            88888775432      3567788888888888888888888888652         22344455557777776666555


Q ss_pred             ccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          287 LPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       287 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      +...+.      +.....+|.+.|++++|++++.++.
T Consensus       733 a~~~~~------~~~A~~~~~~~g~~~~a~~~~~~~~  763 (814)
T 3mkq_A          733 AETTGK------FNLAFNAYWIAGDIQGAKDLLIKSQ  763 (814)
T ss_dssp             HHHTTC------HHHHHHHHHHHTCHHHHHHHHHHTT
T ss_pred             HHHcCc------hHHHHHHHHHcCCHHHHHHHHHHcC
Confidence            544321      2334455667888888888876654

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.91  E-value=0.00012  Score=60.87  Aligned_cols=217  Identities=11%  Similarity=0.090  Sum_probs=128.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      -|+..|..++....+.|++++-+..+....+..  .++..=+.|+.+|++.++..+-.+++    .   .|+..-...+.
T Consensus        81 ~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~--ke~~IDteLi~ayAk~~rL~elEefl----~---~~N~A~iq~VG  151 (624)
T 3lvg_A           81 DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N---GPNNAHIQQVG  151 (624)
T ss_dssp             SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTC--CSTTTTHHHHHHHHTSCSSSTTTSTT----S---CCSSSCTHHHH
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccHHHHHHHHHhhCcHHHHHHHH----c---CCCcccHHHHH
Confidence            467789999999999999999999998777653  34445567899999999877654443    1   35555556666


Q ss_pred             HHHHhCCChHHHHHHHHHHHhc--------------------CCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC
Q 042039           94 DELCKNGKMDEASRLLDLMVQR--------------------DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCK  153 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~--------------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  153 (376)
                      .-|...|.++.|.-+|..+-..                    .-..++.||..+-.+|...+++.-|.-+--.++-..  
T Consensus       152 Drcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvha--  229 (624)
T 3lvg_A          152 DRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHA--  229 (624)
T ss_dssp             HHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCCS--
T ss_pred             HHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhcccH--
Confidence            7777777777666665544321                    012356778888888887777776655544443221  


Q ss_pred             CChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhc-CCC------CCc
Q 042039          154 HDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRD-DVA------ADT  226 (376)
Q Consensus       154 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~------~~~  226 (376)
                         .-...++..|-..|-+++-+.+++..+.. -......|+.|.-.|++- ++++..+.++....+ +++      ...
T Consensus       230 ---deL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~a  304 (624)
T 3lvg_A          230 ---DELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQA  304 (624)
T ss_dssp             ---SCCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTT
T ss_pred             ---HHHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence               11223455566666666666666665532 233455555555555543 334444333322111 111      123


Q ss_pred             chHHHHHHHHHhCCCHHHHH
Q 042039          227 STYNTFIDGLCKNGYIVEAV  246 (376)
Q Consensus       227 ~~~~~l~~~~~~~~~~~~a~  246 (376)
                      ..|..++-.|.+-.+++.|.
T Consensus       305 hLW~ElvfLY~~ydE~DnA~  324 (624)
T 3lvg_A          305 HLWAELVFLYDKYEEYDNAI  324 (624)
T ss_dssp             TCHHHHHHHHHHHTCHHHHH
T ss_pred             hhHHHHHHHHhcchhHHHHH
Confidence            34555555555555555543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.89  E-value=0.052  Score=38.91  Aligned_cols=45  Identities=11%  Similarity=0.130  Sum_probs=22.4

Q ss_pred             hcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHH
Q 042039           62 CHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLM  112 (376)
Q Consensus        62 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  112 (376)
                      .+.|+++.|.++.+.+      .+...|..+.......|+++-|.+.|.+.
T Consensus        16 L~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~   60 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQ   60 (177)
T ss_dssp             HHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHh
Confidence            3445555555554433      13445555555555555555555555443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.86  E-value=0.07  Score=38.26  Aligned_cols=130  Identities=13%  Similarity=0.127  Sum_probs=88.3

Q ss_pred             HHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCCh
Q 042039          198 FLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       198 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      .......|+++.|.++.+.+      .+...|..++......|+++-|.+.|.+...         +..+.-.|...|+.
T Consensus        12 F~LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~   76 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDV   76 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCH
T ss_pred             HHHHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCH
Confidence            34456789999999887765      3677899999999999999999999988753         23444456667888


Q ss_pred             HHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          278 EIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      +.-.++-+.....|      -++.....+...|+++++.++|.+.-.   .|...      ......|-.+.|.++.+.+
T Consensus        77 e~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~~r---~~eA~------~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           77 NKLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEGGS---LPLAY------AVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHTTC---HHHHH------HHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHCCC---hHHHH------HHHHHcCcHHHHHHHHHHh
Confidence            77776665554442      234455667788999999999865422   22111      1122356677788887766

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=96.83  E-value=0.0094  Score=39.95  Aligned_cols=89  Identities=12%  Similarity=0.029  Sum_probs=50.6

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHH---HHHHHHHHHhcCCC-CchHhHHHHHHHHHhCCC
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNE---AKRLFFEMMDQGVQ-PSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~  101 (376)
                      -........+.+.|......| .++..+-..+..++++..+..+   ++.+++.+.+.+.+ -.......+.-++.+.|+
T Consensus        11 ~~~~~~l~~~~~~y~~e~~~~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~   89 (126)
T 1nzn_A           11 LVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKE   89 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCCHHHHHHHHHHHHHHhccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhh
Confidence            333344555555555555444 3566666666666666665444   66666666654311 123344455556666677


Q ss_pred             hHHHHHHHHHHHhc
Q 042039          102 MDEASRLLDLMVQR  115 (376)
Q Consensus       102 ~~~a~~~~~~~~~~  115 (376)
                      +++|.+.++.+++.
T Consensus        90 Y~~A~~~~~~lL~~  103 (126)
T 1nzn_A           90 YEKALKYVRGLLQT  103 (126)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            77777776666664

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=96.69  E-value=0.029  Score=37.64  Aligned_cols=82  Identities=18%  Similarity=0.110  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHH---HHHHHHHhcccCCC-chHHHHHHHHHHHHhCCChHHHHH
Q 042039          207 VEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVE---AVELFRTLGILKCE-LDIQAYNCLIDGLCKSGRLEIALE  282 (376)
Q Consensus       207 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~  282 (376)
                      ...+.+-+......+ .++..+-..++.++.++.....   ++.+++.+...+.+ -.......++.++.+.|++++|.+
T Consensus        17 l~~~~~~y~~e~~~~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~   95 (126)
T 1nzn_A           17 LLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALK   95 (126)
T ss_dssp             HHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHH
Confidence            333444444443333 2445555555555555554444   55555555443311 123334444445555555555555


Q ss_pred             HHhcccc
Q 042039          283 LFRSLPR  289 (376)
Q Consensus       283 ~~~~~~~  289 (376)
                      +++.+++
T Consensus        96 ~~~~lL~  102 (126)
T 1nzn_A           96 YVRGLLQ  102 (126)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555544

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.24  E-value=0.47  Score=40.31  Aligned_cols=256  Identities=12%  Similarity=0.058  Sum_probs=133.6

Q ss_pred             CChHHHHHHHHHHHhc-----CCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHH----ccC
Q 042039          100 GKMDEASRLLDLMVQR-----DVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYC----KNK  170 (376)
Q Consensus       100 ~~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~  170 (376)
                      ++++.|.+.+..+.+.     +..........++..|...++++...+.+..+.... .........++..+.    ...
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr-~qlk~ai~~~V~~~~~~l~~~~  108 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKH-GQLKLSIQYMIQKVMEYLKSSK  108 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTT-TTSHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHh-hhhHHHHHHHHHHHHHHHhcCC
Confidence            6788888877666542     233345667778888888899988877776665432 112222333333222    222


Q ss_pred             cHHH--HHHHHHHHHHC--C-CCC---CHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCC-----cchHHHHHHHHH
Q 042039          171 EVEE--ALSLYREMVSK--G-IKP---TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAAD-----TSTYNTFIDGLC  237 (376)
Q Consensus       171 ~~~~--a~~~~~~~~~~--~-~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~  237 (376)
                      ..+.  -..+.+.+...  | +..   .......+...+...|++.+|.+++..+...-....     ...+...++.|.
T Consensus       109 ~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l  188 (445)
T 4b4t_P          109 SLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSI  188 (445)
T ss_dssp             TTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence            2221  11111111110  1 111   112235667778888888888888888754311111     234566677788


Q ss_pred             hCCCHHHHHHHHHHhcc----cCCCch--HHHHHHHHHHHHhCCChHHHHHHHhcccccC-CCCCHHHH----HHHHHHH
Q 042039          238 KNGYIVEAVELFRTLGI----LKCELD--IQAYNCLIDGLCKSGRLEIALELFRSLPRRV-LVADVVTY----NIMIHGL  306 (376)
Q Consensus       238 ~~~~~~~a~~~~~~~~~----~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~----~~l~~~~  306 (376)
                      ..+++..|..+++++..    ...+|+  ...+...+..+...+++.+|.+.|.++.... ...+...+    ..++.+.
T Consensus       189 ~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~  268 (445)
T 4b4t_P          189 LKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFL  268 (445)
T ss_dssp             HHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHH
Confidence            88888888888877632    222222  2345666777777888888888777764321 11122211    1111111


Q ss_pred             HccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhc--CChhhHHHHHHH
Q 042039          307 CNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRI--NKPSKVIELLHK  356 (376)
Q Consensus       307 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--g~~~~a~~~~~~  356 (376)
                      .-.+....-..++........-++...+..++.+|...  .+++.+.+.|+.
T Consensus       269 iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~  320 (445)
T 4b4t_P          269 VLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEP  320 (445)
T ss_dssp             HHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCS
T ss_pred             HhCCCCchHHHHHHHHhhcccccccHHHHHHHHHHHhchHhhhHHHHHHHHH
Confidence            12222222223333333222234667777777777553  345555554443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.18  E-value=0.16  Score=34.37  Aligned_cols=64  Identities=19%  Similarity=0.216  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCC
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKV  362 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  362 (376)
                      .+...+..+..+|+-++-.+++..+... .+|++.....+..+|.+.|+..++.++++++-++|+
T Consensus        93 ~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A           93 HVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence            3344444444455555544444443221 234444444455555555555555555555554443

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=96.14  E-value=0.84  Score=42.37  Aligned_cols=260  Identities=11%  Similarity=0.005  Sum_probs=143.8

Q ss_pred             HHHhcCCChHHHHHHHHHHHhcC--CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCC-------CCChh--hHHHH
Q 042039           59 HGLCHANDWNEAKRLFFEMMDQG--VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDV-------RPNAF--TYSTL  127 (376)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------~~~~~--~~~~l  127 (376)
                      -+....|+.++++..+...+..+  ..+....-..+.-..+..|..+++..++...+...-       .+...  ....+
T Consensus       382 LGlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGL  461 (963)
T 4ady_A          382 LGVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGI  461 (963)
T ss_dssp             HHHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHH
T ss_pred             hhhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHH
Confidence            44566778888888776655421  112223333344455666766678887777665321       01111  12223


Q ss_pred             HHHHHhcCcHHHHHHHHHHHHhcCCCCCh--hhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhcc
Q 042039          128 MDGFCLTGKINRAEELFGSMESMGCKHDD--VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH  205 (376)
Q Consensus       128 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  205 (376)
                      +.++.-.++ +++.+.+..+.... ....  .+-..++..+.-.|+.+....++..+.+. ...+..-...+.-++...|
T Consensus       462 Gla~~GS~~-eev~e~L~~~L~dd-~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~-~~e~vrR~aalgLGll~~g  538 (963)
T 4ady_A          462 GLAAMGSAN-IEVYEALKEVLYND-SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQET-QHGNITRGLAVGLALINYG  538 (963)
T ss_dssp             HHHSTTCCC-HHHHHHHHHHHHTC-CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTTT
T ss_pred             HHHhcCCCC-HHHHHHHHHHHhcC-CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhcc-CcHHHHHHHHHHHHhhhCC
Confidence            333333344 34555555554432 1111  12234556667788887777777777664 2222222333444455778


Q ss_pred             chHHHHHHHHHHHhcCCCCCcc--hHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHH
Q 042039          206 QVEHALKLFEEMQRDDVAADTS--TYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALEL  283 (376)
Q Consensus       206 ~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  283 (376)
                      +.+.+..+++.+.... .|...  ....+..+|+..|+.....+++..+.... ..+......+.-++...|+.+.+.++
T Consensus       539 ~~e~~~~li~~L~~~~-dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~v~rl  616 (963)
T 4ady_A          539 RQELADDLITKMLASD-ESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTTVPRI  616 (963)
T ss_dssp             CGGGGHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSSHHHH
T ss_pred             ChHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHHHHHH
Confidence            8888888888877642 22222  22344556778899877777888876542 22444444444455567777778888


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHccCCh-hHHHHHHHHHHH
Q 042039          284 FRSLPRRVLVADVVTYNIMIHGLCNDGQM-DKAHDLFLDMEE  324 (376)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~  324 (376)
                      ++.+.+.+ .|....-..+..+....|.. .++++.+..+..
T Consensus       617 v~~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~L~~L~~  657 (963)
T 4ady_A          617 VQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDVLDPLTK  657 (963)
T ss_dssp             TTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHT
T ss_pred             HHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHHHHHHcc
Confidence            87776652 34444333344444444443 578888888865

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=96.11  E-value=0.87  Score=42.28  Aligned_cols=260  Identities=12%  Similarity=0.034  Sum_probs=146.5

Q ss_pred             HHHhcCChhHHHHHHHHhhhCC--CCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC-------CCchHhHHHHHHH
Q 042039           25 GLCKEGFVDKAKALFLQMKGEN--INPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV-------QPSVVTFNVIMDE   95 (376)
Q Consensus        25 ~~~~~g~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------~~~~~~~~~l~~~   95 (376)
                      +....|+.++++.+++.....+  ..+....-..+.-+.+..|..+++..++...+...-       .+....-..+.-+
T Consensus       383 GlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLG  462 (963)
T 4ady_A          383 GVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIG  462 (963)
T ss_dssp             HHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHH
T ss_pred             hhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHH
Confidence            4567788888988888776521  122233334445556666666678887777665321       0112222233333


Q ss_pred             HHhCCC-hHHHHHHHHHHHhcCCCCCh--hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           96 LCKNGK-MDEASRLLDLMVQRDVRPNA--FTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        96 ~~~~~~-~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      .+-.|. -+++...+..++... .+..  ..-..++..+.-.|+-+....++..+.+.. ..+..-...+.-++...|+.
T Consensus       463 la~~GS~~eev~e~L~~~L~dd-~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~-~e~vrR~aalgLGll~~g~~  540 (963)
T 4ady_A          463 LAAMGSANIEVYEALKEVLYND-SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQ-HGNITRGLAVGLALINYGRQ  540 (963)
T ss_dssp             HHSTTCCCHHHHHHHHHHHHTC-CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTCG
T ss_pred             HHhcCCCCHHHHHHHHHHHhcC-CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccC-cHHHHHHHHHHHHhhhCCCh
Confidence            333443 346666676666542 1111  122244555667788888888888776532 22222233344455578888


Q ss_pred             HHHHHHHHHHHHCCCCCCHhH--HHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHH
Q 042039          173 EEALSLYREMVSKGIKPTVVT--YNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFR  250 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  250 (376)
                      +.+..+++.+... ..|....  -..+.-+|+..|+.....+++..+.... ..+..-...+..+....|+.+.+.++++
T Consensus       541 e~~~~li~~L~~~-~dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~v~rlv~  618 (963)
T 4ady_A          541 ELADDLITKMLAS-DESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTTVPRIVQ  618 (963)
T ss_dssp             GGGHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSSHHHHTT
T ss_pred             HHHHHHHHHHHhC-CCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHHHHHHHH
Confidence            8888888888764 2222221  1234456778889888888998887642 2233333334444555677777777777


Q ss_pred             HhcccCCCchHHHHHHHHHHHHhCCCh-HHHHHHHhcccc
Q 042039          251 TLGILKCELDIQAYNCLIDGLCKSGRL-EIALELFRSLPR  289 (376)
Q Consensus       251 ~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~  289 (376)
                      .+...+ .|....-..++.+....|.. .++...+..+..
T Consensus       619 ~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~L~~L~~  657 (963)
T 4ady_A          619 LLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDVLDPLTK  657 (963)
T ss_dssp             TGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHT
T ss_pred             HHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHHHHHHcc
Confidence            665544 44544444444444444443 677888887764

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.06  E-value=0.18  Score=34.05  Aligned_cols=66  Identities=15%  Similarity=0.141  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 042039          262 QAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVA  328 (376)
Q Consensus       262 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  328 (376)
                      ..+...+..+...|+-++-.+++..+... .+|++.....+..+|.+.|+..+|.+++.++-+.|++
T Consensus        92 e~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           92 EHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            34445556666677777777777664332 4566677777777777777777777777777666643

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=95.59  E-value=0.12  Score=36.47  Aligned_cols=139  Identities=10%  Similarity=0.088  Sum_probs=75.4

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCC-CCCC-------hhhHHHHHHHHhcCCChHHHHHHHHHHHhcC--C
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGEN-INPD-------VVTYNSLIHGLCHANDWNEAKRLFFEMMDQG--V   82 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~   82 (376)
                      +-+..++-.-+..+...|.++.|+-+.+.+.... ..|+       ..++..++.++...|++..|...|++.++..  +
T Consensus        17 ~~~~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l   96 (167)
T 3ffl_A           17 RGSHMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKAL   96 (167)
T ss_dssp             ----CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC
T ss_pred             CccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHH
Confidence            3344555666777888888888888777754431 1222       1255667788888888888888888875431  1


Q ss_pred             CCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           83 QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNIL  162 (376)
Q Consensus        83 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  162 (376)
                      .-+......+.   . ......         ......+...-..+..+|.+.+++++|+.+++.+...  ..++.+-..|
T Consensus        97 ~k~~s~~~~~~---~-~ss~p~---------s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k--~Rt~kvnm~L  161 (167)
T 3ffl_A           97 SKTSKVRPSTG---N-SASTPQ---------SQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSR--QRTPKINMLL  161 (167)
T ss_dssp             ---------------------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGG--GCCHHHHHHH
T ss_pred             hcCCCcccccc---c-cCCCcc---------cccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCch--hcCHHHHHHH
Confidence            10111110000   0 000000         0011234455566888888899999999988877554  2344444445


Q ss_pred             HHHH
Q 042039          163 INGY  166 (376)
Q Consensus       163 ~~~~  166 (376)
                      ++.|
T Consensus       162 akLy  165 (167)
T 3ffl_A          162 ANLY  165 (167)
T ss_dssp             HHHC
T ss_pred             HHHh
Confidence            5443

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=95.44  E-value=0.23  Score=44.91  Aligned_cols=127  Identities=14%  Similarity=0.104  Sum_probs=81.4

Q ss_pred             HHHHHHHHHhcCC-hhHHHHHHHHhhhCCCCCChhhH--HHHHHHHhcCC-ChHHHHHHHHHHHhc------CCCC-ch-
Q 042039           19 YNTIIDGLCKEGF-VDKAKALFLQMKGENINPDVVTY--NSLIHGLCHAN-DWNEAKRLFFEMMDQ------GVQP-SV-   86 (376)
Q Consensus        19 ~~~l~~~~~~~g~-~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~-~~~~a~~~~~~~~~~------~~~~-~~-   86 (376)
                      -..++..+...++ ++.|+.+|+++....  |...++  ..++..+...+ +--+|.+++.+.++.      ...+ +. 
T Consensus       251 ~~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~  328 (754)
T 4gns_B          251 MYSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDAD  328 (754)
T ss_dssp             HHHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccc
Confidence            3445555555666 588999999998764  333332  22333333333 223456666555431      1111 11 


Q ss_pred             ---------HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHH
Q 042039           87 ---------VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSME  148 (376)
Q Consensus        87 ---------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  148 (376)
                               .....-...+...|+++-|+.+-++..... +.+-.+|..|+.+|...|+++.|+-.+..+.
T Consensus       329 ~~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          329 SARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             cccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                     122233455677899999999999998863 4457899999999999999999999988874

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=95.35  E-value=0.13  Score=46.42  Aligned_cols=125  Identities=15%  Similarity=0.075  Sum_probs=81.7

Q ss_pred             HHHHHHHhcCCC-hHHHHHHHHHHHhcCCCCchHhHH--HHHHHHHhCC-ChHHHHHHHHHHHhc------CCCC-Ch--
Q 042039           55 NSLIHGLCHAND-WNEAKRLFFEMMDQGVQPSVVTFN--VIMDELCKNG-KMDEASRLLDLMVQR------DVRP-NA--  121 (376)
Q Consensus        55 ~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~-~~~~a~~~~~~~~~~------~~~~-~~--  121 (376)
                      ..++..+...++ .+.|..+|+++...  .|...++.  .++......+ +--+|.+++.+.++.      ..++ +.  
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~--~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKK--DPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhh--CCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            345555555666 57899999999886  33333322  2222222222 223455555554421      1111 11  


Q ss_pred             --------hhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHH
Q 042039          122 --------FTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  182 (376)
Q Consensus       122 --------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  182 (376)
                              .....-+..+...|+++-|+++-++..... |.+-.+|..|..+|...|+++.|+-.++.+
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence                    122333555677899999999999999885 667889999999999999999999998876

>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=95.25  E-value=0.15  Score=42.51  Aligned_cols=74  Identities=3%  Similarity=-0.085  Sum_probs=52.5

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHh-----cCCCCChhhHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQ-----RDVRPNAFTYSTL  127 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~l  127 (376)
                      +...++..+...|++++++..+..+.... +.+...+..++.++...|+..+|++.|+.+.+     .|+.|...+-...
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~  251 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALN  251 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            45556777777888888888887777653 33666788888888888888888888877654     4777776554433

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=95.12  E-value=1.5  Score=42.48  Aligned_cols=52  Identities=12%  Similarity=0.010  Sum_probs=32.7

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHH
Q 042039           21 TIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEM   77 (376)
Q Consensus        21 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~   77 (376)
                      .++..+...+.++-+.++.....     .++..-..++.++...|++++|.+.|++.
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~~-----~~~~~~yl~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWLN-----SDPIAVYLKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHSC-----CCHHHHHHHHHHHHHTTCHHHHHHHHHTC
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcc-----CCcHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            45555666676666665543332     23444456677788888888888888665

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.11  E-value=1.3  Score=37.53  Aligned_cols=260  Identities=11%  Similarity=0.126  Sum_probs=148.6

Q ss_pred             cCChhHHHHHHHHhhhC-----CCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHH----HHHhC
Q 042039           29 EGFVDKAKALFLQMKGE-----NINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMD----ELCKN   99 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~----~~~~~   99 (376)
                      .|+++.|++.+-.+.+.     +..........++..|...|+|+...+.+.-+.+..... ......+++    .....
T Consensus        29 ~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~ql-k~ai~~~V~~~~~~l~~~  107 (445)
T 4b4t_P           29 QNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQL-KLSIQYMIQKVMEYLKSS  107 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTS-HHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhh-HHHHHHHHHHHHHHHhcC
Confidence            36788888877665432     234456678889999999999999888877665542221 122223332    22223


Q ss_pred             CChHHH--HHHHHHHHh--cC-CCC---ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCC----hhhHHHHHHHH
Q 042039          100 GKMDEA--SRLLDLMVQ--RD-VRP---NAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-KHD----DVSYNILINGY  166 (376)
Q Consensus       100 ~~~~~a--~~~~~~~~~--~~-~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~  166 (376)
                      ...+..  ..+.+.+..  .| +-.   .......++..+...|++.+|..++..+...-. ..+    ...+...++.|
T Consensus       108 ~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~  187 (445)
T 4b4t_P          108 KSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELS  187 (445)
T ss_dssp             CTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            332221  111111111  11 111   122345688899999999999999999853211 111    23566778899


Q ss_pred             HccCcHHHHHHHHHHHHH----CCCCCC--HhHHHHHHHHHHhccchHHHHHHHHHHHhcC-CCCCcchH----HHHHHH
Q 042039          167 CKNKEVEEALSLYREMVS----KGIKPT--VVTYNTLFLGLFEIHQVEHALKLFEEMQRDD-VAADTSTY----NTFIDG  235 (376)
Q Consensus       167 ~~~~~~~~a~~~~~~~~~----~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~----~~l~~~  235 (376)
                      ...+++.+|..++.++..    ...+|+  ...+...+..+...+++..|.+.|.++.... ...+...+    ..++.+
T Consensus       188 l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~  267 (445)
T 4b4t_P          188 ILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYF  267 (445)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHH
Confidence            999999999999988753    222222  3445666777788899999988888775531 11122211    122222


Q ss_pred             HHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhC--CChHHHHHHHhcccc
Q 042039          236 LCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKS--GRLEIALELFRSLPR  289 (376)
Q Consensus       236 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~  289 (376)
                      ..-.+..+.-..++........-++...+..++.+|...  .+++.+.+.|.....
T Consensus       268 ~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~  323 (445)
T 4b4t_P          268 LVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLN  323 (445)
T ss_dssp             HHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTT
T ss_pred             HHhCCCCchHHHHHHHHhhcccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhc
Confidence            222222122222222222222234667788888888654  467888887776543

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=94.85  E-value=0.53  Score=31.77  Aligned_cols=66  Identities=15%  Similarity=0.116  Sum_probs=28.2

Q ss_pred             chHHHHHHHHHHHHhCCCh---HHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          259 LDIQAYNCLIDGLCKSGRL---EIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      |++.+-..++.++.+..+.   .+++.+++.+.+.+.......+..+..++.+.|++++|.+..+.+++
T Consensus        38 vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~  106 (134)
T 3o48_A           38 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  106 (134)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             CChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            3444444444444444332   23444444444332111233344444445555555555555554444

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=94.75  E-value=0.44  Score=30.18  Aligned_cols=46  Identities=13%  Similarity=0.209  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          314 KAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       314 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      +..+-+..+...++-|++.+....+++|.+.+++.-|.++++-.+.
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~   73 (109)
T 1v54_E           28 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKD   73 (109)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3444444444444445555555555555555555555555544443

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.54  E-value=0.39  Score=39.97  Aligned_cols=177  Identities=14%  Similarity=0.136  Sum_probs=84.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCC-CChhhHHHHHHHHhcC-CChHHHHHHHHHHHhcC----C---CCc
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENIN-PDVVTYNSLIHGLCHA-NDWNEAKRLFFEMMDQG----V---QPS   85 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~----~---~~~   85 (376)
                      +...+..|.-...+.|+.-...++.+.+-....+ ....+....+.-+.+. +.....-..+......|    .   ..|
T Consensus        32 ~~k~~~LL~~L~~~~g~~vsr~~L~~~lW~~~~~~~a~~~L~~~i~rLRk~L~~~~~~~~~i~~~~~~GY~l~~~~~~~D  111 (388)
T 2ff4_A           32 TPKQRAVLAMLVINRNRPVGVDALITALWEEWPPSGARASIHSYVSNLRKLLGGAGIDPRVVLAAAPPGYRLSIPDNTCD  111 (388)
T ss_dssp             SHHHHHHHHHHHHTTTSEEEHHHHHHHHHTTCCCTTHHHHHHHHHHHHHHHHGGGTSCHHHHEEECSSEEEECCCGGGBH
T ss_pred             ChHHHHHHHHHHhCCCCcccHHHHHHHhCCCCCChhHHHHHHHHHHHHHHhhcccCCCCceEEEEECCEEEEcCCCccch
Confidence            4555665555566668877777777777654322 1223333333222211 11000000110000111    1   123


Q ss_pred             hHhHHHHHHHH---HhCCChHHHHHHHHHHHhc--CCC-CCh----h--------------hHHHHHHHHHhcCcHHHHH
Q 042039           86 VVTFNVIMDEL---CKNGKMDEASRLLDLMVQR--DVR-PNA----F--------------TYSTLMDGFCLTGKINRAE  141 (376)
Q Consensus        86 ~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~--~~~-~~~----~--------------~~~~l~~~~~~~~~~~~a~  141 (376)
                      ...|..++...   ...|+.+.+...+.+++..  |.. ++.    .              +...++..+...|+++++.
T Consensus       112 ~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~~~~w~~~~r~~l~~~~~~a~~~~~~~~l~~g~~~~a~  191 (388)
T 2ff4_A          112 LGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVI  191 (388)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Confidence            44455554432   3458888999999888763  211 111    0              0112233344555666666


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH-----CCCCCCHh
Q 042039          142 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS-----KGIKPTVV  192 (376)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~  192 (376)
                      ..+..+.... |.+...+..++.++.+.|+..+|++.|+.+.+     .|+.|+..
T Consensus       192 ~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~  246 (388)
T 2ff4_A          192 AELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPT  246 (388)
T ss_dssp             HHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHH
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence            5555555443 44555566666666666666666666555433     25555543

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=93.99  E-value=2.2  Score=41.33  Aligned_cols=144  Identities=18%  Similarity=0.160  Sum_probs=86.6

Q ss_pred             HHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC-C------------------
Q 042039          197 LFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK-C------------------  257 (376)
Q Consensus       197 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~------------------  257 (376)
                      ++..+...+..+.+.++..-.     +.++.....++.++...|++++|..+|+++...- .                  
T Consensus       818 l~~~l~~~~~~~~~~~l~~~~-----~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~  892 (1139)
T 4fhn_B          818 LVEKLFLFKQYNACMQLIGWL-----NSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKY  892 (1139)
T ss_dssp             HHHHHHHHSCTTHHHHHHHHS-----CCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTT
T ss_pred             HHHHHHHhhhHHHHHHHhhhc-----cCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccccccccc
Confidence            444455556665555433221     2344445667778888899999998888762110 0                  


Q ss_pred             ---CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCH----HHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc
Q 042039          258 ---ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADV----VTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       258 ---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  330 (376)
                         ..-+.-|..++..+.+.+.++.+.++-+.+.+...+.+.    ..|..+...+...|++++|...+-.+.....  -
T Consensus       893 ~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~--r  970 (1139)
T 4fhn_B          893 HHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPL--K  970 (1139)
T ss_dssp             TSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSS--C
T ss_pred             cccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHH--H
Confidence               001233566777778888888888777766543222221    2567777888888888888887776655322  3


Q ss_pred             HHHHHHHHHHHhhcCCh
Q 042039          331 VIIFVTLIHGFVRINKP  347 (376)
Q Consensus       331 ~~~~~~l~~~~~~~g~~  347 (376)
                      ...+..|+...+..|..
T Consensus       971 ~~cLr~LV~~lce~~~~  987 (1139)
T 4fhn_B          971 KSCLLDFVNQLTKQGKI  987 (1139)
T ss_dssp             HHHHHHHHHHHHHHCCH
T ss_pred             HHHHHHHHHHHHhCCCh
Confidence            44556666655555444

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=93.85  E-value=0.96  Score=30.52  Aligned_cols=67  Identities=9%  Similarity=-0.029  Sum_probs=32.2

Q ss_pred             CCChhhHHHHHHHHHhcCc---HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          118 RPNAFTYSTLMDGFCLTGK---INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       118 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      .|+..+-..++.++.++.+   ...++.+++.+...+.......+..+.-++.+.|++++|.+..+.+++
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~  106 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  106 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            3444444444444444432   334455555554443112233444455555555555555555555555

>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=93.84  E-value=0.91  Score=30.58  Aligned_cols=59  Identities=17%  Similarity=0.260  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchHHHHHHH
Q 042039          314 KAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDASIVSMVV  373 (376)
Q Consensus       314 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~ll  373 (376)
                      +..+-+..+...++-|++.+....+++|.+.+++.-|.++|+-.+.+ ..+...+|..++
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~l  129 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVI  129 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHH
Confidence            34444444444455555555555555555555555555555555433 122233444443

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=93.80  E-value=1.2  Score=31.44  Aligned_cols=60  Identities=8%  Similarity=-0.047  Sum_probs=28.8

Q ss_pred             HHHHHHHHHccCcHHHHHHHHHHHHHCC-CCCC-------HhHHHHHHHHHHhccchHHHHHHHHHHH
Q 042039          159 YNILINGYCKNKEVEEALSLYREMVSKG-IKPT-------VVTYNTLFLGLFEIHQVEHALKLFEEMQ  218 (376)
Q Consensus       159 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~~~  218 (376)
                      +..-+..+...+.++.|+-+...+.... ..|+       ..++..+..++...+++.+|...|++.+
T Consensus        23 l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qAL   90 (167)
T 3ffl_A           23 VIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMAL   90 (167)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            3344455555566666655555544321 1111       1133444455555555555555555543

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=93.34  E-value=1.3  Score=30.36  Aligned_cols=68  Identities=12%  Similarity=0.156  Sum_probs=39.0

Q ss_pred             CCChhhHHHHHHHHhcCCC---hHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           48 NPDVVTYNSLIHGLCHAND---WNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        48 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .|+..+-..+..++++..+   ..+++.+++.+.+.+..........+.-++.+.|++++|.++.+.+++.
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~  106 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  106 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            4555555556666665553   3356666666665433223444455555666666666666666666664

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=92.30  E-value=5.8  Score=35.27  Aligned_cols=142  Identities=11%  Similarity=0.045  Sum_probs=71.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCc-hHhHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPS-VVTFNVIMDEL   96 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~   96 (376)
                      .|..... ..+.|++..+..+...+....+. .-..|..+...+ ......+...++++-.   -.|- ...-...+..+
T Consensus         9 ~~~~a~~-a~~~~~~~~~~~l~~~l~~~pL~-~yl~y~~l~~~l-~~~~~~ev~~Fl~~~~---~~p~~~~Lr~~~l~~l   82 (618)
T 1qsa_A            9 RYAQIKQ-AWDNRQMDVVEQMMPGLKDYPLY-PYLEYRQITDDL-MNQPAVTVTNFVRANP---TLPPARTLQSRFVNEL   82 (618)
T ss_dssp             HHHHHHH-HHHTTCHHHHHHHSGGGTTSTTH-HHHHHHHHHHTG-GGCCHHHHHHHHHHCT---TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-HHHCCCHHHHHHHHHhhcCCCcH-HHHHHHHHHhCc-ccCCHHHHHHHHHHCC---CChhHHHHHHHHHHHH
Confidence            3444444 44668888777776655432111 111222222211 1223444444443321   1122 22233445566


Q ss_pred             HhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc
Q 042039           97 CKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  171 (376)
Q Consensus        97 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  171 (376)
                      .+.+++.....++..     .+.+...-.....+....|+..+|......+-..+ ...+.....++..+.+.|.
T Consensus        83 ~~~~~w~~~l~~~~~-----~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~-~~~p~~c~~l~~~~~~~g~  151 (618)
T 1qsa_A           83 ARREDWRGLLAFSPE-----KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG-KSQPNACDKLFSVWRASGK  151 (618)
T ss_dssp             HHTTCHHHHHHHCCS-----CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS-SCCCTHHHHHHHHHHHTTC
T ss_pred             HhCCCHHHHHHhccC-----CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHCCC
Confidence            667777766554432     13344444556667777788777777777766555 3445566666666665443

>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=92.17  E-value=1.1  Score=28.38  Aligned_cols=43  Identities=9%  Similarity=0.126  Sum_probs=18.2

Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHH
Q 042039          105 ASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSM  147 (376)
Q Consensus       105 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  147 (376)
                      ..+-++.+...+..|++.+....+++|.+.+++..|.++|+.+
T Consensus        29 ~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~i   71 (109)
T 1v54_E           29 LRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVV   71 (109)
T ss_dssp             HHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            3333334433444444444444444444444444444444443

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=92.14  E-value=2  Score=29.47  Aligned_cols=68  Identities=9%  Similarity=-0.025  Sum_probs=38.1

Q ss_pred             CCChhhHHHHHHHHHhcCc---HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          118 RPNAFTYSTLMDGFCLTGK---INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       118 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      .|+..+-..++.++.++..   ..+++.+++.+...+..........+.-++.+.|++++|.+..+.+++.
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~  106 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  106 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            3455555555555555543   3355556666555432223344555666666677777777766666663

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.70  E-value=2.3  Score=35.88  Aligned_cols=98  Identities=12%  Similarity=0.019  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHhcCCC--CChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCChhhH----H
Q 042039           88 TFNVIMDELCKNGKMDEASRLLDLMVQRDVR--PNAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-KHDDVSY----N  160 (376)
Q Consensus        88 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~----~  160 (376)
                      +...++..|.+.|++++|.+.+.++......  .-...+...++.+...+++..+...+.++...-. .++....    .
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            5566777777788888888888777664222  2245666677777777788777777777643210 1122111    1


Q ss_pred             HHHHHHHccCcHHHHHHHHHHHHHC
Q 042039          161 ILINGYCKNKEVEEALSLYREMVSK  185 (376)
Q Consensus       161 ~l~~~~~~~~~~~~a~~~~~~~~~~  185 (376)
                      .-+..+...+++..|.+.|-+....
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~~~t  237 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDSLAT  237 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHHhcc
Confidence            1223344567777777777665543

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=91.44  E-value=5.4  Score=33.09  Aligned_cols=166  Identities=13%  Similarity=0.013  Sum_probs=80.0

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhc-CCCCC---hhhHHHHHHHHHhc-CcHHHHHHHHHHHHhcCCCCChhhH-
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQR-DVRPN---AFTYSTLMDGFCLT-GKINRAEELFGSMESMGCKHDDVSY-  159 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~---~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~-  159 (376)
                      ......+...|.+.|+.++..+++...... +.-+.   ......++..+... +..+.-.++..+..+.. ...-..| 
T Consensus        19 e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a-~~~~r~fl   97 (394)
T 3txn_A           19 EQGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWA-KQEKRTFL   97 (394)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHH-HHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHH-HHHHHHHH
Confidence            345666777888888888877777766432 00111   22344555555543 22333333333332211 0111222 


Q ss_pred             -----HHHHHHHHccCcHHHHHHHHHHHHHCCCCCC-----HhHHHHHHHHHHhccchHHHHHHHHHHHhc--CCCCCcc
Q 042039          160 -----NILINGYCKNKEVEEALSLYREMVSKGIKPT-----VVTYNTLFLGLFEIHQVEHALKLFEEMQRD--DVAADTS  227 (376)
Q Consensus       160 -----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~  227 (376)
                           ..++..|...|++.+|.+++.++.+.--..|     ...+..-++.|...+++.++...+......  .+.+++.
T Consensus        98 r~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~  177 (394)
T 3txn_A           98 RQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPK  177 (394)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHH
Confidence                 2456666677777777666666655311111     233444445566666666666666555433  1112222


Q ss_pred             hH----HHHHHHHH-hCCCHHHHHHHHHHh
Q 042039          228 TY----NTFIDGLC-KNGYIVEAVELFRTL  252 (376)
Q Consensus       228 ~~----~~l~~~~~-~~~~~~~a~~~~~~~  252 (376)
                      ..    ..-+..+. ..+++..|...|-+.
T Consensus       178 i~a~i~~~~Gi~~l~~~rdyk~A~~~F~ea  207 (394)
T 3txn_A          178 VQGALDLQSGILHAADERDFKTAFSYFYEA  207 (394)
T ss_dssp             HHHHHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHhccCHHHHHHHHHHH
Confidence            11    11122344 556666665555443

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.17  E-value=2.9  Score=35.28  Aligned_cols=98  Identities=7%  Similarity=-0.096  Sum_probs=71.7

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhc--CCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc---CCCCChh--hH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQ--GVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR---DVRPNAF--TY  124 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~--~~  124 (376)
                      .++..++..|.+.|+++.|.+.|.++...  +...-...+...++.+...+++..+...+.++...   +..|+..  ..
T Consensus       132 ~~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk  211 (429)
T 4b4t_R          132 QAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYK  211 (429)
T ss_dssp             SCCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            36678899999999999999999999875  33444667888899999999999999999988642   2222221  11


Q ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHh
Q 042039          125 STLMDGFCLTGKINRAEELFGSMES  149 (376)
Q Consensus       125 ~~l~~~~~~~~~~~~a~~~~~~~~~  149 (376)
                      ..-+..+...+++..|...|-+...
T Consensus       212 ~~~gl~~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          212 TYYGIHCLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHHGGGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhChHHHHHHHHHHHhc
Confidence            1223344567889999888877654

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=90.52  E-value=5.6  Score=31.70  Aligned_cols=27  Identities=19%  Similarity=-0.043  Sum_probs=20.0

Q ss_pred             chHHHHHHHHHHHHhCCChHHHHHHHh
Q 042039          259 LDIQAYNCLIDGLCKSGRLEIALELFR  285 (376)
Q Consensus       259 ~~~~~~~~l~~~~~~~~~~~~a~~~~~  285 (376)
                      .++.....++..|.+.|++.+|...|-
T Consensus       132 Gdp~LH~~~a~~~~~e~~~~~A~~H~i  158 (312)
T 2wpv_A          132 GDPYLHNTIGSKLLEGDFVYEAERYFM  158 (312)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhhcCCHHHHHHHHH
Confidence            366777777777888888877777664

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=90.44  E-value=4.4  Score=31.32  Aligned_cols=55  Identities=27%  Similarity=0.291  Sum_probs=33.9

Q ss_pred             HHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccC
Q 042039          201 LFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILK  256 (376)
Q Consensus       201 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  256 (376)
                      ..+.|+++.+++....-++.. |.|...-..+++.++-.|+++.|..-++...+..
T Consensus         7 ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~   61 (273)
T 1zbp_A            7 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLF   61 (273)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            445566666666666665554 4555666666666666666666666666665543

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=90.17  E-value=4.3  Score=29.77  Aligned_cols=55  Identities=16%  Similarity=0.097  Sum_probs=33.0

Q ss_pred             CChHHHHHHHhcccccCCCCC-HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCC
Q 042039          275 GRLEIALELFRSLPRRVLVAD-VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAP  329 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  329 (376)
                      +...++..+|..|...++-.. ...|...+..+...|++.+|.++|+.-++.+-.|
T Consensus        93 ~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A~P  148 (202)
T 3esl_A           93 NNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRP  148 (202)
T ss_dssp             TCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBS
T ss_pred             cccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcc
Confidence            335566666666665544322 3445556666666677777777777666665555

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=87.75  E-value=9.6  Score=30.69  Aligned_cols=83  Identities=7%  Similarity=-0.048  Sum_probs=49.4

Q ss_pred             CchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHH
Q 042039          258 ELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTL  337 (376)
Q Consensus       258 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  337 (376)
                      .-++.....++..|.+.+++.+|...|-  .  +..+++..+..++.-+...+...++              +...-.. 
T Consensus       133 ~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i--l--g~~~s~~~~a~mL~ew~~~~~~~e~--------------dlfiaRa-  193 (336)
T 3lpz_A          133 AGDPELHHVVGTLYVEEGEFEAAEKHLV--L--GTKESPEVLARMEYEWYKQDESHTA--------------PLYCARA-  193 (336)
T ss_dssp             TCCHHHHHHHHHHHHHTTCHHHHHHHHT--T--SCTTHHHHHHHHHHHHHHTSCGGGH--------------HHHHHHH-
T ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHH--h--cCCchHHHHHHHHHHHHHhcCCccH--------------HHHHHHH-
Confidence            3477888888999999999999988873  2  2233345665555544444332222              2222222 


Q ss_pred             HHHHhhcCChhhHHHHHHHHHh
Q 042039          338 IHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       338 ~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      +-.|...++...|..+++...+
T Consensus       194 VL~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          194 VLPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHH
Confidence            2335566777777777666553

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=87.52  E-value=9.5  Score=30.40  Aligned_cols=112  Identities=12%  Similarity=0.096  Sum_probs=57.0

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHH----HHHHHhcCCCCChhhHHHHHH
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRL----LDLMVQRDVRPNAFTYSTLMD  129 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~----~~~~~~~~~~~~~~~~~~l~~  129 (376)
                      |.++..=|.+.+++++|++++..-..               .+.+.|+...|.++    ++-+.+.+.+++......++.
T Consensus        36 ~Rtl~~Ry~~~~~~~eAidlL~~ga~---------------~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~  100 (312)
T 2wpv_A           36 LRTIANRYVRSKSYEHAIELISQGAL---------------SFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVR  100 (312)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHH---------------HHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            33444445566667776666544321               23344554444433    333334455666555555555


Q ss_pred             HHHhcCcHH-HHHHHHHHH----HhcC--CCCChhhHHHHHHHHHccCcHHHHHHHHH
Q 042039          130 GFCLTGKIN-RAEELFGSM----ESMG--CKHDDVSYNILINGYCKNKEVEEALSLYR  180 (376)
Q Consensus       130 ~~~~~~~~~-~a~~~~~~~----~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  180 (376)
                      .+.....-+ .-.++++++    .+.+  ..-++.....++..|.+.+++.+|...|-
T Consensus       101 l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i  158 (312)
T 2wpv_A          101 LIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFM  158 (312)
T ss_dssp             HHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHH
Confidence            554432111 011222222    1221  12366777888888888888888777664

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=87.49  E-value=8.5  Score=29.78  Aligned_cols=56  Identities=20%  Similarity=0.312  Sum_probs=44.6

Q ss_pred             HHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           24 DGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        24 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      ..+.+.|++++|++....-++.. |.|...-..++..++-.|+|+.|.+-++...+.
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l   60 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL   60 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            45667888888888888777765 677888888888888888888888888887775

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=87.00  E-value=12  Score=31.04  Aligned_cols=168  Identities=11%  Similarity=-0.014  Sum_probs=106.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCC--C--CCChhhHHHHHHHHhcCC-ChHHHHHHHHHHHhcCCCCchHhH-
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGEN--I--NPDVVTYNSLIHGLCHAN-DWNEAKRLFFEMMDQGVQPSVVTF-   89 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--~--~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~-   89 (376)
                      ..+...|...|.+.|+.++..+++......-  +  .........++..+.... ..+.-.++..+.++..-. ...+| 
T Consensus        19 e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~-~~r~fl   97 (394)
T 3txn_A           19 EQGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQ-EKRTFL   97 (394)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHH-TTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHH-HHHHHH
Confidence            3567788899999999999999998765331  0  112345567777776643 333334444444332111 11222 


Q ss_pred             -----HHHHHHHHhCCChHHHHHHHHHHHhcCCCCC-----hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcC--CCCChh
Q 042039           90 -----NVIMDELCKNGKMDEASRLLDLMVQRDVRPN-----AFTYSTLMDGFCLTGKINRAEELFGSMESMG--CKHDDV  157 (376)
Q Consensus        90 -----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~  157 (376)
                           ..++..|...|++.+|..++.++.+.-...|     ..++..-+..|...+++.++...+.......  +.+++.
T Consensus        98 r~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~  177 (394)
T 3txn_A           98 RQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPK  177 (394)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHH
Confidence                 2578889999999999999988876311112     3345566777888899999999988775432  223332


Q ss_pred             hH----HHHHHHHH-ccCcHHHHHHHHHHHHH
Q 042039          158 SY----NILINGYC-KNKEVEEALSLYREMVS  184 (376)
Q Consensus       158 ~~----~~l~~~~~-~~~~~~~a~~~~~~~~~  184 (376)
                      ..    ..-+..+. ..++|..|...|-+..+
T Consensus       178 i~a~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~  209 (394)
T 3txn_A          178 VQGALDLQSGILHAADERDFKTAFSYFYEAFE  209 (394)
T ss_dssp             HHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHhccCHHHHHHHHHHHHh
Confidence            22    22234456 78899999888877654

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=86.79  E-value=7.6  Score=28.49  Aligned_cols=53  Identities=17%  Similarity=0.110  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCC
Q 042039          137 INRAEELFGSMESMGCKH-DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP  189 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  189 (376)
                      ...+..+|..|...++.. -+..|...+..+...|++.+|.++|+..++.+-.|
T Consensus        95 ~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A~P  148 (202)
T 3esl_A           95 FHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRP  148 (202)
T ss_dssp             HHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBS
T ss_pred             cCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcc
Confidence            445566666665554322 23344555555556666666666666666554444

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=86.39  E-value=17  Score=32.29  Aligned_cols=114  Identities=11%  Similarity=0.041  Sum_probs=64.8

Q ss_pred             cHHHHHHHHHHHHhcCCCCChhh----HHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHH
Q 042039          136 KINRAEELFGSMESMGCKHDDVS----YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       136 ~~~~a~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      +.+.|...+....... ..+...    ...++......+...++...+......  ..+.......+....+.++++.|.
T Consensus       229 d~~~A~~~~~~~~~~~-~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~e~~~r~Alr~~d~~~a~  305 (618)
T 1qsa_A          229 DAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMR--SQSTSLIERRVRMALGTGDRRGLN  305 (618)
T ss_dssp             CHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHT--CCCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CHHHHHHHHHhhhhcc-CCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhcccc--CCChHHHHHHHHHHHHCCCHHHHH
Confidence            6677777777765433 222222    222233333344244555555554443  233333444444555678888888


Q ss_pred             HHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhc
Q 042039          212 KLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLG  253 (376)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  253 (376)
                      ..|..+.... .........+.+++...|+.++|..+|+.+.
T Consensus       306 ~~~~~l~~~~-~~~~r~~YW~~ra~~~~g~~~~a~~~~~~~a  346 (618)
T 1qsa_A          306 TWLARLPMEA-KEKDEWRYWQADLLLERGREAEAKEILHQLM  346 (618)
T ss_dssp             HHHHHSCTTG-GGSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHccccc-cccHhHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            8887775432 2234456667777778888888888887764

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=84.78  E-value=7.2  Score=26.40  Aligned_cols=61  Identities=13%  Similarity=0.082  Sum_probs=36.6

Q ss_pred             hHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHH
Q 042039          277 LEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLI  338 (376)
Q Consensus       277 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  338 (376)
                      .=+..+-++.+......|++......+++|.+.+++..|.++|+-+.... .+...+|..++
T Consensus        69 ~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~l  129 (152)
T 2y69_E           69 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI  129 (152)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHH
Confidence            33445555555555566777777777777777777777777777666442 22334455444

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=84.32  E-value=15  Score=29.63  Aligned_cols=165  Identities=12%  Similarity=0.097  Sum_probs=84.7

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHH----HHHHhcCCCCChhhHHHHH
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLL----DLMVQRDVRPNAFTYSTLM  128 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~----~~~~~~~~~~~~~~~~~l~  128 (376)
                      .|.++..=|.+.+++++|++++..-.               ..+.+.|+...+.++.    +-+.+.+++++......++
T Consensus        37 ~~RTi~~Ry~~~k~y~eAidLL~~GA---------------~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~  101 (336)
T 3lpz_A           37 ETRLVAARYSKQGNWAAAVDILASVS---------------QTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLL  101 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH---------------HHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHHH---------------HHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            34445555667777777777664432               1233444444443333    3333455566665555555


Q ss_pred             HHHHhcCc--------HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHH
Q 042039          129 DGFCLTGK--------INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLG  200 (376)
Q Consensus       129 ~~~~~~~~--------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  200 (376)
                      ..+.....        .++|+.+=.+. .....-++.....++..|.+.+++.+|...|-  .  |..++...+..++..
T Consensus       102 ~L~~~~~~~~p~r~~fi~~ai~WS~~~-g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i--l--g~~~s~~~~a~mL~e  176 (336)
T 3lpz_A          102 GCLRLFQPGEPVRKRFVKEMIDWSKKF-GDYPAGDPELHHVVGTLYVEEGEFEAAEKHLV--L--GTKESPEVLARMEYE  176 (336)
T ss_dssp             HHHTTSCTTCHHHHHHHHHHHHHHHHH-SSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHT--T--SCTTHHHHHHHHHHH
T ss_pred             HHHHhCCCCCcHHHHHHHHHHHHHhhc-CCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH--h--cCCchHHHHHHHHHH
Confidence            55554432        11222222221 11123466777888889999898888887773  1  333444666666555


Q ss_pred             HHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          201 LFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       201 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      +...+...++--+               ....+--|.-.++...|..+++..
T Consensus       177 w~~~~~~~e~dlf---------------iaRaVL~yL~l~n~~~A~~~~~~f  213 (336)
T 3lpz_A          177 WYKQDESHTAPLY---------------CARAVLPYLLVANVRAANTAYRIF  213 (336)
T ss_dssp             HHHTSCGGGHHHH---------------HHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHhcCCccHHHH---------------HHHHHHHHHHhCCHHHHHHHHHHH
Confidence            5444332221111               122223355566777776655443

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=83.93  E-value=6.2  Score=24.98  Aligned_cols=50  Identities=14%  Similarity=0.114  Sum_probs=20.9

Q ss_pred             HHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhc
Q 042039           60 GLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .+.++|++++|..+.+..    ..||...|..+..  .+.|..+++..-+..+...
T Consensus        48 SLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce--~rlGl~s~le~rL~~la~s   97 (115)
T 2uwj_G           48 SLANQGRYQEALAFAHGN----PWPALEPWFALCE--WHLGLGAALDRRLAGLGGS   97 (115)
T ss_dssp             HHHHTTCHHHHHGGGTTC----CCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHTC
T ss_pred             HHHcchhHHHHHHhcCCC----CCchHHHHHHHHH--HhcccHHHHHHHHHHHHhC
Confidence            344445555554443322    1344444433322  3444444444444444433

>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=83.46  E-value=6.5  Score=24.92  Aligned_cols=15  Identities=20%  Similarity=0.184  Sum_probs=7.0

Q ss_pred             HHhcCCChHHHHHHH
Q 042039           60 GLCHANDWNEAKRLF   74 (376)
Q Consensus        60 ~~~~~~~~~~a~~~~   74 (376)
                      .+.++|++++|..+.
T Consensus        49 SLmNrG~Yq~Al~l~   63 (116)
T 2p58_C           49 SLMNRGDYASALQQG   63 (116)
T ss_dssp             HHHHTTCHHHHHHHH
T ss_pred             HHHcchhHHHHHHhc
Confidence            344445555554443

>4a1g_A Mitotic checkpoint serine/threonine-protein kinas; cell cycle, transferase, spindle assembly checkpoint, mitosi repeat, KNL1, KMN network; 2.60A {Homo sapiens} PDB: 2lah_A

Probab=83.19  E-value=9.4  Score=26.54  Aligned_cols=54  Identities=7%  Similarity=0.160  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHcCCCC-cHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCchH
Q 042039          314 KAHDLFLDMEENAVAP-NVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDAS  367 (376)
Q Consensus       314 ~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~  367 (376)
                      ++.++|..|..+|+-. -...|......+...|++++|.++|+.-++.+-.|-..
T Consensus        83 dp~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~~A~P~~r  137 (152)
T 4a1g_A           83 DLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASAVLQRGIQNQAEPREF  137 (152)
T ss_dssp             CHHHHHHHHHTTTTTTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHHH
T ss_pred             CHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHHH
Confidence            3666666666655433 24455555566666666666666666666666565443

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.26  E-value=24  Score=30.48  Aligned_cols=63  Identities=14%  Similarity=0.153  Sum_probs=30.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCC-CCC---hhhHHHHHHHHhcCCChHHHHHHHHHHHh
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENI-NPD---VVTYNSLIHGLCHANDWNEAKRLFFEMMD   79 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   79 (376)
                      ..+|.+++.|...+.+++|..+..+..--.. .++   ..-+..++..+.-.+++.+|.+.+..+.+
T Consensus       232 ~l~nllLRnYL~~~~y~qA~~lvsk~~fP~~~~sn~q~~rY~YY~GRI~a~q~~Y~eA~~~L~~A~r  298 (523)
T 4b4t_S          232 MLINLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEARYFFYLSKINAIQLDYSTANEYIIAAIR  298 (523)
T ss_dssp             HHHHHHHHHHHHSSCSTTHHHHHHHHCSCTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHccCcHHHHHHHHhcCcCCcccCCHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3455555666666666666666555531100 011   11122334455555556666555555544

>2wvi_A Mitotic checkpoint serine/threonine-protein kinase BUB1 beta; tumor suppressor, TPR, apoptosis, cell division, cell cycle, kinetochore, transferase; 1.80A {Homo sapiens} PDB: 3si5_A

Probab=80.46  E-value=13  Score=26.28  Aligned_cols=51  Identities=14%  Similarity=0.145  Sum_probs=24.2

Q ss_pred             HHHHHhcccccCCCC-CHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc
Q 042039          280 ALELFRSLPRRVLVA-DVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN  330 (376)
Q Consensus       280 a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  330 (376)
                      +..+|..|...++-. -+..|...+..+-..|++.+|.++|+.-++.+-.|.
T Consensus        79 p~~if~~L~~~~IG~~~AlfY~~wA~~lE~~~~~~~A~~Iy~~Gi~~~A~P~  130 (164)
T 2wvi_A           79 PLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPL  130 (164)
T ss_dssp             HHHHHHHHHHTTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSH
T ss_pred             HHHHHHHHHHCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcH
Confidence            334444444433322 233344445555555555555555555555544443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	376
d1w3ba_	388	a.118.8.1 (A:) O-GlcNAc transferase p110 subunit,	3e-08
d1w3ba_	388	a.118.8.1 (A:) O-GlcNAc transferase p110 subunit,	3e-08

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]} Length = 388

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]

 Score = 52.8 bits (125), Expect = 3e-08
 Identities = 39/207 (18%), Positives = 79/207 (38%), Gaps = 8/207 (3%)

Query: 12  CKPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVV-TYNSLIHGLCHANDWNEA 70
            +PN     + + G       +   A+    K   ++P+ +  Y +L + L  A  ++ A
Sbjct: 164 TQPNFAVAWSNL-GCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRA 222

Query: 71  KRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDG 130
              +   +      +VV  N +     + G +D A       ++         Y  L + 
Sbjct: 223 VAAYLRALSLSPNHAVVHGN-LACVYYEQGLIDLAIDTYRRAIELQPH-FPDAYCNLANA 280

Query: 131 FCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT 190
               G +  AE+ + +     C     S N L N   +   +EEA+ LYR+ +   + P 
Sbjct: 281 LKEKGSVAEAEDCYNTA-LRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALE--VFPE 337

Query: 191 -VVTYNTLFLGLFEIHQVEHALKLFEE 216
               ++ L   L +  +++ AL  ++E
Sbjct: 338 FAAAHSNLASVLQQQGKLQEALMHYKE 364

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]} Length = 388

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]

 Score = 52.8 bits (125), Expect = 3e-08
 Identities = 47/246 (19%), Positives = 84/246 (34%), Gaps = 7/246 (2%)

Query: 41  QMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNG 100
            +     NPD+    S +  L  A    E  +  +    +      V ++ +       G
Sbjct: 124 YVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQG 183

Query: 101 KMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYN 160
           ++  A    +  V  D       Y  L +        +RA   +    S+   H  V + 
Sbjct: 184 EIWLAIHHFEKAVTLDPN-FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVV-HG 241

Query: 161 ILINGYCKNKEVEEALSLYREMVSKGIKPTVV-TYNTLFLGLFEIHQVEHALKLFEEMQR 219
            L   Y +   ++ A+  YR  +   ++P     Y  L   L E   V  A   +    R
Sbjct: 242 NLACVYYEQGLIDLAIDTYRRAIE--LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALR 299

Query: 220 DDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEI 279
                   + N   +   + G I EAV L+R   +        A++ L   L + G+L+ 
Sbjct: 300 LC-PTHADSLNNLANIKREQGNIEEAVRLYRKA-LEVFPEFAAAHSNLASVLQQQGKLQE 357

Query: 280 ALELFR 285
           AL  ++
Sbjct: 358 ALMHYK 363

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	376
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.96
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.95
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.82
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.82
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.62
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.58
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.57
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.57
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.55
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.51
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.5
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.47
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.47
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.45
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	99.24
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	99.17
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	99.14
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	99.12
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	99.09
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	99.08
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	99.08
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	99.06
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	99.03
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	99.0
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.99
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.94
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.88
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.84
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.82
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.82
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.75
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.73
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.72
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.67
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.64
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.64
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.57
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.55
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.55
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.52
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.51
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.5
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.46
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.35
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	98.31
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	98.26
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.25
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	98.25
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	98.2
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.01
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.96
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.89
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.81
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.71
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	97.6
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	97.49
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	96.34
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	96.19
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.5
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	95.36
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	95.14
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.93
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	94.91
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	89.23

>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=99.96  E-value=2.2e-25  Score=186.28  Aligned_cols=334  Identities=13%  Similarity=0.059  Sum_probs=276.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  101 (376)
                      +...+.+.|++++|++.++++.+.. |.++.++..++.++...|++++|+..|+++++..+. +..++..++.++...|+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~l~~~~~~~g~   82 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPL-LAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHhhhhcc
Confidence            4567889999999999999998775 667889999999999999999999999999987543 67889999999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCChhhHH----------------------------------HHHHHHHhcCcHHHHHHHHHHH
Q 042039          102 MDEASRLLDLMVQRDVRPNAFTYS----------------------------------TLMDGFCLTGKINRAEELFGSM  147 (376)
Q Consensus       102 ~~~a~~~~~~~~~~~~~~~~~~~~----------------------------------~l~~~~~~~~~~~~a~~~~~~~  147 (376)
                      +++|...+....+.... +.....                                  .........+....+...+...
T Consensus        83 ~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (388)
T d1w3ba_          83 LQEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             ccccccccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHh
Confidence            99999999998875422 222222                                  2222333444555566666665


Q ss_pred             HhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcc
Q 042039          148 ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTS  227 (376)
Q Consensus       148 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  227 (376)
                      .... +.....+..++..+...|++++|...+++.++.. +.+...+..+...+...|++++|...+....... +....
T Consensus       162 ~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~  238 (388)
T d1w3ba_         162 IETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAV  238 (388)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHH
T ss_pred             hccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHH
Confidence            5554 5567788889999999999999999999998863 3467788999999999999999999999998875 55677


Q ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHH
Q 042039          228 TYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLC  307 (376)
Q Consensus       228 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  307 (376)
                      .+..++..+.+.|++++|+..++++....+ .++.++..++.++...|++++|...++.+... .+.+...+..++..+.
T Consensus       239 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~  316 (388)
T d1w3ba_         239 VHGNLACVYYEQGLIDLAIDTYRRAIELQP-HFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKR  316 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHH
Confidence            888899999999999999999999987763 36888999999999999999999999998776 5678889999999999


Q ss_pred             ccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCCCCCch
Q 042039          308 NDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKKVMPDA  366 (376)
Q Consensus       308 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  366 (376)
                      ..|++++|+..|+++++..+ .+..++..+..+|.+.|++++|.+.|++..+.  .|+.
T Consensus       317 ~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~  372 (388)
T d1w3ba_         317 EQGNIEEAVRLYRKALEVFP-EFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTF  372 (388)
T ss_dssp             TTTCHHHHHHHHHHHTTSCT-TCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTC
T ss_pred             HCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCC
Confidence            99999999999999988642 25778889999999999999999999999864  5554

>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=99.95  E-value=5.4e-24  Score=177.77  Aligned_cols=324  Identities=15%  Similarity=0.089  Sum_probs=269.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHH--
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNV--   91 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--   91 (376)
                      -++.++..+...+.+.|++++|+..|+++.+.+ |.+..++..++.++...|++++|++.+......... +......  
T Consensus        31 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~  108 (388)
T d1w3ba_          31 DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPD-FIDGYINLA  108 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccccccccccccccccccc-ccccccccc
Confidence            357789999999999999999999999998876 667899999999999999999999999998876433 2222222  


Q ss_pred             --------------------------------HHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHH
Q 042039           92 --------------------------------IMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINR  139 (376)
Q Consensus        92 --------------------------------l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  139 (376)
                                                      ........+....+...+....... +.+...+..++..+...|++++
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  187 (388)
T d1w3ba_         109 AALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWL  187 (388)
T ss_dssp             HHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccC-cchhHHHHhhcccccccCcHHH
Confidence                                            2222333344555555555555543 3356778888999999999999


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          140 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       140 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      |...+++..... |.+..++..++.++...|++++|+..+++..... +.+...+..+...+.+.|++++|...++++.+
T Consensus       188 A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  265 (388)
T d1w3ba_         188 AIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIE  265 (388)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999998875 6677889999999999999999999999998863 44677888899999999999999999999988


Q ss_pred             cCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHH
Q 042039          220 DDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTY  299 (376)
Q Consensus       220 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  299 (376)
                      .. +.+..++..++.++...|++++|...++.+.... +.+...+..++..+...|++++|+..++++.+. .|.+..++
T Consensus       266 ~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-~p~~~~~~  342 (388)
T d1w3ba_         266 LQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEV-FPEFAAAH  342 (388)
T ss_dssp             TC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS-CTTCHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHH
Confidence            75 5567889999999999999999999999987765 447888999999999999999999999998876 45578889


Q ss_pred             HHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCC
Q 042039          300 NIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINK  346 (376)
Q Consensus       300 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  346 (376)
                      ..++.++...|++++|+..|+++++..+. +...|..+..+|.+.||
T Consensus       343 ~~la~~~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         343 SNLASVLQQQGKLQEALMHYKEAIRISPT-FADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999985422 57789999999988875

>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=99.82  E-value=1.9e-17  Score=134.24  Aligned_cols=229  Identities=13%  Similarity=0.017  Sum_probs=149.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      +......+.+.|++++|+..|+++.+.+ |.+..+|..++.++...|++++|...|+++++..+. +...+..++.++..
T Consensus        22 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~   99 (323)
T d1fcha_          22 PFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPD-NQTALMALAVSFTN   99 (323)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccc-cccccccccccccc
Confidence            4456777889999999999999999886 667889999999999999999999999999887544 67788889999999


Q ss_pred             CCChHHHHHHHHHHHhcCCCCChhh-H---------------HHHHHHHHhcCcHHHHHHHHHHHHhcCC-CCChhhHHH
Q 042039           99 NGKMDEASRLLDLMVQRDVRPNAFT-Y---------------STLMDGFCLTGKINRAEELFGSMESMGC-KHDDVSYNI  161 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~~~~~~~~~-~---------------~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~  161 (376)
                      .|++++|.+.++++....  |+... .               ...+..+...+.+.+|...+.++..... ..+..++..
T Consensus       100 ~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~  177 (323)
T d1fcha_         100 ESLQRQACEILRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCG  177 (323)
T ss_dssp             TTCHHHHHHHHHHHHHTS--TTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHH
T ss_pred             cccccccccchhhHHHhc--cchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchh
Confidence            999999999999988753  22111 0               0111122233445555555555544321 123344555


Q ss_pred             HHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCC
Q 042039          162 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGY  241 (376)
Q Consensus       162 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  241 (376)
                      ++.++...|++++|+..+++..... +.+...|..+..++...|++++|.+.++++++.. +.+..++..++.+|.+.|+
T Consensus       178 l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~  255 (323)
T d1fcha_         178 LGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGA  255 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHh-hccHHHHHHHHHHHHHCCC
Confidence            5555666666666666666655532 2234555555555666666666666665555543 3344455555555556666


Q ss_pred             HHHHHHHHHHhc
Q 042039          242 IVEAVELFRTLG  253 (376)
Q Consensus       242 ~~~a~~~~~~~~  253 (376)
                      +++|+..|+++.
T Consensus       256 ~~~A~~~~~~al  267 (323)
T d1fcha_         256 HREAVEHFLEAL  267 (323)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666665555554

>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=99.82  E-value=2.2e-17  Score=133.82  Aligned_cols=276  Identities=14%  Similarity=0.015  Sum_probs=179.8

Q ss_pred             hhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHH
Q 042039           52 VTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGF  131 (376)
Q Consensus        52 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (376)
                      ......+..+.+.|++++|+..|+++++..+. +..+|..++.++...|++++|...+.+.++.. +-+...+..++.++
T Consensus        20 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~   97 (323)
T d1fcha_          20 PQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPK-HMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSF   97 (323)
T ss_dssp             SSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccc
Confidence            33445666777778888888888877776433 56677777777777788888887777777653 33566677777777


Q ss_pred             HhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHH
Q 042039          132 CLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL  211 (376)
Q Consensus       132 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  211 (376)
                      ...|++++|.+.++.+.... +..............                    ..+.......+..+...+.+.++.
T Consensus        98 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~~a~  156 (323)
T d1fcha_          98 TNESLQRQACEILRDWLRYT-PAYAHLVTPAEEGAG--------------------GAGLGPSKRILGSLLSDSLFLEVK  156 (323)
T ss_dssp             HHTTCHHHHHHHHHHHHHTS-TTTGGGCC-----------------------------------CTTHHHHHHHHHHHHH
T ss_pred             cccccccccccchhhHHHhc-cchHHHHHhhhhhhh--------------------hcccccchhhHHHHHHhhHHHHHH
Confidence            77777777777777776653 111111100000000                    000001111122233445667777


Q ss_pred             HHHHHHHhcCC-CCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          212 KLFEEMQRDDV-AADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       212 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      ..+.++.+... ..+..++..++..+...|++++|+..++.+....+. +...+..++.++...|++++|.+.|+++.+.
T Consensus       157 ~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  235 (323)
T d1fcha_         157 ELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPN-DYLLWNKLGATLANGNQSEEAVAAYRRALEL  235 (323)
T ss_dssp             HHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccc-cccchhhhhhcccccccchhHHHHHHHHHHH
Confidence            77777766532 234556777888888889999999999888766533 6778888888999999999999999888775


Q ss_pred             CCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC----------CCcHHHHHHHHHHHhhcCChhhHHH
Q 042039          291 VLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV----------APNVIIFVTLIHGFVRINKPSKVIE  352 (376)
Q Consensus       291 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----------~~~~~~~~~l~~~~~~~g~~~~a~~  352 (376)
                       .+.+..++..++.+|.+.|++++|+..|+++++...          ......|..+-.++...|+.+.+..
T Consensus       236 -~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~~  306 (323)
T d1fcha_         236 -QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGA  306 (323)
T ss_dssp             -CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHH
T ss_pred             -hhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence             345677888899999999999999999988876311          1112345566666666676665543

>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=99.62  E-value=3.9e-13  Score=107.45  Aligned_cols=215  Identities=9%  Similarity=-0.005  Sum_probs=170.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCC-ChHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAN-DWNEAKRLFFEMMDQGVQPSVVTFNVIMD   94 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   94 (376)
                      ..+|+.+...+.+.+.+++|+++++++++.+ |.+..+|+....++...| ++++|+..++++++..+. +..+|..+..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~-~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHh-hhhHHHHHhH
Confidence            5577788888889999999999999999987 778889999999988876 589999999999987655 7889999999


Q ss_pred             HHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCc---
Q 042039           95 ELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE---  171 (376)
Q Consensus        95 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---  171 (376)
                      ++...|++++|+..++++++.. +.+..+|..++.++...|++++|.+.++++.+.+ |.+..+|+.+..++.+.+.   
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHccccch
Confidence            9999999999999999999875 4478899999999999999999999999999986 6678888888777666554   


Q ss_pred             ---HHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC-CcchHHHHHHHH
Q 042039          172 ---VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA-DTSTYNTFIDGL  236 (376)
Q Consensus       172 ---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~  236 (376)
                         +++|+..+.++++.. +.+...|..+...+.. ...+++.+.+....+....+ +...+..++..|
T Consensus       199 ~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y  265 (315)
T d2h6fa1         199 RAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIY  265 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHH
T ss_pred             hhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHH
Confidence               678999998888863 3366777766665544 34567777777776653222 233444455544

>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=99.58  E-value=1.2e-14  Score=117.98  Aligned_cols=251  Identities=10%  Similarity=-0.055  Sum_probs=141.3

Q ss_pred             cCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHh----------cCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           29 EGFVDKAKALFLQMKGENINPDVVTYNSLIHGLC----------HANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        29 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~----------~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      .+..++|+++++++.+.+ |.+...|+.....+.          ..|++++|+.+++.+++..++ +...|..+..++..
T Consensus        42 ~~~~~~al~~~~~~l~~~-P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk-~~~~~~~~~~~~~~  119 (334)
T d1dcea1          42 GELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSR  119 (334)
T ss_dssp             TCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHT
T ss_pred             ccccHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCC-cHHHHHHhhHHHHH
Confidence            334477788888777664 445555544333322          223466777777777665433 55566666655555


Q ss_pred             CC--ChHHHHHHHHHHHhcCCCCChhhH-HHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHH
Q 042039           99 NG--KMDEASRLLDLMVQRDVRPNAFTY-STLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA  175 (376)
Q Consensus        99 ~~--~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  175 (376)
                      .+  +++++...+.++++.. +++...+ ......+...+.++.|...++.+...+ |.+..+|..++.++.+.|++++|
T Consensus       120 ~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l~~~~~~~~~~~~A  197 (334)
T d1dcea1         120 LPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDS  197 (334)
T ss_dssp             CSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCS
T ss_pred             hccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCHHHH
Confidence            54  3667777777776653 2334443 334455566677777777777776665 45666677777777777776666


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc
Q 042039          176 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL  255 (376)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  255 (376)
                      ...+......  .|.   .......+...+..+.+...+....... ++....+..++..+...++.++|...+......
T Consensus       198 ~~~~~~~~~~--~~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  271 (334)
T d1dcea1         198 GPQGRLPENV--LLK---ELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESCKELQELEPE  271 (334)
T ss_dssp             SSCCSSCHHH--HHH---HHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHhHHh--HHH---HHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            5544443331  111   1122233344455555666665555543 344444455555555566666666666665554


Q ss_pred             CCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc
Q 042039          256 KCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR  290 (376)
Q Consensus       256 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  290 (376)
                      . +.+...+..++.++...|++++|.+.++++.+.
T Consensus       272 ~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l  305 (334)
T d1dcea1         272 N-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  305 (334)
T ss_dssp             C-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH
T ss_pred             C-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            3 224455556666666666666666666666553

>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=99.57  E-value=7.2e-13  Score=105.87  Aligned_cols=195  Identities=10%  Similarity=0.055  Sum_probs=110.3

Q ss_pred             HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC-cHHHHHHHHHHHHhcCCCCChhhHHHHHHH
Q 042039           87 VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG-KINRAEELFGSMESMGCKHDDVSYNILING  165 (376)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  165 (376)
                      ..++.+...+.+.+.+++|+.+++++++.+ +-+..+|+....++...| ++++|+..++++.... |.+..+|..++.+
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~  121 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHH
Confidence            345555556666666677777777766653 334556666666666554 3666666666666654 4556666666666


Q ss_pred             HHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCC----
Q 042039          166 YCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGY----  241 (376)
Q Consensus       166 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----  241 (376)
                      +.+.|++++|+..++++++.. +.+...|..+...+...|++++|+..++.+++.+ +.+...|..+...+.+.+.    
T Consensus       122 ~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~~~~~  199 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDR  199 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHccccchh
Confidence            666666666666666666642 3346666666666666666666666666666654 3445555555555444443    


Q ss_pred             --HHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcc
Q 042039          242 --IVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSL  287 (376)
Q Consensus       242 --~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  287 (376)
                        +++|+..+..+....+ .+...|..+...+... ..+++.+.++.+
T Consensus       200 ~~~~~ai~~~~~al~~~P-~~~~~~~~l~~ll~~~-~~~~~~~~~~~~  245 (315)
T d2h6fa1         200 AVLEREVQYTLEMIKLVP-HNESAWNYLKGILQDR-GLSKYPNLLNQL  245 (315)
T ss_dssp             HHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTTT-CGGGCHHHHHHH
T ss_pred             hhhHHhHHHHHHHHHhCC-CchHHHHHHHHHHHhc-ChHHHHHHHHHH
Confidence              3445555555444432 2444444444433322 234444444433

>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=99.57  E-value=2.2e-12  Score=105.39  Aligned_cols=295  Identities=11%  Similarity=0.037  Sum_probs=150.4

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCc----hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-CC----hhhHHHHH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPS----VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR-PN----AFTYSTLM  128 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~  128 (376)
                      ...+...|++++|++++++.+......+    ...+..+..++...|++++|...+++..+.... ++    ...+..+.
T Consensus        19 A~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~   98 (366)
T d1hz4a_          19 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQS   98 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHH
Confidence            3444444555555555544444321111    123333444444555555555555444331100 00    12333444


Q ss_pred             HHHHhcCcHHHHHHHHHHHHhc----CCCC---ChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCC----CCCHhHHHHH
Q 042039          129 DGFCLTGKINRAEELFGSMESM----GCKH---DDVSYNILINGYCKNKEVEEALSLYREMVSKGI----KPTVVTYNTL  197 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~~----~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~l  197 (376)
                      ..+...|++..+...+......    ..+.   ....+..+...+...|+++.+...+........    ......+...
T Consensus        99 ~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (366)
T d1hz4a_          99 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML  178 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence            4455555555555555544321    1011   112334455556666666666666666554311    1123334444


Q ss_pred             HHHHHhccchHHHHHHHHHHHhcCC--CC----CcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCC---chHHHHHHHH
Q 042039          198 FLGLFEIHQVEHALKLFEEMQRDDV--AA----DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCE---LDIQAYNCLI  268 (376)
Q Consensus       198 ~~~~~~~~~~~~a~~~~~~~~~~~~--~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~  268 (376)
                      ...+...++...+...+........  ..    ....+......+...|++++|...++........   .....+..++
T Consensus       179 ~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la  258 (366)
T d1hz4a_         179 IQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIA  258 (366)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHH
Confidence            4555556666666666555433210  00    1123445556677778888888888776554322   2234556677


Q ss_pred             HHHHhCCChHHHHHHHhccccc----CCCC-CHHHHHHHHHHHHccCChhHHHHHHHHHHHc----CCCC----cHHHHH
Q 042039          269 DGLCKSGRLEIALELFRSLPRR----VLVA-DVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN----AVAP----NVIIFV  335 (376)
Q Consensus       269 ~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~----~~~~~~  335 (376)
                      .++...|++++|...++.+...    +..| ...++..++.+|...|++++|.+.++++.+.    |...    ....+.
T Consensus       259 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~~~~~~~~~~  338 (366)
T d1hz4a_         259 RAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEAMA  338 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTTHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHHHHHHHHHHH
Confidence            7888888888888888776421    2222 2456777788888888888888888877643    2111    112334


Q ss_pred             HHHHHHhhcCChhhHHH
Q 042039          336 TLIHGFVRINKPSKVIE  352 (376)
Q Consensus       336 ~l~~~~~~~g~~~~a~~  352 (376)
                      .++..+...++.+++..
T Consensus       339 ~~~~~l~~~~~l~e~e~  355 (366)
T d1hz4a_         339 QQLRQLIQLNTLPELEQ  355 (366)
T ss_dssp             HHHHHHHHTTCSCHHHH
T ss_pred             HHHHHHHhcCCChHHHH
Confidence            44555555666655543

>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=99.55  E-value=8.9e-12  Score=101.70  Aligned_cols=273  Identities=12%  Similarity=0.017  Sum_probs=199.2

Q ss_pred             HhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCC----hhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC-----CChh
Q 042039           87 VTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPN----AFTYSTLMDGFCLTGKINRAEELFGSMESMGCK-----HDDV  157 (376)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~  157 (376)
                      .........+...|++++|..++++.++.....+    ..++..++.++...|++++|...+++.......     ....
T Consensus        13 e~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   92 (366)
T d1hz4a_          13 EFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALW   92 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHH
Confidence            3444556778899999999999999988632211    245677888999999999999999988654211     1123


Q ss_pred             hHHHHHHHHHccCcHHHHHHHHHHHHHC----CCCCC---HhHHHHHHHHHHhccchHHHHHHHHHHHhcCC----CCCc
Q 042039          158 SYNILINGYCKNKEVEEALSLYREMVSK----GIKPT---VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDV----AADT  226 (376)
Q Consensus       158 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~  226 (376)
                      .+..+...+...|++..+...+......    +....   ...+..+...+...|+++.+...+........    ....
T Consensus        93 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  172 (366)
T d1hz4a_          93 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  172 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHH
Confidence            5667788889999999999999887642    11111   23556677888999999999999988876532    1223


Q ss_pred             chHHHHHHHHHhCCCHHHHHHHHHHhcc----cCCCc--hHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCC---CHH
Q 042039          227 STYNTFIDGLCKNGYIVEAVELFRTLGI----LKCEL--DIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVA---DVV  297 (376)
Q Consensus       227 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~  297 (376)
                      ..+......+...++...+...+.....    .+..+  ....+...+..+...|++++|...++.........   ...
T Consensus       173 ~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  252 (366)
T d1hz4a_         173 QCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQG  252 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHH
Confidence            3455666777888999988888776532    11111  23456677788899999999999999877543222   234


Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHHc----CCCCc-HHHHHHHHHHHhhcCChhhHHHHHHHHHh
Q 042039          298 TYNIMIHGLCNDGQMDKAHDLFLDMEEN----AVAPN-VIIFVTLIHGFVRINKPSKVIELLHKMKE  359 (376)
Q Consensus       298 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  359 (376)
                      .+..++.++...|++++|...++++...    +..|+ ...+..+...|.+.|++++|.+.+++..+
T Consensus       253 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         253 QWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5667888999999999999999988642    33333 45778888999999999999999998764

>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=99.51  E-value=8.5e-12  Score=99.53  Aligned_cols=184  Identities=12%  Similarity=0.064  Sum_probs=80.5

Q ss_pred             HHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHh
Q 042039          173 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTL  252 (376)
Q Consensus       173 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  252 (376)
                      ++|..+|++.++...+.+...|...+......|+++.|..+++.++.........++...+..+.+.|+.+.|.++|+++
T Consensus        81 ~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~a  160 (308)
T d2onda1          81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKA  160 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            44444444444432222333444444444444555555555554444321111223444444444445555555555554


Q ss_pred             cccCCCchHHHHHHHHHH-HHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcC-CCCc
Q 042039          253 GILKCELDIQAYNCLIDG-LCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENA-VAPN  330 (376)
Q Consensus       253 ~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~  330 (376)
                      ....+. +...+...+.. +...|+.+.|..+|+.+... .+.+...+...+..+...|++++|..+|++++... ..|.
T Consensus       161 l~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~  238 (308)
T d2onda1         161 REDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPE  238 (308)
T ss_dssp             HTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGG
T ss_pred             HHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChH
Confidence            443321 22223222222 22234555555555554443 33344455555555555555555555555554432 1221


Q ss_pred             --HHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          331 --VIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       331 --~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                        ...|...+..-...|+.+.+.++++++.
T Consensus       239 ~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~  268 (308)
T d2onda1         239 KSGEIWARFLAFESNIGDLASILKVEKRRF  268 (308)
T ss_dssp             GCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence              2344444444444555555555555543

>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=99.50  E-value=2.4e-12  Score=100.18  Aligned_cols=150  Identities=13%  Similarity=-0.023  Sum_probs=83.6

Q ss_pred             hhHHHHHHHHhhhCCCCC---ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHH
Q 042039           32 VDKAKALFLQMKGENINP---DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRL  108 (376)
Q Consensus        32 ~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  108 (376)
                      .+.++..++++.......   ...+|..++.+|.+.|++++|++.|++.++..+. +..+|..++.++...|++++|+..
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~-~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCC-CHHHHhhhchHHHHHHHHHHhhhh
Confidence            344444555554432111   2345666666677777777777777776665333 556666666666677777777777


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          109 LDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      |+++++.. +.+..++..++.++...|++++|...|++..+.. |.+......+...+.+.+..+.+..+......
T Consensus        94 ~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (259)
T d1xnfa_          94 FDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  167 (259)
T ss_dssp             HHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHH-hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence            76666653 2245556666666666666666666666666554 33333333344444444444444444333333

>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=99.47  E-value=2.4e-11  Score=96.88  Aligned_cols=188  Identities=12%  Similarity=-0.012  Sum_probs=142.6

Q ss_pred             cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHH
Q 042039          136 KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFE  215 (376)
Q Consensus       136 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  215 (376)
                      ..++|..+|++..+...+.+...|..++......|+++.|..+|+++++.........|...+....+.++.+.|.++|.
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            45778888888887554566667888888888889999999999998875333334567888888888899999999999


Q ss_pred             HHHhcCCCCCcchHHHHHHH-HHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccC-CC
Q 042039          216 EMQRDDVAADTSTYNTFIDG-LCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRV-LV  293 (376)
Q Consensus       216 ~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~  293 (376)
                      ++.+.. +.+...+...+.. +...|+.+.|..+|+.+.... +.++..|...+..+...|+.+.|..+|+++.+.. ..
T Consensus       159 ~al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~  236 (308)
T d2onda1         159 KAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  236 (308)
T ss_dssp             HHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSC
T ss_pred             HHHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCC
Confidence            888765 4455555554443 344688899999999988764 3467888889999999999999999999887652 22


Q ss_pred             CC--HHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          294 AD--VVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       294 ~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      |.  ...|...+..-...|+.+.+.++++++.+.
T Consensus       237 ~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         237 PEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             GGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            22  346777777777889999999999888764

>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=99.47  E-value=2.6e-12  Score=99.96  Aligned_cols=151  Identities=8%  Similarity=-0.089  Sum_probs=106.0

Q ss_pred             ChHHHHHHHHHHHhcCCCC---chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHH
Q 042039           66 DWNEAKRLFFEMMDQGVQP---SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEE  142 (376)
Q Consensus        66 ~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  142 (376)
                      +.+.++.-++++.......   ...++..+..+|.+.|++++|...|++.++.. +-++.++..++.++...|++++|..
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~   92 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYE   92 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhh
Confidence            4556666666766542211   23467777888888899999999998888864 3467788888888888899999999


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHh
Q 042039          143 LFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQR  219 (376)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  219 (376)
                      .|+++.... |.+..++..++.++...|++++|...++..++.. +.+......+.......+..+....+......
T Consensus        93 ~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (259)
T d1xnfa_          93 AFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  167 (259)
T ss_dssp             HHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHH-hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence            998888876 5567788888888888888899988888888753 23444444444444555555555444444443

>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=99.45  E-value=4.3e-13  Score=108.67  Aligned_cols=275  Identities=7%  Similarity=-0.047  Sum_probs=187.8

Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHH----------HhCCChHHHHHHHHHHHhcCCCCChhhH
Q 042039           55 NSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDEL----------CKNGKMDEASRLLDLMVQRDVRPNAFTY  124 (376)
Q Consensus        55 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~~~a~~~~~~~~~~~~~~~~~~~  124 (376)
                      ..++......+..++|+++++++++.++. +...|+.....+          ...|++++|+.+++.+++.. +.+...|
T Consensus        33 ~~~~~~~~~~~~~~~al~~~~~~l~~~P~-~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~  110 (334)
T d1dcea1          33 QAVFQKRQAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTW  110 (334)
T ss_dssp             HHHHHHHHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHH
Confidence            33444444444568999999999886433 444454333322          23345788888999888764 3466677


Q ss_pred             HHHHHHHHhcC--cHHHHHHHHHHHHhcCCCCChhhH-HHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHH
Q 042039          125 STLMDGFCLTG--KINRAEELFGSMESMGCKHDDVSY-NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL  201 (376)
Q Consensus       125 ~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  201 (376)
                      ..+..++...+  ++++|...+.++.... +++...+ ......+...+.+++|+..++.++..+ +-+...|..+..++
T Consensus       111 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l~~~~  188 (334)
T d1dcea1         111 HHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLL  188 (334)
T ss_dssp             HHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHH
T ss_pred             HHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHHHHHH
Confidence            77777776665  4889999999988875 4455554 455677778899999999999888863 34678888888889


Q ss_pred             HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHH
Q 042039          202 FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIAL  281 (376)
Q Consensus       202 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  281 (376)
                      ...|++++|...+....+..  |.   .......+...+..+++...+....... +++...+..++..+...+++++|.
T Consensus       189 ~~~~~~~~A~~~~~~~~~~~--~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~  262 (334)
T d1dcea1         189 PQLHPQPDSGPQGRLPENVL--LK---ELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESC  262 (334)
T ss_dssp             HHHSCCCCSSSCCSSCHHHH--HH---HHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHhHHhH--HH---HHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHH
Confidence            89888887765554443321  11   1223334455666777777777766554 334555666677777788899999


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCc-HHHHHHHHHHHh
Q 042039          282 ELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPN-VIIFVTLIHGFV  342 (376)
Q Consensus       282 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~  342 (376)
                      ..+.+.... .+.+..++..++.++...|++++|.+.++++.+.  .|+ ...|..|...+.
T Consensus       263 ~~~~~~~~~-~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         263 KELQELEPE-NKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHHHCTT-CHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHhh-CchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHHHHHHHHHHh
Confidence            988887765 3445677888888999999999999999999885  453 455665654444

>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=99.24  E-value=1e-09  Score=86.33  Aligned_cols=197  Identities=11%  Similarity=-0.054  Sum_probs=111.0

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhc----CCCC-ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-----CCChhhHHHH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQR----DVRP-NAFTYSTLMDGFCLTGKINRAEELFGSMESMGC-----KHDDVSYNIL  162 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l  162 (376)
                      ...|...+++++|...|.++.+.    +.++ ...+|..++.+|.+.|++++|.+.+++......     .....++..+
T Consensus        44 a~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l  123 (290)
T d1qqea_          44 ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFEL  123 (290)
T ss_dssp             HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHH
Confidence            45666777777777777776552    1111 134666777777777777777777776644310     1112345555


Q ss_pred             HHHHH-ccCcHHHHHHHHHHHHHC----CCCC-CHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCc------chHH
Q 042039          163 INGYC-KNKEVEEALSLYREMVSK----GIKP-TVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADT------STYN  230 (376)
Q Consensus       163 ~~~~~-~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~  230 (376)
                      +..|. ..|++++|++.+++..+.    +.++ ...++..++..+...|++++|...++++.........      ..+.
T Consensus       124 ~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (290)
T d1qqea_         124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFL  203 (290)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHH
T ss_pred             HHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHH
Confidence            65553 357788888877776542    1111 1344666677777777777777777776665321111      1233


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhcccCCC-ch---HHHHHHHHHHHHh--CCChHHHHHHHhcccc
Q 042039          231 TFIDGLCKNGYIVEAVELFRTLGILKCE-LD---IQAYNCLIDGLCK--SGRLEIALELFRSLPR  289 (376)
Q Consensus       231 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~---~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~  289 (376)
                      ..+..+...|+++.|...+++.....+. ++   ......++.++..  .+.+++|+..|+++.+
T Consensus       204 ~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~  268 (290)
T d1qqea_         204 KKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (290)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhh
Confidence            4445566677777777777777655321 11   1233445555443  2346666666665544

>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=99.17  E-value=3e-09  Score=77.73  Aligned_cols=126  Identities=15%  Similarity=0.050  Sum_probs=91.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      .|+. ...+...|++++|++.|+++.    +|++.+|..++.+|...|++++|++.|++.++.++. +...|..+..++.
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~-~~~a~~~~g~~~~   81 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYY   81 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh-hhhhHHHHHHHHH
Confidence            4544 556778888999988887653    567778888888888999999999999988887544 6778888888888


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCC----------------hhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPN----------------AFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      +.|++++|...|++.+... +.+                ..++..+..++...|++++|.+.++.....
T Consensus        82 ~~g~~~~A~~~~~kAl~~~-~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_          82 QTEKYDLAIKDLKEALIQL-RGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             HTTCHHHHHHHHHHHHHTT-TTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hhccHHHHHHHHHHHHHhC-ccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            8899999988888887532 111                123445555666666666666666666554

>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=99.14  E-value=1.6e-09  Score=79.32  Aligned_cols=125  Identities=9%  Similarity=-0.067  Sum_probs=85.6

Q ss_pred             HHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCCh
Q 042039          198 FLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRL  277 (376)
Q Consensus       198 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  277 (376)
                      +..+...|+++.|++.|..+    .++++.++..++.+|...|++++|++.|+++++.++. .+..|..++.++.+.|++
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~-~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh-hhhhHHHHHHHHHhhccH
Confidence            55566777788887777653    2456667777777788888888888888877776633 667777777777788888


Q ss_pred             HHHHHHHhcccccCCCCC----------------HHHHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 042039          278 EIALELFRSLPRRVLVAD----------------VVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVA  328 (376)
Q Consensus       278 ~~a~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  328 (376)
                      ++|...|++..... +.+                ..++..++.++.+.|++++|.+.+..+.+....
T Consensus        87 ~~A~~~~~kAl~~~-~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_          87 DLAIKDLKEALIQL-RGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HHHHHHHHHHHHTT-TTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHHhC-ccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            88877777765431 111                244556677777777777777777777665433

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=99.12  E-value=2.1e-07  Score=71.81  Aligned_cols=224  Identities=13%  Similarity=0.036  Sum_probs=132.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----CCChHHHHHHHHHHHhcCCCCchHhHH
Q 042039           15 NTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCH----ANDWNEAKRLFFEMMDQGVQPSVVTFN   90 (376)
Q Consensus        15 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~   90 (376)
                      |+..+..|...+.+.+++++|++.|++..+.|   +..++..|...|..    ..++..|...+......+   +.....
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~   74 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   74 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhh
Confidence            45677777777888888888888888887765   56677777777765    457778888887777654   333334


Q ss_pred             HHHHHHHh----CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           91 VIMDELCK----NGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCKHDDVSYNIL  162 (376)
Q Consensus        91 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  162 (376)
                      .+...+..    ..+.+.|...++...+.|.   ......+...+..    ......+...+......   .+...+..+
T Consensus        75 ~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~L  148 (265)
T d1ouva_          75 LLGNLYYSGQGVSQNTNKALQYYSKACDLKY---AEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDGDGCTIL  148 (265)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCHHHHHHH
T ss_pred             ccccccccccccchhhHHHHHHHhhhhhhhh---hhHHHhhcccccCCCcccchhHHHHHHhhhhhcc---cccchhhhh
Confidence            44444332    3566777777777776652   2223333333332    33455666666665553   345556666


Q ss_pred             HHHHHc----cCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----ccchHHHHHHHHHHHhcCCCCCcchHHHHHH
Q 042039          163 INGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE----IHQVEHALKLFEEMQRDDVAADTSTYNTFID  234 (376)
Q Consensus       163 ~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  234 (376)
                      ...+..    ..+...+...++...+.|   +..+...+...+..    ..+++.|...|....+.+   ++..+..++.
T Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~  222 (265)
T d1ouva_         149 GSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGA  222 (265)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             hhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHH
Confidence            666654    345566666666666543   44444555544443    345666666666665554   3344555555


Q ss_pred             HHHh----CCCHHHHHHHHHHhcccC
Q 042039          235 GLCK----NGYIVEAVELFRTLGILK  256 (376)
Q Consensus       235 ~~~~----~~~~~~a~~~~~~~~~~~  256 (376)
                      +|..    ..+.++|.++|+++...|
T Consensus       223 ~y~~G~g~~~n~~~A~~~~~kAa~~g  248 (265)
T d1ouva_         223 MQYNGEGVTRNEKQAIENFKKGCKLG  248 (265)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHcCCCCccCHHHHHHHHHHHHHCc
Confidence            5543    225556666666655544

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=99.09  E-value=2.3e-07  Score=71.61  Aligned_cols=94  Identities=11%  Similarity=0.123  Sum_probs=49.4

Q ss_pred             hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcCCCCChhhHHH
Q 042039           86 VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMGCKHDDVSYNI  161 (376)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  161 (376)
                      +..+..+...+...+++++|+++|++..+.|   +...+..|...|..    ..++..|..++......+   ++.....
T Consensus         2 p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~~   75 (265)
T d1ouva_           2 PKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHL   75 (265)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhhc
Confidence            3445555556666666666666666665544   44455555555554    345566666666655543   2333333


Q ss_pred             HHHHHHc----cCcHHHHHHHHHHHHHC
Q 042039          162 LINGYCK----NKEVEEALSLYREMVSK  185 (376)
Q Consensus       162 l~~~~~~----~~~~~~a~~~~~~~~~~  185 (376)
                      +...+..    ..+.+.|...++.....
T Consensus        76 l~~~~~~~~~~~~~~~~a~~~~~~a~~~  103 (265)
T d1ouva_          76 LGNLYYSGQGVSQNTNKALQYYSKACDL  103 (265)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             cccccccccccchhhHHHHHHHhhhhhh
Confidence            3333322    34455555555555554

>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=99.08  E-value=3.5e-09  Score=70.45  Aligned_cols=92  Identities=13%  Similarity=0.058  Sum_probs=54.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  101 (376)
                      -...+.+.|++++|+..|+++++.. |.+...|..++.++...|++++|+..+++.++.++. +...|..+..++...|+
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhccc-hhhHHHHHHHHHHHccC
Confidence            3445556666666666666665554 445556666666666666666666666666655333 55556666666666666


Q ss_pred             hHHHHHHHHHHHhc
Q 042039          102 MDEASRLLDLMVQR  115 (376)
Q Consensus       102 ~~~a~~~~~~~~~~  115 (376)
                      +++|+..|++.++.
T Consensus        87 ~~~A~~~~~~a~~~  100 (117)
T d1elwa_          87 FEEAKRTYEEGLKH  100 (117)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            66666666666654

>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=99.08  E-value=1.2e-08  Score=80.21  Aligned_cols=203  Identities=14%  Similarity=0.062  Sum_probs=137.2

Q ss_pred             hHHHHHHHHhcCCChHHHHHHHHHHHhc----CCCC-chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCC-----CChh
Q 042039           53 TYNSLIHGLCHANDWNEAKRLFFEMMDQ----GVQP-SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVR-----PNAF  122 (376)
Q Consensus        53 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~  122 (376)
                      .|...+..|...|++++|.+.|.++...    +.++ -..+|..+..+|.+.|++++|...+++..+....     ....
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  118 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHH
Confidence            3555677788889999999999888763    1111 2357888888999999999999999887653111     1134


Q ss_pred             hHHHHHHHHHh-cCcHHHHHHHHHHHHhc----CCCC-ChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC------
Q 042039          123 TYSTLMDGFCL-TGKINRAEELFGSMESM----GCKH-DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT------  190 (376)
Q Consensus       123 ~~~~l~~~~~~-~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------  190 (376)
                      ++..++..|.. .|++++|.+.+++..+.    +.++ ...++..++.++...|++++|+..|+++........      
T Consensus       119 ~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~  198 (290)
T d1qqea_         119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSL  198 (290)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGH
T ss_pred             HHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhH
Confidence            55666666644 69999999999887543    1111 234578889999999999999999999887532211      


Q ss_pred             HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCC-CC---cchHHHHHHHHHh--CCCHHHHHHHHHHhccc
Q 042039          191 VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVA-AD---TSTYNTFIDGLCK--NGYIVEAVELFRTLGIL  255 (376)
Q Consensus       191 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~---~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~  255 (376)
                      ...+...+..+...++++.|...+++..+.... ++   ......++.++..  .+.+++|+..|+.+.+.
T Consensus       199 ~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~l  269 (290)
T d1qqea_         199 KDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRL  269 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhc
Confidence            123445566677889999999999988776421 11   2234556666554  34588888888776644

>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=99.06  E-value=6.6e-09  Score=69.11  Aligned_cols=91  Identities=11%  Similarity=0.043  Sum_probs=42.8

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKI  137 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  137 (376)
                      +..+...|++++|+..|+++++..+. +...|..+..++...|++++|+..+...++.+ +.+...|..++.++...|++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLDPH-NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCc-chhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCH
Confidence            34444445555555555555444222 34444444444555555555555555544442 22344444444444455555


Q ss_pred             HHHHHHHHHHHhc
Q 042039          138 NRAEELFGSMESM  150 (376)
Q Consensus       138 ~~a~~~~~~~~~~  150 (376)
                      ++|...|++..+.
T Consensus        88 ~~A~~~~~~a~~~  100 (117)
T d1elwa_          88 EEAKRTYEEGLKH  100 (117)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh
Confidence            5555555444443

>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=99.03  E-value=7.5e-09  Score=73.24  Aligned_cols=95  Identities=13%  Similarity=0.054  Sum_probs=56.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh
Q 042039           19 YNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK   98 (376)
Q Consensus        19 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   98 (376)
                      +......|.+.|++++|+..|+++.+.+ |.+...|..++.++...|++++|.+.|+++++..+. +..+|..++.++..
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~-~~~a~~~~g~~~~~   90 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNMA   90 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc-chHHHHHHHHHHHH
Confidence            3344445566666666666666666554 445566666666666666666666666666655322 44556666666666


Q ss_pred             CCChHHHHHHHHHHHhc
Q 042039           99 NGKMDEASRLLDLMVQR  115 (376)
Q Consensus        99 ~~~~~~a~~~~~~~~~~  115 (376)
                      .|++++|...+++....
T Consensus        91 ~g~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          91 LGKFRAALRDYETVVKV  107 (159)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHc
Confidence            66666666666666554

>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=99.00  E-value=1.4e-09  Score=80.62  Aligned_cols=100  Identities=15%  Similarity=-0.023  Sum_probs=73.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHH
Q 042039           14 PNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIM   93 (376)
Q Consensus        14 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   93 (376)
                      |++..+......+.+.|++++|+..|++++..+ |.++.+|..++.+|.+.|++++|+..|+++++..+. +..+|..++
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~-~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCC-cHHHHHHHH
Confidence            666667777777778888888888887777665 567777777777777788888888888777765332 466777777


Q ss_pred             HHHHhCCChHHHHHHHHHHHhc
Q 042039           94 DELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        94 ~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      .++...|++++|...|+++++.
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh
Confidence            7777777777777777776653

>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=98.99  E-value=1.7e-08  Score=71.38  Aligned_cols=93  Identities=10%  Similarity=0.071  Sum_probs=53.9

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCc
Q 042039           57 LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGK  136 (376)
Q Consensus        57 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  136 (376)
                      .+..|.+.|++++|+..|+++++..+. +...|..+..++...|++++|...|+++++.. +.+..+|..++.++...|+
T Consensus        16 ~gn~~~~~~~y~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          16 QANDYFKAKDYENAIKFYSQAIELNPS-NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHhhhccccchh-hhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCC
Confidence            344555666666666666666655332 45555566666666666666666666665543 2244555566666666666


Q ss_pred             HHHHHHHHHHHHhcC
Q 042039          137 INRAEELFGSMESMG  151 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~  151 (376)
                      +++|...++++....
T Consensus        94 ~~eA~~~~~~a~~~~  108 (159)
T d1a17a_          94 FRAALRDYETVVKVK  108 (159)
T ss_dssp             HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHcC
Confidence            666666666665553

>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=98.94  E-value=4.7e-09  Score=77.68  Aligned_cols=99  Identities=11%  Similarity=-0.052  Sum_probs=62.1

Q ss_pred             CChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHH
Q 042039           49 PDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLM  128 (376)
Q Consensus        49 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  128 (376)
                      |+...+...+..+.+.|++++|+..|++++...+. +...|..++.+|.+.|++++|+..|+++++.. +-+..+|..++
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~-~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~-p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC-CCcHHHHHHHH
Confidence            45555666666666666677777666666665432 55566666666666666666666666666542 22355666666


Q ss_pred             HHHHhcCcHHHHHHHHHHHHh
Q 042039          129 DGFCLTGKINRAEELFGSMES  149 (376)
Q Consensus       129 ~~~~~~~~~~~a~~~~~~~~~  149 (376)
                      .+|...|++++|...|+++..
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            666666666666666666554

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.88  E-value=9.4e-09  Score=67.68  Aligned_cols=88  Identities=9%  Similarity=-0.083  Sum_probs=42.1

Q ss_pred             HHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC
Q 042039           22 IIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK  101 (376)
Q Consensus        22 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  101 (376)
                      ....+.+.|++++|+..|++....+ |.++.+|..++.++...|++++|+..|++.++..+. +...+..+..++...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccc-cccchHHHHHHHHHCCC
Confidence            3344444555555555555544443 334445555555555555555555555554444222 34444444445555555


Q ss_pred             hHHHHHHHHH
Q 042039          102 MDEASRLLDL  111 (376)
Q Consensus       102 ~~~a~~~~~~  111 (376)
                      +++|.+.+++
T Consensus       100 ~~~A~~~l~~  109 (112)
T d1hxia_         100 ANAALASLRA  109 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555544444

>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=98.84  E-value=2.3e-09  Score=90.97  Aligned_cols=228  Identities=10%  Similarity=-0.087  Sum_probs=130.9

Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCch-HhHHHHHHHHHhCCChHHHHHHHHHH
Q 042039           34 KAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSV-VTFNVIMDELCKNGKMDEASRLLDLM  112 (376)
Q Consensus        34 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~  112 (376)
                      +|.+.|++..+.. +....++..+..++...+++++|   |++++..  .|+. ..++...  ..-...+..+.+.++..
T Consensus         4 eA~q~~~qA~~l~-p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~--dp~~a~~~~~e~--~Lw~~~y~~~ie~~r~~   75 (497)
T d1ya0a1           4 QSAQYLRQAEVLK-ADMTDSKLGPAEVWTSRQALQDL---YQKMLVT--DLEYALDKKVEQ--DLWNHAFKNQITTLQGQ   75 (497)
T ss_dssp             HHHHHHHHHHHHH-GGGTCSSSCSSSSHHHHHHHHHH---HHHHHHH--CHHHHHHHTHHH--HHHHHHTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCCHHHHhhHHHHHHHHchHHHH---HHHHHHc--ChhhHHHHhHHH--HHHHHHHHHHHHHHHHh
Confidence            6778888887653 33455667777778878888766   6777654  2221 1111111  11111245566777776


Q ss_pred             HhcCCCCChhhHHHH--HHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCC
Q 042039          113 VQRDVRPNAFTYSTL--MDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT  190 (376)
Q Consensus       113 ~~~~~~~~~~~~~~l--~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  190 (376)
                      .+....++..-....  .......+.++.+...+....+.. +++...+..++..+.+.|+.++|...+.......   .
T Consensus        76 ~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---~  151 (497)
T d1ya0a1          76 AKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVD-LPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI---C  151 (497)
T ss_dssp             HSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHH---H
T ss_pred             cccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---H
Confidence            654433333222211  222233455666666666555443 4566778888899999999999998888776531   2


Q ss_pred             HhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHH
Q 042039          191 VVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDG  270 (376)
Q Consensus       191 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  270 (376)
                      ..++..++..+...+++++|...|.++.+.. |.+...|+.++..+...|+..+|+..|.+..... +|.+.++..|...
T Consensus       152 ~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~  229 (497)
T d1ya0a1         152 QHCLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKA  229 (497)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHH
Confidence            4567788899999999999999999999885 6677899999999999999999999999998776 5578888888887


Q ss_pred             HHhCC
Q 042039          271 LCKSG  275 (376)
Q Consensus       271 ~~~~~  275 (376)
                      +.+..
T Consensus       230 ~~~~~  234 (497)
T d1ya0a1         230 LSKAL  234 (497)
T ss_dssp             HHHHT
T ss_pred             HHHhh
Confidence            76543

>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=98.82  E-value=2e-08  Score=66.91  Aligned_cols=96  Identities=11%  Similarity=0.062  Sum_probs=71.6

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC---hHHHHHHHHHHHhcCCCCc-hHhHHHHHHH
Q 042039           20 NTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND---WNEAKRLFFEMMDQGVQPS-VVTFNVIMDE   95 (376)
Q Consensus        20 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~   95 (376)
                      ..+++.+...+++++|.+.|++....+ |.++.++..++.++.+.++   +++|+.+|++++..+..|+ ..++..++.+
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            356777778888888888888888776 6677888888888876554   4468888888776544333 2467778888


Q ss_pred             HHhCCChHHHHHHHHHHHhcC
Q 042039           96 LCKNGKMDEASRLLDLMVQRD  116 (376)
Q Consensus        96 ~~~~~~~~~a~~~~~~~~~~~  116 (376)
                      |.+.|++++|.+.|+++++..
T Consensus        82 y~~~g~~~~A~~~~~~aL~~~  102 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQTE  102 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhhhHHHHHHHHHHHHhC
Confidence            888888888888888888753

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.82  E-value=2.9e-08  Score=65.25  Aligned_cols=57  Identities=14%  Similarity=0.018  Sum_probs=21.5

Q ss_pred             hHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHH
Q 042039          123 TYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR  180 (376)
Q Consensus       123 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  180 (376)
                      +|..++.++.+.|++++|+..|+++.+.. |.+..++..++.+|...|++++|++.++
T Consensus        52 a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~A~~~l~  108 (112)
T d1hxia_          52 AWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLR  108 (112)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHHHHHHHH
Confidence            33333333333333333333333333332 2233333333333333333333333333

>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=98.75  E-value=2.1e-05  Score=61.70  Aligned_cols=146  Identities=16%  Similarity=0.137  Sum_probs=96.3

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHH
Q 042039           13 KPNTVTYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVI   92 (376)
Q Consensus        13 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   92 (376)
                      .||..--..+++.|.+.|.++.|..+|..+..         |..++.++.+.++++.|.+.+.+.      -+..+|..+
T Consensus        11 ~~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~   75 (336)
T d1b89a_          11 GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEV   75 (336)
T ss_dssp             CC----------------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHH
Confidence            35666667788889999999999999986653         667888889999999998887654      267788888


Q ss_pred             HHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcH
Q 042039           93 MDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  172 (376)
Q Consensus        93 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  172 (376)
                      ...+........+     .+.......++.....++..|-..|.+++...+++...... +.+...++.++..|++.+ .
T Consensus        76 ~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~-~  148 (336)
T d1b89a_          76 CFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFK-P  148 (336)
T ss_dssp             HHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTC-H
T ss_pred             HHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhC-h
Confidence            8888887766543     22233334455666788999999999999999999887553 567778888999998865 3


Q ss_pred             HHHHHHHH
Q 042039          173 EEALSLYR  180 (376)
Q Consensus       173 ~~a~~~~~  180 (376)
                      ++-.+.+.
T Consensus       149 ~kl~e~l~  156 (336)
T d1b89a_         149 QKMREHLE  156 (336)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            44444443

>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=98.73  E-value=4.8e-08  Score=65.00  Aligned_cols=93  Identities=13%  Similarity=0.047  Sum_probs=43.8

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCC---hHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHH
Q 042039           57 LIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGK---MDEASRLLDLMVQRDVRPN-AFTYSTLMDGFC  132 (376)
Q Consensus        57 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~  132 (376)
                      ++..+...+++++|.+.|++.+..++. +..++..++.++.+.++   +++|+.++++++..+..|+ ..++..++.+|.
T Consensus         5 l~n~~~~~~~l~~Ae~~Y~~aL~~~p~-~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~   83 (122)
T d1nzna_           5 VLNELVSVEDLLKFEKKFQSEKAAGSV-SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNY   83 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCC-CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHH
Confidence            444444555555555555555554322 44455555555544332   2335555555544322221 124444555555


Q ss_pred             hcCcHHHHHHHHHHHHhc
Q 042039          133 LTGKINRAEELFGSMESM  150 (376)
Q Consensus       133 ~~~~~~~a~~~~~~~~~~  150 (376)
                      +.|++++|.+.|+++.+.
T Consensus        84 ~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          84 RLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHHh
Confidence            555555555555555544

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=5.1e-07  Score=64.16  Aligned_cols=61  Identities=11%  Similarity=-0.033  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      |..+..+|.+.|++++|+..++..++.+ +.++.++..++.++...|++++|...|+.+.+.
T Consensus        65 ~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          65 HLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            3334444444455555555554444442 223444444444444445555555544444444

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=4.5e-07  Score=64.45  Aligned_cols=117  Identities=9%  Similarity=-0.090  Sum_probs=91.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCCCC--------------ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCC
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENINP--------------DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGV   82 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~--------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   82 (376)
                      ..+......+.+.|++++|+..|++.+......              ...+|..+..+|.+.|++++|+..++..+...+
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p   93 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDS   93 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhccc
Confidence            345566778999999999999999887542111              124567788999999999999999999999854


Q ss_pred             CCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC
Q 042039           83 QPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG  135 (376)
Q Consensus        83 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  135 (376)
                      . ++.++..++.++...|++++|...|+.+++.+ +.+..+...+..+..+.+
T Consensus        94 ~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~-P~n~~~~~~l~~~~~~~~  144 (170)
T d1p5qa1          94 N-NEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIR  144 (170)
T ss_dssp             T-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHH
T ss_pred             c-chhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Confidence            4 78899999999999999999999999999874 235555555555544433

>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=98.64  E-value=2.7e-07  Score=62.18  Aligned_cols=97  Identities=12%  Similarity=0.143  Sum_probs=65.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCC-Cc-----hHhHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQ-PS-----VVTFNV   91 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~-----~~~~~~   91 (376)
                      .+..+...+.+.|++++|+..|++.++.+ |.+..++..+..+|.+.|++++|++.++++++.... +.     ..+|..
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            35556677777788888888888777765 556777777788888888888888887777664211 00     124555


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhc
Q 042039           92 IMDELCKNGKMDEASRLLDLMVQR  115 (376)
Q Consensus        92 l~~~~~~~~~~~~a~~~~~~~~~~  115 (376)
                      +...+...+++++|...|++.+..
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhc
Confidence            666666677777777777766654

>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=98.64  E-value=1.9e-08  Score=85.22  Aligned_cols=228  Identities=8%  Similarity=-0.089  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHhcCCCCc-hHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh-hhHHHHHHHHHhcCcHHHHHHHHHH
Q 042039           69 EAKRLFFEMMDQGVQPS-VVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA-FTYSTLMDGFCLTGKINRAEELFGS  146 (376)
Q Consensus        69 ~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~  146 (376)
                      +|.+.|+++.+.  +|+ ...+..+..++...+++++|   |++++..+  |+. ..........  ...+..+.+.++.
T Consensus         4 eA~q~~~qA~~l--~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~d--p~~a~~~~~e~~Lw--~~~y~~~ie~~r~   74 (497)
T d1ya0a1           4 QSAQYLRQAEVL--KADMTDSKLGPAEVWTSRQALQDL---YQKMLVTD--LEYALDKKVEQDLW--NHAFKNQITTLQG   74 (497)
T ss_dssp             HHHHHHHHHHHH--HGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHC--HHHHHHHTHHHHHH--HHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHc--CCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcC--hhhHHHHhHHHHHH--HHHHHHHHHHHHH
Confidence            688899998875  444 45667777888888888775   67776542  221 1111111111  1224566777777


Q ss_pred             HHhcCCCCChhhHHH--HHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCC
Q 042039          147 MESMGCKHDDVSYNI--LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAA  224 (376)
Q Consensus       147 ~~~~~~~~~~~~~~~--l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  224 (376)
                      .......++..-...  ........+.++.++..+....+. .+++...+..+...+.+.++.+.|...+.......   
T Consensus        75 ~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---  150 (497)
T d1ya0a1          75 QAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNV-DLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI---  150 (497)
T ss_dssp             HHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHH---
T ss_pred             hcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---
Confidence            665432233222221  122223344555555555544443 23356677788888889999999998887776543   


Q ss_pred             CcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHH
Q 042039          225 DTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIH  304 (376)
Q Consensus       225 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  304 (376)
                      ...++..++..+...|++++|+..|+++....+ .+...|+.++..+...|+..+|...|.+.... .+|...++..|..
T Consensus       151 ~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P-~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~-~~~~~~a~~nL~~  228 (497)
T d1ya0a1         151 CQHCLVHLGDIARYRNQTSQAESYYRHAAQLVP-SNGQPYNQLAILASSKGDHLTTIFYYCRSIAV-KFPFPAASTNLQK  228 (497)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSS-SBCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCC-CchHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHH
Confidence            235778889999999999999999999988863 37789999999999999999999999998876 4677888888888


Q ss_pred             HHHccCC
Q 042039          305 GLCNDGQ  311 (376)
Q Consensus       305 ~~~~~~~  311 (376)
                      .+.+..+
T Consensus       229 ~~~~~~~  235 (497)
T d1ya0a1         229 ALSKALE  235 (497)
T ss_dssp             HHHHHTT
T ss_pred             HHHHhhh
Confidence            7765443

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.57  E-value=1.4e-06  Score=60.66  Aligned_cols=61  Identities=16%  Similarity=0.033  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039           89 FNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus        89 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      |..+..+|.+.|++++|+..++.+++.+ +.+..+|..++.++...|++++|...|++..+.
T Consensus        70 ~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1          70 NLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3344444444444444444444444432 223444444444444444444444444444444

>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=98.55  E-value=9.6e-07  Score=59.35  Aligned_cols=95  Identities=9%  Similarity=0.132  Sum_probs=54.8

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCCh-------hhHHH
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNA-------FTYST  126 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~  126 (376)
                      +..++..+...|++++|++.|++.++.++. +...+..+..+|...|++++|+..++++++... .+.       .+|..
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~-~~~~~~~~~a~~~~~   84 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR-ENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH-HSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHH
Confidence            445566666667777777777766665433 556666666666666777777766666655321 111       23444


Q ss_pred             HHHHHHhcCcHHHHHHHHHHHHhc
Q 042039          127 LMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       127 l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      +...+...+++++|.+.|++....
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhc
Confidence            444555555566666666555443

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.55  E-value=1.5e-06  Score=60.45  Aligned_cols=109  Identities=12%  Similarity=0.006  Sum_probs=87.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCCC----CCC-----------hhhHHHHHHHHhcCCChHHHHHHHHHHHhcC
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGENI----NPD-----------VVTYNSLIHGLCHANDWNEAKRLFFEMMDQG   81 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~----~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   81 (376)
                      ..+..-...+.+.|++.+|+..|+++...-.    .++           ..+|..++.+|.+.|++++|++.++++++.+
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~   97 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID   97 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc
Confidence            3456677789999999999999999875421    111           2367778999999999999999999999985


Q ss_pred             CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHH
Q 042039           82 VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTL  127 (376)
Q Consensus        82 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  127 (376)
                      +. +..+|..++.++...|++++|...|++.++.+ +-+..+...+
T Consensus        98 p~-~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~-P~n~~~~~~l  141 (153)
T d2fbna1          98 KN-NVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSY  141 (153)
T ss_dssp             TT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHH
T ss_pred             ch-hhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence            43 78899999999999999999999999999874 2245444443

>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=98.52  E-value=1.1e-06  Score=62.45  Aligned_cols=86  Identities=13%  Similarity=-0.035  Sum_probs=59.4

Q ss_pred             chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHH
Q 042039           85 SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILIN  164 (376)
Q Consensus        85 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  164 (376)
                      ....+..+..++.+.|++++|+..++++++.. +.+..+|..++.++...|++++|...|+++.+.. |.+..+...+..
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-p~n~~~~~~l~~  153 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLK  153 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            34456667777777888888888888877764 3456777777888888888888888888777765 455666666665


Q ss_pred             HHHccCcH
Q 042039          165 GYCKNKEV  172 (376)
Q Consensus       165 ~~~~~~~~  172 (376)
                      +..+....
T Consensus       154 ~~~~l~~~  161 (169)
T d1ihga1         154 VKQKIKAQ  161 (169)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55444333

>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=98.51  E-value=2.1e-06  Score=60.81  Aligned_cols=96  Identities=10%  Similarity=-0.017  Sum_probs=41.7

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhc---CCCC-----------chHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCC
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQ---GVQP-----------SVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRP  119 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  119 (376)
                      +...+..+.+.|++.+|+..|++.+..   ....           ...+|..+..+|.+.|++++|+..++..++.+ +.
T Consensus        18 ~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~   96 (168)
T d1kt1a1          18 VKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SA   96 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-cc
Confidence            444455555566666666666555432   0000           01123333444444444444444444444432 22


Q ss_pred             ChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039          120 NAFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       120 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      +..++..++.++...|++++|...|+++...
T Consensus        97 ~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          97 NEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3444444444444444444444444444443

>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=98.50  E-value=1.8e-06  Score=61.31  Aligned_cols=132  Identities=8%  Similarity=-0.004  Sum_probs=88.3

Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhc
Q 042039           55 NSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLT  134 (376)
Q Consensus        55 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  134 (376)
                      ......+...|++++|++.|.++++.  .+.          .........       .... -+.....+..++.++.+.
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~--~~~----------~~~~~~~~~-------~~~~-~~~~~~~~~nla~~~~~~   90 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRY--VEG----------SRAAAEDAD-------GAKL-QPVALSCVLNIGACKLKM   90 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--HHH----------HHHHSCHHH-------HGGG-HHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh--hhh----------hhhhhhhHH-------HHHh-ChhhHHHHHHHHHHHHhh
Confidence            34556667778888888888776642  000          000000000       0010 012355677788899999


Q ss_pred             CcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchH
Q 042039          135 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVE  208 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  208 (376)
                      |++++|+..+.++.+.. |.++.+|..++.++...|++++|+..|+++++.. +.+..+...+..+........
T Consensus        91 ~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-p~n~~~~~~l~~~~~~l~~~~  162 (169)
T d1ihga1          91 SDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVKQKIKAQK  162 (169)
T ss_dssp             TCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHH
Confidence            99999999999999886 6788899999999999999999999999999862 335566666665554444433

>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=98.46  E-value=2.6e-06  Score=60.28  Aligned_cols=118  Identities=6%  Similarity=-0.068  Sum_probs=91.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhhhC---CCCC-----------ChhhHHHHHHHHhcCCChHHHHHHHHHHHhcC
Q 042039           16 TVTYNTIIDGLCKEGFVDKAKALFLQMKGE---NINP-----------DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQG   81 (376)
Q Consensus        16 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~---~~~~-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   81 (376)
                      ...+......+.+.|++++|+..|++.+..   ....           ...+|..+..+|...|++++|+..+++.++..
T Consensus        15 a~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          15 AAIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            345667788899999999999999887642   1111           12346678889999999999999999999975


Q ss_pred             CCCchHhHHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcC
Q 042039           82 VQPSVVTFNVIMDELCKNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTG  135 (376)
Q Consensus        82 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  135 (376)
                      +. +..+|..+..++...|++++|...|+++++.. +.+..+...+..+....+
T Consensus        95 p~-~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~-P~n~~~~~~l~~~~~~~~  146 (168)
T d1kt1a1          95 SA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQIFMCQKKAK  146 (168)
T ss_dssp             TT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHH
T ss_pred             cc-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Confidence            44 78899999999999999999999999999874 345555555555544443

>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=98.35  E-value=7.5e-06  Score=58.25  Aligned_cols=124  Identities=9%  Similarity=0.016  Sum_probs=70.8

Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHcc
Q 042039          230 NTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCND  309 (376)
Q Consensus       230 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  309 (376)
                      ...+......|++++|.+.|..+......+ ..         ......+-+...-..+..    .....+..++.++...
T Consensus        15 ~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~-~l---------~~~~~~~w~~~~r~~l~~----~~~~a~~~la~~~~~~   80 (179)
T d2ff4a2          15 KTAGVHAAAAGRFEQASRHLSAALREWRGP-VL---------DDLRDFQFVEPFATALVE----DKVLAHTAKAEAEIAC   80 (179)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCSS-TT---------GGGTTSTTHHHHHHHHHH----HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhCccc-cc---------ccCcchHHHHHHHHHHHH----HHHHHHHHHHHHHHHC
Confidence            344456677888888888888876543111 00         000000000000001111    0234556667777777


Q ss_pred             CChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHh-----CCCCCchHH
Q 042039          310 GQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKE-----KKVMPDASI  368 (376)
Q Consensus       310 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~  368 (376)
                      |++++|+..++++++... -+...|..++.+|.+.|++++|++.|+++.+     .|+.|...+
T Consensus        81 g~~~~Al~~~~~al~~~P-~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          81 GRASAVIAELEALTFEHP-YREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             TCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             CCchHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            777777777777776542 2666777777777777777777777777643     477777654

>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=98.31  E-value=5.5e-07  Score=68.65  Aligned_cols=123  Identities=11%  Similarity=0.068  Sum_probs=69.1

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHhCCChHHH
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCKNGKMDEA  105 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  105 (376)
                      ..+.|++++|+..+++.++.. |.+...+..++..++..|++++|.+.++...+..+. +...+..+...+...+..+++
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-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhccccHHH
Confidence            456788888888888877775 667778888888888888888888888887775322 233443343333322222221


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhc
Q 042039          106 SRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESM  150 (376)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  150 (376)
                      ..........+.+++...+...+..+...|+.++|.+.++++.+.
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            111111000111112233334455566667777777777666554

>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=98.26  E-value=5.4e-06  Score=56.86  Aligned_cols=56  Identities=18%  Similarity=0.236  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccC-----------cHHHHHHHHHHHHHCCCCCCHhHHH
Q 042039          137 INRAEELFGSMESMGCKHDDVSYNILINGYCKNK-----------EVEEALSLYREMVSKGIKPTVVTYN  195 (376)
Q Consensus       137 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----------~~~~a~~~~~~~~~~~~~~~~~~~~  195 (376)
                      +++|...|+++.+.+ |.+..+|..++.+|...|           .+++|.+.|++.++.  .|+...+.
T Consensus        57 ~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~  123 (145)
T d1zu2a1          57 IQEAITKFEEALLID-PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYL  123 (145)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHHHHHHHHHHHHhc-chhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHH
Confidence            455666666666554 455556666666655443           246666666666663  44444443

>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=98.25  E-value=1.5e-05  Score=56.72  Aligned_cols=125  Identities=10%  Similarity=0.012  Sum_probs=88.6

Q ss_pred             HHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhC
Q 042039          195 NTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKS  274 (376)
Q Consensus       195 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  274 (376)
                      ..........|++++|...|...+...  +....        ......+.+...-..+.    +.....+..++..+...
T Consensus        15 ~~~g~~~~~~g~~e~A~~~~~~AL~l~--rG~~l--------~~~~~~~w~~~~r~~l~----~~~~~a~~~la~~~~~~   80 (179)
T d2ff4a2          15 KTAGVHAAAAGRFEQASRHLSAALREW--RGPVL--------DDLRDFQFVEPFATALV----EDKVLAHTAKAEAEIAC   80 (179)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTC--CSSTT--------GGGTTSTTHHHHHHHHH----HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhC--ccccc--------ccCcchHHHHHHHHHHH----HHHHHHHHHHHHHHHHC
Confidence            344567788999999999999998752  11100        00011111111111111    11346778889999999


Q ss_pred             CChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH-----cCCCCcHHHH
Q 042039          275 GRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEE-----NAVAPNVIIF  334 (376)
Q Consensus       275 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  334 (376)
                      |++++|+..++++... .+.+...|..++.++...|+..+|++.|+++.+     .|+.|...+-
T Consensus        81 g~~~~Al~~~~~al~~-~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          81 GRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             TCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             CCchHHHHHHHHHHHh-CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            9999999999999887 567889999999999999999999999998843     5888887653

>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=98.25  E-value=3.5e-06  Score=57.82  Aligned_cols=72  Identities=11%  Similarity=-0.080  Sum_probs=46.7

Q ss_pred             HHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCC----------hHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 042039           26 LCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHAND----------WNEAKRLFFEMMDQGVQPSVVTFNVIMDE   95 (376)
Q Consensus        26 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   95 (376)
                      |-+.+.+++|+..|+...+.+ |.++.++..+..++...++          +++|+..|+++++.++. +..+|..+..+
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~-~~~a~~~lG~~   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcch-hhHHHhhHHHH
Confidence            345566888888888888776 7778888888877765433          45566666666655332 45555555555


Q ss_pred             HHhC
Q 042039           96 LCKN   99 (376)
Q Consensus        96 ~~~~   99 (376)
                      |...
T Consensus        85 y~~~   88 (145)
T d1zu2a1          85 YTSF   88 (145)
T ss_dssp             HHHH
T ss_pred             HHHc
Confidence            5443

>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=98.20  E-value=2.8e-06  Score=64.69  Aligned_cols=123  Identities=17%  Similarity=0.079  Sum_probs=67.9

Q ss_pred             HHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHH
Q 042039          201 LFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIA  280 (376)
Q Consensus       201 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  280 (376)
                      ..+.|++++|+..+++.++.. |.+...+..++..++..|++++|...++.+.+..+. +...+..+...+...+..+++
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-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhccccHHH
Confidence            345566677777776666664 556666666777777777777777777766655422 344444444444433444333


Q ss_pred             HHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          281 LELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       281 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      ..-.......+.+++...+...+..+...|+.++|.+.++++.+.
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            322222111112223333444455566677777777777776654

>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=98.01  E-value=0.0017  Score=50.62  Aligned_cols=253  Identities=11%  Similarity=0.068  Sum_probs=138.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 042039           18 TYNTIIDGLCKEGFVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELC   97 (376)
Q Consensus        18 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   97 (376)
                      -|..++..+.+.++++.|.+++.+..      +..+|..+...+.+..+..-+.     +.......++.....++..|-
T Consensus        42 d~~rl~~~~v~l~~~~~avd~~~k~~------~~~~~k~~~~~l~~~~e~~la~-----i~~~~~~~~~d~l~~~v~~ye  110 (336)
T d1b89a_          42 NFGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVCFACVDGKEFRLAQ-----MCGLHIVVHADELEELINYYQ  110 (336)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHHHHHHHTTCHHHHH-----HTTTTTTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhhccHHHHHHHHHHcC------CHHHHHHHHHHHHhCcHHHHHH-----HHHHHhhcCHHHHHHHHHHHH
Confidence            35567777778888888777765432      5678888888888877665432     223333345566677889999


Q ss_pred             hCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHccCcHHHHHH
Q 042039           98 KNGKMDEASRLLDLMVQRDVRPNAFTYSTLMDGFCLTGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  177 (376)
Q Consensus        98 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  177 (376)
                      ..|.+++...+++...... ..+...++.++..|++.+. ++..+.+.....   .   .....++..|.+.+-++++.-
T Consensus       111 ~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~~-~kl~e~l~~~s~---~---y~~~k~~~~c~~~~l~~elv~  182 (336)
T d1b89a_         111 DRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKP-QKMREHLELFWS---R---VNIPKVLRAAEQAHLWAELVF  182 (336)
T ss_dssp             HTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCH-HHHHHHHHHHST---T---SCHHHHHHHHHTTTCHHHHHH
T ss_pred             HcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhCh-HHHHHHHHhccc---c---CCHHHHHHHHHHcCChHHHHH
Confidence            9999999999999887542 4567788889999988754 344444433211   1   112233444444444444444


Q ss_pred             HHHHHHHC--------CCCCCHhHHHHHHHHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHH
Q 042039          178 LYREMVSK--------GIKPTVVTYNTLFLGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELF  249 (376)
Q Consensus       178 ~~~~~~~~--------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  249 (376)
                      ++.++...        ..+++..-....+..+.+..+++...++....++.    ++.....++......-+..+.+   
T Consensus       183 Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~----~p~~i~~lL~~v~~~~d~~r~V---  255 (336)
T d1b89a_         183 LYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEF----KPLLLNDLLMVLSPRLDHTRAV---  255 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH----CGGGHHHHHHHHGGGCCHHHHH---
T ss_pred             HHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHHHHHc----CHHHHHHHHHHhccCCCHHHHH---
Confidence            44332110        01222222233334444444444444333333322    1222333333333333333333   


Q ss_pred             HHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHH
Q 042039          250 RTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDL  318 (376)
Q Consensus       250 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  318 (376)
                                         ..+.+.++..-...+++.....+   +..+.+.+...|...++++.-.+.
T Consensus       256 -------------------~~~~k~~~l~li~p~Le~v~~~n---~~~vn~al~~lyie~~d~~~l~~~  302 (336)
T d1b89a_         256 -------------------NYFSKVKQLPLVKPYLRSVQNHN---NKSVNESLNNLFITEEDYQALRTS  302 (336)
T ss_dssp             -------------------HHHHHTTCTTTTHHHHHHHHTTC---CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             -------------------HHHHhcCCcHHHHHHHHHHHHcC---hHHHHHHHHHHHhCcchhHHHHHH
Confidence                               33344455555555555544432   345777788888888886554333

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.96  E-value=8.2e-05  Score=51.55  Aligned_cols=98  Identities=16%  Similarity=0.083  Sum_probs=53.1

Q ss_pred             hhHHHH--HHHHHhcCChhHHHHHHHHhhhCCC-CC----------ChhhHHHHHHHHhcCCChHHHHHHHHHHHhc---
Q 042039           17 VTYNTI--IDGLCKEGFVDKAKALFLQMKGENI-NP----------DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ---   80 (376)
Q Consensus        17 ~~~~~l--~~~~~~~g~~~~a~~~~~~~~~~~~-~~----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---   80 (376)
                      .+|..+  ...+.+.|++++|+..|++.++... .|          ....|+.+..+|...|++++|...+++.++.   
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            455555  4455566777777777777765321 01          1245666666666666666666666665542   


Q ss_pred             --CCCCc-----hHhHHHHHHHHHhCCChHHHHHHHHHHHh
Q 042039           81 --GVQPS-----VVTFNVIMDELCKNGKMDEASRLLDLMVQ  114 (376)
Q Consensus        81 --~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  114 (376)
                        ...++     ...+..+..+|...|++++|+..|++.++
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              01111     11344455555555555555555555543

>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=97.89  E-value=4.1e-05  Score=47.87  Aligned_cols=64  Identities=11%  Similarity=-0.029  Sum_probs=34.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhhhCC-----CCC-ChhhHHHHHHHHhcCCChHHHHHHHHHHHhc
Q 042039           17 VTYNTIIDGLCKEGFVDKAKALFLQMKGEN-----INP-DVVTYNSLIHGLCHANDWNEAKRLFFEMMDQ   80 (376)
Q Consensus        17 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-----~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   80 (376)
                      ..+..+...+.+.|++++|+..|++..+..     ..+ ...++..++.++.+.|++++|++.++++++.
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            334455555666666666666666554321     011 1344555566666666666666666665554

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.81  E-value=0.00025  Score=49.03  Aligned_cols=56  Identities=18%  Similarity=0.162  Sum_probs=28.1

Q ss_pred             HHHHhcCCChHHHHHHHHHHHhcCCC-Cc----------hHhHHHHHHHHHhCCChHHHHHHHHHHH
Q 042039           58 IHGLCHANDWNEAKRLFFEMMDQGVQ-PS----------VVTFNVIMDELCKNGKMDEASRLLDLMV  113 (376)
Q Consensus        58 ~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~  113 (376)
                      +..+...|++++|++.|++.++.... |+          ...|+.+..+|...|++++|...+++.+
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al   82 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL   82 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhh
Confidence            34455556666666666666553111 11          1334445555555555555555554444

>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=97.71  E-value=0.00037  Score=43.33  Aligned_cols=61  Identities=13%  Similarity=0.108  Sum_probs=25.8

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHhcCC-----CC-chHhHHHHHHHHHhCCChHHHHHHHHHHHh
Q 042039           54 YNSLIHGLCHANDWNEAKRLFFEMMDQGV-----QP-SVVTFNVIMDELCKNGKMDEASRLLDLMVQ  114 (376)
Q Consensus        54 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  114 (376)
                      +..++..+.+.|++++|+..|++.++...     .+ ...++..+..++.+.|++++|...++++++
T Consensus         8 c~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_           8 SFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            33444444555555555555544443200     00 122344444444444444444444444444

>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=97.60  E-value=0.0021  Score=42.68  Aligned_cols=48  Identities=15%  Similarity=0.211  Sum_probs=21.9

Q ss_pred             cHHHHHHHHHHHHhcCCCCChhhHHHHHHHHHc----cCcHHHHHHHHHHHHHCC
Q 042039          136 KINRAEELFGSMESMGCKHDDVSYNILINGYCK----NKEVEEALSLYREMVSKG  186 (376)
Q Consensus       136 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  186 (376)
                      +.++|.++|++..+.+   ++.+...|...|..    ..+.++|.++|++..+.|
T Consensus        74 d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          74 DLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            3445555555554443   23333344444433    234555555555555443

>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=97.49  E-value=0.0029  Score=41.95  Aligned_cols=110  Identities=11%  Similarity=0.014  Sum_probs=55.2

Q ss_pred             ChhHHHHHHHHhhhCCCCCChhhHHHHHHHHhcCCChHHHHHHHHHHHhcCCCCchHhHHHHHHHHHh----CCChHHHH
Q 042039           31 FVDKAKALFLQMKGENINPDVVTYNSLIHGLCHANDWNEAKRLFFEMMDQGVQPSVVTFNVIMDELCK----NGKMDEAS  106 (376)
Q Consensus        31 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~  106 (376)
                      |+++|+.+|++..+.|   +......|..  ....+.++|.+++++..+.|   ++.....+...|..    ..+.++|.
T Consensus         8 d~~~A~~~~~kaa~~g---~~~a~~~l~~--~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~   79 (133)
T d1klxa_           8 DLKKAIQYYVKACELN---EMFGCLSLVS--NSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTT---CTTHHHHHHT--CTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHCC---Chhhhhhhcc--ccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHH
Confidence            4556666666665554   2223333322  22345566666666655543   33344444444443    23456666


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHh----cCcHHHHHHHHHHHHhcC
Q 042039          107 RLLDLMVQRDVRPNAFTYSTLMDGFCL----TGKINRAEELFGSMESMG  151 (376)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  151 (376)
                      ++|++..+.+   ++.....+...|..    ..+.++|.++|++..+.|
T Consensus        80 ~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          80 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            6666665554   33444445554443    235566666666655554

>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=96.34  E-value=0.029  Score=35.88  Aligned_cols=64  Identities=9%  Similarity=-0.006  Sum_probs=34.8

Q ss_pred             ChhhHHHHHHHHHhc---CcHHHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHccCcHHHHHHHHHHHHH
Q 042039          120 NAFTYSTLMDGFCLT---GKINRAEELFGSMESMGCKHD-DVSYNILINGYCKNKEVEEALSLYREMVS  184 (376)
Q Consensus       120 ~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  184 (376)
                      ...+-...+.++.++   .+.++++.+++.+...+ +.+ ...+..|.-+|.+.|++++|.+.++.+++
T Consensus        34 s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          34 TIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            344444455555544   23455666666665543 222 23555566666666666666666666666

>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=96.19  E-value=0.03  Score=35.77  Aligned_cols=64  Identities=16%  Similarity=0.114  Sum_probs=28.6

Q ss_pred             hHHHHHHHHHHHHhCC---ChHHHHHHHhcccccCCCCC-HHHHHHHHHHHHccCChhHHHHHHHHHHH
Q 042039          260 DIQAYNCLIDGLCKSG---RLEIALELFRSLPRRVLVAD-VVTYNIMIHGLCNDGQMDKAHDLFLDMEE  324 (376)
Q Consensus       260 ~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  324 (376)
                      +..+-...+.++.+..   +.++++.+++.+.+. .+.+ ...+..++.+|.+.|++++|.+.++.+++
T Consensus        34 s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~-~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          34 TIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKE-AESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHH-CGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhc-CchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            3444444444444432   233455555544432 1112 23444455555555555555555555554

>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=95.50  E-value=0.14  Score=32.41  Aligned_cols=61  Identities=15%  Similarity=0.135  Sum_probs=28.7

Q ss_pred             HHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCC
Q 042039          266 CLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAV  327 (376)
Q Consensus       266 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  327 (376)
                      ..+..+..+|+-++-.+++..+.+. -.+++.....++.+|.+.|...++-+++.++-+.|+
T Consensus        91 lALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~  151 (161)
T d1wy6a1          91 KALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGE  151 (161)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhH
Confidence            3344444455555555554443332 334444444555555555555555555555554443

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=95.36  E-value=0.53  Score=38.08  Aligned_cols=181  Identities=11%  Similarity=-0.052  Sum_probs=99.4

Q ss_pred             CcHHHHHHHHHHHHHCCCCCCHhHHHHHH----HHHHhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHH
Q 042039          170 KEVEEALSLYREMVSKGIKPTVVTYNTLF----LGLFEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEA  245 (376)
Q Consensus       170 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  245 (376)
                      .+.+.+...+........ .+...+..+.    ......+..+.+...+.......  .+.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQQ-LNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHTT-CCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhccc-ccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc--cchHHHHHHHHHHHHcCChHHH
Confidence            456666666666554321 1222222221    22223445566666665554442  2333344444455566777777


Q ss_pred             HHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHHHHHhccccc------------CCCC-----------CH----HH
Q 042039          246 VELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIALELFRSLPRR------------VLVA-----------DV----VT  298 (376)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------------~~~~-----------~~----~~  298 (376)
                      ...+..+.... ........-+++++...|+.+.|...|..+...            |.++           ..    ..
T Consensus       305 ~~~~~~l~~~~-~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~~~~fYG~LAa~~Lg~~~~~~~~~~~~~~~~~~~~~~  383 (450)
T d1qsaa1         305 NTWLARLPMEA-KEKDEWRYWQADLLLERGREAEAKEILHQLMQQRGFYPMVAAQRIGEEYELKIDKAPQNVDSALTQGP  383 (450)
T ss_dssp             HHHHHHSCTTG-GGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSHHHHHHHHHTTCCCCCCCCCCCSCCCCHHHHSH
T ss_pred             HHHHHhcCccc-ccHHHHHHHHHHHHHHcCChhhHHHHHHHHhcCCChHHHHHHHHcCCCCCCCcCCCCccHHHhhhcCh
Confidence            77777764322 223445556677777778887777777764321            0000           00    00


Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHH
Q 042039          299 YNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKM  357 (376)
Q Consensus       299 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  357 (376)
                      -..-+..+...|+...|...|..+...   .+......+.....+.|.++.|+....+.
T Consensus       384 ~~~ra~~L~~~g~~~~A~~e~~~l~~~---~~~~~~~~la~lA~~~g~~~~aI~a~~~~  439 (450)
T d1qsaa1         384 EMARVRELMYWNLDNTARSEWANLVKS---KSKTEQAQLARYAFNNQWWDLSVQATIAG  439 (450)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTT---CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCchHHHHHHHHHHhC---CCHHHHHHHHHHHHHCCChhHHHHHHHHH
Confidence            112345566778888888887777653   24445556666777788888887766655

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=95.14  E-value=0.63  Score=37.64  Aligned_cols=182  Identities=10%  Similarity=-0.004  Sum_probs=118.0

Q ss_pred             CcHHHHHHHHHHHHhcCCCCChhhHH----HHHHHHHccCcHHHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhccchHHH
Q 042039          135 GKINRAEELFGSMESMGCKHDDVSYN----ILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  210 (376)
Q Consensus       135 ~~~~~a~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  210 (376)
                      .+.+.+...+....... ..+...+.    .+.......+..+.+...+......+  .+.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhcc-cccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc--cchHHHHHHHHHHHHcCChHHH
Confidence            46777777777776543 22222222    22233344566778888877776643  3444444455556677889988


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhccc------------CCCc-----------h----HHH
Q 042039          211 LKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGIL------------KCEL-----------D----IQA  263 (376)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------------~~~~-----------~----~~~  263 (376)
                      ...+..+... ..........+++++...|+.+.|...|..+...            |.++           .    ...
T Consensus       305 ~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~~~~fYG~LAa~~Lg~~~~~~~~~~~~~~~~~~~~~~  383 (450)
T d1qsaa1         305 NTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQQRGFYPMVAAQRIGEEYELKIDKAPQNVDSALTQGP  383 (450)
T ss_dssp             HHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSHHHHHHHHHTTCCCCCCCCCCCSCCCCHHHHSH
T ss_pred             HHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhcCCChHHHHHHHHcCCCCCCCcCCCCccHHHhhhcCh
Confidence            8888877443 2334556678888999999999999988886211            1000           0    001


Q ss_pred             HHHHHHHHHhCCChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHH
Q 042039          264 YNCLIDGLCKSGRLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDME  323 (376)
Q Consensus       264 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  323 (376)
                      -...+..+...|+...|...|..+...   .+......++....+.|.++.|+....+..
T Consensus       384 ~~~ra~~L~~~g~~~~A~~e~~~l~~~---~~~~~~~~la~lA~~~g~~~~aI~a~~~~~  440 (450)
T d1qsaa1         384 EMARVRELMYWNLDNTARSEWANLVKS---KSKTEQAQLARYAFNNQWWDLSVQATIAGK  440 (450)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTT---CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCchHHHHHHHHHHhC---CCHHHHHHHHHHHHHCCChhHHHHHHHHHH
Confidence            123356677889999999999887654   255666778888899999999998776653

>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=94.93  E-value=0.23  Score=31.49  Aligned_cols=140  Identities=19%  Similarity=0.161  Sum_probs=97.1

Q ss_pred             HhccchHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCCCHHHHHHHHHHhcccCCCchHHHHHHHHHHHHhCCChHHHH
Q 042039          202 FEIHQVEHALKLFEEMQRDDVAADTSTYNTFIDGLCKNGYIVEAVELFRTLGILKCELDIQAYNCLIDGLCKSGRLEIAL  281 (376)
Q Consensus       202 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  281 (376)
                      .-.|..++..+++.+...+.   +..-++.++--....-+-+-....++.+...-   |          ...+++.....
T Consensus        13 ildG~ve~Gveii~k~~~ss---~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~F---D----------ls~C~Nlk~vv   76 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSYF---D----------LDKCQNLKSVV   76 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGS---C----------GGGCSCTHHHH
T ss_pred             HHhhhHHhHHHHHHHHcccC---CccccceeeeecccccchHHHHHHHHHHhhhc---C----------chhhhcHHHHH
Confidence            34567777777777766542   34445555555555566666666666654321   1          12355555555


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHHhCC
Q 042039          282 ELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMKEKK  361 (376)
Q Consensus       282 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  361 (376)
                      ..+-.+-.     +...+...+.....+|+-+.-.++++.+.+. -+|++.....+..+|.+.|...++.+++.++-++|
T Consensus        77 ~C~~~~n~-----~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G  150 (161)
T d1wy6a1          77 ECGVINNT-----LNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKG  150 (161)
T ss_dssp             HHHHHTTC-----CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHhcc-----hHHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHh
Confidence            55544322     4566777788899999999999999998775 47788899999999999999999999999999998


Q ss_pred             CC
Q 042039          362 VM  363 (376)
Q Consensus       362 ~~  363 (376)
                      +.
T Consensus       151 ~K  152 (161)
T d1wy6a1         151 EK  152 (161)
T ss_dssp             CH
T ss_pred             HH
Confidence            64

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.91  E-value=0.18  Score=30.19  Aligned_cols=45  Identities=13%  Similarity=0.194  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHhhcCChhhHHHHHHHHH
Q 042039          314 KAHDLFLDMEENAVAPNVIIFVTLIHGFVRINKPSKVIELLHKMK  358 (376)
Q Consensus       314 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  358 (376)
                      ++.+-+..+...++.|++.+....+++|.+.+++.-|.++++...
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK   68 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVK   68 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            344444444444455555555555555555555555555555444

>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=89.23  E-value=1.3  Score=26.38  Aligned_cols=50  Identities=8%  Similarity=-0.025  Sum_probs=30.8

Q ss_pred             ChHHHHHHHhcccccCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHc
Q 042039          276 RLEIALELFRSLPRRVLVADVVTYNIMIHGLCNDGQMDKAHDLFLDMEEN  325 (376)
Q Consensus       276 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  325 (376)
                      +.=++.+-+..+......|++......+++|.+.+++..|.++|+.+...
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            33345555555555556666666666777777777777777776666543