Citrus Sinensis ID: 011378

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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-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------
Protein Sequence
MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDAF
Secondary Structure (PSIPRED)
cHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
mvnalckdhkidSAKMFLCemeqkgvypdtvtYNTLINAYCREGFLEEAFQLMNsmsgkglkpgvfTYNSLINGLCKKGRCDRAKEVLDEMLqmglspdtatYNTLLVESCRKENMSEAEEIFCEMsrrgvapdiVSFSTLIGIFSRNGQLDRALMYFREMksaglvpdnVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMlergvfpdfytfttlihghckdgnmnkaLNLFdimtqksikpdivtYNTLIDGFCKVGEMEKANKLWADMISrkispnyisYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKgycrsgdaskADEFLSKMVsegvdpdsisynTLINGFVREENMDKAFALVSKMenqglvpdviTYNVILTGfcrqgrmhdSELILWRMIEkglnpdrstyTTLINGHVSQNNLKEAFRFHDemlqrgfvpddaf
Flexible Loop (DISEMBL)
mvnalckdhkidsAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLqmglspdtatYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVsegvdpdsisYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQrgfvpddaf
Low Complexity Region (SEG)
MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDAF
Disordered region (IsUnstruct)
*****CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA*****FLSKMV**GVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM***********
Disordered Region (DISOPRED)
MVNALC*DHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDAF
Disordered Region (DISEMBL)
MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDAF
Disordered Region (DISPRO)
MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVP****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDAF
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	487	2.2.26 [Sep-21-2011]
Q9LFC5	729	Pentatricopeptide repeat-	yes	no	1.0	0.668	0.623	0.0
Q6NQ83	619	Pentatricopeptide repeat-	no	no	0.995	0.783	0.339	1e-89
Q0WVK7	741	Pentatricopeptide repeat-	no	no	0.928	0.609	0.335	5e-88
Q9ASZ8	621	Pentatricopeptide repeat-	no	no	0.991	0.777	0.324	5e-84
Q9CA58	763	Putative pentatricopeptid	no	no	0.993	0.634	0.334	2e-83
Q9FIX3	747	Pentatricopeptide repeat-	no	no	0.948	0.618	0.329	4e-83
Q3EDF8	598	Pentatricopeptide repeat-	no	no	0.950	0.774	0.326	2e-82
Q9CAN5	614	Pentatricopeptide repeat-	no	no	0.991	0.786	0.330	5e-82
Q76C99	791	Protein Rf1, mitochondria	N/A	no	0.942	0.580	0.321	1e-81
Q0WKV3	637	Pentatricopeptide repeat-	no	no	0.991	0.758	0.318	1e-81

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

 Score =  666 bits (1719), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 305/489 (62%), Positives = 389/489 (79%), Gaps = 2/489 (0%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K++    FL ++++KGVYPD VTYNTLI+AY  +G +EEAF+LMN+M GKG
Sbjct: 241 MVNALCKDGKMEKVGTFLSQVQEKGVYPDIVTYNTLISAYSSKGLMEEAFELMNAMPGKG 300

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
             PGV+TYN++INGLCK G+ +RAKEV  EML+ GLSPD+ TY +LL+E+C+K ++ E E
Sbjct: 301 FSPGVYTYNTVINGLCKHGKYERAKEVFAEMLRSGLSPDSTTYRSLLMEACKKGDVVETE 360

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           ++F +M  R V PD+V FS+++ +F+R+G LD+ALMYF  +K AGL+PDNV+YTI+I GY
Sbjct: 361 KVFSDMRSRDVVPDLVCFSSMMSLFTRSGNLDKALMYFNSVKEAGLIPDNVIYTILIQGY 420

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CR G +  A+ +R+EML++GC MDVVTYNTIL+GLC+ KML EAD LFNEM ER +FPD 
Sbjct: 421 CRKGMISVAMNLRNEMLQQGCAMDVVTYNTILHGLCKRKMLGEADKLFNEMTERALFPDS 480

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YT T LI GHCK GN+  A+ LF  M +K I+ D+VTYNTL+DGF KVG+++ A ++WAD
Sbjct: 481 YTLTILIDGHCKLGNLQNAMELFQKMKEKRIRLDVVTYNTLLDGFGKVGDIDTAKEIWAD 540

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+S++I P  ISY IL+N  CS GH+ EAFR+W EM+ K IKPT++ CN++IKGYCRSG+
Sbjct: 541 MVSKEILPTPISYSILVNALCSKGHLAEAFRVWDEMISKNIKPTVMICNSMIKGYCRSGN 600

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ--GLVPDVITY 418
           AS  + FL KM+SEG  PD ISYNTLI GFVREENM KAF LV KME +  GLVPDV TY
Sbjct: 601 ASDGESFLEKMISEGFVPDCISYNTLIYGFVREENMSKAFGLVKKMEEEQGGLVPDVFTY 660

Query: 419 NVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ 478
           N IL GFCRQ +M ++E++L +MIE+G+NPDRSTYT +ING VSQ+NL EAFR HDEMLQ
Sbjct: 661 NSILHGFCRQNQMKEAEVVLRKMIERGVNPDRSTYTCMINGFVSQDNLTEAFRIHDEMLQ 720

Query: 479 RGFVPDDAF 487
           RGF PDD F
Sbjct: 721 RGFSPDDKF 729

Arabidopsis thaliana (taxid: 3702)

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

 Score =  330 bits (846), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 165/486 (33%), Positives = 278/486 (57%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           M+N  C+  K+  A   L    + G  PDT+T++TL+N +C EG + EA  L++ M    
Sbjct: 111 MINCYCRKKKLLFAFSVLGRAWKLGYEPDTITFSTLVNGFCLEGRVSEAVALVDRMVEMK 170

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
            +P + T ++LINGLC KGR   A  ++D M++ G  PD  TY  +L   C+  N + A 
Sbjct: 171 QRPDLVTVSTLINGLCLKGRVSEALVLIDRMVEYGFQPDEVTYGPVLNRLCKSGNSALAL 230

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           ++F +M  R +   +V +S +I    ++G  D AL  F EM+  G+  D V Y+ +I G 
Sbjct: 231 DLFRKMEERNIKASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGL 290

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           C +G   +  KM  EM+ +  + DVVT++ +++   +   L EA +L+NEM+ RG+ PD 
Sbjct: 291 CNDGKWDDGAKMLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPDT 350

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
            T+ +LI G CK+  +++A  +FD+M  K  +PDIVTY+ LI+ +CK   ++   +L+ +
Sbjct: 351 ITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFRE 410

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           + S+ + PN I+Y  L+ G+C  G +  A  L+ EMV +G+ P++V+   ++ G C +G+
Sbjct: 411 ISSKGLIPNTITYNTLVLGFCQSGKLNAAKELFQEMVSRGVPPSVVTYGILLDGLCDNGE 470

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
            +KA E   KM    +      YN +I+G      +D A++L   + ++G+ PDV+TYNV
Sbjct: 471 LNKALEIFEKMQKSRMTLGIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNV 530

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           ++ G C++G + +++++  +M E G  PD  TY  LI  H+  + L  +    +EM   G
Sbjct: 531 MIGGLCKKGSLSEADMLFRKMKEDGCTPDDFTYNILIRAHLGGSGLISSVELIEEMKVCG 590

Query: 481 FVPDDA 486
           F  D +
Sbjct: 591 FSADSS 596

Arabidopsis thaliana (taxid: 3702)

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

 Score =  325 bits (833), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 152/453 (33%), Positives = 268/453 (59%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           +++ +C+  +I  A   L  ME KG  PD ++Y+T++N YCR G L++ ++L+  M  KG
Sbjct: 252 VIHFVCQLGRIKEAHHLLLLMELKGYTPDVISYSTVVNGYCRFGELDKVWKLIEVMKRKG 311

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKP  + Y S+I  LC+  +   A+E   EM++ G+ PDT  Y TL+   C++ ++  A 
Sbjct: 312 LKPNSYIYGSIIGLLCRICKLAEAEEAFSEMIRQGILPDTVVYTTLIDGFCKRGDIRAAS 371

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           + F EM  R + PD+++++ +I  F + G +  A   F EM   GL PD+V +T +INGY
Sbjct: 372 KFFYEMHSRDITPDVLTYTAIISGFCQIGDMVEAGKLFHEMFCKGLEPDSVTFTELINGY 431

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           C+ G + +A ++ + M++ GC  +VVTY T+++GLC+   L  A++L +EM + G+ P+ 
Sbjct: 432 CKAGHMKDAFRVHNHMIQAGCSPNVVTYTTLIDGLCKEGDLDSANELLHEMWKIGLQPNI 491

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           +T+ ++++G CK GN+ +A+ L        +  D VTY TL+D +CK GEM+KA ++  +
Sbjct: 492 FTYNSIVNGLCKSGNIEEAVKLVGEFEAAGLNADTVTYTTLMDAYCKSGEMDKAQEILKE 551

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+ + + P  +++ +L+NG+C  G + +  +L   M+ KGI P   + N+++K YC   +
Sbjct: 552 MLGKGLQPTIVTFNVLMNGFCLHGMLEDGEKLLNWMLAKGIAPNATTFNSLVKQYCIRNN 611

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
              A      M S GV PD  +Y  L+ G  +  NM +A+ L  +M+ +G    V TY+V
Sbjct: 612 LKAATAIYKDMCSRGVGPDGKTYENLVKGHCKARNMKEAWFLFQEMKGKGFSVSVSTYSV 671

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTY 453
           ++ GF ++ +  ++  +  +M  +GL  D+  +
Sbjct: 672 LIKGFLKRKKFLEAREVFDQMRREGLAADKEIF 704

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ASZ8|PPR37_ARATH Pentatricopeptide repeat-containing protein At1g12620 OS=Arabidopsis thaliana GN=At1g12620 PE=2 SV=1

 Score =  312 bits (799), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 157/484 (32%), Positives = 275/484 (56%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           M+N  C+  K+  A   + ++ + G  PDTVT++TLIN  C EG + EA +L++ M   G
Sbjct: 113 MINCCCRCRKLSLAFSAMGKIIKLGYEPDTVTFSTLINGLCLEGRVSEALELVDRMVEMG 172

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
            KP + T N+L+NGLC  G+   A  ++D M++ G  P+  TY  +L   C+    + A 
Sbjct: 173 HKPTLITLNALVNGLCLNGKVSDAVLLIDRMVETGFQPNEVTYGPVLKVMCKSGQTALAM 232

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           E+  +M  R +  D V +S +I    ++G LD A   F EM+  G   D ++YT +I G+
Sbjct: 233 ELLRKMEERKIKLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIIIYTTLIRGF 292

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           C  G   +  K+  +M+++    DVV ++ +++   +   L EA++L  EM++RG+ PD 
Sbjct: 293 CYAGRWDDGAKLLRDMIKRKITPDVVAFSALIDCFVKEGKLREAEELHKEMIQRGISPDT 352

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
            T+T+LI G CK+  ++KA ++ D+M  K   P+I T+N LI+G+CK   ++   +L+  
Sbjct: 353 VTYTSLIDGFCKENQLDKANHMLDLMVSKGCGPNIRTFNILINGYCKANLIDDGLELFRK 412

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M  R +  + ++Y  LI G+C +G +  A  L+ EMV + ++P +VS   ++ G C +G+
Sbjct: 413 MSLRGVVADTVTYNTLIQGFCELGKLEVAKELFQEMVSRRVRPDIVSYKILLDGLCDNGE 472

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
             KA E   K+    ++ D   YN +I+G      +D A+ L   +  +G+ PDV TYN+
Sbjct: 473 PEKALEIFEKIEKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPDVKTYNI 532

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           ++ G C++G + +++L+  +M E G +P+  TY  LI  H+ + +  ++ +  +E+ + G
Sbjct: 533 MIGGLCKKGSLSEADLLFRKMEEDGHSPNGCTYNILIRAHLGEGDATKSAKLIEEIKRCG 592

Query: 481 FVPD 484
           F  D
Sbjct: 593 FSVD 596

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CA58|PP120_ARATH Putative pentatricopeptide repeat-containing protein At1g74580 OS=Arabidopsis thaliana GN=At1g74580 PE=3 SV=1

 Score =  310 bits (793), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 162/485 (33%), Positives = 262/485 (54%), Gaps = 1/485 (0%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           ++  LCK   +   +  L ++ ++GV P+  TYN  I   C+ G L+ A +++  +  +G
Sbjct: 222 LLRVLCKKGDVKECEKLLDKVIKRGVLPNLFTYNLFIQGLCQRGELDGAVRMVGCLIEQG 281

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
            KP V TYN+LI GLCK  +   A+  L +M+  GL PD+ TYNTL+   C+   +  AE
Sbjct: 282 PKPDVITYNNLIYGLCKNSKFQEAEVYLGKMVNEGLEPDSYTYNTLIAGYCKGGMVQLAE 341

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            I  +    G  PD  ++ +LI      G+ +RAL  F E    G+ P+ +LY  +I G 
Sbjct: 342 RIVGDAVFNGFVPDQFTYRSLIDGLCHEGETNRALALFNEALGKGIKPNVILYNTLIKGL 401

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
              G +LEA ++ +EM EKG + +V T+N ++NGLC+   +++AD L   M+ +G FPD 
Sbjct: 402 SNQGMILEAAQLANEMSEKGLIPEVQTFNILVNGLCKMGCVSDADGLVKVMISKGYFPDI 461

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           +TF  LIHG+     M  AL + D+M    + PD+ TYN+L++G CK  + E   + +  
Sbjct: 462 FTFNILIHGYSTQLKMENALEILDVMLDNGVDPDVYTYNSLLNGLCKTSKFEDVMETYKT 521

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+ +  +PN  ++ IL+   C    + EA  L  EM  K + P  V+  T+I G+C++GD
Sbjct: 522 MVEKGCAPNLFTFNILLESLCRYRKLDEALGLLEEMKNKSVNPDAVTFGTLIDGFCKNGD 581

Query: 361 ASKADEFLSKM-VSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYN 419
              A     KM  +  V   + +YN +I+ F  + N+  A  L  +M ++ L PD  TY 
Sbjct: 582 LDGAYTLFRKMEEAYKVSSSTPTYNIIIHAFTEKLNVTMAEKLFQEMVDRCLGPDGYTYR 641

Query: 420 VILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQR 479
           +++ GFC+ G ++     L  M+E G  P  +T   +IN    ++ + EA      M+Q+
Sbjct: 642 LMVDGFCKTGNVNLGYKFLLEMMENGFIPSLTTLGRVINCLCVEDRVYEAAGIIHRMVQK 701

Query: 480 GFVPD 484
           G VP+
Sbjct: 702 GLVPE 706

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIX3|PP407_ARATH Pentatricopeptide repeat-containing protein At5g39710 OS=Arabidopsis thaliana GN=EMB2745 PE=2 SV=1

 Score =  309 bits (791), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 159/482 (32%), Positives = 277/482 (57%), Gaps = 20/482 (4%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           ++   C    ID A     +ME KG  P+ VTYNTLI+ YC+   +++ F+L+ SM+ KG
Sbjct: 211 LIRGFCFAGNIDVALTLFDKMETKGCLPNVVTYNTLIDGYCKLRKIDDGFKLLRSMALKG 270

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           L+P + +YN +INGLC++GR      VL EM + G S D  TYNTL+   C++ N  +A 
Sbjct: 271 LEPNLISYNVVINGLCREGRMKEVSFVLTEMNRRGYSLDEVTYNTLIKGYCKEGNFHQAL 330

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            +  EM R G+ P ++++++LI    + G ++RA+ +  +M+  GL P+   YT +++G+
Sbjct: 331 VMHAEMLRHGLTPSVITYTSLIHSMCKAGNMNRAMEFLDQMRVRGLCPNERTYTTLVDGF 390

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
            + G++ EA ++  EM + G    VVTYN ++NG C    + +A  +  +M E+G+ PD 
Sbjct: 391 SQKGYMNEAYRVLREMNDNGFSPSVVTYNALINGHCVTGKMEDAIAVLEDMKEKGLSPDV 450

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
            +++T++ G C+  ++++AL +   M +K IKPD +TY++LI GFC+    ++A  L+ +
Sbjct: 451 VSYSTVLSGFCRSYDVDEALRVKREMVEKGIKPDTITYSSLIQGFCEQRRTKEACDLYEE 510

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+   + P+  +Y  LIN YC  G + +A +L  EMV KG+ P +V+ + +I G  +   
Sbjct: 511 MLRVGLPPDEFTYTALINAYCMEGDLEKALQLHNEMVEKGVLPDVVTYSVLINGLNKQSR 570

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
             +A   L K+  E   P  ++Y+TLI      EN        S +E + +V        
Sbjct: 571 TREAKRLLLKLFYEESVPSDVTYHTLI------EN-------CSNIEFKSVVS------- 610

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           ++ GFC +G M +++ +   M+ K   PD + Y  +I+GH    ++++A+  + EM++ G
Sbjct: 611 LIKGFCMKGMMTEADQVFESMLGKNHKPDGTAYNIMIHGHCRAGDIRKAYTLYKEMVKSG 670

Query: 481 FV 482
           F+
Sbjct: 671 FL 672

Arabidopsis thaliana (taxid: 3702)

>sp|Q3EDF8|PPR28_ARATH Pentatricopeptide repeat-containing protein At1g09900 OS=Arabidopsis thaliana GN=At1g09900 PE=2 SV=1

 Score =  306 bits (784), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 152/466 (32%), Positives = 256/466 (54%), Gaps = 3/466 (0%)

Query: 17  FLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLC 76
           FL  M   G  PD +   TLI  +CR G   +A +++  + G G  P V TYN +I+G C
Sbjct: 124 FLENMVYHGNVPDIIPCTTLIRGFCRLGKTRKAAKILEILEGSGAVPDVITYNVMISGYC 183

Query: 77  KKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIV 136
           K G  + A  VLD   +M +SPD  TYNT+L   C    + +A E+   M +R   PD++
Sbjct: 184 KAGEINNALSVLD---RMSVSPDVVTYNTILRSLCDSGKLKQAMEVLDRMLQRDCYPDVI 240

Query: 137 SFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEM 196
           +++ LI    R+  +  A+    EM+  G  PD V Y +++NG C+ G + EA+K  ++M
Sbjct: 241 TYTILIEATCRDSGVGHAMKLLDEMRDRGCTPDVVTYNVLVNGICKEGRLDEAIKFLNDM 300

Query: 197 LEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM 256
              GC  +V+T+N IL  +C      +A+ L  +ML +G  P   TF  LI+  C+ G +
Sbjct: 301 PSSGCQPNVITHNIILRSMCSTGRWMDAEKLLADMLRKGFSPSVVTFNILINFLCRKGLL 360

Query: 257 NKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGIL 316
            +A+++ + M Q   +P+ ++YN L+ GFCK  +M++A +    M+SR   P+ ++Y  +
Sbjct: 361 GRAIDILEKMPQHGCQPNSLSYNPLLHGFCKEKKMDRAIEYLERMVSRGCYPDIVTYNTM 420

Query: 317 INGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGV 376
           +   C  G V +A  +  ++  KG  P L++ NT+I G  ++G   KA + L +M ++ +
Sbjct: 421 LTALCKDGKVEDAVEILNQLSSKGCSPVLITYNTVIDGLAKAGKTGKAIKLLDEMRAKDL 480

Query: 377 DPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSEL 436
            PD+I+Y++L+ G  RE  +D+A     + E  G+ P+ +T+N I+ G C+  +   +  
Sbjct: 481 KPDTITYSSLVGGLSREGKVDEAIKFFHEFERMGIRPNAVTFNSIMLGLCKSRQTDRAID 540

Query: 437 ILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFV 482
            L  MI +G  P+ ++YT LI G   +   KEA    +E+  +G +
Sbjct: 541 FLVFMINRGCKPNETSYTILIEGLAYEGMAKEALELLNELCNKGLM 586

Arabidopsis thaliana (taxid: 3702)

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

 Score =  305 bits (781), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 160/484 (33%), Positives = 269/484 (55%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           +++A+ K  K D    F  +ME  GV  +  TYN +IN  CR   L  A  ++  M   G
Sbjct: 71  LLSAIAKMKKFDLVISFGEKMEILGVSHNLYTYNIMINCLCRRSQLSFALAILGKMMKLG 130

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
             P + T NSL+NG C   R   A  ++D+M++MG  PDT T+ TL+    +    SEA 
Sbjct: 131 YGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMGYQPDTVTFTTLVHGLFQHNKASEAV 190

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            +   M  +G  PD+V++  +I    + G+ D AL    +M+   +  D V+Y+ +I+  
Sbjct: 191 ALVERMVVKGCQPDLVTYGAVINGLCKRGEPDLALNLLNKMEKGKIEADVVIYSTVIDSL 250

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           C+   V +AL +  EM  KG   DV TY+++++ LC     ++A  L ++MLER + P+ 
Sbjct: 251 CKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDASRLLSDMLERKINPNV 310

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
            TF +LI    K+G + +A  LFD M Q+SI P+IVTYN+LI+GFC    +++A +++  
Sbjct: 311 VTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTYNSLINGFCMHDRLDEAQQIFTL 370

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+S+   P+ ++Y  LING+C    V +   L+ +M  +G+    V+  T+I G+ ++ D
Sbjct: 371 MVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSRRGLVGNTVTYTTLIHGFFQASD 430

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
              A     +MVS+GV P+ ++YNTL++G  +   ++KA  +   ++   + PD+ TYN+
Sbjct: 431 CDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVFEYLQKSKMEPDIYTYNI 490

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           +  G C+ G++ D   +   +  KG+ PD   Y T+I+G   +   +EA+    +M + G
Sbjct: 491 MSEGMCKAGKVEDGWDLFCSLSLKGVKPDVIAYNTMISGFCKKGLKEEAYTLFIKMKEDG 550

Query: 481 FVPD 484
            +PD
Sbjct: 551 PLPD 554

Arabidopsis thaliana (taxid: 3702)

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

 Score =  304 bits (778), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 160/498 (32%), Positives = 273/498 (54%), Gaps = 39/498 (7%)

Query: 1   MVNALCKDHKI-DSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMS-- 57
           ++  LC D +  D+  + L  M + G  P+  +YN L+   C E   +EA +L++ M+  
Sbjct: 128 LLKGLCADKRTSDAMDIVLRRMTELGCIPNVFSYNILLKGLCDENRSQEALELLHMMADD 187

Query: 58  -GKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENM 116
            G G  P V +Y ++ING  K+G  D+A     EML  G+ PD  TYN+++   C+ + M
Sbjct: 188 RGGGSPPDVVSYTTVINGFFKEGDSDKAYSTYHEMLDRGILPDVVTYNSIIAALCKAQAM 247

Query: 117 SEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTII 176
            +A E+   M + GV PD +++++++  +  +GQ   A+ + ++M+S G+ PD V Y+++
Sbjct: 248 DKAMEVLNTMVKNGVMPDCMTYNSILHGYCSSGQPKEAIGFLKKMRSDGVEPDVVTYSLL 307

Query: 177 INGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGV 236
           ++  C+NG  +EA K+ D M ++G   ++ TY T+L G      L E   L + M+  G+
Sbjct: 308 MDYLCKNGRCMEARKIFDSMTKRGLKPEITTYGTLLQGYATKGALVEMHGLLDLMVRNGI 367

Query: 237 FPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTY------------------ 278
            PD Y F+ LI  + K G +++A+ +F  M Q+ + P+ VTY                  
Sbjct: 368 HPDHYVFSILICAYAKQGKVDQAMLVFSKMRQQGLNPNAVTYGAVIGILCKSGRVEDAML 427

Query: 279 -----------------NTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYC 321
                            N+LI G C   + E+A +L  +M+ R I  N I +  +I+ +C
Sbjct: 428 YFEQMIDEGLSPGNIVYNSLIHGLCTCNKWERAEELILEMLDRGICLNTIFFNSIIDSHC 487

Query: 322 SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSI 381
             G V E+ +L+  MV  G+KP +++ NT+I GYC +G   +A + LS MVS G+ P+++
Sbjct: 488 KEGRVIESEKLFELMVRIGVKPNVITYNTLINGYCLAGKMDEAMKLLSGMVSVGLKPNTV 547

Query: 382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRM 441
           +Y+TLING+ +   M+ A  L  +ME+ G+ PD+ITYN+IL G  +  R   ++ +  R+
Sbjct: 548 TYSTLINGYCKISRMEDALVLFKEMESSGVSPDIITYNIILQGLFQTRRTAAAKELYVRI 607

Query: 442 IEKGLNPDRSTYTTLING 459
            E G   + STY  +++G
Sbjct: 608 TESGTQIELSTYNIILHG 625

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

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q0WKV3|PPR36_ARATH Pentatricopeptide repeat-containing protein At1g12300, mitochondrial OS=Arabidopsis thaliana GN=At1g12300 PE=2 SV=1

 Score =  303 bits (777), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 154/484 (31%), Positives = 273/484 (56%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           M+N  C+  K+  A   + ++ + G  P+T+T++TLIN  C EG + EA +L++ M   G
Sbjct: 129 MINCFCRCRKLCLAFSAMGKIIKLGYEPNTITFSTLINGLCLEGRVSEALELVDRMVEMG 188

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
            KP + T N+L+NGLC  G+   A  ++D+M++ G  P+  TY  +L   C+    + A 
Sbjct: 189 HKPDLITINTLVNGLCLSGKEAEAMLLIDKMVEYGCQPNAVTYGPVLNVMCKSGQTALAM 248

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           E+  +M  R +  D V +S +I    ++G LD A   F EM+  G+  + + Y I+I G+
Sbjct: 249 ELLRKMEERNIKLDAVKYSIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGF 308

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           C  G   +  K+  +M+++    +VVT++ +++   +   L EA++L  EM+ RG+ PD 
Sbjct: 309 CNAGRWDDGAKLLRDMIKRKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDT 368

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
            T+T+LI G CK+ +++KA  + D+M  K   P+I T+N LI+G+CK   ++   +L+  
Sbjct: 369 ITYTSLIDGFCKENHLDKANQMVDLMVSKGCDPNIRTFNILINGYCKANRIDDGLELFRK 428

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M  R +  + ++Y  LI G+C +G +  A  L+ EMV + + P +V+   ++ G C +G+
Sbjct: 429 MSLRGVVADTVTYNTLIQGFCELGKLNVAKELFQEMVSRKVPPNIVTYKILLDGLCDNGE 488

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
           + KA E   K+    ++ D   YN +I+G      +D A+ L   +  +G+ P V TYN+
Sbjct: 489 SEKALEIFEKIEKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPGVKTYNI 548

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           ++ G C++G + ++EL+  +M E G  PD  TY  LI  H+   +  ++ +  +E+ + G
Sbjct: 549 MIGGLCKKGPLSEAELLFRKMEEDGHAPDGWTYNILIRAHLGDGDATKSVKLIEELKRCG 608

Query: 481 FVPD 484
           F  D
Sbjct: 609 FSVD 612

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	487
224059754	610	predicted protein [Populus trichocarpa]	0.928	0.740	0.743	0.0
255572227	677	pentatricopeptide repeat-containing prot	0.913	0.657	0.753	0.0
359479250	746	PREDICTED: pentatricopeptide repeat-cont	0.928	0.605	0.735	0.0
147840312	850	hypothetical protein VITISV_001389 [Viti	0.928	0.531	0.733	0.0
296083846	589	unnamed protein product [Vitis vinifera]	0.928	0.767	0.735	0.0
357494043	716	Pentatricopeptide repeat-containing prot	0.950	0.646	0.694	0.0
449476143	749	PREDICTED: LOW QUALITY PROTEIN: pentatri	0.963	0.626	0.655	0.0
449442579	749	PREDICTED: pentatricopeptide repeat-cont	0.963	0.626	0.655	0.0
297806115	719	pentatricopeptide repeat-containing prot	1.0	0.677	0.627	0.0
15240891	729	pentatricopeptide repeat-containing prot	1.0	0.668	0.623	0.0

>gi|224059754|ref|XP_002299984.1| predicted protein [Populus trichocarpa] gi|222847242|gb|EEE84789.1| predicted protein [Populus trichocarpa]

 Score =  790 bits (2041), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/487 (74%), Positives = 428/487 (87%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K D  K FL EME  G+Y D VTYNTLI AYCREG LEEAF++MNSM+ KG
Sbjct: 124 MVNALCKDGKFDDVKSFLSEMEGNGIYADMVTYNTLIGAYCREGLLEEAFEIMNSMADKG 183

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKP +FTYN++INGLCKKGR  RAK +L EML +GLSPDT TYNTLLVESCR++N SEA+
Sbjct: 184 LKPSLFTYNAIINGLCKKGRYARAKGILIEMLNIGLSPDTTTYNTLLVESCRRDNFSEAK 243

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           EIF EM R+GV PD+VSFS+LI +FSRN  LD+AL+YFR+MK  GLVPDNV+YT++++GY
Sbjct: 244 EIFGEMLRQGVVPDLVSFSSLIAVFSRNRHLDQALVYFRDMKKFGLVPDNVIYTVLMHGY 303

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG +LEALK+RDEMLE+GCV+DV+ YNTILNGLC+ KMLT+AD LF+EM+ERG  PDF
Sbjct: 304 CRNGNMLEALKIRDEMLEQGCVLDVIAYNTILNGLCKEKMLTDADKLFDEMVERGALPDF 363

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YTFTTLIHGHC+DGNM KAL+LF  MTQ++IKPDIV YNTLIDGFCKVGEMEKA++LW  
Sbjct: 364 YTFTTLIHGHCQDGNMTKALSLFGTMTQRNIKPDIVAYNTLIDGFCKVGEMEKASELWDG 423

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MISRKI PN+I+YGILIN YCS+GHV+EAFRLW  M+ KGIKPTLV+CNT+IKGYCRSGD
Sbjct: 424 MISRKIFPNHITYGILINAYCSVGHVSEAFRLWDVMIEKGIKPTLVTCNTVIKGYCRSGD 483

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
           +SKADEFL +M+++GV PD ISYNTLINGFVRE+NMDKAF  ++KME +GL+PD+ITYNV
Sbjct: 484 SSKADEFLGRMIAKGVAPDHISYNTLINGFVREDNMDKAFLWINKMEKEGLLPDIITYNV 543

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           ++ GFCRQGRM ++EL+L +MIEKG+NPDRSTYT LINGHV+Q+NL EAFRFHDEMLQRG
Sbjct: 544 VMNGFCRQGRMQEAELVLRKMIEKGINPDRSTYTALINGHVTQDNLNEAFRFHDEMLQRG 603

Query: 481 FVPDDAF 487
           F PDD F
Sbjct: 604 FAPDDVF 610

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255572227|ref|XP_002527053.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223533615|gb|EEF35353.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  788 bits (2035), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/487 (75%), Positives = 431/487 (88%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKDHKID  K FL +MEQKG++ D VTYNTLINAYCREG L EAF++MNSMSGKG
Sbjct: 191 MVNALCKDHKIDDVKPFLIDMEQKGIFADIVTYNTLINAYCREGLLGEAFEVMNSMSGKG 250

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKP +FTYN++INGLCKKGR  RAK V +EML +GLSPDT TYNTLLVESCR  N  EA+
Sbjct: 251 LKPTLFTYNAVINGLCKKGRYVRAKGVFNEMLSIGLSPDTTTYNTLLVESCRNNNFLEAK 310

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           +IF +M  RGV+PD++SFS+LIG+ SRNG LD+ALMYFR+MK++GLVPDNV+YTI+INGY
Sbjct: 311 DIFSDMLHRGVSPDLISFSSLIGVSSRNGHLDQALMYFRDMKTSGLVPDNVIYTILINGY 370

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG + EAL++RD+MLE+GC +DVV YNTILNGLC+ K+L +A+ LF+EM+ERGV PDF
Sbjct: 371 CRNGMMSEALEIRDKMLEQGCALDVVAYNTILNGLCKKKLLADANALFDEMVERGVVPDF 430

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
            TFTTLIHGHCK+GNM KAL+LF IMTQK+IKPDIVTYN LIDGFCK  EMEKAN+LW +
Sbjct: 431 CTFTTLIHGHCKEGNMGKALSLFGIMTQKNIKPDIVTYNILIDGFCKTTEMEKANELWNE 490

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MISRKI PN+ISY IL+NGYC++G V+EAFRLW EM+ KGIKPTLV+CNT+IKGYCRSGD
Sbjct: 491 MISRKIFPNHISYAILVNGYCNLGFVSEAFRLWDEMIRKGIKPTLVTCNTVIKGYCRSGD 550

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
            SKADEFL KM+SEGV PDSI+YNTLINGFV+ E MDKAF L++KME +GL PDV+TYNV
Sbjct: 551 LSKADEFLGKMISEGVGPDSITYNTLINGFVKGEYMDKAFFLINKMETKGLQPDVVTYNV 610

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GFCRQGRM ++ELIL +MIE+G++PDRSTYTTLING+VSQ+NLKEAFRFHDEMLQRG
Sbjct: 611 ILNGFCRQGRMQEAELILRKMIERGIDPDRSTYTTLINGYVSQDNLKEAFRFHDEMLQRG 670

Query: 481 FVPDDAF 487
           FVPDD F
Sbjct: 671 FVPDDDF 677

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479250|ref|XP_002275790.2| PREDICTED: pentatricopeptide repeat-containing protein At5g01110-like [Vitis vinifera]

 Score =  778 bits (2008), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/487 (73%), Positives = 431/487 (88%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           M+NALCK+ KI++ K FL +ME+KGV+PD VTYNTLINAYCR+G LEEAF+LM+SMSGKG
Sbjct: 260 MINALCKNQKIENTKSFLSDMEEKGVFPDVVTYNTLINAYCRQGLLEEAFELMDSMSGKG 319

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKP VFTYN++INGLCK G+  RAK VLDEML++G+SPDTATYN LLVE CR +NM +AE
Sbjct: 320 LKPCVFTYNAIINGLCKTGKYLRAKGVLDEMLKIGMSPDTATYNILLVECCRNDNMMDAE 379

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            IF EM  +GV PD+VSFS LIG+ S+NG LD+AL YFR+MK+AGL PDNV+YTI+I G+
Sbjct: 380 RIFDEMPSQGVVPDLVSFSALIGLLSKNGCLDQALKYFRDMKNAGLAPDNVIYTILIGGF 439

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG + EALK+RDEMLE+GCV+DVVTYNTILNGLC+ KML+EAD+LF EM ERGVFPDF
Sbjct: 440 CRNGVMSEALKVRDEMLEQGCVLDVVTYNTILNGLCKEKMLSEADELFTEMTERGVFPDF 499

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YTFTTLI+G+ KDGNMNKA+ LF++M Q+++KPD+VTYNTLIDGFCK  EMEK N+LW D
Sbjct: 500 YTFTTLINGYSKDGNMNKAVTLFEMMIQRNLKPDVVTYNTLIDGFCKGSEMEKVNELWND 559

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MISR+I PN+ISYGILINGYC+MG V+EAFRLW EMV KG + T+++CNTI+KGYCR+G+
Sbjct: 560 MISRRIYPNHISYGILINGYCNMGCVSEAFRLWDEMVEKGFEATIITCNTIVKGYCRAGN 619

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
           A KADEFLS M+ +G+ PD I+YNTLINGF++EENMD+AFALV+KMEN GL+PDVITYNV
Sbjct: 620 AVKADEFLSNMLLKGIVPDGITYNTLINGFIKEENMDRAFALVNKMENSGLLPDVITYNV 679

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GF RQGRM ++ELI+ +MIE+G+NPDRSTYT+LINGHV+QNNLKEAFR HDEMLQRG
Sbjct: 680 ILNGFSRQGRMQEAELIMLKMIERGVNPDRSTYTSLINGHVTQNNLKEAFRVHDEMLQRG 739

Query: 481 FVPDDAF 487
           FVPDD F
Sbjct: 740 FVPDDKF 746

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147840312|emb|CAN63985.1| hypothetical protein VITISV_001389 [Vitis vinifera]

 Score =  773 bits (1997), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/487 (73%), Positives = 430/487 (88%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           M+NALCK+ KI++ K FL +ME+KGV+PD VTYNTLINAYCR+G LEEAF+LM+SMSGKG
Sbjct: 364 MINALCKNQKIENTKSFLSDMEEKGVFPDVVTYNTLINAYCRQGLLEEAFELMDSMSGKG 423

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKP VFTYN++INGLCK G+  RAK VLDEML++G+SPDTATYN LLVE CR +NM +AE
Sbjct: 424 LKPCVFTYNAIINGLCKTGKYLRAKGVLDEMLKIGMSPDTATYNILLVECCRNDNMMDAE 483

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            IF EM  +GV PD+VSFS LIG+ S+NG LD+AL YFR+MK+AGL PDNV+YTI+I G+
Sbjct: 484 RIFDEMPSQGVVPDLVSFSALIGLLSKNGCLDQALKYFRDMKNAGLAPDNVIYTILIGGF 543

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG + EALK+RDEMLE+GC +DVVTYNTILNGLC+ KML+EAD+LF EM ERGVFPDF
Sbjct: 544 CRNGVMSEALKVRDEMLEQGCXLDVVTYNTILNGLCKEKMLSEADELFTEMTERGVFPDF 603

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YTFTTLI+G+ KDGNMNKA+ LF++M Q+++KPD+VTYNTLIDGFCK  EMEK N+LW D
Sbjct: 604 YTFTTLINGYXKDGNMNKAVTLFEMMIQRNLKPDVVTYNTLIDGFCKGSEMEKVNELWND 663

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MISR+I PN+ISYGILINGYC+MG V+EAFRLW EMV KG + T+++CNTI+KGYCR+G+
Sbjct: 664 MISRRIYPNHISYGILINGYCNMGCVSEAFRLWDEMVEKGFEATIITCNTIVKGYCRAGN 723

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
           A KADEFLS M+ +G+ PD I+YNTLINGF++EENMD+AFALV+KMEN GL+PDVITYNV
Sbjct: 724 AVKADEFLSNMLLKGIVPDGITYNTLINGFIKEENMDRAFALVNKMENSGLLPDVITYNV 783

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GF RQGRM ++ELI+ +MIE+G+NPDRSTYT+LINGHV+QNNLKEAFR HDEMLQRG
Sbjct: 784 ILNGFSRQGRMQEAELIMLKMIERGVNPDRSTYTSLINGHVTQNNLKEAFRVHDEMLQRG 843

Query: 481 FVPDDAF 487
           FVPDD F
Sbjct: 844 FVPDDKF 850

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083846|emb|CBI24234.3| unnamed protein product [Vitis vinifera]

 Score =  773 bits (1997), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/487 (73%), Positives = 431/487 (88%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           M+NALCK+ KI++ K FL +ME+KGV+PD VTYNTLINAYCR+G LEEAF+LM+SMSGKG
Sbjct: 103 MINALCKNQKIENTKSFLSDMEEKGVFPDVVTYNTLINAYCRQGLLEEAFELMDSMSGKG 162

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKP VFTYN++INGLCK G+  RAK VLDEML++G+SPDTATYN LLVE CR +NM +AE
Sbjct: 163 LKPCVFTYNAIINGLCKTGKYLRAKGVLDEMLKIGMSPDTATYNILLVECCRNDNMMDAE 222

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            IF EM  +GV PD+VSFS LIG+ S+NG LD+AL YFR+MK+AGL PDNV+YTI+I G+
Sbjct: 223 RIFDEMPSQGVVPDLVSFSALIGLLSKNGCLDQALKYFRDMKNAGLAPDNVIYTILIGGF 282

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG + EALK+RDEMLE+GCV+DVVTYNTILNGLC+ KML+EAD+LF EM ERGVFPDF
Sbjct: 283 CRNGVMSEALKVRDEMLEQGCVLDVVTYNTILNGLCKEKMLSEADELFTEMTERGVFPDF 342

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YTFTTLI+G+ KDGNMNKA+ LF++M Q+++KPD+VTYNTLIDGFCK  EMEK N+LW D
Sbjct: 343 YTFTTLINGYSKDGNMNKAVTLFEMMIQRNLKPDVVTYNTLIDGFCKGSEMEKVNELWND 402

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MISR+I PN+ISYGILINGYC+MG V+EAFRLW EMV KG + T+++CNTI+KGYCR+G+
Sbjct: 403 MISRRIYPNHISYGILINGYCNMGCVSEAFRLWDEMVEKGFEATIITCNTIVKGYCRAGN 462

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
           A KADEFLS M+ +G+ PD I+YNTLINGF++EENMD+AFALV+KMEN GL+PDVITYNV
Sbjct: 463 AVKADEFLSNMLLKGIVPDGITYNTLINGFIKEENMDRAFALVNKMENSGLLPDVITYNV 522

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GF RQGRM ++ELI+ +MIE+G+NPDRSTYT+LINGHV+QNNLKEAFR HDEMLQRG
Sbjct: 523 ILNGFSRQGRMQEAELIMLKMIERGVNPDRSTYTSLINGHVTQNNLKEAFRVHDEMLQRG 582

Query: 481 FVPDDAF 487
           FVPDD F
Sbjct: 583 FVPDDKF 589

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357494043|ref|XP_003617310.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355518645|gb|AET00269.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  739 bits (1909), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 338/487 (69%), Positives = 421/487 (86%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K+D+  ++L EME+KGVY D VTYNTL+NAYCR G + EAF L++ M+GKG
Sbjct: 230 MVNALCKDGKLDNVGVYLSEMEEKGVYADLVTYNTLVNAYCRRGLVSEAFGLVDCMAGKG 289

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           LKPG+FTYN+LINGLCK+G  +RAK VLDEML +GL P+ AT+N +LVESCRKE++ EAE
Sbjct: 290 LKPGLFTYNALINGLCKEGSYERAKRVLDEMLGVGLCPNAATFNPMLVESCRKEDVWEAE 349

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            +F EM +RGV PD++SFS+++G+FSRNG+L RAL YF +MK  GLVPD V+YTI+INGY
Sbjct: 350 RVFNEMLQRGVVPDLISFSSIVGVFSRNGELGRALAYFEKMKGVGLVPDTVIYTILINGY 409

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRN  V  ALKMR+EM+E+GCVMDVVTYNT+LNGLCR KML +AD+LF EM+ERGVFPDF
Sbjct: 410 CRNDDVSGALKMRNEMVERGCVMDVVTYNTLLNGLCRGKMLDDADELFKEMVERGVFPDF 469

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YT TTLIHG+CKDGNM KAL+LF+ MT +S+KPD+VTYNTL+DGFCKVGEMEKA +LW D
Sbjct: 470 YTLTTLIHGYCKDGNMTKALSLFETMTLRSLKPDVVTYNTLMDGFCKVGEMEKAKELWYD 529

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MISR+I P+YIS+ ILING+CS+G V+EAFRLW EM  KGIKPTLV+CNTIIKGY R+G+
Sbjct: 530 MISREIFPSYISFSILINGFCSLGLVSEAFRLWDEMKEKGIKPTLVTCNTIIKGYLRAGN 589

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
            SKA++FL+ M+SEGV PD I+YNTLIN FV+EEN D+AF L++ ME +GL+P+++TYN 
Sbjct: 590 LSKANDFLNTMISEGVPPDCITYNTLINSFVKEENFDRAFFLINNMEERGLLPNLVTYNA 649

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GF R GRM ++E++L +MI+KG+NPD+STYT+LING+VS++N+KEAFR HDEMLQRG
Sbjct: 650 ILGGFSRHGRMQEAEMVLHKMIDKGINPDKSTYTSLINGYVSKDNMKEAFRVHDEMLQRG 709

Query: 481 FVPDDAF 487
           FVPDD F
Sbjct: 710 FVPDDKF 716

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449476143|ref|XP_004154653.1| PREDICTED: LOW QUALITY PROTEIN: pentatricopeptide repeat-containing protein At5g01110-like [Cucumis sativus]

 Score =  697 bits (1799), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/487 (65%), Positives = 409/487 (83%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K ++   FL +ME KGV+ D VTYNTLINAYCREG +EEAFQL+NS S +G
Sbjct: 263 MVNALCKDRKFENVMFFLSDMEGKGVFADIVTYNTLINAYCREGLVEEAFQLLNSFSSRG 322

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           ++PG+ TYN+++ GLCK G+ DRAK+VL EMLQ+GL+P+ ATYNTLLVE CR++N+ EA+
Sbjct: 323 MEPGLLTYNAILYGLCKIGKYDRAKDVLIEMLQLGLTPNAATYNTLLVEICRRDNILEAQ 382

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           EIF EMSRRGV PD+VSFS+LIG+ +RNG L +ALM+FREM+ +G+VPDNV+YTI+I+G+
Sbjct: 383 EIFDEMSRRGVLPDLVSFSSLIGVLARNGHLYQALMHFREMERSGIVPDNVIYTILIDGF 442

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG + +ALKMRDEML +GC MDVVTYNT LNGLC+ KM  +AD LFNEM+ERG+ PDF
Sbjct: 443 CRNGALSDALKMRDEMLARGCFMDVVTYNTFLNGLCKKKMFADADMLFNEMVERGMVPDF 502

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YTFTTLI G+CKDGNM+KALNLF+ M + ++KPD VTYNTLIDGFCK GEM +A +LW D
Sbjct: 503 YTFTTLIRGYCKDGNMDKALNLFEAMVRTNLKPDKVTYNTLIDGFCKAGEMGRAKELWDD 562

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MI + I P++ISYG ++NG+CS G + EA  L  +M+ KGI+P LV+CNT+IKGYCRSGD
Sbjct: 563 MIRKDIIPDHISYGTVLNGFCSSGLLPEALNLCDQMLEKGIRPNLVTCNTLIKGYCRSGD 622

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
             KA E+LSKM+S G+ PDS SYNTLI+G+++E N++KAF L+++ME +GL  ++ITYN+
Sbjct: 623 MPKAYEYLSKMISNGIIPDSFSYNTLIDGYLKEANLEKAFILINEMEKRGLQFNIITYNL 682

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GFC +G+M ++E +L +MIE G+NPD +TY++LINGHVSQ+N+KEAFRFHDEMLQRG
Sbjct: 683 ILNGFCAEGKMQEAEQVLRKMIEIGINPDGATYSSLINGHVSQDNMKEAFRFHDEMLQRG 742

Query: 481 FVPDDAF 487
            VPDD F
Sbjct: 743 LVPDDRF 749

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449442579|ref|XP_004139059.1| PREDICTED: pentatricopeptide repeat-containing protein At5g01110-like [Cucumis sativus]

 Score =  697 bits (1798), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/487 (65%), Positives = 409/487 (83%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K ++   FL +ME KGV+ D VTYNTLINAYCREG +EEAFQL+NS S +G
Sbjct: 263 MVNALCKDRKFENVMFFLSDMEGKGVFADIVTYNTLINAYCREGLVEEAFQLLNSFSSRG 322

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           ++PG+ TYN+++ GLCK G+ DRAK+VL EMLQ+GL+P+ ATYNTLLVE CR++N+ EA+
Sbjct: 323 MEPGLLTYNAILYGLCKIGKYDRAKDVLIEMLQLGLTPNAATYNTLLVEICRRDNILEAQ 382

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           EIF EMSRRGV PD+VSFS+LIG+ +RNG L +ALM+FREM+ +G+VPDNV+YTI+I+G+
Sbjct: 383 EIFDEMSRRGVLPDLVSFSSLIGVLARNGHLYQALMHFREMERSGIVPDNVIYTILIDGF 442

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CRNG + +ALKMRDEML +GC MDVVTYNT LNGLC+ KM  +AD LFNEM+ERG+ PDF
Sbjct: 443 CRNGALSDALKMRDEMLARGCFMDVVTYNTFLNGLCKKKMFADADMLFNEMVERGMVPDF 502

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YTFTTLI G+CKDGNM+KALNLF+ M + ++KPD VTYNTLIDGFCK GEM +A +LW D
Sbjct: 503 YTFTTLIRGYCKDGNMDKALNLFEAMVRTNLKPDKVTYNTLIDGFCKAGEMGRAKELWDD 562

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MI + I P++ISYG ++NG+CS G + EA  L  +M+ KGI+P LV+CNT+IKGYCRSGD
Sbjct: 563 MIRKDIIPDHISYGTVLNGFCSSGLLPEALNLCDQMLEKGIRPNLVTCNTLIKGYCRSGD 622

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
             KA E+LSKM+S G+ PDS SYNTLI+G+++E N++KAF L+++ME +GL  ++ITYN+
Sbjct: 623 MPKAYEYLSKMISNGIIPDSFSYNTLIDGYLKEANLEKAFILINEMEKRGLQFNIITYNL 682

Query: 421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
           IL GFC +G+M ++E +L +MIE G+NPD +TY++LINGHVSQ+N+KEAFRFHDEMLQRG
Sbjct: 683 ILNGFCAEGKMQEAEQVLRKMIEIGINPDGATYSSLINGHVSQDNMKEAFRFHDEMLQRG 742

Query: 481 FVPDDAF 487
            VPDD F
Sbjct: 743 LVPDDRF 749

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297806115|ref|XP_002870941.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297316778|gb|EFH47200.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  668 bits (1724), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 307/489 (62%), Positives = 390/489 (79%), Gaps = 2/489 (0%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K++    FL E+++KGVYPD VTYNTLI+AY  +G +EEAF+LM++M  KG
Sbjct: 231 MVNALCKDGKMEKVGTFLSEVQEKGVYPDIVTYNTLISAYSSQGLMEEAFELMHAMPSKG 290

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
             PGV+TYN++INGLCK G+ +RAKEV  EML+ GLSPD+ TY +LL+E+C+K +  E E
Sbjct: 291 FSPGVYTYNTVINGLCKHGKYERAKEVFAEMLRSGLSPDSTTYRSLLMEACKKGDAVETE 350

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            IF +M  R V PD+V FS+++ +F+R+G LD+ALMYF  +K AGL+PDNV+YTI+I GY
Sbjct: 351 NIFSDMRSRDVVPDLVCFSSMMSLFTRSGNLDKALMYFNSVKEAGLIPDNVIYTILIQGY 410

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CR G + EA+ +R+EML++GC MDVVTYNTIL+GLC+ KML EAD LFNEM ERG+FPD 
Sbjct: 411 CRKGMISEAMNLRNEMLQQGCAMDVVTYNTILHGLCKRKMLGEADKLFNEMTERGLFPDS 470

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YT T LI GHCK GN+  A+ LF  M +K IK D+VTYNTL+DGF KVG+++ A ++WAD
Sbjct: 471 YTLTILIDGHCKLGNLQNAMELFKKMKEKRIKLDVVTYNTLLDGFGKVGDIDTAKEIWAD 530

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+S++I P  IS+ IL+N  CS GH++EAFR+W EM+ K IKPT++ CN++IKGYCRSG+
Sbjct: 531 MVSKEILPTPISFSILVNALCSKGHLSEAFRVWDEMISKSIKPTVMICNSMIKGYCRSGN 590

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ--GLVPDVITY 418
           AS  + FL KM+SEG  PD ISYNTLI GFV+EENM KAF LV KME +  GLVPDV TY
Sbjct: 591 ASDGEIFLEKMISEGFVPDCISYNTLIYGFVKEENMSKAFGLVKKMEEKQGGLVPDVFTY 650

Query: 419 NVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ 478
           N IL GFCR+ +M ++E +L +MIE+G+NPDRSTYT+LING VSQ+NL EAFRFHDEMLQ
Sbjct: 651 NSILHGFCRENQMKEAEAVLRKMIERGVNPDRSTYTSLINGFVSQDNLTEAFRFHDEMLQ 710

Query: 479 RGFVPDDAF 487
           RGF PDD F
Sbjct: 711 RGFSPDDKF 719

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240891|ref|NP_195731.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75174092|sp|Q9LFC5.1|PP360_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At5g01110 gi|6759434|emb|CAB69839.1| putative protein [Arabidopsis thaliana] gi|28973740|gb|AAO64186.1| unknown protein [Arabidopsis thaliana] gi|110736884|dbj|BAF00399.1| hypothetical protein [Arabidopsis thaliana] gi|332002917|gb|AED90300.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  666 bits (1719), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 305/489 (62%), Positives = 389/489 (79%), Gaps = 2/489 (0%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           MVNALCKD K++    FL ++++KGVYPD VTYNTLI+AY  +G +EEAF+LMN+M GKG
Sbjct: 241 MVNALCKDGKMEKVGTFLSQVQEKGVYPDIVTYNTLISAYSSKGLMEEAFELMNAMPGKG 300

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
             PGV+TYN++INGLCK G+ +RAKEV  EML+ GLSPD+ TY +LL+E+C+K ++ E E
Sbjct: 301 FSPGVYTYNTVINGLCKHGKYERAKEVFAEMLRSGLSPDSTTYRSLLMEACKKGDVVETE 360

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           ++F +M  R V PD+V FS+++ +F+R+G LD+ALMYF  +K AGL+PDNV+YTI+I GY
Sbjct: 361 KVFSDMRSRDVVPDLVCFSSMMSLFTRSGNLDKALMYFNSVKEAGLIPDNVIYTILIQGY 420

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
           CR G +  A+ +R+EML++GC MDVVTYNTIL+GLC+ KML EAD LFNEM ER +FPD 
Sbjct: 421 CRKGMISVAMNLRNEMLQQGCAMDVVTYNTILHGLCKRKMLGEADKLFNEMTERALFPDS 480

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
           YT T LI GHCK GN+  A+ LF  M +K I+ D+VTYNTL+DGF KVG+++ A ++WAD
Sbjct: 481 YTLTILIDGHCKLGNLQNAMELFQKMKEKRIRLDVVTYNTLLDGFGKVGDIDTAKEIWAD 540

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           M+S++I P  ISY IL+N  CS GH+ EAFR+W EM+ K IKPT++ CN++IKGYCRSG+
Sbjct: 541 MVSKEILPTPISYSILVNALCSKGHLAEAFRVWDEMISKNIKPTVMICNSMIKGYCRSGN 600

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ--GLVPDVITY 418
           AS  + FL KM+SEG  PD ISYNTLI GFVREENM KAF LV KME +  GLVPDV TY
Sbjct: 601 ASDGESFLEKMISEGFVPDCISYNTLIYGFVREENMSKAFGLVKKMEEEQGGLVPDVFTY 660

Query: 419 NVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ 478
           N IL GFCRQ +M ++E++L +MIE+G+NPDRSTYT +ING VSQ+NL EAFR HDEMLQ
Sbjct: 661 NSILHGFCRQNQMKEAEVVLRKMIERGVNPDRSTYTCMINGFVSQDNLTEAFRIHDEMLQ 720

Query: 479 RGFVPDDAF 487
           RGF PDD F
Sbjct: 721 RGFSPDDKF 729

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	487
TAIR|locus:2150024	729	AT5G01110 [Arabidopsis thalian	1.0	0.668	0.623	8.9e-173
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.997	0.785	0.339	4.9e-85
TAIR|locus:2195047	621	AT1G12620 [Arabidopsis thalian	0.993	0.779	0.324	1.2e-79
TAIR|locus:2019085	763	AT1G74580 "AT1G74580" [Arabido	0.993	0.634	0.334	1.6e-79
TAIR|locus:2034760	637	AT1G12300 [Arabidopsis thalian	0.993	0.759	0.318	3.8e-78
TAIR|locus:2015228	614	AT1G63080 [Arabidopsis thalian	0.993	0.788	0.330	1.3e-77
TAIR|locus:2024296	598	AT1G09900 "AT1G09900" [Arabido	0.963	0.784	0.324	3.4e-77
TAIR|locus:2168078	907	AT5G59900 "AT5G59900" [Arabido	0.987	0.530	0.338	1.5e-76
TAIR|locus:2173403	730	AT5G64320 "AT5G64320" [Arabido	0.983	0.656	0.351	1.9e-76
TAIR|locus:2015494	629	RPF3 "RNA processing factor 3"	0.993	0.769	0.330	3.9e-76

TAIR|locus:2150024 AT5G01110 [Arabidopsis thaliana (taxid:3702)]

 Score = 1679 (596.1 bits), Expect = 8.9e-173, P = 8.9e-173
 Identities = 305/489 (62%), Positives = 389/489 (79%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             MVNALCKD K++    FL ++++KGVYPD VTYNTLI+AY  +G +EEAF+LMN+M GKG
Sbjct:   241 MVNALCKDGKMEKVGTFLSQVQEKGVYPDIVTYNTLISAYSSKGLMEEAFELMNAMPGKG 300

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
               PGV+TYN++INGLCK G+ +RAKEV  EML+ GLSPD+ TY +LL+E+C+K ++ E E
Sbjct:   301 FSPGVYTYNTVINGLCKHGKYERAKEVFAEMLRSGLSPDSTTYRSLLMEACKKGDVVETE 360

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
             ++F +M  R V PD+V FS+++ +F+R+G LD+ALMYF  +K AGL+PDNV+YTI+I GY
Sbjct:   361 KVFSDMRSRDVVPDLVCFSSMMSLFTRSGNLDKALMYFNSVKEAGLIPDNVIYTILIQGY 420

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             CR G +  A+ +R+EML++GC MDVVTYNTIL+GLC+ KML EAD LFNEM ER +FPD 
Sbjct:   421 CRKGMISVAMNLRNEMLQQGCAMDVVTYNTILHGLCKRKMLGEADKLFNEMTERALFPDS 480

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
             YT T LI GHCK GN+  A+ LF  M +K I+ D+VTYNTL+DGF KVG+++ A ++WAD
Sbjct:   481 YTLTILIDGHCKLGNLQNAMELFQKMKEKRIRLDVVTYNTLLDGFGKVGDIDTAKEIWAD 540

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             M+S++I P  ISY IL+N  CS GH+ EAFR+W EM+ K IKPT++ CN++IKGYCRSG+
Sbjct:   541 MVSKEILPTPISYSILVNALCSKGHLAEAFRVWDEMISKNIKPTVMICNSMIKGYCRSGN 600

Query:   361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ--GLVPDVITY 418
             AS  + FL KM+SEG  PD ISYNTLI GFVREENM KAF LV KME +  GLVPDV TY
Sbjct:   601 ASDGESFLEKMISEGFVPDCISYNTLIYGFVREENMSKAFGLVKKMEEEQGGLVPDVFTY 660

Query:   419 NVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ 478
             N IL GFCRQ +M ++E++L +MIE+G+NPDRSTYT +ING VSQ+NL EAFR HDEMLQ
Sbjct:   661 NSILHGFCRQNQMKEAEVVLRKMIERGVNPDRSTYTCMINGFVSQDNLTEAFRIHDEMLQ 720

Query:   479 RGFVPDDAF 487
             RGF PDD F
Sbjct:   721 RGFSPDDKF 729

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 851 (304.6 bits), Expect = 4.9e-85, P = 4.9e-85
 Identities = 165/486 (33%), Positives = 278/486 (57%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             M+N  C+  K+  A   L    + G  PDT+T++TL+N +C EG + EA  L++ M    
Sbjct:   111 MINCYCRKKKLLFAFSVLGRAWKLGYEPDTITFSTLVNGFCLEGRVSEAVALVDRMVEMK 170

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
              +P + T ++LINGLC KGR   A  ++D M++ G  PD  TY  +L   C+  N + A 
Sbjct:   171 QRPDLVTVSTLINGLCLKGRVSEALVLIDRMVEYGFQPDEVTYGPVLNRLCKSGNSALAL 230

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
             ++F +M  R +   +V +S +I    ++G  D AL  F EM+  G+  D V Y+ +I G 
Sbjct:   231 DLFRKMEERNIKASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGL 290

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             C +G   +  KM  EM+ +  + DVVT++ +++   +   L EA +L+NEM+ RG+ PD 
Sbjct:   291 CNDGKWDDGAKMLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPDT 350

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
              T+ +LI G CK+  +++A  +FD+M  K  +PDIVTY+ LI+ +CK   ++   +L+ +
Sbjct:   351 ITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFRE 410

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             + S+ + PN I+Y  L+ G+C  G +  A  L+ EMV +G+ P++V+   ++ G C +G+
Sbjct:   411 ISSKGLIPNTITYNTLVLGFCQSGKLNAAKELFQEMVSRGVPPSVVTYGILLDGLCDNGE 470

Query:   361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
              +KA E   KM    +      YN +I+G      +D A++L   + ++G+ PDV+TYNV
Sbjct:   471 LNKALEIFEKMQKSRMTLGIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNV 530

Query:   421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
             ++ G C++G + +++++  +M E G  PD  TY  LI  H+  + L  +    +EM   G
Sbjct:   531 MIGGLCKKGSLSEADMLFRKMKEDGCTPDDFTYNILIRAHLGGSGLISSVELIEEMKVCG 590

Query:   481 FVPDDA 486
             F  D +
Sbjct:   591 FSADSS 596

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 800 (286.7 bits), Expect = 1.2e-79, P = 1.2e-79
 Identities = 157/484 (32%), Positives = 275/484 (56%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             M+N  C+  K+  A   + ++ + G  PDTVT++TLIN  C EG + EA +L++ M   G
Sbjct:   113 MINCCCRCRKLSLAFSAMGKIIKLGYEPDTVTFSTLINGLCLEGRVSEALELVDRMVEMG 172

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
              KP + T N+L+NGLC  G+   A  ++D M++ G  P+  TY  +L   C+    + A 
Sbjct:   173 HKPTLITLNALVNGLCLNGKVSDAVLLIDRMVETGFQPNEVTYGPVLKVMCKSGQTALAM 232

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
             E+  +M  R +  D V +S +I    ++G LD A   F EM+  G   D ++YT +I G+
Sbjct:   233 ELLRKMEERKIKLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIIIYTTLIRGF 292

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             C  G   +  K+  +M+++    DVV ++ +++   +   L EA++L  EM++RG+ PD 
Sbjct:   293 CYAGRWDDGAKLLRDMIKRKITPDVVAFSALIDCFVKEGKLREAEELHKEMIQRGISPDT 352

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
              T+T+LI G CK+  ++KA ++ D+M  K   P+I T+N LI+G+CK   ++   +L+  
Sbjct:   353 VTYTSLIDGFCKENQLDKANHMLDLMVSKGCGPNIRTFNILINGYCKANLIDDGLELFRK 412

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             M  R +  + ++Y  LI G+C +G +  A  L+ EMV + ++P +VS   ++ G C +G+
Sbjct:   413 MSLRGVVADTVTYNTLIQGFCELGKLEVAKELFQEMVSRRVRPDIVSYKILLDGLCDNGE 472

Query:   361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
               KA E   K+    ++ D   YN +I+G      +D A+ L   +  +G+ PDV TYN+
Sbjct:   473 PEKALEIFEKIEKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPDVKTYNI 532

Query:   421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
             ++ G C++G + +++L+  +M E G +P+  TY  LI  H+ + +  ++ +  +E+ + G
Sbjct:   533 MIGGLCKKGSLSEADLLFRKMEEDGHSPNGCTYNILIRAHLGEGDATKSAKLIEEIKRCG 592

Query:   481 FVPD 484
             F  D
Sbjct:   593 FSVD 596

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2019085 AT1G74580 "AT1G74580" [Arabidopsis thaliana (taxid:3702)]

 Score = 799 (286.3 bits), Expect = 1.6e-79, P = 1.6e-79
 Identities = 162/485 (33%), Positives = 261/485 (53%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             ++  LCK   +   +  L ++ ++GV P+  TYN  I   C+ G L+ A +++  +  +G
Sbjct:   222 LLRVLCKKGDVKECEKLLDKVIKRGVLPNLFTYNLFIQGLCQRGELDGAVRMVGCLIEQG 281

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
              KP V TYN+LI GLCK  +   A+  L +M+  GL PD+ TYNTL+   C+   +  AE
Sbjct:   282 PKPDVITYNNLIYGLCKNSKFQEAEVYLGKMVNEGLEPDSYTYNTLIAGYCKGGMVQLAE 341

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
              I  +    G  PD  ++ +LI      G+ +RAL  F E    G+ P+ +LY  +I G 
Sbjct:   342 RIVGDAVFNGFVPDQFTYRSLIDGLCHEGETNRALALFNEALGKGIKPNVILYNTLIKGL 401

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
                G +LEA ++ +EM EKG + +V T+N ++NGLC+   +++AD L   M+ +G FPD 
Sbjct:   402 SNQGMILEAAQLANEMSEKGLIPEVQTFNILVNGLCKMGCVSDADGLVKVMISKGYFPDI 461

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
             +TF  LIHG+     M  AL + D+M    + PD+ TYN+L++G CK  + E   + +  
Sbjct:   462 FTFNILIHGYSTQLKMENALEILDVMLDNGVDPDVYTYNSLLNGLCKTSKFEDVMETYKT 521

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             M+ +  +PN  ++ IL+   C    + EA  L  EM  K + P  V+  T+I G+C++GD
Sbjct:   522 MVEKGCAPNLFTFNILLESLCRYRKLDEALGLLEEMKNKSVNPDAVTFGTLIDGFCKNGD 581

Query:   361 ASKADEFLSKMVSE-GVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYN 419
                A     KM     V   + +YN +I+ F  + N+  A  L  +M ++ L PD  TY 
Sbjct:   582 LDGAYTLFRKMEEAYKVSSSTPTYNIIIHAFTEKLNVTMAEKLFQEMVDRCLGPDGYTYR 641

Query:   420 VILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQR 479
             +++ GFC+ G ++     L  M+E G  P  +T   +IN    ++ + EA      M+Q+
Sbjct:   642 LMVDGFCKTGNVNLGYKFLLEMMENGFIPSLTTLGRVINCLCVEDRVYEAAGIIHRMVQK 701

Query:   480 GFVPD 484
             G VP+
Sbjct:   702 GLVPE 706

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 786 (281.7 bits), Expect = 3.8e-78, P = 3.8e-78
 Identities = 154/484 (31%), Positives = 273/484 (56%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             M+N  C+  K+  A   + ++ + G  P+T+T++TLIN  C EG + EA +L++ M   G
Sbjct:   129 MINCFCRCRKLCLAFSAMGKIIKLGYEPNTITFSTLINGLCLEGRVSEALELVDRMVEMG 188

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
              KP + T N+L+NGLC  G+   A  ++D+M++ G  P+  TY  +L   C+    + A 
Sbjct:   189 HKPDLITINTLVNGLCLSGKEAEAMLLIDKMVEYGCQPNAVTYGPVLNVMCKSGQTALAM 248

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
             E+  +M  R +  D V +S +I    ++G LD A   F EM+  G+  + + Y I+I G+
Sbjct:   249 ELLRKMEERNIKLDAVKYSIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGF 308

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             C  G   +  K+  +M+++    +VVT++ +++   +   L EA++L  EM+ RG+ PD 
Sbjct:   309 CNAGRWDDGAKLLRDMIKRKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDT 368

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
              T+T+LI G CK+ +++KA  + D+M  K   P+I T+N LI+G+CK   ++   +L+  
Sbjct:   369 ITYTSLIDGFCKENHLDKANQMVDLMVSKGCDPNIRTFNILINGYCKANRIDDGLELFRK 428

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             M  R +  + ++Y  LI G+C +G +  A  L+ EMV + + P +V+   ++ G C +G+
Sbjct:   429 MSLRGVVADTVTYNTLIQGFCELGKLNVAKELFQEMVSRKVPPNIVTYKILLDGLCDNGE 488

Query:   361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
             + KA E   K+    ++ D   YN +I+G      +D A+ L   +  +G+ P V TYN+
Sbjct:   489 SEKALEIFEKIEKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPGVKTYNI 548

Query:   421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
             ++ G C++G + ++EL+  +M E G  PD  TY  LI  H+   +  ++ +  +E+ + G
Sbjct:   549 MIGGLCKKGPLSEAELLFRKMEEDGHAPDGWTYNILIRAHLGDGDATKSVKLIEELKRCG 608

Query:   481 FVPD 484
             F  D
Sbjct:   609 FSVD 612

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 781 (280.0 bits), Expect = 1.3e-77, P = 1.3e-77
 Identities = 160/484 (33%), Positives = 269/484 (55%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             +++A+ K  K D    F  +ME  GV  +  TYN +IN  CR   L  A  ++  M   G
Sbjct:    71 LLSAIAKMKKFDLVISFGEKMEILGVSHNLYTYNIMINCLCRRSQLSFALAILGKMMKLG 130

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
               P + T NSL+NG C   R   A  ++D+M++MG  PDT T+ TL+    +    SEA 
Sbjct:   131 YGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMGYQPDTVTFTTLVHGLFQHNKASEAV 190

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
              +   M  +G  PD+V++  +I    + G+ D AL    +M+   +  D V+Y+ +I+  
Sbjct:   191 ALVERMVVKGCQPDLVTYGAVINGLCKRGEPDLALNLLNKMEKGKIEADVVIYSTVIDSL 250

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             C+   V +AL +  EM  KG   DV TY+++++ LC     ++A  L ++MLER + P+ 
Sbjct:   251 CKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDASRLLSDMLERKINPNV 310

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
              TF +LI    K+G + +A  LFD M Q+SI P+IVTYN+LI+GFC    +++A +++  
Sbjct:   311 VTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTYNSLINGFCMHDRLDEAQQIFTL 370

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             M+S+   P+ ++Y  LING+C    V +   L+ +M  +G+    V+  T+I G+ ++ D
Sbjct:   371 MVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSRRGLVGNTVTYTTLIHGFFQASD 430

Query:   361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
                A     +MVS+GV P+ ++YNTL++G  +   ++KA  +   ++   + PD+ TYN+
Sbjct:   431 CDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVFEYLQKSKMEPDIYTYNI 490

Query:   421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
             +  G C+ G++ D   +   +  KG+ PD   Y T+I+G   +   +EA+    +M + G
Sbjct:   491 MSEGMCKAGKVEDGWDLFCSLSLKGVKPDVIAYNTMISGFCKKGLKEEAYTLFIKMKEDG 550

Query:   481 FVPD 484
              +PD
Sbjct:   551 PLPD 554

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2024296 AT1G09900 "AT1G09900" [Arabidopsis thaliana (taxid:3702)]

 Score = 777 (278.6 bits), Expect = 3.4e-77, P = 3.4e-77
 Identities = 154/474 (32%), Positives = 260/474 (54%)

Query:    10 KIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYN 69
             +++    FL  M   G  PD +   TLI  +CR G   +A +++  + G G  P V TYN
Sbjct:   117 ELEEGFKFLENMVYHGNVPDIIPCTTLIRGFCRLGKTRKAAKILEILEGSGAVPDVITYN 176

Query:    70 SLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRR 129
              +I+G CK G  + A  VLD   +M +SPD  TYNT+L   C    + +A E+   M +R
Sbjct:   177 VMISGYCKAGEINNALSVLD---RMSVSPDVVTYNTILRSLCDSGKLKQAMEVLDRMLQR 233

Query:   130 GVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEA 189
                PD+++++ LI    R+  +  A+    EM+  G  PD V Y +++NG C+ G + EA
Sbjct:   234 DCYPDVITYTILIEATCRDSGVGHAMKLLDEMRDRGCTPDVVTYNVLVNGICKEGRLDEA 293

Query:   190 LKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHG 249
             +K  ++M   GC  +V+T+N IL  +C      +A+ L  +ML +G  P   TF  LI+ 
Sbjct:   294 IKFLNDMPSSGCQPNVITHNIILRSMCSTGRWMDAEKLLADMLRKGFSPSVVTFNILINF 353

Query:   250 HCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN 309
              C+ G + +A+++ + M Q   +P+ ++YN L+ GFCK  +M++A +    M+SR   P+
Sbjct:   354 LCRKGLLGRAIDILEKMPQHGCQPNSLSYNPLLHGFCKEKKMDRAIEYLERMVSRGCYPD 413

Query:   310 YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLS 369
              ++Y  ++   C  G V +A  +  ++  KG  P L++ NT+I G  ++G   KA + L 
Sbjct:   414 IVTYNTMLTALCKDGKVEDAVEILNQLSSKGCSPVLITYNTVIDGLAKAGKTGKAIKLLD 473

Query:   370 KMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG 429
             +M ++ + PD+I+Y++L+ G  RE  +D+A     + E  G+ P+ +T+N I+ G C+  
Sbjct:   474 EMRAKDLKPDTITYSSLVGGLSREGKVDEAIKFFHEFERMGIRPNAVTFNSIMLGLCKS- 532

Query:   430 RMHDSEL-ILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFV 482
             R  D  +  L  MI +G  P+ ++YT LI G   +   KEA    +E+  +G +
Sbjct:   533 RQTDRAIDFLVFMINRGCKPNETSYTILIEGLAYEGMAKEALELLNELCNKGLM 586

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0016020 "membrane" evidence=IDA

TAIR|locus:2168078 AT5G59900 "AT5G59900" [Arabidopsis thaliana (taxid:3702)]

 Score = 771 (276.5 bits), Expect = 1.5e-76, P = 1.5e-76
 Identities = 165/487 (33%), Positives = 274/487 (56%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             ++++LCK  K   A++    M + G+ P+ VTY+ LI+ +CR G L+ A   +  M   G
Sbjct:   373 LIDSLCKGRKFHEAELLFDRMGKIGLRPNDVTYSILIDMFCRRGKLDTALSFLGEMVDTG 432

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
             LK  V+ YNSLING CK G    A+  + EM+   L P   TY +L+   C K  +++A 
Sbjct:   433 LKLSVYPYNSLINGHCKFGDISAAEGFMAEMINKKLEPTVVTYTSLMGGYCSKGKINKAL 492

Query:   121 EIFCEMSRRGVAPDIVSFSTLI-GIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIING 179
              ++ EM+ +G+AP I +F+TL+ G+F R G +  A+  F EM    + P+ V Y ++I G
Sbjct:   493 RLYHEMTGKGIAPSIYTFTTLLSGLF-RAGLIRDAVKLFNEMAEWNVKPNRVTYNVMIEG 551

Query:   180 YCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFP- 238
             YC  G + +A +   EM EKG V D  +Y  +++GLC     +EA  +F + L +G    
Sbjct:   552 YCEEGDMSKAFEFLKEMTEKGIVPDTYSYRPLIHGLCLTGQASEAK-VFVDGLHKGNCEL 610

Query:   239 DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLW 298
             +   +T L+HG C++G + +AL++   M Q+ +  D+V Y  LIDG  K  + +    L 
Sbjct:   611 NEICYTGLLHGFCREGKLEEALSVCQEMVQRGVDLDLVCYGVLIDGSLKHKDRKLFFGLL 670

Query:   299 ADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRS 358
              +M  R + P+ + Y  +I+     G   EAF +W  M+ +G  P  V+   +I G C++
Sbjct:   671 KEMHDRGLKPDDVIYTSMIDAKSKTGDFKEAFGIWDLMINEGCVPNEVTYTAVINGLCKA 730

Query:   359 GDASKADEFLSKMVSEGVDPDSISYNTLINGFVREE-NMDKAFALVSKMENQGLVPDVIT 417
             G  ++A+   SKM      P+ ++Y   ++   + E +M KA  L + +  +GL+ +  T
Sbjct:   731 GFVNEAEVLCSKMQPVSSVPNQVTYGCFLDILTKGEVDMQKAVELHNAIL-KGLLANTAT 789

Query:   418 YNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML 477
             YN+++ GFCRQGR+ ++  ++ RMI  G++PD  TYTT+IN    +N++K+A    + M 
Sbjct:   790 YNMLIRGFCRQGRIEEASELITRMIGDGVSPDCITYTTMINELCRRNDVKKAIELWNSMT 849

Query:   478 QRGFVPD 484
             ++G  PD
Sbjct:   850 EKGIRPD 856

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2173403 AT5G64320 "AT5G64320" [Arabidopsis thaliana (taxid:3702)]

 Score = 770 (276.1 bits), Expect = 1.9e-76, P = 1.9e-76
 Identities = 171/486 (35%), Positives = 275/486 (56%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             ++ A C  ++IDSA   L +M + G  P++V Y TLI++  +   + EA QL+  M   G
Sbjct:   223 VMKAFCAVNEIDSALSLLRDMTKHGCVPNSVIYQTLIHSLSKCNRVNEALQLLEEMFLMG 282

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
               P   T+N +I GLCK  R + A ++++ ML  G +PD  TY  L+   C+   +  A+
Sbjct:   283 CVPDAETFNDVILGLCKFDRINEAAKMVNRMLIRGFAPDDITYGYLMNGLCKIGRVDAAK 342

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREM-KSAGLVPDNVLYTIIING 179
             ++F  + +    P+IV F+TLI  F  +G+LD A     +M  S G+VPD   Y  +I G
Sbjct:   343 DLFYRIPK----PEIVIFNTLIHGFVTHGRLDDAKAVLSDMVTSYGIVPDVCTYNSLIYG 398

Query:   180 YCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD 239
             Y + G V  AL++  +M  KGC  +V +Y  +++G C+   + EA ++ NEM   G+ P+
Sbjct:   399 YWKEGLVGLALEVLHDMRNKGCKPNVYSYTILVDGFCKLGKIDEAYNVLNEMSADGLKPN 458

Query:   240 FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWA 299
                F  LI   CK+  + +A+ +F  M +K  KPD+ T+N+LI G C+V E++ A  L  
Sbjct:   459 TVGFNCLISAFCKEHRIPEAVEIFREMPRKGCKPDVYTFNSLISGLCEVDEIKHALWLLR 518

Query:   300 DMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG 359
             DMIS  +  N ++Y  LIN +   G + EA +L  EMV +G     ++ N++IKG CR+G
Sbjct:   519 DMISEGVVANTVTYNTLINAFLRRGEIKEARKLVNEMVFQGSPLDEITYNSLIKGLCRAG 578

Query:   360 DASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYN 419
             +  KA     KM+ +G  P +IS N LING  R   +++A     +M  +G  PD++T+N
Sbjct:   579 EVDKARSLFEKMLRDGHAPSNISCNILINGLCRSGMVEEAVEFQKEMVLRGSTPDIVTFN 638

Query:   420 VILTGFCRQGRMHDSELILWRMIE-KGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ 478
              ++ G CR GR+ D  L ++R ++ +G+ PD  T+ TL++       + +A    DE ++
Sbjct:   639 SLINGLCRAGRIEDG-LTMFRKLQAEGIPPDTVTFNTLMSWLCKGGFVYDACLLLDEGIE 697

Query:   479 RGFVPD 484
              GFVP+
Sbjct:   698 DGFVPN 703

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 767 (275.1 bits), Expect = 3.9e-76, P = 3.9e-76
 Identities = 160/484 (33%), Positives = 266/484 (54%)

Query:     1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
             +++A+ K +K D        M+   +  D  +YN LIN +CR   L  A  ++  M   G
Sbjct:    86 LLSAIAKMNKFDLVISLGERMQNLRISYDLYSYNILINCFCRRSQLPLALAVLGKMMKLG 145

Query:    61 LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
              +P + T +SL+NG C   R   A  ++D+M  M   P+T T+NTL+         SEA 
Sbjct:   146 YEPDIVTLSSLLNGYCHGKRISEAVALVDQMFVMEYQPNTVTFNTLIHGLFLHNKASEAV 205

Query:   121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
              +   M  RG  PD+ ++ T++    + G +D AL   ++M+   +  D V+YT II+  
Sbjct:   206 ALIDRMVARGCQPDLFTYGTVVNGLCKRGDIDLALSLLKKMEKGKIEADVVIYTTIIDAL 265

Query:   181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             C    V +AL +  EM  KG   +VVTYN+++  LC     ++A  L ++M+ER + P+ 
Sbjct:   266 CNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWSDASRLLSDMIERKINPNV 325

Query:   241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
              TF+ LI    K+G + +A  L+D M ++SI PDI TY++LI+GFC    +++A  ++  
Sbjct:   326 VTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFCMHDRLDEAKHMFEL 385

Query:   301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
             MIS+   PN ++Y  LI G+C    V E   L+ EM  +G+    V+ NT+I+G  ++GD
Sbjct:   386 MISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQRGLVGNTVTYNTLIQGLFQAGD 445

Query:   361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
                A +   KMVS+GV PD I+Y+ L++G  +   ++KA  +   ++   + PD+ TYN+
Sbjct:   446 CDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLEKALVVFEYLQKSKMEPDIYTYNI 505

Query:   421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG 480
             ++ G C+ G++ D   +   +  KG+ P+   YTT+I+G   +   +EA     EM + G
Sbjct:   506 MIEGMCKAGKVEDGWDLFCSLSLKGVKPNVIIYTTMISGFCRKGLKEEADALFREMKEDG 565

Query:   481 FVPD 484
              +P+
Sbjct:   566 TLPN 569

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006397 "mRNA processing" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LFC5	PP360_ARATH	No assigned EC number	0.6237	1.0	0.6680	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	487
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-42
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	3e-37
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-32
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-31
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	6e-31
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-28
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	8e-25
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-23
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-20
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-19
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-19
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-17
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-17
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-16
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-14
pfam13041	50	pfam13041, PPR_2, PPR repeat family	6e-14
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-14
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-11
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-11
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-11
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-11
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-11
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-09
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-08
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-08
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-08
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	6e-08
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	6e-07
pfam01535	31	pfam01535, PPR, PPR repeat	6e-07
pfam01535	31	pfam01535, PPR, PPR repeat	7e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	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	1e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	4e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	6e-06
pfam01535	31	pfam01535, PPR, PPR repeat	6e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	7e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	3e-05
pfam01535	31	pfam01535, PPR, PPR repeat	4e-05
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-05
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-05
pfam01535	31	pfam01535, PPR, PPR repeat	6e-05
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	9e-05
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	1e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	1e-04
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	3e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	3e-04
pfam01535	31	pfam01535, PPR, PPR repeat	4e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	6e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	6e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	7e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	9e-04
COG0457	291	COG0457, NrfG, FOG: TPR repeat [General function p	0.001
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.003
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.004

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

 Score =  161 bits (408), Expect = 2e-42
 Identities = 110/432 (25%), Positives = 212/432 (49%), Gaps = 14/432 (3%)

Query: 3   NALCKDHKIDSAKMFLCEMEQKGVYP-DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGL 61
           N L +D +I      L +ME++G+   D + +     A  ++  ++EAF+    +     
Sbjct: 378 NRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLI----R 433

Query: 62  KPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE- 120
            P + T+N L++        D A  VL  + + GL  D   Y TL + +C K    +A  
Sbjct: 434 NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTL-ISTCAKSGKVDAMF 492

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           E+F EM   GV  ++ +F  LI   +R GQ+ +A   +  M+S  + PD V++  +I+  
Sbjct: 493 EVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISAC 552

Query: 181 CRNGFVLEALKMRDEMLEKGCVM--DVVTYNTILNGLCRAKMLTEADDLFNEMLERGV-- 236
            ++G V  A  +  EM  +   +  D +T   ++     A  +  A +++  + E  +  
Sbjct: 553 GQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKG 612

Query: 237 FPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANK 296
            P+ YT    ++   + G+ + AL+++D M +K +KPD V ++ L+D     G+++KA +
Sbjct: 613 TPEVYTIA--VNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFE 670

Query: 297 LWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYC 356
           +  D   + I    +SY  L+    +  +  +A  L+ ++    ++PT+ + N +I   C
Sbjct: 671 ILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALC 730

Query: 357 RSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVI 416
                 KA E LS+M   G+ P++I+Y+ L+    R+++ D    L+S+ +  G+ P+++
Sbjct: 731 EGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLV 790

Query: 417 TYNVILTGFCRQ 428
               I TG C +
Sbjct: 791 MCRCI-TGLCLR 801

Length = 1060

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

 Score =  145 bits (368), Expect = 3e-37
 Identities = 113/437 (25%), Positives = 191/437 (43%), Gaps = 48/437 (10%)

Query: 55  SMSGKGLKPG--VFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCR 112
           +    G+        Y    N L + GR     ++L++M + GL      Y+    ++C+
Sbjct: 358 AAYNGGVSGKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACK 417

Query: 113 KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVL 172
           K+   +    F ++ R    P + +F+ L+ + + +  +D AL   R ++ AGL  D  L
Sbjct: 418 KQRAVKEAFRFAKLIRN---PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKL 474

Query: 173 YTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEML 232
           YT +I+   ++G V       D M E                            +F+EM+
Sbjct: 475 YTTLISTCAKSGKV-------DAMFE----------------------------VFHEMV 499

Query: 233 ERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME 292
             GV  + +TF  LI G  + G + KA   + IM  K++KPD V +N LI    + G ++
Sbjct: 500 NAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVD 559

Query: 293 KANKLWADMI--SRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGK-GIKPTLVSCN 349
           +A  + A+M   +  I P++I+ G L+    + G V  A  + Y+M+ +  IK T     
Sbjct: 560 RAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEV-YQMIHEYNIKGTP-EVY 617

Query: 350 TIIKGYC-RSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN 408
           TI    C + GD   A      M  +GV PD + ++ L++      ++DKAF ++     
Sbjct: 618 TIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK 677

Query: 409 QGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK-GLNPDRSTYTTLINGHVSQNNLK 467
           QG+    ++Y+  L G C   +     L L+  I+   L P  ST   LI      N L 
Sbjct: 678 QGIKLGTVSYSS-LMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLP 736

Query: 468 EAFRFHDEMLQRGFVPD 484
           +A     EM + G  P+
Sbjct: 737 KALEVLSEMKRLGLCPN 753

Length = 1060

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

 Score =  131 bits (330), Expect = 2e-32
 Identities = 94/359 (26%), Positives = 156/359 (43%), Gaps = 40/359 (11%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           +++   K  K+D+      EM   GV  +  T+  LI+   R G + +AF     M  K 
Sbjct: 478 LISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKN 537

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           +KP    +N+LI+   + G  DRA +VL EM                         +E  
Sbjct: 538 VKPDRVVFNALISACGQSGAVDRAFDVLAEM------------------------KAETH 573

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
            I          PD ++   L+   +  GQ+DRA   ++ +    +     +YTI +N  
Sbjct: 574 PI---------DPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSC 624

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
            + G    AL + D+M +KG   D V ++ +++    A  L +A ++  +  ++G+    
Sbjct: 625 SQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGT 684

Query: 241 YTFTTLIHGHCKDGNMNKALNLF-DIMTQKSIK--PDIVTYNTLIDGFCKVGEMEKANKL 297
            ++++L+       N  KAL L+ DI   KSIK  P + T N LI   C+  ++ KA ++
Sbjct: 685 VSYSSLMGACSNAKNWKKALELYEDI---KSIKLRPTVSTMNALITALCEGNQLPKALEV 741

Query: 298 WADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYC 356
            ++M    + PN I+Y IL+              L  +    GIKP LV C  I  G C
Sbjct: 742 LSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLC 799

Length = 1060

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

 Score =  126 bits (319), Expect = 6e-31
 Identities = 105/464 (22%), Positives = 204/464 (43%), Gaps = 53/464 (11%)

Query: 29  DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVL 88
           D  ++N L+  Y + G+ +EA  L + M   G++P V+T+  ++          R +EV 
Sbjct: 151 DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVH 210

Query: 89  DEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRN 148
             +++ G   D    N L+    +  ++  A  +F  M RR    D +S++ +I  +  N
Sbjct: 211 AHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFEN 266

Query: 149 GQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTY 208
           G+    L  F  M+   + PD +  T +I+     G      +M   +++ G  +DV   
Sbjct: 267 GECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVC 326

Query: 209 NTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ 268
           N+++          EA+ +F+ M  +    D  ++T +I G+ K+G  +KAL  + +M Q
Sbjct: 327 NSLIQMYLSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKALETYALMEQ 382

Query: 269 KSIKPDIVTY-----------------------------------NTLIDGFCKVGEMEK 293
            ++ PD +T                                    N LI+ + K   ++K
Sbjct: 383 DNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDK 442

Query: 294 ANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK 353
           A +++ ++  +    + IS+  +I G        EA   + +M+   +KP  V+    + 
Sbjct: 443 ALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALS 497

Query: 354 GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP 413
              R G      E  + ++  G+  D    N L++ +VR   M+ A+   +  E      
Sbjct: 498 ACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEK----- 552

Query: 414 DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLI 457
           DV+++N++LTG+   G+   +  +  RM+E G+NPD  T+ +L+
Sbjct: 553 DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLL 596

Length = 857

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

 Score =  126 bits (318), Expect = 6e-31
 Identities = 104/482 (21%), Positives = 201/482 (41%), Gaps = 54/482 (11%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG 60
           +V A      I   K     +E  G  PD    N ++  + + G L +A +L + M  + 
Sbjct: 129 LVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERN 188

Query: 61  LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE 120
           L     ++ ++I GL   G    A  +  EM + G   +  T+  +L  S    +    +
Sbjct: 189 L----ASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQ 244

Query: 121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY 180
           ++ C + + GV  D      LI ++S+ G ++ A   F  M     V  N     ++ GY
Sbjct: 245 QLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNS----MLAGY 300

Query: 181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF 240
             +G+  EAL +  EM + G  +D  T++ ++    R  +L  A      ++  G   D 
Sbjct: 301 ALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDI 360

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD 300
              T L+  + K G M  A N+FD M +K    +++++N LI G+   G   KA +++  
Sbjct: 361 VANTALVDLYSKWGRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFER 416

Query: 301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGD 360
           MI+  ++PN++++  +++     G   + + +                            
Sbjct: 417 MIAEGVAPNHVTFLAVLSACRYSGLSEQGWEI---------------------------- 448

Query: 361 ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNV 420
                 F S   +  + P ++ Y  +I    RE  +D+A+A++ +       P V  +  
Sbjct: 449 ------FQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAP---FKPTVNMWAA 499

Query: 421 ILTGFCR-QGRMHDSELILWRMIEKGLNPDR-STYTTLINGHVSQNNLKEAFRFHDEMLQ 478
           +LT  CR    +    L   ++   G+ P++ + Y  L+N + S     EA +  + + +
Sbjct: 500 LLTA-CRIHKNLELGRLAAEKLY--GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKR 556

Query: 479 RG 480
           +G
Sbjct: 557 KG 558

Length = 697

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

 Score =  119 bits (299), Expect = 2e-28
 Identities = 103/466 (22%), Positives = 212/466 (45%), Gaps = 30/466 (6%)

Query: 1   MVNAL------CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMN 54
           +VNAL      C D  + SA++    M ++    D +++N +I+ Y   G   E  +L  
Sbjct: 224 VVNALITMYVKCGD--VVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFF 277

Query: 55  SMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKE 114
           +M    + P + T  S+I+     G     +E+   +++ G + D +  N+L+       
Sbjct: 278 TMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLG 337

Query: 115 NMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYT 174
           +  EAE++F  M  +    D VS++ +I  + +NG  D+AL  +  M+   + PD +   
Sbjct: 338 SWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIA 393

Query: 175 IIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLER 234
            +++     G +   +K+ +    KG +  VV  N ++    + K + +A ++F+ + E+
Sbjct: 394 SVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK 453

Query: 235 GVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKA 294
            V     ++T++I G   +    +AL  F  M    +KP+ VT    +    ++G +   
Sbjct: 454 DVI----SWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGALMCG 508

Query: 295 NKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKG 354
            ++ A ++   I  +      L++ Y   G +  A   W +      +  +VS N ++ G
Sbjct: 509 KEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYA---WNQFNSH--EKDVVSWNILLTG 563

Query: 355 YCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ-GLVP 413
           Y   G  S A E  ++MV  GV+PD +++ +L+    R   + +       ME +  + P
Sbjct: 564 YVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITP 623

Query: 414 DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLING 459
           ++  Y  ++    R G++ ++   + +M    + PD + +  L+N 
Sbjct: 624 NLKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWGALLNA 666

Length = 857

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

 Score =  108 bits (270), Expect = 8e-25
 Identities = 104/453 (22%), Positives = 193/453 (42%), Gaps = 34/453 (7%)

Query: 34  NTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRA-----KEVL 88
           N+ + A C  G LE+A +L+ SM    +      Y +L   LC+  R            L
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFR-LCEWKRAVEEGSRVCSRAL 113

Query: 89  DEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRN 148
                +G+       N +L    R   +  A  +F +M  R    D+ S++ L+G +++ 
Sbjct: 114 SSHPSLGVRLG----NAMLSMFVRFGELVHAWYVFGKMPER----DLFSWNVLVGGYAKA 165

Query: 149 GQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDE----MLEKGCVMD 204
           G  D AL  +  M  AG+ PD   +  ++    R    +  L    E    ++  G  +D
Sbjct: 166 GYFDEALCLYHRMLWAGVRPDVYTFPCVL----RTCGGIPDLARGREVHAHVVRFGFELD 221

Query: 205 VVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFD 264
           V   N ++    +   +  A  +F+ M  R    D  ++  +I G+ ++G   + L LF 
Sbjct: 222 VDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFF 277

Query: 265 IMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMG 324
            M + S+ PD++T  ++I     +G+     ++   ++    + +      LI  Y S+G
Sbjct: 278 TMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLG 337

Query: 325 HVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYN 384
              EA +++  M  K      VS   +I GY ++G   KA E  + M  + V PD I+  
Sbjct: 338 SWGEAEKVFSRMETKDA----VSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIA 393

Query: 385 TLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK 444
           ++++      ++D    L    E +GL+  V+  N ++  + +   +  +  +   + EK
Sbjct: 394 SVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK 453

Query: 445 GLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML 477
               D  ++T++I G    N   EA  F  +ML
Sbjct: 454 ----DVISWTSIIAGLRLNNRCFEALIFFRQML 482

Length = 857

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

 Score =  104 bits (261), Expect = 1e-23
 Identities = 83/356 (23%), Positives = 149/356 (41%), Gaps = 45/356 (12%)

Query: 2   VNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGL 61
           VN+  +    D A     +M++KGV PD V ++ L++     G L++AF+++     +G+
Sbjct: 621 VNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGI 680

Query: 62  KPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEE 121
           K G  +Y+SL+          +A E+ +++  + L P  +T N L+   C    + +A E
Sbjct: 681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALE 740

Query: 122 IFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYC 181
           +  EM R G+ P+ +++S L+    R    D  L    + K  G+ P+ V+   I  G C
Sbjct: 741 VLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLC 799

Query: 182 RNGFVLEALKMRDEMLEKGCVMD--VVTYNT----ILNGLCRAKMLTEADDLFNEMLERG 235
                           EK C +   VV++++    I N     K  + A  ++ E +  G
Sbjct: 800 L------------RRFEKACALGEPVVSFDSGRPQIEN-----KWTSWALMVYRETISAG 842

Query: 236 VFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE----- 290
             P     + ++       +      L + +   +        +TL+DGF   GE     
Sbjct: 843 TLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGF---GEYDPRA 899

Query: 291 ---MEKANKLWA-DMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIK 342
              +E+A  L     +S K SP      I+I+         E + L    + KG+K
Sbjct: 900 FSLLEEAASLGVVPSVSFKKSP------IVIDAEELPVFAAEVYLL---TILKGLK 946

Length = 1060

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

 Score = 83.2 bits (207), Expect = 3e-20
 Identities = 30/50 (60%), Positives = 40/50 (80%)

Query: 28 PDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCK 77
          PD VTYNTLI+ YC++G +EEA +L N M  +G+KP V+TY+ LI+GLCK
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 79.8 bits (198), Expect = 7e-19
 Identities = 26/49 (53%), Positives = 36/49 (73%)

Query: 204 DVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCK 252
           DVVTYNT+++G C+   + EA  LFNEM +RG+ P+ YT++ LI G CK
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 = 79.4 bits (197), Expect = 8e-19
 Identities = 29/49 (59%), Positives = 38/49 (77%)

Query: 273 PDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYC 321
           PD+VTYNTLIDG+CK G++E+A KL+ +M  R I PN  +Y ILI+G 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|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 85.7 bits (212), Expect = 2e-17
 Identities = 67/302 (22%), Positives = 127/302 (42%), Gaps = 41/302 (13%)

Query: 214 GLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD--GNMNKALNLFDIM----- 266
           G+   +   E  D +N +L  G   D           C D   +M K   L D+      
Sbjct: 363 GVSGKRKSPEYIDAYNRLLRDGRIKD-----------CIDLLEDMEKR-GLLDMDKIYHA 410

Query: 267 -------TQKSIK-----------PDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP 308
                   Q+++K           P + T+N L+       +++ A ++   +    +  
Sbjct: 411 KFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKA 470

Query: 309 NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFL 368
           +   Y  LI+     G V   F +++EMV  G++  + +   +I G  R+G  +KA    
Sbjct: 471 DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAY 530

Query: 369 SKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKM--ENQGLVPDVITYNVILTGFC 426
             M S+ V PD + +N LI+   +   +D+AF ++++M  E   + PD IT   ++    
Sbjct: 531 GIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACA 590

Query: 427 RQGRMHDSELILWRMIEK-GLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD 485
             G++ D    +++MI +  +      YT  +N    + +   A   +D+M ++G  PD+
Sbjct: 591 NAGQV-DRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDE 649

Query: 486 AF 487
            F
Sbjct: 650 VF 651

Length = 1060

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

 Score = 74.7 bits (185), Expect = 3e-17
 Identities = 26/50 (52%), Positives = 36/50 (72%)

Query: 238 PDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCK 287
           PD  T+ TLI G+CK G + +AL LF+ M ++ IKP++ TY+ LIDG 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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 71.3 bits (176), Expect = 7e-16
 Identities = 23/50 (46%), Positives = 36/50 (72%)

Query: 168 PDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCR 217
           PD V Y  +I+GYC+ G V EALK+ +EM ++G   +V TY+ +++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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 70.9 bits (175), Expect = 8e-16
 Identities = 18/50 (36%), Positives = 38/50 (76%)

Query: 378 PDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCR 427
           PD ++YNTLI+G+ ++  +++A  L ++M+ +G+ P+V TY++++ G C+
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|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 79.5 bits (196), Expect = 1e-15
 Identities = 67/328 (20%), Positives = 127/328 (38%), Gaps = 51/328 (15%)

Query: 195 EMLEKGC--VMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCK 252
           E+LE GC   +   TY+ ++      K +     ++  +   G  PD Y    ++  H K
Sbjct: 111 EILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVK 170

Query: 253 DGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP---- 308
            G +  A  LFD M +++    + ++ T+I G    G   +A  L+ +M           
Sbjct: 171 CGMLIDARRLFDEMPERN----LASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRT 226

Query: 309 --------------------------------NYISYGILINGYCSMGHVTEAFRLWYEM 336
                                            ++S   LI+ Y   G + +A  ++  M
Sbjct: 227 FVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCA-LIDMYSKCGDIEDARCVFDGM 285

Query: 337 VGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENM 396
             K    T V+ N+++ GY   G + +A     +M   GV  D  +++ +I  F R   +
Sbjct: 286 PEK----TTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALL 341

Query: 397 DKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTL 456
           + A    + +   G   D++    ++  + + GRM D+  +  RM  K L     ++  L
Sbjct: 342 EHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL----ISWNAL 397

Query: 457 INGHVSQNNLKEAFRFHDEMLQRGFVPD 484
           I G+ +     +A    + M+  G  P+
Sbjct: 398 IAGYGNHGRGTKAVEMFERMIAEGVAPN 425

Length = 697

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

 Score = 69.0 bits (170), Expect = 4e-15
 Identities = 20/45 (44%), Positives = 32/45 (71%)

Query: 63  PGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLL 107
           P V TYN+LI+G CKKG+ + A ++ +EM + G+ P+  TY+ L+
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILI 45

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 = 66.3 bits (163), Expect = 4e-14
 Identities = 20/50 (40%), Positives = 35/50 (70%)

Query: 133 PDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCR 182
           PD+V+++TLI  + + G+++ AL  F EMK  G+ P+   Y+I+I+G C+
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 65.5 bits (161), Expect = 6e-14
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 343 PTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR 392
           P +V+ NT+I GYC+ G   +A +  ++M   G+ P+  +Y+ LI+G  +
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 65.1 bits (160), Expect = 9e-14
 Identities = 21/50 (42%), Positives = 33/50 (66%)

Query: 308 PNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR 357
           P+ ++Y  LI+GYC  G V EA +L+ EM  +GIKP + + + +I G C+
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 59.3 bits (145), Expect = 1e-11
 Identities = 17/48 (35%), Positives = 34/48 (70%)

Query: 413 PDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGH 460
           PDV+TYN ++ G+C++G++ ++  +   M ++G+ P+  TY+ LI+G 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 58.1 bits (142), Expect = 2e-11
 Identities = 18/34 (52%), Positives = 25/34 (73%)

Query: 24 KGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMS 57
          KG+ PD VTYNTLI+  CR G ++EA +L++ 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 = 58.1 bits (142), Expect = 2e-11
 Identities = 23/33 (69%), Positives = 27/33 (81%)

Query: 59 KGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEM 91
          KGLKP V TYN+LI+GLC+ GR D A E+LDEM
Sbjct: 1  KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 57.4 bits (140), Expect = 4e-11
 Identities = 13/42 (30%), Positives = 26/42 (61%)

Query: 1  MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCR 42
          +++  CK  K++ A     EM+++G+ P+  TY+ LI+  C+
Sbjct: 9  LIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 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 = 57.0 bits (139), Expect = 7e-11
 Identities = 20/45 (44%), Positives = 31/45 (68%)

Query: 98  PDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLI 142
           PD  TYNTL+   C+K  + EA ++F EM +RG+ P++ ++S LI
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILI 45

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 = 53.1 bits (129), Expect = 1e-09
 Identities = 19/33 (57%), Positives = 25/33 (75%)

Query: 199 KGCVMDVVTYNTILNGLCRAKMLTEADDLFNEM 231
           KG   DVVTYNT+++GLCRA  + EA +L +EM
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 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|205109 pfam12854, PPR_1, PPR repeat

 Score = 51.6 bits (125), Expect = 3e-09
 Identities = 14/33 (42%), Positives = 22/33 (66%)

Query: 234 RGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIM 266
           +G+ PD  T+ TLI G C+ G +++A+ L D M
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 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|205109 pfam12854, PPR_1, PPR repeat

 Score = 51.2 bits (124), Expect = 5e-09
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 269 KSIKPDIVTYNTLIDGFCKVGEMEKANKLWADM 301
           K +KPD+VTYNTLIDG C+ G +++A +L  +M
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 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|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 57.6 bits (139), Expect = 1e-08
 Identities = 46/203 (22%), Positives = 87/203 (42%), Gaps = 37/203 (18%)

Query: 34  NTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQ 93
           N L++ Y R G +  A+   NS      +  V ++N L+ G    G+   A E+ + M++
Sbjct: 528 NALLDLYVRCGRMNYAWNQFNSH-----EKDVVSWNILLTGYVAHGKGSMAVELFNRMVE 582

Query: 94  MGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRR-GVAPDIVSFSTLIGIFSRNGQLD 152
            G++PD  T+ +LL    R   +++  E F  M  +  + P++  ++ ++ +  R G+L 
Sbjct: 583 SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLT 642

Query: 153 RALMYFREMK--------------------------SAGLV----PDNVLYTIII-NGYC 181
            A  +  +M                           +A  +    P++V Y I++ N Y 
Sbjct: 643 EAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYA 702

Query: 182 RNGFVLEALKMRDEMLEKGCVMD 204
             G   E  ++R  M E G  +D
Sbjct: 703 DAGKWDEVARVRKTMRENGLTVD 725

Length = 857

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

 Score = 57.6 bits (139), Expect = 1e-08
 Identities = 57/227 (25%), Positives = 97/227 (42%), Gaps = 29/227 (12%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGK- 59
           ++  L  +++   A +F  +M    + P++VT    ++A  R G L         M GK 
Sbjct: 461 IIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGAL---------MCGKE 510

Query: 60  ----GLKPGV----FTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESC 111
                L+ G+    F  N+L++   + GR + A    +         D  ++N LL    
Sbjct: 511 IHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-----EKDVVSWNILLTGYV 565

Query: 112 RKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSA-GLVPDN 170
                S A E+F  M   GV PD V+F +L+   SR+G + + L YF  M+    + P+ 
Sbjct: 566 AHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNL 625

Query: 171 VLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCR 217
             Y  +++   R G + EA    ++M       D   +  +LN  CR
Sbjct: 626 KHYACVVDLLGRAGKLTEAYNFINKMPITP---DPAVWGALLNA-CR 668

Length = 857

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

 Score = 50.0 bits (121), Expect = 1e-08
 Identities = 17/32 (53%), Positives = 22/32 (68%)

Query: 165 GLVPDNVLYTIIINGYCRNGFVLEALKMRDEM 196
           GL PD V Y  +I+G CR G V EA+++ DEM
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 = 49.8 bits (120), Expect = 2e-08
 Identities = 20/34 (58%), Positives = 27/34 (79%)

Query: 206 VTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD 239
           VTYNT+++GLC+A  + EA +LF EM ERG+ PD
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 48.6 bits (117), Expect = 6e-08
 Identities = 15/38 (39%), Positives = 24/38 (63%)

Query: 448 PDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD 485
           PD  TY TLI+G+  +  ++EA +  +EM +RG  P+ 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNV 38

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

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

 Score = 47.5 bits (114), Expect = 1e-07
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 276 VTYNTLIDGFCKVGEMEKANKLWADMISRKISPN 309
           VTYNTLIDG CK G +E+A +L+ +M  R I P+
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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 = 47.5 bits (114), Expect = 1e-07
 Identities = 18/35 (51%), Positives = 24/35 (68%)

Query: 66  FTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDT 100
            TYN+LI+GLCK GR + A E+  EM + G+ 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|205109 pfam12854, PPR_1, PPR repeat

 Score = 46.6 bits (112), Expect = 2e-07
 Identities = 15/33 (45%), Positives = 23/33 (69%)

Query: 375 GVDPDSISYNTLINGFVREENMDKAFALVSKME 407
           G+ PD ++YNTLI+G  R   +D+A  L+ +ME
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 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 = 45.4 bits (109), Expect = 5e-07
 Identities = 16/34 (47%), Positives = 23/34 (67%)

Query: 339 KGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMV 372
           KG+KP +V+ NT+I G CR+G   +A E L +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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 45.5 bits (109), Expect = 6e-07
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGV 65
          VTYNTLI+  C+ G +EEA +L   M  +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|144943 pfam01535, PPR, PPR repeat

 Score = 45.1 bits (108), Expect = 6e-07
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 66 FTYNSLINGLCKKGRCDRAKEVLDEMLQMGL 96
           TYNSLI+G CK G+ + A E+  EM + 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 = 45.1 bits (108), Expect = 7e-07
 Identities = 17/31 (54%), Positives = 22/31 (70%)

Query: 31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGL 61
          VTYN+LI+ YC+ G LEEA +L   M  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 = 44.6 bits (107), Expect = 1e-06
 Identities = 13/34 (38%), Positives = 19/34 (55%)

Query: 304 RKISPNYISYGILINGYCSMGHVTEAFRLWYEMV 337
           + + P+ ++Y  LI+G C  G 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 = 44.4 bits (106), Expect = 1e-06
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 171 VLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDV 205
           V Y  +I+G C+ G V EAL++  EM E+G   DV
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 = 44.8 bits (107), Expect = 1e-06
 Identities = 17/31 (54%), Positives = 24/31 (77%)

Query: 206 VTYNTILNGLCRAKMLTEADDLFNEMLERGV 236
           VTYN++++G C+A  L EA +LF EM E+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|144943 pfam01535, PPR, PPR repeat

 Score = 44.4 bits (106), Expect = 1e-06
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 171 VLYTIIINGYCRNGFVLEALKMRDEMLEKGC 201
           V Y  +I+GYC+ G + EAL++  EM EKG 
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 = 43.5 bits (104), Expect = 3e-06
 Identities = 16/33 (48%), Positives = 18/33 (54%)

Query: 444 KGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM 476
           KGL PD  TY TLI+G      + EA    DEM
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 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 = 43.2 bits (103), Expect = 4e-06
 Identities = 13/35 (37%), Positives = 24/35 (68%)

Query: 381 ISYNTLINGFVREENMDKAFALVSKMENQGLVPDV 415
           ++YNTLI+G  +   +++A  L  +M+ +G+ 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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 42.4 bits (101), Expect = 6e-06
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS 380
           V+ NT+I G C++G   +A E   +M   G++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|144943 pfam01535, PPR, PPR repeat

 Score = 42.4 bits (101), Expect = 6e-06
 Identities = 14/31 (45%), Positives = 24/31 (77%)

Query: 276 VTYNTLIDGFCKVGEMEKANKLWADMISRKI 306
           VTYN+LI G+CK G++E+A +L+ +M  + +
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 = 42.3 bits (101), Expect = 7e-06
 Identities = 13/25 (52%), Positives = 19/25 (76%)

Query: 409 QGLVPDVITYNVILTGFCRQGRMHD 433
           +GL PDV+TYN ++ G CR GR+ +
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDE 25

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 = 42.1 bits (100), Expect = 1e-05
 Identities = 15/34 (44%), Positives = 21/34 (61%)

Query: 311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT 344
           ++Y  LI+G C  G V EA  L+ EM  +GI+P 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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 = 41.7 bits (99), Expect = 1e-05
 Identities = 14/34 (41%), Positives = 18/34 (52%)

Query: 452 TYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD 485
           TY TLI+G      ++EA     EM +RG  PD 
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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 40.9 bits (97), Expect = 2e-05
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI 275
            T+ TLI G CK G + +AL LF  M ++ I+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 = 40.5 bits (96), Expect = 3e-05
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 136 VSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD 169
           V+++TLI    + G+++ AL  F+EMK  G+ PD
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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 = 40.1 bits (95), Expect = 4e-05
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGI 341
           ++Y  LI+GYC  G + EA  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 = 40.0 bits (95), Expect = 5e-05
 Identities = 13/34 (38%), Positives = 23/34 (67%)

Query: 129 RGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMK 162
           +G+ PD+V+++TLI    R G++D A+    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|205109 pfam12854, PPR_1, PPR repeat

 Score = 40.0 bits (95), Expect = 5e-05
 Identities = 16/34 (47%), Positives = 19/34 (55%)

Query: 94  MGLSPDTATYNTLLVESCRKENMSEAEEIFCEMS 127
            GL PD  TYNTL+   CR   + EA E+  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|144943 pfam01535, PPR, PPR repeat

 Score = 39.7 bits (94), Expect = 6e-05
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGV 376
           V+ N++I GYC++G   +A E   +M  +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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 39.1 bits (92), Expect = 9e-05
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKISP 308
           + TYN L+    K G+ + 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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 30 TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKP 63
            TYN L+ A  + G  + A  ++  M   GLKP
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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 205 VVTYNTILNGLCRAKMLTEADDLFNEMLERGVFP 238
           + TYN +L  L +A     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 = 38.2 bits (90), Expect = 2e-04
 Identities = 12/31 (38%), Positives = 22/31 (70%)

Query: 136 VSFSTLIGIFSRNGQLDRALMYFREMKSAGL 166
           V++++LI  + + G+L+ AL  F+EMK  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 = 13/31 (41%), Positives = 20/31 (64%)

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSI 271
            T+ +LI G+CK G + +AL LF  M +K +
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 = 37.8 bits (89), Expect = 3e-04
 Identities = 9/31 (29%), Positives = 22/31 (70%)

Query: 381 ISYNTLINGFVREENMDKAFALVSKMENQGL 411
           ++YN+LI+G+ +   +++A  L  +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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 382 SYNTLINGFVREENMDKAFALVSKMENQGLVP 413
           +YN L+    +  + D A A++ +M+  GL P
Sbjct: 3   TYNALLLALAKAGDPDLALAVLEEMKASGLKP 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 = 37.0 bits (87), Expect = 4e-04
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 451 STYTTLINGHVSQNNLKEAFRFHDEMLQRGF 481
            TY +LI+G+     L+EA     EM ++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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 9/33 (27%), Positives = 16/33 (48%)

Query: 241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP 273
            T+  L+    K G+ + AL + + M    +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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 11/34 (32%), Positives = 20/34 (58%)

Query: 135 IVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVP 168
           + +++ L+   ++ G  D AL    EMK++GL 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 = 36.7 bits (86), Expect = 7e-04
 Identities = 16/34 (47%), Positives = 22/34 (64%)

Query: 102 TYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDI 135
           TYNTL+   C+   + EA E+F EM  RG+ PD+
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 = 36.4 bits (85), Expect = 9e-04
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 345 LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP 378
           L + N ++    ++GD   A   L +M + 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|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only]

 Score = 41.0 bits (94), Expect = 0.001
 Identities = 48/256 (18%), Positives = 83/256 (32%), Gaps = 5/256 (1%)

Query: 82  DRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEM-SRRGVAPDIVSFST 140
             A  +L E L   L+   A     L        ++EA E+  E       +        
Sbjct: 5   LLALAILLEALAKLLAEALALLEAGLALLELLGELAEALELLEEALELLPNSDLAGLLLL 64

Query: 141 LIGIFSRNGQLDRALMYFREMKSAGLVPDN-VLYTIIINGYCRNGFVLEALKMRDEMLEK 199
           L     + G+L+ AL    +     L+P+       +       G   EAL++ ++ L  
Sbjct: 65  LALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALAL 124

Query: 200 GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHG--HCKDGNMN 257
               D+      L  L       EA +L+ + LE     +      L  G      G   
Sbjct: 125 DPDPDLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYE 184

Query: 258 KALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILI 317
           +AL L +   + +   D      L   + K+G+ E+A + +   +      N  +   L 
Sbjct: 185 EALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDP-DNAEALYNLA 243

Query: 318 NGYCSMGHVTEAFRLW 333
                +G   EA    
Sbjct: 244 LLLLELGRYEEALEAL 259

Length = 291

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

 Score = 35.1 bits (82), Expect = 0.003
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 416 ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD 449
           +TYN ++ G C+ GR+ ++  +   M E+G+ PD
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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 = 0.004
 Identities = 8/32 (25%), Positives = 11/32 (34%)

Query: 452 TYTTLINGHVSQNNLKEAFRFHDEMLQRGFVP 483
           TY  L+       +   A    +EM   G  P
Sbjct: 3   TYNALLLALAKAGDPDLALAVLEEMKASGLKP 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	487
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	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	99.96
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.89
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.88
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.87
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.83
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.82
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.82
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.75
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.73
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.73
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.72
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.72
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.72
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.7
PRK14574	822	hmsH outer membrane protein; Provisional	99.69
PRK14574	822	hmsH outer membrane protein; Provisional	99.68
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.68
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.67
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.6
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.59
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.57
KOG2076	895	consensus RNA polymerase III transcription factor	99.49
PF13041	50	PPR_2: PPR repeat family	99.44
PF13041	50	PPR_2: PPR repeat family	99.43
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.42
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.37
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.37
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.35
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.35
KOG2003	840	consensus TPR repeat-containing protein [General f	99.34
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.32
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.32
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.31
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.31
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.29
KOG2076	895	consensus RNA polymerase III transcription factor	99.28
KOG2003	840	consensus TPR repeat-containing protein [General f	99.21
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.16
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.11
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.09
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.08
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.05
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.04
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.01
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.99
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.97
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.96
KOG1126	638	consensus DNA-binding cell division cycle control	98.95
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.95
PF12854	34	PPR_1: PPR repeat	98.92
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.92
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.89
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.87
KOG1126	638	consensus DNA-binding cell division cycle control	98.87
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.86
PRK12370	553	invasion protein regulator; Provisional	98.86
PF12854	34	PPR_1: PPR repeat	98.83
PRK12370	553	invasion protein regulator; Provisional	98.79
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.77
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.77
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.72
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.7
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.69
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.63
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.61
KOG1129	478	consensus TPR repeat-containing protein [General f	98.6
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.59
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.59
PRK04841	903	transcriptional regulator MalT; Provisional	98.57
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.56
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.49
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.48
PRK04841	903	transcriptional regulator MalT; Provisional	98.48
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.46
KOG1129	478	consensus TPR repeat-containing protein [General f	98.45
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.42
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.42
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.42
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.41
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.38
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.32
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.32
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.26
PRK11189	296	lipoprotein NlpI; Provisional	98.26
PRK11189	296	lipoprotein NlpI; Provisional	98.26
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.24
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.18
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.18
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.17
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.17
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.11
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.09
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.08
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.07
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.06
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.06
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.03
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.0
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.99
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.98
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.97
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.9
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.88
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.88
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.85
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.82
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.81
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.76
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.75
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.69
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.66
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	97.62
KOG1125	579	consensus TPR repeat-containing protein [General f	97.62
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.59
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	97.47
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.46
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.44
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.4
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.4
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.34
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.33
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.33
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.32
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.32
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.31
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.29
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.25
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.24
KOG1125	579	consensus TPR repeat-containing protein [General f	97.22
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.2
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.17
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.17
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.13
PRK15359	144	type III secretion system chaperone protein SscB;	97.11
PRK15359	144	type III secretion system chaperone protein SscB;	97.08
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.07
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.01
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.99
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.94
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.93
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.76
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.75
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.74
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.69
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.66
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.61
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.57
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.55
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.54
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.53
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	96.47
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.39
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.37
KOG3941	406	consensus Intermediate in Toll signal transduction	96.37
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.33
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.29
KOG3941	406	consensus Intermediate in Toll signal transduction	96.29
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	96.21
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.16
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.07
PLN02789	320	farnesyltranstransferase	95.98
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	95.97
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.84
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.82
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	95.76
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.75
KOG2796	366	consensus Uncharacterized conserved protein [Funct	95.73
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	95.73
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.69
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.68
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.66
PF12688	120	TPR_5: Tetratrico peptide repeat	95.51
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.49
PLN02789	320	farnesyltranstransferase	95.48
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.45
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	95.37
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.37
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.34
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	95.34
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.32
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.26
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.1
KOG2041	1189	consensus WD40 repeat protein [General function pr	95.07
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.05
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	94.89
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.87
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.73
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.65
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	94.63
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.53
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.43
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.43
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	94.34
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.31
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	94.27
PF12688	120	TPR_5: Tetratrico peptide repeat	94.07
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.03
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	94.0
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.97
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.74
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	93.57
PRK10803	263	tol-pal system protein YbgF; Provisional	93.46
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.32
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.03
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	92.96
PF13929	292	mRNA_stabil: mRNA stabilisation	92.77
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	92.7
PRK10803	263	tol-pal system protein YbgF; Provisional	92.67
PF13371	73	TPR_9: Tetratricopeptide repeat	92.53
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	92.46
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.32
PF13371	73	TPR_9: Tetratricopeptide repeat	92.11
KOG0553	304	consensus TPR repeat-containing protein [General f	92.11
KOG0553	304	consensus TPR repeat-containing protein [General f	92.01
COG4700	251	Uncharacterized protein conserved in bacteria cont	91.99
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	91.69
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.65
PF13762	145	MNE1: Mitochondrial splicing apparatus component	91.45
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	91.15
KOG2610	491	consensus Uncharacterized conserved protein [Funct	91.15
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	90.94
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.9
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	90.58
COG3629	280	DnrI DNA-binding transcriptional activator of the	90.51
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	90.23
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	90.19
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	89.62
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	89.54
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	88.87
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	88.76
COG3629	280	DnrI DNA-binding transcriptional activator of the	88.6
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	88.53
PF13762	145	MNE1: Mitochondrial splicing apparatus component	88.2
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	88.08
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	87.58
PF13929	292	mRNA_stabil: mRNA stabilisation	87.43
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	87.2
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.57
PF13512	142	TPR_18: Tetratricopeptide repeat	86.39
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	86.2
KOG2796	366	consensus Uncharacterized conserved protein [Funct	86.19
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	86.09
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	85.92
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	85.91
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	85.78
KOG2297	412	consensus Predicted translation factor, contains W	85.73
PHA02875	413	ankyrin repeat protein; Provisional	85.38
PRK15331	165	chaperone protein SicA; Provisional	85.35
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	85.29
PHA02875	413	ankyrin repeat protein; Provisional	85.16
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	84.24
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	83.8
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	83.7
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	83.51
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	83.07
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	82.97
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	82.94
COG4700	251	Uncharacterized protein conserved in bacteria cont	81.86
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	81.8
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	81.7
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	81.53

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=4.4e-79  Score=631.53  Aligned_cols=484  Identities=22%  Similarity=0.350  Sum_probs=430.8

Q ss_pred             hhhHHhcCChhhHHHHHHHHHhCCCC--------------------------------CChhhHHHHHHHHHhcCChhHH
Q 011378            2 VNALCKDHKIDSAKMFLCEMEQKGVY--------------------------------PDTVTYNTLINAYCREGFLEEA   49 (487)
Q Consensus         2 i~~~~~~~~~~~a~~~~~~~~~~g~~--------------------------------p~~~~~~~ll~~~~~~~~~~~a   49 (487)
                      ++.|++.|+++.|.++|++|.+.|+.                                ||..+|+.+|.+|++.|+++.|
T Consensus       377 y~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~a~~k~g~~e~A  456 (1060)
T PLN03218        377 YNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGA  456 (1060)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHhCcCHHHH
Confidence            45566677777777777777776643                                7888899999999999999999


Q ss_pred             HHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHC
Q 011378           50 FQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRR  129 (487)
Q Consensus        50 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  129 (487)
                      .++|+.|.+.|+.||..+|+++|++|++.|+++.|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.
T Consensus       457 ~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~  536 (1060)
T PLN03218        457 LRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK  536 (1060)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHH--CCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhh
Q 011378          130 GVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKS--AGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVT  207 (487)
Q Consensus       130 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~  207 (487)
                      |+.||..+|+.+|.+|++.|++++|.++|++|..  .|+.||..+|++||.+|++.|++++|.++|++|.+.|+.|+..+
T Consensus       537 Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~t  616 (1060)
T PLN03218        537 NVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEV  616 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHH
Confidence            9999999999999999999999999999999976  67889999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHc
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCK  287 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  287 (487)
                      ||++|.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|+.|.+.|+.||..+|++||.+|++
T Consensus       617 ynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k  696 (1060)
T PLN03218        617 YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSN  696 (1060)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHH
Q 011378          288 VGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEF  367 (487)
Q Consensus       288 ~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  367 (487)
                      .|++++|.++|++|...|+.||..+|+.||.+|++.|++++|.++|++|...|+.||..||+++|.+|++.|+++.|.++
T Consensus       697 ~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l  776 (1060)
T PLN03218        697 AKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDL  776 (1060)
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            99999999999999988999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCCCChhhHHHHHHHHhc----c-------------------CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH
Q 011378          368 LSKMVSEGVDPDSISYNTLINGFVR----E-------------------ENMDKAFALVSKMENQGLVPDVITYNVILTG  424 (487)
Q Consensus       368 ~~~m~~~g~~p~~~~~~~li~~~~~----~-------------------~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  424 (487)
                      +++|.+.|+.||..+|++|+..|.+    .                   +..+.|..+|++|.+.|+.||..||+.+|..
T Consensus       777 ~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~c  856 (1060)
T PLN03218        777 LSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGC  856 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Confidence            9999999999999999999876542    1                   2346788899999999999999999999987


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCCCC
Q 011378          425 FCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDAF  487 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~  487 (487)
                      +++.+..+.+..++++|...+..|+..+|+++|+++...  .++|+.++++|.+.|+.|+-.|
T Consensus       857 l~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~~--~~~A~~l~~em~~~Gi~p~~~~  917 (1060)
T PLN03218        857 LQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEY--DPRAFSLLEEAASLGVVPSVSF  917 (1060)
T ss_pred             hcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhccC--hHHHHHHHHHHHHcCCCCCccc
Confidence            788888888888888888888889999999999988533  4689999999999999998753

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.4e-75  Score=603.79  Aligned_cols=457  Identities=20%  Similarity=0.330  Sum_probs=441.2

Q ss_pred             CCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCC-CCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHH
Q 011378           26 VYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGL-KPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYN  104 (487)
Q Consensus        26 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  104 (487)
                      -.++...|..++..+++.|++++|+++|+.|...|+ .|+..+++.++.+|.+.|..++|.++|..|..    ||..+|+
T Consensus       366 ~~~~~~~~~~~y~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~----pd~~Tyn  441 (1060)
T PLN03218        366 GKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRN----PTLSTFN  441 (1060)
T ss_pred             CCCCchHHHHHHHHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCC----CCHHHHH
Confidence            356778899999999999999999999999999986 56778888999999999999999999999974    9999999


Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcC
Q 011378          105 TLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG  184 (487)
Q Consensus       105 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~  184 (487)
                      .+|.+|++.|+++.|.++|++|.+.|+.||..+|+++|.+|++.|+++.|.++|++|.+.|+.||..+|+.||++|++.|
T Consensus       442 ~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G  521 (1060)
T PLN03218        442 MLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAG  521 (1060)
T ss_pred             HHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 011378          185 FVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLE--RGVFPDFYTFTTLIHGHCKDGNMNKALNL  262 (487)
Q Consensus       185 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~t~~~li~~~~~~g~~~~a~~~  262 (487)
                      ++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+  .|+.||..||+++|.+|++.|++++|.++
T Consensus       522 ~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~el  601 (1060)
T PLN03218        522 QVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEV  601 (1060)
T ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence            9999999999999999999999999999999999999999999999986  68999999999999999999999999999


Q ss_pred             HHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 011378          263 FDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIK  342 (487)
Q Consensus       263 ~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  342 (487)
                      |+.|.+.|+.|+..+|+++|.+|++.|++++|.++|.+|...|+.||..||+.+|.+|++.|++++|.++|++|.+.|+.
T Consensus       602 f~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~  681 (1060)
T PLN03218        602 YQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK  681 (1060)
T ss_pred             HHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHH
Q 011378          343 PTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVIL  422 (487)
Q Consensus       343 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  422 (487)
                      ||..+|++||.+|++.|++++|.++|++|.+.|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..||+++|
T Consensus       682 pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL  761 (1060)
T PLN03218        682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL  761 (1060)
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh-----------------------cCCHHHHHHHHHHHHHC
Q 011378          423 TGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVS-----------------------QNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~-----------------------~~~~~~a~~~~~~m~~~  479 (487)
                      .+|++.|++++|.+++.+|.+.|+.||..+|++++..|..                       .++.+.|..+|++|++.
T Consensus       762 ~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~~  841 (1060)
T PLN03218        762 VASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISA  841 (1060)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHHC
Confidence            9999999999999999999999999999999999976542                       23457899999999999


Q ss_pred             CCCCCCC
Q 011378          480 GFVPDDA  486 (487)
Q Consensus       480 g~~p~~~  486 (487)
                      |++||..
T Consensus       842 Gi~Pd~~  848 (1060)
T PLN03218        842 GTLPTME  848 (1060)
T ss_pred             CCCCCHH
Confidence            9999963

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.2e-73  Score=601.26  Aligned_cols=469  Identities=22%  Similarity=0.317  Sum_probs=312.4

Q ss_pred             ChhhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCC
Q 011378            1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGR   80 (487)
Q Consensus         1 li~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~   80 (487)
                      ||.+|++.|+++.|.++|++|.+.|++||..||++++++|++.+++..+.+++..|...|+.||..+||++|.+|++.|+
T Consensus       158 li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~  237 (857)
T PLN03077        158 LVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGD  237 (857)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCC
Confidence            46777888888888888888877788787777777666666666666666666666666666666666666666666666


Q ss_pred             hhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHH
Q 011378           81 CDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFRE  160 (487)
Q Consensus        81 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  160 (487)
                      ++.|.++|++|.    .||..+||++|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|+++.|.+++..
T Consensus       238 ~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~  313 (857)
T PLN03077        238 VVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGY  313 (857)
T ss_pred             HHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHH
Confidence            666666666665    3566666666666666666666666666666666666666666666666666666666666666


Q ss_pred             HHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH
Q 011378          161 MKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF  240 (487)
Q Consensus       161 m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  240 (487)
                      |.+.|+.||..+|++||++|++.|++++|.++|++|.    .||..+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus       314 ~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~  389 (857)
T PLN03077        314 VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDE  389 (857)
T ss_pred             HHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC----CCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCc
Confidence            6666666666666666666666666666666666664    255666666666666666666666666666666666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011378          241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGY  320 (487)
Q Consensus       241 ~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~  320 (487)
                      .||+++|.+|++.|+++.|.++++.|.+.|+.|+..+||+||++|+++|++++|.++|++|..    ||..+|+.+|.+|
T Consensus       390 ~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~vs~~~mi~~~  465 (857)
T PLN03077        390 ITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPE----KDVISWTSIIAGL  465 (857)
T ss_pred             eeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCC----CCeeeHHHHHHHH
Confidence            666666666666666666666666666666666666666666666666666666666665542    4555555555555


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCC------------------------
Q 011378          321 CSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGV------------------------  376 (487)
Q Consensus       321 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~------------------------  376 (487)
                      ++.|+.++|..+|++|.. +++||..||+.+|.+|++.|+.+.+.+++..+.+.|+                        
T Consensus       466 ~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~  544 (857)
T PLN03077        466 RLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAW  544 (857)
T ss_pred             HHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHH
Confidence            555555555555555543 3555555555555555555555555555444444444                        


Q ss_pred             ------CCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH-HcCCCCC
Q 011378          377 ------DPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMI-EKGLNPD  449 (487)
Q Consensus       377 ------~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-~~g~~p~  449 (487)
                            .||..+||+||.+|++.|+.++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|++|. ..|+.|+
T Consensus       545 ~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~  624 (857)
T PLN03077        545 NQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPN  624 (857)
T ss_pred             HHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCc
Confidence                  456667777777777777777777777777777777777777777777777777777777777777 5677777


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCC
Q 011378          450 RSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD  485 (487)
Q Consensus       450 ~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~~  485 (487)
                      ..+|++|+++|++.|++++|.+++++|   +++||.
T Consensus       625 ~~~y~~lv~~l~r~G~~~eA~~~~~~m---~~~pd~  657 (857)
T PLN03077        625 LKHYACVVDLLGRAGKLTEAYNFINKM---PITPDP  657 (857)
T ss_pred             hHHHHHHHHHHHhCCCHHHHHHHHHHC---CCCCCH
Confidence            777777777777777777777777777   466764

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

Probab=100.00  E-value=1e-72  Score=580.78  Aligned_cols=468  Identities=22%  Similarity=0.312  Sum_probs=450.0

Q ss_pred             ChhhHHhcCChhhHHHHHHHHHhCC-CCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcC
Q 011378            1 MVNALCKDHKIDSAKMFLCEMEQKG-VYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKG   79 (487)
Q Consensus         1 li~~~~~~~~~~~a~~~~~~~~~~g-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~   79 (487)
                      +|..|++.|+++.|.++|+.|...+ +.||..+|+.++.+|++.++++.+.+++..|...|+.||..+|+.+|++|++.|
T Consensus        93 ~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g  172 (697)
T PLN03081         93 QIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCG  172 (697)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCC
Confidence            3678999999999999999998764 789999999999999999999999999999999999999999999999999999


Q ss_pred             ChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHH
Q 011378           80 RCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFR  159 (487)
Q Consensus        80 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  159 (487)
                      +++.|.++|++|.+    ||..+||+++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+|++.|..+.+.+++.
T Consensus       173 ~~~~A~~lf~~m~~----~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~  248 (697)
T PLN03081        173 MLIDARRLFDEMPE----RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHC  248 (697)
T ss_pred             CHHHHHHHHhcCCC----CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHH
Confidence            99999999999974    89999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011378          160 EMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD  239 (487)
Q Consensus       160 ~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~  239 (487)
                      .+.+.|+.||..+|++||++|++.|++++|.++|++|.+    +|..+||++|.+|++.|+.++|.++|++|.+.|+.||
T Consensus       249 ~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd  324 (697)
T PLN03081        249 CVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSID  324 (697)
T ss_pred             HHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence            999999999999999999999999999999999999964    6899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011378          240 FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILING  319 (487)
Q Consensus       240 ~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~  319 (487)
                      ..||++++.+|++.|++++|.++++.|.+.|+.||..+||+||++|+++|++++|.++|++|.    .||..|||.||.+
T Consensus       325 ~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d~~t~n~lI~~  400 (697)
T PLN03081        325 QFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLISWNALIAG  400 (697)
T ss_pred             HHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCCeeeHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999986    4899999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH-CCCCCChhhHHHHHHHHhccCCHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS-EGVDPDSISYNTLINGFVREENMDK  398 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p~~~~~~~li~~~~~~~~~~~  398 (487)
                      |++.|+.++|.++|++|.+.|+.||..||+++|.+|++.|+.++|.++|+.|.+ .|+.|+..+|++|+++|++.|++++
T Consensus       401 y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~e  480 (697)
T PLN03081        401 YGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDE  480 (697)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHH
Confidence            999999999999999999999999999999999999999999999999999986 6999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      |.+++++|   +..|+..+|++|+.+|+..|+++.|..+++++.  ++.|+ ..+|..|++.|++.|++++|.+++++|.
T Consensus       481 A~~~~~~~---~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~--~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~  555 (697)
T PLN03081        481 AYAMIRRA---PFKPTVNMWAALLTACRIHKNLELGRLAAEKLY--GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLK  555 (697)
T ss_pred             HHHHHHHC---CCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHh--CCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            99998765   678999999999999999999999999999985  45665 6799999999999999999999999999


Q ss_pred             HCCCCCCC
Q 011378          478 QRGFVPDD  485 (487)
Q Consensus       478 ~~g~~p~~  485 (487)
                      +.|+++.+
T Consensus       556 ~~g~~k~~  563 (697)
T PLN03081        556 RKGLSMHP  563 (697)
T ss_pred             HcCCccCC
Confidence            99997654

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.8e-72  Score=590.84  Aligned_cols=468  Identities=20%  Similarity=0.332  Sum_probs=372.4

Q ss_pred             ChhhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCC
Q 011378            1 MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGR   80 (487)
Q Consensus         1 li~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~   80 (487)
                      +|++|++.++++.+.+++..|.+.|+.||..+||++|.+|++.|+++.|.++|+.|..    ||..+||++|++|++.|+
T Consensus       193 ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~----~d~~s~n~li~~~~~~g~  268 (857)
T PLN03077        193 VLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR----RDCISWNAMISGYFENGE  268 (857)
T ss_pred             HHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCC----CCcchhHHHHHHHHhCCC
Confidence            3566777777777777777777777777777777777777777777777777777753    577777777777777777


Q ss_pred             hhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHH
Q 011378           81 CDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFRE  160 (487)
Q Consensus        81 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  160 (487)
                      +++|.++|.+|.+.|+.||..||+.+|.+|++.|+++.+.+++..|.+.|+.||..+||++|.+|++.|++++|.++|++
T Consensus       269 ~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~  348 (857)
T PLN03077        269 CLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSR  348 (857)
T ss_pred             HHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhh
Confidence            77777777777777777777777777777777777777777777777777777777777777777777777777777777


Q ss_pred             HHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH
Q 011378          161 MKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF  240 (487)
Q Consensus       161 m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  240 (487)
                      |.    .||..+|+++|.+|++.|+.++|.++|++|.+.|+.||..||++++.+|++.|+++.+.++++.|.+.|+.|+.
T Consensus       349 m~----~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~  424 (857)
T PLN03077        349 ME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYV  424 (857)
T ss_pred             CC----CCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcch
Confidence            75    36677777777777777777777777777777777777777777777777777777777777777777777777


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011378          241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGY  320 (487)
Q Consensus       241 ~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~  320 (487)
                      .+|++||++|++.|++++|.++|+.|.+    +|..+||++|.+|++.|+.++|.++|++|.. ++.||..||+.+|.+|
T Consensus       425 ~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~  499 (857)
T PLN03077        425 VVANALIEMYSKCKCIDKALEVFHNIPE----KDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSAC  499 (857)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHH
Confidence            7777777777777777777777777653    4666777777777777777777777777754 4666666666666555


Q ss_pred             HhcCCHHHHHHHHHHHHhCCC------------------------------CCChhhHHHHHHHHHhcCChHHHHHHHHH
Q 011378          321 CSMGHVTEAFRLWYEMVGKGI------------------------------KPTLVSCNTIIKGYCRSGDASKADEFLSK  370 (487)
Q Consensus       321 ~~~~~~~~a~~~~~~m~~~~~------------------------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~  370 (487)
                      ++.|.++.+.+++..|.+.|+                              +||..+||++|.+|++.|+.++|.++|++
T Consensus       500 ~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~  579 (857)
T PLN03077        500 ARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNR  579 (857)
T ss_pred             hhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHH
Confidence            555555555555554444443                              67888999999999999999999999999


Q ss_pred             HHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHH-hCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 011378          371 MVSEGVDPDSISYNTLINGFVREENMDKAFALVSKME-NQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD  449 (487)
Q Consensus       371 m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~-~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  449 (487)
                      |.+.|+.||..||+++|.+|.+.|.+++|.++|+.|. +.|+.|+..+|++++++|++.|++++|.+++++|   +++||
T Consensus       580 M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m---~~~pd  656 (857)
T PLN03077        580 MVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM---PITPD  656 (857)
T ss_pred             HHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHC---CCCCC
Confidence            9999999999999999999999999999999999998 6799999999999999999999999999999998   48999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCCC
Q 011378          450 RSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDDA  486 (487)
Q Consensus       450 ~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  486 (487)
                      ..+|++|+.+|..+|+.+.+....+++.+  +.|++.
T Consensus       657 ~~~~~aLl~ac~~~~~~e~~e~~a~~l~~--l~p~~~  691 (857)
T PLN03077        657 PAVWGALLNACRIHRHVELGELAAQHIFE--LDPNSV  691 (857)
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHh--hCCCCc
Confidence            99999999999999999999988888874  577653

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

Probab=100.00  E-value=4.1e-68  Score=546.69  Aligned_cols=443  Identities=19%  Similarity=0.345  Sum_probs=426.4

Q ss_pred             CCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhC-CCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHH
Q 011378           26 VYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGK-GLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYN  104 (487)
Q Consensus        26 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  104 (487)
                      ..++..+|+.+|.++++.|++++|+++|+.|... ++.||..+|+.++.+|++.++++.+.+++..|.+.|+.||..+||
T Consensus        83 ~~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n  162 (697)
T PLN03081         83 IRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN  162 (697)
T ss_pred             CCCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHH
Confidence            3456679999999999999999999999999876 478999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcC
Q 011378          105 TLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG  184 (487)
Q Consensus       105 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~  184 (487)
                      .|+..|++.|+++.|.++|++|.    .||.++||++|.+|++.|++++|+++|++|.+.|+.||..+|+.++.++++.|
T Consensus       163 ~Li~~y~k~g~~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~  238 (697)
T PLN03081        163 RVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLG  238 (697)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCC
Confidence            99999999999999999999996    48999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          185 FVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFD  264 (487)
Q Consensus       185 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~  264 (487)
                      ....+.+++..+.+.|+.+|..+||+||++|++.|++++|.++|++|.+    +|..+||+||.+|++.|+.++|+++|+
T Consensus       239 ~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~  314 (697)
T PLN03081        239 SARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYY  314 (697)
T ss_pred             cHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999964    689999999999999999999999999


Q ss_pred             HHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 011378          265 IMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT  344 (487)
Q Consensus       265 ~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~  344 (487)
                      .|.+.|+.||..||+++|++|++.|++++|.+++.+|.+.|+.||..+|+.||++|++.|++++|.++|++|.    +||
T Consensus       315 ~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d  390 (697)
T PLN03081        315 EMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKN  390 (697)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999995    589


Q ss_pred             hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHh-CCCCCCHhhHHHHHH
Q 011378          345 LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN-QGLVPDVITYNVILT  423 (487)
Q Consensus       345 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p~~~~~~~li~  423 (487)
                      ..+||+||.+|++.|+.++|.++|++|.+.|+.||..||++++.+|.+.|.+++|.++|+.|.+ .|+.|+..+|+++|+
T Consensus       391 ~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~  470 (697)
T PLN03081        391 LISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIE  470 (697)
T ss_pred             eeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999975 699999999999999


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCC
Q 011378          424 GFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD  485 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~~  485 (487)
                      +|+++|++++|.+++++|   ++.|+..+|+.|+.+|..+|+++.|.+++++|.  ++.|+.
T Consensus       471 ~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~--~~~p~~  527 (697)
T PLN03081        471 LLGREGLLDEAYAMIRRA---PFKPTVNMWAALLTACRIHKNLELGRLAAEKLY--GMGPEK  527 (697)
T ss_pred             HHHhcCCHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHh--CCCCCC
Confidence            999999999999998765   789999999999999999999999999999996  666764

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

Probab=99.97  E-value=5.7e-26  Score=243.83  Aligned_cols=460  Identities=14%  Similarity=0.081  Sum_probs=343.3

Q ss_pred             hhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChh
Q 011378            3 NALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCD   82 (487)
Q Consensus         3 ~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~   82 (487)
                      ..+.+.|+++.|..+++.+.... +++..++..+...+.+.|++++|.+.|+.+.+.. +.+...+..+...+...|+++
T Consensus       439 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~  516 (899)
T TIGR02917       439 LSYLRSGQFDKALAAAKKLEKKQ-PDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPD  516 (899)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHH
Confidence            34566677777777777765532 3455677777777777788888887777765532 223345666667777778888


Q ss_pred             hHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHH
Q 011378           83 RAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMK  162 (487)
Q Consensus        83 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  162 (487)
                      +|.+.++++.+.. +.+..++..+...+.+.|+.++|...++++.+.+ +.+...+..+...+.+.|++++|..+++.+.
T Consensus       517 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  594 (899)
T TIGR02917       517 DAIQRFEKVLTID-PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAA  594 (899)
T ss_pred             HHHHHHHHHHHhC-cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            8888887776543 2356677777777777888888888887776543 2345566677778888888888888888876


Q ss_pred             HCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH
Q 011378          163 SAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYT  242 (487)
Q Consensus       163 ~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t  242 (487)
                      ... ..+..+|..+...+.+.|+.++|...++.+.+.. +.+...+..+...+.+.|+++.|...|+++.+.. +.+..+
T Consensus       595 ~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  671 (899)
T TIGR02917       595 DAA-PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEA  671 (899)
T ss_pred             HcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHH
Confidence            532 3456678888888888888888888888876643 2355667778888888888888888888877642 335677


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          243 FTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCS  322 (487)
Q Consensus       243 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~  322 (487)
                      +..+...+...|++++|.++++.+.+.. +.+...+..+...+.+.|++++|.+.|..+...+  |+..++..+..++..
T Consensus       672 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~  748 (899)
T TIGR02917       672 QIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLA  748 (899)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHH
Confidence            8888888888888888888888877654 3355567777788888888888888888877654  445677778888888


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHH
Q 011378          323 MGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFAL  402 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~  402 (487)
                      .|++++|...++.+.... +.+...+..+...|...|+.++|.+.++++.+.. +++...++.+...+...|+ ++|...
T Consensus       749 ~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~  825 (899)
T TIGR02917       749 SGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEY  825 (899)
T ss_pred             CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHH
Confidence            888888888888877643 5567778888888888899999999998887654 3567788888888888888 778888


Q ss_pred             HHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          403 VSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       403 ~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      +++..+.. .-+...+..+...+.+.|++++|...++++.+.+.. +..+|..+...+...|++++|.+++++|+
T Consensus       826 ~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       826 AEKALKLA-PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLALALLATGRKAEARKELDKLL  898 (899)
T ss_pred             HHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            88876542 224456777788888999999999999999886643 78889999999999999999999999886

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=99.96  E-value=5.2e-24  Score=228.67  Aligned_cols=463  Identities=13%  Similarity=0.094  Sum_probs=281.7

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCC-----------------------
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKG-----------------------   60 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-----------------------   60 (487)
                      .+.+.|+++.|..+++++.+.. +.+...+..+...+...|++++|.+.++......                       
T Consensus       372 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A  450 (899)
T TIGR02917       372 AYLALGDFEKAAEYLAKATELD-PENAAARTQLGISKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKA  450 (899)
T ss_pred             HHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhCCChHHHHHHHHHHHhhCCcchhhHHHHHHHHHhcCCHHHH
Confidence            4555666666666666655432 1133444445555555555555555555443321                       


Q ss_pred             ----------CCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCC
Q 011378           61 ----------LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRG  130 (487)
Q Consensus        61 ----------~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g  130 (487)
                                .+++..+|..+...+.+.|++++|.+.|+++.+.. +.+...+..+...+...|++++|.+.++++.+..
T Consensus       451 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  529 (899)
T TIGR02917       451 LAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTID  529 (899)
T ss_pred             HHHHHHHHHhCCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence                      12233445555555555555555555555554321 1223344444555555555555555555554432


Q ss_pred             CCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHH
Q 011378          131 VAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNT  210 (487)
Q Consensus       131 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  210 (487)
                       +.+..++..+...+.+.|+.++|..+++++...+ ..+...+..+...+.+.|+.++|..+++.+.+. .+.+...|..
T Consensus       530 -~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~  606 (899)
T TIGR02917       530 -PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADA-APDSPEAWLM  606 (899)
T ss_pred             -cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHc-CCCCHHHHHH
Confidence             2234455555556666666666666666654432 223345555666666666666666666666543 2344556666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCC
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE  290 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~  290 (487)
                      +..++.+.|++++|...|+++.+.. +.+...+..+...+...|+.++|..+|+.+.+.. +.+..++..+...+...|+
T Consensus       607 l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~  684 (899)
T TIGR02917       607 LGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKR  684 (899)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCC
Confidence            6677777777777777776665532 2345556666666777777777777776655432 2234566667777777777


Q ss_pred             HHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHH
Q 011378          291 MEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSK  370 (487)
Q Consensus       291 ~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  370 (487)
                      +++|.+++..+...+ +++...+..+...+...|++++|...++.+...+  |+..++..+...+.+.|+.++|.+.++.
T Consensus       685 ~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~  761 (899)
T TIGR02917       685 TESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEA  761 (899)
T ss_pred             HHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            777777777665543 3345566667777777777777777777766543  4445666677777777777777777777


Q ss_pred             HHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH
Q 011378          371 MVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR  450 (487)
Q Consensus       371 m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  450 (487)
                      +.+.. +.+...+..+...|.+.|+.++|.+.++++.+.. .+++..++.+...+.+.|+ .+|...+++..... .-+.
T Consensus       762 ~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~-~~~~  837 (899)
T TIGR02917       762 WLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEYAEKALKLA-PNIP  837 (899)
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhC-CCCc
Confidence            66532 3456677777777777888888888887776543 3456677777777777777 77777777776532 1234


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          451 STYTTLINGHVSQNNLKEAFRFHDEMLQRG  480 (487)
Q Consensus       451 ~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g  480 (487)
                      .++..+...+...|++++|.++++++++.+
T Consensus       838 ~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~  867 (899)
T TIGR02917       838 AILDTLGWLLVEKGEADRALPLLRKAVNIA  867 (899)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            466677778888899999999998888754

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=99.89  E-value=7e-20  Score=177.22  Aligned_cols=305  Identities=15%  Similarity=0.155  Sum_probs=169.2

Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCC---hhhHHHHHHHHHhcCC
Q 011378          144 IFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMD---VVTYNTILNGLCRAKM  220 (487)
Q Consensus       144 ~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~li~~~~~~~~  220 (487)
                      .+...|++++|...|.++.+.+ ..+..++..+...+.+.|++++|..+++.+.+.+..++   ...+..+...|.+.|+
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            3455666777777777666542 11233555566666666666666666666554322111   1234455555555555


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHH
Q 011378          221 LTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD  300 (487)
Q Consensus       221 ~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  300 (487)
                      ++.|..+|+++.+.. +++..++..+...+.+.|++++|.+.++.+.+.+..+....                       
T Consensus       123 ~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-----------------------  178 (389)
T PRK11788        123 LDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVE-----------------------  178 (389)
T ss_pred             HHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHH-----------------------
Confidence            555555555554431 22344555555555555555555555555443321111000                       


Q ss_pred             HHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh
Q 011378          301 MISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS  380 (487)
Q Consensus       301 m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  380 (487)
                              ....+..+...+...|++++|...++++.+.. +.+...+..+...|.+.|+.++|.+.++++...+-....
T Consensus       179 --------~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~  249 (389)
T PRK11788        179 --------IAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLS  249 (389)
T ss_pred             --------HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHH
Confidence                    01123344445555566666666666555432 223344555556666666666666666666543211123


Q ss_pred             hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011378          381 ISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGH  460 (487)
Q Consensus       381 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~  460 (487)
                      .+++.+..+|.+.|++++|...++++.+.  .|+...+..++..+.+.|++++|..+++++.+.  .|+..++..++..+
T Consensus       250 ~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~  325 (389)
T PRK11788        250 EVLPKLMECYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYH  325 (389)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHh
Confidence            45566666777777777777777766553  455555666667777777777777777766543  56777777666665


Q ss_pred             Hh---cCCHHHHHHHHHHHHHCCCCCCCC
Q 011378          461 VS---QNNLKEAFRFHDEMLQRGFVPDDA  486 (487)
Q Consensus       461 ~~---~~~~~~a~~~~~~m~~~g~~p~~~  486 (487)
                      ..   .|+.++++.++++|.+.+++|++.
T Consensus       326 ~~~~~~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        326 LAEAEEGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             hhccCCccchhHHHHHHHHHHHHHhCCCC
Confidence            53   346677777777777777766653

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.88  E-value=4.6e-19  Score=171.50  Aligned_cols=313  Identities=13%  Similarity=0.114  Sum_probs=235.2

Q ss_pred             HHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC---hhhHHHHHHHHHhcCC
Q 011378          109 ESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD---NVLYTIIINGYCRNGF  185 (487)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~---~~~~~~ll~~~~~~~~  185 (487)
                      .+...|++++|...|+++.+.+ +.+..++..+...+.+.|++++|..+++.+...+..++   ...+..+...|.+.|+
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            4567899999999999998863 23556788899999999999999999999987543222   2468888999999999


Q ss_pred             HHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCCHHHHHH
Q 011378          186 VLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD----FYTFTTLIHGHCKDGNMNKALN  261 (487)
Q Consensus       186 ~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~----~~t~~~li~~~~~~g~~~~a~~  261 (487)
                      .++|..+++++.+. .+.+..+++.+...+.+.|++++|.+.++.+.+.+..++    ...+..+...+.+.|+.++|..
T Consensus       123 ~~~A~~~~~~~l~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  201 (389)
T PRK11788        123 LDRAEELFLQLVDE-GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARA  201 (389)
T ss_pred             HHHHHHHHHHHHcC-CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence            99999999999875 335677899999999999999999999999987653332    1235567777888899999999


Q ss_pred             HHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 011378          262 LFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGI  341 (487)
Q Consensus       262 ~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~  341 (487)
                      .|+.+.+.. +.+...+..+...+.+.|++++|.+.|.++..........+++.+..+|...|++++|...++.+...  
T Consensus       202 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--  278 (389)
T PRK11788        202 LLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE--  278 (389)
T ss_pred             HHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--
Confidence            998877643 22344666777888888888888888888775432222456677778888888888888888877654  


Q ss_pred             CCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc---cCCHHHHHHHHHHHHhCCCCCCHhhH
Q 011378          342 KPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR---EENMDKAFALVSKMENQGLVPDVITY  418 (487)
Q Consensus       342 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~~~  418 (487)
                      .|+...+..+...+.+.|+.++|..+++++.+.  .|+..+++.++..+..   .|+.+++..++++|.+.+++|++.  
T Consensus       279 ~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~--  354 (389)
T PRK11788        279 YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR--  354 (389)
T ss_pred             CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC--
Confidence            456566677777788888888888888777654  4777777777776664   447777788888777777777666  


Q ss_pred             HHHHHHHHhcCChHHH
Q 011378          419 NVILTGFCRQGRMHDS  434 (487)
Q Consensus       419 ~~li~~~~~~g~~~~a  434 (487)
                          ..|.++|-..+.
T Consensus       355 ----~~c~~cg~~~~~  366 (389)
T PRK11788        355 ----YRCRNCGFTART  366 (389)
T ss_pred             ----EECCCCCCCCcc
Confidence                235566654443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.87  E-value=2.5e-17  Score=147.32  Aligned_cols=362  Identities=17%  Similarity=0.205  Sum_probs=257.9

Q ss_pred             CCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHH
Q 011378           98 PDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIII  177 (487)
Q Consensus        98 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll  177 (487)
                      -+..||.++|.++|+....+.|.+++++-.....+.+..+||.+|.+-+-.-.    .+++.+|.+..+.||..|+|+++
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL  280 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALL  280 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHH
Confidence            46678899999999999999999999888888788888899998876543222    67888888888999999999999


Q ss_pred             HHHHhcCCHHH----HHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHH-HHHHHHHHHH----cCCCC----CHHHHH
Q 011378          178 NGYCRNGFVLE----ALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTE-ADDLFNEMLE----RGVFP----DFYTFT  244 (487)
Q Consensus       178 ~~~~~~~~~~~----a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~-a~~~~~~m~~----~~~~~----~~~t~~  244 (487)
                      +..++.|+++.    +++++.+|++-|+.|...+|..+|..+++.++... +..++.+...    +.++|    |..-|.
T Consensus       281 ~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~  360 (625)
T KOG4422|consen  281 SCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQ  360 (625)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHH
Confidence            99999987664    46678888999999999999999999988887643 4444444332    33333    445677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHC----CCCCCe---eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHH
Q 011378          245 TLIHGHCKDGNMNKALNLFDIMTQK----SIKPDI---VTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILI  317 (487)
Q Consensus       245 ~li~~~~~~g~~~~a~~~~~~m~~~----~~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li  317 (487)
                      ..|..|.+..+.+.|.++...+...    -+.|+.   .-|..+....|....++...+.+..|.-+-.-|+..+..-++
T Consensus       361 ~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~l  440 (625)
T KOG4422|consen  361 SAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLL  440 (625)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHHH
Confidence            8888888999999999888776532    244442   236778888899999999999999999888888888999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhcc--CC
Q 011378          318 NGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVRE--EN  395 (487)
Q Consensus       318 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~--~~  395 (487)
                      ++....|+++-.-++|.+++..|.+-+...-                ++++..|......|+..--.-|-.+.++.  ..
T Consensus       441 rA~~v~~~~e~ipRiw~D~~~~ght~r~~l~----------------eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~  504 (625)
T KOG4422|consen  441 RALDVANRLEVIPRIWKDSKEYGHTFRSDLR----------------EEILMLLARDKLHPLTPEREQLQVAFAKCAADI  504 (625)
T ss_pred             HHHhhcCcchhHHHHHHHHHHhhhhhhHHHH----------------HHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHH
Confidence            9999999999999999999876643333322                33333343334344433222222222211  11


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHhcCCHHHHHH
Q 011378          396 MDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKG----LNPDRSTYTTLINGHVSQNNLKEAFR  471 (487)
Q Consensus       396 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~ty~~l~~~~~~~~~~~~a~~  471 (487)
                      .+..+.-..+|....+.  ....+.+.-.+.+.|+.++|+++|..+..++    ..|.......+++.-.+.++...|..
T Consensus       505 ~e~~e~~~~R~r~~~~~--~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~  582 (625)
T KOG4422|consen  505 KEAYESQPIRQRAQDWP--ATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIE  582 (625)
T ss_pred             HHHHHhhHHHHHhccCC--hhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHH
Confidence            22223334555554443  3456777778888888888888888876544    23555555577788888888888888


Q ss_pred             HHHHHHHCCC
Q 011378          472 FHDEMLQRGF  481 (487)
Q Consensus       472 ~~~~m~~~g~  481 (487)
                      .++-|...++
T Consensus       583 ~lQ~a~~~n~  592 (625)
T KOG4422|consen  583 VLQLASAFNL  592 (625)
T ss_pred             HHHHHHHcCc
Confidence            8888876654

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.83  E-value=4.6e-15  Score=161.30  Aligned_cols=431  Identities=14%  Similarity=0.099  Sum_probs=317.5

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCC-CCHHHHHHH--------
Q 011378           37 INAYCREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLS-PDTATYNTL--------  106 (487)
Q Consensus        37 l~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~l--------  106 (487)
                      -..+...|++++|...|+.....  .| +...+..+-..+.+.|++++|...|++..+..-. +....|..+        
T Consensus       276 G~~~~~~g~~~~A~~~l~~aL~~--~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~  353 (1157)
T PRK11447        276 GLAAVDSGQGGKAIPELQQAVRA--NPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWL  353 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHH
Confidence            45667889999999999988764  34 5677888888999999999999999998764321 122222222        


Q ss_pred             ----HHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHH
Q 011378          107 ----LVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYC  181 (487)
Q Consensus       107 ----l~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~  181 (487)
                          -..+.+.|++++|...|++..+.. +.+...+..+-..+.+.|++++|.+.|++..+..  |+ ...+..+...|.
T Consensus       354 ~~~~g~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~--p~~~~a~~~L~~l~~  430 (1157)
T PRK11447        354 LIQQGDAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD--PGNTNAVRGLANLYR  430 (1157)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHH
Confidence                235678899999999999998753 2345667778889999999999999999988643  43 445566666664


Q ss_pred             hcCCHHHHHHHHHHHHHcCC--------cCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 011378          182 RNGFVLEALKMRDEMLEKGC--------VMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD  253 (487)
Q Consensus       182 ~~~~~~~a~~~~~~m~~~g~--------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~  253 (487)
                       .+..++|..+++.+....-        ......+..+...+...|++++|.+.|++..+.. +-+...+..+...|.+.
T Consensus       431 -~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~  508 (1157)
T PRK11447        431 -QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQA  508 (1157)
T ss_pred             -hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc
Confidence             4577888888765432210        0112245566777888999999999999988753 22567778888999999


Q ss_pred             CCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChh---------hHHHHHHHHHhc
Q 011378          254 GNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYI---------SYGILINGYCSM  323 (487)
Q Consensus       254 g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~---------t~~~li~~~~~~  323 (487)
                      |+.++|...++...+..  | +...+..+...+.+.++.++|...+..+......++..         .+..+...+...
T Consensus       509 G~~~~A~~~l~~al~~~--P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~  586 (1157)
T PRK11447        509 GQRSQADALMRRLAQQK--PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDS  586 (1157)
T ss_pred             CCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHC
Confidence            99999999999877532  3 33334444455677899999999988764433323221         123456678889


Q ss_pred             CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHH
Q 011378          324 GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALV  403 (487)
Q Consensus       324 ~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~  403 (487)
                      |+.++|..+++.     .+.+...+..+-..+.+.|+.++|...+++..+.. +.+...+..+...|...|+.++|.+.+
T Consensus       587 G~~~eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l  660 (1157)
T PRK11447        587 GKEAEAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQL  660 (1157)
T ss_pred             CCHHHHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            999999998872     34455667778888999999999999999988753 234668889999999999999999999


Q ss_pred             HHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC--C---CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          404 SKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIEKGLN--P---DRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       404 ~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~--p---~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      +...+.  .|+ ...+..+...+.+.|++++|..+++++....-.  |   +...+..+.+.+...|++++|...+++-.
T Consensus       661 ~~ll~~--~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al  738 (1157)
T PRK11447        661 AKLPAT--ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAM  738 (1157)
T ss_pred             HHHhcc--CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            977653  444 455666777888999999999999998764321  2   22456666788899999999999988775


Q ss_pred             -HCCCCCC
Q 011378          478 -QRGFVPD  484 (487)
Q Consensus       478 -~~g~~p~  484 (487)
                       ..|+.|+
T Consensus       739 ~~~~~~~~  746 (1157)
T PRK11447        739 VASGITPT  746 (1157)
T ss_pred             hhcCCCCC
Confidence             4566654

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.82  E-value=1.6e-14  Score=157.11  Aligned_cols=458  Identities=13%  Similarity=0.075  Sum_probs=284.4

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChhh-HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChh
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTVT-YNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCD   82 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~~-~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~   82 (487)
                      .+.+.|++++|...++...+.. .|+... ...........|+.++|.+.++.+.... +-+...+..+-..+.+.|+++
T Consensus       121 ll~~~g~~~eA~~~~~~~l~~~-p~~~~la~~y~~~~~~~~g~~~~A~~~L~~ll~~~-P~~~~~~~~LA~ll~~~g~~~  198 (1157)
T PRK11447        121 LLATTGRTEEALASYDKLFNGA-PPELDLAVEYWRLVAKLPAQRPEAINQLQRLNADY-PGNTGLRNTLALLLFSSGRRD  198 (1157)
T ss_pred             HHHhCCCHHHHHHHHHHHccCC-CCChHHHHHHHHHHhhCCccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHccCCHH
Confidence            4678899999999999987643 333221 1111222234589999999999987752 223455667777888899999


Q ss_pred             hHHHHHHHHHHCCC------------------CCCH-HHHH----------------------------------HHHHH
Q 011378           83 RAKEVLDEMLQMGL------------------SPDT-ATYN----------------------------------TLLVE  109 (487)
Q Consensus        83 ~a~~~~~~m~~~g~------------------~~~~-~~~~----------------------------------~ll~~  109 (487)
                      +|.+.++++.+..-                  .+.. ..+.                                  ..-..
T Consensus       199 eAl~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~~~~G~~  278 (1157)
T PRK11447        199 EGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRARAQGLA  278 (1157)
T ss_pred             HHHHHHHHHhhCCCchHHHHHHHHHHHhccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHHHHHHHH
Confidence            99999988754321                  0000 0010                                  01123


Q ss_pred             HHccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC-ChhhHHH------------
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVP-DNVLYTI------------  175 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~~~~------------  175 (487)
                      +...|++++|...|++..+.  .| +...+..+-..+.+.|++++|...|++..+..... ....|..            
T Consensus       279 ~~~~g~~~~A~~~l~~aL~~--~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~  356 (1157)
T PRK11447        279 AVDSGQGGKAIPELQQAVRA--NPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQ  356 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHH
Confidence            45678888888888887764  34 56677788888888999999999888877643221 1111211            


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 011378          176 IINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGN  255 (487)
Q Consensus       176 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~  255 (487)
                      .-..+.+.|+.++|...+++..+.. +.+...+..+-..+...|++++|.+.|++..+.. +.+...+..+...|. .++
T Consensus       357 ~g~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~-~~~  433 (1157)
T PRK11447        357 QGDAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYR-QQS  433 (1157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH-hcC
Confidence            1335667888899988888887653 2345566777888888899999999998887642 223344444444432 234


Q ss_pred             HHHHHHHHHHHHHCCCC--------CCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCH
Q 011378          256 MNKALNLFDIMTQKSIK--------PDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHV  326 (487)
Q Consensus       256 ~~~a~~~~~~m~~~~~~--------~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~  326 (487)
                      .++|+.+++.+......        .....+..+...+...|++++|...+++....  .| +...+..+...|...|++
T Consensus       434 ~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~--~P~~~~~~~~LA~~~~~~G~~  511 (1157)
T PRK11447        434 PEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLAL--DPGSVWLTYRLAQDLRQAGQR  511 (1157)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCH
Confidence            44444444322111000        00112223334444455555555555544432  12 223334444455555555


Q ss_pred             HHHHHHHHHHHhC----------------------------------CCCCChhh---------HHHHHHHHHhcCChHH
Q 011378          327 TEAFRLWYEMVGK----------------------------------GIKPTLVS---------CNTIIKGYCRSGDASK  363 (487)
Q Consensus       327 ~~a~~~~~~m~~~----------------------------------~~~~~~~~---------~~~li~~~~~~~~~~~  363 (487)
                      ++|...++.....                                  ...++...         +..+...+...|+.++
T Consensus       512 ~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~e  591 (1157)
T PRK11447        512 SQADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAE  591 (1157)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHH
Confidence            5555555544332                                  11111111         1123345566677777


Q ss_pred             HHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          364 ADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       364 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      |..+++.     .+++...+..|-..+.+.|++++|.+.+++..+.  .| +...+..+...+...|++++|...++...
T Consensus       592 A~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll  664 (1157)
T PRK11447        592 AEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTR--EPGNADARLGLIEVDIAQGDLAAARAQLAKLP  664 (1157)
T ss_pred             HHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            7777661     2345556777888889999999999999988764  34 56788889999999999999999999876


Q ss_pred             HcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          443 EKGLNPD-RSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       443 ~~g~~p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      +.  .|+ ..++..+...+...|++++|.+++++.+..
T Consensus       665 ~~--~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        665 AT--ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             cc--CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            43  443 456666778888999999999999998754

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.82  E-value=5.2e-16  Score=138.96  Aligned_cols=239  Identities=18%  Similarity=0.267  Sum_probs=190.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHH
Q 011378           28 PDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLL  107 (487)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  107 (487)
                      .+..||..+|.++|+....+.|.+++++-.+...+.+..+||.+|.+-+-    ....+++.+|.+..+.||..|+|+++
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~----~~~K~Lv~EMisqkm~Pnl~TfNalL  280 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSY----SVGKKLVAEMISQKMTPNLFTFNALL  280 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHh----hccHHHHHHHHHhhcCCchHhHHHHH
Confidence            36678999999999999999999999999888888899999999876443    22378999999999999999999999


Q ss_pred             HHHHccCChhHH----HHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHH-HHHHHHHHHH----CCCCC----ChhhHH
Q 011378          108 VESCRKENMSEA----EEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDR-ALMYFREMKS----AGLVP----DNVLYT  174 (487)
Q Consensus       108 ~~~~~~~~~~~a----~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~----~g~~~----~~~~~~  174 (487)
                      .+.++.|+++.|    .+++.+|++-|+.|...+|..+|..+.+.++..+ |..+..+...    +-++|    |...|.
T Consensus       281 ~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~  360 (625)
T KOG4422|consen  281 SCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQ  360 (625)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHH
Confidence            999999988765    5678899999999999999999999999888744 4444444432    22333    345677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcC----CcCChh---hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011378          175 IIINGYCRNGFVLEALKMRDEMLEKG----CVMDVV---TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLI  247 (487)
Q Consensus       175 ~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li  247 (487)
                      ..+..|.+..+.+-|.++..-++...    +.|+..   =|..+....|+....+.....|+.|.-+-..|+..+-.-++
T Consensus       361 ~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~l  440 (625)
T KOG4422|consen  361 SAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLL  440 (625)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHHH
Confidence            77888888888888888876655321    223322   35677788888888999999999998888889999999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCC
Q 011378          248 HGHCKDGNMNKALNLFDIMTQKS  270 (487)
Q Consensus       248 ~~~~~~g~~~~a~~~~~~m~~~~  270 (487)
                      .+.-..++++-.-++|..+...|
T Consensus       441 rA~~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  441 RALDVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             HHHhhcCcchhHHHHHHHHHHhh
Confidence            99888888888888888777654

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

Probab=99.75  E-value=8.1e-15  Score=142.35  Aligned_cols=222  Identities=24%  Similarity=0.296  Sum_probs=152.2

Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCC
Q 011378           16 MFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMG   95 (487)
Q Consensus        16 ~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g   95 (487)
                      .+|..++..|+.|+-+||.++|.-||..|+++.|- +|..|..+.++.+...++.++.++.+.++.+.+.          
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            67889999999999999999999999999999999 9999999999889999999999999999887665          


Q ss_pred             CCCCHHHHHHHHHHHHccCChhHHHHHHHHH-------HHCCC-----------------CCCHhHHHHHHHHHHhCCCH
Q 011378           96 LSPDTATYNTLLVESCRKENMSEAEEIFCEM-------SRRGV-----------------APDIVSFSTLIGIFSRNGQL  151 (487)
Q Consensus        96 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m-------~~~g~-----------------~p~~~~~~~li~~~~~~g~~  151 (487)
                       .|...||+.|+.+|..+||+..-..+=+.|       ...|+                 -||..   +++....-.|.+
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~---n~illlv~eglw  155 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAE---NAILLLVLEGLW  155 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHH---HHHHHHHHHHHH
Confidence             588999999999999999977633222212       12232                 23332   233333333444


Q ss_pred             HHHHHHHHHH------------------------------HHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011378          152 DRALMYFREM------------------------------KSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGC  201 (487)
Q Consensus       152 ~~a~~~~~~m------------------------------~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~  201 (487)
                      +.+++++..+                              ++.--.|++.+|..+++.-...|+++.|..++.+|.+.|+
T Consensus       156 aqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gf  235 (1088)
T KOG4318|consen  156 AQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGF  235 (1088)
T ss_pred             HHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCC
Confidence            4444333222                              1111135666666666666666666666666666666666


Q ss_pred             cCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 011378          202 VMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGN  255 (487)
Q Consensus       202 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~  255 (487)
                      +.+.+-+..|+-+   .++...++.+...|.+.|+.|+..|+..-+..+.++|.
T Consensus       236 pir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  236 PIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             Ccccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            6666655555544   55666666666666666666666666666666665443

>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=99.73  E-value=3e-12  Score=130.85  Aligned_cols=424  Identities=11%  Similarity=0.025  Sum_probs=193.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCC-CHHHHHHHHHHHH
Q 011378           33 YNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSP-DTATYNTLLVESC  111 (487)
Q Consensus        33 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~  111 (487)
                      +...-..+.+.|+++.|...|+....  +.|+...|..+-.++.+.|++++|.+.++...+.  .| +...|..+-.++.
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~--~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l--~p~~~~a~~~~a~a~~  205 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIE--CKPDPVYYSNRAACHNALGDWEKVVEDTTAALEL--DPDYSKALNRRANAYD  205 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh--cCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHH
Confidence            34455667777888888888877654  3566667777777788888888888888877654  34 3556777777778


Q ss_pred             ccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011378          112 RKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALK  191 (487)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~  191 (487)
                      ..|++++|..-|......+-..+. ....++....+......+...++   ..  .++...+.. +..|...........
T Consensus       206 ~lg~~~eA~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~a~~~~~~~l~---~~--~~~~~~~~~-~~~~~~~~~~~~~~~  278 (615)
T TIGR00990       206 GLGKYADALLDLTASCIIDGFRNE-QSAQAVERLLKKFAESKAKEILE---TK--PENLPSVTF-VGNYLQSFRPKPRPA  278 (615)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCccH-HHHHHHHHHHHHHHHHHHHHHHh---cC--CCCCCCHHH-HHHHHHHccCCcchh
Confidence            888888887777655433211111 11111111111111111111111   10  011111111 111111000000000


Q ss_pred             HHHHHHHcCCcCCh-hhHHHHHHH---HHhcCCHHHHHHHHHHHHHcC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          192 MRDEMLEKGCVMDV-VTYNTILNG---LCRAKMLTEADDLFNEMLERG-VFP-DFYTFTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       192 ~~~~m~~~g~~~~~-~~~~~li~~---~~~~~~~~~a~~~~~~m~~~~-~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      -++.-  ....++. ..+..+-..   ....+.+++|.+.|++..+.+ ..| +...+..+-..+...|++++|+..|+.
T Consensus       279 ~~~~~--~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~k  356 (615)
T TIGR00990       279 GLEDS--NELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSK  356 (615)
T ss_pred             hhhcc--cccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            00000  0000000 000000000   012244555555555555433 122 223444444555555555555555554


Q ss_pred             HHHCCCCCC-eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 011378          266 MTQKSIKPD-IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT  344 (487)
Q Consensus       266 m~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~  344 (487)
                      ..+.  .|+ ...|..+-..+...|++++|...|....... +.+...|..+...+...|++++|...|+...... +.+
T Consensus       357 al~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~  432 (615)
T TIGR00990       357 SIEL--DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDF  432 (615)
T ss_pred             HHHc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccC
Confidence            4432  232 2244444455555555555555555544321 1223445555555555555555555555554331 223


Q ss_pred             hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH--------h
Q 011378          345 LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDV--------I  416 (487)
Q Consensus       345 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~--------~  416 (487)
                      ...+..+-..+.+.|+.++|...++...+.. +-+...++.+-..+...|++++|.+.+++..+.  .|+.        .
T Consensus       433 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l--~p~~~~~~~~~~~  509 (615)
T TIGR00990       433 IFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIEL--EKETKPMYMNVLP  509 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCccccccccHHH
Confidence            3344444455555555555555555554321 112344555555555555555555555554332  1110        0


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      .++.....+...|++++|..++++...... .+...+..+...+.+.|++++|++.+++..
T Consensus       510 l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p-~~~~a~~~la~~~~~~g~~~eAi~~~e~A~  569 (615)
T TIGR00990       510 LINKALALFQWKQDFIEAENLCEKALIIDP-ECDIAVATMAQLLLQQGDVDEALKLFERAA  569 (615)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            111111222334555555555555443321 122345555555555566655555555543

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.73  E-value=3.6e-13  Score=137.34  Aligned_cols=329  Identities=11%  Similarity=0.054  Sum_probs=223.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCC-HHHHHHHHHHHH
Q 011378           33 YNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPD-TATYNTLLVESC  111 (487)
Q Consensus        33 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~  111 (487)
                      ...++..+.+.|+++.|..+++......-.+ ...+..+..+....|+++.|...++++.+.  .|+ ...+..+-..+.
T Consensus        45 ~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~-~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~--~P~~~~a~~~la~~l~  121 (656)
T PRK15174         45 IILFAIACLRKDETDVGLTLLSDRVLTAKNG-RDLLRRWVISPLASSQPDAVLQVVNKLLAV--NVCQPEDVLLVASVLL  121 (656)
T ss_pred             HHHHHHHHHhcCCcchhHHHhHHHHHhCCCc-hhHHHHHhhhHhhcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHH
Confidence            4456677778888888888887776543222 233444555566688888888888887764  343 455666667777


Q ss_pred             ccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHH
Q 011378          112 RKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEAL  190 (487)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~  190 (487)
                      ..|++++|...+++..+.  .| +...+..+...+...|++++|...++.+......+. ..+..+ ..+.+.|+.++|.
T Consensus       122 ~~g~~~~Ai~~l~~Al~l--~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~~-~a~~~~-~~l~~~g~~~eA~  197 (656)
T PRK15174        122 KSKQYATVADLAEQAWLA--FSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPRG-DMIATC-LSFLNKSRLPEDH  197 (656)
T ss_pred             HcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCCH-HHHHHH-HHHHHcCCHHHHH
Confidence            888888888888887664  33 455667777888888888888888887755432222 222222 3467788888888


Q ss_pred             HHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHH----HHHHHHHH
Q 011378          191 KMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNK----ALNLFDIM  266 (487)
Q Consensus       191 ~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~----a~~~~~~m  266 (487)
                      ..++.+.+..-.++...+..+...+.+.|++++|...+++..+.. +.+...+..+-..+...|+.++    |+..|+..
T Consensus       198 ~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~A  276 (656)
T PRK15174        198 DLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHA  276 (656)
T ss_pred             HHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHH
Confidence            888877665433344444555677778888888888888877653 3356667777788888888775    67777766


Q ss_pred             HHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh
Q 011378          267 TQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL  345 (487)
Q Consensus       267 ~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  345 (487)
                      .+.  .| +...+..+-..+.+.|++++|...+++..... +.+...+..+..++...|++++|...++.+...  .|+.
T Consensus       277 l~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~--~P~~  351 (656)
T PRK15174        277 LQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLARE--KGVT  351 (656)
T ss_pred             Hhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--Cccc
Confidence            643  34 34567777888888888888888888776542 123445666777888888888888888877654  3443


Q ss_pred             hh-HHHHHHHHHhcCChHHHHHHHHHHHHC
Q 011378          346 VS-CNTIIKGYCRSGDASKADEFLSKMVSE  374 (487)
Q Consensus       346 ~~-~~~li~~~~~~~~~~~a~~~~~~m~~~  374 (487)
                      .. +..+..++...|+.++|...++...+.
T Consensus       352 ~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        352 SKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            33 333455677888888888888877654

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.72  E-value=4.1e-13  Score=136.91  Aligned_cols=358  Identities=9%  Similarity=0.036  Sum_probs=255.5

Q ss_pred             HhcCChhHHHHHHHHHhhCC-CC-CCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhH
Q 011378           41 CREGFLEEAFQLMNSMSGKG-LK-PGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSE  118 (487)
Q Consensus        41 ~~~~~~~~a~~~~~~m~~~~-~~-p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~  118 (487)
                      .+..+++.---.|..-.++. -. -+..-..-++..+.+.|+++.|..++.......-.+ ...+..+..+....|++++
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~-~~~l~~l~~~~l~~g~~~~   94 (656)
T PRK15174         16 LKQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTAKNG-RDLLRRWVISPLASSQPDA   94 (656)
T ss_pred             hhhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhCCCc-hhHHHHHhhhHhhcCCHHH
Confidence            45566665554554433321 11 123345567778889999999999999877654332 3344455566677999999


Q ss_pred             HHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          119 AEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEML  197 (487)
Q Consensus       119 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~  197 (487)
                      |.+.++++.+.. +-+...+..+...+.+.|++++|...+++....  .|+ ...+..+...+...|+.++|...++.+.
T Consensus        95 A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l--~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~  171 (656)
T PRK15174         95 VLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLA--FSGNSQIFALHLRTLVLMDKELQAISLARTQA  171 (656)
T ss_pred             HHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            999999987652 224556777888889999999999999988764  444 5577888888999999999999888776


Q ss_pred             HcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeee
Q 011378          198 EKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVT  277 (487)
Q Consensus       198 ~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~  277 (487)
                      ...-. +...+..+ ..+.+.|++++|...++.+.+..-.++...+..+..++...|+.++|+..++...+.. +.+...
T Consensus       172 ~~~P~-~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~  248 (656)
T PRK15174        172 QEVPP-RGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAAL  248 (656)
T ss_pred             HhCCC-CHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHH
Confidence            54322 22233233 3477889999999999988765433444555666778888999999999998877653 224556


Q ss_pred             hHHHHHHHHccCCHHH----HHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          278 YNTLIDGFCKVGEMEK----ANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK  353 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~----a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  353 (487)
                      +..+-..+...|++++    |...|+...... +.+...+..+...+...|++++|...++...... +.+...+..+-.
T Consensus       249 ~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~  326 (656)
T PRK15174        249 RRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYAR  326 (656)
T ss_pred             HHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            7778888888998885    788888776542 2355678888888899999999999998877643 233456667778


Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCChhh-HHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPDSIS-YNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~-~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      +|.+.|+.++|...++.+...  .|+... +..+..++...|+.++|...+++..+.
T Consensus       327 ~l~~~G~~~eA~~~l~~al~~--~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        327 ALRQVGQYTAASDEFVQLARE--KGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            888899999999999888764  355433 333456778889999999998887653

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.72  E-value=2.3e-12  Score=134.32  Aligned_cols=402  Identities=9%  Similarity=0.014  Sum_probs=237.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011378           29 DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLV  108 (487)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  108 (487)
                      +..-....+......|+.++|.++|....... +.+...+..+-..+.+.|++++|.+++++..+.. +.+...+..+..
T Consensus        14 ~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~   91 (765)
T PRK10049         14 SNNQIADWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLIL   91 (765)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            44455667777788889999988888876521 2334457778888888889999998888876542 233555667777


Q ss_pred             HHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHH
Q 011378          109 ESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVL  187 (487)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~  187 (487)
                      .+...|+.++|...+++..+. -+.+.. +..+..++.+.|+.++|+..+++..+.  .|+ ...+..+..++.+.+..+
T Consensus        92 ~l~~~g~~~eA~~~l~~~l~~-~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~--~P~~~~~~~~la~~l~~~~~~e  167 (765)
T PRK10049         92 TLADAGQYDEALVKAKQLVSG-APDKAN-LLALAYVYKRAGRHWDELRAMTQALPR--APQTQQYPTEYVQALRNNRLSA  167 (765)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh-CCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCChH
Confidence            788888899999888888765 222444 777777888888899998888888764  343 334455666777778888


Q ss_pred             HHHHHHHHHHHcCCcCCh------hhHHHHHHHHHhc-----CCH---HHHHHHHHHHHHc-CCCCCHH-HH----HHHH
Q 011378          188 EALKMRDEMLEKGCVMDV------VTYNTILNGLCRA-----KML---TEADDLFNEMLER-GVFPDFY-TF----TTLI  247 (487)
Q Consensus       188 ~a~~~~~~m~~~g~~~~~------~~~~~li~~~~~~-----~~~---~~a~~~~~~m~~~-~~~~~~~-t~----~~li  247 (487)
                      +|++.++....   .|+.      .....++......     +.+   +.|.+.++.+.+. ...|+.. .+    ...+
T Consensus       168 ~Al~~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l  244 (765)
T PRK10049        168 PALGAIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRL  244 (765)
T ss_pred             HHHHHHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHH
Confidence            88877765443   2221      0111222222111     123   4566666666543 1222221 11    1112


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCC-CCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC---ChhhHHHHHHHHHhc
Q 011378          248 HGHCKDGNMNKALNLFDIMTQKSIK-PDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP---NYISYGILINGYCSM  323 (487)
Q Consensus       248 ~~~~~~g~~~~a~~~~~~m~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p---~~~t~~~li~~~~~~  323 (487)
                      .++...|+.++|+..|+.+.+.+-. |+. .-..+...|...|++++|...|+.........   .......+..++...
T Consensus       245 ~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~  323 (765)
T PRK10049        245 GALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLES  323 (765)
T ss_pred             HHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhc
Confidence            3345567777777777776655421 221 11124556677777777777777665432111   123345555566777


Q ss_pred             CCHHHHHHHHHHHHhCC-----------CCCC---hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHH
Q 011378          324 GHVTEAFRLWYEMVGKG-----------IKPT---LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLING  389 (487)
Q Consensus       324 ~~~~~a~~~~~~m~~~~-----------~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  389 (487)
                      |++++|..+++.+....           -.|+   ...+..+...+...|+.++|.++++++... .+-+...+..+...
T Consensus       324 g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~-~P~n~~l~~~lA~l  402 (765)
T PRK10049        324 ENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYN-APGNQGLRIDYASV  402 (765)
T ss_pred             ccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHH
Confidence            77777777777665431           0122   123344555566666677776666666543 12234456666666


Q ss_pred             HhccCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          390 FVREENMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       390 ~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +...|+.++|++.+++..+.  .|| ...+-.....+.+.|++++|+.+++++.+
T Consensus       403 ~~~~g~~~~A~~~l~~al~l--~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~  455 (765)
T PRK10049        403 LQARGWPRAAENELKKAEVL--EPRNINLEVEQAWTALDLQEWRQMDVLTDDVVA  455 (765)
T ss_pred             HHhcCCHHHHHHHHHHHHhh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            66666666666666655542  354 33444444456666666666666666654

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.72  E-value=2.6e-12  Score=133.87  Aligned_cols=390  Identities=12%  Similarity=-0.007  Sum_probs=173.7

Q ss_pred             HHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChhh
Q 011378            5 LCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCDR   83 (487)
Q Consensus         5 ~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~   83 (487)
                      ..-.|+.+.|..++.+..... ..+...+..+...+.+.|++++|.++|+...+.  .| +...+..+...+.+.|++++
T Consensus        25 a~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~l~~~g~~~e  101 (765)
T PRK10049         25 ALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSL--EPQNDDYQRGLILTLADAGQYDE  101 (765)
T ss_pred             HHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHH
Confidence            344555555555555554311 122334555555555555666665555554432  12 23334444455555556666


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHH
Q 011378           84 AKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMK  162 (487)
Q Consensus        84 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  162 (487)
                      |...+++..+.. +.+.. +..+-..+...|+.++|...+++..+.  .| +...+..+...+.+.|..+.|++.++...
T Consensus       102 A~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~--~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~  177 (765)
T PRK10049        102 ALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPR--APQTQQYPTEYVQALRNNRLSAPALGAIDDAN  177 (765)
T ss_pred             HHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCChHHHHHHHHhCC
Confidence            655555554431 12223 444545555555566666555555543  22 22333344444555555555555554433


Q ss_pred             HCCCCCCh------hhHHHHHHHHHhc-----CCH---HHHHHHHHHHHHc-CCcCChh-hHH----HHHHHHHhcCCHH
Q 011378          163 SAGLVPDN------VLYTIIINGYCRN-----GFV---LEALKMRDEMLEK-GCVMDVV-TYN----TILNGLCRAKMLT  222 (487)
Q Consensus       163 ~~g~~~~~------~~~~~ll~~~~~~-----~~~---~~a~~~~~~m~~~-g~~~~~~-~~~----~li~~~~~~~~~~  222 (487)
                      .   .|+.      .....++......     +..   ++|+..++.+.+. .-.|+.. .+.    ..+..+...|+++
T Consensus       178 ~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~  254 (765)
T PRK10049        178 L---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYK  254 (765)
T ss_pred             C---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHH
Confidence            2   2221      0111111111111     111   3444455554432 1112111 110    0022233445555


Q ss_pred             HHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC---CeeehHHHHHHHHccCCHHHHHHHH
Q 011378          223 EADDLFNEMLERGVF-PDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP---DIVTYNTLIDGFCKVGEMEKANKLW  298 (487)
Q Consensus       223 ~a~~~~~~m~~~~~~-~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~  298 (487)
                      +|...|+.+.+.+-. |+. .-..+..+|...|++++|+..|+.+.+..-..   .......|..++...|++++|..++
T Consensus       255 eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l  333 (765)
T PRK10049        255 DVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVT  333 (765)
T ss_pred             HHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHH
Confidence            565555555544321 211 11113445555555666655555544321100   0122333444555555566665555


Q ss_pred             HHHHhCC-----------CCCC---hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHH
Q 011378          299 ADMISRK-----------ISPN---YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKA  364 (487)
Q Consensus       299 ~~m~~~~-----------~~p~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a  364 (487)
                      ..+....           ..|+   ...+..+...+...|++++|..+++++... .+-+...+..+...+...|+.++|
T Consensus       334 ~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~-~P~n~~l~~~lA~l~~~~g~~~~A  412 (765)
T PRK10049        334 AHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYN-APGNQGLRIDYASVLQARGWPRAA  412 (765)
T ss_pred             HHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHH
Confidence            5554321           0112   112334444555555566666555555433 133344455555555555556666


Q ss_pred             HHHHHHHHHCCCCCC-hhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          365 DEFLSKMVSEGVDPD-SISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       365 ~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      .+.+++....  .|| ...+-.+...+...+++++|+.+++++.+
T Consensus       413 ~~~l~~al~l--~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~  455 (765)
T PRK10049        413 ENELKKAEVL--EPRNINLEVEQAWTALDLQEWRQMDVLTDDVVA  455 (765)
T ss_pred             HHHHHHHHhh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            5555555442  233 23334444455555556666555555544

>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=99.70  E-value=5.6e-12  Score=128.87  Aligned_cols=421  Identities=14%  Similarity=0.036  Sum_probs=279.8

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChh
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCD   82 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~   82 (487)
                      .+.+.|+++.|...+++..+.  .|+...|..+-.++.+.|++++|++.++...+.  .| +...|..+-.++...|+++
T Consensus       136 ~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l--~p~~~~a~~~~a~a~~~lg~~~  211 (615)
T TIGR00990       136 KAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALEL--DPDYSKALNRRANAYDGLGKYA  211 (615)
T ss_pred             HHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHcCCHH
Confidence            567789999999999988764  588888999999999999999999999987764  34 3457888888999999999


Q ss_pred             hHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHH
Q 011378           83 RAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMK  162 (487)
Q Consensus        83 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  162 (487)
                      +|..-|......+-..+. ....++.....    ..+........+.. .++...+.. +..+...........-+..-.
T Consensus       212 eA~~~~~~~~~~~~~~~~-~~~~~~~~~l~----~~a~~~~~~~l~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  284 (615)
T TIGR00990       212 DALLDLTASCIIDGFRNE-QSAQAVERLLK----KFAESKAKEILETK-PENLPSVTF-VGNYLQSFRPKPRPAGLEDSN  284 (615)
T ss_pred             HHHHHHHHHHHhCCCccH-HHHHHHHHHHH----HHHHHHHHHHHhcC-CCCCCCHHH-HHHHHHHccCCcchhhhhccc
Confidence            999988766543211111 11122221111    11222222222211 111112222 222222211111111111111


Q ss_pred             HCCCCCChh-hHHHHHHH---HHhcCCHHHHHHHHHHHHHcC-CcC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011378          163 SAGLVPDNV-LYTIIING---YCRNGFVLEALKMRDEMLEKG-CVM-DVVTYNTILNGLCRAKMLTEADDLFNEMLERGV  236 (487)
Q Consensus       163 ~~g~~~~~~-~~~~ll~~---~~~~~~~~~a~~~~~~m~~~g-~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  236 (487)
                        ...++.. .+..+-..   ....+..++|.+.++...+.+ ..| +...|+.+...+...|++++|...|++..+.  
T Consensus       285 --~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l--  360 (615)
T TIGR00990       285 --ELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL--  360 (615)
T ss_pred             --ccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--
Confidence              1111110 11111100   123467888999998888765 223 3456777778888899999999999988764  


Q ss_pred             CCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHH
Q 011378          237 FPD-FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGI  315 (487)
Q Consensus       237 ~~~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~  315 (487)
                      .|+ ...|..+...+...|++++|+..|+...+.. +.+..+|..+-..+...|++++|...|.+..... +.+...+..
T Consensus       361 ~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~  438 (615)
T TIGR00990       361 DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQ  438 (615)
T ss_pred             CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHH
Confidence            344 5678888888899999999999998876542 2245678888888999999999999998876542 224566777


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC--C---Ch-hhHHHHHHH
Q 011378          316 LINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVD--P---DS-ISYNTLING  389 (487)
Q Consensus       316 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~--p---~~-~~~~~li~~  389 (487)
                      +...+.+.|++++|...++...+. .+.+...++.+-..+...|++++|...++......-.  +   +. ..++.....
T Consensus       439 la~~~~~~g~~~eA~~~~~~al~~-~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~  517 (615)
T TIGR00990       439 LGVTQYKEGSIASSMATFRRCKKN-FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALAL  517 (615)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh-CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHH
Confidence            888888999999999999987754 2345677888888999999999999999987764311  1   11 112222233


Q ss_pred             HhccCCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          390 FVREENMDKAFALVSKMENQGLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       390 ~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      +...|++++|.+++++....  .|+. ..+..+...+.+.|++++|...|++..+.
T Consensus       518 ~~~~~~~~eA~~~~~kAl~l--~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       518 FQWKQDFIEAENLCEKALII--DPECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHhhhHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            44468999999999886553  3543 46888899999999999999999987654

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.69  E-value=1.6e-11  Score=126.00  Aligned_cols=191  Identities=10%  Similarity=0.049  Sum_probs=90.7

Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCC-----CCCChhhHHHHHHHHHh
Q 011378          283 DGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKG-----IKPTLVSCNTIIKGYCR  357 (487)
Q Consensus       283 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~~~~~~~~~li~~~~~  357 (487)
                      -++.+.|+..++.+.++.+...+.+.....-..+.++|...++.++|+.++..+....     ..++......|.-+|..
T Consensus       300 ~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld  379 (822)
T PRK14574        300 GALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNE  379 (822)
T ss_pred             HHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHh
Confidence            3444455555555555555555543222244455555555555555555555554321     11222223455555555


Q ss_pred             cCChHHHHHHHHHHHHCCC-----------CC--Chh-hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          358 SGDASKADEFLSKMVSEGV-----------DP--DSI-SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       358 ~~~~~~a~~~~~~m~~~g~-----------~p--~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                      ++++++|..+++.+.+.--           .|  |-. .+..++..++..|++.+|++.++++.... .-|......+.+
T Consensus       380 ~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~  458 (822)
T PRK14574        380 SEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTA-PANQNLRIALAS  458 (822)
T ss_pred             cccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            5555555555555554100           01  111 12333444455555555555555554321 224455555555


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          424 GFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      .+..+|.+.+|+..++.....  .|+ ..+......++...+++++|..+...+
T Consensus       459 v~~~Rg~p~~A~~~~k~a~~l--~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l  510 (822)
T PRK14574        459 IYLARDLPRKAEQELKAVESL--APRSLILERAQAETAMALQEWHQMELLTDDV  510 (822)
T ss_pred             HHHhcCCHHHHHHHHHHHhhh--CCccHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            555555555555555443222  332 233334444555555555555555444

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.68  E-value=2.3e-11  Score=124.89  Aligned_cols=436  Identities=13%  Similarity=0.106  Sum_probs=308.6

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHH---HHHHHhcC
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTV-TYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSL---INGLCKKG   79 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l---i~~~~~~~   79 (487)
                      ...+.|+++.|...|.+..+..  |+.. ....++..+...|+.++|...++...    .|+...+..+   ...+...|
T Consensus        43 i~~r~Gd~~~Al~~L~qaL~~~--P~~~~av~dll~l~~~~G~~~~A~~~~eka~----~p~n~~~~~llalA~ly~~~g  116 (822)
T PRK14574         43 IRARAGDTAPVLDYLQEESKAG--PLQSGQVDDWLQIAGWAGRDQEVIDVYERYQ----SSMNISSRGLASAARAYRNEK  116 (822)
T ss_pred             HHHhCCCHHHHHHHHHHHHhhC--ccchhhHHHHHHHHHHcCCcHHHHHHHHHhc----cCCCCCHHHHHHHHHHHHHcC
Confidence            3578999999999999987654  5532 22388888899999999999999877    3444444333   34667789


Q ss_pred             ChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHH
Q 011378           80 RCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFR  159 (487)
Q Consensus        80 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  159 (487)
                      +++.|.++++++.+.. +-+...+..+...+...++.++|++.++.+...  .|+...+-.++..+...++..+|++.++
T Consensus       117 dyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~e  193 (822)
T PRK14574        117 RWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASS  193 (822)
T ss_pred             CHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHH
Confidence            9999999999998753 223566667788889999999999999998765  4565556445555555666666999999


Q ss_pred             HHHHCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhH------HHHHHHH-----HhcCCHHHHHHH
Q 011378          160 EMKSAGLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTY------NTILNGL-----CRAKMLTEADDL  227 (487)
Q Consensus       160 ~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~------~~li~~~-----~~~~~~~~a~~~  227 (487)
                      ++....  | +...+..+..++.+.|-...|.++..+-.. -+.+...-+      ...+..-     .....+..+.+.
T Consensus       194 kll~~~--P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~-~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~a  270 (822)
T PRK14574        194 EAVRLA--PTSEEVLKNHLEILQRNRIVEPALRLAKENPN-LVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKA  270 (822)
T ss_pred             HHHHhC--CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCcc-ccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHH
Confidence            998753  5 456778888899999988888876554210 011111000      0111110     012233444444


Q ss_pred             HHHH---HHc-CCCCCH-H----HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHH
Q 011378          228 FNEM---LER-GVFPDF-Y----TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLW  298 (487)
Q Consensus       228 ~~~m---~~~-~~~~~~-~----t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  298 (487)
                      +..+   ... +-.|.. .    ...-.+-++...|+.+++++.|+.+...+.+....+-.++.++|...+++++|..++
T Consensus       271 la~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~  350 (822)
T PRK14574        271 LADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPIL  350 (822)
T ss_pred             HHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHH
Confidence            4443   321 222321 1    223456678889999999999999998887655567889999999999999999999


Q ss_pred             HHHHhCC-----CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-----------CCCh---hhHHHHHHHHHhcC
Q 011378          299 ADMISRK-----ISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGI-----------KPTL---VSCNTIIKGYCRSG  359 (487)
Q Consensus       299 ~~m~~~~-----~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----------~~~~---~~~~~li~~~~~~~  359 (487)
                      +......     ..++......|.-++...+++++|..+.+.+.+.--           .||.   ..+..+...+...|
T Consensus       351 ~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~g  430 (822)
T PRK14574        351 SSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALN  430 (822)
T ss_pred             HHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcC
Confidence            9986543     233444467899999999999999999999987310           1222   23445677788999


Q ss_pred             ChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHH
Q 011378          360 DASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      +..+|++.++++... -+-|......+-+.+...|+..+|++.++.....  .|+ ..+.-.....+-..|++.+|..+.
T Consensus       431 dl~~Ae~~le~l~~~-aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l--~P~~~~~~~~~~~~al~l~e~~~A~~~~  507 (822)
T PRK14574        431 DLPTAQKKLEDLSST-APANQNLRIALASIYLARDLPRKAEQELKAVESL--APRSLILERAQAETAMALQEWHQMELLT  507 (822)
T ss_pred             CHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh--CCccHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            999999999999653 3446778889999999999999999999766543  565 455667777888899999999999


Q ss_pred             HHHHHcCCCCCHHHHHHH
Q 011378          439 WRMIEKGLNPDRSTYTTL  456 (487)
Q Consensus       439 ~~m~~~g~~p~~~ty~~l  456 (487)
                      +.+.+.  .|+......|
T Consensus       508 ~~l~~~--~Pe~~~~~~l  523 (822)
T PRK14574        508 DDVISR--SPEDIPSQEL  523 (822)
T ss_pred             HHHHhh--CCCchhHHHH
Confidence            888653  4555444443

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.68  E-value=3.1e-11  Score=126.39  Aligned_cols=79  Identities=16%  Similarity=0.155  Sum_probs=42.1

Q ss_pred             cCChhhHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHH
Q 011378            8 DHKIDSAKMFLCEMEQKGVYP-DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKE   86 (487)
Q Consensus         8 ~~~~~~a~~~~~~~~~~g~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~   86 (487)
                      .|+++.|...|....+..  | +..++..+...|.+.|+.++|...+++..+.  .|+-..|..++..+   +++++|..
T Consensus        57 ~Gd~~~A~~~l~~Al~~d--P~n~~~~~~LA~~yl~~g~~~~A~~~~~kAv~l--dP~n~~~~~~La~i---~~~~kA~~  129 (987)
T PRK09782         57 NNDEATAIREFEYIHQQV--PDNIPLTLYLAEAYRHFGHDDRARLLLEDQLKR--HPGDARLERSLAAI---PVEVKSVT  129 (987)
T ss_pred             CCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CcccHHHHHHHHHh---ccChhHHH
Confidence            366666666666654432  3 3345556666666666666666666655443  33333333333222   55556666


Q ss_pred             HHHHHHH
Q 011378           87 VLDEMLQ   93 (487)
Q Consensus        87 ~~~~m~~   93 (487)
                      +++++..
T Consensus       130 ~ye~l~~  136 (987)
T PRK09782        130 TVEELLA  136 (987)
T ss_pred             HHHHHHH
Confidence            6666554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.67  E-value=6.6e-11  Score=124.02  Aligned_cols=227  Identities=12%  Similarity=0.060  Sum_probs=141.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011378          240 FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILING  319 (487)
Q Consensus       240 ~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~  319 (487)
                      ...|..+-..+.. ++.++|+..+......  .|+......+...+...|++++|...|+.+...  .|+...+..+..+
T Consensus       477 ~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~a  551 (987)
T PRK09782        477 AAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANT  551 (987)
T ss_pred             HHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHH
Confidence            3444444444444 5666666655544433  244322222233345677777777777765433  3444445556666


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKA  399 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a  399 (487)
                      +...|++++|...++...+.. +.+...+..+.....+.|+.++|...+++..+.  .|+...+..+-..+.+.|+.++|
T Consensus       552 ll~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA  628 (987)
T PRK09782        552 AQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAA  628 (987)
T ss_pred             HHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHH
Confidence            777778887777777776543 222222323333444557888888888777643  36666777777778888888888


Q ss_pred             HHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          400 FALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       400 ~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      ...+++....  .|+ ...++.+-..+...|+.++|...+++..+.  .| +...+..+-.++...|++++|...+++-.
T Consensus       629 ~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l--~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al  704 (987)
T PRK09782        629 VSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREMLERAHKG--LPDDPALIRQLAYVNQRLDDMAATQHYARLVI  704 (987)
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            8888776653  454 445566666777888888888887776653  34 34567777778888888888888877766


Q ss_pred             H
Q 011378          478 Q  478 (487)
Q Consensus       478 ~  478 (487)
                      +
T Consensus       705 ~  705 (987)
T PRK09782        705 D  705 (987)
T ss_pred             h
Confidence            3

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

Probab=99.60  E-value=3e-12  Score=124.83  Aligned_cols=223  Identities=19%  Similarity=0.230  Sum_probs=142.9

Q ss_pred             HHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCC
Q 011378           51 QLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRG  130 (487)
Q Consensus        51 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g  130 (487)
                      .++..+...|+.||..||.++|.-|+..|+.+.|- +|.-|+-..+..+...|+.++.++...++.+.+.          
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            46677888999999999999999999999999999 9999988888888899999999999999888877          


Q ss_pred             CCCCHhHHHHHHHHHHhCCCHHHHHHHHHH-HHH-------CC-----------------CCCChh----------hHHH
Q 011378          131 VAPDIVSFSTLIGIFSRNGQLDRALMYFRE-MKS-------AG-----------------LVPDNV----------LYTI  175 (487)
Q Consensus       131 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~-m~~-------~g-----------------~~~~~~----------~~~~  175 (487)
                       .|...||+.|..+|.+.|++.. ++..++ |.+       .|                 .-||..          .|..
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~-fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaq  157 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLIL-FEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQ  157 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHH-HHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHH
Confidence             7888999999999999999875 222222 321       11                 122221          1222


Q ss_pred             HHHHHHhcCC------HH-----------HHHHHHHHHHHcCC-cCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011378          176 IINGYCRNGF------VL-----------EALKMRDEMLEKGC-VMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVF  237 (487)
Q Consensus       176 ll~~~~~~~~------~~-----------~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  237 (487)
                      +++.+.+..-      ..           ...+ +..|.+.+. .|++.+|+.++.+-...|+.+.|..+..+|+++|++
T Consensus       158 llkll~~~Pvsa~~~p~~vfLrqnv~~ntpvek-Ll~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfp  236 (1088)
T KOG4318|consen  158 LLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEK-LLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFP  236 (1088)
T ss_pred             HHHHHhhCCcccccchHHHHHHHhccCCchHHH-HHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCC
Confidence            2222211110      00           0000 111122222 255666666666666666666666666666666666


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCC
Q 011378          238 PDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE  290 (487)
Q Consensus       238 ~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~  290 (487)
                      .+.+-|-.++-+   .++...+..+++.|...|+.|+..|+.--+-.+.++|.
T Consensus       237 ir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  237 IRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             cccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            555555555444   55555566666666666666666666555555555443

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

Probab=99.59  E-value=3.1e-11  Score=113.61  Aligned_cols=365  Identities=16%  Similarity=0.246  Sum_probs=257.4

Q ss_pred             ccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHH-HH
Q 011378           65 VFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSP-DTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFST-LI  142 (487)
Q Consensus        65 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~-li  142 (487)
                      ..+|..+-..+-..|+++.|+..+..+.+.  .| ....|..+-.++...|+.+.|.+.|.+..+  +.|+.....+ +-
T Consensus       116 ae~ysn~aN~~kerg~~~~al~~y~~aiel--~p~fida~inla~al~~~~~~~~a~~~~~~alq--lnP~l~ca~s~lg  191 (966)
T KOG4626|consen  116 AEAYSNLANILKERGQLQDALALYRAAIEL--KPKFIDAYINLAAALVTQGDLELAVQCFFEALQ--LNPDLYCARSDLG  191 (966)
T ss_pred             HHHHHHHHHHHHHhchHHHHHHHHHHHHhc--CchhhHHHhhHHHHHHhcCCCcccHHHHHHHHh--cCcchhhhhcchh
Confidence            356666777777777777788777777764  34 355677777777777777777777776654  3455443333 33


Q ss_pred             HHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCC-hhhHHHHHHHHHhcCC
Q 011378          143 GIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMD-VVTYNTILNGLCRAKM  220 (487)
Q Consensus       143 ~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~~~  220 (487)
                      +.....|++.+|...+.+..+.  .|. ...|+.|--.+-..|++..|..-|++..+.  .|+ ...|-.|-..|...+.
T Consensus       192 nLlka~Grl~ea~~cYlkAi~~--qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~  267 (966)
T KOG4626|consen  192 NLLKAEGRLEEAKACYLKAIET--QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARI  267 (966)
T ss_pred             HHHHhhcccchhHHHHHHHHhh--CCceeeeehhcchHHhhcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhc
Confidence            3334467777777666655442  343 345777777777778888888777776542  222 2356667777777777


Q ss_pred             HHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCe-eehHHHHHHHHccCCHHHHHHHH
Q 011378          221 LTEADDLFNEMLERGVFPD-FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI-VTYNTLIDGFCKVGEMEKANKLW  298 (487)
Q Consensus       221 ~~~a~~~~~~m~~~~~~~~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~g~~~~a~~~~  298 (487)
                      ++.|...+......  .|+ ...+..|-..|-..|.+|.|++.|+...+.  .|+- ..|+.|-.++...|++.+|.+.+
T Consensus       268 ~d~Avs~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cY  343 (966)
T KOG4626|consen  268 FDRAVSCYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCY  343 (966)
T ss_pred             chHHHHHHHHHHhc--CCcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHH
Confidence            77777777766542  343 456677777788888888888888876543  4543 47888999999999999999988


Q ss_pred             HHHHhCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCChHHHHHHHHHHHHCCC
Q 011378          299 ADMISRKISPN-YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL-VSCNTIIKGYCRSGDASKADEFLSKMVSEGV  376 (487)
Q Consensus       299 ~~m~~~~~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  376 (487)
                      ......  .|+ ....+.|-..|...|.+++|..+|..-.  .+.|.. ..+|.|-..|-..|++++|...+++.++  |
T Consensus       344 nkaL~l--~p~hadam~NLgni~~E~~~~e~A~~ly~~al--~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I  417 (966)
T KOG4626|consen  344 NKALRL--CPNHADAMNNLGNIYREQGKIEEATRLYLKAL--EVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--I  417 (966)
T ss_pred             HHHHHh--CCccHHHHHHHHHHHHHhccchHHHHHHHHHH--hhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--c
Confidence            876543  333 3567788888989999999988887653  344543 4578888889999999999999988774  6


Q ss_pred             CCCh-hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHH
Q 011378          377 DPDS-ISYNTLINGFVREENMDKAFALVSKMENQGLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRS  451 (487)
Q Consensus       377 ~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  451 (487)
                      +|+- ..|+.+-..|-..|+++.|...+.+-..  +.|.. ..++.|.+.|-..|++.+|..-+++.+.  ++||.+
T Consensus       418 ~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~--~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfp  490 (966)
T KOG4626|consen  418 KPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQ--INPTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFP  490 (966)
T ss_pred             CchHHHHHHhcchHHHHhhhHHHHHHHHHHHHh--cCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCc
Confidence            7774 3788888888888999999888876654  34543 4678888899999999999888888654  567654

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

Probab=99.57  E-value=4.4e-11  Score=112.64  Aligned_cols=374  Identities=21%  Similarity=0.280  Sum_probs=294.9

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCC-ccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011378           30 TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPG-VFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLV  108 (487)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  108 (487)
                      ..+|+.+-+.+-..|++++|+.+++.+.+.  .|+ ...|..+-.++...|+.+.|...|.+..+  +.|+.....+-+.
T Consensus       116 ae~ysn~aN~~kerg~~~~al~~y~~aiel--~p~fida~inla~al~~~~~~~~a~~~~~~alq--lnP~l~ca~s~lg  191 (966)
T KOG4626|consen  116 AEAYSNLANILKERGQLQDALALYRAAIEL--KPKFIDAYINLAAALVTQGDLELAVQCFFEALQ--LNPDLYCARSDLG  191 (966)
T ss_pred             HHHHHHHHHHHHHhchHHHHHHHHHHHHhc--CchhhHHHhhHHHHHHhcCCCcccHHHHHHHHh--cCcchhhhhcchh
Confidence            468999999999999999999999999874  453 46799999999999999999999988776  3576665544443


Q ss_pred             HHH-ccCChhHHHHHHHHHHHCCCCCC-HhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCC
Q 011378          109 ESC-RKENMSEAEEIFCEMSRRGVAPD-IVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGF  185 (487)
Q Consensus       109 ~~~-~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~  185 (487)
                      -+. ..|++++|..-+.+..+.  .|. .+.|+.|-..+-..|++..|++.|++...  +.|+ ...|-.|-+.|...+.
T Consensus       192 nLlka~Grl~ea~~cYlkAi~~--qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvk--ldP~f~dAYiNLGnV~ke~~~  267 (966)
T KOG4626|consen  192 NLLKAEGRLEEAKACYLKAIET--QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVK--LDPNFLDAYINLGNVYKEARI  267 (966)
T ss_pred             HHHHhhcccchhHHHHHHHHhh--CCceeeeehhcchHHhhcchHHHHHHHHHHhhc--CCCcchHHHhhHHHHHHHHhc
Confidence            333 358888998888776653  333 35788899999999999999999998876  4565 3467777777777777


Q ss_pred             HHHHHHHHHHHHHcCCcC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHH
Q 011378          186 VLEALKMRDEMLEKGCVM-DVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD-FYTFTTLIHGHCKDGNMNKALNLF  263 (487)
Q Consensus       186 ~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~t~~~li~~~~~~g~~~~a~~~~  263 (487)
                      ++.|...+.....  ..| ....+..+-..|...|.++.|.+.+++..+.  .|+ +..|+.|-+++-..|++.+|++.|
T Consensus       268 ~d~Avs~Y~rAl~--lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cY  343 (966)
T KOG4626|consen  268 FDRAVSCYLRALN--LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCY  343 (966)
T ss_pred             chHHHHHHHHHHh--cCCcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHH
Confidence            8888777665443  334 3456777888899999999999999998864  465 458999999999999999999999


Q ss_pred             HHHHHCCCCCC-eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 011378          264 DIMTQKSIKPD-IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-ISYGILINGYCSMGHVTEAFRLWYEMVGKGI  341 (487)
Q Consensus       264 ~~m~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~  341 (487)
                      .....-  .|+ ....+.|-..|...|.+++|.++|....  .+.|.. ..+|.|-..|-..|.+++|..-+++..  .+
T Consensus       344 nkaL~l--~p~hadam~NLgni~~E~~~~e~A~~ly~~al--~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykeal--rI  417 (966)
T KOG4626|consen  344 NKALRL--CPNHADAMNNLGNIYREQGKIEEATRLYLKAL--EVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEAL--RI  417 (966)
T ss_pred             HHHHHh--CCccHHHHHHHHHHHHHhccchHHHHHHHHHH--hhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHH--hc
Confidence            876643  333 3467889999999999999999998754  344543 568999999999999999999999875  46


Q ss_pred             CCCh-hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh-hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH-hhH
Q 011378          342 KPTL-VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS-ISYNTLINGFVREENMDKAFALVSKMENQGLVPDV-ITY  418 (487)
Q Consensus       342 ~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~  418 (487)
                      .|+. ..|+.+=..|...|+.+.|.+.+...+.  +.|.- ..++.|-+.|-..|++.+|+.-+++-.+  ++||. ..|
T Consensus       418 ~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~--~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfpdA~  493 (966)
T KOG4626|consen  418 KPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQ--INPTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFPDAY  493 (966)
T ss_pred             CchHHHHHHhcchHHHHhhhHHHHHHHHHHHHh--cCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCchhh
Confidence            7765 4788888899999999999999988775  44653 4789999999999999999998887654  67875 346


Q ss_pred             HHHHHHH
Q 011378          419 NVILTGF  425 (487)
Q Consensus       419 ~~li~~~  425 (487)
                      ..++...
T Consensus       494 cNllh~l  500 (966)
T KOG4626|consen  494 CNLLHCL  500 (966)
T ss_pred             hHHHHHH
Confidence            5665544

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

Probab=99.49  E-value=2.9e-08  Score=98.10  Aligned_cols=468  Identities=15%  Similarity=0.164  Sum_probs=318.1

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChh
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCD   82 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~   82 (487)
                      .+++ |+++.|..++.++.+..- .....|-+|-..|-+.|+.+.+...+-  ....+.| |..-|..+-.-..+.|.++
T Consensus       149 lfar-g~~eeA~~i~~EvIkqdp-~~~~ay~tL~~IyEqrGd~eK~l~~~l--lAAHL~p~d~e~W~~ladls~~~~~i~  224 (895)
T KOG2076|consen  149 LFAR-GDLEEAEEILMEVIKQDP-RNPIAYYTLGEIYEQRGDIEKALNFWL--LAAHLNPKDYELWKRLADLSEQLGNIN  224 (895)
T ss_pred             HHHh-CCHHHHHHHHHHHHHhCc-cchhhHHHHHHHHHHcccHHHHHHHHH--HHHhcCCCChHHHHHHHHHHHhcccHH
Confidence            3455 999999999999987652 366789999999999999999987763  3333444 4567888888888999999


Q ss_pred             hHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHH----HHHHHHHhCCCHHHHHHHH
Q 011378           83 RAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFS----TLIGIFSRNGQLDRALMYF  158 (487)
Q Consensus        83 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~----~li~~~~~~g~~~~a~~~~  158 (487)
                      .|.-.|.+..+.. +++...+-.-...|-+.|+...|..-|.++.+.--+.|..-+-    .++..|...++-+.|.+.+
T Consensus       225 qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~l  303 (895)
T KOG2076|consen  225 QARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKAL  303 (895)
T ss_pred             HHHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            9999999988754 3455555555667888999999999999998764322333233    3456677778889999888


Q ss_pred             HHHHHCC-CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC---------------------------CcCChhhHHH
Q 011378          159 REMKSAG-LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKG---------------------------CVMDVVTYNT  210 (487)
Q Consensus       159 ~~m~~~g-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g---------------------------~~~~~~~~~~  210 (487)
                      +.....+ -..+...++++...|.+....+.+......+....                           ..++... --
T Consensus       304 e~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v-~r  382 (895)
T KOG2076|consen  304 EGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRV-IR  382 (895)
T ss_pred             HHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchh-Hh
Confidence            8876632 23445578888888888888888887776665522                           2222222 12


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFP--DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV  288 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  288 (487)
                      ++-++......+...-+.....+.++.|  +...|.-+..+|...|++++|+.+|..+...-.--+...|-.+-.+|-..
T Consensus       383 l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l  462 (895)
T KOG2076|consen  383 LMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMEL  462 (895)
T ss_pred             HhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHH
Confidence            3344445556666666677777777554  45678889999999999999999999988765555677899999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCCHHHHHHHHHHHH--------hCCCCCChhhHHHHHHHHHhcC
Q 011378          289 GEMEKANKLWADMISRKISPNY-ISYGILINGYCSMGHVTEAFRLWYEMV--------GKGIKPTLVSCNTIIKGYCRSG  359 (487)
Q Consensus       289 g~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~--------~~~~~~~~~~~~~li~~~~~~~  359 (487)
                      |..+.|.+.+......  .|+. ..--.|-..+...|+.++|.+.+..+.        ..++.|+....--..+.+...|
T Consensus       463 ~e~e~A~e~y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~g  540 (895)
T KOG2076|consen  463 GEYEEAIEFYEKVLIL--APDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVG  540 (895)
T ss_pred             hhHHHHHHHHHHHHhc--CCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhh
Confidence            9999999999887643  3432 222345566778899999999998854        3345566655555566677778


Q ss_pred             ChHHHHHHHHHHHHCC-----C-----------------CCChhhHHHHHHHHhccCCHHHHHHHHH------HHHhCCC
Q 011378          360 DASKADEFLSKMVSEG-----V-----------------DPDSISYNTLINGFVREENMDKAFALVS------KMENQGL  411 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g-----~-----------------~p~~~~~~~li~~~~~~~~~~~a~~~~~------~m~~~g~  411 (487)
                      +.++=......|...+     +                 +....+-...+.+-.+.++.....+-+.      --...|+
T Consensus       541 k~E~fi~t~~~Lv~~~~~~~~~f~~~~k~r~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~l~d~~~~~~~e~~~L  620 (895)
T KOG2076|consen  541 KREEFINTASTLVDDFLKKRYIFPRNKKKRRRAIAGTTSKRYSELLKQIIRAREKATDDNVMEKALSDGTEFRAVELRGL  620 (895)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHhhccccccccchhHHHHHHHHhccCchHHhhhcccchhhhhhhhhccC
Confidence            7666433333333211     1                 1112223333444444444322222111      1111233


Q ss_pred             CCCH--hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-CCHH---HH-HHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          412 VPDV--ITYNVILTGFCRQGRMHDSELILWRMIEKGLN-PDRS---TY-TTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       412 ~p~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~---ty-~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      .-|.  ..+.-+|...++.+++++|..++..+.+..+- -+..   +. ..++.+....+++..|+.+++.|...
T Consensus       621 siddwfel~~e~i~~L~k~~r~qeAl~vv~~a~~~~~f~~~~~~~k~l~~~~l~~s~~~~d~~~a~~~lR~~i~~  695 (895)
T KOG2076|consen  621 SIDDWFELFRELILSLAKLQRVQEALSVVFTALEAYIFFQDSEIRKELQFLGLKASLYARDPGDAFSYLRSVITQ  695 (895)
T ss_pred             cHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            3222  23456677889999999999999988765432 2222   33 34467778889999999999999754

>PF13041 PPR_2: PPR repeat family

Probab=99.44  E-value=2.9e-13  Score=87.82  Aligned_cols=48  Identities=40%  Similarity=0.908  Sum_probs=21.3

Q ss_pred             CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011378          413 PDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGH  460 (487)
Q Consensus       413 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~  460 (487)
                      ||+.+||++|++|++.|++++|.++|++|.+.|+.||..||+.|+++|
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~   48 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGL   48 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            344444444444444444444444444444444444444444444444

>PF13041 PPR_2: PPR repeat family

Probab=99.43  E-value=4.1e-13  Score=87.11  Aligned_cols=50  Identities=38%  Similarity=0.935  Sum_probs=48.9

Q ss_pred             CChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh
Q 011378          378 PDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCR  427 (487)
Q Consensus       378 p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  427 (487)
                      ||..+||++|++|++.|++++|.++|++|.+.|+.||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            89999999999999999999999999999999999999999999999985

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.42  E-value=1.7e-09  Score=104.21  Aligned_cols=250  Identities=11%  Similarity=0.081  Sum_probs=134.6

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHH
Q 011378          216 CRAKMLTEADDLFNEMLERGVFPDFYTFT--TLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEK  293 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~~~~~t~~--~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~  293 (487)
                      .+.|+++.+.+.+.++.+.  .|+.....  .....+...|+.+.|...++.+.+.. +-+......+...|.+.|++++
T Consensus       129 ~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~  205 (398)
T PRK10747        129 QQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSS  205 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHH
Confidence            4445555555555554432  22221111  11334444555555555555444332 1123344445555555555555


Q ss_pred             HHHHHHHHHhCCCCCCh-------hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHH
Q 011378          294 ANKLWADMISRKISPNY-------ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADE  366 (487)
Q Consensus       294 a~~~~~~m~~~~~~p~~-------~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  366 (487)
                      |.+++..+.+.+..++.       ..|..++.......+.+...++|+.+.+. .+.+......+...+...|+.++|..
T Consensus       206 a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~  284 (398)
T PRK10747        206 LLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQ  284 (398)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            55555555544333211       12222333333334445555555554322 24455566667777777777777777


Q ss_pred             HHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011378          367 FLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIEKG  445 (487)
Q Consensus       367 ~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  445 (487)
                      ++++..+.  .||..  -.++.+.+..++.+++.+..+.+.+.  .|+ ...+..+-..|.++|++++|...|+...+  
T Consensus       285 ~L~~~l~~--~~~~~--l~~l~~~l~~~~~~~al~~~e~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~--  356 (398)
T PRK10747        285 IILDGLKR--QYDER--LVLLIPRLKTNNPEQLEKVLRQQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALK--  356 (398)
T ss_pred             HHHHHHhc--CCCHH--HHHHHhhccCCChHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh--
Confidence            77766653  33331  12334444557777777777776654  343 34455666677777777777777777665  


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          446 LNPDRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       446 ~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      ..|+..+|-.+-..+.+.|+.++|..++++=+
T Consensus       357 ~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        357 QRPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            35777777777777777777777777766543

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.37  E-value=3.3e-09  Score=102.18  Aligned_cols=251  Identities=10%  Similarity=0.058  Sum_probs=160.8

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCcCChhhHH--HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHH
Q 011378          181 CRNGFVLEALKMRDEMLEKGCVMDVVTYN--TILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNK  258 (487)
Q Consensus       181 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~  258 (487)
                      .+.|+.+.+.+.+.++.+.  .|+...+-  .....+...|+++.|...++++.+.. +-++.....+...|.+.|++++
T Consensus       129 ~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~  205 (398)
T PRK10747        129 QQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSS  205 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHH
Confidence            4555555555555555432  23322221  22345556666666666666665543 2245556666666666666666


Q ss_pred             HHHHHHHHHHCCCCCCe-------eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011378          259 ALNLFDIMTQKSIKPDI-------VTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFR  331 (487)
Q Consensus       259 a~~~~~~m~~~~~~~~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~  331 (487)
                      |.+++..+.+.+..++.       ..|..++.......+.+...++|+...+. .+.+......+..++...|+.++|.+
T Consensus       206 a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~  284 (398)
T PRK10747        206 LLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQ  284 (398)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            66666666655443211       12333344444444566666666655322 23466677788888888899999888


Q ss_pred             HHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCC
Q 011378          332 LWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGL  411 (487)
Q Consensus       332 ~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  411 (487)
                      ++++..+.  +|+...  .++.+....++.+++....+...+.. +-|...+.++-..|.+.+++++|.+.|+...+.  
T Consensus       285 ~L~~~l~~--~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--  357 (398)
T PRK10747        285 IILDGLKR--QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--  357 (398)
T ss_pred             HHHHHHhc--CCCHHH--HHHHhhccCCChHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--
Confidence            88887763  444422  23445556688888888888877532 224456777788888999999999999888764  


Q ss_pred             CCCHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          412 VPDVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       412 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      .|+..+|-.+...+.+.|+.++|..++++-.
T Consensus       358 ~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        358 RPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            6888888888899999999999988888754

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

Probab=99.37  E-value=1.4e-07  Score=94.21  Aligned_cols=456  Identities=14%  Similarity=0.113  Sum_probs=246.9

Q ss_pred             HHhcCChhhHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCC---hhHHHHHHHHH-hhCCCCCCccchHHHHHHHHhcC
Q 011378            5 LCKDHKIDSAKMFLCEMEQKGVYPDTV-TYNTLINAYCREGF---LEEAFQLMNSM-SGKGLKPGVFTYNSLINGLCKKG   79 (487)
Q Consensus         5 ~~~~~~~~~a~~~~~~~~~~g~~p~~~-~~~~ll~~~~~~~~---~~~a~~~~~~m-~~~~~~p~~~~~~~li~~~~~~~   79 (487)
                      +.+.++.+.|+..|.+..+..  |+.+ ++-.|--.-....+   +..++.++... ...+  -|+...+.|-+.+.-.|
T Consensus       209 f~kl~~~~~a~~a~~ralqLd--p~~v~alv~L~~~~l~~~d~~s~~~~~~ll~~ay~~n~--~nP~~l~~LAn~fyfK~  284 (1018)
T KOG2002|consen  209 FWKLGMSEKALLAFERALQLD--PTCVSALVALGEVDLNFNDSDSYKKGVQLLQRAYKENN--ENPVALNHLANHFYFKK  284 (1018)
T ss_pred             HHhccchhhHHHHHHHHHhcC--hhhHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhhcC--CCcHHHHHHHHHHhhcc
Confidence            346677777777777766532  3221 11111111111222   33444444333 2222  34556777788888889


Q ss_pred             ChhhHHHHHHHHHHCCCC--CCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhH--HHHHHHHHHhCCCHHHHH
Q 011378           80 RCDRAKEVLDEMLQMGLS--PDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVS--FSTLIGIFSRNGQLDRAL  155 (487)
Q Consensus        80 ~~~~a~~~~~~m~~~g~~--~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~--~~~li~~~~~~g~~~~a~  155 (487)
                      ++..++.+.+.+...-..  .-+..|--+-++|-..|++++|...+.+-.+.  .|+..+  +-.|...+.+.|+++.+.
T Consensus       285 dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~--~~d~~~l~~~GlgQm~i~~~dle~s~  362 (1018)
T KOG2002|consen  285 DYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKA--DNDNFVLPLVGLGQMYIKRGDLEESK  362 (1018)
T ss_pred             cHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHcc--CCCCccccccchhHHHHHhchHHHHH
Confidence            999999888887754321  11334566777888889999999888776543  333333  334778888999999998


Q ss_pred             HHHHHHHHCCCCCCh-hhHHHHHHHHHhcC----CHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          156 MYFREMKSAGLVPDN-VLYTIIINGYCRNG----FVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNE  230 (487)
Q Consensus       156 ~~~~~m~~~g~~~~~-~~~~~ll~~~~~~~----~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (487)
                      ..|+..-..  .||. .+-.+|-..|+..+    ..+.|..++.+-.+.- +.|...|-.+-..+-. ++...+...+..
T Consensus       363 ~~fEkv~k~--~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-~~d~~a~l~laql~e~-~d~~~sL~~~~~  438 (1018)
T KOG2002|consen  363 FCFEKVLKQ--LPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-PVDSEAWLELAQLLEQ-TDPWASLDAYGN  438 (1018)
T ss_pred             HHHHHHHHh--CcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-cccHHHHHHHHHHHHh-cChHHHHHHHHH
Confidence            888887653  3543 34444444555443    2344444444333322 2344455444444433 333333444443


Q ss_pred             ----HHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC---CCCCCee------ehHHHHHHHHccCCHHHHHHH
Q 011378          231 ----MLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQK---SIKPDIV------TYNTLIDGFCKVGEMEKANKL  297 (487)
Q Consensus       231 ----m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~------~~~~li~~~~~~g~~~~a~~~  297 (487)
                          +...+-.+.+...|++-..+...|++.+|...|+.....   ...+|..      +--.+-..+-..++.+.|.+.
T Consensus       439 A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~  518 (1018)
T KOG2002|consen  439 ALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEM  518 (1018)
T ss_pred             HHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHH
Confidence                445555677888888888888888888888888766544   2223331      112233334445577777787


Q ss_pred             HHHHHhCCCCCChhhHHHHHHHHH-hcCCHHHHHHHHHHHHhC-------------------CCC---------------
Q 011378          298 WADMISRKISPNYISYGILINGYC-SMGHVTEAFRLWYEMVGK-------------------GIK---------------  342 (487)
Q Consensus       298 ~~~m~~~~~~p~~~t~~~li~~~~-~~~~~~~a~~~~~~m~~~-------------------~~~---------------  342 (487)
                      +..+.+.  .|+.+..-.=+-+.+ ..+...+|...+++....                   .+.               
T Consensus       519 Yk~Ilke--hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~  596 (1018)
T KOG2002|consen  519 YKSILKE--HPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTST  596 (1018)
T ss_pred             HHHHHHH--CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhcc
Confidence            7777654  244333211111111 123444555544443211                   111               


Q ss_pred             -CChhhHHHHHHHHHh------------cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          343 -PTLVSCNTIIKGYCR------------SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       343 -~~~~~~~~li~~~~~------------~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                       +|.++.-+|=..|..            .+..++|.++|.+..+.. +-|...-|.+--.++..|+++.|..+|....+.
T Consensus       597 ~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa  675 (1018)
T KOG2002|consen  597 KTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREA  675 (1018)
T ss_pred             CCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHH
Confidence             233332222222221            122345555555554321 224445555555566667777777777766655


Q ss_pred             CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          410 GLVPDVITYNVILTGFCRQGRMHDSELILWRMIE-KGLNPDRSTYTTLINGHVSQNNLKEAFRFHD  474 (487)
Q Consensus       410 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~  474 (487)
                      .- -+..+|-.|.+.|..+|++..|.+.|+.... .+-.-+......|-+++.+.|.+.+|.+.+.
T Consensus       676 ~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll  740 (1018)
T KOG2002|consen  676 TS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALL  740 (1018)
T ss_pred             Hh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            32 1333566666677777777777777666443 3333445556666667777777777666543

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

Probab=99.35  E-value=8e-12  Score=114.76  Aligned_cols=159  Identities=18%  Similarity=0.173  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC-hhhHHHHHHH
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGK-GIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD-SISYNTLING  389 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~  389 (487)
                      .+..++..+...++++++..+++..... ..+++...|..+-..+.+.|+.++|.+.+++..+.  .|+ ....+.++..
T Consensus       112 ~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~  189 (280)
T PF13429_consen  112 YLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWL  189 (280)
T ss_dssp             ------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHH
Confidence            3334444444444444444444443321 12233444444444444455555555555444432  232 3344444445


Q ss_pred             HhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHH
Q 011378          390 FVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNLKE  468 (487)
Q Consensus       390 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~~~  468 (487)
                      +...|+.+++.++++...+.. ..|...+..+..++...|+.++|...+++....  .| |+.....+.+.+...|+.++
T Consensus       190 li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~--~p~d~~~~~~~a~~l~~~g~~~~  266 (280)
T PF13429_consen  190 LIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKL--NPDDPLWLLAYADALEQAGRKDE  266 (280)
T ss_dssp             HCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH--STT-HHHHHHHHHHHT-------
T ss_pred             HHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccccccccccc--ccccccccccccccccccccccc
Confidence            555555555444444444321 223334444445555555555555555554331  22 33444444455555555555


Q ss_pred             HHHHHHH
Q 011378          469 AFRFHDE  475 (487)
Q Consensus       469 a~~~~~~  475 (487)
                      |.++.++
T Consensus       267 A~~~~~~  273 (280)
T PF13429_consen  267 ALRLRRQ  273 (280)
T ss_dssp             -------
T ss_pred             ccccccc
Confidence            5554433

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

Probab=99.35  E-value=1.5e-11  Score=113.05  Aligned_cols=259  Identities=17%  Similarity=0.161  Sum_probs=85.6

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCCCCCc-cchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 011378           35 TLINAYCREGFLEEAFQLMNSMSGKGLKPGV-FTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRK  113 (487)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  113 (487)
                      .+-..+.+.|++++|++++..-....-+|+. .-|..+-......++++.|.+.++++.+.+.. +...+..++.. ...
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            4456666777777777777543333212333 33333333444566777777777777655432 34445555555 567


Q ss_pred             CChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCC-CCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          114 ENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAG-LVPDNVLYTIIINGYCRNGFVLEALKM  192 (487)
Q Consensus       114 ~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~~~~~~a~~~  192 (487)
                      +++++|.+++....+..  ++...+...+..+.+.++++.+.++++...... ..++...|..+-..+.+.|+.++|.+.
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            77777777766554432  344556666777777777777777777765422 334556666677777777777777777


Q ss_pred             HHHHHHcCCcC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 011378          193 RDEMLEKGCVM-DVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSI  271 (487)
Q Consensus       193 ~~~m~~~g~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~  271 (487)
                      +++..+..  | |....+.++..+...|+.+++.++++...+.. +.|+..+..+-.+|...|+.++|+..|+...+.. 
T Consensus       169 ~~~al~~~--P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-  244 (280)
T PF13429_consen  169 YRKALELD--PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-  244 (280)
T ss_dssp             HHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-
T ss_pred             HHHHHHcC--CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-
Confidence            77666532  3 35556667777777777777777776665543 3445566667777777777777777777655421 


Q ss_pred             CCCeeehHHHHHHHHccCCHHHHHHHHHHH
Q 011378          272 KPDIVTYNTLIDGFCKVGEMEKANKLWADM  301 (487)
Q Consensus       272 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  301 (487)
                      +.|..+...+.+++...|+.++|.++.++.
T Consensus       245 p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  245 PDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             TT-HHHHHHHHHHHT---------------
T ss_pred             cccccccccccccccccccccccccccccc
Confidence            225556666777777777777777766543

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

Probab=99.34  E-value=1e-08  Score=93.49  Aligned_cols=205  Identities=13%  Similarity=0.124  Sum_probs=143.4

Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHH---HHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHH
Q 011378          251 CKDGNMNKALNLFDIMTQKSIKPDIVTYNTLID---GFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVT  327 (487)
Q Consensus       251 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~---~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~  327 (487)
                      ...|++++|.+.|++....    |.....+|.+   .+-+.|++++|++.|-.+.. -+.-+....--+.+.|-...+..
T Consensus       501 f~ngd~dka~~~ykeal~n----dasc~ealfniglt~e~~~~ldeald~f~klh~-il~nn~evl~qianiye~led~a  575 (840)
T KOG2003|consen  501 FANGDLDKAAEFYKEALNN----DASCTEALFNIGLTAEALGNLDEALDCFLKLHA-ILLNNAEVLVQIANIYELLEDPA  575 (840)
T ss_pred             eecCcHHHHHHHHHHHHcC----chHHHHHHHHhcccHHHhcCHHHHHHHHHHHHH-HHHhhHHHHHHHHHHHHHhhCHH
Confidence            3457788888888776643    3333223322   24567888888888866532 11224445555666677777777


Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHH
Q 011378          328 EAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKME  407 (487)
Q Consensus       328 ~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  407 (487)
                      .|++++.+.. .-++.|..+.+.|-..|-+.|+-..|.+++=+-- +-++.+..|..=|-..|....-++++..+|++..
T Consensus       576 qaie~~~q~~-slip~dp~ilskl~dlydqegdksqafq~~ydsy-ryfp~nie~iewl~ayyidtqf~ekai~y~ekaa  653 (840)
T KOG2003|consen  576 QAIELLMQAN-SLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSY-RYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA  653 (840)
T ss_pred             HHHHHHHHhc-ccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcc-cccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            8888775543 2345577788888899999999888877653322 1345566777777777888888899999998765


Q ss_pred             hCCCCCCHhhHHHHHHHH-HhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 011378          408 NQGLVPDVITYNVILTGF-CRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNN  465 (487)
Q Consensus       408 ~~g~~p~~~~~~~li~~~-~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~  465 (487)
                      -  +.|+..-|..+|..| .+.|++..|..++++... .+..|..+..-|++.+..-|.
T Consensus       654 l--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hr-kfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  654 L--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHR-KFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             h--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHH-hCccchHHHHHHHHHhccccc
Confidence            4  579999999998876 578999999999998864 466778888888888877764

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

Probab=99.32  E-value=1.9e-07  Score=93.12  Aligned_cols=421  Identities=14%  Similarity=0.132  Sum_probs=267.0

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCC--CCccchHHHHHHHHhcCChhhHHHHH
Q 011378           11 IDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLK--PGVFTYNSLINGLCKKGRCDRAKEVL   88 (487)
Q Consensus        11 ~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~--p~~~~~~~li~~~~~~~~~~~a~~~~   88 (487)
                      +..+...+...-... .-++...+.|-+-+.-.|+++.++.+..-+......  .-+.+|-.+-+++-..|+++.|..+|
T Consensus       252 ~~~~~~ll~~ay~~n-~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY  330 (1018)
T KOG2002|consen  252 YKKGVQLLQRAYKEN-NENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYY  330 (1018)
T ss_pred             HHHHHHHHHHHHhhc-CCCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHH
Confidence            344444444332221 135566888888888899999999998877654311  12345667788888999999999999


Q ss_pred             HHHHHCCCCCCHHHHH--HHHHHHHccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCC----CHHHHHHHHHHH
Q 011378           89 DEMLQMGLSPDTATYN--TLLVESCRKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNG----QLDRALMYFREM  161 (487)
Q Consensus        89 ~~m~~~g~~~~~~~~~--~ll~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g----~~~~a~~~~~~m  161 (487)
                      .+-.+.  .|+.+++.  -|-..+.+.|+++.+...|+...+.  .| +..|...|-..|+..+    ..+.|..++.+.
T Consensus       331 ~~s~k~--~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~--~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~  406 (1018)
T KOG2002|consen  331 MESLKA--DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQ--LPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKV  406 (1018)
T ss_pred             HHHHcc--CCCCccccccchhHHHHHhchHHHHHHHHHHHHHh--CcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHH
Confidence            876653  35544333  4566788899999999999888664  34 3445555555666654    456666666655


Q ss_pred             HHCCCCCChhhHHHHHHHHHhcCCHHHHHHHH----HHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc---
Q 011378          162 KSAGLVPDNVLYTIIINGYCRNGFVLEALKMR----DEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLER---  234 (487)
Q Consensus       162 ~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~----~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---  234 (487)
                      ...- ..|...|-.+-..+- .++...++..+    +.|...+-.+.+...|.+-......|+++.|...|+.....   
T Consensus       407 ~~~~-~~d~~a~l~laql~e-~~d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~  484 (1018)
T KOG2002|consen  407 LEQT-PVDSEAWLELAQLLE-QTDPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLE  484 (1018)
T ss_pred             Hhcc-cccHHHHHHHHHHHH-hcChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhh
Confidence            4422 233445544444443 33333334433    34556666677888888888888999999999888887654   


Q ss_pred             CCCCCHH-------HHHHHHHHHHhcCCHHHHHHHHHHHHHC-----------------------------------CCC
Q 011378          235 GVFPDFY-------TFTTLIHGHCKDGNMNKALNLFDIMTQK-----------------------------------SIK  272 (487)
Q Consensus       235 ~~~~~~~-------t~~~li~~~~~~g~~~~a~~~~~~m~~~-----------------------------------~~~  272 (487)
                      ...+|..       -|| +-...-..++.+.|.++|....+.                                   .-.
T Consensus       485 ~~n~de~~~~~lt~~YN-larl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~n  563 (1018)
T KOG2002|consen  485 VANKDEGKSTNLTLKYN-LARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSN  563 (1018)
T ss_pred             hcCccccccchhHHHHH-HHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCC
Confidence            1222221       122 222223334555555555544332                                   111


Q ss_pred             CCeeehHHHHH-HHHccCCHHHHHHHHHHHHhC-CCCCChhhHHHHHHHHHh------------cCCHHHHHHHHHHHHh
Q 011378          273 PDIVTYNTLID-GFCKVGEMEKANKLWADMISR-KISPNYISYGILINGYCS------------MGHVTEAFRLWYEMVG  338 (487)
Q Consensus       273 ~~~~~~~~li~-~~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~------------~~~~~~a~~~~~~m~~  338 (487)
                      |+  . .+++. .+.+...+..|.+-|..+.+. -..+|..+.-.|-+.|..            .++.++|+++|....+
T Consensus       564 p~--a-rsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~  640 (1018)
T KOG2002|consen  564 PN--A-RSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLR  640 (1018)
T ss_pred             cH--H-HHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHh
Confidence            11  1 12222 444444444555444333322 112454444444443332            2457789999988876


Q ss_pred             CCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC-CCCCCHhh
Q 011378          339 KGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ-GLVPDVIT  417 (487)
Q Consensus       339 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~~~  417 (487)
                      .. +.|...-|-+--+++..|++..|..+|....+... -+.-+|-.|-++|+..|++..|.++|+..... .-+-++..
T Consensus       641 ~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~v  718 (1018)
T KOG2002|consen  641 ND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEV  718 (1018)
T ss_pred             cC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHH
Confidence            53 55777777777788899999999999999998765 23345778889999999999999999877554 44457778


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          418 YNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       418 ~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      .+.|..++-++|++.+|...+......
T Consensus       719 l~~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  719 LHYLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            899999999999999998877665554

>TIGR00540 hemY_coli hemY protein

Probab=99.32  E-value=1.1e-08  Score=99.13  Aligned_cols=129  Identities=12%  Similarity=0.057  Sum_probs=75.7

Q ss_pred             ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhh---HHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHh---h
Q 011378          344 TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSIS---YNTLINGFVREENMDKAFALVSKMENQGLVPDVI---T  417 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~---~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~---~  417 (487)
                      +...+-.+...+...|+.++|.+++++..+..  ||...   ...........++.+.+.+.+++..+.  .|+..   .
T Consensus       262 ~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~--~p~~~~~~l  337 (409)
T TIGR00540       262 NIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN--VDDKPKCCI  337 (409)
T ss_pred             CHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh--CCCChhHHH
Confidence            55556666666666677777766666665532  33221   111112223345566666666655443  34333   3


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          418 YNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       418 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      ..++-..+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.+++++-
T Consensus       338 l~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       338 NRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34555666777777777777775444445677777777777777777777777777664

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.

>TIGR00540 hemY_coli hemY protein

Probab=99.31  E-value=1.1e-08  Score=98.98  Aligned_cols=130  Identities=11%  Similarity=0.028  Sum_probs=77.6

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH--HHhcCChHHHHHHHHHHHHCCCCCCh---hhH
Q 011378          309 NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKG--YCRSGDASKADEFLSKMVSEGVDPDS---ISY  383 (487)
Q Consensus       309 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~--~~~~~~~~~a~~~~~~m~~~g~~p~~---~~~  383 (487)
                      +...+..+...+...|+.++|.++.++..+.........+. ++..  ....++.+.+.+.++...+.  .|+.   ...
T Consensus       262 ~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~-~l~~~~~l~~~~~~~~~~~~e~~lk~--~p~~~~~~ll  338 (409)
T TIGR00540       262 NIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLP-LCLPIPRLKPEDNEKLEKLIEKQAKN--VDDKPKCCIN  338 (409)
T ss_pred             CHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhH-HHHHhhhcCCCChHHHHHHHHHHHHh--CCCChhHHHH
Confidence            44555556666666666666666666655442211111111 2222  22345666666666665532  2332   445


Q ss_pred             HHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          384 NTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRM  441 (487)
Q Consensus       384 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  441 (487)
                      .++-..|.+.|++++|.+.|+........||...+..+...+-+.|+.++|.+++++-
T Consensus       339 ~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       339 RALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            5666777788888888888875333334678777778888888888888888877774

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.

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

Probab=99.31  E-value=1.9e-08  Score=90.68  Aligned_cols=285  Identities=14%  Similarity=0.129  Sum_probs=166.8

Q ss_pred             cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          113 KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKM  192 (487)
Q Consensus       113 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  192 (487)
                      .|++..|++....-.+++-.|-. .|....++--+.|+.+.+..++.+..+.--.++...+-+........|+.+.|.  
T Consensus        97 eG~~~qAEkl~~rnae~~e~p~l-~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~--  173 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQPVL-AYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAR--  173 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcchHH-HHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHH--
Confidence            46666666666666666554432 344455555566666666666666655322333333444444444444444444  


Q ss_pred             HHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 011378          193 RDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIK  272 (487)
Q Consensus       193 ~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~  272 (487)
                                                       .-.+++.+.+ +-++.........|.+.|++.....++..|.+.++-
T Consensus       174 ---------------------------------~~v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l  219 (400)
T COG3071         174 ---------------------------------ENVDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLL  219 (400)
T ss_pred             ---------------------------------HHHHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCC
Confidence                                             4444443322 123344445555555555555555555555554443


Q ss_pred             CCe-------eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh
Q 011378          273 PDI-------VTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL  345 (487)
Q Consensus       273 ~~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  345 (487)
                      -+.       .+|+.+++-....+..+.-...|++..+ ..+-+...-..++.-+.++|+.++|.++..+-.+++..|..
T Consensus       220 ~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr-~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L  298 (400)
T COG3071         220 SDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPR-KLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRL  298 (400)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccH-HhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhH
Confidence            332       3566666665555555555555554432 23333444456677777778888888877777777777662


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHH-HCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLSKMV-SEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTG  424 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~~m~-~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  424 (487)
                      ..    +-.+.+.++.+.-.+..++-. ..+-.|  -.+.+|-..|.+.+.+.+|...|+.--  ...|+..+|+-+.++
T Consensus       299 ~~----~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~kA~~~leaAl--~~~~s~~~~~~la~~  370 (400)
T COG3071         299 CR----LIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGKASEALEAAL--KLRPSASDYAELADA  370 (400)
T ss_pred             HH----HHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHHHHHHHHHHH--hcCCChhhHHHHHHH
Confidence            22    224456666666666666544 334444  556777777888888888888887443  356888888888888


Q ss_pred             HHhcCChHHHHHHHHHHHH
Q 011378          425 FCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~  443 (487)
                      |.+.|+..+|..+.++-..
T Consensus       371 ~~~~g~~~~A~~~r~e~L~  389 (400)
T COG3071         371 LDQLGEPEEAEQVRREALL  389 (400)
T ss_pred             HHHcCChHHHHHHHHHHHH
Confidence            8888888888877776553

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

Probab=99.29  E-value=2.9e-08  Score=89.51  Aligned_cols=291  Identities=17%  Similarity=0.139  Sum_probs=202.5

Q ss_pred             cCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHH
Q 011378           43 EGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEI  122 (487)
Q Consensus        43 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  122 (487)
                      .|++..|.++...-.+++-.|- ..|..-..+.-+.|+.+.+-.++.+.-+..-.++...+-+.-......|+...|..-
T Consensus        97 eG~~~qAEkl~~rnae~~e~p~-l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQPV-LAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcchH-HHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            7888888888887766655442 234444556667888888888888877654455666666777777888888888888


Q ss_pred             HHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCh-------hhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          123 FCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDN-------VLYTIIINGYCRNGFVLEALKMRDE  195 (487)
Q Consensus       123 ~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~-------~~~~~ll~~~~~~~~~~~a~~~~~~  195 (487)
                      ++++.+.+-. +.........+|.+.|++..+..+...|.+.|+--|.       .+|..+++-....+..+.-...|+.
T Consensus       176 v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~  254 (400)
T COG3071         176 VDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKN  254 (400)
T ss_pred             HHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHh
Confidence            8888776533 4556777888888888888888888888888765544       3688888877766666665555554


Q ss_pred             HHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH-HHHCCCCCC
Q 011378          196 MLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDI-MTQKSIKPD  274 (487)
Q Consensus       196 m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~-m~~~~~~~~  274 (487)
                      .-+ ...-++..-.+++.-+.+.|+.++|.++..+..+++..|+.    ...-.+.+-++...=++..+. ..+.+..| 
T Consensus       255 ~pr-~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L----~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p-  328 (400)
T COG3071         255 QPR-KLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRL----CRLIPRLRPGDPEPLIKAAEKWLKQHPEDP-  328 (400)
T ss_pred             ccH-HhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhH----HHHHhhcCCCCchHHHHHHHHHHHhCCCCh-
Confidence            422 22334555667777788888888888888888877665552    222344555665555555543 33444444 


Q ss_pred             eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 011378          275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT  344 (487)
Q Consensus       275 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~  344 (487)
                       ..+.+|=.-|.+.+.+.+|...|+..  -...|+..+|+.+-.++.+.|+..+|.++.++-...-.+|+
T Consensus       329 -~L~~tLG~L~~k~~~w~kA~~~leaA--l~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~  395 (400)
T COG3071         329 -LLLSTLGRLALKNKLWGKASEALEAA--LKLRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPN  395 (400)
T ss_pred             -hHHHHHHHHHHHhhHHHHHHHHHHHH--HhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCC
Confidence             56777777788888888888888744  34568888888888888888888888888877654434443

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

Probab=99.28  E-value=3.8e-07  Score=90.43  Aligned_cols=362  Identities=14%  Similarity=0.125  Sum_probs=228.8

Q ss_pred             HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHH
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEA  189 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  189 (487)
                      +++ |++++|.+++.+..+.. +-+...|-.|-..|-+.|+.++++..+-..-..+ +-|...|..+-+...+.|++.+|
T Consensus       150 far-g~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~i~qA  226 (895)
T KOG2076|consen  150 FAR-GDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGNINQA  226 (895)
T ss_pred             HHh-CCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhcccHHHH
Confidence            444 88888888888776553 2355567788888888888888776655444332 23456777777777788888888


Q ss_pred             HHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH----HHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          190 LKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFY----TFTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       190 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~----t~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      .-.+.+..+.. ++++..+-.=+..|-+.|+...|.+-|.++....-+.|..    +.-.+++.+...++-+.|...++.
T Consensus       227 ~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~  305 (895)
T KOG2076|consen  227 RYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEG  305 (895)
T ss_pred             HHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            88777776643 2445454555667777888888888888877643222222    233445666666777777777765


Q ss_pred             HHH-CCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCC---------------------------CCChhhHHHHH
Q 011378          266 MTQ-KSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKI---------------------------SPNYISYGILI  317 (487)
Q Consensus       266 m~~-~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---------------------------~p~~~t~~~li  317 (487)
                      ... .+-..+...++.++..|.+...++.+.....++.....                           .++...+. +.
T Consensus       306 ~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~r-l~  384 (895)
T KOG2076|consen  306 ALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIR-LM  384 (895)
T ss_pred             HHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHh-Hh
Confidence            544 23334556777888888888888887777766655211                           12222211 11


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCC
Q 011378          318 NGYCSMGHVTEAFRLWYEMVGKGI--KPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREEN  395 (487)
Q Consensus       318 ~~~~~~~~~~~a~~~~~~m~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~  395 (487)
                      -++......+...-+..-.....+  .-+...|.-+.++|...|++.+|..++........--+...|-.+-.+|...|.
T Consensus       385 icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e  464 (895)
T KOG2076|consen  385 ICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGE  464 (895)
T ss_pred             hhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhh
Confidence            122222222222223333333332  233456777788888888888888888887765444456778888888888888


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhh-HHHHHHHHHhcCChHHHHHHHHHHH--------HcCCCCCHHHHHHHHHHHHhcCCH
Q 011378          396 MDKAFALVSKMENQGLVPDVIT-YNVILTGFCRQGRMHDSELILWRMI--------EKGLNPDRSTYTTLINGHVSQNNL  466 (487)
Q Consensus       396 ~~~a~~~~~~m~~~g~~p~~~~-~~~li~~~~~~g~~~~a~~~~~~m~--------~~g~~p~~~ty~~l~~~~~~~~~~  466 (487)
                      .+.|.+.+++....  .||... =-.|-..+-+.|+.++|.+++.++.        ..++.|+...--.....+-..|+.
T Consensus       465 ~e~A~e~y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~  542 (895)
T KOG2076|consen  465 YEEAIEFYEKVLIL--APDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKR  542 (895)
T ss_pred             HHHHHHHHHHHHhc--CCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhH
Confidence            88888888776543  344322 2233345677888888888888743        344566666666677777788888


Q ss_pred             HHHHHHHHHHHH
Q 011378          467 KEAFRFHDEMLQ  478 (487)
Q Consensus       467 ~~a~~~~~~m~~  478 (487)
                      ++=..+-.+|+.
T Consensus       543 E~fi~t~~~Lv~  554 (895)
T KOG2076|consen  543 EEFINTASTLVD  554 (895)
T ss_pred             HHHHHHHHHHHH
Confidence            877777666654

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

Probab=99.21  E-value=4.6e-08  Score=89.34  Aligned_cols=426  Identities=14%  Similarity=0.129  Sum_probs=268.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCCccchH-HHHHHHHhcCChhhHHHHHHHHHHCCCCCC------HHHHHHHHH
Q 011378           36 LINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYN-SLINGLCKKGRCDRAKEVLDEMLQMGLSPD------TATYNTLLV  108 (487)
Q Consensus        36 ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~g~~~~------~~~~~~ll~  108 (487)
                      |..-|.-..-..+|+..++-+.....-||.-... .+-..+.+.+.+..|.+++.-.+..  .|+      ....+.+-.
T Consensus       207 laqqy~~ndm~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldq--vpsink~~rikil~nigv  284 (840)
T KOG2003|consen  207 LAQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQ--VPSINKDMRIKILNNIGV  284 (840)
T ss_pred             HHHHhhhhHHHHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhh--ccccchhhHHHHHhhcCe
Confidence            3444444556788999999888877778764432 2345677888899999988654432  232      334555566


Q ss_pred             HHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChh--------hHHHHHHHH
Q 011378          109 ESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNV--------LYTIIINGY  180 (487)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~--------~~~~ll~~~  180 (487)
                      .+.+.|.++.|...|+...+.  .|+..+--.|+-++..-|+-++..+.|.+|......||..        .-..|++--
T Consensus       285 tfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~ea  362 (840)
T KOG2003|consen  285 TFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEA  362 (840)
T ss_pred             eEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHHH
Confidence            788999999999999987665  5887766666767777889999999999987644333221        112222221


Q ss_pred             Hh---------cC--CHHHHHHHHHHHHHcCCcCChhh---H----------H--------HHHHHHHhcCCHHHHHHHH
Q 011378          181 CR---------NG--FVLEALKMRDEMLEKGCVMDVVT---Y----------N--------TILNGLCRAKMLTEADDLF  228 (487)
Q Consensus       181 ~~---------~~--~~~~a~~~~~~m~~~g~~~~~~~---~----------~--------~li~~~~~~~~~~~a~~~~  228 (487)
                      .+         .+  +.+++.-.-.++...-+.||-..   |          .        .-.--+.+.|+++.|.+++
T Consensus       363 i~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aieil  442 (840)
T KOG2003|consen  363 IKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEIL  442 (840)
T ss_pred             HhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHH
Confidence            11         11  11121111111222112222110   0          0        0012356788999998888


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHCCCCCCeeehHHHH-----HHHHccCCHHHHHHHHHHH
Q 011378          229 NEMLERGVFPDFYTFTTLIHGHCK--DGNMNKALNLFDIMTQKSIKPDIVTYNTLI-----DGFCKVGEMEKANKLWADM  301 (487)
Q Consensus       229 ~~m~~~~~~~~~~t~~~li~~~~~--~g~~~~a~~~~~~m~~~~~~~~~~~~~~li-----~~~~~~g~~~~a~~~~~~m  301 (487)
                      +-..++.-+.-+..-+.|-..+.-  ..++..|.++-+...      +..-||.-.     +.-...|++++|...+++.
T Consensus       443 kv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~al------n~dryn~~a~~nkgn~~f~ngd~dka~~~ykea  516 (840)
T KOG2003|consen  443 KVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIAL------NIDRYNAAALTNKGNIAFANGDLDKAAEFYKEA  516 (840)
T ss_pred             HHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHh------cccccCHHHhhcCCceeeecCcHHHHHHHHHHH
Confidence            877665433333333333322222  334666665555433      222232221     1123478999999999998


Q ss_pred             HhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChh
Q 011378          302 ISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSI  381 (487)
Q Consensus       302 ~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  381 (487)
                      ....-.-....||+=+ .+-..|++++|+..|-.+..- +.-+..+.--+-..|-...+...|.+++-...+ =++.|+.
T Consensus       517 l~ndasc~ealfnigl-t~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~s-lip~dp~  593 (840)
T KOG2003|consen  517 LNNDASCTEALFNIGL-TAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQANS-LIPNDPA  593 (840)
T ss_pred             HcCchHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcc-cCCCCHH
Confidence            7653322333344333 245678999999998776421 223444555566677777888888888765432 3556788


Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHV  461 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~  461 (487)
                      +.+.|-+.|-+.|+-.+|.+..=.-.. =+..+..+..=|...|....-++.+.+.|++..  =++|+.+-|..|+..|.
T Consensus       594 ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ayyidtqf~ekai~y~ekaa--liqp~~~kwqlmiasc~  670 (840)
T KOG2003|consen  594 ILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--LIQPNQSKWQLMIASCF  670 (840)
T ss_pred             HHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--hcCccHHHHHHHHHHHH
Confidence            999999999999999998886533221 123467777778888888888999999999853  47899999999997665


Q ss_pred             h-cCCHHHHHHHHHHHH
Q 011378          462 S-QNNLKEAFRFHDEML  477 (487)
Q Consensus       462 ~-~~~~~~a~~~~~~m~  477 (487)
                      + .|+++.|+.++.+..
T Consensus       671 rrsgnyqka~d~yk~~h  687 (840)
T KOG2003|consen  671 RRSGNYQKAFDLYKDIH  687 (840)
T ss_pred             HhcccHHHHHHHHHHHH
Confidence            5 699999999998874

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

Probab=99.16  E-value=2.7e-07  Score=80.96  Aligned_cols=225  Identities=15%  Similarity=0.188  Sum_probs=132.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCe----eehHHHHHHHH
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI----VTYNTLIDGFC  286 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~li~~~~  286 (487)
                      |-.-|...|-++.|+.+|..+.+.+. .-.....-|+..|-...++++|+++-+.+.+.+-.+..    ..|.-|-..+.
T Consensus       113 L~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~  191 (389)
T COG2956         113 LGRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQAL  191 (389)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHh
Confidence            33446677778888888877766432 12335566777788888888888877766655443332    13444555555


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCChhhH-HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHH
Q 011378          287 KVGEMEKANKLWADMISRKISPNYISY-GILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKAD  365 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m~~~~~~p~~~t~-~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~  365 (487)
                      ...+++.|..++.......  |+.+-- -++-+.....|++..|.+.|+...+....--..+...|..+|...|+.++..
T Consensus       192 ~~~~~d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~  269 (389)
T COG2956         192 ASSDVDRARELLKKALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGL  269 (389)
T ss_pred             hhhhHHHHHHHHHHHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHH
Confidence            5667777777776654432  222211 2344556677788888888877776655555566777778888888888887


Q ss_pred             HHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh---cCChHHHHHHHHHHH
Q 011378          366 EFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCR---QGRMHDSELILWRMI  442 (487)
Q Consensus       366 ~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~---~g~~~~a~~~~~~m~  442 (487)
                      .++..+.+....++..  ..+-..-....-.+.|...+-+-...  +|+..-+..+|+....   .|...+..-++++|.
T Consensus       270 ~fL~~~~~~~~g~~~~--l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mv  345 (389)
T COG2956         270 NFLRRAMETNTGADAE--LMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMV  345 (389)
T ss_pred             HHHHHHHHccCCccHH--HHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHH
Confidence            7777776654444432  11111111222334444444332222  5777777777776643   333444455555554

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

Probab=99.11  E-value=8.3e-06  Score=75.46  Aligned_cols=426  Identities=13%  Similarity=0.113  Sum_probs=292.3

Q ss_pred             HHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCChh
Q 011378           39 AYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPD-TATYNTLLVESCRKENMS  117 (487)
Q Consensus        39 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~  117 (487)
                      .=...+++..|.++|+...... .-+...|---+..=.+...+..|..++++....  .|- ...|-..+..=-..|++.
T Consensus        82 wEesq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~--lPRVdqlWyKY~ymEE~LgNi~  158 (677)
T KOG1915|consen   82 WEESQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI--LPRVDQLWYKYIYMEEMLGNIA  158 (677)
T ss_pred             HHHhHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh--cchHHHHHHHHHHHHHHhcccH
Confidence            3344566777888888766533 234445666666777888888899998886542  233 345556666666678999


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          118 EAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEML  197 (487)
Q Consensus       118 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  197 (487)
                      .|.++|+...+.  .|+...|.+.|+.-.+-..++.|..+++...-.  -|+...|-....-=-++|.+..+..+++...
T Consensus       159 gaRqiferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~VyerAi  234 (677)
T KOG1915|consen  159 GARQIFERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVYERAI  234 (677)
T ss_pred             HHHHHHHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            999999887664  799999999999999999999999999988753  4888888877777778898888888887665


Q ss_pred             Hc-CCc-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHH--------HH
Q 011378          198 EK-GCV-MDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD--FYTFTTLIHGHCKDGNMNKALNLF--------DI  265 (487)
Q Consensus       198 ~~-g~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~t~~~li~~~~~~g~~~~a~~~~--------~~  265 (487)
                      +. |-. .+...+.+...-=.++..++.|.-+|+-..++ ++-+  ...|......=-+.|+-....++.        +.
T Consensus       235 e~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~  313 (677)
T KOG1915|consen  235 EFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEK  313 (677)
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHH
Confidence            42 211 11222333333333567788888888877764 2222  234444444334445544333332        22


Q ss_pred             HHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChh--h---HHHH-----HHHHHhcCCHHHHHHHHHH
Q 011378          266 MTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYI--S---YGIL-----INGYCSMGHVTEAFRLWYE  335 (487)
Q Consensus       266 m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~--t---~~~l-----i~~~~~~~~~~~a~~~~~~  335 (487)
                      +.+.+ +.|-.+|--.++.-...|+.+...++|..... +++|-..  .   |-.|     +--=....+++.+.++++.
T Consensus       314 ~v~~n-p~nYDsWfdylrL~e~~g~~~~Ire~yErAIa-nvpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~  391 (677)
T KOG1915|consen  314 EVSKN-PYNYDSWFDYLRLEESVGDKDRIRETYERAIA-NVPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQA  391 (677)
T ss_pred             HHHhC-CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHc-cCCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            22221 23455666677777778999999999988764 4444221  1   1111     1112346788889999988


Q ss_pred             HHhCCCCC-ChhhHHHHHH----HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCC
Q 011378          336 MVGKGIKP-TLVSCNTIIK----GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQG  410 (487)
Q Consensus       336 m~~~~~~~-~~~~~~~li~----~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  410 (487)
                      ..+  +-| ..+||.-+=-    --.++.++..|.+++...+  |..|-..+|..-|..=.+.+++|...+++++..+.+
T Consensus       392 ~l~--lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~  467 (677)
T KOG1915|consen  392 CLD--LIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFS  467 (677)
T ss_pred             HHh--hcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            876  344 4455554433    3347889999999988655  788999999888888889999999999999988754


Q ss_pred             CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          411 LVPDVITYNVILTGFCRQGRMHDSELILWRMIEK-GLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       411 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                       .-+..+|.-....=..-|+++.|+.+|.-.... .+.-....|...|+--...|.++.|..+++++++.
T Consensus       468 -Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  468 -PENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             -hHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh
Confidence             235677887777777889999999999876643 23345567788888888899999999999999864

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

Probab=99.09  E-value=7.8e-07  Score=78.19  Aligned_cols=270  Identities=14%  Similarity=0.119  Sum_probs=145.8

Q ss_pred             cCChhhHHHHHHHHHHCCCCCCHH-HHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCH---hHHHHHHHHHHhCCCHHH
Q 011378           78 KGRCDRAKEVLDEMLQMGLSPDTA-TYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDI---VSFSTLIGIFSRNGQLDR  153 (487)
Q Consensus        78 ~~~~~~a~~~~~~m~~~g~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~---~~~~~li~~~~~~g~~~~  153 (487)
                      ..+.++|.+.|-+|.+.  .|.+. +--+|-..|-+.|.++.|.++.+.+.++.--+..   ...--|-.-|-.+|-+|.
T Consensus        48 s~Q~dKAvdlF~e~l~~--d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DR  125 (389)
T COG2956          48 SNQPDKAVDLFLEMLQE--DPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDR  125 (389)
T ss_pred             hcCcchHHHHHHHHHhc--CchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhH
Confidence            45667777777777652  22222 2223444566667777777777776653111111   112234455667777777


Q ss_pred             HHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCCh----hhHHHHHHHHHhcCCHHHHHHHHH
Q 011378          154 ALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDV----VTYNTILNGLCRAKMLTEADDLFN  229 (487)
Q Consensus       154 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~~~~~~a~~~~~  229 (487)
                      |..+|..+.+.|- .-....-.|+..|-...++++|.++-+++.+.+-.+..    ..|.-+-..+....+++.|...++
T Consensus       126 AE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~  204 (389)
T COG2956         126 AEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLK  204 (389)
T ss_pred             HHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            7777777765321 11234556677777777777777777776665443322    134444444445566666777666


Q ss_pred             HHHHcCCCCCHHHHH-HHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC
Q 011378          230 EMLERGVFPDFYTFT-TLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP  308 (487)
Q Consensus       230 ~m~~~~~~~~~~t~~-~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p  308 (487)
                      +..+.+  |+..--+ .+-+.....|+++.|++.++...+.+...-..+...|..+|...|+.++....+..+......+
T Consensus       205 kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~  282 (389)
T COG2956         205 KALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGA  282 (389)
T ss_pred             HHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCc
Confidence            665532  2222222 2334566667777777777666655433334456666677777777777666666665543333


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011378          309 NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYC  356 (487)
Q Consensus       309 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  356 (487)
                      +..  ..+-.--....-.+.|.....+-.+.  +|+...+..||+...
T Consensus       283 ~~~--l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l  326 (389)
T COG2956         283 DAE--LMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHL  326 (389)
T ss_pred             cHH--HHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhh
Confidence            322  22222222233344444444433322  566666666665544

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.08  E-value=1.7e-07  Score=83.36  Aligned_cols=197  Identities=14%  Similarity=0.147  Sum_probs=110.0

Q ss_pred             hHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          278 YNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR  357 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  357 (487)
                      +..+...+...|++++|...+.+..... +.+...+..+...+...|++++|...++...... +.+...+..+...+..
T Consensus        34 ~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~  111 (234)
T TIGR02521        34 RVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLCQ  111 (234)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHH
Confidence            3344444455555555555554443321 1123444555555555566666666555554432 2233444555555566


Q ss_pred             cCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHH
Q 011378          358 SGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       358 ~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  436 (487)
                      .|+.++|.+.++........| ....+..+...+...|++++|...+++..... ..+...+..+...+...|++++|..
T Consensus       112 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  190 (234)
T TIGR02521       112 QGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARA  190 (234)
T ss_pred             cccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHH
Confidence            666666666666655432212 23345555566667777777777776665432 1234456666677777777777777


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          437 ILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       437 ~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      .+++.... ...+...+..+...+...|+.+.|..+.+.+..
T Consensus       191 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       191 YLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            77776654 233445555666667777777777777666643

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.05  E-value=1.9e-07  Score=82.99  Aligned_cols=195  Identities=15%  Similarity=0.073  Sum_probs=84.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFC  286 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  286 (487)
                      .+..+...+...|+++.|.+.+++..+.. +.+...+..+...+...|+.++|...++...+.. +.+...+..+...+.
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            34444455555555555555555554332 1223444445555555555555555555444321 112223344444445


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHH
Q 011378          287 KVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKAD  365 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~  365 (487)
                      ..|++++|.+.+.+.......| ....+..+...+...|++++|...+....... +.+...+..+...+...|+.++|.
T Consensus       111 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~  189 (234)
T TIGR02521       111 QQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDAR  189 (234)
T ss_pred             HcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHH
Confidence            5555555555555444321111 12233334444444455555555444443321 112233334444444444444444


Q ss_pred             HHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHH
Q 011378          366 EFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSK  405 (487)
Q Consensus       366 ~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~  405 (487)
                      ..+++..+. .+.+...+..+...+...|+.+.|..+.+.
T Consensus       190 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  228 (234)
T TIGR02521       190 AYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQ  228 (234)
T ss_pred             HHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            444444333 112223333334444444444444444433

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.

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

Probab=99.04  E-value=1.5e-05  Score=73.61  Aligned_cols=343  Identities=15%  Similarity=0.089  Sum_probs=212.7

Q ss_pred             HHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCC-HHHHHH-HHHHHHccCChh
Q 011378           40 YCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPD-TATYNT-LLVESCRKENMS  117 (487)
Q Consensus        40 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~-ll~~~~~~~~~~  117 (487)
                      +.+.|..+.|.+.|......    -+..|.+.+.-..-..+.+.+..+..     |...| ...-.. +..++-.....+
T Consensus       174 ~k~~~~~s~A~~sfv~~v~~----~P~~W~AWleL~~lit~~e~~~~l~~-----~l~~~~h~M~~~F~~~a~~el~q~~  244 (559)
T KOG1155|consen  174 LKELGLLSLAIDSFVEVVNR----YPWFWSAWLELSELITDIEILSILVV-----GLPSDMHWMKKFFLKKAYQELHQHE  244 (559)
T ss_pred             HHhhchHHHHHHHHHHHHhc----CCcchHHHHHHHHhhchHHHHHHHHh-----cCcccchHHHHHHHHHHHHHHHHHH
Confidence            44566667777666554431    23456555554433333333322221     11111 111111 223344445677


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC--CCChhhHHHHHHHHHhcCCH-HHHHHHHH
Q 011378          118 EAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGL--VPDNVLYTIIINGYCRNGFV-LEALKMRD  194 (487)
Q Consensus       118 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~--~~~~~~~~~ll~~~~~~~~~-~~a~~~~~  194 (487)
                      ++.+-.+.....|..-+...-+-...+.-...++|+|+.+|++..+...  --|..+|+.++-.--....+ --|..+..
T Consensus       245 e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~  324 (559)
T KOG1155|consen  245 EALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSN  324 (559)
T ss_pred             HHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHH
Confidence            7777777777777765554444444455677889999999999887632  12456777766432221111 11111111


Q ss_pred             HHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 011378          195 EMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPD  274 (487)
Q Consensus       195 ~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~  274 (487)
                         -.  .--+.|+.++-+-|+-.++.+.|...|+...+-+ +-....|+.|-+-|..-.+...|++-++...+-. +.|
T Consensus       325 ---id--KyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~D  397 (559)
T KOG1155|consen  325 ---ID--KYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRD  397 (559)
T ss_pred             ---hc--cCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chh
Confidence               11  2334677778888888889999999999887643 1234568888888999999999998888765432 236


Q ss_pred             eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK  353 (487)
Q Consensus       275 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  353 (487)
                      -..|-.|=++|.-.+...=|+-.|++..  .++| |...|..|-++|.+.++.++|++-|......| ..+...+..|-+
T Consensus       398 yRAWYGLGQaYeim~Mh~YaLyYfqkA~--~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~Lak  474 (559)
T KOG1155|consen  398 YRAWYGLGQAYEIMKMHFYALYYFQKAL--ELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAK  474 (559)
T ss_pred             HHHHhhhhHHHHHhcchHHHHHHHHHHH--hcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHH
Confidence            6678888888888888888888887654  3444 67889999999999999999999888776655 235567778888


Q ss_pred             HHHhcCChHHHHHHHHHHHH----CCCCCChhhH--HHHHHHHhccCCHHHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVS----EGVDPDSISY--NTLINGFVREENMDKAFA  401 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~----~g~~p~~~~~--~~li~~~~~~~~~~~a~~  401 (487)
                      .|-+.++.++|...+.+-.+    .|...|....  -=|-.-+.+.+++++|..
T Consensus       475 Lye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~  528 (559)
T KOG1155|consen  475 LYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASY  528 (559)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHH
Confidence            88888888888888776553    2332221111  113344455566655544

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

Probab=99.01  E-value=2.2e-05  Score=72.76  Aligned_cols=421  Identities=12%  Similarity=0.115  Sum_probs=255.6

Q ss_pred             cCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHH
Q 011378           43 EGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEI  122 (487)
Q Consensus        43 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  122 (487)
                      .|++..|.++|+.-.+  ..|+...|.+.|+.=.+-...+.|..++++..-  +.|+..+|-...+-=-++|++..+..+
T Consensus       154 LgNi~gaRqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~V  229 (677)
T KOG1915|consen  154 LGNIAGARQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARSV  229 (677)
T ss_pred             hcccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHH
Confidence            4666666666665443  357777777777766667777777777776653  346777766666666666777777777


Q ss_pred             HHHHHHC-CC-CCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC--hhhHHHHHHHHHhcCCHHHHHHH------
Q 011378          123 FCEMSRR-GV-APDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD--NVLYTIIINGYCRNGFVLEALKM------  192 (487)
Q Consensus       123 ~~~m~~~-g~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~~~------  192 (487)
                      ++...+. |- .-+...|.+...--.++..++.|.-+|.-.... ++.+  ...|..+..-=-+-|+.......      
T Consensus       230 yerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk  308 (677)
T KOG1915|consen  230 YERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRK  308 (677)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhh
Confidence            6655432 10 001122223333333445566666666554432 1111  22344443333344544333222      


Q ss_pred             --HHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-------HHHHHHHHH---HHhcCCHHHHH
Q 011378          193 --RDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDF-------YTFTTLIHG---HCKDGNMNKAL  260 (487)
Q Consensus       193 --~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-------~t~~~li~~---~~~~g~~~~a~  260 (487)
                        ++.+.+. .+.|=.+|--.+..-...|+.+...++|+.... +++|-.       +.|.-+=-+   =....+++.+.
T Consensus       309 ~qYE~~v~~-np~nYDsWfdylrL~e~~g~~~~Ire~yErAIa-nvpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr  386 (677)
T KOG1915|consen  309 FQYEKEVSK-NPYNYDSWFDYLRLEESVGDKDRIRETYERAIA-NVPPASEKRYWRRYIYLWINYALYEELEAEDVERTR  386 (677)
T ss_pred             hHHHHHHHh-CCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHc-cCCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence              2222221 234445666667777778999999999999875 455532       122222122   23467889999


Q ss_pred             HHHHHHHHCCCCCCeeehHHHHHHHH----ccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          261 NLFDIMTQKSIKPDIVTYNTLIDGFC----KVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEM  336 (487)
Q Consensus       261 ~~~~~m~~~~~~~~~~~~~~li~~~~----~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m  336 (487)
                      ++|+...+ -++-...||..+=-.|+    ++.++..|.+++...  -|..|-..+|..-|..=.+.+.++.+..+++..
T Consensus       387 ~vyq~~l~-lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~A--IG~cPK~KlFk~YIelElqL~efDRcRkLYEkf  463 (677)
T KOG1915|consen  387 QVYQACLD-LIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNA--IGKCPKDKLFKGYIELELQLREFDRCRKLYEKF  463 (677)
T ss_pred             HHHHHHHh-hcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHH--hccCCchhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            99988776 44445677776655554    567889999988765  378899999999999999999999999999998


Q ss_pred             HhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCC-CCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH
Q 011378          337 VGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEG-VDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDV  415 (487)
Q Consensus       337 ~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  415 (487)
                      ...+ +-|..+|.-.-.-=...|+.+.|..+|+-..+.. .......|-+-|+-=...|.+++|..+++++.+..  +.+
T Consensus       464 le~~-Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt--~h~  540 (677)
T KOG1915|consen  464 LEFS-PENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRT--QHV  540 (677)
T ss_pred             HhcC-hHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhc--ccc
Confidence            7654 4466677666555567799999999999887642 12223334444444457899999999999987652  333


Q ss_pred             hhHHHHHHHHH-----hcC-----------ChHHHHHHHHHHHH--cCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          416 ITYNVILTGFC-----RQG-----------RMHDSELILWRMIE--KGLNPDR---STYTTLINGHVSQNNLKEAFRFHD  474 (487)
Q Consensus       416 ~~~~~li~~~~-----~~g-----------~~~~a~~~~~~m~~--~g~~p~~---~ty~~l~~~~~~~~~~~~a~~~~~  474 (487)
                      -+|-++...=.     +.|           .+..|+++|++...  +...|..   ...+.+.+.-...|.-.+...+-.
T Consensus       541 kvWisFA~fe~s~~~~~~~~~~~~~e~~~~~~~~AR~iferAn~~~k~~~~KeeR~~LLEaw~~~E~~~G~~~d~~~V~s  620 (677)
T KOG1915|consen  541 KVWISFAKFEASASEGQEDEDLAELEITDENIKRARKIFERANTYLKESTPKEERLMLLEAWKNMEETFGTEGDVERVQS  620 (677)
T ss_pred             hHHHhHHHHhccccccccccchhhhhcchhHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCchhhHHHHHH
Confidence            35555544322     444           56678888887642  1222322   244455555555565444444433


Q ss_pred             HH
Q 011378          475 EM  476 (487)
Q Consensus       475 ~m  476 (487)
                      .|
T Consensus       621 ~m  622 (677)
T KOG1915|consen  621 KM  622 (677)
T ss_pred             hc
Confidence            33

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

Probab=98.99  E-value=3.6e-05  Score=74.17  Aligned_cols=451  Identities=12%  Similarity=0.085  Sum_probs=305.4

Q ss_pred             ChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHH
Q 011378           10 KIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLD   89 (487)
Q Consensus        10 ~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~   89 (487)
                      ..+.|.-++++..+.  -|   +-..|.-++++..-++.|..+++..++. ++-+...|.+--.-=-+.|+.+.+.++++
T Consensus       391 ~~~darilL~rAvec--cp---~s~dLwlAlarLetYenAkkvLNkaRe~-iptd~~IWitaa~LEE~ngn~~mv~kii~  464 (913)
T KOG0495|consen  391 EPEDARILLERAVEC--CP---QSMDLWLALARLETYENAKKVLNKAREI-IPTDREIWITAAKLEEANGNVDMVEKIID  464 (913)
T ss_pred             ChHHHHHHHHHHHHh--cc---chHHHHHHHHHHHHHHHHHHHHHHHHhh-CCCChhHHHHHHHHHHhcCCHHHHHHHHH
Confidence            445577777776552  12   2345667778888888888888887653 44466677655554456888888888876


Q ss_pred             H----HHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCC--HhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 011378           90 E----MLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPD--IVSFSTLIGIFSRNGQLDRALMYFREMKS  163 (487)
Q Consensus        90 ~----m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~  163 (487)
                      +    +...|+..+..-|-.=-..|-+.|.+-.+..+.......|+.-.  ..||..--..|.+.+.++-|..+|....+
T Consensus       465 rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alq  544 (913)
T KOG0495|consen  465 RGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQ  544 (913)
T ss_pred             HHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHh
Confidence            5    45668888888888877888888888888888888877776542  35788888888999999988888888766


Q ss_pred             CCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 011378          164 AGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTF  243 (487)
Q Consensus       164 ~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~  243 (487)
                      - ..-+...|......=-..|..++...++.+.....- -....|--....+-..|+...|..++....+.. +.+...|
T Consensus       545 v-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~p-kae~lwlM~ake~w~agdv~~ar~il~~af~~~-pnseeiw  621 (913)
T KOG0495|consen  545 V-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCP-KAEILWLMYAKEKWKAGDVPAARVILDQAFEAN-PNSEEIW  621 (913)
T ss_pred             h-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCC-cchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhC-CCcHHHH
Confidence            3 233456777777777777888888888887776532 223345445566667788888888888887754 2256678


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHh
Q 011378          244 TTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-ISYGILINGYCS  322 (487)
Q Consensus       244 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~~~  322 (487)
                      -+-+..-..+..++.|..+|...+.  ..|+...|.--++.-.-.+..++|.+++++..+.  -|+. ..|-.+-..+-+
T Consensus       622 laavKle~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~--fp~f~Kl~lmlGQi~e~  697 (913)
T KOG0495|consen  622 LAAVKLEFENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEALRLLEEALKS--FPDFHKLWLMLGQIEEQ  697 (913)
T ss_pred             HHHHHHhhccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh--CCchHHHHHHHhHHHHH
Confidence            8888888888888888888876654  4566666666666666677888888888766543  2443 345555555666


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHH
Q 011378          323 MGHVTEAFRLWYEMVGKGIKPTL-VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  401 (487)
                      .++++.|...|..=.  ..-|+. -.|-.|-+.=-+.|.+.+|..+++.-.-++ +-+...|-..|..=.+.|+.+.|..
T Consensus       698 ~~~ie~aR~aY~~G~--k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~  774 (913)
T KOG0495|consen  698 MENIEMAREAYLQGT--KKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAEL  774 (913)
T ss_pred             HHHHHHHHHHHHhcc--ccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHH
Confidence            666666666554321  123333 334444444455667777777777655433 2345567777777777777777776


Q ss_pred             HHHHHH----hCCC-------------------------CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH-H
Q 011378          402 LVSKME----NQGL-------------------------VPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR-S  451 (487)
Q Consensus       402 ~~~~m~----~~g~-------------------------~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~  451 (487)
                      ++.+..    ..|+                         .-|.+..-.+...|-...+++.|+..|.+....  .||- -
T Consensus       775 lmakALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~--d~d~GD  852 (913)
T KOG0495|consen  775 LMAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKK--DPDNGD  852 (913)
T ss_pred             HHHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHcc--CCccch
Confidence            654322    1222                         234555666667777788899999999987654  4544 3


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          452 TYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       452 ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      +|.-+..-+.++|.=++-.+++..-.+
T Consensus       853 ~wa~fykfel~hG~eed~kev~~~c~~  879 (913)
T KOG0495|consen  853 AWAWFYKFELRHGTEEDQKEVLKKCET  879 (913)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence            777788889999977777777666543

>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=98.97  E-value=3.2e-06  Score=82.73  Aligned_cols=288  Identities=14%  Similarity=0.150  Sum_probs=163.6

Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHH-HHHHHHHh-----
Q 011378          144 IFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYN-TILNGLCR-----  217 (487)
Q Consensus       144 ~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~-~li~~~~~-----  217 (487)
                      .+...|++++|++.++.-.. .+...........+.+.+.|+.++|..++..+.+.+  ||-..|- .+..+.+-     
T Consensus        13 il~e~g~~~~AL~~L~~~~~-~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g~~~~~~   89 (517)
T PF12569_consen   13 ILEEAGDYEEALEHLEKNEK-QILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALGLQLQLS   89 (517)
T ss_pred             HHHHCCCHHHHHHHHHhhhh-hCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHhhhcccc
Confidence            34455555555555544222 122222333444455555556666655555555543  3333332 22222211     


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH-HHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHH
Q 011378          218 AKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM-NKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANK  296 (487)
Q Consensus       218 ~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~-~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  296 (487)
                      ....+...++++++...-  |.......+.-.+.....+ ..+..++..+.++|+++   +|+.|-..|......+-..+
T Consensus        90 ~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K~~~i~~  164 (517)
T PF12569_consen   90 DEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPEKAAIIES  164 (517)
T ss_pred             cccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChhHHHHHHH
Confidence            123455556666554432  3322222222122221112 22233334445555543   45555555554444444444


Q ss_pred             HHHHHHhC--------------CCCCChh--hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcC
Q 011378          297 LWADMISR--------------KISPNYI--SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT-LVSCNTIIKGYCRSG  359 (487)
Q Consensus       297 ~~~~m~~~--------------~~~p~~~--t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~  359 (487)
                      ++......              .-.|+..  ++..+-..|-..|++++|+...+.-+.+  +|+ +..|..--+.+.+.|
T Consensus       165 l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G  242 (517)
T PF12569_consen  165 LVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAG  242 (517)
T ss_pred             HHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCC
Confidence            44443321              1234443  3455677788899999999999987765  455 556777788899999


Q ss_pred             ChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhh--------HHHHHHHHHhcCCh
Q 011378          360 DASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVIT--------YNVILTGFCRQGRM  431 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~--------~~~li~~~~~~g~~  431 (487)
                      ++.+|.+.++....... -|...-+.....+.+.|++++|.+++......+..|-...        ..-.-.+|.++|++
T Consensus       243 ~~~~Aa~~~~~Ar~LD~-~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~  321 (517)
T PF12569_consen  243 DLKEAAEAMDEARELDL-ADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDY  321 (517)
T ss_pred             CHHHHHHHHHHHHhCCh-hhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhH
Confidence            99999999998876543 3777888888889999999999999998876654443221        13344688899999


Q ss_pred             HHHHHHHHHHH
Q 011378          432 HDSELILWRMI  442 (487)
Q Consensus       432 ~~a~~~~~~m~  442 (487)
                      ..|.+-|....
T Consensus       322 ~~ALk~~~~v~  332 (517)
T PF12569_consen  322 GLALKRFHAVL  332 (517)
T ss_pred             HHHHHHHHHHH
Confidence            99977555543

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 [], [].

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

Probab=98.96  E-value=3.3e-05  Score=71.51  Aligned_cols=256  Identities=12%  Similarity=0.146  Sum_probs=161.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhcC
Q 011378          177 INGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGV--FPDFYTFTTLIHGHCKDG  254 (487)
Q Consensus       177 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~--~~~~~t~~~li~~~~~~g  254 (487)
                      ..++-.....+++..-.+.+...|++-+...-+-...+.....++++|+.+|++..++.-  .-|..+|+.++  |.+..
T Consensus       234 ~~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~L--Yv~~~  311 (559)
T KOG1155|consen  234 KKAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVL--YVKND  311 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHH--HHHhh
Confidence            345555566777777777777777766655555555556677888888888888877631  12566777776  34443


Q ss_pred             CHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHH
Q 011378          255 NMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN-YISYGILINGYCSMGHVTEAFRLW  333 (487)
Q Consensus       255 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~~~~a~~~~  333 (487)
                      ..+.+.-......-...+|  .|...+-+-|+-.++-++|...|+...+-  .|. ...|+.+-.=|....+...|..-+
T Consensus       312 ~skLs~LA~~v~~idKyR~--ETCCiIaNYYSlr~eHEKAv~YFkRALkL--Np~~~~aWTLmGHEyvEmKNt~AAi~sY  387 (559)
T KOG1155|consen  312 KSKLSYLAQNVSNIDKYRP--ETCCIIANYYSLRSEHEKAVMYFKRALKL--NPKYLSAWTLMGHEYVEMKNTHAAIESY  387 (559)
T ss_pred             hHHHHHHHHHHHHhccCCc--cceeeehhHHHHHHhHHHHHHHHHHHHhc--CcchhHHHHHhhHHHHHhcccHHHHHHH
Confidence            3222221111112233333  35555666667777777788877765533  343 345666666677777777777777


Q ss_pred             HHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCC
Q 011378          334 YEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLV  412 (487)
Q Consensus       334 ~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  412 (487)
                      +.-++-. +.|-..|-.|=++|.-.+...-|.-.|++...  .+| |...|.+|-.+|.+.++.++|++.+.+.-..| .
T Consensus       388 RrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-d  463 (559)
T KOG1155|consen  388 RRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALE--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-D  463 (559)
T ss_pred             HHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHh--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-c
Confidence            6654332 34556666777777777777777777776554  334 56677777777777777777777777766543 2


Q ss_pred             CCHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          413 PDVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       413 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      .+...+..|...|-+-++..+|.+.+.+-.
T Consensus       464 te~~~l~~LakLye~l~d~~eAa~~yek~v  493 (559)
T KOG1155|consen  464 TEGSALVRLAKLYEELKDLNEAAQYYEKYV  493 (559)
T ss_pred             cchHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            344667777777777777777776666544

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

Probab=98.95  E-value=2.9e-07  Score=88.43  Aligned_cols=277  Identities=15%  Similarity=0.103  Sum_probs=179.1

Q ss_pred             ChhHHHHHHHHHhhCCCCCCcc-chHHHHHHHHhcCChhhHHHHHHHHHHCC--CCCCHHHHHHHHHHHHccCChh-HHH
Q 011378           45 FLEEAFQLMNSMSGKGLKPGVF-TYNSLINGLCKKGRCDRAKEVLDEMLQMG--LSPDTATYNTLLVESCRKENMS-EAE  120 (487)
Q Consensus        45 ~~~~a~~~~~~m~~~~~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g--~~~~~~~~~~ll~~~~~~~~~~-~a~  120 (487)
                      +.++|..+|+....+  .+|+. +..-+-.+|...++++++.++|+...+..  ..-+..+|.++|..+-+.-.+. .|.
T Consensus       334 ~~~~A~~~~~klp~h--~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq  411 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH--HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQ  411 (638)
T ss_pred             HHHHHHHHHHhhHHh--cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHH
Confidence            457888888885554  34443 33445678888999999999999887542  1236778888888764432211 222


Q ss_pred             HHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011378          121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEK  199 (487)
Q Consensus       121 ~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  199 (487)
                      .+.+.+     +-.+.+|.++-++|+-.++.+.|++.|+...+.  .| ...+|+.+=.-+......+.|...|+.-   
T Consensus       412 ~Li~~~-----~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~A---  481 (638)
T KOG1126|consen  412 DLIDTD-----PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKA---  481 (638)
T ss_pred             HHHhhC-----CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhh---
Confidence            222222     234668999999999999999999999987763  45 4667777766677777778887777654   


Q ss_pred             CCcCChhhHHHH---HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCee
Q 011378          200 GCVMDVVTYNTI---LNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIV  276 (487)
Q Consensus       200 g~~~~~~~~~~l---i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~  276 (487)
                       +..|+..||+.   --.|.+.++++.|+-.|++..+-+ +-+.+....+...+.+.|+.|+|+++++....-.-+ |..
T Consensus       482 -l~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l  558 (638)
T KOG1126|consen  482 -LGVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPL  558 (638)
T ss_pred             -hcCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-Cch
Confidence             44677777764   455778888888888888776533 224555666667777888888888888766532211 222


Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISRKISPN-YISYGILINGYCSMGHVTEAFRLWYEMVG  338 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~  338 (487)
                      .--.....+...++.++|+..+++++.-  .|+ ...+..+...|-+.|+.+.|..-|..+.+
T Consensus       559 ~~~~~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  559 CKYHRASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             hHHHHHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            2122333444556667777766666432  333 34455566666666666666666655543

>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=98.95  E-value=4.2e-06  Score=81.93  Aligned_cols=289  Identities=18%  Similarity=0.220  Sum_probs=198.8

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCcCChhh-HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHh---
Q 011378          178 NGYCRNGFVLEALKMRDEMLEKGCVMDVVT-YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTF-TTLIHGHCK---  252 (487)
Q Consensus       178 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~-~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~-~~li~~~~~---  252 (487)
                      ..+...|+.++|++.++.-.  ...+|... .......+.+.|+.++|..+|..+.+++  |+-..| ..+..+..-   
T Consensus        12 ~il~e~g~~~~AL~~L~~~~--~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   12 SILEEAGDYEEALEHLEKNE--KQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhh--hhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHhhhcc
Confidence            44567899999999987633  33456554 4566688889999999999999999876  555554 444444422   


Q ss_pred             --cCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHH-HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHH
Q 011378          253 --DGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME-KANKLWADMISRKISPNYISYGILINGYCSMGHVTEA  329 (487)
Q Consensus       253 --~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~-~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a  329 (487)
                        ....+....+++.+...-  |.......+.-.+.....++ .+...+..+...|+++   +|+.|-..|.......-.
T Consensus        88 ~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K~~~i  162 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPEKAAII  162 (517)
T ss_pred             cccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChhHHHHH
Confidence              235778888888876543  33333333332233323343 3455556666777654   566666666666566666


Q ss_pred             HHHHHHHHhC----C----------CCCChhhH--HHHHHHHHhcCChHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHhc
Q 011378          330 FRLWYEMVGK----G----------IKPTLVSC--NTIIKGYCRSGDASKADEFLSKMVSEGVDPD-SISYNTLINGFVR  392 (487)
Q Consensus       330 ~~~~~~m~~~----~----------~~~~~~~~--~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~  392 (487)
                      ..++......    +          -.|....|  .-+-+.|...|+.++|.+.+++.++.  .|+ +..|..--..+-+
T Consensus       163 ~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh  240 (517)
T PF12569_consen  163 ESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKH  240 (517)
T ss_pred             HHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHH
Confidence            6666665432    1          12333334  45577788999999999999988864  465 4567777788889


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHH------H--HHHHHHHHhcC
Q 011378          393 EENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRST------Y--TTLINGHVSQN  464 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t------y--~~l~~~~~~~~  464 (487)
                      .|++++|.+.++...... .-|...-+-.+..+.++|++++|++++......+..|-...      |  ...-.+|.+.|
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 AGDLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQG  319 (517)
T ss_pred             CCCHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999887654 23777888888889999999999999988876665443221      1  23467999999


Q ss_pred             CHHHHHHHHHHHHH
Q 011378          465 NLKEAFRFHDEMLQ  478 (487)
Q Consensus       465 ~~~~a~~~~~~m~~  478 (487)
                      ++..|++.+....+
T Consensus       320 ~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  320 DYGLALKRFHAVLK  333 (517)
T ss_pred             hHHHHHHHHHHHHH
Confidence            99999998877654

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 [], [].

>PF12854 PPR_1: PPR repeat

Probab=98.92  E-value=1.4e-09  Score=63.32  Aligned_cols=32  Identities=38%  Similarity=0.855  Sum_probs=19.4

Q ss_pred             CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          410 GLVPDVITYNVILTGFCRQGRMHDSELILWRM  441 (487)
Q Consensus       410 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  441 (487)
                      |+.||..|||+||++||+.|++++|.++|++|
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            55566666666666666666666666666555

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.92  E-value=6.3e-07  Score=86.58  Aligned_cols=166  Identities=18%  Similarity=0.187  Sum_probs=102.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHh---C--C-CCCChh-hHHHHHHHHHhcCChHHHHHHHHHHHHC---CCCCC--
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVG---K--G-IKPTLV-SCNTIIKGYCRSGDASKADEFLSKMVSE---GVDPD--  379 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~---~--~-~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~p~--  379 (487)
                      +++.|-.+|.+.|++++|...++...+   +  | ..|.+. -++.+...|+..+++++|..+++...+.   -..++  
T Consensus       285 ~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~  364 (508)
T KOG1840|consen  285 TLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNV  364 (508)
T ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccch
Confidence            344444455555555555444443211   1  1 112222 2455556666777777777777654431   12222  


Q ss_pred             --hhhHHHHHHHHhccCCHHHHHHHHHHHH----hCCCCCCH---hhHHHHHHHHHhcCChHHHHHHHHHHHH----cCC
Q 011378          380 --SISYNTLINGFVREENMDKAFALVSKME----NQGLVPDV---ITYNVILTGFCRQGRMHDSELILWRMIE----KGL  446 (487)
Q Consensus       380 --~~~~~~li~~~~~~~~~~~a~~~~~~m~----~~g~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~  446 (487)
                        ..+++.|-..|.+.|++++|++++++..    +.+-+-+.   ..++-|-..|.+.+++++|.++|.+-..    .|.
T Consensus       365 ~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~  444 (508)
T KOG1840|consen  365 NLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGP  444 (508)
T ss_pred             HHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCC
Confidence              2468888888888888888888877553    22222222   3467777788888888888888877543    232


Q ss_pred             C-CCH-HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          447 N-PDR-STYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       447 ~-p~~-~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      . |+. .+|..|...|...|+++.|.++.+...
T Consensus       445 ~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  445 DHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             CCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            2 333 478888889999999999998887765

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

Probab=98.89  E-value=6.6e-05  Score=70.01  Aligned_cols=232  Identities=13%  Similarity=0.065  Sum_probs=159.7

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHH
Q 011378          217 RAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANK  296 (487)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  296 (487)
                      -.|+.-++..-|+...+..-.++. .|.-+-..|....+.++....|....+-.- -|..+|..=-..+.-.+++++|..
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp-~n~dvYyHRgQm~flL~q~e~A~a  415 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDLDP-ENPDVYYHRGQMRFLLQQYEEAIA  415 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhcCC-CCCchhHhHHHHHHHHHHHHHHHH
Confidence            357788888888888765433222 266666778899999999999987665321 144566555566666678889988


Q ss_pred             HHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCC
Q 011378          297 LWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEG  375 (487)
Q Consensus       297 ~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  375 (487)
                      =|.+.++-  .| +...|--+--+.-+.++++++...|++.+++ ++.....|+..-..+...++++.|.+.++..++..
T Consensus       416 DF~Kai~L--~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE  492 (606)
T KOG0547|consen  416 DFQKAISL--DPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELE  492 (606)
T ss_pred             HHHHHhhc--ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhc
Confidence            88776543  34 3344545555556788999999999998754 66677889999999999999999999999877532


Q ss_pred             -----CC--CChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 011378          376 -----VD--PDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKGLN  447 (487)
Q Consensus       376 -----~~--p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  447 (487)
                           +.  +.+.+--.++-.-.+ ++++.|.+++.+--+.  .| ....|..|...-.++|++++|..+|++-...   
T Consensus       493 ~~~~~~~v~~~plV~Ka~l~~qwk-~d~~~a~~Ll~KA~e~--Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~l---  566 (606)
T KOG0547|consen  493 PREHLIIVNAAPLVHKALLVLQWK-EDINQAENLLRKAIEL--DPKCEQAYETLAQFELQRGKIDEAIELFEKSAQL---  566 (606)
T ss_pred             cccccccccchhhhhhhHhhhchh-hhHHHHHHHHHHHHcc--CchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH---
Confidence                 21  222223333333333 8899999999877553  34 3356888888889999999999999885431   


Q ss_pred             CCHHHHHHHHHHHH
Q 011378          448 PDRSTYTTLINGHV  461 (487)
Q Consensus       448 p~~~ty~~l~~~~~  461 (487)
                        ..|-..++++|.
T Consensus       567 --Art~~E~~~a~s  578 (606)
T KOG0547|consen  567 --ARTESEMVHAYS  578 (606)
T ss_pred             --HHhHHHHHHHHH
Confidence              234455555544

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.87  E-value=2.3e-06  Score=82.82  Aligned_cols=129  Identities=20%  Similarity=0.207  Sum_probs=66.5

Q ss_pred             hHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CC--CC-
Q 011378          278 YNTLIDGFCKVGEMEKANKLWADMISR---KISPN----YISYGILINGYCSMGHVTEAFRLWYEMVGK----GI--KP-  343 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----~~--~~-  343 (487)
                      ++.+...++..+++++|..++....+.   -+.++    ..+++.|-..|...|++++|.++++..+..    +-  .+ 
T Consensus       328 l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~  407 (508)
T KOG1840|consen  328 LSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYG  407 (508)
T ss_pred             HHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChh
Confidence            344444455555555555555433221   11121    135566666666666666666666554321    11  11 


Q ss_pred             ChhhHHHHHHHHHhcCChHHHHHHHHHHHH----CCC-CCC-hhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          344 TLVSCNTIIKGYCRSGDASKADEFLSKMVS----EGV-DPD-SISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~-~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      .-..++-|-..|.+.++.+.|.++|.+...    -|. .|| ..+|..|...|-+.|++++|.++.+..
T Consensus       408 ~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~  476 (508)
T KOG1840|consen  408 VGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKV  476 (508)
T ss_pred             hhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            123455555566666666666666554332    121 122 346777777777777777777766544

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

Probab=98.87  E-value=1.7e-06  Score=83.23  Aligned_cols=196  Identities=17%  Similarity=0.112  Sum_probs=89.0

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHH
Q 011378          205 VVTYNTILNGLCRAKMLTEADDLFNEMLERGVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLID  283 (487)
Q Consensus       205 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~  283 (487)
                      +.+|.++-++|.-+++.+.|.+.|++..+.  .| ..++|+.+-+-+....++|.|...|+...    ..|...||+.  
T Consensus       421 PesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al----~~~~rhYnAw--  492 (638)
T KOG1126|consen  421 PESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKAL----GVDPRHYNAW--  492 (638)
T ss_pred             cHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhh----cCCchhhHHH--
Confidence            345555555555555555555555554432  23 33444444444444445555554443322    2333333332  


Q ss_pred             HHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCChH
Q 011378          284 GFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKP-TLVSCNTIIKGYCRSGDAS  362 (487)
Q Consensus       284 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~~~~~  362 (487)
                                                    -.|-..|.+.++++.|+-.|+....  +.| +.+....+-..+-+.|+.+
T Consensus       493 ------------------------------YGlG~vy~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d  540 (638)
T KOG1126|consen  493 ------------------------------YGLGTVYLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKD  540 (638)
T ss_pred             ------------------------------HhhhhheeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhh
Confidence                                          2233344444555555444443321  222 2233333444444555555


Q ss_pred             HHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHh-hHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          363 KADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVI-TYNVILTGFCRQGRMHDSELILWRM  441 (487)
Q Consensus       363 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~g~~~~a~~~~~~m  441 (487)
                      +|.+++++.....-+ |+..----...+...++.++|...++++++  +.|+.. .|-.+...|.+.|+.+.|..-|--+
T Consensus       541 ~AL~~~~~A~~ld~k-n~l~~~~~~~il~~~~~~~eal~~LEeLk~--~vP~es~v~~llgki~k~~~~~~~Al~~f~~A  617 (638)
T KOG1126|consen  541 KALQLYEKAIHLDPK-NPLCKYHRASILFSLGRYVEALQELEELKE--LVPQESSVFALLGKIYKRLGNTDLALLHFSWA  617 (638)
T ss_pred             HHHHHHHHHHhcCCC-CchhHHHHHHHHHhhcchHHHHHHHHHHHH--hCcchHHHHHHHHHHHHHHccchHHHHhhHHH
Confidence            555555554432211 111111112223345566666666666665  245443 3444444666666666665555544


Q ss_pred             HH
Q 011378          442 IE  443 (487)
Q Consensus       442 ~~  443 (487)
                      .+
T Consensus       618 ~~  619 (638)
T KOG1126|consen  618 LD  619 (638)
T ss_pred             hc
Confidence            33

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

Probab=98.86  E-value=2.8e-05  Score=78.29  Aligned_cols=42  Identities=24%  Similarity=0.242  Sum_probs=31.2

Q ss_pred             HhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhH
Q 011378            6 CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEE   48 (487)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~   48 (487)
                      -|..++.-...+++...+.|. .|..++|++.+.|...++-.+
T Consensus       849 EkRNRLklLlp~LE~~i~eG~-~d~a~hnAlaKIyIDSNNnPE  890 (1666)
T KOG0985|consen  849 EKRNRLKLLLPWLESLIQEGS-QDPATHNALAKIYIDSNNNPE  890 (1666)
T ss_pred             HhhhhHHHHHHHHHHHHhccC-cchHHHhhhhheeecCCCChH
Confidence            456667777778888888886 488888888888877665444

>PRK12370 invasion protein regulator; Provisional

Probab=98.86  E-value=3.1e-06  Score=85.40  Aligned_cols=178  Identities=12%  Similarity=0.040  Sum_probs=99.1

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC-eeehHHHHHHHHccCCHHHHHHHH
Q 011378          220 MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPD-IVTYNTLIDGFCKVGEMEKANKLW  298 (487)
Q Consensus       220 ~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~  298 (487)
                      ++++|...+++..+.. +-+...+..+-..+...|+.++|...|+...+..  |+ ...+..+-..+...|++++|...+
T Consensus       319 ~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~G~~~eAi~~~  395 (553)
T PRK12370        319 AMIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS--PISADIKYYYGWNLFMAGQLEEALQTI  395 (553)
T ss_pred             HHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4666777776666542 2245556666666666777777777776665442  32 334555666667777777777777


Q ss_pred             HHHHhCCCCCChh-hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCC
Q 011378          299 ADMISRKISPNYI-SYGILINGYCSMGHVTEAFRLWYEMVGKGIKP-TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGV  376 (487)
Q Consensus       299 ~~m~~~~~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  376 (487)
                      ++.....  |+.. .+..+...+...|++++|...+++..... .| +...+..+-.++...|+.++|...++++...  
T Consensus       396 ~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--  470 (553)
T PRK12370        396 NECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--  470 (553)
T ss_pred             HHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--
Confidence            6665432  3221 22223334555667777777776655432 23 2333445555666677777777777665432  


Q ss_pred             CCCh-hhHHHHHHHHhccCCHHHHHHHHHHHH
Q 011378          377 DPDS-ISYNTLINGFVREENMDKAFALVSKME  407 (487)
Q Consensus       377 ~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~  407 (487)
                      .|+. ...+.|-..|+..|  ++|...++++.
T Consensus       471 ~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll  500 (553)
T PRK12370        471 EITGLIAVNLLYAEYCQNS--ERALPTIREFL  500 (553)
T ss_pred             cchhHHHHHHHHHHHhccH--HHHHHHHHHHH
Confidence            2332 23344444555555  35666555554

>PF12854 PPR_1: PPR repeat

Probab=98.83  E-value=4.6e-09  Score=61.09  Aligned_cols=32  Identities=44%  Similarity=0.941  Sum_probs=20.4

Q ss_pred             CCCCChhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          375 GVDPDSISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       375 g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      |+.||..|||+||++|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            55666666666666666666666666666665

>PRK12370 invasion protein regulator; Provisional

Probab=98.79  E-value=4.7e-06  Score=84.04  Aligned_cols=261  Identities=13%  Similarity=0.029  Sum_probs=173.8

Q ss_pred             hhhHHHHHHHHHh-----cCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHH---------hcCCHHHHHHHHHHHHHC
Q 011378          205 VVTYNTILNGLCR-----AKMLTEADDLFNEMLERGVFPD-FYTFTTLIHGHC---------KDGNMNKALNLFDIMTQK  269 (487)
Q Consensus       205 ~~~~~~li~~~~~-----~~~~~~a~~~~~~m~~~~~~~~-~~t~~~li~~~~---------~~g~~~~a~~~~~~m~~~  269 (487)
                      ...|...+.+-..     .+.++.|...|++..+.  .|+ ...|..+-.++.         ..++.++|...++...+.
T Consensus       256 ~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~l--dP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l  333 (553)
T PRK12370        256 IDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNM--SPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL  333 (553)
T ss_pred             hHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc
Confidence            3445455554321     23467888999888764  354 344544444333         234578999999877654


Q ss_pred             CCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh-hh
Q 011378          270 SIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL-VS  347 (487)
Q Consensus       270 ~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~  347 (487)
                        .| +...+..+-..+...|++++|...|++..+.. +.+...+..+-..+...|++++|...++...+.  .|+. ..
T Consensus       334 --dP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l--~P~~~~~  408 (553)
T PRK12370        334 --DHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKL--DPTRAAA  408 (553)
T ss_pred             --CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCChhh
Confidence              34 44567777777888999999999999887653 223556778888999999999999999998765  3443 23


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHh-hHHHHHHHH
Q 011378          348 CNTIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVI-TYNVILTGF  425 (487)
Q Consensus       348 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~  425 (487)
                      +..+...+...|+.++|...+++..+.. .| +...+..+-.++...|+.++|...+.++...  .|+.. ..+.+...|
T Consensus       409 ~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~  485 (553)
T PRK12370        409 GITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEY  485 (553)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHH
Confidence            3334445667899999999999887543 24 3445677778888999999999999887543  34433 345555567


Q ss_pred             HhcCChHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          426 CRQGRMHDSELILWRMIEK-GLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG  480 (487)
Q Consensus       426 ~~~g~~~~a~~~~~~m~~~-g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g  480 (487)
                      .+.|  +.+...++.+.+. +-.|.-.-+..+  .|.-.|+.+.+... +++.+.|
T Consensus       486 ~~~g--~~a~~~l~~ll~~~~~~~~~~~~~~~--~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        486 CQNS--ERALPTIREFLESEQRIDNNPGLLPL--VLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             hccH--HHHHHHHHHHHHHhhHhhcCchHHHH--HHHHHhhhHHHHHH-HHhhccc
Confidence            7777  5787777777642 223333333333  44455777777666 7776654

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

Probab=98.77  E-value=0.00024  Score=68.79  Aligned_cols=392  Identities=14%  Similarity=0.064  Sum_probs=299.0

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh
Q 011378           37 INAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENM  116 (487)
Q Consensus        37 l~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  116 (487)
                      =++.+...+.+.|.-+++...+.  -|.+   .-|.-++++..-|+.|.++++...+. ++-+...|.+--..--..|+.
T Consensus       383 WKaAVelE~~~darilL~rAvec--cp~s---~dLwlAlarLetYenAkkvLNkaRe~-iptd~~IWitaa~LEE~ngn~  456 (913)
T KOG0495|consen  383 WKAAVELEEPEDARILLERAVEC--CPQS---MDLWLALARLETYENAKKVLNKAREI-IPTDREIWITAAKLEEANGNV  456 (913)
T ss_pred             HHHHHhccChHHHHHHHHHHHHh--ccch---HHHHHHHHHHHHHHHHHHHHHHHHhh-CCCChhHHHHHHHHHHhcCCH
Confidence            34455566777788777776552  3332   23556788888999999999988753 555677887766666778999


Q ss_pred             hHHHHHHHH----HHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC--hhhHHHHHHHHHhcCCHHHHH
Q 011378          117 SEAEEIFCE----MSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD--NVLYTIIINGYCRNGFVLEAL  190 (487)
Q Consensus       117 ~~a~~~~~~----m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~~~~~~a~  190 (487)
                      +.+.+++++    +...|+..+...|-.=...|-+.|..-.+-.+.......|++-.  ..||..--+.|.+.+.++-+.
T Consensus       457 ~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~car  536 (913)
T KOG0495|consen  457 DMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECAR  536 (913)
T ss_pred             HHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHH
Confidence            999998764    56789999999998888899999998888878777776666543  458999999999999999999


Q ss_pred             HHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          191 KMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKS  270 (487)
Q Consensus       191 ~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~  270 (487)
                      .++....+- ++-+...|......=-..|..+..+.+|++....- +-....|--....+-..|++..|..++...-+..
T Consensus       537 AVya~alqv-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~  614 (913)
T KOG0495|consen  537 AVYAHALQV-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEAN  614 (913)
T ss_pred             HHHHHHHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhC
Confidence            998877653 34456678877777778899999999999998752 2233455555567778899999999998877654


Q ss_pred             CCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHH
Q 011378          271 IKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNT  350 (487)
Q Consensus       271 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  350 (487)
                      -. +..+|-+-++--..+.+++.|..+|.+...  ..|+...|.--+..---.+..++|.+++++-.+. ++--...|..
T Consensus       615 pn-seeiwlaavKle~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~-fp~f~Kl~lm  690 (913)
T KOG0495|consen  615 PN-SEEIWLAAVKLEFENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEALRLLEEALKS-FPDFHKLWLM  690 (913)
T ss_pred             CC-cHHHHHHHHHHhhccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh-CCchHHHHHH
Confidence            33 556788888888999999999999987654  5677777766666666678999999999887653 3333456777


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHCCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcC
Q 011378          351 IIKGYCRSGDASKADEFLSKMVSEGVDPDSI-SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG  429 (487)
Q Consensus       351 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  429 (487)
                      +=+.+-+.++++.|.+.|..  .....|+.. .|-.|...=-+.|.+-+|..++++-...+ .-+...|-..|..=.+.|
T Consensus       691 lGQi~e~~~~ie~aR~aY~~--G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~g  767 (913)
T KOG0495|consen  691 LGQIEEQMENIEMAREAYLQ--GTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAG  767 (913)
T ss_pred             HhHHHHHHHHHHHHHHHHHh--ccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcC
Confidence            77888899999999888763  223456654 55555555567789999999999887654 346788999999999999


Q ss_pred             ChHHHHHHHHHHHH
Q 011378          430 RMHDSELILWRMIE  443 (487)
Q Consensus       430 ~~~~a~~~~~~m~~  443 (487)
                      ..+.|+.++.+.++
T Consensus       768 n~~~a~~lmakALQ  781 (913)
T KOG0495|consen  768 NKEQAELLMAKALQ  781 (913)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999988777654

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=98.77  E-value=0.00024  Score=68.73  Aligned_cols=131  Identities=15%  Similarity=0.206  Sum_probs=79.9

Q ss_pred             CCChhhH--HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhH
Q 011378          307 SPNYISY--GILINGYCSMGHVTEAFRLWYEMVGKGIKPTLV-SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISY  383 (487)
Q Consensus       307 ~p~~~t~--~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~  383 (487)
                      +|+...|  -.++..+-..|+++.|....+.-+.+  +|+.. -|..=-+.+...|++++|..++++..+... ||...-
T Consensus       366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~-aDR~IN  442 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT-ADRAIN  442 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc-hhHHHH
Confidence            4444433  34666777888888888887766533  55543 344444667788888888888887765432 555554


Q ss_pred             HHHHHHHhccCCHHHHHHHHHHHHhCCCCC-----CHh-hHHHH--HHHHHhcCChHHHHHHHHH
Q 011378          384 NTLINGFVREENMDKAFALVSKMENQGLVP-----DVI-TYNVI--LTGFCRQGRMHDSELILWR  440 (487)
Q Consensus       384 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-----~~~-~~~~l--i~~~~~~g~~~~a~~~~~~  440 (487)
                      +--.....++.+.++|.++.......|...     ++. .|=.+  -.+|.++|++.+|.+=|..
T Consensus       443 sKcAKYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkfh~  507 (700)
T KOG1156|consen  443 SKCAKYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKFHE  507 (700)
T ss_pred             HHHHHHHHHccccHHHHHHHHHhhhcccchhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHHhh
Confidence            455556677888888888888777665310     011 11111  1366677777666544333

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=98.72  E-value=0.00032  Score=67.85  Aligned_cols=420  Identities=18%  Similarity=0.173  Sum_probs=260.8

Q ss_pred             HHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHH
Q 011378           40 YCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEA  119 (487)
Q Consensus        40 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  119 (487)
                      +...|+.++|......-.... .-+.+.|..+--.+-...++++|.+.+......+ +-|...|-.+--.-++.++++..
T Consensus        51 L~~lg~~~ea~~~vr~glr~d-~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~  128 (700)
T KOG1156|consen   51 LNCLGKKEEAYELVRLGLRND-LKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGY  128 (700)
T ss_pred             hhcccchHHHHHHHHHHhccC-cccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhH
Confidence            456788999998876544322 2345667765555555778999999999877644 23566777766666777888888


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCC-CCCChhhHHHHHHH------HHhcCCHHHHHHH
Q 011378          120 EEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAG-LVPDNVLYTIIING------YCRNGFVLEALKM  192 (487)
Q Consensus       120 ~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~~~~~~~~~ll~~------~~~~~~~~~a~~~  192 (487)
                      ...-.++.+... -.-..|..+..++--.|+...|..+.++..+.. -.|+...|.-....      ..+.|..++|++.
T Consensus       129 ~~tr~~LLql~~-~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~  207 (700)
T KOG1156|consen  129 LETRNQLLQLRP-SQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEH  207 (700)
T ss_pred             HHHHHHHHHhhh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHH
Confidence            877777765421 134567788888888999999999999998754 35666655544433      3456777777666


Q ss_pred             HHHHHHcCCcCChhhH-HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHHhcCCHHHHH-HHHHHHHHC
Q 011378          193 RDEMLEKGCVMDVVTY-NTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLI-HGHCKDGNMNKAL-NLFDIMTQK  269 (487)
Q Consensus       193 ~~~m~~~g~~~~~~~~-~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li-~~~~~~g~~~~a~-~~~~~m~~~  269 (487)
                      +..-+..  ..|-..+ .+--..+.+.+++++|..++..+..++  ||-.-|.-.+ .++++-.+.-+++ .+|....+.
T Consensus       208 L~~~e~~--i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rn--Pdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~  283 (700)
T KOG1156|consen  208 LLDNEKQ--IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERN--PDNLDYYEGLEKALGKIKDMLEALKALYAILSEK  283 (700)
T ss_pred             HHhhhhH--HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhC--chhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhc
Confidence            5443221  1222222 233456778899999999999998764  6666555544 4444343433333 666655442


Q ss_pred             ---CCCCCeeehHHHHHHHHccCCH-HHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH----hCC-
Q 011378          270 ---SIKPDIVTYNTLIDGFCKVGEM-EKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMV----GKG-  340 (487)
Q Consensus       270 ---~~~~~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~----~~~-  340 (487)
                         ...|-....+.     .....+ +...++++.+.+.|+++-   +..+..-|-.....+-..++.-.+.    ..| 
T Consensus       284 y~r~e~p~Rlplsv-----l~~eel~~~vdkyL~~~l~Kg~p~v---f~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~  355 (700)
T KOG1156|consen  284 YPRHECPRRLPLSV-----LNGEELKEIVDKYLRPLLSKGVPSV---FKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGM  355 (700)
T ss_pred             CcccccchhccHHH-----hCcchhHHHHHHHHHHHhhcCCCch---hhhhHHHHhchhHhHHHHHHHHHHHhhcccccC
Confidence               22222111111     111233 334555666667776653   3333333322222221122222221    111 


Q ss_pred             ---------CCCChhhHH--HHHHHHHhcCChHHHHHHHHHHHHCCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          341 ---------IKPTLVSCN--TIIKGYCRSGDASKADEFLSKMVSEGVDPDSI-SYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       341 ---------~~~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                               -+|....|+  -+.+.|-+.|+++.|...++..+.  ..|+.+ .|-.=-..+.+.|+++.|...+++-.+
T Consensus       356 f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AId--HTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~e  433 (700)
T KOG1156|consen  356 FNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAID--HTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQE  433 (700)
T ss_pred             CCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc--cCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Confidence                     144544444  477889999999999999998774  456643 444444667889999999999998876


Q ss_pred             CCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC--CCHHHHHHH------HHHHHhcCCHHHHHHHHHHHH
Q 011378          409 QGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLN--PDRSTYTTL------INGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       409 ~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~--p~~~ty~~l------~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      .. .||+..-+--.....++.+.++|++++......|..  -+..--.+|      -.+|.+.|++..|++=++...
T Consensus       434 lD-~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkfh~i~  509 (700)
T KOG1156|consen  434 LD-TADRAINSKCAKYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKFHEIE  509 (700)
T ss_pred             cc-chhHHHHHHHHHHHHHccccHHHHHHHHHhhhcccchhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHHhhHH
Confidence            54 467766556677778999999999999888877651  122111111      357888888888887766654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.70  E-value=0.00019  Score=64.23  Aligned_cols=188  Identities=14%  Similarity=0.121  Sum_probs=108.1

Q ss_pred             HHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH-----HHhcCCHHHHHHHHHHHHhCCCCCChh-hHHHHHHHHHh
Q 011378          284 GFCKVGEMEKANKLWADMISRKISPNYISYGILING-----YCSMGHVTEAFRLWYEMVGKGIKPTLV-SCNTIIKGYCR  357 (487)
Q Consensus       284 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~-----~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~li~~~~~  357 (487)
                      -|.+.+++.+|..+.++..  ...|-....-.++.+     .....++..|.+.|...-.++.+.|.. --.++-+.+.-
T Consensus       294 YyL~q~dVqeA~~L~Kdl~--PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL  371 (557)
T KOG3785|consen  294 YYLNQNDVQEAISLCKDLD--PTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFL  371 (557)
T ss_pred             eecccccHHHHHHHHhhcC--CCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHH
Confidence            3677778888877776542  112222222222111     112234666777776665666554432 23344555555


Q ss_pred             cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH-HHHhcCChHHHHH
Q 011378          358 SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILT-GFCRQGRMHDSEL  436 (487)
Q Consensus       358 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~-~~~~~g~~~~a~~  436 (487)
                      ..++++..-.++...+-=..-|.+.|| +..+++..|++.+|+++|-......++ |..+|.+++. .|.++|+.+.|+.
T Consensus       372 ~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~  449 (557)
T KOG3785|consen  372 SFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWD  449 (557)
T ss_pred             HHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHH
Confidence            566777766666666544445555554 567788888888888888766544433 4456655554 5678888888877


Q ss_pred             HHHHHHHcCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          437 ILWRMIEKGLNPDRS-TYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       437 ~~~~m~~~g~~p~~~-ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      ++-++-.   ..++- ....+-+-|-..+.+--|-+-|.++..
T Consensus       450 ~~lk~~t---~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~  489 (557)
T KOG3785|consen  450 MMLKTNT---PSERFSLLQLIANDCYKANEFYYAAKAFDELEI  489 (557)
T ss_pred             HHHhcCC---chhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHc
Confidence            6655422   11222 233334556667777777777777653

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

Probab=98.69  E-value=0.00027  Score=66.10  Aligned_cols=216  Identities=15%  Similarity=0.152  Sum_probs=145.8

Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCC-CCCChhhHHHHHHHHHhcCCHHHH
Q 011378          251 CKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRK-ISPNYISYGILINGYCSMGHVTEA  329 (487)
Q Consensus       251 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~~~~~~~~~~a  329 (487)
                      .-.|+...|..-|+...+....++. .|--+-..|....+.++..+.|.+..+-. -.||  +|.-=-....-.+++++|
T Consensus       337 fL~g~~~~a~~d~~~~I~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~d--vYyHRgQm~flL~q~e~A  413 (606)
T KOG0547|consen  337 FLKGDSLGAQEDFDAAIKLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDLDPENPD--VYYHRGQMRFLLQQYEEA  413 (606)
T ss_pred             hhcCCchhhhhhHHHHHhcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCc--hhHhHHHHHHHHHHHHHH
Confidence            3456777777777766654333322 25556667888888888888888765432 2233  444434444556778888


Q ss_pred             HHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          330 FRLWYEMVGKGIKPT-LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       330 ~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      ..-|+.-+.  +.|+ +..|--+--+.-|.+.++++...|++.++ .++--+..|+..-..+.-.+++++|.+.++.-.+
T Consensus       414 ~aDF~Kai~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kk-kFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~  490 (606)
T KOG0547|consen  414 IADFQKAIS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKK-KFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIE  490 (606)
T ss_pred             HHHHHHHhh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHh
Confidence            888877653  3342 33444444444578899999999999876 4555567888888999999999999999987764


Q ss_pred             CCCCCC---------HhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          409 QGLVPD---------VITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       409 ~g~~p~---------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      .  .|+         +...-.++..- =.+++..|.+++.+..+.  .|. ...|..|-..-+++|+.++|+++|++-.
T Consensus       491 L--E~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~--Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  491 L--EPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIEL--DPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             h--ccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHcc--CchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            2  333         22222232222 338889999988887553  443 4589999999999999999999998753

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

Probab=98.63  E-value=0.00042  Score=66.13  Aligned_cols=57  Identities=11%  Similarity=-0.041  Sum_probs=27.3

Q ss_pred             HHHHHhccCCHHHHHHHHHHHHhCCCC-------C-CHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          386 LINGFVREENMDKAFALVSKMENQGLV-------P-DVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       386 li~~~~~~~~~~~a~~~~~~m~~~g~~-------p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      ...+++..|+.+.|..+++.+....-.       . .+..--...-++.+.|+.++|..++....
T Consensus       270 ~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al  334 (355)
T cd05804         270 AALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVR  334 (355)
T ss_pred             HHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            444555666666666666665432111       0 01111111123346666666666666544

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.

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

Probab=98.61  E-value=0.00071  Score=65.49  Aligned_cols=219  Identities=11%  Similarity=0.167  Sum_probs=121.5

Q ss_pred             cCCHHHHHHHHHHHHHCCCCCC------eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC---hhhHHHHHHHHHhc
Q 011378          253 DGNMNKALNLFDIMTQKSIKPD------IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN---YISYGILINGYCSM  323 (487)
Q Consensus       253 ~g~~~~a~~~~~~m~~~~~~~~------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~---~~t~~~li~~~~~~  323 (487)
                      .|+..+-..+|.+..+. +.|-      ...|..+-+.|-..|+++.|..+|.+...-..+.-   ..+|..-...=.+.
T Consensus       360 e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh  438 (835)
T KOG2047|consen  360 EGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRH  438 (835)
T ss_pred             cCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhh
Confidence            45556666666555432 2221      12466677777777888888888776554322111   12333333333455


Q ss_pred             CCHHHHHHHHHHHHh-----------CCC------CCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChh--hHH
Q 011378          324 GHVTEAFRLWYEMVG-----------KGI------KPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSI--SYN  384 (487)
Q Consensus       324 ~~~~~a~~~~~~m~~-----------~~~------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~--~~~  384 (487)
                      .+++.|+++.+.-..           .+.      ..+...|...++---..|-++....+++.+++..+.....  .|.
T Consensus       439 ~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyA  518 (835)
T KOG2047|consen  439 ENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYA  518 (835)
T ss_pred             hhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            566677766654321           111      1223456566666666788888888888888776543222  333


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHh---cCChHHHHHHHHHHHHcCCCCCHHHHHHHH--H
Q 011378          385 TLINGFVREENMDKAFALVSKMENQGLVPDV-ITYNVILTGFCR---QGRMHDSELILWRMIEKGLNPDRSTYTTLI--N  458 (487)
Q Consensus       385 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~---~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~--~  458 (487)
                      .++.   ....++++.+.+++-...---|++ ..||..+..|.+   .-+++.|+.+|++.++ |..|...-+--|+  .
T Consensus       519 mfLE---eh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~  594 (835)
T KOG2047|consen  519 MFLE---EHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAK  594 (835)
T ss_pred             HHHH---hhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHH
Confidence            3332   233466777666643222112444 346666665543   3367888889998887 6656544333232  2


Q ss_pred             HHHhcCCHHHHHHHHHHH
Q 011378          459 GHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       459 ~~~~~~~~~~a~~~~~~m  476 (487)
                      .--+.|....|++++++-
T Consensus       595 lEEe~GLar~amsiyera  612 (835)
T KOG2047|consen  595 LEEEHGLARHAMSIYERA  612 (835)
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            223457788888888873

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

Probab=98.60  E-value=7.6e-06  Score=72.17  Aligned_cols=234  Identities=15%  Similarity=0.043  Sum_probs=163.6

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeee-hHHH
Q 011378          203 MDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVT-YNTL  281 (487)
Q Consensus       203 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~-~~~l  281 (487)
                      .|+.--+-+-.+|.+.|.+.+|++.|+...+.  .|-+.||..|-.+|.+-..+..|+.+|..-...  .|-.+| ..-+
T Consensus       221 ~dwwWk~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~  296 (478)
T KOG1129|consen  221 LDWWWKQQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQ  296 (478)
T ss_pred             HhHHHHHHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhh
Confidence            34444466778888999999999988887765  455668888888899999999998888765432  233333 3445


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCh
Q 011378          282 IDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA  361 (487)
Q Consensus       282 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~  361 (487)
                      .+.+-..++.++|.++++...+.. +.++....++-.+|.-.++.+-|++.++.+.+.|+. +...|+.+--+|.-.+++
T Consensus       297 ARi~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~  374 (478)
T KOG1129|consen  297 ARIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQI  374 (478)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcch
Confidence            556666778888888888766542 345666666777777778888888888888888854 445566666666677888


Q ss_pred             HHHHHHHHHHHHCCCCCChh--hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHH
Q 011378          362 SKADEFLSKMVSEGVDPDSI--SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILW  439 (487)
Q Consensus       362 ~~a~~~~~~m~~~g~~p~~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  439 (487)
                      +.+...|+.....-..|+..  +|-.|-...+..|++..|.+.|.--.... .-....+|.|...-.+.|++++|..++.
T Consensus       375 D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~  453 (478)
T KOG1129|consen  375 DLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLN  453 (478)
T ss_pred             hhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHH
Confidence            88888877766554444432  45555555667788888888876554322 2234678888888888888888888887


Q ss_pred             HHHH
Q 011378          440 RMIE  443 (487)
Q Consensus       440 ~m~~  443 (487)
                      ....
T Consensus       454 ~A~s  457 (478)
T KOG1129|consen  454 AAKS  457 (478)
T ss_pred             Hhhh
Confidence            7644

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.59  E-value=0.00031  Score=68.82  Aligned_cols=193  Identities=18%  Similarity=0.251  Sum_probs=134.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCH
Q 011378          247 IHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHV  326 (487)
Q Consensus       247 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~  326 (487)
                      |.+......+.+|+.+++.+......  ..-|.-+.+.|+..|+++.|+++|.+-         ..++--|..|.+.|++
T Consensus       739 ieaai~akew~kai~ildniqdqk~~--s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQKTA--SGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhccc--cccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccH
Confidence            34455566777888888776654332  235777889999999999999999753         2456778899999999


Q ss_pred             HHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          327 TEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       327 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      .+|+++-.+.  .|-+..+..|-+--.-+-..|++.+|++++-...    .||..     |..|-+.|..++..++.++-
T Consensus       808 ~da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~~a-----iqmydk~~~~ddmirlv~k~  876 (1636)
T KOG3616|consen  808 EDAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPDKA-----IQMYDKHGLDDDMIRLVEKH  876 (1636)
T ss_pred             HHHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhheeEEcc----CchHH-----HHHHHhhCcchHHHHHHHHh
Confidence            9999987665  4445555666666666777888888888775433    26643     77888999999888887764


Q ss_pred             HhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 011378          407 ENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFH  473 (487)
Q Consensus       407 ~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~  473 (487)
                      ....+   ..|...+..-+-..|++..|+.-|-+..         -|..-+++|-.++.|++|.++-
T Consensus       877 h~d~l---~dt~~~f~~e~e~~g~lkaae~~flea~---------d~kaavnmyk~s~lw~dayria  931 (1636)
T KOG3616|consen  877 HGDHL---HDTHKHFAKELEAEGDLKAAEEHFLEAG---------DFKAAVNMYKASELWEDAYRIA  931 (1636)
T ss_pred             Chhhh---hHHHHHHHHHHHhccChhHHHHHHHhhh---------hHHHHHHHhhhhhhHHHHHHHH
Confidence            32211   2345556667777888888886665432         3456677777777787777764

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

Probab=98.59  E-value=2.6e-06  Score=77.52  Aligned_cols=222  Identities=17%  Similarity=0.200  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHH-HHH
Q 011378          241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGIL-ING  319 (487)
Q Consensus       241 ~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~l-i~~  319 (487)
                      ....-+.+++...|..+.++.   ..... -.|.......+...+....+-+.+..-+.+.......++-.++..+ -..
T Consensus        36 e~~~~~~Rs~iAlg~~~~vl~---ei~~~-~~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i  111 (290)
T PF04733_consen   36 ERDFYQYRSYIALGQYDSVLS---EIKKS-SSPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATI  111 (290)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHH---HS-TT-SSCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChhHHHH---HhccC-CChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHH
Confidence            344455566666666554432   22222 2444444434433333323344444433333222222222222222 223


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc----cCC
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR----EEN  395 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~  395 (487)
                      +...|++++|++++..    +  .+.......+..|.+.++.+.|.+.++.|.+.  ..|. +-..|..+|+.    .++
T Consensus       112 ~~~~~~~~~AL~~l~~----~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~eD~-~l~qLa~awv~l~~g~e~  182 (290)
T PF04733_consen  112 LFHEGDYEEALKLLHK----G--GSLELLALAVQILLKMNRPDLAEKELKNMQQI--DEDS-ILTQLAEAWVNLATGGEK  182 (290)
T ss_dssp             HCCCCHHHHHHCCCTT----T--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--SCCH-HHHHHHHHHHHHHHTTTC
T ss_pred             HHHcCCHHHHHHHHHc----c--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcH-HHHHHHHHHHHHHhCchh
Confidence            4445777777776542    1  34555556677777777777777777777643  2332 33334444432    235


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCH-HHHHHHH
Q 011378          396 MDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNL-KEAFRFH  473 (487)
Q Consensus       396 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~-~~a~~~~  473 (487)
                      +.+|..+|+++.+. ..+++.+.|.+..++...|++++|+.++.+....  .| +..|...++-.....|+. +.+.+++
T Consensus       183 ~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~--~~~~~d~LaNliv~~~~~gk~~~~~~~~l  259 (290)
T PF04733_consen  183 YQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEK--DPNDPDTLANLIVCSLHLGKPTEAAERYL  259 (290)
T ss_dssp             CCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             HHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--ccCCHHHHHHHHHHHHHhCCChhHHHHHH
Confidence            77777777776553 4566777777777777777777777777775432  23 334555566666666665 5566666


Q ss_pred             HHHHH
Q 011378          474 DEMLQ  478 (487)
Q Consensus       474 ~~m~~  478 (487)
                      +++.+
T Consensus       260 ~qL~~  264 (290)
T PF04733_consen  260 SQLKQ  264 (290)
T ss_dssp             HHCHH
T ss_pred             HHHHH
Confidence            66653

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.57  E-value=0.0011  Score=71.89  Aligned_cols=336  Identities=10%  Similarity=0.039  Sum_probs=202.2

Q ss_pred             HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC------CCChh--hHHHHHHHHH
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGL------VPDNV--LYTIIINGYC  181 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~------~~~~~--~~~~ll~~~~  181 (487)
                      ....|+++.+...++.+.......+..........+...|+++++..++......--      .+...  ....+-..+.
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            334567777766666553221111222223344555678899999988887654210      11111  1122223455


Q ss_pred             hcCCHHHHHHHHHHHHHcCCcCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CCCHHHHHHHHHHHHh
Q 011378          182 RNGFVLEALKMRDEMLEKGCVMDV----VTYNTILNGLCRAKMLTEADDLFNEMLER----GV-FPDFYTFTTLIHGHCK  252 (487)
Q Consensus       182 ~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~-~~~~~t~~~li~~~~~  252 (487)
                      ..|+++++...+++..+.--..+.    ...+.+...+...|+++.|...+.+....    |- .+...++..+-..+..
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            788999999988877653111121    23455666677899999999999887642    11 1112345566677888


Q ss_pred             cCCHHHHHHHHHHHHH----CCCCC---CeeehHHHHHHHHccCCHHHHHHHHHHHHhC--CCCC--ChhhHHHHHHHHH
Q 011378          253 DGNMNKALNLFDIMTQ----KSIKP---DIVTYNTLIDGFCKVGEMEKANKLWADMISR--KISP--NYISYGILINGYC  321 (487)
Q Consensus       253 ~g~~~~a~~~~~~m~~----~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--~~~p--~~~t~~~li~~~~  321 (487)
                      .|+++.|...++....    .+...   ....+..+-..+...|++++|...+.+....  ...+  ....+..+.....
T Consensus       544 ~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~  623 (903)
T PRK04841        544 QGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISL  623 (903)
T ss_pred             CCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHH
Confidence            9999999998876543    22211   1122344455667779999999888876432  1112  2334455666778


Q ss_pred             hcCCHHHHHHHHHHHHhC--CCCCChh--hH--HHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh---hhHHHHHHHHhc
Q 011378          322 SMGHVTEAFRLWYEMVGK--GIKPTLV--SC--NTIIKGYCRSGDASKADEFLSKMVSEGVDPDS---ISYNTLINGFVR  392 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~--~~~~~~~--~~--~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~---~~~~~li~~~~~  392 (487)
                      ..|+.++|...+......  .......  ..  ...+..+...|+.+.|.+.+............   ..+..+..++..
T Consensus       624 ~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~  703 (903)
T PRK04841        624 ARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQIL  703 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHH
Confidence            899999999988876432  1111111  10  11224445678999998888765432211111   113456677888


Q ss_pred             cCCHHHHHHHHHHHHh----CCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011378          393 EENMDKAFALVSKMEN----QGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIEKG  445 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~----~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  445 (487)
                      .|+.++|...+++...    .|..++ ..+...+-.++.+.|+.++|...+.+..+..
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            9999999998887643    243332 2456666778889999999999999987543

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

Probab=98.56  E-value=0.00097  Score=64.60  Aligned_cols=452  Identities=13%  Similarity=0.133  Sum_probs=262.2

Q ss_pred             hhhHHhcCChhhHHHHHHHHHhCC------CCCChhhHHHHHHHHHhcCChhHHH---HHHHHHhhCCCCCCc--cchHH
Q 011378            2 VNALCKDHKIDSAKMFLCEMEQKG------VYPDTVTYNTLINAYCREGFLEEAF---QLMNSMSGKGLKPGV--FTYNS   70 (487)
Q Consensus         2 i~~~~~~~~~~~a~~~~~~~~~~g------~~p~~~~~~~ll~~~~~~~~~~~a~---~~~~~m~~~~~~p~~--~~~~~   70 (487)
                      |..+++.++.+.|.+.++.+....      -+.+--.|+.+-...++.-+.-..+   .++..+.  +.-+|.  ..|++
T Consensus       176 ie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi--~rftDq~g~Lw~S  253 (835)
T KOG2047|consen  176 IEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGI--RRFTDQLGFLWCS  253 (835)
T ss_pred             HHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhc--ccCcHHHHHHHHH
Confidence            567889999999999888765431      2334455666655555554433322   2333332  223453  56899


Q ss_pred             HHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc----------------C------ChhHHHHHHHHHHH
Q 011378           71 LINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRK----------------E------NMSEAEEIFCEMSR  128 (487)
Q Consensus        71 li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~----------------~------~~~~a~~~~~~m~~  128 (487)
                      |-+-|.+.|.++.|..++++-.+.-  .+..-|+.+...|+..                +      +++....-|+.+.+
T Consensus       254 LAdYYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~  331 (835)
T KOG2047|consen  254 LADYYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMN  331 (835)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHh
Confidence            9999999999999999999876542  2333334444333322                1      12222233444333


Q ss_pred             CCC-----------CCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC------hhhHHHHHHHHHhcCCHHHHHH
Q 011378          129 RGV-----------APDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD------NVLYTIIINGYCRNGFVLEALK  191 (487)
Q Consensus       129 ~g~-----------~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~------~~~~~~ll~~~~~~~~~~~a~~  191 (487)
                      ++-           .-++.+|..-+..  ..|+..+....|.+..+. +.|.      ...|..+-+.|-++|+++.|..
T Consensus       332 rr~~~lNsVlLRQn~~nV~eW~kRV~l--~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRv  408 (835)
T KOG2047|consen  332 RRPLLLNSVLLRQNPHNVEEWHKRVKL--YEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARV  408 (835)
T ss_pred             ccchHHHHHHHhcCCccHHHHHhhhhh--hcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHH
Confidence            210           1122333333222  245566666677666542 2332      2368888888999999999999


Q ss_pred             HHHHHHHcCCcCC---hhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----------CCCC-------CHHHHHHHHHHHH
Q 011378          192 MRDEMLEKGCVMD---VVTYNTILNGLCRAKMLTEADDLFNEMLER----------GVFP-------DFYTFTTLIHGHC  251 (487)
Q Consensus       192 ~~~~m~~~g~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----------~~~~-------~~~t~~~li~~~~  251 (487)
                      +|++-.+..++-=   ..+|.....+=.+..+++.|.++.+....-          |-.|       +...|+-.++.--
T Consensus       409 ifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleE  488 (835)
T KOG2047|consen  409 IFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEE  488 (835)
T ss_pred             HHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHH
Confidence            9998776544321   234555555556677788888877665421          1111       2234555555555


Q ss_pred             hcCCHHHHHHHHHHHHHCCC-CCCee-ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHh---cCC
Q 011378          252 KDGNMNKALNLFDIMTQKSI-KPDIV-TYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-ISYGILINGYCS---MGH  325 (487)
Q Consensus       252 ~~g~~~~a~~~~~~m~~~~~-~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~~~---~~~  325 (487)
                      ..|-++....+++.+..-.+ .|.+. -|..++   -.+.-++++.++++.-..-.-.|++ ..|+.-+.-+.+   ...
T Consensus       489 s~gtfestk~vYdriidLriaTPqii~NyAmfL---Eeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~k  565 (835)
T KOG2047|consen  489 SLGTFESTKAVYDRIIDLRIATPQIIINYAMFL---EEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTK  565 (835)
T ss_pred             HhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHH---HhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCC
Confidence            56777777777777765433 33322 122222   2344578888888764444445665 356666666654   236


Q ss_pred             HHHHHHHHHHHHhCCCCCChhhHHHHHHHH--HhcCChHHHHHHHHHHHHCCCCCC--hhhHHHHHHHHhccCCHHHHHH
Q 011378          326 VTEAFRLWYEMVGKGIKPTLVSCNTIIKGY--CRSGDASKADEFLSKMVSEGVDPD--SISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       326 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~--~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~  401 (487)
                      ++.|..+|++-.+ |.+|...-+--|+-+=  -+-|-...|..+++... .++++.  ...||+.|.--+..--+.....
T Consensus       566 lEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat-~~v~~a~~l~myni~I~kaae~yGv~~TR~  643 (835)
T KOG2047|consen  566 LERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERAT-SAVKEAQRLDMYNIYIKKAAEIYGVPRTRE  643 (835)
T ss_pred             HHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHHHHHHhCCcccHH
Confidence            8899999998887 6666544332232221  13477778888888744 355554  3478888876655444444555


Q ss_pred             HHHHHHhCCCCCCHhhHHHH---HHHHHhcCChHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCCHH
Q 011378          402 LVSKMENQGLVPDVITYNVI---LTGFCRQGRMHDSELILWRMIEK-GLNPDRSTYTTLINGHVSQNNLK  467 (487)
Q Consensus       402 ~~~~m~~~g~~p~~~~~~~l---i~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~ty~~l~~~~~~~~~~~  467 (487)
                      ++++..+.  -||...-.-.   .+.=++-|.++.|+.++..-.+. +-+-+..-|.+.=.--+++|+-+
T Consensus       644 iYekaIe~--Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~twk~FEvrHGned  711 (835)
T KOG2047|consen  644 IYEKAIES--LPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWDTWKEFEVRHGNED  711 (835)
T ss_pred             HHHHHHHh--CChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHHHHHHHHHhcCCHH
Confidence            55555443  3554432222   23447789999998888775432 22334456777777777777733

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.49  E-value=0.00087  Score=66.65  Aligned_cols=239  Identities=16%  Similarity=0.178  Sum_probs=139.2

Q ss_pred             ChhhHHHHHHH--HHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCC-C--------C
Q 011378           29 DTVTYNTLINA--YCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMG-L--------S   97 (487)
Q Consensus        29 ~~~~~~~ll~~--~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~--------~   97 (487)
                      |..|--.+++-  |.-.|+.+.|++-.+.+++      -.+|..+-+.|.+..+.|-|.-.+-.|.+.. .        .
T Consensus       725 d~~TRkaml~FSfyvtiG~MD~AfksI~~IkS------~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~  798 (1416)
T KOG3617|consen  725 DESTRKAMLDFSFYVTIGSMDAAFKSIQFIKS------DSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQN  798 (1416)
T ss_pred             CHHHHHhhhceeEEEEeccHHHHHHHHHHHhh------hHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhC
Confidence            33444444432  4556778888777766653      4578888888888888887777776666432 0        1


Q ss_pred             CCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHH
Q 011378           98 PDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIII  177 (487)
Q Consensus        98 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll  177 (487)
                      |+ .+=..+-......|.+++|+.++.+-++         |..+=..|-..|.|++|+++-+.=....+.   .||-.-.
T Consensus       799 ~~-e~eakvAvLAieLgMlEeA~~lYr~ckR---------~DLlNKlyQs~g~w~eA~eiAE~~DRiHLr---~Tyy~yA  865 (1416)
T KOG3617|consen  799 GE-EDEAKVAVLAIELGMLEEALILYRQCKR---------YDLLNKLYQSQGMWSEAFEIAETKDRIHLR---NTYYNYA  865 (1416)
T ss_pred             Cc-chhhHHHHHHHHHhhHHHHHHHHHHHHH---------HHHHHHHHHhcccHHHHHHHHhhccceehh---hhHHHHH
Confidence            21 2222233334466888888888887765         334555667788888888876643222222   2444444


Q ss_pred             HHHHhcCCHHHHHHHHHHH----------HHcC---------CcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 011378          178 NGYCRNGFVLEALKMRDEM----------LEKG---------CVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFP  238 (487)
Q Consensus       178 ~~~~~~~~~~~a~~~~~~m----------~~~g---------~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~  238 (487)
                      .-+-..++.+.|++.+++-          ....         -.-|...|.-.-...-..|+.+.|..+|...++     
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            4444566677776665532          1110         012333344444444556777777777766543     


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHH
Q 011378          239 DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADM  301 (487)
Q Consensus       239 ~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  301 (487)
                          |-+++...|-.|+.++|-++-++-      -|....-.|-+.|-..|++.+|...|...
T Consensus       941 ----~fs~VrI~C~qGk~~kAa~iA~es------gd~AAcYhlaR~YEn~g~v~~Av~FfTrA  993 (1416)
T KOG3617|consen  941 ----YFSMVRIKCIQGKTDKAARIAEES------GDKAACYHLARMYENDGDVVKAVKFFTRA  993 (1416)
T ss_pred             ----hhhheeeEeeccCchHHHHHHHhc------ccHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence                445555556666666666554432      14445556777777777777777777654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.48  E-value=0.00088  Score=60.19  Aligned_cols=418  Identities=11%  Similarity=0.118  Sum_probs=229.4

Q ss_pred             HhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHH
Q 011378            6 CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAK   85 (487)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~   85 (487)
                      ...+++..|..+++--...+-+-...+--=+...+-+.|++++|...+..+.++. .|+...+..|--...-.|.+.+|.
T Consensus        33 ls~rDytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y~eA~  111 (557)
T KOG3785|consen   33 LSNRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQYIEAK  111 (557)
T ss_pred             HhcccchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHHHHHH
Confidence            3456667777776655443322221121223444556778888887777665533 344444544443334456666666


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHH-HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHC
Q 011378           86 EVLDEMLQMGLSPDTATYNTLLVE-SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSA  164 (487)
Q Consensus        86 ~~~~~m~~~g~~~~~~~~~~ll~~-~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  164 (487)
                      .+-+..      |+....+-|+-. .-+.++-++...+.+.+.+.     ...--+|.....-.-.+.+|.+++......
T Consensus       112 ~~~~ka------~k~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----~EdqLSLAsvhYmR~HYQeAIdvYkrvL~d  180 (557)
T KOG3785|consen  112 SIAEKA------PKTPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----LEDQLSLASVHYMRMHYQEAIDVYKRVLQD  180 (557)
T ss_pred             HHHhhC------CCChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----HHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            655542      333333333333 33445555555444444321     111123333333333456677777666543


Q ss_pred             CCCCChhhHHHHH-HHHHhcCCHHHHHHHHHHHHHcCCcCChh-hHHHHHHHHHhc--C---------------------
Q 011378          165 GLVPDNVLYTIII-NGYCRNGFVLEALKMRDEMLEKGCVMDVV-TYNTILNGLCRA--K---------------------  219 (487)
Q Consensus       165 g~~~~~~~~~~ll-~~~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~li~~~~~~--~---------------------  219 (487)
                      +  |+....|.-+ -.|.+....+-+.+++....+.  .||.. .-|.......+.  |                     
T Consensus       181 n--~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~  256 (557)
T KOG3785|consen  181 N--PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFI  256 (557)
T ss_pred             C--hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhH
Confidence            2  3322233222 2345555555555555544432  13322 122222111111  1                     


Q ss_pred             ------------CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHH--
Q 011378          220 ------------MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGF--  285 (487)
Q Consensus       220 ------------~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~--  285 (487)
                                  +-+.|.+++-.+.+  +  =+..--.++--|.+.+++++|..+.+.+.     |.. -|.-++++.  
T Consensus       257 ~~l~rHNLVvFrngEgALqVLP~L~~--~--IPEARlNL~iYyL~q~dVqeA~~L~Kdl~-----Ptt-P~EyilKgvv~  326 (557)
T KOG3785|consen  257 EYLCRHNLVVFRNGEGALQVLPSLMK--H--IPEARLNLIIYYLNQNDVQEAISLCKDLD-----PTT-PYEYILKGVVF  326 (557)
T ss_pred             HHHHHcCeEEEeCCccHHHhchHHHh--h--ChHhhhhheeeecccccHHHHHHHHhhcC-----CCC-hHHHHHHHHHH
Confidence                        11222222222211  0  11233345556889999999988765442     322 122333332  


Q ss_pred             Hcc-------CCHHHHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          286 CKV-------GEMEKANKLWADMISRKISPNYI-SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR  357 (487)
Q Consensus       286 ~~~-------g~~~~a~~~~~~m~~~~~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  357 (487)
                      ...       ..+.-|.+.|.-.-.++..-|.. ---++.+.+.-..++++++...+.+...-..-|.+.|| +-++++.
T Consensus       327 aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~a  405 (557)
T KOG3785|consen  327 AALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLA  405 (557)
T ss_pred             HHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHH
Confidence            222       23556777776554444432322 12345566666778999999888887766666666664 7789999


Q ss_pred             cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhh-HHHHHHHHHhcCChHHHHH
Q 011378          358 SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVIT-YNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       358 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~-~~~li~~~~~~g~~~~a~~  436 (487)
                      .|+..+|+++|-......++-+..-.+.|..+|.+.++.+.|++++-++...   .+..+ ...+..-|.+.+.+--|.+
T Consensus       406 tgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~---~e~fsLLqlIAn~CYk~~eFyyaaK  482 (557)
T KOG3785|consen  406 TGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKTNTP---SERFSLLQLIANDCYKANEFYYAAK  482 (557)
T ss_pred             hcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhcCCc---hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999987766555544444455668889999999999988776532   24444 3445568889999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHH
Q 011378          437 ILWRMIEKGLNPDRSTYTT  455 (487)
Q Consensus       437 ~~~~m~~~g~~p~~~ty~~  455 (487)
                      .|+.+..  +.|++..|+.
T Consensus       483 AFd~lE~--lDP~pEnWeG  499 (557)
T KOG3785|consen  483 AFDELEI--LDPTPENWEG  499 (557)
T ss_pred             hhhHHHc--cCCCccccCC
Confidence            9998754  4677777754

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.48  E-value=0.004  Score=67.56  Aligned_cols=335  Identities=14%  Similarity=0.044  Sum_probs=202.5

Q ss_pred             HHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC------cCChh--hHHHHHHHHH
Q 011378          145 FSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGC------VMDVV--TYNTILNGLC  216 (487)
Q Consensus       145 ~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~------~~~~~--~~~~li~~~~  216 (487)
                      ....|+++.+..+++.+.......+..........+...|+.+++...+....+.--      .+...  ....+-..+.
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            344566666666665542211111222223344455677899998888877654211      11111  1122224456


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-----CCeeehHHHHHHHHc
Q 011378          217 RAKMLTEADDLFNEMLERGVFPDF----YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIK-----PDIVTYNTLIDGFCK  287 (487)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~~~~~~~----~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-----~~~~~~~~li~~~~~  287 (487)
                      ..|+++.|...+++..+.--..+.    ...+.+-..+...|+++.|...++......-.     +...++..+-..+..
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            789999999999987653111121    23455666678899999999998876532111     112344556667788


Q ss_pred             cCCHHHHHHHHHHHHh----CCCC--C-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCC--hhhHHHHHHHHH
Q 011378          288 VGEMEKANKLWADMIS----RKIS--P-NYISYGILINGYCSMGHVTEAFRLWYEMVGK--GIKPT--LVSCNTIIKGYC  356 (487)
Q Consensus       288 ~g~~~~a~~~~~~m~~----~~~~--p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~~~--~~~~~~li~~~~  356 (487)
                      .|+++.|...+.+...    .+..  | ....+..+...+...|++++|...+.+....  ...+.  ...+..+-..+.
T Consensus       544 ~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~  623 (903)
T PRK04841        544 QGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISL  623 (903)
T ss_pred             CCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHH
Confidence            9999999998877553    2221  1 2233445556677789999999988876432  11122  234444566777


Q ss_pred             hcCChHHHHHHHHHHHHC----CCCCChhh--HHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC---HhhHHHHHHHHHh
Q 011378          357 RSGDASKADEFLSKMVSE----GVDPDSIS--YNTLINGFVREENMDKAFALVSKMENQGLVPD---VITYNVILTGFCR  427 (487)
Q Consensus       357 ~~~~~~~a~~~~~~m~~~----g~~p~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~li~~~~~  427 (487)
                      ..|+.+.|.+.++.....    +..+....  -...+..+...|+.+.|...+...........   ...+..+..++..
T Consensus       624 ~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~  703 (903)
T PRK04841        624 ARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQIL  703 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHH
Confidence            899999999988887532    11111101  11123445568899999998776543211111   1113456677889


Q ss_pred             cCChHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          428 QGRMHDSELILWRMIEK----GLNPDR-STYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       428 ~g~~~~a~~~~~~m~~~----g~~p~~-~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      .|+.++|...+.+....    |..++. .+...+-.++...|+.++|...+.+-.+.
T Consensus       704 ~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        704 LGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            99999999999987643    333322 35555667888999999999998888753

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.46  E-value=0.0016  Score=62.46  Aligned_cols=159  Identities=13%  Similarity=0.106  Sum_probs=96.4

Q ss_pred             hHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHH--------HHHHCCCCCChh
Q 011378          312 SYGILINGYCSM--GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLS--------KMVSEGVDPDSI  381 (487)
Q Consensus       312 t~~~li~~~~~~--~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~--------~m~~~g~~p~~~  381 (487)
                      .+.+++..+.+.  ....++..++.......-.-...+.-.+++.....|+++.|.+++.        ...+.+..|.. 
T Consensus       341 ~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~-  419 (652)
T KOG2376|consen  341 LFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGT-  419 (652)
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhH-
Confidence            344444444322  2355666666655443222234455566777788888888888888        55555555544 


Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhC--CCCCCHhh----HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQ--GLVPDVIT----YNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTT  455 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p~~~~----~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~  455 (487)
                       ...++..|.+.++-+.|..++++-...  .-.+....    +.-+...--+.|..++|..+++++... -.+|..+...
T Consensus       420 -V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~-n~~d~~~l~~  497 (652)
T KOG2376|consen  420 -VGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKF-NPNDTDLLVQ  497 (652)
T ss_pred             -HHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHh-CCchHHHHHH
Confidence             455667777777777788887654321  11222222    333334445778888888888888763 2356778888


Q ss_pred             HHHHHHhcCCHHHHHHHHH
Q 011378          456 LINGHVSQNNLKEAFRFHD  474 (487)
Q Consensus       456 l~~~~~~~~~~~~a~~~~~  474 (487)
                      ++.+|++. +++.|..+-.
T Consensus       498 lV~a~~~~-d~eka~~l~k  515 (652)
T KOG2376|consen  498 LVTAYARL-DPEKAESLSK  515 (652)
T ss_pred             HHHHHHhc-CHHHHHHHhh
Confidence            88888865 4666665533

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

Probab=98.45  E-value=1.7e-05  Score=70.06  Aligned_cols=228  Identities=15%  Similarity=0.066  Sum_probs=145.4

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHH-HHHHHHHHc
Q 011378           34 NTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATY-NTLLVESCR  112 (487)
Q Consensus        34 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~-~~ll~~~~~  112 (487)
                      +.+-+.|.+.|-+.+|...+++-.+.  .|-+.||-.|-++|.+..++..|+.++.+-.+.  .|-.+|| .-.-+.+-.
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~ea  302 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEA  302 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHH
Confidence            45667777777777777777665443  244456666677777777777777777765542  3444443 233444555


Q ss_pred             cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          113 KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKM  192 (487)
Q Consensus       113 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  192 (487)
                      .++.++|.+++....+.. .-++....++...|.-.++++.|+.+++.+.+.|+.. ...|+.+--.|.-.++++-++..
T Consensus       303 m~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~s-peLf~NigLCC~yaqQ~D~~L~s  380 (478)
T KOG1129|consen  303 MEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQS-PELFCNIGLCCLYAQQIDLVLPS  380 (478)
T ss_pred             HHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCC-hHHHhhHHHHHHhhcchhhhHHH
Confidence            677777777777665432 2244444555666677777788888888777777543 34555555555566666666666


Q ss_pred             HHHHHHcCCcCCh--hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          193 RDEMLEKGCVMDV--VTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       193 ~~~m~~~g~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      |......--.|+.  ..|-.+-....-.|++..|.+.|+-...++ .-+...+++|--.-.+.|+++.|..++.....
T Consensus       381 f~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~A~s  457 (478)
T KOG1129|consen  381 FQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNAAKS  457 (478)
T ss_pred             HHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHHhhh
Confidence            6655543332322  235455555566788888888888766543 23567788888888888888888888876554

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

Probab=98.42  E-value=2.3e-05  Score=71.43  Aligned_cols=223  Identities=16%  Similarity=0.131  Sum_probs=136.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHH-HH
Q 011378           31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLL-VE  109 (487)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll-~~  109 (487)
                      ...-.+.+++...|..+.++   .++.... .|.......+-..+...++-+.+..-+++.......++..++..+. ..
T Consensus        36 e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i  111 (290)
T PF04733_consen   36 ERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATI  111 (290)
T ss_dssp             HHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHH
Confidence            34456777888888776544   4443333 5665555444444433344444444444333333332233333222 34


Q ss_pred             HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHh----cCC
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCR----NGF  185 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~  185 (487)
                      +...|++++|++++..-      .+.......+..+.+.+++|.|.+.++.|++.  ..|. +...+..++..    ...
T Consensus       112 ~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~eD~-~l~qLa~awv~l~~g~e~  182 (290)
T PF04733_consen  112 LFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQI--DEDS-ILTQLAEAWVNLATGGEK  182 (290)
T ss_dssp             HCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--SCCH-HHHHHHHHHHHHHHTTTC
T ss_pred             HHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcH-HHHHHHHHHHHHHhCchh
Confidence            56678999998887542      35666677888999999999999999999864  3443 33344444433    336


Q ss_pred             HHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH-HHHHHHHH
Q 011378          186 VLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM-NKALNLFD  264 (487)
Q Consensus       186 ~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~-~~a~~~~~  264 (487)
                      +.+|..+|+++.+ .+.+++.+.|.+..++...|++++|++++.+..+.+ +-|+.+..+++......|+. +.+.+.+.
T Consensus       183 ~~~A~y~f~El~~-~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~  260 (290)
T PF04733_consen  183 YQDAFYIFEELSD-KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLS  260 (290)
T ss_dssp             CCHHHHHHHHHHC-CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHh-ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHH
Confidence            8888889988754 456778888888888888999999998888876543 33667777788777777776 56667777


Q ss_pred             HHHH
Q 011378          265 IMTQ  268 (487)
Q Consensus       265 ~m~~  268 (487)
                      .++.
T Consensus       261 qL~~  264 (290)
T PF04733_consen  261 QLKQ  264 (290)
T ss_dssp             HCHH
T ss_pred             HHHH
Confidence            6664

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.42  E-value=0.00026  Score=62.01  Aligned_cols=337  Identities=13%  Similarity=0.138  Sum_probs=215.2

Q ss_pred             CCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHH
Q 011378           59 KGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSF  138 (487)
Q Consensus        59 ~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~  138 (487)
                      .|+....--+++++..+.+..++..|.+++....+.. +.+....+.|-.+|-+..++..|...++++...  -|...-|
T Consensus         4 ~g~~i~EGeftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qY   80 (459)
T KOG4340|consen    4 SGAQIPEGEFTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQY   80 (459)
T ss_pred             ccccCCCCchHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHH
Confidence            4554444557888888899999999999988765542 236777778888888999999999999998764  4555555


Q ss_pred             HH-HHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHH--HhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHH
Q 011378          139 ST-LIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY--CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGL  215 (487)
Q Consensus       139 ~~-li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~--~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~  215 (487)
                      .. -.....+++.+..|+.+...|...   |+...-..-+++-  ...+++..+..++++.-..|   +..+.+..-...
T Consensus        81 rlY~AQSLY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCll  154 (459)
T KOG4340|consen   81 RLYQAQSLYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLL  154 (459)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchhee
Confidence            43 345667888999999998888653   3333222223332  24567777777777764322   223333444445


Q ss_pred             HhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-------------Ceee----
Q 011378          216 CRAKMLTEADDLFNEMLER-GVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-------------DIVT----  277 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~-~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-------------~~~~----  277 (487)
                      .+.|+++.|.+-|+...+- |..| ...||..+. ..+.|+.+.|++...+..++|++-             |+..    
T Consensus       155 ykegqyEaAvqkFqaAlqvsGyqp-llAYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt  232 (459)
T KOG4340|consen  155 YKEGQYEAAVQKFQAALQVSGYQP-LLAYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNT  232 (459)
T ss_pred             eccccHHHHHHHHHHHHhhcCCCc-hhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccch
Confidence            6889999999999998774 4444 456776664 456789999999999888887652             2211    


Q ss_pred             ----hHHHHHH-------HHccCCHHHHHHHHHHHHhC-CCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh
Q 011378          278 ----YNTLIDG-------FCKVGEMEKANKLWADMISR-KISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL  345 (487)
Q Consensus       278 ----~~~li~~-------~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  345 (487)
                          -+.++.+       +.+.|+.+.|.+-+.+|.-+ ....|.+|...+.-.=. .+++.+..+-+.-+.... +-..
T Consensus       233 ~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~n-PfP~  310 (459)
T KOG4340|consen  233 LVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQN-PFPP  310 (459)
T ss_pred             HHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcC-CCCh
Confidence                1344444       34567888888888777533 33456677665543222 234444444444443331 2345


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC-CChhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGVD-PDSISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      .||..++-.||+..-++.|..++.+-...-.+ .+...|+.|=..-......++|.+-++.+.+
T Consensus       311 ETFANlLllyCKNeyf~lAADvLAEn~~lTyk~L~~Yly~LLdaLIt~qT~pEea~KKL~~La~  374 (459)
T KOG4340|consen  311 ETFANLLLLYCKNEYFDLAADVLAENAHLTYKFLTPYLYDLLDALITCQTAPEEAFKKLDGLAG  374 (459)
T ss_pred             HHHHHHHHHHhhhHHHhHHHHHHhhCcchhHHHhhHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            67888888899888888888888754332211 2344455433333345567777776666554

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

Probab=98.42  E-value=0.0033  Score=64.15  Aligned_cols=319  Identities=15%  Similarity=0.179  Sum_probs=167.3

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHhhC--CCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHH
Q 011378           29 DTVTYNTLINAYCREGFLEEAFQLMNSMSGK--GLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTL  106 (487)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  106 (487)
                      |+.-.+..++++...+-..+-.++++.+.-.  .+.-+...-|.||-.. -.-+...+.++.+++.+.. .|+..     
T Consensus       983 dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtA-ikad~trVm~YI~rLdnyD-a~~ia----- 1055 (1666)
T KOG0985|consen  983 DPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTA-IKADRTRVMEYINRLDNYD-APDIA----- 1055 (1666)
T ss_pred             ChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHH-hhcChHHHHHHHHHhccCC-chhHH-----
Confidence            4455666677777777777777777766432  1111111222233222 2335556666666665432 23322     


Q ss_pred             HHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCH
Q 011378          107 LVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFV  186 (487)
Q Consensus       107 l~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  186 (487)
                       ..+...+-.++|..+|+..-     .+....+.||.   ..+.+|+|.++-+...      ....|+.+-.+--+.|.+
T Consensus      1056 -~iai~~~LyEEAF~ifkkf~-----~n~~A~~VLie---~i~~ldRA~efAe~~n------~p~vWsqlakAQL~~~~v 1120 (1666)
T KOG0985|consen 1056 -EIAIENQLYEEAFAIFKKFD-----MNVSAIQVLIE---NIGSLDRAYEFAERCN------EPAVWSQLAKAQLQGGLV 1120 (1666)
T ss_pred             -HHHhhhhHHHHHHHHHHHhc-----ccHHHHHHHHH---HhhhHHHHHHHHHhhC------ChHHHHHHHHHHHhcCch
Confidence             22334455667776666542     12322333332   3456666666555432      234677777777777777


Q ss_pred             HHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          187 LEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       187 ~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      .+|.+-+-+.      -|+..|..+++...+.|.+++..+.+...+++.-.|...  +.+|-+|++.+++.+-++.+   
T Consensus      1121 ~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi--- 1189 (1666)
T KOG0985|consen 1121 KDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFI--- 1189 (1666)
T ss_pred             HHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHh---
Confidence            7776555332      355567777777777777777777776555554444433  35666777777766654433   


Q ss_pred             HHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChh
Q 011378          267 TQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLV  346 (487)
Q Consensus       267 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  346 (487)
                          ..||......+=+-|...|.++.|.-++.         ++.-|.-|...+...|.++-|.+--+.      ..+..
T Consensus      1190 ----~gpN~A~i~~vGdrcf~~~~y~aAkl~y~---------~vSN~a~La~TLV~LgeyQ~AVD~aRK------Ans~k 1250 (1666)
T KOG0985|consen 1190 ----AGPNVANIQQVGDRCFEEKMYEAAKLLYS---------NVSNFAKLASTLVYLGEYQGAVDAARK------ANSTK 1250 (1666)
T ss_pred             ----cCCCchhHHHHhHHHhhhhhhHHHHHHHH---------HhhhHHHHHHHHHHHHHHHHHHHHhhh------ccchh
Confidence                13555555555555566666666655554         344555666666666665555443221      12344


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVS  404 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~  404 (487)
                      ||.-.--+|...+.+..|     .|-..++.....-..-|+..|-..|.+++...+++
T Consensus      1251 tWK~VcfaCvd~~EFrlA-----QiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~E 1303 (1666)
T KOG0985|consen 1251 TWKEVCFACVDKEEFRLA-----QICGLNIIVHADELEELIEYYQDRGYFEELISLLE 1303 (1666)
T ss_pred             HHHHHHHHHhchhhhhHH-----HhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHH
Confidence            555555555444433332     22222232333334455555655666555444443

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

Probab=98.41  E-value=0.0022  Score=61.25  Aligned_cols=195  Identities=10%  Similarity=-0.035  Sum_probs=102.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhC-CCCCCccchHH-HHHHHHhcCChhhHHHHHHHHHHCCCCCC-HHHHHH---H
Q 011378           33 YNTLINAYCREGFLEEAFQLMNSMSGK-GLKPGVFTYNS-LINGLCKKGRCDRAKEVLDEMLQMGLSPD-TATYNT---L  106 (487)
Q Consensus        33 ~~~ll~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~-li~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~---l  106 (487)
                      |..+...+...++.+.+.+.+...... ...++...-.. -...+...|++++|.+.+++..+.  .|+ ...+..   .
T Consensus         9 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~--~P~~~~a~~~~~~~   86 (355)
T cd05804           9 HAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDD--YPRDLLALKLHLGA   86 (355)
T ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHhHHH
Confidence            444444455566666655555443322 11122111111 112345577888888888876654  233 333331   1


Q ss_pred             HHHHHccCChhHHHHHHHHHHHCCCCCCH-hHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCC
Q 011378          107 LVESCRKENMSEAEEIFCEMSRRGVAPDI-VSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGF  185 (487)
Q Consensus       107 l~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~  185 (487)
                      .......+....+.+.++.  ..+..|+. .....+...+...|++++|...+++..+.. +.+...+..+-..+...|+
T Consensus        87 ~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~  163 (355)
T cd05804          87 FGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGR  163 (355)
T ss_pred             HHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCC
Confidence            1111223444455554443  11222332 233344456677888888888888776643 2224456666667777777


Q ss_pred             HHHHHHHHHHHHHcCC-cCCh--hhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          186 VLEALKMRDEMLEKGC-VMDV--VTYNTILNGLCRAKMLTEADDLFNEML  232 (487)
Q Consensus       186 ~~~a~~~~~~m~~~g~-~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (487)
                      .++|...+++..+..- .++.  ..|..+...+...|++++|.+++++..
T Consensus       164 ~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         164 FKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             HHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            7777777776654321 1222  234456666777777777777777764

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.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.38  E-value=7e-07  Score=52.71  Aligned_cols=33  Identities=45%  Similarity=0.797  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 011378          452 TYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPD  484 (487)
Q Consensus       452 ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~  484 (487)
                      ||+.+|.+|++.|++++|.+++++|.+.|++||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            456666666666666666666666666666665

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.

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

Probab=98.32  E-value=0.002  Score=61.64  Aligned_cols=287  Identities=14%  Similarity=0.117  Sum_probs=193.7

Q ss_pred             CCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHH
Q 011378           60 GLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFS  139 (487)
Q Consensus        60 ~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~  139 (487)
                      ++.-++.....--+-|...+++.++.++.+...+.. ++....+..=|.++...|+-.+-..+=.+|.+. .+-...+|=
T Consensus       239 ~l~~~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~  316 (611)
T KOG1173|consen  239 GLAENLDLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWF  316 (611)
T ss_pred             hhhhcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchh
Confidence            344455555555666777888888888888776542 455556666666777777777766666666654 233556777


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHH--cC-CcCChhhHHHHHHHH
Q 011378          140 TLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLE--KG-CVMDVVTYNTILNGL  215 (487)
Q Consensus       140 ~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--~g-~~~~~~~~~~li~~~  215 (487)
                      ++---|.-.|..++|.++|.+...  +.|. ...|-.+-.+|+-.|.-++|...+...-+  .| ..|.  .|  +---|
T Consensus       317 aVg~YYl~i~k~seARry~SKat~--lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~--LY--lgmey  390 (611)
T KOG1173|consen  317 AVGCYYLMIGKYSEARRYFSKATT--LDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPS--LY--LGMEY  390 (611)
T ss_pred             hHHHHHHHhcCcHHHHHHHHHHhh--cCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchH--HH--HHHHH
Confidence            777777777888888888887654  3333 34677777788888888877766554332  12 2232  12  22336


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH--CCCCC----CeeehHHHHHHHHccC
Q 011378          216 CRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ--KSIKP----DIVTYNTLIDGFCKVG  289 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~----~~~~~~~li~~~~~~g  289 (487)
                      .+.++++.|.++|.+.... .+-|+...+-+--.....+.+.+|..+|+....  +.+.+    -..+++.|=..|.+.+
T Consensus       391 ~~t~n~kLAe~Ff~~A~ai-~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~  469 (611)
T KOG1173|consen  391 MRTNNLKLAEKFFKQALAI-APSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLN  469 (611)
T ss_pred             HHhccHHHHHHHHHHHHhc-CCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHh
Confidence            6788888899888876643 233667777776667777888888888875542  11111    2235677778888889


Q ss_pred             CHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc
Q 011378          290 EMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRS  358 (487)
Q Consensus       290 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  358 (487)
                      ..++|+..++..... .+-+..+++++--.|...|.++.|.+.|..-  ..+.|+-.+...+++.+...
T Consensus       470 ~~~eAI~~~q~aL~l-~~k~~~~~asig~iy~llgnld~Aid~fhKa--L~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  470 KYEEAIDYYQKALLL-SPKDASTHASIGYIYHLLGNLDKAIDHFHKA--LALKPDNIFISELLKLAIED  535 (611)
T ss_pred             hHHHHHHHHHHHHHc-CCCchhHHHHHHHHHHHhcChHHHHHHHHHH--HhcCCccHHHHHHHHHHHHh
Confidence            999998888876543 2347778888888888889999998888865  45688887777777766543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.32  E-value=1.1e-06  Score=51.82  Aligned_cols=33  Identities=36%  Similarity=0.924  Sum_probs=24.6

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEKGLNPD  449 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  449 (487)
                      +||++|.+|++.|++++|.++|++|...|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            577777777777777777777777777777776

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=98.26  E-value=1.8e-06  Score=50.53  Aligned_cols=33  Identities=27%  Similarity=0.530  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC
Q 011378          451 STYTTLINGHVSQNNLKEAFRFHDEMLQRGFVP  483 (487)
Q Consensus       451 ~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p  483 (487)
                      .||+.++++|++.|+++.|.+++++|.+.|++|
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            356666666666666666666666666666655

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.26  E-value=0.001  Score=61.43  Aligned_cols=217  Identities=13%  Similarity=0.022  Sum_probs=120.7

Q ss_pred             CChhHHHHHHHHHhhC-CCCCCc--cchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHH
Q 011378           44 GFLEEAFQLMNSMSGK-GLKPGV--FTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE  120 (487)
Q Consensus        44 ~~~~~a~~~~~~m~~~-~~~p~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~  120 (487)
                      +..+.++.-+.++... ...|+.  ..|..+-..+.+.|+.+.|...|++..+.. +.+...|+.+-..+...|++++|.
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            3455555555555532 222322  334445555667777777777777766542 224566777777777777777777


Q ss_pred             HHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011378          121 EIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEK  199 (487)
Q Consensus       121 ~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  199 (487)
                      +.|+...+.  .| +..++..+..++...|++++|.+.|+...+.  .|+..............++.++|...+.+....
T Consensus       119 ~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~  194 (296)
T PRK11189        119 EAFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYEK  194 (296)
T ss_pred             HHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhh
Confidence            777777653  34 3455666666677777777777777776653  343322122222233456677777777554432


Q ss_pred             CCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CC--CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          200 GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLER---GV--FP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKS  270 (487)
Q Consensus       200 g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~--~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~  270 (487)
                      . .++...| .+..  ...|+...+ +.+..+.+.   ..  .| ....|..+-..+.+.|+.++|...|+...+..
T Consensus       195 ~-~~~~~~~-~~~~--~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~  266 (296)
T PRK11189        195 L-DKEQWGW-NIVE--FYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANN  266 (296)
T ss_pred             C-CccccHH-HHHH--HHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            2 2222112 2222  223444333 244444321   11  11 23467777777778888888888887766544

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.26  E-value=0.0019  Score=59.70  Aligned_cols=27  Identities=19%  Similarity=0.240  Sum_probs=15.6

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      .|..+-..+...|+.++|...|++..+
T Consensus       238 a~~~Lg~~~~~~g~~~~A~~~~~~Al~  264 (296)
T PRK11189        238 TYFYLAKYYLSLGDLDEAAALFKLALA  264 (296)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            445555555566666666666665554

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.24  E-value=2e-06  Score=50.33  Aligned_cols=33  Identities=27%  Similarity=0.467  Sum_probs=19.8

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 011378          416 ITYNVILTGFCRQGRMHDSELILWRMIEKGLNP  448 (487)
Q Consensus       416 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  448 (487)
                      .+|+++|.+|++.|+++.|..+|++|.+.|++|
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            356666666666666666666666666666555

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

Probab=98.18  E-value=0.003  Score=53.63  Aligned_cols=202  Identities=14%  Similarity=0.050  Sum_probs=135.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC-eeehHHHHHHHHcc
Q 011378          210 TILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPD-IVTYNTLIDGFCKV  288 (487)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~  288 (487)
                      -|--.|.+.|+...|..-+++..+.. +-+.-+|..+-..|.+.|+.+.|.+.|+...+.  .|+ ..+.|..=-.+|..
T Consensus        40 qLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~FLC~q  116 (250)
T COG3063          40 QLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSL--APNNGDVLNNYGAFLCAQ  116 (250)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHHHHhC
Confidence            44566788888888888888887753 224457788888888888888888888866542  343 34455555556888


Q ss_pred             CCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHH
Q 011378          289 GEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEF  367 (487)
Q Consensus       289 g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  367 (487)
                      |++++|...|+.....-.-| -..||..+.-+..+.|+.+.|...++.-.... +-...+...+.+...+.|++-.|...
T Consensus       117 g~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar~~  195 (250)
T COG3063         117 GRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPARLY  195 (250)
T ss_pred             CChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHHHH
Confidence            88888888888766542222 23567777777778888888888887765442 22233455566667777888888777


Q ss_pred             HHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhH
Q 011378          368 LSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITY  418 (487)
Q Consensus       368 ~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~  418 (487)
                      ++.....+. ++..+.-..|.--.+.|+.+.+.+.=..+...  .|.+..|
T Consensus       196 ~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~--fP~s~e~  243 (250)
T COG3063         196 LERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL--FPYSEEY  243 (250)
T ss_pred             HHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCcHHH
Confidence            777776655 66666666666666777777776655555442  3444433

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.18  E-value=0.0039  Score=54.88  Aligned_cols=298  Identities=15%  Similarity=0.117  Sum_probs=195.5

Q ss_pred             CCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHH
Q 011378           24 KGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTAT  102 (487)
Q Consensus        24 ~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~  102 (487)
                      .|+.....-+.+++..+.+..++++|++++..-.++  .| +......+-..|....++..|-..++++-+.  .|...-
T Consensus         4 ~g~~i~EGeftaviy~lI~d~ry~DaI~~l~s~~Er--~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~q   79 (459)
T KOG4340|consen    4 SGAQIPEGEFTAVVYRLIRDARYADAIQLLGSELER--SPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQ   79 (459)
T ss_pred             ccccCCCCchHHHHHHHHHHhhHHHHHHHHHHHHhc--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHH
Confidence            344444555888999999999999999999887665  34 4555666667778889999999999998764  466655


Q ss_pred             HHHH-HHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHH--HHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHH
Q 011378          103 YNTL-LVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGI--FSRNGQLDRALMYFREMKSAGLVPDNVLYTIIING  179 (487)
Q Consensus       103 ~~~l-l~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~--~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  179 (487)
                      |... -..+-+.+.+.+|++|...|.+.   |+...-..-+.+  -...+++..+..+.++....|   +..+.+..--.
T Consensus        80 YrlY~AQSLY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCl  153 (459)
T KOG4340|consen   80 YRLYQAQSLYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCL  153 (459)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchhe
Confidence            5432 23455778899999999998764   333322222222  345788889999988875432   22233333333


Q ss_pred             HHhcCCHHHHHHHHHHHHH-cCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-------------CCHH----
Q 011378          180 YCRNGFVLEALKMRDEMLE-KGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVF-------------PDFY----  241 (487)
Q Consensus       180 ~~~~~~~~~a~~~~~~m~~-~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-------------~~~~----  241 (487)
                      ..+.|+.+.|.+-|....+ .|+.| ...||.-+..| +.++.+.|.+...+..++|++             ||..    
T Consensus       154 lykegqyEaAvqkFqaAlqvsGyqp-llAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgN  231 (459)
T KOG4340|consen  154 LYKEGQYEAAVQKFQAALQVSGYQP-LLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGN  231 (459)
T ss_pred             eeccccHHHHHHHHHHHHhhcCCCc-hhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccc
Confidence            4588999999998888766 46655 55788777654 678999999999999999874             2321    


Q ss_pred             ----HHHHHHHH-------HHhcCCHHHHHHHHHHHHHC-CCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 011378          242 ----TFTTLIHG-------HCKDGNMNKALNLFDIMTQK-SIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN  309 (487)
Q Consensus       242 ----t~~~li~~-------~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~  309 (487)
                          .-+.++.+       +.+.|+.+.|.+.+-.|.-+ .-..|..|...+.-.=. .+++-+..+-+.-+.... +-.
T Consensus       232 t~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~n-PfP  309 (459)
T KOG4340|consen  232 TLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQN-PFP  309 (459)
T ss_pred             hHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcC-CCC
Confidence                12334433       45677888887777666432 23345566544332211 222222222222222221 124


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          310 YISYGILINGYCSMGHVTEAFRLWYE  335 (487)
Q Consensus       310 ~~t~~~li~~~~~~~~~~~a~~~~~~  335 (487)
                      ..||..++-.||++.-++.|-.++-+
T Consensus       310 ~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  310 PETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             hHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            57999999999999999999988865

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.17  E-value=0.008  Score=57.95  Aligned_cols=118  Identities=17%  Similarity=0.199  Sum_probs=52.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHH--------HHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH--CCCCCChhhHH
Q 011378          315 ILINGYCSMGHVTEAFRLWY--------EMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS--EGVDPDSISYN  384 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~--------~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~g~~p~~~~~~  384 (487)
                      .++......|+++.|.+++.        .+...+..|-.  ...+...+.+.++.+.|..++.+...  ..-.+......
T Consensus       381 ~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~--V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~  458 (652)
T KOG2376|consen  381 LRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGT--VGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALL  458 (652)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhH--HHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHH
Confidence            34444455555555555555        23223333322  22344445555555555555544432  11122222222


Q ss_pred             HHHHHH----hccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHH
Q 011378          385 TLINGF----VREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       385 ~li~~~----~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  436 (487)
                      +++.-.    .+.|+-++|..+++++-+.+ .+|..+...++.+|++- +.+.|+.
T Consensus       459 ~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~-d~eka~~  512 (652)
T KOG2376|consen  459 SLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL-DPEKAES  512 (652)
T ss_pred             hHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc-CHHHHHH
Confidence            222222    24455555555555554432 34555555555555554 3444443

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

Probab=98.17  E-value=0.0078  Score=57.74  Aligned_cols=285  Identities=13%  Similarity=0.086  Sum_probs=200.2

Q ss_pred             CCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHH
Q 011378          131 VAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNT  210 (487)
Q Consensus       131 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  210 (487)
                      ..-+......-..-|-..+++.+..++++...+. .++....+..=|..+...|+..+-+.+=.+|.+. .+-...+|-+
T Consensus       240 l~~~~dll~~~ad~~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~a  317 (611)
T KOG1173|consen  240 LAENLDLLAEKADRLYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFA  317 (611)
T ss_pred             hhhcHHHHHHHHHHHHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhh
Confidence            3344444555566778889999999999987763 2344455666677888889888777776677654 3456678888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCe-eehHHHHHHHHcc
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFPD-FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI-VTYNTLIDGFCKV  288 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~  288 (487)
                      +---|.-.|..++|.+.|.+...-  .|. ...|-..-++|+-.|.-|.|+..+....+--..-.. ..|-.  --|.+.
T Consensus       318 Vg~YYl~i~k~seARry~SKat~l--D~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlg--mey~~t  393 (611)
T KOG1173|consen  318 VGCYYLMIGKYSEARRYFSKATTL--DPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLG--MEYMRT  393 (611)
T ss_pred             HHHHHHHhcCcHHHHHHHHHHhhc--CccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHH--HHHHHh
Confidence            888888889999999999986542  222 356888889999999999999988766543211111 12222  236778


Q ss_pred             CCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHh--C----CCCCChhhHHHHHHHHHhcCCh
Q 011378          289 GEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVG--K----GIKPTLVSCNTIIKGYCRSGDA  361 (487)
Q Consensus       289 g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~--~----~~~~~~~~~~~li~~~~~~~~~  361 (487)
                      +.++.|.+.|.+..  ++.| |....+-+--..-..+.+.+|...|+.-..  +    .......+++.|=.+|.+.+..
T Consensus       394 ~n~kLAe~Ff~~A~--ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~  471 (611)
T KOG1173|consen  394 NNLKLAEKFFKQAL--AIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKY  471 (611)
T ss_pred             ccHHHHHHHHHHHH--hcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhH
Confidence            89999999998764  4455 344444444444456788899888886551  1    1112344577777888899999


Q ss_pred             HHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHH
Q 011378          362 SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFC  426 (487)
Q Consensus       362 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  426 (487)
                      ++|...+++..... +-|..++.++--.|...|+++.|...|.+--  .++||-.+-..++..+.
T Consensus       472 ~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~ai  533 (611)
T KOG1173|consen  472 EEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLAI  533 (611)
T ss_pred             HHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHHH
Confidence            99999999877543 3467788888888899999999999887653  56888766666666443

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

Probab=98.11  E-value=0.0033  Score=53.40  Aligned_cols=194  Identities=14%  Similarity=0.083  Sum_probs=132.0

Q ss_pred             HHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHh
Q 011378          104 NTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCR  182 (487)
Q Consensus       104 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~  182 (487)
                      .-|--.|...|+...|..-+++..+.. +.+..+|..+...|-+.|+.+.|.+.|++..+.  .|+ ..+.|..=.-+|.
T Consensus        39 lqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~FLC~  115 (250)
T COG3063          39 LQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSL--APNNGDVLNNYGAFLCA  115 (250)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHHHHh
Confidence            345556778888888888888877653 224456777788888888888888888887653  343 3455666666778


Q ss_pred             cCCHHHHHHHHHHHHHc-CCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 011378          183 NGFVLEALKMRDEMLEK-GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALN  261 (487)
Q Consensus       183 ~~~~~~a~~~~~~m~~~-g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~  261 (487)
                      .|.+++|...|++-... ...--..+|..+.-+..+.|+.+.|++.|++..+.. +-.+.+...+-....+.|+.-.|..
T Consensus       116 qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar~  194 (250)
T COG3063         116 QGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPARL  194 (250)
T ss_pred             CCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHHH
Confidence            88888888888776653 233334577777777788888888888888877643 1233456666777777788878877


Q ss_pred             HHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHH
Q 011378          262 LFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       262 ~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  302 (487)
                      .++.....+. ++..+.---|+.-...|+.+.+.+.=..+.
T Consensus       195 ~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~  234 (250)
T COG3063         195 YLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQ  234 (250)
T ss_pred             HHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            7776665554 555555555666666677666665544444

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.09  E-value=0.014  Score=57.80  Aligned_cols=308  Identities=16%  Similarity=0.169  Sum_probs=166.4

Q ss_pred             CChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHH
Q 011378          114 ENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMR  193 (487)
Q Consensus       114 ~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~  193 (487)
                      .++.+|+.+|-+-       |.  --..|..|..-..||+|+.+-+.   .|-+.-...-.+.++++...|+-+.|-++-
T Consensus       545 kkfk~ae~ifleq-------n~--te~aigmy~~lhkwde~i~lae~---~~~p~~eklk~sy~q~l~dt~qd~ka~elk  612 (1636)
T KOG3616|consen  545 KKFKEAEMIFLEQ-------NA--TEEAIGMYQELHKWDEAIALAEA---KGHPALEKLKRSYLQALMDTGQDEKAAELK  612 (1636)
T ss_pred             hhhhHHHHHHHhc-------cc--HHHHHHHHHHHHhHHHHHHHHHh---cCChHHHHHHHHHHHHHHhcCchhhhhhhc
Confidence            4566777766432       11  13467777777788888776543   222222233445566777777777765443


Q ss_pred             HHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC
Q 011378          194 DEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP  273 (487)
Q Consensus       194 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~  273 (487)
                      +        .|..+ -+.|+.|.+.|.+..|.+.-..  +..+..|.....-+-.++.+..-+++|=++|+.+..     
T Consensus       613 ~--------sdgd~-laaiqlyika~~p~~a~~~a~n--~~~l~~de~il~~ia~alik~elydkagdlfeki~d-----  676 (1636)
T KOG3616|consen  613 E--------SDGDG-LAAIQLYIKAGKPAKAARAALN--DEELLADEEILEHIAAALIKGELYDKAGDLFEKIHD-----  676 (1636)
T ss_pred             c--------ccCcc-HHHHHHHHHcCCchHHHHhhcC--HHHhhccHHHHHHHHHHHHhhHHHHhhhhHHHHhhC-----
Confidence            2        11112 2457888888888777655321  112334555555555555555555555555554431     


Q ss_pred             CeeehHHHHHHHHccCCHHHHHHHHHHH---------------HhCCCCCCh--------hhHHHHHHHHHhcCCHHHHH
Q 011378          274 DIVTYNTLIDGFCKVGEMEKANKLWADM---------------ISRKISPNY--------ISYGILINGYCSMGHVTEAF  330 (487)
Q Consensus       274 ~~~~~~~li~~~~~~g~~~~a~~~~~~m---------------~~~~~~p~~--------~t~~~li~~~~~~~~~~~a~  330 (487)
                          +..-+.+|.+-..+-+|.++-+-.               ....-+-|.        ...---|.+-.....+.+|+
T Consensus       677 ----~dkale~fkkgdaf~kaielarfafp~evv~lee~wg~hl~~~~q~daainhfiea~~~~kaieaai~akew~kai  752 (1636)
T KOG3616|consen  677 ----FDKALECFKKGDAFGKAIELARFAFPEEVVKLEEAWGDHLEQIGQLDAAINHFIEANCLIKAIEAAIGAKEWKKAI  752 (1636)
T ss_pred             ----HHHHHHHHHcccHHHHHHHHHHhhCcHHHhhHHHHHhHHHHHHHhHHHHHHHHHHhhhHHHHHHHHhhhhhhhhhH
Confidence                112222332222223332221100               000000000        00111233444556677777


Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCC
Q 011378          331 RLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQG  410 (487)
Q Consensus       331 ~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  410 (487)
                      .+++.+.....  -..-|--+-+.|+..|+++.|+++|.+.-         .++--|..|.+.|++++|.++-++..  |
T Consensus       753 ~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw~da~kla~e~~--~  819 (1636)
T KOG3616|consen  753 SILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKWEDAFKLAEECH--G  819 (1636)
T ss_pred             hHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccHHHHHHHHHHhc--C
Confidence            77776654432  22235566778888888888888876422         24455777888888888877665543  2


Q ss_pred             CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          411 LVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDE  475 (487)
Q Consensus       411 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~  475 (487)
                      -...+..|-.-..-.-++|++.+|++++-...    .|+     .-|.+|-++|..++.+++.++
T Consensus       820 ~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~-----~aiqmydk~~~~ddmirlv~k  875 (1636)
T KOG3616|consen  820 PEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPD-----KAIQMYDKHGLDDDMIRLVEK  875 (1636)
T ss_pred             chhHHHHHHHhHHhHHhhcchhhhhheeEEcc----Cch-----HHHHHHHhhCcchHHHHHHHH
Confidence            22344555555566677888888877654431    244     236678888888888877654

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

Probab=98.08  E-value=0.00034  Score=68.66  Aligned_cols=215  Identities=15%  Similarity=0.149  Sum_probs=164.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYC  321 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~  321 (487)
                      .-..+-..+.+.|-...|+.+|+...         .|...|.+|+..|+-.+|..+.++-.+  -+||...|..+.+...
T Consensus       400 ~q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~  468 (777)
T KOG1128|consen  400 LQRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLH  468 (777)
T ss_pred             HHHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhcc
Confidence            33456677888999999999998654         678899999999999999999887665  5788899999888887


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHH
Q 011378          322 SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAF  400 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~  400 (487)
                      ...-+++|.++++.....       .-..+-....+.++++++.+.++.-.+.+  | -..+|-.+=.+..+.+++..|.
T Consensus       469 d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n--plq~~~wf~~G~~ALqlek~q~av  539 (777)
T KOG1128|consen  469 DPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN--PLQLGTWFGLGCAALQLEKEQAAV  539 (777)
T ss_pred             ChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC--ccchhHHHhccHHHHHHhhhHHHH
Confidence            777789999988765322       00001111223688899988887655432  2 2345655666667888999998


Q ss_pred             HHHHHHHhCCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          401 ALVSKMENQGLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       401 ~~~~~m~~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      +.|..-..  +.||- ..||.+-.+|.+.|+-.+|...+++..+.. .-+-..|+..+-.....|.+++|++.+++|...
T Consensus       540 ~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~  616 (777)
T KOG1128|consen  540 KAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDL  616 (777)
T ss_pred             HHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHh
Confidence            88877654  46765 569999999999999999999999988776 556667777777788899999999999988753

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

Probab=98.07  E-value=6.3e-05  Score=71.30  Aligned_cols=123  Identities=16%  Similarity=0.131  Sum_probs=72.7

Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 011378          166 LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEK--GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTF  243 (487)
Q Consensus       166 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~  243 (487)
                      ...+.....++++.+....+++++..++-.++..  ....-..|.+++|+.|.+.|..+.+..+++.=..-|+.||.+|+
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            3344555666666666666666666666655543  22223334456666666666666666666666666666666666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc
Q 011378          244 TTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV  288 (487)
Q Consensus       244 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  288 (487)
                      +.+|+.+.+.|++..|.+|...|.......+..|+.--+.+|.+.
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            666666666666666666666665555555555555555444444

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 [].

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

Probab=98.06  E-value=0.012  Score=56.16  Aligned_cols=424  Identities=10%  Similarity=0.108  Sum_probs=209.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHH
Q 011378           28 PDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLL  107 (487)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  107 (487)
                      -|+.+|+.||+-+-.. .++++.+.++++... ++.++..|..-|++-.+..+++.+.++|.+.+..-+  +...|...|
T Consensus        18 ~di~sw~~lire~qt~-~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkvL--nlDLW~lYl   93 (656)
T KOG1914|consen   18 YDIDSWSQLIREAQTQ-PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCLVKVL--NLDLWKLYL   93 (656)
T ss_pred             ccHHHHHHHHHHHccC-CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHh--hHhHHHHHH
Confidence            5889999999988544 999999999998652 333457799999999999999999999999876543  455555555


Q ss_pred             HHHHc-cCChhHHHHH----HHH-HHHCCCCCC-HhHHHHHH---------HHHHhCCCHHHHHHHHHHHHHCCCCC---
Q 011378          108 VESCR-KENMSEAEEI----FCE-MSRRGVAPD-IVSFSTLI---------GIFSRNGQLDRALMYFREMKSAGLVP---  168 (487)
Q Consensus       108 ~~~~~-~~~~~~a~~~----~~~-m~~~g~~p~-~~~~~~li---------~~~~~~g~~~~a~~~~~~m~~~g~~~---  168 (487)
                      .---+ .++...+...    |+- +.+-|+.+- ...|+.-+         .-+....+++.+.+++..+....+.-   
T Consensus        94 ~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~nlEk  173 (656)
T KOG1914|consen   94 SYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHNLEK  173 (656)
T ss_pred             HHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccccHHH
Confidence            43222 2333332222    222 223444332 22344333         23555567778888888886532211   


Q ss_pred             ---ChhhHHHHHHHHHh-------cCCHHHHHHHHHHHHH--cCCcCChhhHHHHHHHHHhcCCHH--HHHHHHHHHHH-
Q 011378          169 ---DNVLYTIIINGYCR-------NGFVLEALKMRDEMLE--KGCVMDVVTYNTILNGLCRAKMLT--EADDLFNEMLE-  233 (487)
Q Consensus       169 ---~~~~~~~ll~~~~~-------~~~~~~a~~~~~~m~~--~g~~~~~~~~~~li~~~~~~~~~~--~a~~~~~~m~~-  233 (487)
                         |-..|-.=|+....       ......|.++..++..  .|...+..+       .=..|--+  ...++|..+.+ 
T Consensus       174 LW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~-------vp~~~T~~e~~qv~~W~n~I~w  246 (656)
T KOG1914|consen  174 LWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPA-------VPPKGTKDEIQQVELWKNWIKW  246 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCC-------CCCCCChHHHHHHHHHHHHHHH
Confidence               11122222222211       2233445555555432  233222111       00001111  11122222211 


Q ss_pred             ---cCCC-CC--------HHHHHHHHHHHHhcCC-HHHHHHHHHHH----HHCCCCCCeeehHHHHHHHHccCCHHHHHH
Q 011378          234 ---RGVF-PD--------FYTFTTLIHGHCKDGN-MNKALNLFDIM----TQKSIKPDIVTYNTLIDGFCKVGEMEKANK  296 (487)
Q Consensus       234 ---~~~~-~~--------~~t~~~li~~~~~~g~-~~~a~~~~~~m----~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  296 (487)
                         .++. .+        .++|+-.|..+.-+.+ +-.+-..+...    .+.|-.|+...            ..+++..
T Consensus       247 EksNpL~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~------------~t~e~~~  314 (656)
T KOG1914|consen  247 EKSNPLRTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKS------------LTDEAAS  314 (656)
T ss_pred             HhcCCcccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchh------------hHHHHHH
Confidence               1111 00        0122222222111111 11111111111    11111111111            0223333


Q ss_pred             HHHHHHhCCCCCChhhHHHHHHHHH---hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          297 LWADMISRKISPNYISYGILINGYC---SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       297 ~~~~m~~~~~~p~~~t~~~li~~~~---~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      +++.....-..-+..+|..+.+-=-   .-...+.....++.....-..--..+|..+++.-.|..-++.|..+|.+..+
T Consensus       315 ~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~  394 (656)
T KOG1914|consen  315 IYERAIEGLLKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKARE  394 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhh
Confidence            3332221111112222222111100   0012333444444444332222233566666666677777777777777777


Q ss_pred             CCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH-
Q 011378          374 EGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR-  450 (487)
Q Consensus       374 ~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-  450 (487)
                      .+..+ ++.+++++|..|+ .++.+-|.++|+.-.+.  -+|. .--...++.+..-++=..++.+|++....++.|+. 
T Consensus       395 ~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkk--f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks  471 (656)
T KOG1914|consen  395 DKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKK--FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKS  471 (656)
T ss_pred             ccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHh--cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhh
Confidence            77666 6667777777664 35556677777543221  1232 33355666666777777777777777766555544 


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          451 -STYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       451 -~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                       ..|..+++--+..|+...+.++-+++.
T Consensus       472 ~~Iw~r~l~yES~vGdL~si~~lekR~~  499 (656)
T KOG1914|consen  472 KEIWDRMLEYESNVGDLNSILKLEKRRF  499 (656)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence             477777777777777777777766554

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.06  E-value=0.018  Score=57.85  Aligned_cols=50  Identities=26%  Similarity=0.355  Sum_probs=33.5

Q ss_pred             ChHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          430 RMHDSELILWRMIEKGLNPD----RSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       430 ~~~~a~~~~~~m~~~g~~p~----~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      +..+...-+..|.+..+-|+    ...|.-+|..|++..+|.+|.+.+.+|+..
T Consensus      1306 D~~~~i~qc~~lleep~ld~~Ir~~~~~a~lie~~v~~k~y~~AyRal~el~~k 1359 (1416)
T KOG3617|consen 1306 DAADGIRQCTTLLEEPILDDIIRCTRLFALLIEDHVSRKNYKPAYRALTELQKK 1359 (1416)
T ss_pred             hHHHHHHHHHHHhhCcCCCCcchhHHHHHHHHHHHHhhhhccHHHHHHHHHhhc
Confidence            33334444444555544443    347788889999999999999999998753

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

Probab=98.03  E-value=9.5e-05  Score=70.09  Aligned_cols=121  Identities=12%  Similarity=0.108  Sum_probs=63.1

Q ss_pred             CCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCC--CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHH
Q 011378          133 PDIVSFSTLIGIFSRNGQLDRALMYFREMKSAG--LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNT  210 (487)
Q Consensus       133 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  210 (487)
                      .+......+++.+....+++.+..++-.++...  ...-..|..++++.|.+.|..++++.++..=...|+-||..++|.
T Consensus        64 vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~  143 (429)
T PF10037_consen   64 VSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNL  143 (429)
T ss_pred             CcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHH
Confidence            344444555555555555555555555554431  111122334555555555555555555555555555555555555


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD  253 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~  253 (487)
                      ||+.+.+.|++..|.++..+|..++...++.|+...+.+|.+.
T Consensus       144 Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  144 LMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            5555555555555555555555555555555555555554444

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 [].

>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=0.00015  Score=53.88  Aligned_cols=79  Identities=18%  Similarity=0.385  Sum_probs=57.6

Q ss_pred             HHHHHHHhccCCHHHHHHHHHHHHhCCC-CCCHhhHHHHHHHHHhcC--------ChHHHHHHHHHHHHcCCCCCHHHHH
Q 011378          384 NTLINGFVREENMDKAFALVSKMENQGL-VPDVITYNVILTGFCRQG--------RMHDSELILWRMIEKGLNPDRSTYT  454 (487)
Q Consensus       384 ~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~~~~~~~li~~~~~~g--------~~~~a~~~~~~m~~~g~~p~~~ty~  454 (487)
                      ...|..|...+++.....+++.++..|+ .|++.+|+.++.+.++..        ++-....++++|...+++|+..||+
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            3445555556777777777777777777 777777777777766543        3445567888898889999999999


Q ss_pred             HHHHHHHh
Q 011378          455 TLINGHVS  462 (487)
Q Consensus       455 ~l~~~~~~  462 (487)
                      .++..+..
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            99888764

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 [, , ].

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

Probab=97.99  E-value=5.8e-05  Score=56.06  Aligned_cols=76  Identities=24%  Similarity=0.331  Sum_probs=44.3

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCC-CCCccchHHHHHHHHhcCC--------hhhHHHHHHHHHHCCCCCCHHHHHH
Q 011378           35 TLINAYCREGFLEEAFQLMNSMSGKGL-KPGVFTYNSLINGLCKKGR--------CDRAKEVLDEMLQMGLSPDTATYNT  105 (487)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~~~--------~~~a~~~~~~m~~~g~~~~~~~~~~  105 (487)
                      .-|..+...+++.....+|+.++..|+ .|+..+|+.++++.++..-        .-..+.++++|...+++|+..+|+.
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            345555556777777777777777777 6777777777776655321        1134445555555555555555555


Q ss_pred             HHHHH
Q 011378          106 LLVES  110 (487)
Q Consensus       106 ll~~~  110 (487)
                      ++..+
T Consensus       110 vl~~L  114 (120)
T PF08579_consen  110 VLGSL  114 (120)
T ss_pred             HHHHH
Confidence            55444

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 [, , ].

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

Probab=97.98  E-value=0.0027  Score=66.95  Aligned_cols=222  Identities=11%  Similarity=0.121  Sum_probs=144.0

Q ss_pred             CCc-cchHHHHHHHHhcCChhhHHHHHHHHHHC-CCCCC---HHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhH
Q 011378           63 PGV-FTYNSLINGLCKKGRCDRAKEVLDEMLQM-GLSPD---TATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVS  137 (487)
Q Consensus        63 p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~  137 (487)
                      ||+ ..|..-|..+.+.++.+.|++++++.+.. .++-.   .-.|.+++..-.-.|.-+...++|++..+.--  .-..
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd--~~~V 1532 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCD--AYTV 1532 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcc--hHHH
Confidence            554 55888888888889999999999887642 11111   23566777766667777788888888776421  1234


Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCC---hhhHHHHHHH
Q 011378          138 FSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMD---VVTYNTILNG  214 (487)
Q Consensus       138 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~li~~  214 (487)
                      |..|...|.+.+..++|.++++.|.+. +.-....|...++.+.+....+.|..++.+..+.  .|-   ..........
T Consensus      1533 ~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqL 1609 (1710)
T KOG1070|consen 1533 HLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQL 1609 (1710)
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHH
Confidence            667888888888888888888888653 2244567777778887877777777777665542  222   2233444455


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCe--eehHHHHHHHHccCC
Q 011378          215 LCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI--VTYNTLIDGFCKVGE  290 (487)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~--~~~~~li~~~~~~g~  290 (487)
                      -.+.|+.+.+..+|+.....- +--...|+..|+.=.++|+.+.+.++|+.....++.|--  ..|...+..=.+.|+
T Consensus      1610 EFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gd 1686 (1710)
T KOG1070|consen 1610 EFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGD 1686 (1710)
T ss_pred             HhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCc
Confidence            566777777777777766432 113346777777777777777777777777766666532  334444444444444

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

Probab=97.97  E-value=1e-05  Score=46.01  Aligned_cols=26  Identities=27%  Similarity=0.727  Sum_probs=10.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          418 YNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       418 ~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ||++|++|++.|++++|.++|++|.+
T Consensus         3 y~~li~~~~~~~~~~~a~~~~~~M~~   28 (31)
T PF01535_consen    3 YNSLISGYCKMGQFEEALEVFDEMRE   28 (31)
T ss_pred             HHHHHHHHHccchHHHHHHHHHHHhH
Confidence            33334444444444444444333333

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.

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

Probab=97.90  E-value=1.7e-05  Score=45.14  Aligned_cols=31  Identities=39%  Similarity=0.654  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 011378          451 STYTTLINGHVSQNNLKEAFRFHDEMLQRGF  481 (487)
Q Consensus       451 ~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~  481 (487)
                      .||+.++++|++.|++++|.+++++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            3899999999999999999999999999986

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.

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

Probab=97.88  E-value=0.01  Score=58.78  Aligned_cols=219  Identities=12%  Similarity=0.075  Sum_probs=144.1

Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 011378          167 VPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTL  246 (487)
Q Consensus       167 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~l  246 (487)
                      .|-...-..+...+...|-..+|..+++++         ..|..+|.+|+..|+...|+.+..+..+  -+||+.-|..+
T Consensus       395 pp~Wq~q~~laell~slGitksAl~I~Erl---------emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~L  463 (777)
T KOG1128|consen  395 PPIWQLQRLLAELLLSLGITKSALVIFERL---------EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLL  463 (777)
T ss_pred             CCcchHHHHHHHHHHHcchHHHHHHHHHhH---------HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHh
Confidence            344444556677788888889998888875         3678889999999999999999887766  46888888888


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHC-CCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCC
Q 011378          247 IHGHCKDGNMNKALNLFDIMTQK-SIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGH  325 (487)
Q Consensus       247 i~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~  325 (487)
                      .+......-+++|.++++....+ ......        .....++++++.+-|+.-.... +-...+|=.+-.+..+.++
T Consensus       464 GDv~~d~s~yEkawElsn~~sarA~r~~~~--------~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek  534 (777)
T KOG1128|consen  464 GDVLHDPSLYEKAWELSNYISARAQRSLAL--------LILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEK  534 (777)
T ss_pred             hhhccChHHHHHHHHHhhhhhHHHHHhhcc--------ccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhh
Confidence            88877777788888888654322 011011        1122567777777776543221 1123455555555566677


Q ss_pred             HHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHH
Q 011378          326 VTEAFRLWYEMVGKGIKPTL-VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVS  404 (487)
Q Consensus       326 ~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~  404 (487)
                      ++.|.+.|..-..  ..||. ..||.+-.+|.+.++-.+|...+.+..+-+ .-+...|..-+-.-.+.|.+++|.+.+.
T Consensus       535 ~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~  611 (777)
T KOG1128|consen  535 EQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYH  611 (777)
T ss_pred             hHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHH
Confidence            7777777665542  34443 467777777777777777777777777655 2333445555556667777777777776


Q ss_pred             HHHh
Q 011378          405 KMEN  408 (487)
Q Consensus       405 ~m~~  408 (487)
                      ++.+
T Consensus       612 rll~  615 (777)
T KOG1128|consen  612 RLLD  615 (777)
T ss_pred             HHHH
Confidence            6653

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

Probab=97.88  E-value=0.0085  Score=63.43  Aligned_cols=227  Identities=13%  Similarity=0.083  Sum_probs=159.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHC-CCCC---CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHH
Q 011378          240 FYTFTTLIHGHCKDGNMNKALNLFDIMTQK-SIKP---DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGI  315 (487)
Q Consensus       240 ~~t~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~  315 (487)
                      ...|...|......++.++|..+++..... +++-   -...|.++++.--..|.-+...++|++..+.  .-....|..
T Consensus      1458 Si~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy--cd~~~V~~~ 1535 (1710)
T KOG1070|consen 1458 SILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY--CDAYTVHLK 1535 (1710)
T ss_pred             chHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--cchHHHHHH
Confidence            345777777777777888887777765431 1111   1246777777766677777777788766542  223455677


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC---hhhHHHHHHHHhc
Q 011378          316 LINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD---SISYNTLINGFVR  392 (487)
Q Consensus       316 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~li~~~~~  392 (487)
                      |...|.+.+.+++|.++++.|.++ +.....+|......+.+..+.+.|..++....+.  -|.   ...-+-....=.+
T Consensus      1536 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 1536 LLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQLEFK 1612 (1710)
T ss_pred             HHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHHHhh
Confidence            888888888888888888888764 3366778888888888888888888888776542  222   2222333333357


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHhcCCHHHHH
Q 011378          393 EENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR--STYTTLINGHVSQNNLKEAF  470 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~ty~~l~~~~~~~~~~~~a~  470 (487)
                      .|+.+++..+|+..... ..--...|++.|+.=.++|+...++.+|++..+.++.|..  ..|..++..--++|+-+.+.
T Consensus      1613 ~GDaeRGRtlfEgll~a-yPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~vE 1691 (1710)
T KOG1070|consen 1613 YGDAERGRTLFEGLLSA-YPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEKNVE 1691 (1710)
T ss_pred             cCCchhhHHHHHHHHhh-CccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchhhHH
Confidence            88999999999877543 2224568999999999999999999999999999988865  47888888877778755544


Q ss_pred             HH
Q 011378          471 RF  472 (487)
Q Consensus       471 ~~  472 (487)
                      .+
T Consensus      1692 ~V 1693 (1710)
T KOG1070|consen 1692 YV 1693 (1710)
T ss_pred             HH
Confidence            33

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.85  E-value=0.024  Score=52.46  Aligned_cols=292  Identities=15%  Similarity=0.079  Sum_probs=188.7

Q ss_pred             HHHHHHHHHh--CCCHHHHHHHHHHHHHCC-CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChh-hHHHHHH
Q 011378          138 FSTLIGIFSR--NGQLDRALMYFREMKSAG-LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVV-TYNTILN  213 (487)
Q Consensus       138 ~~~li~~~~~--~g~~~~a~~~~~~m~~~g-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~li~  213 (487)
                      .+.-+.+++.  .++-..+...+-.+.... +.-|......+-+.+...|+.+++...|++.+..  .|+.. ....---
T Consensus       197 ls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~  274 (564)
T KOG1174|consen  197 LSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAV  274 (564)
T ss_pred             HHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHH
Confidence            3334444433  444445554444444333 3445667888888999999999998888876542  22221 1122223


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHH---HHHHccCC
Q 011378          214 GLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLI---DGFCKVGE  290 (487)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li---~~~~~~g~  290 (487)
                      .+.+.|++++...+-..+.... .-+...|-.-.......++.+.|+.+-+...    ..+....-.+|   ..+...|+
T Consensus       275 LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I----~~~~r~~~alilKG~lL~~~~R  349 (564)
T KOG1174|consen  275 LLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCI----DSEPRNHEALILKGRLLIALER  349 (564)
T ss_pred             HHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHh----ccCcccchHHHhccHHHHhccc
Confidence            3456788888777777765432 1122223333344456677888877665544    33444443444   45677889


Q ss_pred             HHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHH-HHHHH-hcCChHHHHHH
Q 011378          291 MEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTI-IKGYC-RSGDASKADEF  367 (487)
Q Consensus       291 ~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~l-i~~~~-~~~~~~~a~~~  367 (487)
                      .++|.=-|+..+.  +.| +..+|..|+.+|...|.+.+|.-+-++..+. ++.+..+.+.+ -.+|. ...--++|+.+
T Consensus       350 ~~~A~IaFR~Aq~--Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf  426 (564)
T KOG1174|consen  350 HTQAVIAFRTAQM--LAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKF  426 (564)
T ss_pred             hHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHH
Confidence            9999888887653  444 6789999999999999999998877665432 23344444333 12332 22335778888


Q ss_pred             HHHHHHCCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          368 LSKMVSEGVDPDSI-SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       368 ~~~m~~~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +++-.  .+.|+.. ..+.+-..|...|..+++..++++-..  ..||....+.|-+.+...+.+.+|...|.....
T Consensus       427 ~ek~L--~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr  499 (564)
T KOG1174|consen  427 AEKSL--KINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALR  499 (564)
T ss_pred             HHhhh--ccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            87654  3557643 566777888899999999999987654  479999999999999999999999988887654

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.82  E-value=0.0062  Score=54.21  Aligned_cols=185  Identities=12%  Similarity=0.024  Sum_probs=114.9

Q ss_pred             eeehHHHHHHHHccCCHHHHHHHHHHHHhCCC-CCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CCh-hhHHH
Q 011378          275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKI-SPN-YISYGILINGYCSMGHVTEAFRLWYEMVGKGIK-PTL-VSCNT  350 (487)
Q Consensus       275 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~-~~~~~  350 (487)
                      ...+-.+...+.+.|++++|...|.+...... .|. ...+..+..++...|++++|...++.+.+..-. |.. .++..
T Consensus        33 ~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~  112 (235)
T TIGR03302        33 AEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYL  112 (235)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHH
Confidence            34566666778888899999888888765431 111 235667778888888999999988888754311 111 12333


Q ss_pred             HHHHHHhc--------CChHHHHHHHHHHHHCCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHH
Q 011378          351 IIKGYCRS--------GDASKADEFLSKMVSEGVDPDSI-SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVI  421 (487)
Q Consensus       351 li~~~~~~--------~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  421 (487)
                      +-.++...        |+.+.|.+.++.....  .|+.. .+..+.... .   ..      ....        ...-.+
T Consensus       113 ~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~-~---~~------~~~~--------~~~~~~  172 (235)
T TIGR03302       113 RGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMD-Y---LR------NRLA--------GKELYV  172 (235)
T ss_pred             HHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHH-H---HH------HHHH--------HHHHHH
Confidence            33344433        5677777777777653  23322 121111100 0   00      0000        011245


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCC-CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          422 LTGFCRQGRMHDSELILWRMIEKGL-NP-DRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       422 i~~~~~~g~~~~a~~~~~~m~~~g~-~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      ...+.+.|++.+|...+.+.....- .| ....+..+..++...|++++|..+++.+...
T Consensus       173 a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       173 ARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5678899999999999999876421 23 3568889999999999999999998888654

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).

>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=97.81  E-value=0.00034  Score=58.85  Aligned_cols=104  Identities=19%  Similarity=0.304  Sum_probs=66.8

Q ss_pred             CCChhhHHHHHHHHHhc-----CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChh
Q 011378          307 SPNYISYGILINGYCSM-----GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSI  381 (487)
Q Consensus       307 ~p~~~t~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  381 (487)
                      ..+-.+|..+++.|...     |+++-....+..|...|++-|..+|+.||+.+-+ |.+.               |...
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv---------------p~n~  107 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV---------------PRNF  107 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc---------------cccH
Confidence            45667777777777543     5666666666677777777777777777776654 2211               1111


Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcC
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG  429 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  429 (487)
                      ... +---|  ..+-+-|.+++++|+..|+-||..++..++..|++.+
T Consensus       108 fQ~-~F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s  152 (228)
T PF06239_consen  108 FQA-EFMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKS  152 (228)
T ss_pred             HHH-HhccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcccc
Confidence            111 11111  2345678888999999999999999999999987665

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

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

Probab=97.76  E-value=0.023  Score=49.52  Aligned_cols=167  Identities=17%  Similarity=0.179  Sum_probs=103.5

Q ss_pred             HHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC
Q 011378          300 DMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD  379 (487)
Q Consensus       300 ~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  379 (487)
                      .+.......+...-..-...|+..|++++|++....    +-  +....-.=...+.+..+.+-|...+++|.+-   -+
T Consensus        98 ~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~----~~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i---de  168 (299)
T KOG3081|consen   98 LVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHL----GE--NLEAAALNVQILLKMHRFDLAEKELKKMQQI---DE  168 (299)
T ss_pred             HHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhc----cc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc---ch
Confidence            333333333333333344557788888888887654    11  2222222233455667788888888888752   24


Q ss_pred             hhhHHHHHHHHhc----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHH
Q 011378          380 SISYNTLINGFVR----EENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTT  455 (487)
Q Consensus       380 ~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~  455 (487)
                      ..|.+-|-.+|++    .+++.+|.-+|++|-+. ..|+..+-+.....+...|++++|+.+++..+.+.-. ++.|...
T Consensus       169 d~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL~N  246 (299)
T KOG3081|consen  169 DATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETLAN  246 (299)
T ss_pred             HHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHHHH
Confidence            5566666666654    35688888888888653 5788888888888888888888888888888765432 3445555


Q ss_pred             HHHHHHhcCC-HHHHHHHHHHHH
Q 011378          456 LINGHVSQNN-LKEAFRFHDEML  477 (487)
Q Consensus       456 l~~~~~~~~~-~~~a~~~~~~m~  477 (487)
                      ++-+-...|. .+-.-+.+.++.
T Consensus       247 liv~a~~~Gkd~~~~~r~l~QLk  269 (299)
T KOG3081|consen  247 LIVLALHLGKDAEVTERNLSQLK  269 (299)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHH
Confidence            5444444444 333445555554

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.75  E-value=0.0058  Score=54.42  Aligned_cols=61  Identities=18%  Similarity=0.074  Sum_probs=35.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-H---HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          206 VTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD-F---YTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~---~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      ..+-.+...+.+.|+++.|...|++.....  |+ +   ..+..+..++...|++++|...++.+.+
T Consensus        34 ~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~   98 (235)
T TIGR03302        34 EELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIR   98 (235)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            344555556666677777776666665432  22 1   2445555666666666666666666554

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).

>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=97.69  E-value=0.00037  Score=58.63  Aligned_cols=105  Identities=18%  Similarity=0.219  Sum_probs=64.6

Q ss_pred             CCCHHHHHHHHHHHHc-----cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChh
Q 011378           97 SPDTATYNTLLVESCR-----KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNV  171 (487)
Q Consensus        97 ~~~~~~~~~ll~~~~~-----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~  171 (487)
                      ..|..+|..++..+.+     .|.++-....+..|.+.|+.-|..+|+.||..+-+..-.                |...
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fv----------------p~n~  107 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFV----------------PRNF  107 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcc----------------cccH
Confidence            3566666666666653     467777777788888888888888888888877653211                1111


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC
Q 011378          172 LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM  220 (487)
Q Consensus       172 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~  220 (487)
                      ......   -...+.+-+.+++++|+..|+.||..|+..|++.+++.+.
T Consensus       108 fQ~~F~---hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  108 FQAEFM---HYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHhc---cCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            111000   0122345566677777777777777777777777766554

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

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

Probab=97.66  E-value=0.053  Score=56.69  Aligned_cols=57  Identities=14%  Similarity=0.165  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWAD  300 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  300 (487)
                      .+..+-.+|-+.|+.+++..+|+.+.+.. +-|....|.+-..|+.. ++++|..++..
T Consensus       118 Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~K  174 (906)
T PRK14720        118 ALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKK  174 (906)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHH
Confidence            33444444445555555555555444433 22334444444444444 55555544443

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=97.62  E-value=0.092  Score=52.61  Aligned_cols=212  Identities=17%  Similarity=0.100  Sum_probs=126.5

Q ss_pred             HHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCC
Q 011378           19 CEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSP   98 (487)
Q Consensus        19 ~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~   98 (487)
                      .+++...++-|+..|..+.=++.+.|+++.+-+.|++..-. ..-..+.|+.+-..++..|.-..|..+++.-....-.|
T Consensus       312 ~k~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~-~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~p  390 (799)
T KOG4162|consen  312 RKLRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPF-SFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQP  390 (799)
T ss_pred             HHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh-hhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCC
Confidence            34444456678888888888888889988888888875432 22244667777777888888888888887654332224


Q ss_pred             CH-HHHHHHHHHHH-ccCChhHHHHHHHHHHH--CCCC--CCHhHHHHHHHHHHh----C-------CCHHHHHHHHHHH
Q 011378           99 DT-ATYNTLLVESC-RKENMSEAEEIFCEMSR--RGVA--PDIVSFSTLIGIFSR----N-------GQLDRALMYFREM  161 (487)
Q Consensus        99 ~~-~~~~~ll~~~~-~~~~~~~a~~~~~~m~~--~g~~--p~~~~~~~li~~~~~----~-------g~~~~a~~~~~~m  161 (487)
                      +. ..+-..-+.|. +.+.++++.+.-.+...  .|..  .....|-.+--+|..    .       ....++++.+++.
T Consensus       391 s~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~a  470 (799)
T KOG4162|consen  391 SDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEA  470 (799)
T ss_pred             CcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHH
Confidence            32 22222222232 33566666655544443  1111  111222222222221    1       1223566777776


Q ss_pred             HHCCC-CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          162 KSAGL-VPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       162 ~~~g~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (487)
                      .+.+. .|+...|-++ . |+-.+++..|.+...+..+-+-.-+...|.-+.-.+...+++.+|+.+.+...+
T Consensus       471 v~~d~~dp~~if~lal-q-~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~  541 (799)
T KOG4162|consen  471 VQFDPTDPLVIFYLAL-Q-YAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALE  541 (799)
T ss_pred             HhcCCCCchHHHHHHH-H-HHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence            66443 3333333332 2 556778888888888887776666778888888888888888888888776654

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

Probab=97.62  E-value=0.018  Score=55.45  Aligned_cols=245  Identities=18%  Similarity=0.155  Sum_probs=165.4

Q ss_pred             HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHH
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLE  188 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~  188 (487)
                      +.+.|++.+|.-.|+...+.. +-+...|.-|-...+..++=..|+..+.+..+  +.|+ ......|--.|...|.-.+
T Consensus       295 lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~--LdP~NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLE--LDPTNLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHh--cCCccHHHHHHHHHHHhhhhhHHH
Confidence            457788888888888776653 22566787788888888888888888777665  3454 4456667777888898899


Q ss_pred             HHHHHHHHHHcCCc--------CChhhHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhcCCHHHH
Q 011378          189 ALKMRDEMLEKGCV--------MDVVTYNTILNGLCRAKMLTEADDLFNEMLE-RGVFPDFYTFTTLIHGHCKDGNMNKA  259 (487)
Q Consensus       189 a~~~~~~m~~~g~~--------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~~~~~t~~~li~~~~~~g~~~~a  259 (487)
                      |+++++.+.....+        ++...-+.  ..+.....+..+.++|-++.. .+.++|+.....|--.|--.|++++|
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            99999888654321        01110000  222233345667777777644 45557777888888888889999999


Q ss_pred             HHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCCHHHHHHHHHHH-
Q 011378          260 LNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-ISYGILINGYCSMGHVTEAFRLWYEM-  336 (487)
Q Consensus       260 ~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m-  336 (487)
                      .+.|+...+  ++| |..+||.|=-.++...+.++|..-|++..+  ++|+. ...-.|--+|...|.+++|.+.|-.. 
T Consensus       450 iDcf~~AL~--v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  450 VDCFEAALQ--VKPNDYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPGYVRVRYNLGISCMNLGAYKEAVKHLLEAL  525 (579)
T ss_pred             HHHHHHHHh--cCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHH
Confidence            999987764  356 456789988888888889999999987764  45654 23445666788999999998877653 


Q ss_pred             --HhCCC------CCChhhHHHHHHHHHhcCChHH
Q 011378          337 --VGKGI------KPTLVSCNTIIKGYCRSGDASK  363 (487)
Q Consensus       337 --~~~~~------~~~~~~~~~li~~~~~~~~~~~  363 (487)
                        .+++-      .++-..|.+|=.++...++.+.
T Consensus       526 ~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~  560 (579)
T KOG1125|consen  526 SMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDL  560 (579)
T ss_pred             HhhhcccccccCCcchHHHHHHHHHHHHHcCCchH
Confidence              33311      1223456666555555555443

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

Probab=97.59  E-value=0.021  Score=59.55  Aligned_cols=236  Identities=10%  Similarity=0.091  Sum_probs=121.9

Q ss_pred             ccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHH-HHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 011378           65 VFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLV-ESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIG  143 (487)
Q Consensus        65 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~-~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  143 (487)
                      ...|..|++.+...+++++|.++.+.-.+.  .|+...+-.+.. .+...++.+++.-+                 .++.
T Consensus        31 ~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv-----------------~~l~   91 (906)
T PRK14720         31 FKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL-----------------NLID   91 (906)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh-----------------hhhh
Confidence            455666777777777777777777744432  344322211111 33333333333222                 2333


Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHH
Q 011378          144 IFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTE  223 (487)
Q Consensus       144 ~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~  223 (487)
                      .+....++..+..+...|...  .-+...+..+..+|-+.|..+++..++++..+.. +-|+...|.+-..|... +++.
T Consensus        92 ~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~K  167 (906)
T PRK14720         92 SFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEK  167 (906)
T ss_pred             hcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHH
Confidence            344444443333344444332  1223355566666666677777777777666655 44556666666666666 6666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHh
Q 011378          224 ADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMIS  303 (487)
Q Consensus       224 a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  303 (487)
                      |.+++.+....               +...+++..+.++|..+....  |+               +++.-.++.+.+..
T Consensus       168 A~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~--~~---------------d~d~f~~i~~ki~~  215 (906)
T PRK14720        168 AITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYN--SD---------------DFDFFLRIERKVLG  215 (906)
T ss_pred             HHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcC--cc---------------cchHHHHHHHHHHh
Confidence            66666665442               455556666666666655431  11               12222222222222


Q ss_pred             C-CCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011378          304 R-KISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYC  356 (487)
Q Consensus       304 ~-~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  356 (487)
                      . +..--+.++-.+-..|-...+++++..+++.+.+.. +.|.....-|+.+|.
T Consensus       216 ~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~-~~n~~a~~~l~~~y~  268 (906)
T PRK14720        216 HREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHD-NKNNKAREELIRFYK  268 (906)
T ss_pred             hhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcC-CcchhhHHHHHHHHH
Confidence            1 223334455555566666677777777777766543 234445555665554

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=97.47  E-value=0.15  Score=51.21  Aligned_cols=206  Identities=12%  Similarity=0.092  Sum_probs=114.9

Q ss_pred             CCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhH
Q 011378           94 MGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLY  173 (487)
Q Consensus        94 ~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~  173 (487)
                      ..+.-|...|.-|.-+..+.|+++.+.+.|++....-+. ....|..+-..++-+|.-..|..+++.-....-.|+..+-
T Consensus       317 ~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~-~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~  395 (799)
T KOG4162|consen  317 KKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFG-EHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISV  395 (799)
T ss_pred             hhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-hHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchH
Confidence            345567777777777888888888888888776543222 3445777777777777777777777765433222432222


Q ss_pred             HHHH-HHHH-hcCCHHHHHHHHHHHHH----cCCcCChhhHHHHHHHHHhc-----------CCHHHHHHHHHHHHHcC-
Q 011378          174 TIII-NGYC-RNGFVLEALKMRDEMLE----KGCVMDVVTYNTILNGLCRA-----------KMLTEADDLFNEMLERG-  235 (487)
Q Consensus       174 ~~ll-~~~~-~~~~~~~a~~~~~~m~~----~g~~~~~~~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~-  235 (487)
                      -.++ ..|. +.+.+++++++-.+..+    ..-...+..|..+--+|...           .....+.+.+++..+.+ 
T Consensus       396 ~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~  475 (799)
T KOG4162|consen  396 LLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDP  475 (799)
T ss_pred             HHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCC
Confidence            2222 2222 23455555554443333    11112233444333333321           12334445555554432 


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHH
Q 011378          236 VFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       236 ~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  302 (487)
                      -.|+..-|-++  -|+..++++.|.+..+...+-+-.-+...|.-|.-.+...+++.+|+.+.....
T Consensus       476 ~dp~~if~lal--q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al  540 (799)
T KOG4162|consen  476 TDPLVIFYLAL--QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAAL  540 (799)
T ss_pred             CCchHHHHHHH--HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence            23333333333  456667778887777777666555666777777777777777777777776544

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.46  E-value=0.051  Score=55.96  Aligned_cols=229  Identities=13%  Similarity=0.080  Sum_probs=146.9

Q ss_pred             HHHHHHHHhcCChhHH-HHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 011378           34 NTLINAYCREGFLEEA-FQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCR  112 (487)
Q Consensus        34 ~~ll~~~~~~~~~~~a-~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  112 (487)
                      .-+=.+++.-|..++| .+++++..+            ++...++.....+++.-...... ....+...+-.|-.....
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~La~i~~~   98 (694)
T PRK15179         32 DLLEAALAEPGESEEAGRELLQQARQ------------VLERHAAVHKPAAALPELLDYVR-RYPHTELFQVLVARALEA   98 (694)
T ss_pred             hHHHHHhcCcccchhHHHHHHHHHHH------------HHHHhhhhcchHhhHHHHHHHHH-hccccHHHHHHHHHHHHH
Confidence            3333445556666655 344544432            44444444444433333322221 234457777778888888


Q ss_pred             cCChhHHHHHHHHHHHCCCCCC-HhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCh-hhHHHHHHHHHhcCCHHHHH
Q 011378          113 KENMSEAEEIFCEMSRRGVAPD-IVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDN-VLYTIIINGYCRNGFVLEAL  190 (487)
Q Consensus       113 ~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~-~~~~~ll~~~~~~~~~~~a~  190 (487)
                      .|..++|+.+++...+.  .|+ ......+..++.+.+++++|+...++....  .|+. .....+-.++.+.|..++|.
T Consensus        99 ~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~~a~~l~~~g~~~~A~  174 (694)
T PRK15179         99 AHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILLEAKSWDEIGQSEQAD  174 (694)
T ss_pred             cCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHhcchHHHH
Confidence            99999999999988774  564 445666788889999999999999888764  4554 45666677788899999999


Q ss_pred             HHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          191 KMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKS  270 (487)
Q Consensus       191 ~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~  270 (487)
                      .+|++.... .+-+..++-.+-.++...|+.++|...|+...+. ..|...-|+..+.      ++..-...++.+.-.+
T Consensus       175 ~~y~~~~~~-~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~-~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~  246 (694)
T PRK15179        175 ACFERLSRQ-HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA-IGDGARKLTRRLV------DLNADLAALRRLGVEG  246 (694)
T ss_pred             HHHHHHHhc-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-hCcchHHHHHHHH------HHHHHHHHHHHcCccc
Confidence            999999873 2234667888888888899999999999988764 2344555555442      3344445555443332


Q ss_pred             ----CCCCeeehHHHHHHHHc
Q 011378          271 ----IKPDIVTYNTLIDGFCK  287 (487)
Q Consensus       271 ----~~~~~~~~~~li~~~~~  287 (487)
                          ....+.....+|..|.+
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~  267 (694)
T PRK15179        247 DGRDVPVSILVLEKMLQEIGR  267 (694)
T ss_pred             ccCCCceeeeeHHHHHHHHhh
Confidence                22233344555555443

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

Probab=97.44  E-value=0.022  Score=49.53  Aligned_cols=159  Identities=11%  Similarity=0.016  Sum_probs=103.0

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc
Q 011378          279 NTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRS  358 (487)
Q Consensus       279 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  358 (487)
                      ..+-..+-..|+-+....+...... ....|....+.......+.|++..|...+++.... -++|...|+.+=-+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~-~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAI-AYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhc-cCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHc
Confidence            3344455555665555555544321 11223344455777777778888888877776543 366777788777788888


Q ss_pred             CChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHH
Q 011378          359 GDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       359 ~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      |+.+.|..-+.+..+.-. -+....|.|--.|.-.|+++.|..++.+-...+ .-|...-..+.-.-..+|++++|+.+.
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 GRFDEARRAYRQALELAP-NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             cChhHHHHHHHHHHHhcc-CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhhc
Confidence            888888877777665322 133456666666677788888888887776654 225556677777778888888887766


Q ss_pred             HHH
Q 011378          439 WRM  441 (487)
Q Consensus       439 ~~m  441 (487)
                      .+-
T Consensus       226 ~~e  228 (257)
T COG5010         226 VQE  228 (257)
T ss_pred             ccc
Confidence            554

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

Probab=97.40  E-value=0.0088  Score=56.74  Aligned_cols=118  Identities=16%  Similarity=0.195  Sum_probs=51.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCC
Q 011378          316 LINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREEN  395 (487)
Q Consensus       316 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~  395 (487)
                      |+..+...++++.|..+++++.+..  |+.  .-.+.+.+...++-.+|.+++++..+. .+-|......-..-|.+.++
T Consensus       175 Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~~  249 (395)
T PF09295_consen  175 LLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKKK  249 (395)
T ss_pred             HHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCC
Confidence            3334444455555555555554443  332  223444444445555555555544421 11122223333333444444


Q ss_pred             HHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHH
Q 011378          396 MDKAFALVSKMENQGLVPDV-ITYNVILTGFCRQGRMHDSELILWR  440 (487)
Q Consensus       396 ~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~  440 (487)
                      .+.|.++.++..+.  .|+. .+|..|...|.+.|+++.|...+..
T Consensus       250 ~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs  293 (395)
T PF09295_consen  250 YELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNS  293 (395)
T ss_pred             HHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhc
Confidence            55555544444332  3332 2444444455555555544444443

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

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.40  E-value=0.12  Score=48.63  Aligned_cols=441  Identities=16%  Similarity=0.211  Sum_probs=220.3

Q ss_pred             HHhcCChhhHHHHHHHHHhCCCCCChh------hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHH--HH
Q 011378            5 LCKDHKIDSAKMFLCEMEQKGVYPDTV------TYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLING--LC   76 (487)
Q Consensus         5 ~~~~~~~~~a~~~~~~~~~~g~~p~~~------~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~--~~   76 (487)
                      +-+.+++.++..+|.++-+..- -+++      .-+.++++|-.. +++..........+.  .| ...|-.+..+  +.
T Consensus        16 Lqkq~~~~esEkifskI~~e~~-~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~Y   90 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDEKE-SSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQ--FG-KSAYLPLFKALVAY   90 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhh-cchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHh--cC-CchHHHHHHHHHHH
Confidence            4578899999999999865431 2222      345566676544 344444444344332  23 3346666665  34


Q ss_pred             hcCChhhHHHHHHHHHHC--CCCC------------CHHHHHHHHHHHHccCChhHHHHHHHHHHHC----CCCCCHhHH
Q 011378           77 KKGRCDRAKEVLDEMLQM--GLSP------------DTATYNTLLVESCRKENMSEAEEIFCEMSRR----GVAPDIVSF  138 (487)
Q Consensus        77 ~~~~~~~a~~~~~~m~~~--g~~~------------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~p~~~~~  138 (487)
                      +.+.++.|.+.+....+.  +-.|            |..-=+....++...|.+.++..+++.|...    ...-+..+|
T Consensus        91 ~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~y  170 (549)
T PF07079_consen   91 KQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMY  170 (549)
T ss_pred             HhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHH
Confidence            788999999998877655  3222            2222244556677889999999988888653    334688889


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHH---CCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHH
Q 011378          139 STLIGIFSRNGQLDRALMYFREMKS---AGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGL  215 (487)
Q Consensus       139 ~~li~~~~~~g~~~~a~~~~~~m~~---~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~  215 (487)
                      +.++-.++|+        +|-++++   ..+-||   |--++-.|-+.=...++.. +     ..+.|.......++...
T Consensus       171 d~~vlmlsrS--------YfLEl~e~~s~dl~pd---yYemilfY~kki~~~d~~~-Y-----~k~~peeeL~s~imqhl  233 (549)
T PF07079_consen  171 DRAVLMLSRS--------YFLELKESMSSDLYPD---YYEMILFYLKKIHAFDQRP-Y-----EKFIPEEELFSTIMQHL  233 (549)
T ss_pred             HHHHHHHhHH--------HHHHHHHhcccccChH---HHHHHHHHHHHHHHHhhch-H-----HhhCcHHHHHHHHHHHH
Confidence            9888887775        3333332   223332   2233333322111100000 0     00112222222222222


Q ss_pred             Hhc--CCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC----CeeehHHHHHHHHcc
Q 011378          216 CRA--KMLTEADDLFNEMLERGVFPDFY-TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP----DIVTYNTLIDGFCKV  288 (487)
Q Consensus       216 ~~~--~~~~~a~~~~~~m~~~~~~~~~~-t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~----~~~~~~~li~~~~~~  288 (487)
                      .-.  ....--.+++..+.+.-+.|+-. ....++..+..  +.+.+..+-+.+....+.+    =+.+|..++....+.
T Consensus       234 fi~p~e~l~~~mq~l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~  311 (549)
T PF07079_consen  234 FIVPKERLPPLMQILENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQ  311 (549)
T ss_pred             HhCCHhhccHHHHHHHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            111  11122223333334444455432 22333333333  3333333333222211111    123566666666666


Q ss_pred             CCHHHHHHHHHHHHhCCCCCChhh-------HHHHHHHHH----hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH---
Q 011378          289 GEMEKANKLWADMISRKISPNYIS-------YGILINGYC----SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKG---  354 (487)
Q Consensus       289 g~~~~a~~~~~~m~~~~~~p~~~t-------~~~li~~~~----~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~---  354 (487)
                      ++..+|...+.-...-  .|+...       -..+-+..+    ..-+..+-+.+|++.....+..-. ..+-|+.+   
T Consensus       312 ~~T~~a~q~l~lL~~l--dp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrqQ-Lvh~L~~~Ak~  388 (549)
T PF07079_consen  312 VQTEEAKQYLALLKIL--DPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQQ-LVHYLVFGAKH  388 (549)
T ss_pred             HhHHHHHHHHHHHHhc--CCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHHH-HHHHHHHHHHH
Confidence            6666666666544321  122110       011111111    112345566677766655432221 12223322   


Q ss_pred             HHhcCC-hHHHHHHHHHHHHCCCCC-ChhhHHHHH----HHHhc---cCCHHHHHHHHHHHHhCCCCCCH----hhHHHH
Q 011378          355 YCRSGD-ASKADEFLSKMVSEGVDP-DSISYNTLI----NGFVR---EENMDKAFALVSKMENQGLVPDV----ITYNVI  421 (487)
Q Consensus       355 ~~~~~~-~~~a~~~~~~m~~~g~~p-~~~~~~~li----~~~~~---~~~~~~a~~~~~~m~~~g~~p~~----~~~~~l  421 (487)
                      +=+.|. -++|.++++...+  +.| |..+-|+..    .+|..   ...+..-.++-+-..+.|+.|-.    ..-|.|
T Consensus       389 lW~~g~~dekalnLLk~il~--ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~L  466 (549)
T PF07079_consen  389 LWEIGQCDEKALNLLKLILQ--FTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFL  466 (549)
T ss_pred             HHhcCCccHHHHHHHHHHHH--hccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHH
Confidence            334444 6777777777664  222 222222221    22221   22344444444555677877743    334555


Q ss_pred             HHH--HHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          422 LTG--FCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       422 i~~--~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      .+|  +-.+|+++++...-.-+.  .+.|++.+|..+--++....++++|-.+++++
T Consensus       467 aDAEyLysqgey~kc~~ys~WL~--~iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~L  521 (549)
T PF07079_consen  467 ADAEYLYSQGEYHKCYLYSSWLT--KIAPSPQAYRLLGLCLMENKRYQEAWEYLQKL  521 (549)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHH--HhCCcHHHHHHHHHHHHHHhhHHHHHHHHHhC
Confidence            543  356788888865444443  46788889888888888888899998888754

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

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

Probab=97.34  E-value=0.012  Score=47.86  Aligned_cols=86  Identities=16%  Similarity=0.273  Sum_probs=40.4

Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCCh--hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCC
Q 011378          353 KGYCRSGDASKADEFLSKMVSEGVDPDS--ISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGR  430 (487)
Q Consensus       353 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  430 (487)
                      +.+...|++++|...|+......-.|+.  ...-.|-..+...|++++|...++......  .....+...-+.+.+.|+
T Consensus        56 ~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~--~~~~~~~~~Gdi~~~~g~  133 (145)
T PF09976_consen   56 KAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPDEA--FKALAAELLGDIYLAQGD  133 (145)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcc--hHHHHHHHHHHHHHHCCC
Confidence            4455556666666666555554422221  122234444555555555555554432221  122233444445555555


Q ss_pred             hHHHHHHHHH
Q 011378          431 MHDSELILWR  440 (487)
Q Consensus       431 ~~~a~~~~~~  440 (487)
                      +++|...|++
T Consensus       134 ~~~A~~~y~~  143 (145)
T PF09976_consen  134 YDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHH
Confidence            5555555543

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

Probab=97.33  E-value=0.094  Score=45.83  Aligned_cols=86  Identities=16%  Similarity=0.262  Sum_probs=43.2

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH----hcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCC
Q 011378          215 LCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHC----KDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE  290 (487)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~----~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~  290 (487)
                      +.+..+++.|++.+++|.+-   -+..|.+-|-.++.    -.+.+.+|.-+|++|.+ ...|+..+.+....++...|+
T Consensus       147 ~lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~  222 (299)
T KOG3081|consen  147 LLKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGR  222 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcC
Confidence            34445566666666666542   12334433333322    23345566666665543 234445555555555555566


Q ss_pred             HHHHHHHHHHHHhC
Q 011378          291 MEKANKLWADMISR  304 (487)
Q Consensus       291 ~~~a~~~~~~m~~~  304 (487)
                      +++|..++++....
T Consensus       223 ~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  223 YEEAESLLEEALDK  236 (299)
T ss_pred             HHHHHHHHHHHHhc
Confidence            66666666555443

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

Probab=97.33  E-value=0.009  Score=56.66  Aligned_cols=124  Identities=18%  Similarity=0.190  Sum_probs=99.5

Q ss_pred             hHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          278 YNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR  357 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  357 (487)
                      ..+|++.+...++++.|..+|+++....  |+.  ...+...+...++-.+|.++.++.... .+-+....+.-.+.|.+
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHh
Confidence            4566677777899999999999998765  554  345788888888889999998888743 24456666666777889


Q ss_pred             cCChHHHHHHHHHHHHCCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          358 SGDASKADEFLSKMVSEGVDPDSI-SYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       358 ~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      .++.+.|..+.+++..  ..|+.. +|..|..+|...|+++.|...+..+.-
T Consensus       247 k~~~~lAL~iAk~av~--lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  247 KKKYELALEIAKKAVE--LSPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             cCCHHHHHHHHHHHHH--hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            9999999999998875  457665 999999999999999999998887753

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

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

Probab=97.32  E-value=0.012  Score=47.81  Aligned_cols=126  Identities=13%  Similarity=0.131  Sum_probs=88.7

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhH--HHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH--hhHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISY--NTLINGFVREENMDKAFALVSKMENQGLVPDV--ITYNVIL  422 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~--~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~--~~~~~li  422 (487)
                      .|..++..+. .++...+...++.+.+..-.......  -.+-..+...|++++|...|+...+..-.|+.  ...-.|.
T Consensus        14 ~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA   92 (145)
T PF09976_consen   14 LYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLA   92 (145)
T ss_pred             HHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHH
Confidence            4555555653 78888888888888875322112222  23447778899999999999999886522221  2344567


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDE  475 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~  475 (487)
                      ..+...|++++|...++......+  ....+...-+.|...|++++|...|+.
T Consensus        93 ~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   93 RILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            788899999999999977433332  334566677899999999999998874

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.32  E-value=0.092  Score=45.54  Aligned_cols=184  Identities=15%  Similarity=0.203  Sum_probs=110.2

Q ss_pred             HhcCCHHHHHHHHHHHHH---cC-CCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCee----ehHHHHHHHH
Q 011378          216 CRAKMLTEADDLFNEMLE---RG-VFPDFYT-FTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIV----TYNTLIDGFC  286 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~---~~-~~~~~~t-~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~li~~~~  286 (487)
                      ....+.+++.+++.++..   .| ..++.++ |.-++-+....|+.+.|...++.++.+-  |...    ....++   -
T Consensus        23 ~~~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~l---E   97 (289)
T KOG3060|consen   23 ETVRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLL---E   97 (289)
T ss_pred             ccccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHH---H
Confidence            345677778877777753   34 5566554 4555666677777888887777776553  3321    122222   2


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHH
Q 011378          287 KVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADE  366 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  366 (487)
                      ..|+.++|.+++....... +.|.+++---+...-..|+--+|++-+.+..+. +..|...|.-+-..|...|++++|.-
T Consensus        98 a~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~f  175 (289)
T KOG3060|consen   98 ATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAF  175 (289)
T ss_pred             HhhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHH
Confidence            3567777777777766554 345556655555555566666666666655432 45677777777777777777777777


Q ss_pred             HHHHHHHCCCCC-ChhhHHHHHHHHhccC---CHHHHHHHHHHHHh
Q 011378          367 FLSKMVSEGVDP-DSISYNTLINGFVREE---NMDKAFALVSKMEN  408 (487)
Q Consensus       367 ~~~~m~~~g~~p-~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~  408 (487)
                      +++++.-  +.| ++..+..+-+.+...|   +++.+.+.+.+-.+
T Consensus       176 ClEE~ll--~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alk  219 (289)
T KOG3060|consen  176 CLEELLL--IQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALK  219 (289)
T ss_pred             HHHHHHH--cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            7777764  234 3334445554444333   44555555555443

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

Probab=97.31  E-value=0.076  Score=45.66  Aligned_cols=154  Identities=7%  Similarity=0.057  Sum_probs=94.0

Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChH
Q 011378          283 DGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDAS  362 (487)
Q Consensus       283 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~  362 (487)
                      -.|...|+++.+......+..    |. .       .+...++.+++...++...... +.|...|..+-..|...|+.+
T Consensus        24 ~~Y~~~g~~~~v~~~~~~~~~----~~-~-------~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~   90 (198)
T PRK10370         24 GSYLLSPKWQAVRAEYQRLAD----PL-H-------QFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYD   90 (198)
T ss_pred             HHHHHcchHHHHHHHHHHHhC----cc-c-------cccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHH
Confidence            557778887775433322111    11 0       1112455566666565554432 456667777777888888888


Q ss_pred             HHHHHHHHHHHCCCCC-ChhhHHHHHHH-HhccCC--HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHH
Q 011378          363 KADEFLSKMVSEGVDP-DSISYNTLING-FVREEN--MDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       363 ~a~~~~~~m~~~g~~p-~~~~~~~li~~-~~~~~~--~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      +|...++...+..  | +...+..+-.+ |...|+  .++|.+++++..+.. .-+...+..+...+.+.|++++|...+
T Consensus        91 ~A~~a~~~Al~l~--P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~  167 (198)
T PRK10370         91 NALLAYRQALQLR--GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELW  167 (198)
T ss_pred             HHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHH
Confidence            8888888776543  3 44555555554 355565  478888888776643 225566777777778888888888888


Q ss_pred             HHHHHcCCCCCHHHH
Q 011378          439 WRMIEKGLNPDRSTY  453 (487)
Q Consensus       439 ~~m~~~g~~p~~~ty  453 (487)
                      +++.+. ..|+...+
T Consensus       168 ~~aL~l-~~~~~~r~  181 (198)
T PRK10370        168 QKVLDL-NSPRVNRT  181 (198)
T ss_pred             HHHHhh-CCCCccHH
Confidence            887653 23444333

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

Probab=97.29  E-value=0.071  Score=45.86  Aligned_cols=160  Identities=11%  Similarity=0.093  Sum_probs=111.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCC
Q 011378          246 LIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGH  325 (487)
Q Consensus       246 li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~  325 (487)
                      -+-.|...|+++......+.+.    .|. .       .+...++.+++...++..... -+.|...|..|-..|...|+
T Consensus        22 ~~~~Y~~~g~~~~v~~~~~~~~----~~~-~-------~~~~~~~~~~~i~~l~~~L~~-~P~~~~~w~~Lg~~~~~~g~   88 (198)
T PRK10370         22 CVGSYLLSPKWQAVRAEYQRLA----DPL-H-------QFASQQTPEAQLQALQDKIRA-NPQNSEQWALLGEYYLWRND   88 (198)
T ss_pred             HHHHHHHcchHHHHHHHHHHHh----Ccc-c-------cccCchhHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCC
Confidence            3457889999888644432111    111 1       222366777777777665543 24577789999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCChhhHHHHHHHH-HhcCC--hHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHH
Q 011378          326 VTEAFRLWYEMVGKGIKPTLVSCNTIIKGY-CRSGD--ASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFAL  402 (487)
Q Consensus       326 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~-~~~~~--~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~  402 (487)
                      +++|...++...+.. +-+...+..+-.++ ...|+  .++|.+++++..+..- -+...+..|-..+.+.|++++|...
T Consensus        89 ~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP-~~~~al~~LA~~~~~~g~~~~Ai~~  166 (198)
T PRK10370         89 YDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDA-NEVTALMLLASDAFMQADYAQAIEL  166 (198)
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC-CChhHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999877653 33566666666664 56676  5899999999887542 2556788888889999999999999


Q ss_pred             HHHHHhCCCCCCHhhHHHH
Q 011378          403 VSKMENQGLVPDVITYNVI  421 (487)
Q Consensus       403 ~~~m~~~g~~p~~~~~~~l  421 (487)
                      ++++.+. ..|+..-+..+
T Consensus       167 ~~~aL~l-~~~~~~r~~~i  184 (198)
T PRK10370        167 WQKVLDL-NSPRVNRTQLV  184 (198)
T ss_pred             HHHHHhh-CCCCccHHHHH
Confidence            9998765 25555544433

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

Probab=97.25  E-value=0.19  Score=47.80  Aligned_cols=113  Identities=12%  Similarity=0.083  Sum_probs=48.5

Q ss_pred             ccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHH
Q 011378          112 RKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEA  189 (487)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a  189 (487)
                      ..++.+.|+..++.+...  .| |..-+......+.+.++.++|.+.++.+...  .|+ ....-.+-++|.+.|+..++
T Consensus       318 ~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~ea  393 (484)
T COG4783         318 LAGQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEA  393 (484)
T ss_pred             HhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHH
Confidence            344455555555544332  22 2222223334444555555555555544432  233 23333344444444444444


Q ss_pred             HHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHH
Q 011378          190 LKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFN  229 (487)
Q Consensus       190 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~  229 (487)
                      ..++...... .+-|+..|..|-.+|...|+..++..-..
T Consensus       394 i~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~A  432 (484)
T COG4783         394 IRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARA  432 (484)
T ss_pred             HHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHH
Confidence            4444443322 12344444444444444444444444333

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

Probab=97.24  E-value=0.035  Score=52.59  Aligned_cols=108  Identities=14%  Similarity=0.172  Sum_probs=44.8

Q ss_pred             CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHhccCCHHHHHHH
Q 011378          324 GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD-SISYNTLINGFVREENMDKAFAL  402 (487)
Q Consensus       324 ~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~  402 (487)
                      |++++|+..++.+.+. .+-|...+....+.+.+.++.++|.+.++++...  .|+ ....-.+-.+|.+.|+..+|...
T Consensus       320 ~~~d~A~~~l~~L~~~-~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~  396 (484)
T COG4783         320 GQYDEALKLLQPLIAA-QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRI  396 (484)
T ss_pred             cccchHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHH
Confidence            4444444444444332 1222333333344444444444444444444432  233 22233333444444444444444


Q ss_pred             HHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHH
Q 011378          403 VSKMENQGLVPDVITYNVILTGFCRQGRMHDSE  435 (487)
Q Consensus       403 ~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  435 (487)
                      ++..... .+-|+..|..|..+|...|+..++.
T Consensus       397 L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~  428 (484)
T COG4783         397 LNRYLFN-DPEDPNGWDLLAQAYAELGNRAEAL  428 (484)
T ss_pred             HHHHhhc-CCCCchHHHHHHHHHHHhCchHHHH
Confidence            4443322 1233444444444444444444443

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

Probab=97.22  E-value=0.082  Score=51.18  Aligned_cols=216  Identities=15%  Similarity=0.123  Sum_probs=93.0

Q ss_pred             HhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCC-ccchHHHHHHHHhcCChhhH
Q 011378            6 CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPG-VFTYNSLINGLCKKGRCDRA   84 (487)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a   84 (487)
                      .+.|++..|.-.|+...+.. +-+...|--|-......++-..|+..+....+  +.|+ ....-+|--.|...|.-..|
T Consensus       296 m~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~--LdP~NleaLmaLAVSytNeg~q~~A  372 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLE--LDPTNLEALMALAVSYTNEGLQNQA  372 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHh--cCCccHHHHHHHHHHHhhhhhHHHH
Confidence            44555555555555544432 11344555555555555555555555544433  2232 23333333344445555555


Q ss_pred             HHHHHHHHHCCCC-----C---CHHHHHHHHHHHHccCChhHHHHHHHHH-HHCCCCCCHhHHHHHHHHHHhCCCHHHHH
Q 011378           85 KEVLDEMLQMGLS-----P---DTATYNTLLVESCRKENMSEAEEIFCEM-SRRGVAPDIVSFSTLIGIFSRNGQLDRAL  155 (487)
Q Consensus        85 ~~~~~~m~~~g~~-----~---~~~~~~~ll~~~~~~~~~~~a~~~~~~m-~~~g~~p~~~~~~~li~~~~~~g~~~~a~  155 (487)
                      .+.++.......+     +   +...-+.  +.+.....+....++|-++ .+.+..+|....+.|--.|--.|++++|.
T Consensus       373 l~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  373 LKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHH
Confidence            5555444322100     0   0000000  1111122223333333333 23343344444555555555556666666


Q ss_pred             HHHHHHHHCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCCh-hhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          156 MYFREMKSAGLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDV-VTYNTILNGLCRAKMLTEADDLFNE  230 (487)
Q Consensus       156 ~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~  230 (487)
                      ..|+...+.  .| |..+||.|=-.++...+.++|..-+.+..+.  .|+- ...-.|--+|...|.+++|.+.|-.
T Consensus       451 Dcf~~AL~v--~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~  523 (579)
T KOG1125|consen  451 DCFEAALQV--KPNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLE  523 (579)
T ss_pred             HHHHHHHhc--CCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHH
Confidence            666555442  23 2345555555555555555555555544431  2211 1222233334555555555544443

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.20  E-value=0.075  Score=52.08  Aligned_cols=89  Identities=20%  Similarity=0.264  Sum_probs=56.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHh-----------
Q 011378          348 CNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVI-----------  416 (487)
Q Consensus       348 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-----------  416 (487)
                      ...+-.-+.+......|.++|.+|-+         ..++++..+..+++++|..+-++..+  +.||+.           
T Consensus       750 l~~~a~ylk~l~~~gLAaeIF~k~gD---------~ksiVqlHve~~~W~eAFalAe~hPe--~~~dVy~pyaqwLAE~D  818 (1081)
T KOG1538|consen  750 LLLCATYLKKLDSPGLAAEIFLKMGD---------LKSLVQLHVETQRWDEAFALAEKHPE--FKDDVYMPYAQWLAEND  818 (1081)
T ss_pred             HHHHHHHHhhccccchHHHHHHHhcc---------HHHHhhheeecccchHhHhhhhhCcc--ccccccchHHHHhhhhh
Confidence            33333334455556667777776653         23456667777777777777666554  344442           


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEKGLN  447 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  447 (487)
                      -|.--=.+|.++|+..||.++++++....+.
T Consensus       819 rFeEAqkAfhkAGr~~EA~~vLeQLtnnav~  849 (1081)
T KOG1538|consen  819 RFEEAQKAFHKAGRQREAVQVLEQLTNNAVA  849 (1081)
T ss_pred             hHHHHHHHHHHhcchHHHHHHHHHhhhhhhh
Confidence            2334446889999999999999998766554

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

Probab=97.17  E-value=0.2  Score=46.45  Aligned_cols=125  Identities=15%  Similarity=0.185  Sum_probs=85.0

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGF  390 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  390 (487)
                      .+.+..|.-|...|+...|.++-.+..    -|+...|..-+++++..+++++...+-..    +  -.+.-|..++.+|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s----k--KsPIGyepFv~~~  247 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS----K--KSPIGYEPFVEAC  247 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC----C--CCCCChHHHHHHH
Confidence            456666777778888888887766652    37777888888888888888876665432    2  2346678888888


Q ss_pred             hccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          391 VREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHV  461 (487)
Q Consensus       391 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~  461 (487)
                      .+.|+..+|..++.++          ++.--+..|.+.|++.+|-+.-.+.      -|......+.+.+.
T Consensus       248 ~~~~~~~eA~~yI~k~----------~~~~rv~~y~~~~~~~~A~~~A~~~------kd~~~L~~i~~~~~  302 (319)
T PF04840_consen  248 LKYGNKKEASKYIPKI----------PDEERVEMYLKCGDYKEAAQEAFKE------KDIDLLKQILKRCP  302 (319)
T ss_pred             HHCCCHHHHHHHHHhC----------ChHHHHHHHHHCCCHHHHHHHHHHc------CCHHHHHHHHHHCC
Confidence            8888888888887762          2356677788888888886654443      24444444444443

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

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

Probab=97.17  E-value=0.14  Score=44.66  Aligned_cols=118  Identities=17%  Similarity=0.053  Sum_probs=47.2

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC
Q 011378          141 LIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM  220 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~  220 (487)
                      ......+.|++..|...+.+.... -.+|...|+.+--+|.+.|+.++|..-+.+..+-- .-+...+|.+.-.+.-.|+
T Consensus       106 ~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd  183 (257)
T COG5010         106 QGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGD  183 (257)
T ss_pred             HHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCC
Confidence            444445555555555555544331 12334444444444444444444444333333211 0122233344444444444


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 011378          221 LTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALN  261 (487)
Q Consensus       221 ~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~  261 (487)
                      ++.|..++......+ .-|...-.++..+-...|++++|.+
T Consensus       184 ~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~  223 (257)
T COG5010         184 LEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAED  223 (257)
T ss_pred             HHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHh
Confidence            444444444433321 1133333333334444444444443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.13  E-value=0.4  Score=49.55  Aligned_cols=171  Identities=12%  Similarity=0.033  Sum_probs=122.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCH-HHHHHHHHHHHcc
Q 011378           35 TLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDT-ATYNTLLVESCRK  113 (487)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~-~~~~~ll~~~~~~  113 (487)
                      .++....+.....+++--...... ....++..+..|-....+.|.+++|..+++...+.  .|+. .....+...+.+.
T Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~  133 (694)
T PRK15179         57 QVLERHAAVHKPAAALPELLDYVR-RYPHTELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQ  133 (694)
T ss_pred             HHHHHhhhhcchHhhHHHHHHHHH-hccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHh
Confidence            355555555555554433333322 23445677888888888999999999999998874  5664 4566677788899


Q ss_pred             CChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          114 ENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKM  192 (487)
Q Consensus       114 ~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  192 (487)
                      +++++|+...++..+..  | +......+-.++.+.|+.++|..+|++....+ .-+..++..+-.++.+.|+.++|...
T Consensus       134 ~~~eeA~~~~~~~l~~~--p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~  210 (694)
T PRK15179        134 QGIEAGRAEIELYFSGG--SSSAREILLEAKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDV  210 (694)
T ss_pred             ccHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            99999999999987763  4 44556667778889999999999999998732 22366888888889999999999999


Q ss_pred             HHHHHHcCCcCChhhHHHHH
Q 011378          193 RDEMLEKGCVMDVVTYNTIL  212 (487)
Q Consensus       193 ~~~m~~~g~~~~~~~~~~li  212 (487)
                      |+...+.-- +...-|+..+
T Consensus       211 ~~~a~~~~~-~~~~~~~~~~  229 (694)
T PRK15179        211 LQAGLDAIG-DGARKLTRRL  229 (694)
T ss_pred             HHHHHHhhC-cchHHHHHHH
Confidence            988765321 2334454443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.11  E-value=0.013  Score=47.53  Aligned_cols=93  Identities=10%  Similarity=-0.079  Sum_probs=51.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHc
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCK  287 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  287 (487)
                      +...-..+.+.|++++|...|+...... +.+...|..+-.++...|++++|...|+...... +.+...+..+-.++.+
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            3344455556666666666666655432 2345555566666666666666666666555421 2234455555555666


Q ss_pred             cCCHHHHHHHHHHHH
Q 011378          288 VGEMEKANKLWADMI  302 (487)
Q Consensus       288 ~g~~~~a~~~~~~m~  302 (487)
                      .|+.++|...|....
T Consensus       105 ~g~~~eAi~~~~~Al  119 (144)
T PRK15359        105 MGEPGLAREAFQTAI  119 (144)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            666666666665544

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.08  E-value=0.028  Score=45.55  Aligned_cols=92  Identities=11%  Similarity=-0.092  Sum_probs=52.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcC
Q 011378          350 TIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG  429 (487)
Q Consensus       350 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  429 (487)
                      .+-.++...|++++|...++...... +.+...|..+-.++.+.|++++|...+++..... ..+...+..+-..+.+.|
T Consensus        29 ~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g  106 (144)
T PRK15359         29 ASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMG  106 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcC
Confidence            34445555666666666666655322 1234455566666666666666666666655432 224455555656666666


Q ss_pred             ChHHHHHHHHHHHH
Q 011378          430 RMHDSELILWRMIE  443 (487)
Q Consensus       430 ~~~~a~~~~~~m~~  443 (487)
                      +.++|...|++...
T Consensus       107 ~~~eAi~~~~~Al~  120 (144)
T PRK15359        107 EPGLAREAFQTAIK  120 (144)
T ss_pred             CHHHHHHHHHHHHH
Confidence            66666666666544

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

Probab=97.07  E-value=0.028  Score=44.93  Aligned_cols=91  Identities=12%  Similarity=0.015  Sum_probs=44.1

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCC
Q 011378          351 IIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGR  430 (487)
Q Consensus       351 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  430 (487)
                      +...+...|+.++|.+.++.....+ +.+...+..+-..|.+.|++++|...++...+.+ ..+...+..+-..+...|+
T Consensus        23 ~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~  100 (135)
T TIGR02552        23 LAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGE  100 (135)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCC
Confidence            3344445555555555555544432 1233444445555555555555555555443332 2233444444445555555


Q ss_pred             hHHHHHHHHHHHH
Q 011378          431 MHDSELILWRMIE  443 (487)
Q Consensus       431 ~~~a~~~~~~m~~  443 (487)
                      .++|...+++..+
T Consensus       101 ~~~A~~~~~~al~  113 (135)
T TIGR02552       101 PESALKALDLAIE  113 (135)
T ss_pred             HHHHHHHHHHHHH
Confidence            5555555555443

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=97.01  E-value=0.033  Score=44.48  Aligned_cols=94  Identities=10%  Similarity=-0.011  Sum_probs=51.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR  392 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  392 (487)
                      ...+...+...|++++|...|+.....+ +.+...+..+-..+...|+.+.|...++...+.+ +.+...+..+-..|..
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            3344455555666666666666554432 2344555555556666666666666666554432 2233444445555666


Q ss_pred             cCCHHHHHHHHHHHHh
Q 011378          393 EENMDKAFALVSKMEN  408 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~  408 (487)
                      .|+.++|...+++..+
T Consensus        98 ~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        98 LGEPESALKALDLAIE  113 (135)
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            6666666666655544

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

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

Probab=96.99  E-value=0.3  Score=45.32  Aligned_cols=106  Identities=18%  Similarity=0.215  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFC  286 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  286 (487)
                      +.+..|.-+...|....|.++-++..    .||-.-|-..|.+++..+++++-..+-..      +-++.-|-.++..|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHH
Confidence            44445555555666666655544431    25555666666666666666655443221      112345666666666


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          287 KVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRL  332 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~  332 (487)
                      +.|+.++|..+...          .++.--+..|.+.|++.+|.+.
T Consensus       249 ~~~~~~eA~~yI~k----------~~~~~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  249 KYGNKKEASKYIPK----------IPDEERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             HCCCHHHHHHHHHh----------CChHHHHHHHHHCCCHHHHHHH
Confidence            66666666655543          1223445556666666666554

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

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=96.94  E-value=0.34  Score=45.17  Aligned_cols=257  Identities=18%  Similarity=0.126  Sum_probs=118.4

Q ss_pred             CCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChh----hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhH
Q 011378          133 PDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNV----LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTY  208 (487)
Q Consensus       133 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~----~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~  208 (487)
                      -|+.-...+-..+...|+.+.|...|++....  .|+..    .|..|+   .+.|+.++...+...+.... ..+...|
T Consensus       230 ~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL---~~eg~~e~~~~L~~~Lf~~~-~~ta~~w  303 (564)
T KOG1174|consen  230 CNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLL---GQEGGCEQDSALMDYLFAKV-KYTASHW  303 (564)
T ss_pred             ccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHH---HhccCHhhHHHHHHHHHhhh-hcchhhh
Confidence            34555555666666666666666666655432  23322    233322   34455555555444443321 0111222


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH---HHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHH
Q 011378          209 NTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLI---HGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDG  284 (487)
Q Consensus       209 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li---~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~  284 (487)
                      -.-.+.....++++.|..+-++..+.    |+.....+|   ..+...++++.|.-.|+...  .+.| +..+|..|+.+
T Consensus       304 fV~~~~l~~~K~~~rAL~~~eK~I~~----~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq--~Lap~rL~~Y~GL~hs  377 (564)
T KOG1174|consen  304 FVHAQLLYDEKKFERALNFVEKCIDS----EPRNHEALILKGRLLIALERHTQAVIAFRTAQ--MLAPYRLEIYRGLFHS  377 (564)
T ss_pred             hhhhhhhhhhhhHHHHHHHHHHHhcc----CcccchHHHhccHHHHhccchHHHHHHHHHHH--hcchhhHHHHHHHHHH
Confidence            22223333445555555555544332    111111111   34445566666665555432  2222 44566666666


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCChhhHHHHH-HHHHh-cCCHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhcCCh
Q 011378          285 FCKVGEMEKANKLWADMISRKISPNYISYGILI-NGYCS-MGHVTEAFRLWYEMVGKGIKPTL-VSCNTIIKGYCRSGDA  361 (487)
Q Consensus       285 ~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li-~~~~~-~~~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~~~~  361 (487)
                      |...|++.+|..+-+...+. ++-+..+.+.+- ..|.. ...-++|.++++.-.  .++|+- ...+.+-.-|...|..
T Consensus       378 YLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L--~~~P~Y~~AV~~~AEL~~~Eg~~  454 (564)
T KOG1174|consen  378 YLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSL--KINPIYTPAVNLIAELCQVEGPT  454 (564)
T ss_pred             HHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhh--ccCCccHHHHHHHHHHHHhhCcc
Confidence            66666666655544433221 112333332221 11211 112344555444322  223432 2344455555566666


Q ss_pred             HHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          362 SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       362 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      +.+..+++.-..  ..||....+.|-+.+.....+.+|...|..-
T Consensus       455 ~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~A  497 (564)
T KOG1174|consen  455 KDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKAMEYYYKA  497 (564)
T ss_pred             chHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            666666655442  3466666666666666666666666555443

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

Probab=96.93  E-value=0.028  Score=51.32  Aligned_cols=129  Identities=9%  Similarity=0.094  Sum_probs=65.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCC-CCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEG-VDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGF  425 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  425 (487)
                      +|..+++...|.+..+.|..+|....+.+ ...++....+++..+ ..++.+.|.++|+...+. +..+...|..-++.+
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~-~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Confidence            45555555555555666666666555332 233444444444322 234445566666655432 233445556666666


Q ss_pred             HhcCChHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          426 CRQGRMHDSELILWRMIEKGLNP---DRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       426 ~~~g~~~~a~~~~~~m~~~g~~p---~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      .+.|+.+.|+.+|++.... +.+   ....|..+++--...|+.+.+.++.+++.+
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6666666666666665433 211   123666666666666666666666655543

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.

>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=96.76  E-value=0.031  Score=40.69  Aligned_cols=89  Identities=13%  Similarity=0.134  Sum_probs=41.5

Q ss_pred             HHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 011378          387 INGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNL  466 (487)
Q Consensus       387 i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~  466 (487)
                      ...+...|++++|...+++..+.. ..+...+..+...+...|++++|...+++...... .+...+..+...+...|++
T Consensus         7 a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   84 (100)
T cd00189           7 GNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLAYYKLGKY   84 (100)
T ss_pred             HHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHHHHHHHhH
Confidence            334444555555555555443321 11223344444455555555555555555443221 1223444555555555555


Q ss_pred             HHHHHHHHHHH
Q 011378          467 KEAFRFHDEML  477 (487)
Q Consensus       467 ~~a~~~~~~m~  477 (487)
                      +.|...+.+..
T Consensus        85 ~~a~~~~~~~~   95 (100)
T cd00189          85 EEALEAYEKAL   95 (100)
T ss_pred             HHHHHHHHHHH
Confidence            55555555443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.75  E-value=0.75  Score=46.29  Aligned_cols=323  Identities=12%  Similarity=0.120  Sum_probs=190.6

Q ss_pred             HCCCCCCHhHHH-----HHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCH--HHHHHHHHHHHHcC
Q 011378          128 RRGVAPDIVSFS-----TLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFV--LEALKMRDEMLEKG  200 (487)
Q Consensus       128 ~~g~~p~~~~~~-----~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~--~~a~~~~~~m~~~g  200 (487)
                      .-|+..+..-|.     .+|.-+...+.+..|.++-..+...-..- ..+|.....-+.+..+.  +++++-.++-.+.-
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 RIGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAK  503 (829)
T ss_pred             ccCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHHHHHHHhccCccchHHHHHHHHHhccc
Confidence            356666666555     36778888899999999888875422222 45566666666665433  23333333222222


Q ss_pred             CcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC----CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-----
Q 011378          201 CVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGV----FPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSI-----  271 (487)
Q Consensus       201 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~----~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~-----  271 (487)
                      . -+..+|..+..-....|+.+.|..+.+.=...+-    ..+..-+...+.-+..+|+.+....++-.+.++-.     
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 4456788888888899999999988764222211    11333466777788888998888887765544211     


Q ss_pred             -----CC-CeeehHHHHHH--------HHccCCHHHHHHHHH--HHH----hCCCCCChhhHHHHHHHHHhcCC------
Q 011378          272 -----KP-DIVTYNTLIDG--------FCKVGEMEKANKLWA--DMI----SRKISPNYISYGILINGYCSMGH------  325 (487)
Q Consensus       272 -----~~-~~~~~~~li~~--------~~~~g~~~~a~~~~~--~m~----~~~~~p~~~t~~~li~~~~~~~~------  325 (487)
                           .| ....|.-+++-        +...++-..+...|.  ...    -.+..|+..+   .-++|++...      
T Consensus       583 ~~l~~~p~a~~lY~~~~r~~~~~~l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~---~a~~~a~sk~~s~e~k  659 (829)
T KOG2280|consen  583 MTLRNQPLALSLYRQFMRHQDRATLYDFYNQDDNHQALASFHLQASYAAETIEGRIPALKT---AANAFAKSKEKSFEAK  659 (829)
T ss_pred             HHHHhchhhhHHHHHHHHhhchhhhhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHHH---HHHHHhhhhhhhhHHH
Confidence                 11 12222222220        111111111111111  000    0123333332   3334443332      


Q ss_pred             -HHHHHHHHH---HHH-hCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHH
Q 011378          326 -VTEAFRLWY---EMV-GKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAF  400 (487)
Q Consensus       326 -~~~a~~~~~---~m~-~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~  400 (487)
                       .++-.+++.   .+. +.|..-.--+.+--+.-+...|+..+|.++-++.+    -||...|-.=+.+++..+++++-+
T Consensus       660 a~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLe  735 (829)
T KOG2280|consen  660 ALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELE  735 (829)
T ss_pred             HHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHH
Confidence             112222222   221 12333333455666677778899999988887665    489889988999999999999876


Q ss_pred             HHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          401 ALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHD  474 (487)
Q Consensus       401 ~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~  474 (487)
                      ++-++++      ++.-|-..+.+|.++|+.++|.+++-+..      +.   ...+.+|++.|++.+|.+.--
T Consensus       736 kfAkskk------sPIGy~PFVe~c~~~~n~~EA~KYiprv~------~l---~ekv~ay~~~~~~~eAad~A~  794 (829)
T KOG2280|consen  736 KFAKSKK------SPIGYLPFVEACLKQGNKDEAKKYIPRVG------GL---QEKVKAYLRVGDVKEAADLAA  794 (829)
T ss_pred             HHHhccC------CCCCchhHHHHHHhcccHHHHhhhhhccC------Ch---HHHHHHHHHhccHHHHHHHHH
Confidence            6555443      25568888999999999999998877641      21   268899999999999987643

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

Probab=96.74  E-value=0.033  Score=50.93  Aligned_cols=129  Identities=12%  Similarity=0.147  Sum_probs=62.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCC-CCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011378           32 TYNTLINAYCREGFLEEAFQLMNSMSGKG-LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVES  110 (487)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  110 (487)
                      +|..+|+..-+.+.++.|..+|......+ +........++|.. .-.++.+.|.++|+...+. +..+...|...+..+
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~-~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEY-YCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHH-HTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Confidence            45566666666666666666666655321 11222222222221 1134555566666665432 233445555555555


Q ss_pred             HccCChhHHHHHHHHHHHCCCCCCH---hHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 011378          111 CRKENMSEAEEIFCEMSRRGVAPDI---VSFSTLIGIFSRNGQLDRALMYFREMKS  163 (487)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~g~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~  163 (487)
                      .+.++.+.|..+|+..... +.++.   ..|...+..=.+.|+++.+.++...+.+
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5666666666666655433 22211   2555555555555666666555555544

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.

>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=96.69  E-value=0.024  Score=44.37  Aligned_cols=49  Identities=22%  Similarity=0.284  Sum_probs=24.5

Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCcCChhhHHHHHHH
Q 011378          166 LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLE-KGCVMDVVTYNTILNG  214 (487)
Q Consensus       166 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-~g~~~~~~~~~~li~~  214 (487)
                      +.|+..+..+++.+|+.++++..|.++++...+ .+++.+..+|..|++-
T Consensus        48 l~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   48 LYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            445555555555555555555555555554432 2444444455554443

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

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.66  E-value=0.82  Score=45.64  Aligned_cols=64  Identities=9%  Similarity=0.203  Sum_probs=41.2

Q ss_pred             hhhHHHHHHHHhccCCHHHHHHHHHHHHh-CCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          380 SISYNTLINGFVREENMDKAFALVSKMEN-QGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       380 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ...|-+|..--...|.++.|...--.+.+ ..+-|....|+.|.-+-|....+....+.|-++..
T Consensus      1021 AyHFmilAQrql~eg~v~~Al~Tal~L~DYEd~lpP~eiySllALaaca~raFGtCSKAfmkLe~ 1085 (1189)
T KOG2041|consen 1021 AYHFMILAQRQLFEGRVKDALQTALILSDYEDFLPPAEIYSLLALAACAVRAFGTCSKAFMKLEA 1085 (1189)
T ss_pred             HHHHHHHHHHHHHhchHHHHHHHHhhhccHhhcCCHHHHHHHHHHHHhhhhhhhhhHHHHHHHHh
Confidence            45566666666777888888776555543 24567777787777666666666666666665543

>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=96.61  E-value=0.031  Score=43.78  Aligned_cols=96  Identities=15%  Similarity=0.165  Sum_probs=68.5

Q ss_pred             ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          344 TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                      |..++..+|.++++.|+++....+++..=  |+.++..         ...+.         --....+.|+..+..+++.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~W--gI~~~~~---------~~~~~---------~~~~spl~Pt~~lL~AIv~   60 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVW--GIDVNGK---------KKEGD---------YPPSSPLYPTSRLLIAIVH   60 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhc--CCCCCCc---------cccCc---------cCCCCCCCCCHHHHHHHHH
Confidence            44567778888888888877777765332  4433321         00010         1134567899999999999


Q ss_pred             HHHhcCChHHHHHHHHHHHH-cCCCCCHHHHHHHHHH
Q 011378          424 GFCRQGRMHDSELILWRMIE-KGLNPDRSTYTTLING  459 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~-~g~~p~~~ty~~l~~~  459 (487)
                      +|+..|++..|.++++.... -++..+..+|..|+.=
T Consensus        61 sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   61 SFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             HHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            99999999999999999764 5788888999999873

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

>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=96.57  E-value=0.05  Score=39.54  Aligned_cols=89  Identities=13%  Similarity=0.184  Sum_probs=42.6

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCCh
Q 011378          352 IKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRM  431 (487)
Q Consensus       352 i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~  431 (487)
                      ...+...|+.++|...++...+.. +.+...+..+...+...+++++|.+.+++..... ..+...+..+...+...|+.
T Consensus         7 a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   84 (100)
T cd00189           7 GNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGKY   84 (100)
T ss_pred             HHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHhH
Confidence            334444555555555555544321 1122334444445555555555555555544332 12223455555555556666


Q ss_pred             HHHHHHHHHHH
Q 011378          432 HDSELILWRMI  442 (487)
Q Consensus       432 ~~a~~~~~~m~  442 (487)
                      ++|...+.+..
T Consensus        85 ~~a~~~~~~~~   95 (100)
T cd00189          85 EEALEAYEKAL   95 (100)
T ss_pred             HHHHHHHHHHH
Confidence            66655555543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.55  E-value=0.094  Score=40.55  Aligned_cols=94  Identities=10%  Similarity=0.015  Sum_probs=49.0

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHCCCCCC----hhhHHHHHHHHhccCCHHHHHHHHHHHHhCC--CCCCHhhHHHHH
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVSEGVDPD----SISYNTLINGFVREENMDKAFALVSKMENQG--LVPDVITYNVIL  422 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g--~~p~~~~~~~li  422 (487)
                      -.+...+.+.|+.++|...++.+....  |+    ...+..+...+.+.|+++.|...++......  .......+..+.
T Consensus         6 ~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         6 YDAALLVLKAGDYADAIQAFQAFLKKY--PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            344455556666666666666665432  21    2234445555666666666666666554321  011123344455


Q ss_pred             HHHHhcCChHHHHHHHHHHHHc
Q 011378          423 TGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      ..+.+.|+.++|...+.++.+.
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHH
Confidence            5555666666666666665544

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.

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

Probab=96.54  E-value=0.84  Score=44.25  Aligned_cols=120  Identities=16%  Similarity=0.214  Sum_probs=88.9

Q ss_pred             hHHHHHHHHHHHHC-CCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHH
Q 011378          361 ASKADEFLSKMVSE-GVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       361 ~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      .+.....+++.... .++|+ .+|..+|..--+..-++.|..+|.+..+.+..+ ++..+++++..+|.. +...|.++|
T Consensus       347 ~~~~~~~~~~ll~~~~~~~t-Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~csk-D~~~AfrIF  424 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLT-LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSK-DKETAFRIF  424 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCc-eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcC-ChhHHHHHH
Confidence            44455566665543 34454 468888888888889999999999999988888 889999999999876 568898888


Q ss_pred             HH-HHHcCCCCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCC
Q 011378          439 WR-MIEKGLNPDRSTY-TTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD  485 (487)
Q Consensus       439 ~~-m~~~g~~p~~~ty-~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~~  485 (487)
                      +- |+..   +|..-| ...++-+..-++=..+..+|++.+..++.||.
T Consensus       425 eLGLkkf---~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~k  470 (656)
T KOG1914|consen  425 ELGLKKF---GDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADK  470 (656)
T ss_pred             HHHHHhc---CCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhh
Confidence            75 3333   444433 44566667778888888888888888777765

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.53  E-value=0.48  Score=41.29  Aligned_cols=185  Identities=15%  Similarity=0.123  Sum_probs=100.6

Q ss_pred             cCCHHHHHHHHHHHHH---cC-CcCChh-hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH-HHHhcCCH
Q 011378          183 NGFVLEALKMRDEMLE---KG-CVMDVV-TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIH-GHCKDGNM  256 (487)
Q Consensus       183 ~~~~~~a~~~~~~m~~---~g-~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~-~~~~~g~~  256 (487)
                      ..+.++..+++.++..   .| ..++.. .|.-++-+....+..+.|...++.+.++=  |.+.-...|=. .+-..|+.
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~lEa~~~~  102 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLLEATGNY  102 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHhhch
Confidence            3456666666666653   23 333332 34455556666777777777777766542  44332222211 13345677


Q ss_pred             HHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          257 NKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEM  336 (487)
Q Consensus       257 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m  336 (487)
                      ++|+++++...+.. +.|..++-.=+-.....|..-+|++-+.+-.+ .+.-|...|.-+-..|...|++++|.--++++
T Consensus       103 ~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~-~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~  180 (289)
T KOG3060|consen  103 KEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLD-KFMNDQEAWHELAEIYLSEGDFEKAAFCLEEL  180 (289)
T ss_pred             hhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHH-HhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHH
Confidence            77777777666554 33444554444444445555555555544433 34457777777777777777777777777776


Q ss_pred             HhCCCCCChhh-HHHHHHHH---HhcCChHHHHHHHHHHHH
Q 011378          337 VGKGIKPTLVS-CNTIIKGY---CRSGDASKADEFLSKMVS  373 (487)
Q Consensus       337 ~~~~~~~~~~~-~~~li~~~---~~~~~~~~a~~~~~~m~~  373 (487)
                      .-.  .|-... +-.+-..+   ....+.+.+...+....+
T Consensus       181 ll~--~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alk  219 (289)
T KOG3060|consen  181 LLI--QPFNPLYFQRLAEVLYTQGGAENLELARKYYERALK  219 (289)
T ss_pred             HHc--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            543  333322 22222222   223345556666665554

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=96.47  E-value=0.67  Score=42.22  Aligned_cols=83  Identities=11%  Similarity=0.213  Sum_probs=55.2

Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCC--H---hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCC
Q 011378          392 REENMDKAFALVSKMENQGLVPD--V---ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGHVSQNN  465 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~~g~~p~--~---~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~~~~~~  465 (487)
                      +.+++.++.+--++..+.  .|.  .   ..+.++-..+...|++.+|.+...+.++  +.|+ ..++--=-.+|.-...
T Consensus       281 e~~~~t~cle~ge~vlk~--ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~--~d~~dv~~l~dRAeA~l~dE~  356 (504)
T KOG0624|consen  281 EEKHWTECLEAGEKVLKN--EPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLD--IDPDDVQVLCDRAEAYLGDEM  356 (504)
T ss_pred             hhhhHHHHHHHHHHHHhc--CCcccceeeeeeheeeecccccCCHHHHHHHHHHHHh--cCchHHHHHHHHHHHHhhhHH
Confidence            345555555544443332  343  2   2344555566788899999988888764  5666 6677777789998899


Q ss_pred             HHHHHHHHHHHHH
Q 011378          466 LKEAFRFHDEMLQ  478 (487)
Q Consensus       466 ~~~a~~~~~~m~~  478 (487)
                      |++|+.=++.-++
T Consensus       357 YD~AI~dye~A~e  369 (504)
T KOG0624|consen  357 YDDAIHDYEKALE  369 (504)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999888887654

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.39  E-value=0.2  Score=38.68  Aligned_cols=94  Identities=11%  Similarity=0.000  Sum_probs=37.9

Q ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCCC-C-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CcCChhhHHHHHHHH
Q 011378          140 TLIGIFSRNGQLDRALMYFREMKSAGLV-P-DNVLYTIIINGYCRNGFVLEALKMRDEMLEKG--CVMDVVTYNTILNGL  215 (487)
Q Consensus       140 ~li~~~~~~g~~~~a~~~~~~m~~~g~~-~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~~~~~~~li~~~  215 (487)
                      .+...+.+.|++++|.+.|+++.+.... + ....+..+...+.+.|+.++|...++......  .+.....+..+..++
T Consensus         7 ~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~   86 (119)
T TIGR02795         7 DAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSL   86 (119)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHH
Confidence            3344444445555555555544432100 0 01223334444444444444444444443321  111122333334444


Q ss_pred             HhcCCHHHHHHHHHHHHH
Q 011378          216 CRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~  233 (487)
                      .+.++.+.|...+++..+
T Consensus        87 ~~~~~~~~A~~~~~~~~~  104 (119)
T TIGR02795        87 QELGDKEKAKATLQQVIK  104 (119)
T ss_pred             HHhCChHHHHHHHHHHHH
Confidence            444555555555544444

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.

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

Probab=96.37  E-value=0.0071  Score=43.81  Aligned_cols=18  Identities=11%  Similarity=0.361  Sum_probs=7.4

Q ss_pred             HHHHhccCCHHHHHHHHH
Q 011378          387 INGFVREENMDKAFALVS  404 (487)
Q Consensus       387 i~~~~~~~~~~~a~~~~~  404 (487)
                      -.+|.+.|++++|..+++
T Consensus        32 a~~~~~~~~y~~A~~~~~   49 (84)
T PF12895_consen   32 AQCYFQQGKYEEAIELLQ   49 (84)
T ss_dssp             HHHHHHTTHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHH
Confidence            333444444444444443

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

Probab=96.37  E-value=0.039  Score=48.42  Aligned_cols=104  Identities=16%  Similarity=0.234  Sum_probs=59.4

Q ss_pred             CCHHHHHHHHHHHH-----ccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhh
Q 011378           98 PDTATYNTLLVESC-----RKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVL  172 (487)
Q Consensus        98 ~~~~~~~~ll~~~~-----~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~  172 (487)
                      .|..+|-..+..+.     +.+.++-.-.-+..|++.|+.-|..+|+.||+.+-+-.-+..                ...
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~----------------nvf  128 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQ----------------NVF  128 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccH----------------HHH
Confidence            45555555555443     235666666677888888888888889888888765433221                100


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC
Q 011378          173 YTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM  220 (487)
Q Consensus       173 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~  220 (487)
                      -..++ .|  -..-+-+..++++|+..|+.||-.+-..|++++++.+-
T Consensus       129 Q~~F~-HY--P~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  129 QKVFL-HY--PQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHh-hC--chhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            00000 01  11223345566666666666666666666666666553

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.33  E-value=0.42  Score=40.05  Aligned_cols=61  Identities=18%  Similarity=0.108  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--hhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGKGIKPT--LVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      +..+...+...|++++|...|++..+....++  ...+..+-..+.+.|+.++|...+++..+
T Consensus        38 ~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  100 (172)
T PRK02603         38 YYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE  100 (172)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44444555555666666666655544322221  23444455555555555555555555443

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

Probab=96.29  E-value=0.0098  Score=43.04  Aligned_cols=80  Identities=15%  Similarity=0.235  Sum_probs=57.4

Q ss_pred             cCCHHHHHHHHHHHHhCCC-CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCCHHHHH
Q 011378          393 EENMDKAFALVSKMENQGL-VPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR-STYTTLINGHVSQNNLKEAF  470 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~~g~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~ty~~l~~~~~~~~~~~~a~  470 (487)
                      .|+++.|..+++++.+..- .|+...+-.+...|.+.|++++|..++++ .  ++.|+. ...-.+..+|...|++++|.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~--~~~~~~~~~~~l~a~~~~~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-L--KLDPSNPDIHYLLARCLLKLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-H--THHHCHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-h--CCCCCCHHHHHHHHHHHHHhCCHHHHH
Confidence            4788999999999876421 22444555588899999999999999988 2  223333 33334578899999999999


Q ss_pred             HHHHH
Q 011378          471 RFHDE  475 (487)
Q Consensus       471 ~~~~~  475 (487)
                      +.+++
T Consensus        79 ~~l~~   83 (84)
T PF12895_consen   79 KALEK   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            99875

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

Probab=96.29  E-value=0.038  Score=48.51  Aligned_cols=105  Identities=14%  Similarity=0.218  Sum_probs=64.4

Q ss_pred             CCChhhHHHHHHHHHh-----cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChh
Q 011378          307 SPNYISYGILINGYCS-----MGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSI  381 (487)
Q Consensus       307 ~p~~~t~~~li~~~~~-----~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  381 (487)
                      .-|-.+|-..+..|..     .++++-....++.|...|++.|+.+|+.||..+-+..-                .|...
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkf----------------iP~nv  127 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKF----------------IPQNV  127 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCccccc----------------ccHHH
Confidence            4455667677776654     35677777777888888888888888888877654321                12111


Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCC
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGR  430 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  430 (487)
                      .-..++ .|=  .+-+-+.++++.|+..|+-||-.+--.++.+|++.+.
T Consensus       128 fQ~~F~-HYP--~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  128 FQKVFL-HYP--QQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHh-hCc--hhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            111111 111  2234466777777777777777777777777766654

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=96.21  E-value=0.96  Score=41.43  Aligned_cols=23  Identities=9%  Similarity=0.143  Sum_probs=13.2

Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHH
Q 011378          139 STLIGIFSRNGQLDRALMYFREM  161 (487)
Q Consensus       139 ~~li~~~~~~g~~~~a~~~~~~m  161 (487)
                      .-.-+.|-..|++++|.+.|.+.
T Consensus        39 ~~Aa~~fk~~~~~~~A~~ay~kA   61 (282)
T PF14938_consen   39 EKAANCFKLAKDWEKAAEAYEKA   61 (282)
T ss_dssp             HHHHHHHHHTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccchhHHHHHHH
Confidence            33445566666777666666654

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.16  E-value=0.1  Score=43.59  Aligned_cols=63  Identities=19%  Similarity=0.090  Sum_probs=30.6

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC--CccchHHHHHHHHhcCChhhHHHHHHHHHH
Q 011378           31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKP--GVFTYNSLINGLCKKGRCDRAKEVLDEMLQ   93 (487)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   93 (487)
                      ..|..+...+...|++++|...|+......-.|  ...+|..+-..+...|++++|.+.++....
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~  100 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE  100 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344455555555566666666655543321111  112444444555555555555555555443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.07  E-value=0.17  Score=42.31  Aligned_cols=26  Identities=15%  Similarity=-0.068  Sum_probs=12.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEML  232 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~  232 (487)
                      +|..+-..+...|++++|...++...
T Consensus        74 ~~~~lg~~~~~~g~~~eA~~~~~~Al   99 (168)
T CHL00033         74 ILYNIGLIHTSNGEHTKALEYYFQAL   99 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444455555555555554444

>PLN02789 farnesyltranstransferase

Probab=95.98  E-value=1.4  Score=41.11  Aligned_cols=132  Identities=11%  Similarity=0.108  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc---CC----HHHH
Q 011378          222 TEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV---GE----MEKA  294 (487)
Q Consensus       222 ~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~---g~----~~~a  294 (487)
                      +.+..+++++.+.. +-|...|+..--++...|+++++++.++.+.+.... |...|+.....+.+.   |.    .+++
T Consensus       125 ~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~~~e~e  202 (320)
T PLN02789        125 NKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGLEAMRDSE  202 (320)
T ss_pred             HHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhccccccccccHHHH
Confidence            34445555554432 124445555555555555566666666655544322 222333332222222   11    2234


Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHhc----CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          295 NKLWADMISRKISPNYISYGILINGYCSM----GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR  357 (487)
Q Consensus       295 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  357 (487)
                      .....+.... -+-|...|+.+-..+...    +...+|...+.+....+ ..+......|++.|+.
T Consensus       203 l~y~~~aI~~-~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        203 LKYTIDAILA-NPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             HHHHHHHHHh-CCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence            4444333322 123555666666665552    23344666665544422 2234455566666654

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.97  E-value=1.7  Score=42.11  Aligned_cols=236  Identities=14%  Similarity=0.144  Sum_probs=123.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHH-------
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNT-------  280 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~-------  280 (487)
                      +-.+.++..+..+++.+.+-+....+..  -+..-++..-.+|...|....+...-+...+.|... ..-|+.       
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~-rad~klIak~~~r  303 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGREL-RADYKLIAKALAR  303 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHH-HHHHHHHHHHHHH
Confidence            3456666677778888888777776644  344445555667777777666655544433333211 111221       


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhh-HHHHHHHHHhcC
Q 011378          281 LIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVS-CNTIIKGYCRSG  359 (487)
Q Consensus       281 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~li~~~~~~~  359 (487)
                      +=.+|.+.++.+.+...|.+.......|+..+         +....+++.+......  -+.|.... .-.=-..+.+.|
T Consensus       304 ~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls---------~lk~~Ek~~k~~e~~a--~~~pe~A~e~r~kGne~Fk~g  372 (539)
T KOG0548|consen  304 LGNAYTKREDYEGAIKYYQKALTEHRTPDLLS---------KLKEAEKALKEAERKA--YINPEKAEEEREKGNEAFKKG  372 (539)
T ss_pred             hhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHH---------HHHHHHHHHHHHHHHH--hhChhHHHHHHHHHHHHHhcc
Confidence            22356666788888888887766665555433         1222333333333221  12222211 001123455677


Q ss_pred             ChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHh-hHHHHHHHHHhcCChHHHHHHH
Q 011378          360 DASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVI-TYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      ++..|...+.+++... +-|...|+..--+|.+.+.+..|.+=.+.-.+.  .|+-. -|..=..++....+++.|...|
T Consensus       373 dy~~Av~~YteAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL--~p~~~kgy~RKg~al~~mk~ydkAleay  449 (539)
T KOG0548|consen  373 DYPEAVKHYTEAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIEL--DPNFIKAYLRKGAALRAMKEYDKALEAY  449 (539)
T ss_pred             CHHHHHHHHHHHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888888777655 345667777777777777777776654443332  33321 1211112222233555555555


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHh
Q 011378          439 WRMIEKGLNPDRSTYTTLINGHVS  462 (487)
Q Consensus       439 ~~m~~~g~~p~~~ty~~l~~~~~~  462 (487)
                      ++-++.  .|+..-+..-+.-|..
T Consensus       450 ~eale~--dp~~~e~~~~~~rc~~  471 (539)
T KOG0548|consen  450 QEALEL--DPSNAEAIDGYRRCVE  471 (539)
T ss_pred             HHHHhc--CchhHHHHHHHHHHHH
Confidence            554432  3554444444444444

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.84  E-value=0.65  Score=42.59  Aligned_cols=22  Identities=9%  Similarity=0.386  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHcCCcCChhhHH
Q 011378          188 EALKMRDEMLEKGCVMDVVTYN  209 (487)
Q Consensus       188 ~a~~~~~~m~~~g~~~~~~~~~  209 (487)
                      .+.++++.+.+.|+++....|.
T Consensus       200 r~~~l~~~l~~~~~kik~~~yp  221 (297)
T PF13170_consen  200 RVIELYNALKKNGVKIKYMHYP  221 (297)
T ss_pred             HHHHHHHHHHHcCCcccccccc
Confidence            3444455555555554444443

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

Probab=95.82  E-value=0.44  Score=38.63  Aligned_cols=68  Identities=18%  Similarity=0.276  Sum_probs=35.8

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-----HCCCCCCC
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML-----QRGFVPDD  485 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~-----~~g~~p~~  485 (487)
                      ....++..+...|++++|..+++.+.... .-+...|..+|.+|...|+...|.++++++.     +-|+.|++
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~  136 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSP  136 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----H
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCH
Confidence            34455555666666666666666665431 1245566666666666666666666666654     23666653

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

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=95.76  E-value=0.5  Score=46.66  Aligned_cols=211  Identities=14%  Similarity=0.181  Sum_probs=104.7

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHH---------HHHHhhCCCCCCccchHHHHHHHHhcCChhhH--HHHHHHHHHCC
Q 011378           27 YPDTVTYNTLINAYCREGFLEEAFQL---------MNSMSGKGLKPGVFTYNSLINGLCKKGRCDRA--KEVLDEMLQMG   95 (487)
Q Consensus        27 ~p~~~~~~~ll~~~~~~~~~~~a~~~---------~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a--~~~~~~m~~~g   95 (487)
                      .|....+.+-+..+...|.+++|.++         |+.+...  ..+.-.++..=++|.+.++..--  ..=+++|++.|
T Consensus       553 ~~~evp~~~~m~q~Ieag~f~ea~~iaclgVv~~DW~~LA~~--ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rg  630 (1081)
T KOG1538|consen  553 SAVEVPQSAPMYQYIERGLFKEAYQIACLGVTDTDWRELAME--ALEALDFETARKAYIRVRDLRYLELISELEERKKRG  630 (1081)
T ss_pred             ecccccccccchhhhhccchhhhhcccccceecchHHHHHHH--HHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcC
Confidence            34445566667777788888887654         2222111  01223344444556665554422  22334566777


Q ss_pred             CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHH------------HHHH
Q 011378           96 LSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFR------------EMKS  163 (487)
Q Consensus        96 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~------------~m~~  163 (487)
                      -.|+....   ...++-.|++.+|.++|.+-   |..      |-.++.|..-+.+|.|-+++.            +-.+
T Consensus       631 e~P~~iLl---A~~~Ay~gKF~EAAklFk~~---G~e------nRAlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKRA~  698 (1081)
T KOG1538|consen  631 ETPNDLLL---ADVFAYQGKFHEAAKLFKRS---GHE------NRALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKRAD  698 (1081)
T ss_pred             CCchHHHH---HHHHHhhhhHHHHHHHHHHc---Cch------hhHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHH
Confidence            77776542   23345566677777776532   211      223444444444444433322            1100


Q ss_pred             --CCC-CCChhhHHHHHHHHHhcCCHHHHHHHH------HHHHHcCCcCC---hhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          164 --AGL-VPDNVLYTIIINGYCRNGFVLEALKMR------DEMLEKGCVMD---VVTYNTILNGLCRAKMLTEADDLFNEM  231 (487)
Q Consensus       164 --~g~-~~~~~~~~~ll~~~~~~~~~~~a~~~~------~~m~~~g~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (487)
                        .++ +|     .+....+...|+..+|..+.      +-+.+-+-..|   ..+.-.+-..+-+...+..|-++|..|
T Consensus       699 WAr~~keP-----kaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~  773 (1081)
T KOG1538|consen  699 WARNIKEP-----KAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKM  773 (1081)
T ss_pred             HhhhcCCc-----HHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHh
Confidence              011 11     12233344456666665442      12222222232   233333444445556677778888777


Q ss_pred             HHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          232 LERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       232 ~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      -+.         .+++......+++++|..+-+.
T Consensus       774 gD~---------ksiVqlHve~~~W~eAFalAe~  798 (1081)
T KOG1538|consen  774 GDL---------KSLVQLHVETQRWDEAFALAEK  798 (1081)
T ss_pred             ccH---------HHHhhheeecccchHhHhhhhh
Confidence            542         3566677778888888776654

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

Probab=95.75  E-value=3  Score=43.18  Aligned_cols=223  Identities=18%  Similarity=0.168  Sum_probs=141.4

Q ss_pred             HhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHH--HhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhh
Q 011378            6 CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAY--CREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDR   83 (487)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~--~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~   83 (487)
                      ...+++..|..-.+.+.+.-  |+. .|.-+++++  .+.|..++|..+++....-+.. |..|...+-..|-+.++.++
T Consensus        20 ld~~qfkkal~~~~kllkk~--Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~   95 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKKH--PNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDE   95 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHHC--CCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhH
Confidence            34677888888887764431  332 455666665  5688999999888887654433 66778888888888999999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCC----------HHH
Q 011378           84 AKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQ----------LDR  153 (487)
Q Consensus        84 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~----------~~~  153 (487)
                      +..++++..+.  -|+..-..-+.-+|++.+++..-.++=-+|-+ ..+-+...|-++++...+.-.          +..
T Consensus        96 ~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~L  172 (932)
T KOG2053|consen   96 AVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYK-NFPKRAYYFWSVISLILQSIFSENELLDPILLAL  172 (932)
T ss_pred             HHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCcccchHHHHHHHHHHhccCCcccccchhHHH
Confidence            99999987754  57777777778888888776655544333322 123345566667766654321          224


Q ss_pred             HHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHH-HHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          154 ALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRD-EMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEM  231 (487)
Q Consensus       154 a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~-~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (487)
                      |.+.++.+...+-+.. ..-.-.-+..+-..|..++|.+++. ..-+.-...+...-+--+..+...+.+.+..++-.++
T Consensus       173 A~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~L  252 (932)
T KOG2053|consen  173 AEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRL  252 (932)
T ss_pred             HHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            5555555544331211 1111222233345677888888873 3333333444555566777788888888888888888


Q ss_pred             HHcC
Q 011378          232 LERG  235 (487)
Q Consensus       232 ~~~~  235 (487)
                      ..+|
T Consensus       253 l~k~  256 (932)
T KOG2053|consen  253 LEKG  256 (932)
T ss_pred             HHhC
Confidence            7765

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.73  E-value=1.1  Score=39.31  Aligned_cols=139  Identities=9%  Similarity=0.025  Sum_probs=66.1

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHH-----HHHH
Q 011378          279 NTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCN-----TIIK  353 (487)
Q Consensus       279 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~-----~li~  353 (487)
                      +.++..+.-.|.+.-...++.+..+..-+-+....+.|.+.-.+.|+.+.|...|++..+..-+.|-.+++     ..-.
T Consensus       181 y~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~  260 (366)
T KOG2796|consen  181 YSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAF  260 (366)
T ss_pred             HHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhh
Confidence            45555555555555556666555554433444555555555566666666666666554322222222222     2223


Q ss_pred             HHHhcCChHHHHHHHHHHHHCC-CCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEG-VDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVI  421 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  421 (487)
                      .|..+.++..|...+.+..... -.|-...-.+|+..|  .|+..+|.+.++.|...  .|...+-+++
T Consensus       261 i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllY--lg~l~DAiK~~e~~~~~--~P~~~l~es~  325 (366)
T KOG2796|consen  261 LHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLY--LGKLKDALKQLEAMVQQ--DPRHYLHESV  325 (366)
T ss_pred             heecccchHHHHHHHhhccccCCCchhhhchHHHHHHH--HHHHHHHHHHHHHHhcc--CCccchhhhH
Confidence            3444555555555555544321 111122222333333  45556666666665543  3444444433

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=95.73  E-value=0.92  Score=45.33  Aligned_cols=143  Identities=11%  Similarity=0.094  Sum_probs=78.0

Q ss_pred             CCCCChhhHHHHHHHHHhcC-----CHHHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhc--------CChHHHHHHHHH
Q 011378          305 KISPNYISYGILINGYCSMG-----HVTEAFRLWYEMVGKGIKPTL-VSCNTIIKGYCRS--------GDASKADEFLSK  370 (487)
Q Consensus       305 ~~~p~~~t~~~li~~~~~~~-----~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~--------~~~~~a~~~~~~  370 (487)
                      +.+.+...|...+.+.....     +...|..+|++....  .|+- ..|..+..++...        .+...+.+..+.
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            34455566666666644322     255666666665543  3442 2233222222211        112233333333


Q ss_pred             HHHC-CCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 011378          371 MVSE-GVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD  449 (487)
Q Consensus       371 m~~~-g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  449 (487)
                      .... ....+...|.++--.....|++++|...+++..+.  .|+...|..+-..+...|+.++|...+++...  +.|.
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L--~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~--L~P~  485 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL--EMSWLNYVLLGKVYELKGDNRLAADAYSTAFN--LRPG  485 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--cCCC
Confidence            2222 12234456666655555667888888888777664  36777777777777888888888777777544  3455


Q ss_pred             HHHH
Q 011378          450 RSTY  453 (487)
Q Consensus       450 ~~ty  453 (487)
                      .+||
T Consensus       486 ~pt~  489 (517)
T PRK10153        486 ENTL  489 (517)
T ss_pred             CchH
Confidence            5554

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=95.69  E-value=1.7  Score=39.86  Aligned_cols=110  Identities=21%  Similarity=0.252  Sum_probs=54.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc-CCHHHHHHHHHHHHh----CCCCCC--hhhHHHHHHH
Q 011378          247 IHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV-GEMEKANKLWADMIS----RKISPN--YISYGILING  319 (487)
Q Consensus       247 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~----~~~~p~--~~t~~~li~~  319 (487)
                      +..|...|++..|-+.+..               +-..|-.. |+++.|.+.|.+...    .+ .+.  ...+..+...
T Consensus       101 ~~~y~~~G~~~~aA~~~~~---------------lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l  164 (282)
T PF14938_consen  101 IEIYREAGRFSQAAKCLKE---------------LAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADL  164 (282)
T ss_dssp             HHHHHHCT-HHHHHHHHHH---------------HHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcHHHHHHHHHH---------------HHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHH
Confidence            3455555665555444433               23334444 566666666655432    12 111  1234555666


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChh-------hHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLV-------SCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~-------~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      +.+.|++++|..+|+++.......+..       .+.++| ++...||...|.+.+++...
T Consensus       165 ~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l-~~L~~~D~v~A~~~~~~~~~  224 (282)
T PF14938_consen  165 YARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAIL-CHLAMGDYVAARKALERYCS  224 (282)
T ss_dssp             HHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHH-HHHHTT-HHHHHHHHHHHGT
T ss_pred             HHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHH-HHHHcCCHHHHHHHHHHHHh
Confidence            777777777777777766543332221       122222 44456677777777776653

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=95.68  E-value=3.4  Score=43.39  Aligned_cols=421  Identities=14%  Similarity=0.087  Sum_probs=214.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHH--HH
Q 011378           32 TYNTLINAYCREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTL--LV  108 (487)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l--l~  108 (487)
                      .|..+-.-|+...+...|.+.|+...+-  -| +...+....+.+++..+++.|..+.-.--+... .-...+|-+  --
T Consensus       494 af~~LG~iYrd~~Dm~RA~kCf~KAFeL--Datdaeaaaa~adtyae~~~we~a~~I~l~~~qka~-a~~~k~nW~~rG~  570 (1238)
T KOG1127|consen  494 AFAFLGQIYRDSDDMKRAKKCFDKAFEL--DATDAEAAAASADTYAEESTWEEAFEICLRAAQKAP-AFACKENWVQRGP  570 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcC--CchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhch-HHHHHhhhhhccc
Confidence            4666666666666677777777765442  22 345577778888888888888887433222210 111122222  22


Q ss_pred             HHHccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHH--HHhcCC
Q 011378          109 ESCRKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIING--YCRNGF  185 (487)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~--~~~~~~  185 (487)
                      .|-..+++..+..-|+...+-  .| |...|..+..+|.++|++..|.++|.+....  .|+ .+|...-.+  -+..|.
T Consensus       571 yyLea~n~h~aV~~fQsALR~--dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L--rP~-s~y~~fk~A~~ecd~Gk  645 (1238)
T KOG1127|consen  571 YYLEAHNLHGAVCEFQSALRT--DPKDYNLWLGLGEAYPESGRYSHALKVFTKASLL--RPL-SKYGRFKEAVMECDNGK  645 (1238)
T ss_pred             cccCccchhhHHHHHHHHhcC--CchhHHHHHHHHHHHHhcCceehHHHhhhhhHhc--CcH-hHHHHHHHHHHHHHhhh
Confidence            355667777777777766543  33 5567788899999999999999999877553  343 244433332  355677


Q ss_pred             HHHHHHHHHHHHHc------CCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-C---
Q 011378          186 VLEALKMRDEMLEK------GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDG-N---  255 (487)
Q Consensus       186 ~~~a~~~~~~m~~~------g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g-~---  255 (487)
                      ..+++..+......      +..--..++-.+...+...|-...+..++++-.+.       ..+++++..+... .   
T Consensus       646 Ykeald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~-------f~~~l~h~~~~~~~~Wi~  718 (1238)
T KOG1127|consen  646 YKEALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIES-------FIVSLIHSLQSDRLQWIV  718 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH-------HHHHHHHhhhhhHHHHHH
Confidence            77777666544321      11111112222222233333344444444443321       1112222211110 0   


Q ss_pred             HHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCH---H---HHHHHHHHHHhCCCCCChhhHHHHHHHHHh----c--
Q 011378          256 MNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEM---E---KANKLWADMISRKISPNYISYGILINGYCS----M--  323 (487)
Q Consensus       256 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~---~---~a~~~~~~m~~~~~~p~~~t~~~li~~~~~----~--  323 (487)
                      ...|..+|-... .+ .|+......|..-+-+.+..   |   .+.+.+-  ....+..+..+|..|...|.+    .  
T Consensus       719 asdac~~f~q~e-~~-~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~--~hlsl~~~~~~WyNLGinylr~f~~l~e  794 (1238)
T KOG1127|consen  719 ASDACYIFSQEE-PS-IVNMHYLIILSKQLEKTGALKKNDLLFLGYECGI--AHLSLAIHMYPWYNLGINYLRYFLLLGE  794 (1238)
T ss_pred             HhHHHHHHHHhc-cc-chHHHHHHHHHHHHHhcccCcchhHHHHHHHHhh--HHHHHhhccchHHHHhHHHHHHHHHcCC
Confidence            112222222222 11 22222222222212222222   1   0111110  011122334556555555544    1  


Q ss_pred             CC--HHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHH
Q 011378          324 GH--VTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       324 ~~--~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  401 (487)
                      +.  ...|..-+..-++  +..|...+-..+.+....|++.-+...|-+-.... +....+|..+--.|.+..+++.|..
T Consensus       795 t~~~~~~Ai~c~KkaV~--L~ann~~~WnaLGVlsg~gnva~aQHCfIks~~se-p~~~~~W~NlgvL~l~n~d~E~A~~  871 (1238)
T KOG1127|consen  795 TMKDACTAIRCCKKAVS--LCANNEGLWNALGVLSGIGNVACAQHCFIKSRFSE-PTCHCQWLNLGVLVLENQDFEHAEP  871 (1238)
T ss_pred             cchhHHHHHHHHHHHHH--HhhccHHHHHHHHHhhccchhhhhhhhhhhhhhcc-ccchhheeccceeEEecccHHHhhH
Confidence            22  2234444433322  23344444444555566677777777665544322 2234567777777888899999999


Q ss_pred             HHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHH----HcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          402 LVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMI----EKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       402 ~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~----~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      .|.+...  +.| +...|-....--...|+.-++..+|.+-.    ..|-.|+..-|-+-.......|+.++-+..-+..
T Consensus       872 af~~~qS--LdP~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~f~Yw~c~te~h~~Ng~~e~~I~t~~ki  949 (1238)
T KOG1127|consen  872 AFSSVQS--LDPLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKKFQYWLCATEIHLQNGNIEESINTARKI  949 (1238)
T ss_pred             HHHhhhh--cCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccchhhHHHHHHHHHHhccchHHHHHHhhhh
Confidence            9988765  345 44556555544556788888888887732    2344566666666666666677766555444433

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.66  E-value=0.56  Score=39.30  Aligned_cols=86  Identities=16%  Similarity=0.188  Sum_probs=52.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCC--ccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCC-CHHHHHHHH
Q 011378           31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPG--VFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSP-DTATYNTLL  107 (487)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~ll  107 (487)
                      ..+..+...+...|++++|...|+........+.  ...|..+-..+.+.|+++.|...+.+..+.  .| +...+..+.
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg  113 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIA  113 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHH
Confidence            3466666677777888888888877654322221  245666666777778888888877776653  23 234444444


Q ss_pred             HHHHccCChhH
Q 011378          108 VESCRKENMSE  118 (487)
Q Consensus       108 ~~~~~~~~~~~  118 (487)
                      ..+...|+...
T Consensus       114 ~~~~~~g~~~~  124 (172)
T PRK02603        114 VIYHKRGEKAE  124 (172)
T ss_pred             HHHHHcCChHh
Confidence            55555555433

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.51  E-value=0.86  Score=35.36  Aligned_cols=102  Identities=15%  Similarity=0.161  Sum_probs=63.3

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCCh--hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC---HhhH-HHHHHHHHh
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPDS--ISYNTLINGFVREENMDKAFALVSKMENQGLVPD---VITY-NVILTGFCR  427 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~-~~li~~~~~  427 (487)
                      ++-..|+.++|..+++.....|...+.  ..+-.+-+.+-..|++++|..++++....  .|+   .... ..+..++..
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~--~p~~~~~~~l~~f~Al~L~~   87 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEE--FPDDELNAALRVFLALALYN   87 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCccccHHHHHHHHHHHHH
Confidence            455668888888888888777765542  24555667777788888888888776543  244   2121 222335667


Q ss_pred             cCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          428 QGRMHDSELILWRMIEKGLNPDRSTYTTLINGHV  461 (487)
Q Consensus       428 ~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~  461 (487)
                      .|+.++|...+-....    ++...|..=|..|.
T Consensus        88 ~gr~~eAl~~~l~~la----~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   88 LGRPKEALEWLLEALA----ETLPRYRRAIRFYA  117 (120)
T ss_pred             CCCHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence            7888888776655443    34445555555554

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.49  E-value=0.54  Score=37.78  Aligned_cols=126  Identities=9%  Similarity=0.099  Sum_probs=62.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR  392 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  392 (487)
                      ...++..+...+........++.+...+ ..+....+.++..|++.+. +...+.++.      .++.......+..|-+
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~-~~ll~~l~~------~~~~yd~~~~~~~c~~   81 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDP-QKEIERLDN------KSNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCH-HHHHHHHHh------ccccCCHHHHHHHHHH
Confidence            3455666666666666666666666554 3455566666666665432 233333331      1223333445555656


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhc-CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          393 EENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQ-GRMHDSELILWRMIEKGLNPDRSTYTTLINGHV  461 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~  461 (487)
                      .+.++.+..++.++..         |.-.+..+.+. ++++.|.+.+.+      .-+...|..++..+.
T Consensus        82 ~~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~------~~~~~lw~~~~~~~l  136 (140)
T smart00299       82 AKLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVK------QNNPELWAEVLKALL  136 (140)
T ss_pred             cCcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHh------CCCHHHHHHHHHHHH
Confidence            6666666555555421         22233333333 555555555443      124445555555444

>PLN02789 farnesyltranstransferase

Probab=95.48  E-value=2.2  Score=39.79  Aligned_cols=204  Identities=11%  Similarity=0.114  Sum_probs=96.3

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcC-CHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCC--H
Q 011378          216 CRAKMLTEADDLFNEMLERGVFPDF-YTFTTLIHGHCKDG-NMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE--M  291 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~~~~-~t~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~--~  291 (487)
                      ...+..++|..+..++.+.  .|+. ..|+.--..+...| .+++++..++.+.+...+ +..+|+.---.+.+.|.  .
T Consensus        48 ~~~e~serAL~lt~~aI~l--nP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~l~~l~~~~~  124 (320)
T PLN02789         48 ASDERSPRALDLTADVIRL--NPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWLAEKLGPDAA  124 (320)
T ss_pred             HcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHHHHHcCchhh
Confidence            3344555555555555542  2322 22332222333334 356666666555543221 12233322222233333  2


Q ss_pred             HHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc---CC----hHHH
Q 011378          292 EKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRS---GD----ASKA  364 (487)
Q Consensus       292 ~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~---~~----~~~a  364 (487)
                      +++..+...+.+.. +-+...|+..-..+...|++++++..++.+++.... |...|+-....+.+.   |.    .+..
T Consensus       125 ~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~~~e~e  202 (320)
T PLN02789        125 NKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGLEAMRDSE  202 (320)
T ss_pred             HHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhccccccccccHHHH
Confidence            44555555554322 235666766666666777777777777777665422 233343333333222   11    1344


Q ss_pred             HHHHHHHHHCCCCC-ChhhHHHHHHHHhcc----CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh
Q 011378          365 DEFLSKMVSEGVDP-DSISYNTLINGFVRE----ENMDKAFALVSKMENQGLVPDVITYNVILTGFCR  427 (487)
Q Consensus       365 ~~~~~~m~~~g~~p-~~~~~~~li~~~~~~----~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  427 (487)
                      .+...+.+..  .| |...|+-+-..+...    ++..+|.+++.+....+ ..++.....|++.|+.
T Consensus       203 l~y~~~aI~~--~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        203 LKYTIDAILA--NPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             HHHHHHHHHh--CCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence            4444444432  23 345566555555542    23344666665544322 2244556667776664

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

Probab=95.45  E-value=3.8  Score=42.42  Aligned_cols=193  Identities=16%  Similarity=0.121  Sum_probs=126.5

Q ss_pred             HHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhH
Q 011378            5 LCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRA   84 (487)
Q Consensus         5 ~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a   84 (487)
                      +.+.|+.+.|...++.....+.. |..|...+-.+|-+.+..++|..+|+.....  .|+..-...+..+|+|.+++.+-
T Consensus        53 l~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~q  129 (932)
T KOG2053|consen   53 LFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQ  129 (932)
T ss_pred             HHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHH
Confidence            47889999999999988766643 8889999999999999999999999987654  57766677788889999888876


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHcc-C---------ChhHHHHHHHHHHHCC-CCCCHhHHHHHHHHHHhCCCHHH
Q 011378           85 KEVLDEMLQMGLSPDTATYNTLLVESCRK-E---------NMSEAEEIFCEMSRRG-VAPDIVSFSTLIGIFSRNGQLDR  153 (487)
Q Consensus        85 ~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-~---------~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~g~~~~  153 (487)
                      .+.--+|-+. ++-+...+=+++...... .         -+..|.+.++.+.+.+ .--+..-.-.-.......|.+++
T Consensus       130 Qkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~e  208 (932)
T KOG2053|consen  130 QKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQE  208 (932)
T ss_pred             HHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHH
Confidence            6655555432 122233322333332221 1         1334566677766554 11122222233345567788999


Q ss_pred             HHHHH-HHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011378          154 ALMYF-REMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGC  201 (487)
Q Consensus       154 a~~~~-~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~  201 (487)
                      |.+++ ....+.-..-+...-+--++.+...+.+.+..++-.++...|.
T Consensus       209 al~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~  257 (932)
T KOG2053|consen  209 ALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKGN  257 (932)
T ss_pred             HHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhCC
Confidence            99988 3343332233344445567777888888888888888877664

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=95.37  E-value=1.1  Score=44.67  Aligned_cols=135  Identities=12%  Similarity=0.097  Sum_probs=94.1

Q ss_pred             CCCCCChhhHHHHHHHHHh--cCC---hHHHHHHHHHHHHCCCCCCh-hhHHHHHHHHhcc--------CCHHHHHHHHH
Q 011378          339 KGIKPTLVSCNTIIKGYCR--SGD---ASKADEFLSKMVSEGVDPDS-ISYNTLINGFVRE--------ENMDKAFALVS  404 (487)
Q Consensus       339 ~~~~~~~~~~~~li~~~~~--~~~---~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~--------~~~~~a~~~~~  404 (487)
                      .+.+.|...|...+++...  .++   ...|..+|++..+  ..||- ..|..+..+|...        .++..+.+...
T Consensus       331 ~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~--ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~  408 (517)
T PRK10153        331 QGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILK--SEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELD  408 (517)
T ss_pred             ccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHH
Confidence            4567788999999998653  223   6688889988876  45764 3444443333221        12333333333


Q ss_pred             HHHhC-CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          405 KMENQ-GLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       405 ~m~~~-g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      +.... ....+...|.++.......|++++|...+++..+.  .|+...|..+-..|...|++++|...+++-.
T Consensus       409 ~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L--~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~  480 (517)
T PRK10153        409 NIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL--EMSWLNYVLLGKVYELKGDNRLAADAYSTAF  480 (517)
T ss_pred             HhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            32222 23345577888877777889999999999998775  4788899999999999999999999987754

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

Probab=95.37  E-value=0.11  Score=42.21  Aligned_cols=69  Identities=19%  Similarity=0.331  Sum_probs=42.9

Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH-----HcCCCCCHHH
Q 011378          383 YNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMI-----EKGLNPDRST  452 (487)
Q Consensus       383 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t  452 (487)
                      ...++..+...|+++.|..+.+++.... ..|...|..+|.+|...|+..+|..+|+++.     +.|+.|+..|
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            4455666677778888887777776531 3356677888888888888888887777764     3578887664

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

>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=95.34  E-value=0.067  Score=36.65  Aligned_cols=48  Identities=21%  Similarity=0.384  Sum_probs=21.5

Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          393 EENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      .|++++|.+++++....  .| +...+-.+...|.+.|++++|..+++++.
T Consensus         4 ~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~   52 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELLERLL   52 (68)
T ss_dssp             TTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred             ccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44455555555444332  12 33333444445555555555555555443

...

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=95.34  E-value=5  Score=43.05  Aligned_cols=137  Identities=14%  Similarity=0.164  Sum_probs=83.7

Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHH----HhcCCHHHHHHHHHHHHhCCCCCChhhHHHHH
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGY----CSMGHVTEAFRLWYEMVGKGIKPTLVSCNTII  352 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~----~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  352 (487)
                      .|.-.++---++|-+++|..++        .|+...+.....+|    ....++++|.-.|+..-+         ..--+
T Consensus       910 ~~~e~~n~I~kh~Ly~~aL~ly--------~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl  972 (1265)
T KOG1920|consen  910 YFPECKNYIKKHGLYDEALALY--------KPDSEKQKVIYEAYADHLREELMSDEAALMYERCGK---------LEKAL  972 (1265)
T ss_pred             ccHHHHHHHHhcccchhhhhee--------ccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcc---------HHHHH
Confidence            3344444445555555555554        36666555555444    456777777776654321         12356


Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCCh--hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCC
Q 011378          353 KGYCRSGDASKADEFLSKMVSEGVDPDS--ISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGR  430 (487)
Q Consensus       353 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  430 (487)
                      .+|..+|++.+|..+...+...   -|.  .+--.|..-+...++.-+|.++..+--.        ...-.+..+|+...
T Consensus       973 ~a~~~~~dWr~~l~~a~ql~~~---~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~s--------d~~~av~ll~ka~~ 1041 (1265)
T KOG1920|consen  973 KAYKECGDWREALSLAAQLSEG---KDELVILAEELVSRLVEQRKHYEAAKILLEYLS--------DPEEAVALLCKAKE 1041 (1265)
T ss_pred             HHHHHhccHHHHHHHHHhhcCC---HHHHHHHHHHHHHHHHHcccchhHHHHHHHHhc--------CHHHHHHHHhhHhH
Confidence            7888888888888887766531   122  2235677777788887777777765432        24455667788888


Q ss_pred             hHHHHHHHHHH
Q 011378          431 MHDSELILWRM  441 (487)
Q Consensus       431 ~~~a~~~~~~m  441 (487)
                      +++|.++...-
T Consensus      1042 ~~eAlrva~~~ 1052 (1265)
T KOG1920|consen 1042 WEEALRVASKA 1052 (1265)
T ss_pred             HHHHHHHHHhc
Confidence            89887765543

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=95.32  E-value=4.5  Score=42.53  Aligned_cols=216  Identities=14%  Similarity=0.072  Sum_probs=103.6

Q ss_pred             CChhhHHHHHHHHHh------cC--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-
Q 011378          203 MDVVTYNTILNGLCR------AK--MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-  273 (487)
Q Consensus       203 ~~~~~~~~li~~~~~------~~--~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-  273 (487)
                      .+..+|-.|...|.+      .+  +...|...+++..+.. .-+..+||.|--. .-.|++..+..-|-  ...-..| 
T Consensus       773 ~~~~~WyNLGinylr~f~~l~et~~~~~~Ai~c~KkaV~L~-ann~~~WnaLGVl-sg~gnva~aQHCfI--ks~~sep~  848 (1238)
T KOG1127|consen  773 IHMYPWYNLGINYLRYFLLLGETMKDACTAIRCCKKAVSLC-ANNEGLWNALGVL-SGIGNVACAQHCFI--KSRFSEPT  848 (1238)
T ss_pred             hccchHHHHhHHHHHHHHHcCCcchhHHHHHHHHHHHHHHh-hccHHHHHHHHHh-hccchhhhhhhhhh--hhhhcccc
Confidence            345566555555544      11  1234555555554321 1244455554433 44455555544442  2222223 


Q ss_pred             CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHH--HH--hCCCCCChhhH
Q 011378          274 DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYE--MV--GKGIKPTLVSC  348 (487)
Q Consensus       274 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~--m~--~~~~~~~~~~~  348 (487)
                      ...+|..+--.+.+..+++-|...|...++  +.| |...|-..-...-..|+.-++..+|..  ..  ..|--|+..-|
T Consensus       849 ~~~~W~NlgvL~l~n~d~E~A~~af~~~qS--LdP~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~f~Yw  926 (1238)
T KOG1127|consen  849 CHCQWLNLGVLVLENQDFEHAEPAFSSVQS--LDPLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKKFQYW  926 (1238)
T ss_pred             chhheeccceeEEecccHHHhhHHHHhhhh--cCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccchhhHH
Confidence            445666666667778888888888876553  334 445555544444556666667666654  11  12222333222


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHH---------CCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHh-CCCCCCHhhH
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVS---------EGVDPDSISYNTLINGFVREENMDKAFALVSKMEN-QGLVPDVITY  418 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~---------~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p~~~~~  418 (487)
                      -.-..-....|+.++-..-.++...         .|.+-+...|.+..+..-+.+....|.++..+.-. ...+.|..+|
T Consensus       927 ~c~te~h~~Ng~~e~~I~t~~ki~sAs~al~~yf~~~p~~~fAy~~~gstlEhL~ey~~a~ela~RliglLe~k~d~sqy 1006 (1238)
T KOG1127|consen  927 LCATEIHLQNGNIEESINTARKISSASLALSYYFLGHPQLCFAYAANGSTLEHLEEYRAALELATRLIGLLELKLDESQY 1006 (1238)
T ss_pred             HHHHHHHHhccchHHHHHHhhhhhhhHHHHHHHHhcCcchhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            2222223344444332222221111         23444455666555555555555555555443321 1124566677


Q ss_pred             HHHHHH
Q 011378          419 NVILTG  424 (487)
Q Consensus       419 ~~li~~  424 (487)
                      |++..-
T Consensus      1007 nvak~~ 1012 (1238)
T KOG1127|consen 1007 NVAKPD 1012 (1238)
T ss_pred             hhhhhh
Confidence            765443

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

Probab=95.26  E-value=0.55  Score=44.65  Aligned_cols=86  Identities=14%  Similarity=0.061  Sum_probs=41.8

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDK  398 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~  398 (487)
                      +...|++++|...|++..... +.+...|..+-.+|.+.|++++|...++.....  .| +...|..+-.+|...|++++
T Consensus        12 a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--~P~~~~a~~~lg~~~~~lg~~~e   88 (356)
T PLN03088         12 AFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIEL--DPSLAKAYLRKGTACMKLEEYQT   88 (356)
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCCHHH
Confidence            334455555555555554332 223334444445555555555555555555432  22 23344444455555555555


Q ss_pred             HHHHHHHHHh
Q 011378          399 AFALVSKMEN  408 (487)
Q Consensus       399 a~~~~~~m~~  408 (487)
                      |...+++..+
T Consensus        89 A~~~~~~al~   98 (356)
T PLN03088         89 AKAALEKGAS   98 (356)
T ss_pred             HHHHHHHHHH
Confidence            5555555443

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.10  E-value=1.4  Score=35.35  Aligned_cols=84  Identities=10%  Similarity=0.127  Sum_probs=38.2

Q ss_pred             HHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCC
Q 011378           70 SLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNG  149 (487)
Q Consensus        70 ~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  149 (487)
                      .++..+.+.+.......+++.+...+ ..+....|.++..|++.. .....+.++.      .++......+++.|.+.+
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~~   83 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKAK   83 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHcC
Confidence            34444444455555555555554443 234445555555555432 2222222221      112222334555565555


Q ss_pred             CHHHHHHHHHHH
Q 011378          150 QLDRALMYFREM  161 (487)
Q Consensus       150 ~~~~a~~~~~~m  161 (487)
                      .++++..++.++
T Consensus        84 l~~~~~~l~~k~   95 (140)
T smart00299       84 LYEEAVELYKKD   95 (140)
T ss_pred             cHHHHHHHHHhh
Confidence            555555555544

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=95.07  E-value=4.3  Score=40.87  Aligned_cols=328  Identities=14%  Similarity=0.146  Sum_probs=154.2

Q ss_pred             CCCHHHHHHHHHHHHccCChhHHHHHHHHHHH-CCCCC--------CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC
Q 011378           97 SPDTATYNTLLVESCRKENMSEAEEIFCEMSR-RGVAP--------DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLV  167 (487)
Q Consensus        97 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-~g~~p--------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  167 (487)
                      .|....|..|.......-.++.|+.-|-.... .|++.        +...-.+-|.+|  -|++++|.++|-+|..+.  
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 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDADRRD--  764 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccchhh--
Confidence            47777787777777777777777777765543 23221        111111122222  367888888777775543  


Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 011378          168 PDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMD----VVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTF  243 (487)
Q Consensus       168 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~  243 (487)
                             ..|..+.+.|++..+.++++   ..|...|    ...|+.+-..+.....++.|.+.+..-..         -
T Consensus       765 -------LAielr~klgDwfrV~qL~r---~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~---------~  825 (1189)
T KOG2041|consen  765 -------LAIELRKKLGDWFRVYQLIR---NGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD---------T  825 (1189)
T ss_pred             -------hhHHHHHhhhhHHHHHHHHH---ccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc---------h
Confidence                   23444555555555444332   1111111    12344444444444444444444433211         0


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc
Q 011378          244 TTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSM  323 (487)
Q Consensus       244 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~  323 (487)
                      ...+..+.+...+++-+.+     ...++-+....-.+-+++.+.|.-++|.+.+-...   . |     -.-+..|...
T Consensus       826 e~~~ecly~le~f~~LE~l-----a~~Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s---~-p-----kaAv~tCv~L  891 (1189)
T KOG2041|consen  826 ENQIECLYRLELFGELEVL-----ARTLPEDSELLPVMADMFTSVGMCDQAVEAYLRRS---L-P-----KAAVHTCVEL  891 (1189)
T ss_pred             HhHHHHHHHHHhhhhHHHH-----HHhcCcccchHHHHHHHHHhhchHHHHHHHHHhcc---C-c-----HHHHHHHHHH
Confidence            1222222222222222111     12334455566667777777777777776654321   1 1     1345566677


Q ss_pred             CCHHHHHHHHHHHHhCCCCCChhhHH----------HHHHHHHhcCChHHHHHHHHHHHHC----CCCCCh----hhHHH
Q 011378          324 GHVTEAFRLWYEMVGKGIKPTLVSCN----------TIIKGYCRSGDASKADEFLSKMVSE----GVDPDS----ISYNT  385 (487)
Q Consensus       324 ~~~~~a~~~~~~m~~~~~~~~~~~~~----------~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~~----~~~~~  385 (487)
                      +++.+|.++-+...-..+..-+.-+.          --|..+.++|+.-.|.+++.+|.++    +.+|-.    ....+
T Consensus       892 nQW~~avelaq~~~l~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~e~~K~~p~lr~KklYVL~A  971 (1189)
T KOG2041|consen  892 NQWGEAVELAQRFQLPQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAEREQEKYVPYLRLKKLYVLGA  971 (1189)
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHHHhhccCCHHHHHHHHHHHH
Confidence            77777776655432111111110010          1234456667766777777777543    333321    11222


Q ss_pred             HH-HHHh----------ccCCHHHHHHHHHHHHhC---CC----CCCHhhHHHHH--HHHHhcCChHHHHHHHHHHHH-c
Q 011378          386 LI-NGFV----------REENMDKAFALVSKMENQ---GL----VPDVITYNVIL--TGFCRQGRMHDSELILWRMIE-K  444 (487)
Q Consensus       386 li-~~~~----------~~~~~~~a~~~~~~m~~~---g~----~p~~~~~~~li--~~~~~~g~~~~a~~~~~~m~~-~  444 (487)
                      |+ .-+-          +.|..++|..+++.-...   .+    =.....|.-+|  .-....|.++.|.+.--.+.+ .
T Consensus       972 lLvE~h~~~ik~~~~~~~~g~~~dat~lles~~l~~~~ri~~n~WrgAEAyHFmilAQrql~eg~v~~Al~Tal~L~DYE 1051 (1189)
T KOG2041|consen  972 LLVENHRQTIKELRKIDKHGFLEDATDLLESGLLAEQSRILENTWRGAEAYHFMILAQRQLFEGRVKDALQTALILSDYE 1051 (1189)
T ss_pred             HHHHHHHHHHHHhhhhhhcCcchhhhhhhhhhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHhchHHHHHHHHhhhccHh
Confidence            21 1111          234444554433321100   00    01122344343  444567888888765555543 3


Q ss_pred             CCCCCHHHHHHHHHHHH
Q 011378          445 GLNPDRSTYTTLINGHV  461 (487)
Q Consensus       445 g~~p~~~ty~~l~~~~~  461 (487)
                      .+-|....|..+--+-+
T Consensus      1052 d~lpP~eiySllALaac 1068 (1189)
T KOG2041|consen 1052 DFLPPAEIYSLLALAAC 1068 (1189)
T ss_pred             hcCCHHHHHHHHHHHHh
Confidence            56677788877644333

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

Probab=95.05  E-value=0.67  Score=44.05  Aligned_cols=101  Identities=16%  Similarity=0.080  Sum_probs=71.5

Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChH
Q 011378          283 DGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDAS  362 (487)
Q Consensus       283 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~  362 (487)
                      ..+...|++++|...|.+..... +-+...|..+..+|...|++++|+..++...... +.+...|..+-.+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHH
Confidence            44566788888888888876542 2245667777788888888888888888876543 234556777777888888888


Q ss_pred             HHHHHHHHHHHCCCCCChhhHHHHH
Q 011378          363 KADEFLSKMVSEGVDPDSISYNTLI  387 (487)
Q Consensus       363 ~a~~~~~~m~~~g~~p~~~~~~~li  387 (487)
                      +|...++...+.  .|+......++
T Consensus        88 eA~~~~~~al~l--~P~~~~~~~~l  110 (356)
T PLN03088         88 TAKAALEKGASL--APGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHH
Confidence            888888887753  35544444443

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

Probab=94.89  E-value=0.12  Score=35.43  Aligned_cols=22  Identities=18%  Similarity=0.418  Sum_probs=8.9

Q ss_pred             HHHHHHhccCCHHHHHHHHHHH
Q 011378          385 TLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       385 ~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      .|..+|.+.|++++|..+++++
T Consensus        30 ~la~~~~~~g~~~~A~~~l~~~   51 (68)
T PF14559_consen   30 LLAQCYLKQGQYDEAEELLERL   51 (68)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHCC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH
Confidence            3444444444444444444433

...

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

Probab=94.87  E-value=0.15  Score=34.54  Aligned_cols=52  Identities=15%  Similarity=0.256  Sum_probs=24.3

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          424 GFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      .+.+.|++++|...|++..+..  | +...+..+-..+...|++++|..++++.+
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444555555555555554432  3 23344444445555555555555555443

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.73  E-value=1.7  Score=39.82  Aligned_cols=131  Identities=11%  Similarity=0.148  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh--c----CCHHHHHHHHHHHHhCCC---CCChhhHHHHHHHHHhcCC-
Q 011378          291 MEKANKLWADMISRKISPNYISYGILINGYCS--M----GHVTEAFRLWYEMVGKGI---KPTLVSCNTIIKGYCRSGD-  360 (487)
Q Consensus       291 ~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~--~----~~~~~a~~~~~~m~~~~~---~~~~~~~~~li~~~~~~~~-  360 (487)
                      +++...++..+.+.|+.-+..+|-+-......  .    ....+|..+|+.|++...   .++...+.+|+..  ..++ 
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            44566777777788887777665332222211  1    235667888888876532   2334456556544  2333 


Q ss_pred             ---hHHHHHHHHHHHHCCCCCChh--hHHHHHHHHhccC--CHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          361 ---ASKADEFLSKMVSEGVDPDSI--SYNTLINGFVREE--NMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       361 ---~~~a~~~~~~m~~~g~~p~~~--~~~~li~~~~~~~--~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                         .+.++.+++.+.+.|+..+-.  ..+.++..+-...  ...++.++++.+++.|+++....|..+--
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGl  225 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGL  225 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHH
Confidence               355677777777777765432  2333332222111  14567777778888888877777665533

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

Probab=94.65  E-value=1.2  Score=42.21  Aligned_cols=145  Identities=14%  Similarity=0.225  Sum_probs=103.6

Q ss_pred             eehHHHHHHHHccCCHHHHHHHHHHHHhCC-CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhh-HHHHHH
Q 011378          276 VTYNTLIDGFCKVGEMEKANKLWADMISRK-ISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVS-CNTIIK  353 (487)
Q Consensus       276 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~li~  353 (487)
                      ..|...|+...+..-++.|..+|.+..+.+ +.+++..++++|.-++. |+...|.++|+-=...  -||... .+-.+.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~--f~d~~~y~~kyl~  474 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK--FPDSTLYKEKYLL  474 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh--CCCchHHHHHHHH
Confidence            456778888888888899999999888887 67888899999987765 6677888888753222  344443 345666


Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCC--hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPD--SISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFC  426 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  426 (487)
                      -+.+.++-+.|..+|+....+ +..+  ..+|..+|+.=...|++..+..+=++|.+.  .|...+-.+..+.|.
T Consensus       475 fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry~  546 (660)
T COG5107         475 FLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRYA  546 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHHh
Confidence            777888888888888855432 1122  457888888888889998888887777663  555555555555553

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=94.63  E-value=4.1  Score=38.48  Aligned_cols=77  Identities=9%  Similarity=0.036  Sum_probs=40.8

Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCC--C-ChhhHHHHHHHHHh---cCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          280 TLIDGFCKVGEMEKANKLWADMISRKIS--P-NYISYGILINGYCS---MGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK  353 (487)
Q Consensus       280 ~li~~~~~~g~~~~a~~~~~~m~~~~~~--p-~~~t~~~li~~~~~---~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  353 (487)
                      .|+-+|....+++...++.+.+......  + ....--...-++-+   .|+.++|.+++..+....-.++..+|..+-.
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            4444567777777777777766543111  0 11111122233334   5667777777766555555666666665555


Q ss_pred             HHH
Q 011378          354 GYC  356 (487)
Q Consensus       354 ~~~  356 (487)
                      .|.
T Consensus       226 IyK  228 (374)
T PF13281_consen  226 IYK  228 (374)
T ss_pred             HHH
Confidence            543

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

Probab=94.53  E-value=0.23  Score=33.54  Aligned_cols=54  Identities=17%  Similarity=0.158  Sum_probs=29.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          213 NGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMT  267 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~  267 (487)
                      ..+.+.|++++|.+.|++..+.. +-+...+..+-..+...|++++|...|+...
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34455566666666666665543 2244555555556666666666666665544

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.43  E-value=1.8  Score=33.67  Aligned_cols=19  Identities=21%  Similarity=0.319  Sum_probs=6.9

Q ss_pred             HHHHHhccCCHHHHHHHHH
Q 011378          386 LINGFVREENMDKAFALVS  404 (487)
Q Consensus       386 li~~~~~~~~~~~a~~~~~  404 (487)
                      +-.+|.+.|+..++.+++.
T Consensus       126 ia~Ay~klg~~r~~~ell~  144 (161)
T PF09205_consen  126 IANAYKKLGNTREANELLK  144 (161)
T ss_dssp             HHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHhcchhhHHHHHH
Confidence            3333333333333333333

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

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.43  E-value=0.59  Score=45.57  Aligned_cols=129  Identities=16%  Similarity=0.115  Sum_probs=66.6

Q ss_pred             hHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          278 YNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR  357 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  357 (487)
                      .+.++.-+-+.|-.+.|+.+-.+-.            .-.+...+.|+++.|.++.++      .++...|..|-+...+
T Consensus       298 ~~~i~~fL~~~G~~e~AL~~~~D~~------------~rFeLAl~lg~L~~A~~~a~~------~~~~~~W~~Lg~~AL~  359 (443)
T PF04053_consen  298 GQSIARFLEKKGYPELALQFVTDPD------------HRFELALQLGNLDIALEIAKE------LDDPEKWKQLGDEALR  359 (443)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHSS-HH------------HHHHHHHHCT-HHHHHHHCCC------CSTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHhhcCChH------------HHhHHHHhcCCHHHHHHHHHh------cCcHHHHHHHHHHHHH
Confidence            5556666666666666665543311            123334455666666654432      2355566666666666


Q ss_pred             cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHH
Q 011378          358 SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELI  437 (487)
Q Consensus       358 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  437 (487)
                      .|+++.|++.+++...         |..|+-.|.-.|+.+.-.++.+.-...|      -+|+...++.-.|+.++..++
T Consensus       360 ~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~~------~~n~af~~~~~lgd~~~cv~l  424 (443)
T PF04053_consen  360 QGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEERG------DINIAFQAALLLGDVEECVDL  424 (443)
T ss_dssp             TTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHHHHT-HHHHHHH
T ss_pred             cCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHcc------CHHHHHHHHHHcCCHHHHHHH
Confidence            6666666666665432         4555555666666665555555444443      345555555555555555544


Q ss_pred             HH
Q 011378          438 LW  439 (487)
Q Consensus       438 ~~  439 (487)
                      +.
T Consensus       425 L~  426 (443)
T PF04053_consen  425 LI  426 (443)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=94.34  E-value=7.2  Score=40.14  Aligned_cols=46  Identities=20%  Similarity=0.213  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhC
Q 011378          101 ATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRN  148 (487)
Q Consensus       101 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  148 (487)
                      ..| .+|..|.|+|++++|.++..+..+. .......|-..+..|..+
T Consensus       113 p~W-a~Iyy~LR~G~~~~A~~~~~~~~~~-~~~~~~~f~~~l~~~~~s  158 (613)
T PF04097_consen  113 PIW-ALIYYCLRCGDYDEALEVANENRNQ-FQKIERSFPTYLKAYASS  158 (613)
T ss_dssp             EHH-HHHHHHHTTT-HHHHHHHHHHTGGG-S-TTTTHHHHHHHHCTTT
T ss_pred             ccH-HHHHHHHhcCCHHHHHHHHHHhhhh-hcchhHHHHHHHHHHHhC
Confidence            344 3455666888888888877444332 333344566667776654

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.

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

Probab=94.31  E-value=0.13  Score=36.32  Aligned_cols=61  Identities=20%  Similarity=0.286  Sum_probs=37.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc--CCC---CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEK--GLN---PD-RSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~---p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      +|+.+-..|...|++++|...|++..+.  -..   |+ ..+|..+-..|...|++++|.+++++-.
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            4566666666777777777666665532  111   22 3466677777777777777777776543

...

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=94.27  E-value=1.2  Score=36.14  Aligned_cols=88  Identities=14%  Similarity=0.029  Sum_probs=53.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHH
Q 011378          213 NGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME  292 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~  292 (487)
                      ..+...|++++|.++|+-+..-. +-+..-|-.|--.|-..|++++|+..|........ -|...+-.+-.++.+.|+.+
T Consensus        43 ~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG~~~  120 (157)
T PRK15363         43 MQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACDNVC  120 (157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcCCHH
Confidence            33456677777777777665432 22344455566666667777777777766554442 34455556666677777777


Q ss_pred             HHHHHHHHHH
Q 011378          293 KANKLWADMI  302 (487)
Q Consensus       293 ~a~~~~~~m~  302 (487)
                      .|.+-|+...
T Consensus       121 ~A~~aF~~Ai  130 (157)
T PRK15363        121 YAIKALKAVV  130 (157)
T ss_pred             HHHHHHHHHH
Confidence            7777766543

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=94.07  E-value=2.2  Score=33.12  Aligned_cols=49  Identities=22%  Similarity=0.229  Sum_probs=19.2

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCh--hhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          288 VGEMEKANKLWADMISRKISPNY--ISYGILINGYCSMGHVTEAFRLWYEM  336 (487)
Q Consensus       288 ~g~~~~a~~~~~~m~~~~~~p~~--~t~~~li~~~~~~~~~~~a~~~~~~m  336 (487)
                      .|+.++|..+|++....|.....  ..+-.+-.++-..|++++|..++++.
T Consensus        14 ~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~   64 (120)
T PF12688_consen   14 LGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEA   64 (120)
T ss_pred             cCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34444444444444443333221  12223333344444444444444433

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.03  E-value=1.7  Score=42.47  Aligned_cols=129  Identities=20%  Similarity=0.124  Sum_probs=57.9

Q ss_pred             hHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh
Q 011378           68 YNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR  147 (487)
Q Consensus        68 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  147 (487)
                      .+.+++-+-+.|.++.|+++..+-..            -.....+.|+++.|.++-++.      .+...|..|-....+
T Consensus       298 ~~~i~~fL~~~G~~e~AL~~~~D~~~------------rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~AL~  359 (443)
T PF04053_consen  298 GQSIARFLEKKGYPELALQFVTDPDH------------RFELALQLGNLDIALEIAKEL------DDPEKWKQLGDEALR  359 (443)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHSS-HHH------------HHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHhhcCChHH------------HhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHHHHH
Confidence            45555555555555555554443211            223334455555555443322      234455555555555


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          148 NGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDL  227 (487)
Q Consensus       148 ~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~  227 (487)
                      .|+++.|.+.|.+.+         -|..|+-.|.-.|+.+.-.++.+.-...|-      +|....++.-.|+.++..++
T Consensus       360 ~g~~~lAe~c~~k~~---------d~~~L~lLy~~~g~~~~L~kl~~~a~~~~~------~n~af~~~~~lgd~~~cv~l  424 (443)
T PF04053_consen  360 QGNIELAEECYQKAK---------DFSGLLLLYSSTGDREKLSKLAKIAEERGD------INIAFQAALLLGDVEECVDL  424 (443)
T ss_dssp             TTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHHHHT-HHHHHHH
T ss_pred             cCCHHHHHHHHHhhc---------CccccHHHHHHhCCHHHHHHHHHHHHHccC------HHHHHHHHHHcCCHHHHHHH
Confidence            555555555555432         234444445555555554444444444432      33344444444555555544


Q ss_pred             HH
Q 011378          228 FN  229 (487)
Q Consensus       228 ~~  229 (487)
                      +.
T Consensus       425 L~  426 (443)
T PF04053_consen  425 LI  426 (443)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

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.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.00  E-value=8.1  Score=39.39  Aligned_cols=342  Identities=13%  Similarity=0.128  Sum_probs=185.9

Q ss_pred             CCCCCCccchH-----HHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC---ChhHHHHHHHHHHHCC
Q 011378           59 KGLKPGVFTYN-----SLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKE---NMSEAEEIFCEMSRRG  130 (487)
Q Consensus        59 ~~~~p~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~---~~~~a~~~~~~m~~~g  130 (487)
                      -|++.+..-|.     .+|+-+...+.+..|.++-..+...-..- ...|.....-+.+..   +-+-+..+-+++... 
T Consensus       426 ~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~-~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~-  503 (829)
T KOG2280|consen  426 IGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAK-  503 (829)
T ss_pred             cCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHHHHHHHhccCccchHHHHHHHHHhccc-
Confidence            35555544443     45777778888999999888875321111 455555555554442   222233333333332 


Q ss_pred             CCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC----CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChh
Q 011378          131 VAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGL----VPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVV  206 (487)
Q Consensus       131 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~----~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~  206 (487)
                      ..|. .+|..+...-..+|+.+.|..+++.=...+-    -.+..-+...+.-..+.|+.+-...++..+..+   .+..
T Consensus       504 ~~~~-iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~---~~~s  579 (829)
T KOG2280|consen  504 LTPG-ISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNK---LNRS  579 (829)
T ss_pred             CCCc-eeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHH---HHHH
Confidence            3444 4678888888899999999888764222111    012223555666666777776666665555432   1111


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH---HHHCCCCCCeeehHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDI---MTQKSIKPDIVTYNTLID  283 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~---m~~~~~~~~~~~~~~li~  283 (487)
                      .+.-.      ..+.-.|..+|.+..++.-...       +..+...++-..+...|..   .....+.+-.......-+
T Consensus       580 ~l~~~------l~~~p~a~~lY~~~~r~~~~~~-------l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~~a~  646 (829)
T KOG2280|consen  580 SLFMT------LRNQPLALSLYRQFMRHQDRAT-------LYDFYNQDDNHQALASFHLQASYAAETIEGRIPALKTAAN  646 (829)
T ss_pred             HHHHH------HHhchhhhHHHHHHHHhhchhh-------hhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHHHHHH
Confidence            11111      1223344445544433210000       0111122222222222210   000001111222233334


Q ss_pred             HHHccCC-------HHHHHH---HHHHHH-hCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHH
Q 011378          284 GFCKVGE-------MEKANK---LWADMI-SRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTII  352 (487)
Q Consensus       284 ~~~~~g~-------~~~a~~---~~~~m~-~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  352 (487)
                      .+.+...       .++-.+   +.+... +.+..-.-.|.+-.+.-+...|+-.+|.++-.+.+    -||...|..=+
T Consensus       647 ~~a~sk~~s~e~ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~  722 (829)
T KOG2280|consen  647 AFAKSKEKSFEAKALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKL  722 (829)
T ss_pred             HHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHH
Confidence            4444333       111122   222222 12334445567777888888999999999877764    68888888888


Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChH
Q 011378          353 KGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMH  432 (487)
Q Consensus       353 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  432 (487)
                      .+++..+++++.+++-+.+..      +.-|.-.+.+|.+.|+.++|.+++.+...         +.-...+|.+.|++.
T Consensus       723 ~aLa~~~kweeLekfAkskks------PIGy~PFVe~c~~~~n~~EA~KYiprv~~---------l~ekv~ay~~~~~~~  787 (829)
T KOG2280|consen  723 TALADIKKWEELEKFAKSKKS------PIGYLPFVEACLKQGNKDEAKKYIPRVGG---------LQEKVKAYLRVGDVK  787 (829)
T ss_pred             HHHHhhhhHHHHHHHHhccCC------CCCchhHHHHHHhcccHHHHhhhhhccCC---------hHHHHHHHHHhccHH
Confidence            999999999987776665442      34466678999999999999998876432         114567888888888


Q ss_pred             HHHHHH
Q 011378          433 DSELIL  438 (487)
Q Consensus       433 ~a~~~~  438 (487)
                      +|..+-
T Consensus       788 eAad~A  793 (829)
T KOG2280|consen  788 EAADLA  793 (829)
T ss_pred             HHHHHH
Confidence            886543

>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=93.97  E-value=0.37  Score=32.95  Aligned_cols=62  Identities=15%  Similarity=0.109  Sum_probs=39.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHH
Q 011378          205 VVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDG-NMNKALNLFDIMT  267 (487)
Q Consensus       205 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g-~~~~a~~~~~~m~  267 (487)
                      ..+|..+-..+.+.|++++|...|.+..+.. +-+...|..+-.+|...| ++++|+..|+...
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            3456666666677777777777777766643 224556666666677776 5777776666544

...

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.74  E-value=6.7  Score=37.55  Aligned_cols=422  Identities=14%  Similarity=0.210  Sum_probs=229.8

Q ss_pred             hhhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHH--HhcCChhHHHHHHHHHhhC--CCCCC---c--------c
Q 011378            2 VNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAY--CREGFLEEAFQLMNSMSGK--GLKPG---V--------F   66 (487)
Q Consensus         2 i~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~--~~~~~~~~a~~~~~~m~~~--~~~p~---~--------~   66 (487)
                      |++|..+. ++.....+.+.++.-  | ...|-.+..++  -+.+.++.|.+.+..-.++  +-.|.   .        +
T Consensus        53 lnAffl~n-ld~Me~~l~~l~~~~--~-~s~~l~LF~~L~~Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df  128 (549)
T PF07079_consen   53 LNAFFLNN-LDLMEKQLMELRQQF--G-KSAYLPLFKALVAYKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDF  128 (549)
T ss_pred             HHHHHHhh-HHHHHHHHHHHHHhc--C-CchHHHHHHHHHHHHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHH
Confidence            44554443 666666777765542  2 22344444443  4688899999888766554  32221   1        1


Q ss_pred             c-hHHHHHHHHhcCChhhHHHHHHHHHHCCCC----CCHHHHHHHHHHHHccCChhHHHHHHHHHHH---CCCCCCHhHH
Q 011378           67 T-YNSLINGLCKKGRCDRAKEVLDEMLQMGLS----PDTATYNTLLVESCRKENMSEAEEIFCEMSR---RGVAPDIVSF  138 (487)
Q Consensus        67 ~-~~~li~~~~~~~~~~~a~~~~~~m~~~g~~----~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~---~g~~p~~~~~  138 (487)
                      . =+.....+...|.+.+++.+++++.+.=++    .+..+||.++-.+++.        .|-++++   ..+-|+-  |
T Consensus       129 ~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmlsrS--------YfLEl~e~~s~dl~pdy--Y  198 (549)
T PF07079_consen  129 FLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLSRS--------YFLELKESMSSDLYPDY--Y  198 (549)
T ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHhHH--------HHHHHHHhcccccChHH--H
Confidence            1 134566778899999999999998865444    7889999877777664        3333322   3344442  2


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCcCChh-hHHHHHHHH
Q 011378          139 STLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG--FVLEALKMRDEMLEKGCVMDVV-TYNTILNGL  215 (487)
Q Consensus       139 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~g~~~~~~-~~~~li~~~  215 (487)
                       -+|-.|-+.=      ..+++-.-..+.|.......+++...-..  ...--.++++.+.+.-+.|+-. ....++..+
T Consensus       199 -emilfY~kki------~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~~mq~l~~We~~yv~p~~~LVi~~L~~~f  271 (549)
T PF07079_consen  199 -EMILFYLKKI------HAFDQRPYEKFIPEEELFSTIMQHLFIVPKERLPPLMQILENWENFYVHPNYDLVIEPLKQQF  271 (549)
T ss_pred             -HHHHHHHHHH------HHHhhchHHhhCcHHHHHHHHHHHHHhCCHhhccHHHHHHHHHHhhccCCchhHHHHHHHHHH
Confidence             2333333221      11111111123444444444444433222  1222234444444555555422 223333333


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeee-------hHHHHHH
Q 011378          216 CRAKMLTEADDLFNEMLERGVFP----DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVT-------YNTLIDG  284 (487)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~~----~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~-------~~~li~~  284 (487)
                      .+  +.+++..+=+.+....+.+    =..+|..++....+.++..+|-+.+..+.--  .|+...       -.++-+.
T Consensus       272 ~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~lL~~l--dp~~svs~Kllls~~~lq~I  347 (549)
T PF07079_consen  272 MS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLALLKIL--DPRISVSEKLLLSPKVLQDI  347 (549)
T ss_pred             hc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc--CCcchhhhhhhcCHHHHHHH
Confidence            33  4444444433332221111    2457899999999999999998888766532  333322       1233333


Q ss_pred             HHcc----CCHHHHHHHHHHHHhCCCCCChhhHHHHHHH---HHhcCC-HHHHHHHHHHHHhC---CCCCChhhHHHHHH
Q 011378          285 FCKV----GEMEKANKLWADMISRKISPNYISYGILING---YCSMGH-VTEAFRLWYEMVGK---GIKPTLVSCNTIIK  353 (487)
Q Consensus       285 ~~~~----g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~---~~~~~~-~~~a~~~~~~m~~~---~~~~~~~~~~~li~  353 (487)
                      .|.-    -+...-..+|.......+..- ..-.-|+.+   +-+.|. -++|+++++...+-   .++.-..++..+-.
T Consensus       348 v~~DD~~~Tklr~yL~lwe~~qs~DiDrq-QLvh~L~~~Ak~lW~~g~~dekalnLLk~il~ft~yD~ec~n~v~~fvKq  426 (549)
T PF07079_consen  348 VCEDDESYTKLRDYLNLWEEIQSYDIDRQ-QLVHYLVFGAKHLWEIGQCDEKALNLLKLILQFTNYDIECENIVFLFVKQ  426 (549)
T ss_pred             HhcchHHHHHHHHHHHHHHHHHhhcccHH-HHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            4421    134455666666665433211 111223322   344555 67788888877642   12222223333444


Q ss_pred             HHHhc---CChHHHHHHHHHHHHCCCCCChh----hHHHHHHH--HhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH
Q 011378          354 GYCRS---GDASKADEFLSKMVSEGVDPDSI----SYNTLING--FVREENMDKAFALVSKMENQGLVPDVITYNVILTG  424 (487)
Q Consensus       354 ~~~~~---~~~~~a~~~~~~m~~~g~~p~~~----~~~~li~~--~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  424 (487)
                      +|...   ..+.+...+-+...+.|++|-.+    .-|.|-+|  ....|++.++.-.-.-+.+  +.|++.+|.-+--.
T Consensus       427 ~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~  504 (549)
T PF07079_consen  427 AYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLC  504 (549)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHH
Confidence            55432   34555566666667789887433    34444433  2356888887654433333  68999999877667


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCCHHHHHHH
Q 011378          425 FCRQGRMHDSELILWRMIEKGLNPDRSTYTTL  456 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l  456 (487)
                      ...+.++++|+.+++.+     .|+..++++=
T Consensus       505 l~e~k~Y~eA~~~l~~L-----P~n~~~~dsk  531 (549)
T PF07079_consen  505 LMENKRYQEAWEYLQKL-----PPNERMRDSK  531 (549)
T ss_pred             HHHHhhHHHHHHHHHhC-----CCchhhHHHH
Confidence            77899999999999874     6787777654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=93.57  E-value=5.1  Score=35.69  Aligned_cols=56  Identities=7%  Similarity=-0.023  Sum_probs=31.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLER--GVFPDFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~--~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      +..-|.+.|.+..|..-|+.+.++  +.+......-.++.+|.+.|..++|..+...+
T Consensus       181 ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l  238 (243)
T PRK10866        181 VAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKII  238 (243)
T ss_pred             HHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            334456666666666666666553  22333444555666666666666666555544

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=93.46  E-value=1.9  Score=38.88  Aligned_cols=93  Identities=14%  Similarity=0.046  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh----hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC----HhhH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS----ISYNTLINGFVREENMDKAFALVSKMENQGLVPD----VITY  418 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~  418 (487)
                      .|..-+....+.|++++|...|+.+.+.-  |+.    ..+--+-..|...|++++|...|+.+.+.  .|+    ...+
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~--yP~s~~~~dAl  220 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN--YPKSPKAADAM  220 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCcchhHHH
Confidence            34444444445566666666666666432  322    23334455556666666666666666432  122    1222


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          419 NVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       419 ~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      --+...+...|+.++|..++++..+
T Consensus       221 ~klg~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        221 FKVGVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2233344455666666666555543

>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=93.32  E-value=0.58  Score=31.97  Aligned_cols=60  Identities=17%  Similarity=0.210  Sum_probs=33.2

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcC-CHHHHHHHHHHHH
Q 011378          416 ITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQN-NLKEAFRFHDEML  477 (487)
Q Consensus       416 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~-~~~~a~~~~~~m~  477 (487)
                      .+|..+-..+.+.|++++|...|.+..+.  .| +...|..+-.+|...| ++++|++.+++-+
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~--~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIEL--DPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHH--STTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            34555555566666666666666665543  23 3345555555666666 4666666655443

...

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

Probab=93.03  E-value=0.33  Score=34.23  Aligned_cols=60  Identities=22%  Similarity=0.267  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCC---CC-HHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLER--GVF---PD-FYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~---~~-~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      +|+.+-..|...|++++|...|++..+.  ...   |+ ..++..+-..|...|+.++|+..++..
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4555666666666666666666665432  111   11 345556666666666666666666543

...

>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=92.96  E-value=4.5  Score=33.35  Aligned_cols=132  Identities=14%  Similarity=0.144  Sum_probs=72.2

Q ss_pred             HHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHH-HhCC
Q 011378          332 LWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKM-ENQG  410 (487)
Q Consensus       332 ~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m-~~~g  410 (487)
                      ..+.+...+++|+...+..+++.+.+.|.....    ..+...++-||.......+-.+.  +....+.++--.| +..|
T Consensus        16 YirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L----~qllq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkRL~   89 (167)
T PF07035_consen   16 YIRSLNQHNIPVQHELYELLIDLLIRNGQFSQL----HQLLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKRLG   89 (167)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHH----HHHHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHHhh
Confidence            344455667777777777777777777775553    33344566666554444432222  1222333332222 2211


Q ss_pred             CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          411 LVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       411 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                           ..+..++..+...|++-+|.++.++....    +......++.+-...+|...-..+++-..+
T Consensus        90 -----~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   90 -----TAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             -----hhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                 13667777888888888888877664221    111224466666666665555555555444

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.77  E-value=7.2  Score=35.15  Aligned_cols=114  Identities=11%  Similarity=0.154  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHh-cC-CHHHHHHHHHHHHH-CCCCCCeeehHHHHHHHHccCCHHHHHH
Q 011378          221 LTEADDLFNEMLE-RGVFPDFYTFTTLIHGHCK-DG-NMNKALNLFDIMTQ-KSIKPDIVTYNTLIDGFCKVGEMEKANK  296 (487)
Q Consensus       221 ~~~a~~~~~~m~~-~~~~~~~~t~~~li~~~~~-~g-~~~~a~~~~~~m~~-~~~~~~~~~~~~li~~~~~~g~~~~a~~  296 (487)
                      +.+|.++|+.... ..+--|..+.+.+++.... .+ ....-.++.+.+.+ .+-.++..+...+|+.+++.+++++-.+
T Consensus       144 Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~  223 (292)
T PF13929_consen  144 VVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQ  223 (292)
T ss_pred             HHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHH
Confidence            4455566653322 3355566666666666655 22 23333344444432 3455666677777777777777777777


Q ss_pred             HHHHHHhC-CCCCChhhHHHHHHHHHhcCCHHHHHHHHH
Q 011378          297 LWADMISR-KISPNYISYGILINGYCSMGHVTEAFRLWY  334 (487)
Q Consensus       297 ~~~~m~~~-~~~p~~~t~~~li~~~~~~~~~~~a~~~~~  334 (487)
                      +|...... +..-|...|..+|..-...|+..-..++.+
T Consensus       224 fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  224 FWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             HHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhh
Confidence            77665544 455567777777777777777665555444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=92.70  E-value=7  Score=34.83  Aligned_cols=55  Identities=9%  Similarity=0.033  Sum_probs=29.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          422 LTGFCRQGRMHDSELILWRMIEK--GLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       422 i~~~~~~g~~~~a~~~~~~m~~~--g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      ...|-+.|.+.-|..=++.+.+.  +-.......-.++.+|...|..++|..+..-+
T Consensus       182 a~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l  238 (243)
T PRK10866        182 AEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKII  238 (243)
T ss_pred             HHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            34455666666666666665542  11223334455566666666666666655433

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.67  E-value=3.3  Score=37.36  Aligned_cols=59  Identities=14%  Similarity=0.149  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          137 SFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDN----VLYTIIINGYCRNGFVLEALKMRDEML  197 (487)
Q Consensus       137 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~----~~~~~ll~~~~~~~~~~~a~~~~~~m~  197 (487)
                      .|...+....+.|++++|...|+.+.+..  |+.    ..+-.+-..|...|+.++|...|..+.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv  207 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVV  207 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444455566666666666555432  221    233344444445555555555555444

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.53  E-value=1.1  Score=30.89  Aligned_cols=55  Identities=15%  Similarity=0.183  Sum_probs=29.9

Q ss_pred             HHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          388 NGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       388 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ..|.+.+++++|.++++++...+ +.++..|.-.-..+.+.|++++|...|++..+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            34555666666666666655431 11333444445555666666666666666553

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=92.46  E-value=11  Score=36.73  Aligned_cols=103  Identities=20%  Similarity=0.184  Sum_probs=74.5

Q ss_pred             hhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCc-cchHHHHHHHHhcCCh
Q 011378            3 NALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGV-FTYNSLINGLCKKGRC   81 (487)
Q Consensus         3 ~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~   81 (487)
                      ++.+..|+++.|...|-+..... +++...|+.=..+|++.|++++|++=-..  ...+.|+- ..|...-.++.-.|++
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l~-p~nhvlySnrsaa~a~~~~~~~al~da~k--~~~l~p~w~kgy~r~Gaa~~~lg~~   86 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATK--TRRLNPDWAKGYSRKGAALFGLGDY   86 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHH--HHhcCCchhhHHHHhHHHHHhcccH
Confidence            34577899999999998876654 34778899999999999999998854333  23456663 5677777788888999


Q ss_pred             hhHHHHHHHHHHCCCCCC-HHHHHHHHHHH
Q 011378           82 DRAKEVLDEMLQMGLSPD-TATYNTLLVES  110 (487)
Q Consensus        82 ~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~  110 (487)
                      ++|..-|.+=++.  .|+ ...++-+..++
T Consensus        87 ~eA~~ay~~GL~~--d~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   87 EEAILAYSEGLEK--DPSNKQLKTGLAQAY  114 (539)
T ss_pred             HHHHHHHHHHhhc--CCchHHHHHhHHHhh
Confidence            9999999876553  343 34444444444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.32  E-value=1.6  Score=39.36  Aligned_cols=104  Identities=15%  Similarity=0.152  Sum_probs=62.0

Q ss_pred             cCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC---CCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh
Q 011378          234 RGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQK---SIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY  310 (487)
Q Consensus       234 ~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~  310 (487)
                      .|......+...++..-....+++.++..+=.++..   ...|+... .+.++-+.+- ++++++.++..-...|+-||.
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~-~~~irlllky-~pq~~i~~l~npIqYGiF~dq  135 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTI-HTWIRLLLKY-DPQKAIYTLVNPIQYGIFPDQ  135 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccH-HHHHHHHHcc-ChHHHHHHHhCcchhccccch
Confidence            344455556666665555566677776666555432   22233222 2334433332 556777777766677777777


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGK  339 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~  339 (487)
                      .+++.+|+.+.+.+++.+|.++..+|...
T Consensus       136 f~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  136 FTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             hhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            77777777777777777777776665543

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.11  E-value=0.8  Score=31.67  Aligned_cols=57  Identities=14%  Similarity=0.099  Sum_probs=46.7

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          423 TGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG  480 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g  480 (487)
                      ..|.+++++++|..+++.+...+- .+...|...-..+...|++++|.+.++...+.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDP-DDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCc-ccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            568899999999999999987522 255566777789999999999999999988543

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

Probab=92.11  E-value=2  Score=38.63  Aligned_cols=101  Identities=14%  Similarity=0.276  Sum_probs=77.7

Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCC
Q 011378          353 KGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGR  430 (487)
Q Consensus       353 ~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~  430 (487)
                      .-+.+.+++++|...|.+.+.  +.| |.+-|..=-.+|.+.|.++.|++=.+.-..  +.|. ..+|..|=.+|...|+
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk  164 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGK  164 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCc
Confidence            346678999999999998886  445 566677778899999999999886665433  3443 3578999999999999


Q ss_pred             hHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011378          431 MHDSELILWRMIEKGLNPDRSTYTTLING  459 (487)
Q Consensus       431 ~~~a~~~~~~m~~~g~~p~~~ty~~l~~~  459 (487)
                      +++|...|++.++  +.|+=.+|..=+..
T Consensus       165 ~~~A~~aykKaLe--ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  165 YEEAIEAYKKALE--LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHHHHhhhc--cCCCcHHHHHHHHH
Confidence            9999999888654  68887777765543

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

Probab=92.01  E-value=3.2  Score=37.32  Aligned_cols=97  Identities=22%  Similarity=0.332  Sum_probs=65.7

Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCChH
Q 011378          285 FCKVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT-LVSCNTIIKGYCRSGDAS  362 (487)
Q Consensus       285 ~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~~~~  362 (487)
                      +.+.+++++|...|.+.+.  +.| |.+-|..=-.+|++.|.++.|.+-.+.-+.  +.|. ..+|..|=.+|...|+++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~~  166 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKYE  166 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcHH
Confidence            4556788888888877654  333 566677778888888888888776554432  2232 246777777888888888


Q ss_pred             HHHHHHHHHHHCCCCCChhhHHHHH
Q 011378          363 KADEFLSKMVSEGVDPDSISYNTLI  387 (487)
Q Consensus       363 ~a~~~~~~m~~~g~~p~~~~~~~li  387 (487)
                      +|.+.|++..  .+.|+-.+|-.=+
T Consensus       167 ~A~~aykKaL--eldP~Ne~~K~nL  189 (304)
T KOG0553|consen  167 EAIEAYKKAL--ELDPDNESYKSNL  189 (304)
T ss_pred             HHHHHHHhhh--ccCCCcHHHHHHH
Confidence            8888877655  3667766665444

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=91.99  E-value=6.5  Score=32.85  Aligned_cols=144  Identities=13%  Similarity=0.125  Sum_probs=98.4

Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHC---CCCCChhh
Q 011378          306 ISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSE---GVDPDSIS  382 (487)
Q Consensus       306 ~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~p~~~~  382 (487)
                      ..|++..---|-.+....|+..+|...|.+-..--+--|....-.+-++....++...|...++++.+.   +-.||.. 
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~-  163 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH-  163 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch-
Confidence            357777777788888899999999999888765555667777778888888888888888888887764   3445533 


Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHH
Q 011378          383 YNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYT  454 (487)
Q Consensus       383 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~  454 (487)
                       -.+-..+...|+..+|+.-|+....  ..|+...-...-..+.++|+..++..-+....+. +.-+...|.
T Consensus       164 -Ll~aR~laa~g~~a~Aesafe~a~~--~ypg~~ar~~Y~e~La~qgr~~ea~aq~~~v~d~-~~r~~~H~r  231 (251)
T COG4700         164 -LLFARTLAAQGKYADAESAFEVAIS--YYPGPQARIYYAEMLAKQGRLREANAQYVAVVDT-AKRSRPHYR  231 (251)
T ss_pred             -HHHHHHHHhcCCchhHHHHHHHHHH--hCCCHHHHHHHHHHHHHhcchhHHHHHHHHHHHH-HHhcchhHH
Confidence             3445677788888888888877665  3566554444445567778777776544443321 223444554

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=91.69  E-value=3.7  Score=39.47  Aligned_cols=62  Identities=11%  Similarity=0.048  Sum_probs=39.6

Q ss_pred             hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh----hhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          345 LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS----ISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       345 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      ...++.+-.+|...|++++|...++...+.  .|+.    ..|..+-.+|.+.|+.++|.+.+++..+
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345666666777777777777777665543  3543    2466666677777777777776666654

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.65  E-value=3.2  Score=37.54  Aligned_cols=104  Identities=13%  Similarity=0.271  Sum_probs=69.0

Q ss_pred             HCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CCCC--hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCc
Q 011378          128 RRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAG---LVPD--NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCV  202 (487)
Q Consensus       128 ~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g---~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~  202 (487)
                      ..|...+..+...++..-....+++.+..++-+++...   ..|+  .++|-.++..|    +.+++.-++..-...|+-
T Consensus        57 ~~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllky----~pq~~i~~l~npIqYGiF  132 (418)
T KOG4570|consen   57 ERGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLKY----DPQKAIYTLVNPIQYGIF  132 (418)
T ss_pred             hcCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHcc----ChHHHHHHHhCcchhccc
Confidence            45555566666667777677778888887777776532   2222  23333333332    455777777777778888


Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011378          203 MDVVTYNTILNGLCRAKMLTEADDLFNEMLERG  235 (487)
Q Consensus       203 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (487)
                      ||..+.+.+|+.+.+.+++.+|-++.-.|..++
T Consensus       133 ~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  133 PDQFTFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             cchhhHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            888888888888888888888877777766554

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=91.45  E-value=2.7  Score=33.65  Aligned_cols=45  Identities=18%  Similarity=0.199  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHhCCC-HHHHHHHHHHHHHCCCCCChhhHHHHHHHHH
Q 011378          137 SFSTLIGIFSRNGQ-LDRALMYFREMKSAGLVPDNVLYTIIINGYC  181 (487)
Q Consensus       137 ~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~  181 (487)
                      +|.+++++.++..- ---+..+|..|++.+.+++...|..+|+++.
T Consensus        81 sf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l  126 (145)
T PF13762_consen   81 SFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAAL  126 (145)
T ss_pred             hHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            34444444444333 2233344444444444444444444444433

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=91.15  E-value=14  Score=35.04  Aligned_cols=76  Identities=13%  Similarity=0.027  Sum_probs=41.4

Q ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCC---CCCChhhHHHHHHHHHh---cCCHHHHHHHHHHHHHcCCcCChhhHHHHHH
Q 011378          140 TLIGIFSRNGQLDRALMYFREMKSAG---LVPDNVLYTIIINGYCR---NGFVLEALKMRDEMLEKGCVMDVVTYNTILN  213 (487)
Q Consensus       140 ~li~~~~~~g~~~~a~~~~~~m~~~g---~~~~~~~~~~ll~~~~~---~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~  213 (487)
                      .++-.|-...+++...++.+.+....   +.-...+--...-++-|   .|+.++|.+++.......-.+++.+|..+-.
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            44455777777777777777776531   11111111112223334   6777777777777555555566666655544


Q ss_pred             HH
Q 011378          214 GL  215 (487)
Q Consensus       214 ~~  215 (487)
                      .|
T Consensus       226 Iy  227 (374)
T PF13281_consen  226 IY  227 (374)
T ss_pred             HH
Confidence            43

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.15  E-value=6.8  Score=35.93  Aligned_cols=150  Identities=13%  Similarity=0.135  Sum_probs=80.4

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHH--HHHH--HHhccCCHHH
Q 011378          323 MGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYN--TLIN--GFVREENMDK  398 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~--~li~--~~~~~~~~~~  398 (487)
                      .|.+.+|-..|+.+.+ ..+.|...++---.+|.-.|+.+.-...+++.... ..||...|+  .=|.  ++...|.+++
T Consensus       116 ~g~~h~a~~~wdklL~-d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~d  193 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLD-DYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYDD  193 (491)
T ss_pred             cccccHHHHHHHHHHH-hCchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccchh
Confidence            3555555556666553 34556666666666676677766666666666542 123332222  1122  2235667777


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK---GLNPDRSTYTTLINGHVSQNNLKEAFRFHDE  475 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~  475 (487)
                      |++.-++--+-+ ..|.-.-....+.+-..|+..++.+..++-...   +.-.-...|-..--.+.+.+.++.|..++..
T Consensus       194 AEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~  272 (491)
T KOG2610|consen  194 AEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDR  272 (491)
T ss_pred             HHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHH
Confidence            766555443321 224444455555566677777776665553211   1112234555555566666777777777654

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=90.94  E-value=7.6  Score=31.61  Aligned_cols=84  Identities=7%  Similarity=-0.135  Sum_probs=40.5

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 011378          181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKAL  260 (487)
Q Consensus       181 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~  260 (487)
                      ...|++++|..+|+-+..... -+..-|-.|--++-..|++++|...|....... +-|+..+-.+-.++...|+.+.|.
T Consensus        46 y~~G~l~~A~~~f~~L~~~Dp-~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~L~lG~~~~A~  123 (157)
T PRK15363         46 MEVKEFAGAARLFQLLTIYDA-WSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECYLACDNVCYAI  123 (157)
T ss_pred             HHCCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHH
Confidence            344555555555544433211 122233344444445555555555555554433 234455555555555566666665


Q ss_pred             HHHHHH
Q 011378          261 NLFDIM  266 (487)
Q Consensus       261 ~~~~~m  266 (487)
                      .-|+..
T Consensus       124 ~aF~~A  129 (157)
T PRK15363        124 KALKAV  129 (157)
T ss_pred             HHHHHH
Confidence            555543

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.90  E-value=22  Score=36.93  Aligned_cols=178  Identities=13%  Similarity=0.164  Sum_probs=106.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHH----HHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHH
Q 011378           32 TYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLIN----GLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLL  107 (487)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~----~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  107 (487)
                      ...+-|..+.+...++.|+.+-..   .+.  +..+...+..    .+.+.|++++|...+-+-... +.|     ..++
T Consensus       336 ~le~kL~iL~kK~ly~~Ai~LAk~---~~~--d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi  404 (933)
T KOG2114|consen  336 DLETKLDILFKKNLYKVAINLAKS---QHL--DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVI  404 (933)
T ss_pred             cHHHHHHHHHHhhhHHHHHHHHHh---cCC--CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHH
Confidence            345567777777777777766543   222  2333333333    345688888888877664321 111     2355


Q ss_pred             HHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHH
Q 011378          108 VESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVL  187 (487)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  187 (487)
                      .-|.......+-...++.+.+.|+.- ...-+.|+++|.+-++.+.-.++.+... .|..  .+-....+..+.+.+..+
T Consensus       405 ~kfLdaq~IknLt~YLe~L~~~gla~-~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl~  480 (933)
T KOG2114|consen  405 KKFLDAQRIKNLTSYLEALHKKGLAN-SDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNYLD  480 (933)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHccccc-chhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChHH
Confidence            66666666777777788888888754 3344678889999988888777766544 3322  112445666666777777


Q ss_pred             HHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          188 EALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEML  232 (487)
Q Consensus       188 ~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (487)
                      +|..+-.....     .......+   +-..+++++|.+.++.+.
T Consensus       481 ~a~~LA~k~~~-----he~vl~il---le~~~ny~eAl~yi~slp  517 (933)
T KOG2114|consen  481 EAELLATKFKK-----HEWVLDIL---LEDLHNYEEALRYISSLP  517 (933)
T ss_pred             HHHHHHHHhcc-----CHHHHHHH---HHHhcCHHHHHHHHhcCC
Confidence            77655443322     22222333   334577888888877653

>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=90.58  E-value=7  Score=30.62  Aligned_cols=65  Identities=14%  Similarity=0.226  Sum_probs=41.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVD  377 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  377 (487)
                      ....-++.....|.-+.-.++..++.+. -++++...-.+-.+|.+.|+..++.+++++.-++|++
T Consensus        88 ~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   88 YVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            3445566667777777777777777653 3666677777778888888888888888887777764

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

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

Probab=90.51  E-value=3.6  Score=37.11  Aligned_cols=76  Identities=16%  Similarity=0.162  Sum_probs=41.5

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHH-----CCCCCChhhHHHHH
Q 011378          103 YNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKS-----AGLVPDNVLYTIII  177 (487)
Q Consensus       103 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~~~~~~ll  177 (487)
                      +..++..+...++.+.+.+.++++.... +.+...|..+|.+|.+.|+...|+..|+++++     .|+.|...+.....
T Consensus       156 l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~  234 (280)
T COG3629         156 LTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYE  234 (280)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHH
Confidence            3445555555566666666666655442 23455566666666666666666666665543     34555544444443


Q ss_pred             HH
Q 011378          178 NG  179 (487)
Q Consensus       178 ~~  179 (487)
                      +.
T Consensus       235 ~~  236 (280)
T COG3629         235 EI  236 (280)
T ss_pred             HH
Confidence            33

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

Probab=90.23  E-value=3.5  Score=34.61  Aligned_cols=61  Identities=11%  Similarity=0.129  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPD--FYTFTTLIHGHCKDGNMNKALNLFDIMT  267 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~t~~~li~~~~~~g~~~~a~~~~~~m~  267 (487)
                      .+..+...|++.|+.+.|.+.|.++.+....|.  ...+-.+|......+++..+........
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            456666777777777777777777776554443  2345667777777777777766665544

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.

>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=90.19  E-value=9.5  Score=31.51  Aligned_cols=131  Identities=18%  Similarity=0.246  Sum_probs=68.3

Q ss_pred             HHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHH-C
Q 011378           51 QLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSR-R  129 (487)
Q Consensus        51 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-~  129 (487)
                      +.+.++...+++|+...|..+|+.+.+.|.+..    +..+.+.++-+|.......+-.+...  ...+.++=-+|.. .
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~--~~~~~Ql~lDMLkRL   88 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQ--YPPAYQLGLDMLKRL   88 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHcc--ChHHHHHHHHHHHHh
Confidence            445556666777777777777777777776443    33445556666665555444333322  2223333222221 1


Q ss_pred             CCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          130 GVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEM  196 (487)
Q Consensus       130 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  196 (487)
                      |.     .+..++..+...|++-+|+++.+....    .+......++++-.+.++..--..++.-.
T Consensus        89 ~~-----~~~~iievLL~~g~vl~ALr~ar~~~~----~~~~~~~~fLeAA~~~~D~~lf~~V~~ff  146 (167)
T PF07035_consen   89 GT-----AYEEIIEVLLSKGQVLEALRYARQYHK----VDSVPARKFLEAAANSNDDQLFYAVFRFF  146 (167)
T ss_pred             hh-----hHHHHHHHHHhCCCHHHHHHHHHHcCC----cccCCHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            11     244566777777777777777665422    12223345566655555554444444333

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=89.62  E-value=7.4  Score=37.55  Aligned_cols=60  Identities=17%  Similarity=0.019  Sum_probs=28.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          172 LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDV----VTYNTILNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       172 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (487)
                      .|+.+-.+|.+.|++++|...+++-.+.  .|+.    .+|..+-.+|...|++++|...+++..+
T Consensus        77 a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         77 DAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4445555555555555555555544332  1221    2344555555555555555555555444

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=89.54  E-value=13  Score=32.07  Aligned_cols=44  Identities=18%  Similarity=0.229  Sum_probs=20.0

Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCCh----hhHHHHHHHHHhcCCHH
Q 011378          282 IDGFCKVGEMEKANKLWADMISRKISPNY----ISYGILINGYCSMGHVT  327 (487)
Q Consensus       282 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~t~~~li~~~~~~~~~~  327 (487)
                      .+.|.+.|.+..|..-++.+.+.-  |+.    ...-.++.+|.+.|..+
T Consensus       148 a~~Y~~~~~y~aA~~r~~~v~~~y--p~t~~~~~al~~l~~~y~~l~~~~  195 (203)
T PF13525_consen  148 ARFYYKRGKYKAAIIRFQYVIENY--PDTPAAEEALARLAEAYYKLGLKQ  195 (203)
T ss_dssp             HHHHHCTT-HHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTT-HH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC--CCCchHHHHHHHHHHHHHHhCChH
Confidence            344555555555555555554431  221    23344555555555444

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=88.87  E-value=18  Score=34.19  Aligned_cols=66  Identities=14%  Similarity=0.027  Sum_probs=50.1

Q ss_pred             CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          414 DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP---DRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       414 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p---~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      ...+|.-++..+.++|.++.|...+.++...+..+   .+...-.-.+.....|+.++|+..+++....
T Consensus       145 ~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~  213 (352)
T PF02259_consen  145 LAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKC  213 (352)
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            44578888999999999999999999987644222   3344444567777889999999999888873

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=88.76  E-value=27  Score=34.72  Aligned_cols=52  Identities=10%  Similarity=0.142  Sum_probs=25.4

Q ss_pred             HHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH-HhcCCh-------HHHHHHHHHH
Q 011378          389 GFVREENMDKAFALVSKMENQGLVPDVITYNVILTGF-CRQGRM-------HDSELILWRM  441 (487)
Q Consensus       389 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~-~~~g~~-------~~a~~~~~~m  441 (487)
                      .++-..++++|.+.+.++.+.. ..+...|.-+..+| ...|+.       ++|..+|.+.
T Consensus       314 ~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~v  373 (468)
T PF10300_consen  314 CHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKV  373 (468)
T ss_pred             HHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHH
Confidence            3444556666666666665432 22333444444433 344555       5555555554

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.

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

Probab=88.60  E-value=6.1  Score=35.69  Aligned_cols=57  Identities=11%  Similarity=0.105  Sum_probs=23.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          314 GILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       314 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  371 (487)
                      ..++..+...|+++.+...++++.... +-+...|..+|.+|.+.|+...|...++.+
T Consensus       157 ~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l  213 (280)
T COG3629         157 TKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQL  213 (280)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHH
Confidence            334444444444444444444443221 223334444444444444444444444433

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=88.53  E-value=27  Score=34.66  Aligned_cols=163  Identities=13%  Similarity=0.060  Sum_probs=90.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCCCH-----HHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCee
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLER-GVFPDF-----YTFTTLIHGHCK----DGNMNKALNLFDIMTQKSIKPDIV  276 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~-----~t~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~  276 (487)
                      ....+++..+=.|+-+.+.+.+.+..+. ++.-..     -+|..++..++.    ....+.|.++++.+.++  -|+..
T Consensus       190 ~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~  267 (468)
T PF10300_consen  190 KVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSA  267 (468)
T ss_pred             HHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcH
Confidence            3445555566666666666666655432 221111     223344433333    34567777777776654  45655


Q ss_pred             ehHHHH-HHHHccCCHHHHHHHHHHHHhCC-CCC--ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHH
Q 011378          277 TYNTLI-DGFCKVGEMEKANKLWADMISRK-ISP--NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTII  352 (487)
Q Consensus       277 ~~~~li-~~~~~~g~~~~a~~~~~~m~~~~-~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  352 (487)
                      .|.-.- +.+...|++++|.+.|.+..... -.|  ....+=-+...+....++++|...|..+.+.. ..+..+|.-+.
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~  346 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLA  346 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHH
Confidence            443322 23455677888888887544311 111  11223334555677788999999998887642 23444554444


Q ss_pred             HHH-HhcCCh-------HHHHHHHHHHH
Q 011378          353 KGY-CRSGDA-------SKADEFLSKMV  372 (487)
Q Consensus       353 ~~~-~~~~~~-------~~a~~~~~~m~  372 (487)
                      .+| ...++.       ++|.+++.+..
T Consensus       347 a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  347 AACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            443 245666       77888887765

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=88.20  E-value=10  Score=30.36  Aligned_cols=84  Identities=13%  Similarity=0.160  Sum_probs=47.5

Q ss_pred             HHHHHHHHhcCChhhHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHccCC-hhHHHHHHHHHHHCCCCCCHhHHHHHH
Q 011378           69 NSLINGLCKKGRCDRAKEVLDEMLQMG-----LSPDTATYNTLLVESCRKEN-MSEAEEIFCEMSRRGVAPDIVSFSTLI  142 (487)
Q Consensus        69 ~~li~~~~~~~~~~~a~~~~~~m~~~g-----~~~~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~p~~~~~~~li  142 (487)
                      |.++...+..+++.....+++.+....     -..+..+|++++.+.++... --.+..+|+.|++.+.+++...|..+|
T Consensus        43 N~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li  122 (145)
T PF13762_consen   43 NCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLI  122 (145)
T ss_pred             HHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            444444444445554444444442110     02345567777777766555 345556677777766777777777777


Q ss_pred             HHHHhCCCHH
Q 011378          143 GIFSRNGQLD  152 (487)
Q Consensus       143 ~~~~~~g~~~  152 (487)
                      .++.+-...+
T Consensus       123 ~~~l~g~~~~  132 (145)
T PF13762_consen  123 KAALRGYFHD  132 (145)
T ss_pred             HHHHcCCCCc
Confidence            7766653333

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=88.08  E-value=20  Score=32.47  Aligned_cols=100  Identities=10%  Similarity=0.089  Sum_probs=60.8

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh---cCChHHHHHHHHHHHHCCCCCChhhHH
Q 011378          308 PNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR---SGDASKADEFLSKMVSEGVDPDSISYN  384 (487)
Q Consensus       308 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~~~~  384 (487)
                      -|...|-.|-..|...|++++|..-|..-.+.. .+|...+..+-.++..   ..+..++..+++++.... +-|+....
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral~  231 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHHH
Confidence            366777777778888888887777777655421 2333334344343332   233566777777776532 12344555


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          385 TLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       385 ~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      .|--.+...|++.+|...++.|.+.
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhc
Confidence            5556667777777777777777664

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

Probab=87.58  E-value=1.5  Score=25.43  Aligned_cols=26  Identities=15%  Similarity=0.194  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          452 TYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       452 ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      +|..|-+.|.+.|++++|..++++.+
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45667777777777777777777744

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=87.43  E-value=22  Score=32.18  Aligned_cols=64  Identities=3%  Similarity=-0.047  Sum_probs=34.3

Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCcCChhhHHHHHHHHHhcCCHHHHHHHHH
Q 011378          166 LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEK-GCVMDVVTYNTILNGLCRAKMLTEADDLFN  229 (487)
Q Consensus       166 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~li~~~~~~~~~~~a~~~~~  229 (487)
                      -.++..+...+|+.+++.+++..-.++++..... +..-|...|..+|..-.+.|+..-..++..
T Consensus       198 ~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  198 KSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             cCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhh
Confidence            3444555555555555555555555555554433 344455555555555555555555544443

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=87.20  E-value=25  Score=32.58  Aligned_cols=95  Identities=17%  Similarity=0.181  Sum_probs=54.9

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHH---HHHhcCChhhHHHHHHHHHHCCCCCCHHHHHH
Q 011378           29 DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLIN---GLCKKGRCDRAKEVLDEMLQMGLSPDTATYNT  105 (487)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~---~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  105 (487)
                      |+.-.-.+-+.+.-.|.+..|+.-|....+    .|+..|.++.+   .|...|.-..|+.=+.+..+.  .||-..-..
T Consensus        37 dvekhlElGk~lla~~Q~sDALt~yHaAve----~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARi  110 (504)
T KOG0624|consen   37 DVEKHLELGKELLARGQLSDALTHYHAAVE----GDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARI  110 (504)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHc----CCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHH
Confidence            333344566667777788888877776654    34455655543   455566666666666665543  455322110


Q ss_pred             -HHHHHHccCChhHHHHHHHHHHHC
Q 011378          106 -LLVESCRKENMSEAEEIFCEMSRR  129 (487)
Q Consensus       106 -ll~~~~~~~~~~~a~~~~~~m~~~  129 (487)
                       --..+.+.|.++.|..=|+...++
T Consensus       111 QRg~vllK~Gele~A~~DF~~vl~~  135 (504)
T KOG0624|consen  111 QRGVVLLKQGELEQAEADFDQVLQH  135 (504)
T ss_pred             HhchhhhhcccHHHHHHHHHHHHhc
Confidence             112345677777777777777654

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

Probab=86.57  E-value=11  Score=27.95  Aligned_cols=60  Identities=12%  Similarity=0.155  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHH
Q 011378          118 EAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIIN  178 (487)
Q Consensus       118 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  178 (487)
                      +..+-++.+....+.|++....+.+.+|-|.+++..|.++|+-.+.+ +.+....|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHH
Confidence            45555666667777788888888888888888888888888877653 1222225655554

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 ....

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=86.39  E-value=11  Score=30.09  Aligned_cols=84  Identities=14%  Similarity=0.203  Sum_probs=55.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHhhC-CCCC-CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHH
Q 011378           28 PDTVTYNTLINAYCREGFLEEAFQLMNSMSGK-GLKP-GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNT  105 (487)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  105 (487)
                      |....|+.-..++ +.|++++|.+.|+.+..+ ...| ....--.++.++.+.++++.|...+++..+..-.--..-|..
T Consensus         9 ~~~~ly~~a~~~l-~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~   87 (142)
T PF13512_consen    9 SPQELYQEAQEAL-QKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAY   87 (142)
T ss_pred             CHHHHHHHHHHHH-HhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            3445566555554 789999999999988764 1211 223445678889999999999999998876532111244555


Q ss_pred             HHHHHHc
Q 011378          106 LLVESCR  112 (487)
Q Consensus       106 ll~~~~~  112 (487)
                      .+.+++.
T Consensus        88 Y~~gL~~   94 (142)
T PF13512_consen   88 YMRGLSY   94 (142)
T ss_pred             HHHHHHH
Confidence            5555544

>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=86.20  E-value=13  Score=31.21  Aligned_cols=59  Identities=22%  Similarity=0.377  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh--hhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL--VSCNTIIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m  371 (487)
                      +..+...|++.|+.+.|.+.+..+......+..  ..+-.+|+...-.+++..+...+.+.
T Consensus        39 ~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   39 LEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            444445555555555555555554444333322  22344445555555555554444443

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.

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.19  E-value=24  Score=31.40  Aligned_cols=153  Identities=11%  Similarity=0.148  Sum_probs=103.2

Q ss_pred             HHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          292 EKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       292 ~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  371 (487)
                      +...+.|++-.       ....++++..+.-.+.+.-...++.+.++..-+.+......|.+.-...||.+.|...++..
T Consensus       166 ESsv~lW~KRl-------~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~v  238 (366)
T KOG2796|consen  166 ESSIRLWRKRL-------GRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDV  238 (366)
T ss_pred             hhHHHHHHHHH-------HHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            44556665432       12345666666667778888888888888766677777888888888999999999999988


Q ss_pred             HHCCCCCChhhHHHHHH-----HHhccCCHHHHHHHHHHHHhCCCCCCHhhHH--HHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          372 VSEGVDPDSISYNTLIN-----GFVREENMDKAFALVSKMENQGLVPDVITYN--VILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       372 ~~~g~~p~~~~~~~li~-----~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~--~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      .+..-+.|-.+++.++.     .|.-++++..|...+++..... ..|+..-|  +|+-.|  -|+..+|.+.++.|+..
T Consensus       239 ek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllY--lg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  239 EKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLY--LGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             HHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHH--HHHHHHHHHHHHHHhcc
Confidence            87665666666666653     3455677888888787765542 11222222  333333  57889999999999764


Q ss_pred             CCCCCHHHHHHH
Q 011378          445 GLNPDRSTYTTL  456 (487)
Q Consensus       445 g~~p~~~ty~~l  456 (487)
                        .|...+=+++
T Consensus       316 --~P~~~l~es~  325 (366)
T KOG2796|consen  316 --DPRHYLHESV  325 (366)
T ss_pred             --CCccchhhhH
Confidence              4554444433

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

Probab=86.09  E-value=36  Score=33.35  Aligned_cols=82  Identities=12%  Similarity=0.100  Sum_probs=55.9

Q ss_pred             eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCC-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh-hhHHHHH
Q 011378          275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKIS-PNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL-VSCNTII  352 (487)
Q Consensus       275 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~li  352 (487)
                      ..+=..|-.+..+.|+.++|.+.++++.+..-. -.......|+.++...+.+.++..++..-.+...+.+. ..|+..+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            334455777778889999999999998765322 24456678999999999999999998876443333332 2466544


Q ss_pred             HHHH
Q 011378          353 KGYC  356 (487)
Q Consensus       353 ~~~~  356 (487)
                      -.+.
T Consensus       339 LkaR  342 (539)
T PF04184_consen  339 LKAR  342 (539)
T ss_pred             HHHH
Confidence            4433

The molecular function of this protein is uncertain.

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

Probab=85.92  E-value=34  Score=32.96  Aligned_cols=94  Identities=10%  Similarity=0.120  Sum_probs=69.8

Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCC
Q 011378           16 MFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMG   95 (487)
Q Consensus        16 ~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g   95 (487)
                      ++=++++..  +.|+.+|-.||.-+...+..++..+++++|.. .++.=+..|..-|++=....++..+..+|.+.+...
T Consensus        30 rLRerIkdN--PtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~-pfp~~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~  106 (660)
T COG5107          30 RLRERIKDN--PTNILSYFQLIQYLETQESMDAEREMYEQLSS-PFPIMEHAWRLYMSGELARKDFRSVESLFGRCLKKS  106 (660)
T ss_pred             HHHHHhhcC--chhHHHHHHHHHHHhhhhhHHHHHHHHHHhcC-CCccccHHHHHHhcchhhhhhHHHHHHHHHHHHhhh
Confidence            455556554  35888999999999999999999999999964 233344678888888777889999999999988765


Q ss_pred             CCCCHHHHHHHHHHHHccC
Q 011378           96 LSPDTATYNTLLVESCRKE  114 (487)
Q Consensus        96 ~~~~~~~~~~ll~~~~~~~  114 (487)
                      +.  ...|...|.---+.+
T Consensus       107 l~--ldLW~lYl~YIRr~n  123 (660)
T COG5107         107 LN--LDLWMLYLEYIRRVN  123 (660)
T ss_pred             cc--HhHHHHHHHHHHhhC
Confidence            44  555555555444444

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=85.91  E-value=18  Score=32.80  Aligned_cols=99  Identities=15%  Similarity=0.150  Sum_probs=62.5

Q ss_pred             CCChhhHHHHHHHHHhcCChHHHHHHHHHHHHC-CCCCChhhHHHHHHHHhcc---CCHHHHHHHHHHHHhCCCCC-CHh
Q 011378          342 KPTLVSCNTIIKGYCRSGDASKADEFLSKMVSE-GVDPDSISYNTLINGFVRE---ENMDKAFALVSKMENQGLVP-DVI  416 (487)
Q Consensus       342 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~---~~~~~a~~~~~~m~~~g~~p-~~~  416 (487)
                      +-|...|-.|=..|...|+.+.|..-|+...+. |-.|+  .+..+-.++...   ..-.++..+|++....  .| |+.
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~--~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~--D~~~ir  228 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPE--ILLGLAEALYYQAGQQMTAKARALLRQALAL--DPANIR  228 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHH--HHHHHHHHHHHhcCCcccHHHHHHHHHHHhc--CCccHH
Confidence            456778888888888888888888888776543 33333  333333333322   2345666777776543  34 444


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      +-.-|...+..+|++.+|...++.|.+.
T Consensus       229 al~lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         229 ALSLLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHhc
Confidence            5555556777788888888887777654

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.78  E-value=20  Score=32.07  Aligned_cols=94  Identities=17%  Similarity=0.249  Sum_probs=47.2

Q ss_pred             chHHHHHHHHhcCChhhHHHHHHHHHHCC----CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHC-CCCCC-HhHHHH
Q 011378           67 TYNSLINGLCKKGRCDRAKEVLDEMLQMG----LSPDTATYNTLLVESCRKENMSEAEEIFCEMSRR-GVAPD-IVSFST  140 (487)
Q Consensus        67 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g----~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~p~-~~~~~~  140 (487)
                      .|+.-++.+ +.|++..|...|....+..    ..|+..-|  |-.++...|+.++|..+|..+.+. +-.|- +..+--
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW--LGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallK  220 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW--LGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLK  220 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHH--HHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHH
Confidence            455554443 3445666666555555432    23344444  455555666666666666555432 11111 123334


Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHH
Q 011378          141 LIGIFSRNGQLDRALMYFREMKS  163 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~  163 (487)
                      |-....+.|+.+.|...|++..+
T Consensus       221 lg~~~~~l~~~d~A~atl~qv~k  243 (262)
T COG1729         221 LGVSLGRLGNTDEACATLQQVIK  243 (262)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHH
Confidence            44555566666666666666554

>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]

Probab=85.73  E-value=28  Score=31.69  Aligned_cols=153  Identities=16%  Similarity=0.136  Sum_probs=73.3

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHH
Q 011378          222 TEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADM  301 (487)
Q Consensus       222 ~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  301 (487)
                      .-+.++|+.....      ...+.++.++-+.+.-+.-++.        ++|+..+-..+-..+...|--+...-.-.++
T Consensus       184 ~F~~~lFk~~~~E------k~i~~lis~Lrkg~md~rLmef--------fPpnkrs~E~Fak~Ft~agL~elvey~~~q~  249 (412)
T KOG2297|consen  184 SFAVKLFKEWLVE------KDINDLISSLRKGKMDDRLMEF--------FPPNKRSVEHFAKYFTDAGLKELVEYHRNQQ  249 (412)
T ss_pred             HHHHHHHHHHHhh------ccHHHHHHHHHhcChHhHHHHh--------cCCcchhHHHHHHHHhHhhHHHHHHHHHHHH
Confidence            4466777776543      2456666666555444444333        3666666666666655554322211111111


Q ss_pred             HhCCCCCChhhHHHHHHHHHhcCCHHHHHHHH-HHHHhCCCCCCh---hhHHHHHHHHHhcCChH-HHHHHHHHHHHCCC
Q 011378          302 ISRKISPNYISYGILINGYCSMGHVTEAFRLW-YEMVGKGIKPTL---VSCNTIIKGYCRSGDAS-KADEFLSKMVSEGV  376 (487)
Q Consensus       302 ~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~-~~m~~~~~~~~~---~~~~~li~~~~~~~~~~-~a~~~~~~m~~~g~  376 (487)
                      . .+-  --..-..|.+-..+...+++..... ++|++..++-..   ..|..++++---+.+-+ -|.+.++.+     
T Consensus       250 ~-~~a--~kElq~~L~~q~s~e~p~~evi~~VKee~k~~nlPe~eVi~ivWs~iMsaveWnKkeelva~qalrhl-----  321 (412)
T KOG2297|consen  250 S-EGA--RKELQKELQEQVSEEDPVKEVILYVKEEMKRNNLPETEVIGIVWSGIMSAVEWNKKEELVAEQALRHL-----  321 (412)
T ss_pred             H-HHH--HHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCCCCceEEeeeHhhhhHHHhhchHHHHHHHHHHHHH-----
Confidence            0 000  0000112222223333455544443 456555544332   35777776654443222 133444433     


Q ss_pred             CCChhhHHHHHHHHhccCCHHHHH
Q 011378          377 DPDSISYNTLINGFVREENMDKAF  400 (487)
Q Consensus       377 ~p~~~~~~~li~~~~~~~~~~~a~  400 (487)
                          .+|.-|+.+++..|+.+...
T Consensus       322 ----K~yaPLL~af~s~g~sEL~L  341 (412)
T KOG2297|consen  322 ----KQYAPLLAAFCSQGQSELEL  341 (412)
T ss_pred             ----HhhhHHHHHHhcCChHHHHH
Confidence                35888888888888876543

>PHA02875 ankyrin repeat protein; Provisional

Probab=85.38  E-value=38  Score=32.95  Aligned_cols=68  Identities=12%  Similarity=0.229  Sum_probs=33.9

Q ss_pred             HHHHHHHcCCcCChhh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHhcCCHHHHHHHH
Q 011378          192 MRDEMLEKGCVMDVVT--YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFY--TFTTLIHGHCKDGNMNKALNLF  263 (487)
Q Consensus       192 ~~~~m~~~g~~~~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~--t~~~li~~~~~~g~~~~a~~~~  263 (487)
                      +++.+.+.|..|+...  ..+.+...++.|+.+-+    +.+.+.|..|+..  ...+.+...+..|+.+.+..++
T Consensus        17 iv~~Ll~~g~~~n~~~~~g~tpL~~A~~~~~~~~v----~~Ll~~ga~~~~~~~~~~t~L~~A~~~g~~~~v~~Ll   88 (413)
T PHA02875         17 IARRLLDIGINPNFEIYDGISPIKLAMKFRDSEAI----KLLMKHGAIPDVKYPDIESELHDAVEEGDVKAVEELL   88 (413)
T ss_pred             HHHHHHHCCCCCCccCCCCCCHHHHHHHcCCHHHH----HHHHhCCCCccccCCCcccHHHHHHHCCCHHHHHHHH
Confidence            3444555676665433  23344445566666433    3344455544432  1223455566667766654444

>PRK15331 chaperone protein SicA; Provisional

Probab=85.35  E-value=14  Score=30.34  Aligned_cols=87  Identities=14%  Similarity=0.001  Sum_probs=58.0

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHH
Q 011378          215 LCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKA  294 (487)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a  294 (487)
                      +...|++++|..+|.-+.--+ +-|..-|..|-..|-..++.++|+..|...-.-.. -|...+-..-.+|...|+.+.|
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHH
Confidence            456788888888888776543 22444566666677778888888888876544332 2233333456677788888888


Q ss_pred             HHHHHHHHh
Q 011378          295 NKLWADMIS  303 (487)
Q Consensus       295 ~~~~~~m~~  303 (487)
                      ...|.....
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            888876655

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=85.29  E-value=62  Score=35.36  Aligned_cols=113  Identities=12%  Similarity=0.153  Sum_probs=61.8

Q ss_pred             CCChhhHHHHH----HHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCH--
Q 011378          342 KPTLVSCNTII----KGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDV--  415 (487)
Q Consensus       342 ~~~~~~~~~li----~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~--  415 (487)
                      .|+...+..+.    +.+...+.+++|.-.|+..-+         ..--+.+|..+|++.+|..+-.+|...   -|.  
T Consensus       932 ~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl~a~~~~~dWr~~l~~a~ql~~~---~de~~  999 (1265)
T KOG1920|consen  932 KPDSEKQKVIYEAYADHLREELMSDEAALMYERCGK---------LEKALKAYKECGDWREALSLAAQLSEG---KDELV  999 (1265)
T ss_pred             ccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcc---------HHHHHHHHHHhccHHHHHHHHHhhcCC---HHHHH
Confidence            44544433333    333444555555555543221         122356666667777766666555321   121  


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          416 ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHD  474 (487)
Q Consensus       416 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~  474 (487)
                      .+-..|+.-+..+++.-+|-++..+-..        .+..-+..|+....|++|.++..
T Consensus      1000 ~~a~~L~s~L~e~~kh~eAa~il~e~~s--------d~~~av~ll~ka~~~~eAlrva~ 1050 (1265)
T KOG1920|consen 1000 ILAEELVSRLVEQRKHYEAAKILLEYLS--------DPEEAVALLCKAKEWEEALRVAS 1050 (1265)
T ss_pred             HHHHHHHHHHHHcccchhHHHHHHHHhc--------CHHHHHHHHhhHhHHHHHHHHHH
Confidence            1225667777778888888777666432        23455666676777888877643

>PHA02875 ankyrin repeat protein; Provisional

Probab=85.16  E-value=39  Score=32.88  Aligned_cols=74  Identities=19%  Similarity=0.182  Sum_probs=32.2

Q ss_pred             hcCChhhHHHHHHHHHhCCCCCChhh--HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCcc--chHHHHHHHHhcCChh
Q 011378            7 KDHKIDSAKMFLCEMEQKGVYPDTVT--YNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVF--TYNSLINGLCKKGRCD   82 (487)
Q Consensus         7 ~~~~~~~a~~~~~~~~~~g~~p~~~~--~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--~~~~li~~~~~~~~~~   82 (487)
                      +.|+++.+..++    +.|..|+...  ..+.+..+++.|+.+-+    +.+.+.|..|+..  .....+...++.|+.+
T Consensus        11 ~~g~~~iv~~Ll----~~g~~~n~~~~~g~tpL~~A~~~~~~~~v----~~Ll~~ga~~~~~~~~~~t~L~~A~~~g~~~   82 (413)
T PHA02875         11 LFGELDIARRLL----DIGINPNFEIYDGISPIKLAMKFRDSEAI----KLLMKHGAIPDVKYPDIESELHDAVEEGDVK   82 (413)
T ss_pred             HhCCHHHHHHHH----HCCCCCCccCCCCCCHHHHHHHcCCHHHH----HHHHhCCCCccccCCCcccHHHHHHHCCCHH
Confidence            344544444333    3455444322  33455555566665433    3333445444322  1112233344556655


Q ss_pred             hHHHHH
Q 011378           83 RAKEVL   88 (487)
Q Consensus        83 ~a~~~~   88 (487)
                      .+..++
T Consensus        83 ~v~~Ll   88 (413)
T PHA02875         83 AVEELL   88 (413)
T ss_pred             HHHHHH
Confidence            444433

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.24  E-value=58  Score=34.12  Aligned_cols=170  Identities=18%  Similarity=0.236  Sum_probs=109.9

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHH----HhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcC
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAY----CREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKG   79 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~----~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~   79 (487)
                      .+++...++-|..+-   +.++.  |..+...+.+.|    -+.|++++|...+-+-... +.|     ..+|+-|....
T Consensus       343 iL~kK~ly~~Ai~LA---k~~~~--d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLdaq  411 (933)
T KOG2114|consen  343 ILFKKNLYKVAINLA---KSQHL--DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDAQ  411 (933)
T ss_pred             HHHHhhhHHHHHHHH---HhcCC--CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCHH
Confidence            344444444444433   23332  444445555544    4689999999887654321 122     34577777777


Q ss_pred             ChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHH
Q 011378           80 RCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFR  159 (487)
Q Consensus        80 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  159 (487)
                      ....--.+++.+.+.|+. +...-+.||.+|.+.++.+...++.+.-. .|...  .-....+..|-+.+-.+.|..+-.
T Consensus       412 ~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~~--fd~e~al~Ilr~snyl~~a~~LA~  487 (933)
T KOG2114|consen  412 RIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEWF--FDVETALEILRKSNYLDEAELLAT  487 (933)
T ss_pred             HHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Cccee--eeHHHHHHHHHHhChHHHHHHHHH
Confidence            777888899999998875 44445789999999999998887776554 34332  123468888999999998887665


Q ss_pred             HHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          160 EMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEM  196 (487)
Q Consensus       160 ~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  196 (487)
                      ....     .......+++   ..+++++|++.+..+
T Consensus       488 k~~~-----he~vl~ille---~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  488 KFKK-----HEWVLDILLE---DLHNYEEALRYISSL  516 (933)
T ss_pred             Hhcc-----CHHHHHHHHH---HhcCHHHHHHHHhcC
Confidence            5433     3344455554   467788888887765

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

Probab=83.80  E-value=2.8  Score=24.21  Aligned_cols=26  Identities=12%  Similarity=0.056  Sum_probs=19.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      +|+.|-..|.+.|++++|..++++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46777788888888888888888754

>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=83.70  E-value=0.61  Score=37.60  Aligned_cols=85  Identities=9%  Similarity=0.193  Sum_probs=55.2

Q ss_pred             HHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCC
Q 011378           70 SLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNG  149 (487)
Q Consensus        70 ~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  149 (487)
                      .+|+.+.+.+.+.....+++.+...+..-+....+.++..|++.+..+...++++..       +......++..|-+.|
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~-------~~yd~~~~~~~c~~~~   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTS-------NNYDLDKALRLCEKHG   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS-------SSS-CTHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccc-------cccCHHHHHHHHHhcc
Confidence            356666667777777777777776665566777778888888887777777776621       1122235677777777


Q ss_pred             CHHHHHHHHHHH
Q 011378          150 QLDRALMYFREM  161 (487)
Q Consensus       150 ~~~~a~~~~~~m  161 (487)
                      .++.+.-++..+
T Consensus        85 l~~~a~~Ly~~~   96 (143)
T PF00637_consen   85 LYEEAVYLYSKL   96 (143)
T ss_dssp             SHHHHHHHHHCC
T ss_pred             hHHHHHHHHHHc
Confidence            777776666654

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.

>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=83.51  E-value=0.97  Score=36.41  Aligned_cols=82  Identities=10%  Similarity=0.161  Sum_probs=46.4

Q ss_pred             hhhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCCh
Q 011378            2 VNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRC   81 (487)
Q Consensus         2 i~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~   81 (487)
                      |+.+-+.+.+.....+++.+...+...+....+.++..|++.++.+...++++.       .+......+++.|-+.+.+
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~~~~l~   86 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCEKHGLY   86 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHHTTTSH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHHhcchH
Confidence            455556666777777777776655445566667777777777666666655541       1112334455555555555


Q ss_pred             hhHHHHHHH
Q 011378           82 DRAKEVLDE   90 (487)
Q Consensus        82 ~~a~~~~~~   90 (487)
                      +++.-++.+
T Consensus        87 ~~a~~Ly~~   95 (143)
T PF00637_consen   87 EEAVYLYSK   95 (143)
T ss_dssp             HHHHHHHHC
T ss_pred             HHHHHHHHH
Confidence            555554443

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.

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

Probab=83.07  E-value=5.3  Score=29.58  Aligned_cols=59  Identities=15%  Similarity=0.113  Sum_probs=32.0

Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLIN  458 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~  458 (487)
                      ..+-+..+-...+.|++....+.+.+|.+-+++..|.++|+-.+.+-- +....|..++.
T Consensus        29 ~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~-~~~~~Y~~~lq   87 (108)
T PF02284_consen   29 LRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG-NKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT-T-TTHHHHHHH
T ss_pred             HHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc-ChHHHHHHHHH
Confidence            333444444556677777777777777777777777777777664311 22225555443

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 ....

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.97  E-value=13  Score=37.09  Aligned_cols=98  Identities=18%  Similarity=0.202  Sum_probs=49.5

Q ss_pred             HhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHH
Q 011378           76 CKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRAL  155 (487)
Q Consensus        76 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  155 (487)
                      .+.|+++.|.++..+.      -+..-|..|-.+..+.+++..|.+-|....+         |..|+-.+...|+-+...
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            3455555555555442      2444556666666666666666665554332         445555555555555444


Q ss_pred             HHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHH
Q 011378          156 MYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRD  194 (487)
Q Consensus       156 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  194 (487)
                      .+-...++.|      ..|...-+|...|+++++.+++.
T Consensus       713 ~la~~~~~~g------~~N~AF~~~~l~g~~~~C~~lLi  745 (794)
T KOG0276|consen  713 VLASLAKKQG------KNNLAFLAYFLSGDYEECLELLI  745 (794)
T ss_pred             HHHHHHHhhc------ccchHHHHHHHcCCHHHHHHHHH
Confidence            4444444333      12233334445556665555543

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=82.94  E-value=11  Score=27.62  Aligned_cols=46  Identities=11%  Similarity=0.068  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          187 LEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEML  232 (487)
Q Consensus       187 ~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (487)
                      .+..+-++.+....+.|++....+.+.+|-|.+++..|.++|+..+
T Consensus        24 we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          24 WELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            3444444555555556666666666666666666666666665544

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.

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=81.86  E-value=30  Score=29.10  Aligned_cols=126  Identities=13%  Similarity=0.133  Sum_probs=89.5

Q ss_pred             CCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC---CcCChhh
Q 011378          131 VAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKG---CVMDVVT  207 (487)
Q Consensus       131 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g---~~~~~~~  207 (487)
                      +.|+...--.|-+...+.|+..+|...|++....-+.-|..+.-.+-++....++...+...++.+.+..   -.||  +
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd--~  162 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPD--G  162 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCC--c
Confidence            4577766667888899999999999999988876566777777788888888888888888888877643   2233  3


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKAL  260 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~  260 (487)
                      .-.+-..+...|..++|+.-|+.....  .|++..-.-.-..+.+.|+.+++.
T Consensus       163 ~Ll~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~  213 (251)
T COG4700         163 HLLFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREAN  213 (251)
T ss_pred             hHHHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHH
Confidence            334556777788888888888887764  455544333334456666655554

>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=81.80  E-value=41  Score=30.66  Aligned_cols=102  Identities=10%  Similarity=-0.001  Sum_probs=49.7

Q ss_pred             ehHHHHHHHHccCCHH---HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          277 TYNTLIDGFCKVGEME---KANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK  353 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~---~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  353 (487)
                      +...++.+|...+..+   +|..+++.+.+.... ....+-.-+..+.+.++.+++.+++..|...- .-....+..++.
T Consensus        86 iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~-~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~-~~~e~~~~~~l~  163 (278)
T PF08631_consen   86 ILRLLANAYLEWDTYESVEKALNALRLLESEYGN-KPEVFLLKLEILLKSFDEEEYEEILMRMIRSV-DHSESNFDSILH  163 (278)
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHhccCChhHHHHHHHHHHHhc-ccccchHHHHHH
Confidence            4566666666666543   344455555433222 12233344555555667777777777776542 112233333443


Q ss_pred             HHHh--cCChHHHHHHHHHHHHCCCCCCh
Q 011378          354 GYCR--SGDASKADEFLSKMVSEGVDPDS  380 (487)
Q Consensus       354 ~~~~--~~~~~~a~~~~~~m~~~g~~p~~  380 (487)
                      .+..  ......+...+..+....+.|..
T Consensus       164 ~i~~l~~~~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  164 HIKQLAEKSPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHHhhCcHHHHHHHHHHHHHHhCCCh
Confidence            3311  12334555556555554444443

It is also involved in sporulation [].

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.70  E-value=25  Score=31.40  Aligned_cols=86  Identities=20%  Similarity=0.202  Sum_probs=35.8

Q ss_pred             hcCCHHHHHHHHHHHHHCCC--CCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCC-CCC-hhhHHHHHHHHHhcCCHH
Q 011378          252 KDGNMNKALNLFDIMTQKSI--KPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKI-SPN-YISYGILINGYCSMGHVT  327 (487)
Q Consensus       252 ~~g~~~~a~~~~~~m~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~-~~t~~~li~~~~~~~~~~  327 (487)
                      ++|++..|..-|....+..-  .-....+-.|-.++...|++++|..+|..+.+..- .|- ...+--|-.+..+.|+.+
T Consensus       153 ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d  232 (262)
T COG1729         153 KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTD  232 (262)
T ss_pred             HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHH
Confidence            33445555555544443210  00112233455555555555555555555443211 111 122223333444445555


Q ss_pred             HHHHHHHHHH
Q 011378          328 EAFRLWYEMV  337 (487)
Q Consensus       328 ~a~~~~~~m~  337 (487)
                      +|...|+++.
T Consensus       233 ~A~atl~qv~  242 (262)
T COG1729         233 EACATLQQVI  242 (262)
T ss_pred             HHHHHHHHHH
Confidence            5555554443

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=81.53  E-value=14  Score=34.95  Aligned_cols=129  Identities=15%  Similarity=0.098  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHH----cCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHH----HCC-CCCCee
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLE----RGVF-PDFYTFTTLIHGHCKDGNMNKALNLFDIMT----QKS-IKPDIV  276 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~-~~~~t~~~li~~~~~~g~~~~a~~~~~~m~----~~~-~~~~~~  276 (487)
                      .|..|-+.|.-.|+++.|....+.-.+    -|-. ..-..++.+-+++.-.|+++.|.+.|+.-.    +-| -.....
T Consensus       197 a~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEAQ  276 (639)
T KOG1130|consen  197 AYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEAQ  276 (639)
T ss_pred             hhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHHH
Confidence            455555555566777777665543221    1111 112346666677777777777777775322    111 111223


Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhC-----CCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISR-----KISPNYISYGILINGYCSMGHVTEAFRLWYE  335 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~-----~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  335 (487)
                      ..-+|-+.|.-..++++|+..+..-..-     ...-....|=+|-.+|...|..++|+...+.
T Consensus       277 scYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~  340 (639)
T KOG1130|consen  277 SCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAEL  340 (639)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            4445666666666667776666432210     1111234455667777777777776665443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	487
4g24_A	501	Crystal Structure Of Proteinaceous Rnase P 1 (Prorp		5e-07
4g24_A	501	Crystal Structure Of Proteinaceous Rnase P 1 (Prorp		9e-05
4g24_A	501	Crystal Structure Of Proteinaceous Rnase P 1 (Prorp		7e-04
4g23_A	501	Crystal Structure Of Proteinaceous Rnase P 1 (Prorp		2e-05

>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From A. Thaliana With Mn Length = 501

Iteration: 1
 Score = 52.4 bits (124), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 36/129 (27%), Positives = 59/129 (45%), Gaps = 9/129 (6%)
Query: 182 RNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEAD---------DLFNEML 232
           + G VLEAL++ DE    G  +    YN +L     A+  TE+          D+F +M+
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 233 ERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME 292
              V P+  TFT          +   A ++   M    I+P + +Y   + GFC+ G+ +
Sbjct: 98  VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 293 KANKLWADM 301
           KA ++ A M
Sbjct: 158 KAYEVDAHM 166

>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From A. Thaliana With Mn Length = 501

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 41/167 (24%), Positives = 73/167 (43%), Gaps = 11/167 (6%)
Query: 252 KDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE----------MEKANKLWADM 301
           K G++ +AL L+D   +  ++     YN L+   C + E          + +   ++  M
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 302 ISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA 361
           I  K+ PN  ++        +      AF +  +M   GI+P L S    + G+CR GDA
Sbjct: 97  IVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDA 156
Query: 362 SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN 408
            KA E  + MV   V P+      L+   +  +N DK +  + ++ +
Sbjct: 157 DKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRD 203

>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From A. Thaliana With Mn Length = 501

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/116 (25%), Positives = 55/116 (47%), Gaps = 11/116 (9%)
Query: 324 GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA----------SKADEFLSKMVS 373
           G V EA RL+ E    G++ +    N ++   C   +A          S+  +   +M+ 
Sbjct: 40  GDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQMIV 98
Query: 374 EGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG 429
           + V P+  ++       V +++ + AF +V +M+  G+ P + +Y   L GFCR+G
Sbjct: 99  DKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154

>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From A. Thaliana With Mn Length = 501

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 52/122 (42%), Gaps = 9/122 (7%)
Query: 182 RNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEAD---------DLFNEML 232
           + G VLEAL++ DE    G  +    YN +L     A+  TE+          D+F + +
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 233 ERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME 292
              V P+  TFT          +   A +         I+P + +Y   + GFC+ G+ +
Sbjct: 98  VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 293 KA 294
           KA
Sbjct: 158 KA 159

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	487
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-23
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-23
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-22
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-20
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-18
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-16
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	2e-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 =  102 bits (255), Expect = 3e-23
 Identities = 30/199 (15%), Positives = 62/199 (31%), Gaps = 4/199 (2%)

Query: 10  KIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQL---MNSMSGKGLKPGVF 66
            +D  +    +  Q  +                   L  A  L    +    K     + 
Sbjct: 107 SLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLD 166

Query: 67  TYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEA-EEIFCE 125
            YN+++ G  ++G       VL  +   GL+PD  +Y   L    R++  +   E    +
Sbjct: 167 MYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQ 226

Query: 126 MSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGF 185
           MS+ G+    +  + L+    R   L               +P  V  + ++        
Sbjct: 227 MSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDG 286

Query: 186 VLEALKMRDEMLEKGCVMD 204
            +   K+   +    C+ +
Sbjct: 287 RVSYPKLHLPLKTLQCLFE 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 =  102 bits (254), Expect = 3e-23
 Identities = 32/222 (14%), Positives = 68/222 (30%), Gaps = 4/222 (1%)

Query: 84  AKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIG 143
           A  + D   Q   SP       LL E+  K ++   +    + S+  ++           
Sbjct: 76  AGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFK 135

Query: 144 IFSRNGQLDRA---LMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKG 200
                 QL  A   L+     +    +    +Y  ++ G+ R G   E + +   + + G
Sbjct: 136 CCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAG 195

Query: 201 CVMDVVTYNTILNGLCRAKMLTEA-DDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKA 259
              D+++Y   L  + R        +    +M + G+         L+    +   +   
Sbjct: 196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV 255

Query: 260 LNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADM 301
             +    +     P  V  + L+             KL   +
Sbjct: 256 HKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPL 297

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 98.4 bits (243), Expect = 8e-22
 Identities = 24/224 (10%), Positives = 64/224 (28%), Gaps = 4/224 (1%)

Query: 224 ADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLID 283
           A  L +   +    P       L+       +++         +Q  +            
Sbjct: 76  AGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFK 135

Query: 284 GFCKVGEMEKANKL---WADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKG 340
                 ++  A+ L         ++       Y  ++ G+   G   E   + + +   G
Sbjct: 136 CCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAG 195

Query: 341 IKPTLVSCNTIIKGYCRSGDASKA-DEFLSKMVSEGVDPDSISYNTLINGFVREENMDKA 399
           + P L+S    ++   R    +   +  L +M  EG+   ++    L++   R   +   
Sbjct: 196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV 255

Query: 400 FALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE 443
             +         +P  +  + +L     +        +   +  
Sbjct: 256 HKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKT 299

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 93.0 bits (229), Expect = 4e-20
 Identities = 20/197 (10%), Positives = 56/197 (28%), Gaps = 4/197 (2%)

Query: 217 RAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDI---MTQKSIKP 273
               L        +  +  +                   +  A +L  +     QK    
Sbjct: 104 GKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLL 163

Query: 274 DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAF-RL 332
            +  YN ++ G+ + G  ++   +   +    ++P+ +SY   +              R 
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC 223

Query: 333 WYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR 392
             +M  +G+K   +    ++    R+       +           P  ++ + L+     
Sbjct: 224 LEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYA 283

Query: 393 EENMDKAFALVSKMENQ 409
           ++       L   ++  
Sbjct: 284 KDGRVSYPKLHLPLKTL 300

>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 = 2e-18
 Identities = 14/215 (6%), Positives = 54/215 (25%), Gaps = 4/215 (1%)

Query: 161 MKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM 220
            + A   P       ++        +        +  +                      
Sbjct: 83  TRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQ 142

Query: 221 LTEADDLFN---EMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVT 277
           L  A  L        ++        +  ++ G  + G   + + +  ++    + PD+++
Sbjct: 143 LPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS 202

Query: 278 YNTLIDGFCKVG-EMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEM 336
           Y   +    +   +     +    M    +    +   +L++       +    ++    
Sbjct: 203 YAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTF 262

Query: 337 VGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKM 371
                 P  V+ + +++            +    +
Sbjct: 263 SLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPL 297

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 81.4 bits (199), Expect = 2e-16
 Identities = 29/197 (14%), Positives = 56/197 (28%), Gaps = 4/197 (2%)

Query: 294 ANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK 353
           A  L         SP       L+        +        +     +           K
Sbjct: 76  AGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFK 135

Query: 354 GYCRSGDASKADEFL---SKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQG 410
               +     A   L        +        YN ++ G+ R+    +   ++  +++ G
Sbjct: 136 CCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAG 195

Query: 411 LVPDVITYNVILTGFCRQGR-MHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEA 469
           L PD+++Y   L    RQ +     E  L +M ++GL         L++       LK  
Sbjct: 196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV 255

Query: 470 FRFHDEMLQRGFVPDDA 486
            +          +P   
Sbjct: 256 HKVKPTFSLPPQLPPPV 272

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 62.9 bits (151), Expect = 1e-10
 Identities = 17/130 (13%), Positives = 40/130 (30%), Gaps = 1/130 (0%)

Query: 1   MVNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQ-LMNSMSGK 59
           ++    +          L  ++  G+ PD ++Y   +    R+       +  +  MS +
Sbjct: 171 VMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQE 230

Query: 60  GLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEA 119
           GLK        L++   +        +V          P     + LL +   K+     
Sbjct: 231 GLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSY 290

Query: 120 EEIFCEMSRR 129
            ++   +   
Sbjct: 291 PKLHLPLKTL 300

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.7 bits (102), Expect = 1e-04
 Identities = 77/555 (13%), Positives = 159/555 (28%), Gaps = 170/555 (30%)

Query: 1   MVNALCKDHKIDSAKMFLCE---MEQKGVYPDTVTYNTLINAYCREG--F-------LEE 48
           +   L  ++K      FL      EQ+     T  Y    +    +   F       L+ 
Sbjct: 83  VEEVLRINYK------FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136

Query: 49  AFQLMNSMSGKGLKP--GVFTY-------NSLINGLCKK----------------GRCDR 83
             +L  ++    L+P   V            +   +C                    C+ 
Sbjct: 137 YLKLRQAL--LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194

Query: 84  AKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIG 143
            + VL EMLQ            LL          + +  +   S         S +  + 
Sbjct: 195 PETVL-EMLQ-----------KLL---------YQIDPNWTSRSDH-------SSNIKLR 226

Query: 144 IFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY---CRNGFVLEALKMRDEMLEKG 200
           I S   +L R L+  +  ++  LV  NV      N +   C+   +L  L  R +     
Sbjct: 227 IHSIQAELRR-LLKSKPYENCLLVLLNVQNAKAWNAFNLSCK---IL--LTTRFK----- 275

Query: 201 CVMDVV----TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM 256
            V D +    T +  L+         E   L  + L+            L          
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ-------DLPREVLTTNPR 328

Query: 257 NKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN-----YI 311
              L++      +SI+  + T     D +  V   +    +  +     + P      + 
Sbjct: 329 --RLSII----AESIRDGLAT----WDNWKHVNCDKLTTII--ESSLNVLEPAEYRKMFD 376

Query: 312 SYGILINGYCSMGHVTEAF--RLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLS 369
              +         H+       +W++++                   +S      ++   
Sbjct: 377 RLSVFPPSA----HIPTILLSLIWFDVI-------------------KSDVMVVVNKLHK 413

Query: 370 K-MVSEGVDPDSISYNTLINGFVREENMDKA--------FALVSKMENQGLVPDVIT--- 417
             +V +     +IS  ++      +   + A        + +    ++  L+P  +    
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF 473

Query: 418 YNVILTGF----CRQGRMHD--SELIL-WRMIEKGLNPDRSTYTTLINGHVSQNNLKEAF 470
           Y+ I  G                 + L +R +E+ +  D    +T  N   S  N  +  
Sbjct: 474 YSHI--GHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHD----STAWNASGSILNTLQQL 527

Query: 471 RFHDEMLQRGFVPDD 485
           +F+     + ++ D+
Sbjct: 528 KFY-----KPYICDN 537

>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 Length = 388

 Score = 42.5 bits (101), Expect = 2e-04
 Identities = 33/177 (18%), Positives = 58/177 (32%), Gaps = 26/177 (14%)

Query: 27  YPD-TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLK--PGVF-TYNSLINGLCKKGRCD 82
            PD T     L + + +   L+ +           +K  P +   Y++L N   ++G+  
Sbjct: 29  EPDNTGVLLLLSSIHFQCRRLDRSAHFST----LAIKQNPLLAEAYSNLGNVYKERGQLQ 84

Query: 83  RAKEVLDEMLQMGLSPDTA-TYNTLLVESCRKENMSEAEEIFCEMSRRGVA--PDIV-SF 138
            A E     L+  L PD    Y  L        +M  A + +       +   PD+    
Sbjct: 85  EAIEHYRHALR--LKPDFIDGYINLAAALVAAGDMEGAVQAY----VSALQYNPDLYCVR 138

Query: 139 STLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDE 195
           S L  +    G+L+ A   +   K+    P+          +   G V  A      
Sbjct: 139 SDLGNLLKALGRLEEAKACYL--KAIETQPNFA------VAWSNLGCVFNAQGEIWL 187

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	487
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.93
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.92
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.89
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.89
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.84
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.84
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.83
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.83
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.8
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.79
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.74
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.72
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.72
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.71
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.7
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.7
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.7
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.69
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.69
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.69
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.67
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.67
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.66
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.62
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.61
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.61
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.6
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.59
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.59
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.58
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.41
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.41
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.38
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.37
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.37
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.36
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.35
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.34
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.33
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.33
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.32
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.31
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.29
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.27
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.27
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.25
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.25
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.25
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.24
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.23
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.21
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.19
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.18
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.16
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.16
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.16
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.14
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.14
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.13
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.12
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.11
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.1
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.09
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.08
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.03
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.0
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.99
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.98
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.96
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.96
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.95
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.89
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.88
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.88
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.87
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.86
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.85
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.85
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.7
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.7
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.7
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.67
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.6
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.56
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.56
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.56
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.54
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.53
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.5
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.49
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.41
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.34
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.32
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.29
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.24
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.23
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.22
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.21
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.15
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.14
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.12
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.1
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.1
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.09
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.09
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.08
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.04
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.04
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.03
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.0
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.0
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.0
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.99
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.97
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.94
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.94
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.93
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.91
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.83
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.8
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.76
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.76
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.73
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.69
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.67
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.62
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.58
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.56
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.55
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.55
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.54
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.53
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.52
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.49
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.47
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.45
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.44
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.44
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.43
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.43
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.43
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.42
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.4
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.37
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.37
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.37
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.36
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.36
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.36
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.35
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.32
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.3
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.3
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.25
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.25
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.25
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.24
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.23
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.2
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.2
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.18
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.18
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.17
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.16
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.12
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.08
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.07
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.96
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.88
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.88
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.83
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.79
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.75
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.75
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.63
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.6
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.55
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.5
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	96.46
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.43
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.41
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.4
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.37
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.29
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.27
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	96.21
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.07
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.01
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	95.93
2l6j_A	111	TPR repeat-containing protein associated with HSP;	95.57
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.49
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.45
2l6j_A	111	TPR repeat-containing protein associated with HSP;	95.43
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.41
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	95.38
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.32
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.12
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.12
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	95.05
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.0
2kat_A	115	Uncharacterized protein; NESG, structure, structur	94.94
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	94.89
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	94.73
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	94.62
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	94.49
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	93.74
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	93.19
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	93.18
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	92.78
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	92.55
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.54
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	92.05
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	91.35
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	91.18
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	90.85
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	90.81
1pc2_A	152	Mitochondria fission protein; unknown function; NM	90.46
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	90.37
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	89.93
1pc2_A	152	Mitochondria fission protein; unknown function; NM	89.87
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	89.36
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	88.84
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	88.66
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	88.42
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	88.28
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	88.01
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	87.94
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	87.87
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	87.86
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	86.75
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	86.11
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	85.66
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	85.61
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	84.68
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	84.51
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	84.33
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	84.02
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	83.96
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	82.7
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	82.48
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	82.04
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	81.98
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	81.07
3jxi_A	260	Vanilloid receptor-related osmotically activated p	80.38

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

Probab=100.00  E-value=3.4e-39  Score=329.01  Aligned_cols=454  Identities=11%  Similarity=0.005  Sum_probs=383.1

Q ss_pred             cCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHH
Q 011378            8 DHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEV   87 (487)
Q Consensus         8 ~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~   87 (487)
                      .+.+..+...+..++    .++...|+.++..+.+.|++++|..+|+.|..  ..|+..++..+..+|.+.|++++|..+
T Consensus        66 ~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~  139 (597)
T 2xpi_A           66 DGSFLKERNAQNTDS----LSREDYLRLWRHDALMQQQYKCAAFVGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCL  139 (597)
T ss_dssp             --------------------CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCccCCCCCccccch----HHHHHHHHHHHHHHHHccCchHHHHHHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHH
Confidence            344444555555443    26788999999999999999999999999974  457888999999999999999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHH-HC--------------CCCCCHhHHHHHHHHHHhCCCHH
Q 011378           88 LDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMS-RR--------------GVAPDIVSFSTLIGIFSRNGQLD  152 (487)
Q Consensus        88 ~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~-~~--------------g~~p~~~~~~~li~~~~~~g~~~  152 (487)
                      |+.+...  .++..+++.++.+|.+.|++++|.++|+++. ..              |..++..+|+.++.+|.+.|+++
T Consensus       140 ~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  217 (597)
T 2xpi_A          140 LTKEDLY--NRSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFD  217 (597)
T ss_dssp             HHHTCGG--GTCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHhcc--ccchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHH
Confidence            9988543  6789999999999999999999999998532 22              33456889999999999999999


Q ss_pred             HHHHHHHHHHHCCCCCC-hhh--------------------------------------HHHHHHHHHhcCCHHHHHHHH
Q 011378          153 RALMYFREMKSAGLVPD-NVL--------------------------------------YTIIINGYCRNGFVLEALKMR  193 (487)
Q Consensus       153 ~a~~~~~~m~~~g~~~~-~~~--------------------------------------~~~ll~~~~~~~~~~~a~~~~  193 (487)
                      +|.++|++|.+.+  |+ ...                                      |+.++..|.+.|++++|.+++
T Consensus       218 ~A~~~~~~~~~~~--p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~  295 (597)
T 2xpi_A          218 RAKECYKEALMVD--AKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYL  295 (597)
T ss_dssp             HHHHHHHHHHHHC--TTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--chhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHH
Confidence            9999999998754  32 222                                      333356677889999999999


Q ss_pred             HHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC
Q 011378          194 DEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP  273 (487)
Q Consensus       194 ~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~  273 (487)
                      +++.+.  +++..+|+.++.+|.+.|++++|.++|+++.+.+ +.+..+++.++..|.+.|+.++|..+|+.+.+.. +.
T Consensus       296 ~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~  371 (597)
T 2xpi_A          296 SSINGL--EKSSDLLLCKADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PE  371 (597)
T ss_dssp             HTSTTG--GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHhhcC--CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cc
Confidence            998765  5889999999999999999999999999998765 3477889999999999999999999999987542 44


Q ss_pred             CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          274 DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK  353 (487)
Q Consensus       274 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  353 (487)
                      +..+++.+...|.+.|++++|.++|.++.... +.+..+|+.++.+|.+.|++++|.++|+++...+ +.+..+|+.+..
T Consensus       372 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  449 (597)
T 2xpi_A          372 KAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGM  449 (597)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHH
Confidence            67789999999999999999999999987632 2357799999999999999999999999998764 457889999999


Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC----CCCCC--HhhHHHHHHHHHh
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ----GLVPD--VITYNVILTGFCR  427 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~--~~~~~~li~~~~~  427 (487)
                      +|.+.|+.++|.++++++.+.. +.+..+|+.+...|.+.|++++|.++|+++.+.    +..|+  ..+|..+...|.+
T Consensus       450 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  528 (597)
T 2xpi_A          450 QHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRK  528 (597)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHH
Confidence            9999999999999999998753 346889999999999999999999999999765    77888  7899999999999


Q ss_pred             cCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          428 QGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       428 ~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      .|++++|..+++++.+.+ ..+..+|..+...|...|++++|.+.++++.+.
T Consensus       529 ~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  579 (597)
T 2xpi_A          529 LKMYDAAIDALNQGLLLS-TNDANVHTAIALVYLHKKIPGLAITHLHESLAI  579 (597)
T ss_dssp             TTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            999999999999998764 347899999999999999999999999999863

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

Probab=100.00  E-value=6.6e-37  Score=312.09  Aligned_cols=444  Identities=12%  Similarity=0.027  Sum_probs=382.3

Q ss_pred             hhhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCCh
Q 011378            2 VNALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRC   81 (487)
Q Consensus         2 i~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~   81 (487)
                      +..|.+.|+++.|..+++++..  ..|+..++..+..+|.+.|++++|..+|+.+...  +++..+|+.++.++.+.|++
T Consensus        91 ~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~  166 (597)
T 2xpi_A           91 RHDALMQQQYKCAAFVGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYLAAFCLVKLYDW  166 (597)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHccCchHHHHHHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHHHHHHHHHHhhH
Confidence            5678999999999999999974  4588899999999999999999999999988543  57889999999999999999


Q ss_pred             hhHHHHHHHH-HHC--------------CCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHH--------
Q 011378           82 DRAKEVLDEM-LQM--------------GLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSF--------  138 (487)
Q Consensus        82 ~~a~~~~~~m-~~~--------------g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~--------  138 (487)
                      ++|.++|+++ ...              |..++..+|+.+..+|.+.|++++|.++|++|.+.+.. +...+        
T Consensus       167 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~  245 (597)
T 2xpi_A          167 QGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAK-CYEAFDQLVSNHL  245 (597)
T ss_dssp             HHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHTTC
T ss_pred             HHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCch-hhHHHHHHHHhhc
Confidence            9999999953 222              33456889999999999999999999999999875421 22222        


Q ss_pred             ------------------------------HHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHH
Q 011378          139 ------------------------------STLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLE  188 (487)
Q Consensus       139 ------------------------------~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~  188 (487)
                                                    +.++..|.+.|++++|.++|+++.+.  .++..+|+.++.+|.+.|+.++
T Consensus       246 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~  323 (597)
T 2xpi_A          246 LTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL--EKSSDLLLCKADTLFVRSRFID  323 (597)
T ss_dssp             SCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG--GGCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC--CchHHHHHHHHHHHHHhcCHHH
Confidence                                          22355677889999999999998765  5889999999999999999999


Q ss_pred             HHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          189 ALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       189 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      |.++++++.+.+ +.+..+|+.++.+|.+.|++++|.++|+++.+.. +.+..+|+.+...|.+.|++++|.++|+.+.+
T Consensus       324 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  401 (597)
T 2xpi_A          324 VLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSST  401 (597)
T ss_dssp             HHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            999999998765 3478899999999999999999999999998543 55789999999999999999999999999876


Q ss_pred             CCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhH
Q 011378          269 KSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSC  348 (487)
Q Consensus       269 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  348 (487)
                      .. +.+..+|+.++..|.+.|++++|.++|+++...+ +.+..+|+.+..+|.+.|++++|.++|+.+.... +.+..+|
T Consensus       402 ~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~  478 (597)
T 2xpi_A          402 MD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLL  478 (597)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHH
Confidence            32 2356799999999999999999999999998653 3478899999999999999999999999998753 4478899


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHC----CCCCC--hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHH
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVSE----GVDPD--SISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVIL  422 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  422 (487)
                      +.+...|.+.|+.++|.++++++.+.    +..|+  ..+|..+..+|.+.|++++|.+.++++.+.+ ..+..+|..+.
T Consensus       479 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~  557 (597)
T 2xpi_A          479 NELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIA  557 (597)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHH
Confidence            99999999999999999999999876    77888  7899999999999999999999999987754 34789999999


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGH  460 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~  460 (487)
                      ..|.+.|++++|...++++.+.  .|+ ...|..+...|
T Consensus       558 ~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~l~~~~  594 (597)
T 2xpi_A          558 LVYLHKKIPGLAITHLHESLAI--SPNEIMASDLLKRAL  594 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHTT
T ss_pred             HHHHHhCCHHHHHHHHHHHHhc--CCCChHHHHHHHHHH
Confidence            9999999999999999999874  454 44555554444

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

Probab=100.00  E-value=9.6e-35  Score=285.45  Aligned_cols=206  Identities=21%  Similarity=0.298  Sum_probs=148.1

Q ss_pred             HHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCC---------HH
Q 011378          223 EADDLFNEMLERGVFPDF-YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE---------ME  292 (487)
Q Consensus       223 ~a~~~~~~m~~~~~~~~~-~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~---------~~  292 (487)
                      .++.+.+++.++++.+.+ ..++.+|++|++.|++++|+++|+.|.+.|++||..|||+||++|++.+.         ++
T Consensus         8 ~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~   87 (501)
T 4g26_A            8 PSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLS   87 (501)
T ss_dssp             ----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHH
T ss_pred             hHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHH
Confidence            344455555555554433 24556666666666666666666666666666666666666666655443         67


Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          293 KANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       293 ~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      +|.++|.+|...|+.||..||++||.+|++.|++++|.++|++|.+.|+.||..||++||.+|++.|+.++|.+++++|.
T Consensus        88 ~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~  167 (501)
T 4g26_A           88 RGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMV  167 (501)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHH
Confidence            78888888888888888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             HCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhc
Q 011378          373 SEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQ  428 (487)
Q Consensus       373 ~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  428 (487)
                      +.|+.||..||++||.+|++.|++++|.+++++|++.|..|+..||++|+..|+..
T Consensus       168 ~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          168 ESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             hcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            88888888888888888888888888888888888888888888888888888753

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

Probab=100.00  E-value=1.6e-34  Score=283.81  Aligned_cols=207  Identities=17%  Similarity=0.231  Sum_probs=183.5

Q ss_pred             HHHHHHHHHHHHCCCCCCe-eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCC---------H
Q 011378          257 NKALNLFDIMTQKSIKPDI-VTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGH---------V  326 (487)
Q Consensus       257 ~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~---------~  326 (487)
                      ..+..+.+.++++++.+.. ..++.+|++|++.|++++|.++|.+|.+.|+.||..|||+||.+|++.+.         +
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            3455566777777776543 46899999999999999999999999999999999999999999997764         7


Q ss_pred             HHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          327 TEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       327 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      ++|.++|++|...|+.||..||++||++|++.|+.++|.+++++|.+.|+.||..||++||.+|++.|++++|.++|++|
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            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 011378          407 ENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQ  463 (487)
Q Consensus       407 ~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~  463 (487)
                      .+.|+.||..||++||.+|++.|++++|..+|++|.+.|+.|+..||+.++..+...
T Consensus       167 ~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          167 VESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999998864

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.93  E-value=3.4e-21  Score=185.09  Aligned_cols=372  Identities=15%  Similarity=0.131  Sum_probs=228.2

Q ss_pred             HHhcCChhhHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHH
Q 011378           75 LCKKGRCDRAKEVLDEMLQMGLSPD-TATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDR  153 (487)
Q Consensus        75 ~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~  153 (487)
                      +.+.|++++|.+.+..+.+.  .|+ ...+..+-..+...|++++|...++...+.. +.+..+|..+...+.+.|++++
T Consensus         9 ~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~   85 (388)
T 1w3b_A            9 EYQAGDFEAAERHCMQLWRQ--EPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQE   85 (388)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHH
Confidence            34455555555555554432  232 2333333444455555555555555544331 2345556666666666666666


Q ss_pred             HHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCC-hhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          154 ALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMD-VVTYNTILNGLCRAKMLTEADDLFNEM  231 (487)
Q Consensus       154 a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (487)
                      |...|+++...  .|+ ...|..+..++.+.|+.++|.+.+++..+..  |+ ...+..+-..+...|++++|.+.|+++
T Consensus        86 A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  161 (388)
T 1w3b_A           86 AIEHYRHALRL--KPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN--PDLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHH--CTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC--TTCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc--CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            66666665542  233 3346666666666666666666666655432  32 334455556666667777777777666


Q ss_pred             HHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-Ch
Q 011378          232 LERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP-NY  310 (487)
Q Consensus       232 ~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~  310 (487)
                      .+.. +-+..+|..+...+...|++++|...|+.+.+.. +.+...|..+-..+...|++++|...+.+....  .| +.
T Consensus       162 l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~  237 (388)
T 1w3b_A          162 IETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHA  237 (388)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCH
T ss_pred             HHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCH
Confidence            6542 2245666667777777777777777776665532 112345666666777777777777777665543  23 35


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGF  390 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  390 (487)
                      .++..+...+...|++++|...|+.+.... +.+..+|..+...+.+.|+.++|...++++.+.. +.+..++..+...+
T Consensus       238 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  315 (388)
T 1w3b_A          238 VVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIK  315 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHH
Confidence            667777777777777777777777776542 2345567777777888888888888887776542 34566777788888


Q ss_pred             hccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHh
Q 011378          391 VREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGHVS  462 (487)
Q Consensus       391 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~~~  462 (487)
                      .+.|++++|...++++.+.. ..+..+|..+...+.+.|++++|...++++.+  +.|+ ...|..+-..+..
T Consensus       316 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~--~~p~~~~a~~~lg~~~~~  385 (388)
T 1w3b_A          316 REQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIR--ISPTFADAYSNMGNTLKE  385 (388)
T ss_dssp             HTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT--TCTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCCHHHHHhHHHHHHH
Confidence            88888888888887776531 22456778888888888888888888888765  3453 3455555444443

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.92  E-value=6.2e-21  Score=183.27  Aligned_cols=323  Identities=14%  Similarity=0.057  Sum_probs=155.5

Q ss_pred             HHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhCCCHH
Q 011378           74 GLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRNGQLD  152 (487)
Q Consensus        74 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~  152 (487)
                      .+.+.|++++|...++...+.. +.+...|..+...+.+.|++++|.+.|+++.+.  .| +..+|..+..++.+.|+++
T Consensus        42 ~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~  118 (388)
T 1w3b_A           42 IHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRL--KPDFIDGYINLAAALVAAGDME  118 (388)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHSCSS
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CcchHHHHHHHHHHHHHcCCHH
Confidence            3334444444444444333221 223344444444444444444444444444332  12 2233444444444444444


Q ss_pred             HHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          153 RALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEM  231 (487)
Q Consensus       153 ~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (487)
                      +|.+.|+++.+.  .|+ ...+..+-..+.+.|+.++|.+.++++.+.. +-+..+|+.+...+.+.|+++.|...|+++
T Consensus       119 ~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  195 (388)
T 1w3b_A          119 GAVQAYVSALQY--NPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKA  195 (388)
T ss_dssp             HHHHHHHHHHHH--CTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444444444432  122 2233334444444444444444444444321 112344455555555555555555555555


Q ss_pred             HHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh
Q 011378          232 LERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY  310 (487)
Q Consensus       232 ~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~  310 (487)
                      .+.. +.+...+..+-..+...|++++|+..|+...+.  .| +..++..+...|.+.|++++|...|+++.... +.+.
T Consensus       196 l~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~  271 (388)
T 1w3b_A          196 VTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFP  271 (388)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCH
T ss_pred             HhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCH
Confidence            4432 123344555555555555555555555444332  12 23445555555555555555555555554431 1123


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGF  390 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  390 (487)
                      .+|..+...+...|++++|...|+.+.... +.+..++..+...+...|+.++|...++++.+.. +.+..++..+...|
T Consensus       272 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  349 (388)
T 1w3b_A          272 DAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVL  349 (388)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHH
Confidence            455555666666666666666666555432 3445556666666666666666666666655421 22344566666666


Q ss_pred             hccCCHHHHHHHHHHHHh
Q 011378          391 VREENMDKAFALVSKMEN  408 (487)
Q Consensus       391 ~~~~~~~~a~~~~~~m~~  408 (487)
                      .+.|++++|.+.++++.+
T Consensus       350 ~~~g~~~~A~~~~~~a~~  367 (388)
T 1w3b_A          350 QQQGKLQEALMHYKEAIR  367 (388)
T ss_dssp             HTTTCCHHHHHHHHHHHT
T ss_pred             HHcCCHHHHHHHHHHHHh
Confidence            666666666666666554

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

Probab=99.89  E-value=4.4e-20  Score=183.98  Aligned_cols=402  Identities=10%  Similarity=-0.057  Sum_probs=245.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 011378           33 YNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCR  112 (487)
Q Consensus        33 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  112 (487)
                      +...-..+.+.|++++|...|+.+....  |+...|..+..++.+.|++++|.+.++++.+.. +.+...|..+..++.+
T Consensus         9 ~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~   85 (514)
T 2gw1_A            9 LKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEG   85 (514)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHH
Confidence            3444445555555555555555554432  455555555555555555555555555555432 1233455555555555


Q ss_pred             cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHH-----------------------------------H
Q 011378          113 KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALM-----------------------------------Y  157 (487)
Q Consensus       113 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~-----------------------------------~  157 (487)
                      .|++++|...|+++.+.+ +++......++..+.+......+.+                                   +
T Consensus        86 ~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (514)
T 2gw1_A           86 LGKFADAMFDLSVLSLNG-DFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSM  164 (514)
T ss_dssp             TTCHHHHHHHHHHHHHSS-SCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHH
T ss_pred             HhhHHHHHHHHHHHHhcC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHH
Confidence            555555555555555443 1222222233332222222222221                                   2


Q ss_pred             HHHHHHCCCCC--------C-hhhHHHHHHHHHh---cCCHHHHHHHHHHHHH-----cCC--------cCChhhHHHHH
Q 011378          158 FREMKSAGLVP--------D-NVLYTIIINGYCR---NGFVLEALKMRDEMLE-----KGC--------VMDVVTYNTIL  212 (487)
Q Consensus       158 ~~~m~~~g~~~--------~-~~~~~~ll~~~~~---~~~~~~a~~~~~~m~~-----~g~--------~~~~~~~~~li  212 (487)
                      ...+......+        + ...+......+..   .|+.++|...+++..+     ..-        +.+...|..+.
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (514)
T 2gw1_A          165 ASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTG  244 (514)
T ss_dssp             HHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHH
Confidence            22222111111        1 2223333333333   7788888888888776     211        22345677777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHH
Q 011378          213 NGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME  292 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~  292 (487)
                      ..+...|+++.|...|+++.+..  |+...+..+...+...|++++|...++...+.. +.+...+..+...+...|+++
T Consensus       245 ~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~  321 (514)
T 2gw1_A          245 IFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYD  321 (514)
T ss_dssp             HHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTT
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHH
Confidence            77888888888888888877654  336777778888888888888888887766542 224556777778888888888


Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          293 KANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       293 ~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      +|...+.+..... +.+...+..+...+...|++++|...++...... +.+...+..+...|.+.|+.++|...++++.
T Consensus       322 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  399 (514)
T 2gw1_A          322 QAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAI  399 (514)
T ss_dssp             HHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            8888888776543 2245677777788888888888888888776542 3345677777788888888888888887776


Q ss_pred             HCC-CCCC----hhhHHHHHHHHhc---cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          373 SEG-VDPD----SISYNTLINGFVR---EENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       373 ~~g-~~p~----~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      +.. -.++    ...+..+...|..   .|++++|...+++..+.. ..+...+..+...|.+.|++++|...+++..+.
T Consensus       400 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  478 (514)
T 2gw1_A          400 ELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAITLFEESADL  478 (514)
T ss_dssp             HHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            432 1122    2367777778888   888888888887776532 234566777777888888888888888887664

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

Probab=99.89  E-value=1.4e-19  Score=180.23  Aligned_cols=402  Identities=13%  Similarity=0.012  Sum_probs=310.1

Q ss_pred             hhHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChh
Q 011378            3 NALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCD   82 (487)
Q Consensus         3 ~~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~   82 (487)
                      ..+.+.|+++.|...++++.+..  |+..+|..+..++.+.|++++|.+.++...+.+ +.+..+|..+..++.+.|+++
T Consensus        14 ~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~   90 (514)
T 2gw1_A           14 NQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFA   90 (514)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHH
Confidence            35678999999999999998765  899999999999999999999999999987643 234567888999999999999


Q ss_pred             hHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHH-----------------------------------H
Q 011378           83 RAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEM-----------------------------------S  127 (487)
Q Consensus        83 ~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m-----------------------------------~  127 (487)
                      +|...|+++...+ +++......++..+.+......+.+.+..+                                   .
T Consensus        91 ~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (514)
T 2gw1_A           91 DAMFDLSVLSLNG-DFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFG  169 (514)
T ss_dssp             HHHHHHHHHHHSS-SCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHhcC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHh
Confidence            9999999998775 234444444444443332222222222111                                   1


Q ss_pred             HCCCC--------CC-HhHHHHHHHHHHh---CCCHHHHHHHHHHHHH-----CCCCC--------ChhhHHHHHHHHHh
Q 011378          128 RRGVA--------PD-IVSFSTLIGIFSR---NGQLDRALMYFREMKS-----AGLVP--------DNVLYTIIINGYCR  182 (487)
Q Consensus       128 ~~g~~--------p~-~~~~~~li~~~~~---~g~~~~a~~~~~~m~~-----~g~~~--------~~~~~~~ll~~~~~  182 (487)
                      .....        |+ ...+......+..   .|+++.|..+|+++..     ..-.|        +..++..+...+..
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (514)
T 2gw1_A          170 IFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFL  249 (514)
T ss_dssp             TSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHH
Confidence            11111        11 3333333333443   8999999999999987     32122        24578888899999


Q ss_pred             cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 011378          183 NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNL  262 (487)
Q Consensus       183 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~  262 (487)
                      .|+.++|...+++..+....  ...|..+...+...|+++.|...++++.+.. +.+...+..+...|...|++++|...
T Consensus       250 ~~~~~~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~  326 (514)
T 2gw1_A          250 KNDPLGAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKD  326 (514)
T ss_dssp             SSCHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            99999999999999876533  7789999999999999999999999988653 34667889999999999999999999


Q ss_pred             HHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-
Q 011378          263 FDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGI-  341 (487)
Q Consensus       263 ~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~-  341 (487)
                      |+...+... .+...+..+...+.+.|++++|...+.+..... +.+...+..+...+...|++++|...++......- 
T Consensus       327 ~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~  404 (514)
T 2gw1_A          327 FDKAKELDP-ENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENK  404 (514)
T ss_dssp             HHHHHHTCS-SCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCh-hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhc
Confidence            998876532 256688899999999999999999999987642 23567888999999999999999999998865321 


Q ss_pred             CCC----hhhHHHHHHHHHh---cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC
Q 011378          342 KPT----LVSCNTIIKGYCR---SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPD  414 (487)
Q Consensus       342 ~~~----~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  414 (487)
                      .++    ...+..+...+..   .|+.++|...++...+.. +.+..++..+...|.+.|++++|...+++..+.  .|+
T Consensus       405 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~  481 (514)
T 2gw1_A          405 LDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAITLFEESADL--ART  481 (514)
T ss_dssp             SSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSS
T ss_pred             cchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--ccc
Confidence            122    3488889999999   999999999999988643 235678889999999999999999999988764  455


Q ss_pred             Hh
Q 011378          415 VI  416 (487)
Q Consensus       415 ~~  416 (487)
                      ..
T Consensus       482 ~~  483 (514)
T 2gw1_A          482 ME  483 (514)
T ss_dssp             HH
T ss_pred             cH
Confidence            43

>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=99.84  E-value=1.3e-17  Score=163.25  Aligned_cols=301  Identities=14%  Similarity=0.091  Sum_probs=199.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHH
Q 011378           28 PDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLL  107 (487)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll  107 (487)
                      .+...+..+...+.+.|++++|..+|+.+... .+.+..+|..+...+.+.|++++|...|+++.+.+ +.+...|..+.
T Consensus        24 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~  101 (450)
T 2y4t_A           24 ADVEKHLELGKKLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRG  101 (450)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHH
Confidence            35567788888888888888888888887653 22356677888888888888888888888887654 23466777888


Q ss_pred             HHHHccCChhHHHHHHHHHHHCCCCCCH----hHHHHHH------------HHHHhCCCHHHHHHHHHHHHHCCCCCChh
Q 011378          108 VESCRKENMSEAEEIFCEMSRRGVAPDI----VSFSTLI------------GIFSRNGQLDRALMYFREMKSAGLVPDNV  171 (487)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~~~~~li------------~~~~~~g~~~~a~~~~~~m~~~g~~~~~~  171 (487)
                      ..+.+.|++++|.+.|+++.+.  .|+.    ..+..+.            ..+.+.|++++|...|+++.... +.+..
T Consensus       102 ~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~  178 (450)
T 2y4t_A          102 HLLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAE  178 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChH
Confidence            8888888888888888888764  3432    3444443            33777777777777777776532 23456


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH-----
Q 011378          172 LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTL-----  246 (487)
Q Consensus       172 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~l-----  246 (487)
                      .+..+...|.+.|+.++|.+.++++.+.. +.+..+|..+...|.+.|++++|...|+++.+.. +.+...+..+     
T Consensus       179 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~~~~~~  256 (450)
T 2y4t_A          179 LRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKK  256 (450)
T ss_dssp             HHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHHHHHHH
Confidence            67777777777777777777777766542 2345677777777777777777777777776532 1223333333     


Q ss_pred             -------HHHHHhcCCHHHHHHHHHHHHHCCCCCC-----eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHH
Q 011378          247 -------IHGHCKDGNMNKALNLFDIMTQKSIKPD-----IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYG  314 (487)
Q Consensus       247 -------i~~~~~~g~~~~a~~~~~~m~~~~~~~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~  314 (487)
                             ...|.+.|++++|...|+.+.+.  .|+     ..++..+...+.+.|++++|...+.++.... +.+...|.
T Consensus       257 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~  333 (450)
T 2y4t_A          257 LNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALK  333 (450)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHH
Confidence                   55666666666666666666542  233     2245566666666666666666666654331 22455666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVG  338 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~  338 (487)
                      .+..+|...|++++|...++....
T Consensus       334 ~l~~~~~~~~~~~~A~~~~~~al~  357 (450)
T 2y4t_A          334 DRAEAYLIEEMYDEAIQDYETAQE  357 (450)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHH
Confidence            666666666666666666666654

>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=99.84  E-value=2.4e-17  Score=161.34  Aligned_cols=311  Identities=12%  Similarity=0.046  Sum_probs=174.8

Q ss_pred             CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 011378           64 GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIG  143 (487)
Q Consensus        64 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  143 (487)
                      +...|..+...+.+.|++++|..+|+++.+.. +.+...|..+...+...|++++|...|+++.+.+ +.+...+..+..
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  102 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGH  102 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHH
Confidence            45667788888888889999999888887642 3457788888888888888888888888887754 234667788888


Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCCh----hhHHHHHHH------------HHhcCCHHHHHHHHHHHHHcCCcCChhh
Q 011378          144 IFSRNGQLDRALMYFREMKSAGLVPDN----VLYTIIING------------YCRNGFVLEALKMRDEMLEKGCVMDVVT  207 (487)
Q Consensus       144 ~~~~~g~~~~a~~~~~~m~~~g~~~~~----~~~~~ll~~------------~~~~~~~~~a~~~~~~m~~~g~~~~~~~  207 (487)
                      .|.+.|++++|.+.|+++.+.  .|+.    ..+..+...            +.+.|+.++|...++++.+.. +.+...
T Consensus       103 ~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  179 (450)
T 2y4t_A          103 LLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAEL  179 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHH
Confidence            888888888888888888764  3443    455555444            444555555555555554422 123444


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCee-ehHHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIV-TYNTLIDGFC  286 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-~~~~li~~~~  286 (487)
                      +..+..+|.+.|++++|.+.|+++.+.. +.+..+|..+...|...|+.++|+..|+.+.+.  .|+.. .+..+ ....
T Consensus       180 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~-~~~~  255 (450)
T 2y4t_A          180 RELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHY-KQVK  255 (450)
T ss_dssp             HHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH-HHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHHHHH-HHHH
Confidence            5555555555555555555555544321 223445555555555555555555555544422  22221 12111 0000


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-----hhhHHHHHHHHHhcCCh
Q 011378          287 KVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT-----LVSCNTIIKGYCRSGDA  361 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-----~~~~~~li~~~~~~~~~  361 (487)
                                            ....+..+...|...|++++|...|+.+...  .|+     ...+..+...+.+.|+.
T Consensus       256 ----------------------~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~  311 (450)
T 2y4t_A          256 ----------------------KLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKP  311 (450)
T ss_dssp             ----------------------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCH
T ss_pred             ----------------------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCH
Confidence                                  0000011144555555555555555555442  222     22444555555555555


Q ss_pred             HHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          362 SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       362 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      ++|...++++.+.. +.+...|..+..+|...|++++|...+++..+
T Consensus       312 ~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  357 (450)
T 2y4t_A          312 VEAIRVCSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYETAQE  357 (450)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            55555555554321 12344555555555555555555555555544

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

Probab=99.83  E-value=7.5e-21  Score=192.18  Aligned_cols=116  Identities=18%  Similarity=0.181  Sum_probs=56.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHH---hCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMV---GKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLI  387 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  387 (487)
                      .|||+||++||+.|++++|..+|.+|.   ..|+.||+.|||+||.+||+.|++++|.++|++|.+.|+.||..|||+||
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            345555555555555555555554443   22444555555555555555555555555555555555555555555555


Q ss_pred             HHHhccCC-HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHH
Q 011378          388 NGFVREEN-MDKAFALVSKMENQGLVPDVITYNVILTGFC  426 (487)
Q Consensus       388 ~~~~~~~~-~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  426 (487)
                      +++++.|+ .++|.++|++|.+.|+.||..+|++++.++.
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~e  247 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEED  247 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHH
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhh
Confidence            55554444 2344445555554455555555554444433

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

Probab=99.83  E-value=1.1e-20  Score=190.91  Aligned_cols=149  Identities=15%  Similarity=0.223  Sum_probs=86.5

Q ss_pred             eehHHHHHHHHccCCHHHHHHHHHHHHh---CCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHH
Q 011378          276 VTYNTLIDGFCKVGEMEKANKLWADMIS---RKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTII  352 (487)
Q Consensus       276 ~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  352 (487)
                      .|||+||++||+.|++++|.++|.+|.+   .|+.||+.|||+||.+||+.|++++|.++|++|...|+.||.+|||+||
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            3566666666666666666666655542   3566666666666666666666666666666666666666666666666


Q ss_pred             HHHHhcCCh-HHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC------HhhHHHHHHHH
Q 011378          353 KGYCRSGDA-SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPD------VITYNVILTGF  425 (487)
Q Consensus       353 ~~~~~~~~~-~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~------~~~~~~li~~~  425 (487)
                      .++|+.|+. +.|.++|++|.+.|+.||..+|+++++++-+.    .+.+.+.++ ..+++|+      +.+.+.|.+.|
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~----~vL~~Vrkv-~P~f~p~~~~~~~~~t~~LL~dl~  282 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA----TVLKAVHKV-KPTFSLPPQLPPPVNTSKLLRDVY  282 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH----HHHHHHGGG-CCCCCCCCCCCCCCCCCTTTHHHH
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH----HHHHHHHHh-CcccCCCCCCcccccchHHHHHHH
Confidence            666666653 55666666666666666666666666544433    223333333 2344443      34444455555


Q ss_pred             HhcC
Q 011378          426 CRQG  429 (487)
Q Consensus       426 ~~~g  429 (487)
                      .+.+
T Consensus       283 s~d~  286 (1134)
T 3spa_A          283 AKDG  286 (1134)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            5444

>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=99.80  E-value=5.4e-16  Score=155.29  Aligned_cols=395  Identities=12%  Similarity=0.037  Sum_probs=208.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011378           30 TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVE  109 (487)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  109 (487)
                      ...+..+-..+.+.|++++|.+.|+...... +.++.+|..+...+.+.|++++|.+.+++..+.. +.+...+..+...
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~  102 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASA  102 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHH
Confidence            4567888889999999999999999987643 2356778888899999999999999999988754 3357788888889


Q ss_pred             HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHC------CCCCChhhHHHHHHHHHhc
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSA------GLVPDNVLYTIIINGYCRN  183 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~~~~~~~~~ll~~~~~~  183 (487)
                      +...|++++|.+.|+.+.   ..|+.  .+..+..+...+....|...++++...      ...|+...    +..+...
T Consensus       103 ~~~~g~~~~A~~~~~~~~---~~~~~--~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~----~~~~~~~  173 (537)
T 3fp2_A          103 NESLGNFTDAMFDLSVLS---LNGDF--DGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTS----LASFFGI  173 (537)
T ss_dssp             HHHHTCHHHHHHHHHHHC----------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHH----HHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHh---cCCCC--ChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhH----HHHHHHh
Confidence            999999999999996442   23332  233455666666778899988888542      12233222    2222222


Q ss_pred             C------------------------------------------CHHHHHHHHHHHHHcCCcCC--------hhhHHHHHH
Q 011378          184 G------------------------------------------FVLEALKMRDEMLEKGCVMD--------VVTYNTILN  213 (487)
Q Consensus       184 ~------------------------------------------~~~~a~~~~~~m~~~g~~~~--------~~~~~~li~  213 (487)
                      .                                          ++++|..+++++.+..  |+        ..+|..+..
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~g~  251 (537)
T 3fp2_A          174 FDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN--TVDDPLRENAALALCYTGI  251 (537)
T ss_dssp             SCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC--CCcchhhHHHHHHHHHHHH
Confidence            2                                          3444444444444321  11        112333334


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHH
Q 011378          214 GLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEK  293 (487)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~  293 (487)
                      .+...|+++.|...|++..+.  .|+...+..+...+...|++++|...|+...+.. +.+..++..+...+...|++++
T Consensus       252 ~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  328 (537)
T 3fp2_A          252 FHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKN  328 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHH
Confidence            444555555555555555443  2334445555555555555555555555444321 1123344455555555555555


Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          294 ANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       294 a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      |...+.+..... +.+...+..+...+...|++++|...++...... +.+...+..+-..|...|+.++|...+++..+
T Consensus       329 A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  406 (537)
T 3fp2_A          329 AKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKR  406 (537)
T ss_dssp             HHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            555555444321 1123444455555555555555555555544332 22333444455555555555555555555433


Q ss_pred             CC-----CCCChhhHHHHHHHHhcc----------CCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHH
Q 011378          374 EG-----VDPDSISYNTLINGFVRE----------ENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       374 ~g-----~~p~~~~~~~li~~~~~~----------~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      ..     .......+..+...|.+.          |++++|...+++..+.. ..+...|..+...|.+.|++++|...|
T Consensus       407 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~  485 (537)
T 3fp2_A          407 LEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKIDEAIELF  485 (537)
T ss_dssp             HHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHH
Confidence            21     000111122222333444          55555555555444321 122344455555555555555555555


Q ss_pred             HHHHH
Q 011378          439 WRMIE  443 (487)
Q Consensus       439 ~~m~~  443 (487)
                      ++..+
T Consensus       486 ~~al~  490 (537)
T 3fp2_A          486 EDSAI  490 (537)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>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=99.79  E-value=1.3e-15  Score=152.58  Aligned_cols=391  Identities=12%  Similarity=0.032  Sum_probs=259.2

Q ss_pred             hHHhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhh
Q 011378            4 ALCKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDR   83 (487)
Q Consensus         4 ~~~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~   83 (487)
                      .+.+.|+++.|...+++..+.. +.+..+|..+..++.+.|++++|.+.++.....+ +.+..+|..+...+.+.|++++
T Consensus        34 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~  111 (537)
T 3fp2_A           34 HFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTD  111 (537)
T ss_dssp             HHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHH
Confidence            4667888888888888876643 2366778888888888888888888888876542 2245667777778888888888


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHC------CCCCCHhHH-------------------
Q 011378           84 AKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRR------GVAPDIVSF-------------------  138 (487)
Q Consensus        84 a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~~p~~~~~-------------------  138 (487)
                      |.+.|+.+..   .|+..  +..+..+...+....|...++++...      ...|+....                   
T Consensus       112 A~~~~~~~~~---~~~~~--~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (537)
T 3fp2_A          112 AMFDLSVLSL---NGDFD--GASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTS  186 (537)
T ss_dssp             HHHHHHHHC----------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCC
T ss_pred             HHHHHHHHhc---CCCCC--hHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhc
Confidence            8888863322   23222  22233444455566778888777442      112222211                   


Q ss_pred             -----------HHHHHHHHhC--------CCHHHHHHHHHHHHHCCCCCC--------hhhHHHHHHHHHhcCCHHHHHH
Q 011378          139 -----------STLIGIFSRN--------GQLDRALMYFREMKSAGLVPD--------NVLYTIIINGYCRNGFVLEALK  191 (487)
Q Consensus       139 -----------~~li~~~~~~--------g~~~~a~~~~~~m~~~g~~~~--------~~~~~~ll~~~~~~~~~~~a~~  191 (487)
                                 ..+...+...        |++++|..+++++.+..  |+        ..++..+-..+...|+.++|..
T Consensus       187 ~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~  264 (537)
T 3fp2_A          187 SNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN--TVDDPLRENAALALCYTGIFHFLKNNLLDAQV  264 (537)
T ss_dssp             CSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC--CCcchhhHHHHHHHHHHHHHHHhcccHHHHHH
Confidence                       1122222211        36777888888776543  33        2245556667777888888888


Q ss_pred             HHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 011378          192 MRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSI  271 (487)
Q Consensus       192 ~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~  271 (487)
                      .+++..+..  |+...|..+...+...|+++.|.+.|++..+.. +.+..++..+...+...|++++|...|+...+.. 
T Consensus       265 ~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-  340 (537)
T 3fp2_A          265 LLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-  340 (537)
T ss_dssp             HHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-
Confidence            888877643  456677778888888888888888888877653 3356778888888888888888888888776543 


Q ss_pred             CCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCC-----CCCChh
Q 011378          272 KPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKG-----IKPTLV  346 (487)
Q Consensus       272 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~~~~~  346 (487)
                      +.+...+..+...+...|++++|...+.+..... +.+...+..+...+...|++++|...++......     ......
T Consensus       341 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  419 (537)
T 3fp2_A          341 PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIG  419 (537)
T ss_dssp             TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHH
Confidence            1234577778888888888888888888776542 2345677788888888888888888888765432     111222


Q ss_pred             hHHHHHHHHHhc----------CChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          347 SCNTIIKGYCRS----------GDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       347 ~~~~li~~~~~~----------~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      .+...-..+.+.          |++++|...+++..+.. +.+...+..+...|.+.|++++|.+.+++..+.
T Consensus       420 ~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  491 (537)
T 3fp2_A          420 PLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKIDEAIELFEDSAIL  491 (537)
T ss_dssp             HHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            233444566666          88888888888877642 234567778888888888888888888877653

>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=99.74  E-value=7e-16  Score=145.00  Aligned_cols=346  Identities=12%  Similarity=0.110  Sum_probs=148.4

Q ss_pred             HhcCChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHH
Q 011378            6 CKDHKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAK   85 (487)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~   85 (487)
                      -+.|++++|.++++++..    |  .+|..+..++.+.|++++|.+.|..      .+|..+|..+++++.+.|++++|.
T Consensus        14 ~~~~~ld~A~~fae~~~~----~--~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi   81 (449)
T 1b89_A           14 EHIGNLDRAYEFAERCNE----P--AVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELV   81 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHccCHHHHHHHHHhCCC----h--HHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHH
Confidence            456778899999888842    3  4788999999999999999988864      257778889999999999999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCC
Q 011378           86 EVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAG  165 (487)
Q Consensus        86 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  165 (487)
                      ++++...+.  .++..+.+.++.+|++.|+++++.++++       .|+..+|..+...|...|.++.|..+|..+    
T Consensus        82 ~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a----  148 (449)
T 1b89_A           82 KYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV----  148 (449)
T ss_dssp             -----------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT----
T ss_pred             HHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh----
Confidence            977765553  4567888889999999999999888875       377778999999999999999999999876    


Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 011378          166 LVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTT  245 (487)
Q Consensus       166 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~  245 (487)
                           ..|..+.+++.+.|++++|.+.+.+.      .++.+|..++.+|...|+++.|......     +..++.-...
T Consensus       149 -----~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~-----L~~~ad~l~~  212 (449)
T 1b89_A          149 -----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEE  212 (449)
T ss_dssp             -----TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-----TTTCHHHHHH
T ss_pred             -----hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHH-----HHhCHhhHHH
Confidence                 37889999999999999999888877      3678899999999999999998555443     2233444557


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc--CCHHHHHHHHHHHHhCCCCC------ChhhHHHHH
Q 011378          246 LIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV--GEMEKANKLWADMISRKISP------NYISYGILI  317 (487)
Q Consensus       246 li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~--g~~~~a~~~~~~m~~~~~~p------~~~t~~~li  317 (487)
                      ++..|.+.|++++|..+++...... +-....|+-|--.|++-  +++.+..+.|..  +-.++|      +...|.-+.
T Consensus       213 lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~--~ini~k~~~~~~~~~~w~e~~  289 (449)
T 1b89_A          213 LINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWS--RVNIPKVLRAAEQAHLWAELV  289 (449)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHST--TSCHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHHHHH
Confidence            8888999999999998888665332 23445666666666665  234444444431  112222      345677777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHH
Q 011378          318 NGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMD  397 (487)
Q Consensus       318 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~  397 (487)
                      -.|...++++.|..   .|..+  +|+..--..+.+...+..+.+--.+.+....  +..|.  ..|-|+.++...=+..
T Consensus       290 ~ly~~~~e~d~A~~---tm~~h--~~~a~~~~~f~~~~~kv~n~elyYkai~fyl--~~~p~--~l~~ll~~l~~~ld~~  360 (449)
T 1b89_A          290 FLYDKYEEYDNAII---TMMNH--PTDAWKEGQFKDIITKVANVELYYRAIQFYL--EFKPL--LLNDLLMVLSPRLDHT  360 (449)
T ss_dssp             HHHHHTTCHHHHHH---HHHHS--TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH--HHCGG--GHHHHHHHHGGGCCHH
T ss_pred             HHHHhhchHHHHHH---HHHhC--ChhhhhhHHHHHHHhchhHHHHHHHHHHHHH--hcCHH--HHHHHHHHHHhccCcH
Confidence            77777777777766   33332  2232223334444455555554444444433  12233  2555555555555555


Q ss_pred             HHHHHHH
Q 011378          398 KAFALVS  404 (487)
Q Consensus       398 ~a~~~~~  404 (487)
                      ++..+|+
T Consensus       361 r~v~~~~  367 (449)
T 1b89_A          361 RAVNYFS  367 (449)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5544443

>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=99.72  E-value=5.2e-16  Score=145.87  Aligned_cols=239  Identities=13%  Similarity=0.106  Sum_probs=82.4

Q ss_pred             hcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHH
Q 011378           42 REGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEE  121 (487)
Q Consensus        42 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~  121 (487)
                      +.|++++|.++++.+      +++.+|..+..++.+.|++++|.+.|.+      .+|..+|..++..+...|++++|.+
T Consensus        15 ~~~~ld~A~~fae~~------~~~~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           15 HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhC------CChHHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHH
Confidence            457788888877766      3445788888888888888888888764      2566777778888878888888888


Q ss_pred             HHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011378          122 IFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGC  201 (487)
Q Consensus       122 ~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~  201 (487)
                      .++...+.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..+.+.|...|.+++|...|..+     
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            66655553  3445667778888888888887777664       266667777777777888888877777754     


Q ss_pred             cCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHH
Q 011378          202 VMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTL  281 (487)
Q Consensus       202 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~l  281 (487)
                          ..|..+..++.+.|++++|.+.+.++      .++.+|..++.+|...|+++.|......     +..+..-...+
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------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEEL  213 (449)
T ss_dssp             ----TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-----TTTCHHHHHHH
T ss_pred             ----hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHH-----HHhCHhhHHHH
Confidence                47777777777778887777777776      2567777777777777777777443322     11222224456


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          282 IDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCS  322 (487)
Q Consensus       282 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~  322 (487)
                      +..|.+.|++++|..+++...... +.....|+-|--+|++
T Consensus       214 v~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~k  253 (449)
T 1b89_A          214 INYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSK  253 (449)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHh
Confidence            667777777777777776654332 2334455555555544

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

Probab=99.72  E-value=4.5e-13  Score=133.95  Aligned_cols=413  Identities=10%  Similarity=0.100  Sum_probs=234.7

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011378           29 DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLV  108 (487)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  108 (487)
                      |...|..++. +.+.|+++.|..+|+.+.+. .+-+...|...+..+.+.|+++.|.++|++....  .|+...|..++.
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~-~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw~~~~~   87 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQ-FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLWKCYLS   87 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTT-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHHHHHHH
Confidence            6678888888 47899999999999998764 2334567999999999999999999999998865  478777777765


Q ss_pred             H-HHccCChhHHHH----HHHHHHH-CCCCC-CHhHHHHHHHHHHh---------CCCHHHHHHHHHHHHHCCCCCCh--
Q 011378          109 E-SCRKENMSEAEE----IFCEMSR-RGVAP-DIVSFSTLIGIFSR---------NGQLDRALMYFREMKSAGLVPDN--  170 (487)
Q Consensus       109 ~-~~~~~~~~~a~~----~~~~m~~-~g~~p-~~~~~~~li~~~~~---------~g~~~~a~~~~~~m~~~g~~~~~--  170 (487)
                      . ....|+.+.|.+    +|+...+ .|..| +...|...+....+         .|+++.|..+|+...+.   |+.  
T Consensus        88 ~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~---P~~~~  164 (530)
T 2ooe_A           88 YVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVN---PMINI  164 (530)
T ss_dssp             HHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTS---CCTTH
T ss_pred             HHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhc---hhhhH
Confidence            3 335577777665    6665543 35544 45667777766554         68899999999988762   332  


Q ss_pred             -hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHH------HcC---CCCC-
Q 011378          171 -VLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEML------ERG---VFPD-  239 (487)
Q Consensus       171 -~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~------~~~---~~~~-  239 (487)
                       ..|......--..|.                    .+...++.  .+.+++..|..++++..      +..   ++|+ 
T Consensus       165 ~~~~~~~~~~e~~~~~--------------------~~~~~~l~--~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~  222 (530)
T 2ooe_A          165 EQLWRDYNKYEEGINI--------------------HLAKKMIE--DRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQN  222 (530)
T ss_dssp             HHHHHHHHHHHHHHCH--------------------HHHHHHHH--TTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC-
T ss_pred             HHHHHHHHHHHHhhch--------------------hHHHHHHH--HhhHHHHHHHHHHHHHHHHHHHhccccccCCCCC
Confidence             233322221100110                    00011110  01223344444443321      111   2222 


Q ss_pred             -------HHHHHHHHHHHHhc----CCH----HHHHHHHHHHHHCCCCCCeeehHHHHHHHHc-------cCCHH-----
Q 011378          240 -------FYTFTTLIHGHCKD----GNM----NKALNLFDIMTQKSIKPDIVTYNTLIDGFCK-------VGEME-----  292 (487)
Q Consensus       240 -------~~t~~~li~~~~~~----g~~----~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~-------~g~~~-----  292 (487)
                             ...|...+......    ++.    +.+..+|+..... .+-+...|..+...+.+       .|+++     
T Consensus       223 ~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~  301 (530)
T 2ooe_A          223 TPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLF  301 (530)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhh
Confidence                   13344433322221    121    2455555554432 11233445555555443       46655     


Q ss_pred             --HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh--hhHHHHHHHHHhcCChHHHHHHH
Q 011378          293 --KANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTL--VSCNTIIKGYCRSGDASKADEFL  368 (487)
Q Consensus       293 --~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~--~~~~~li~~~~~~~~~~~a~~~~  368 (487)
                        +|..++.+....-.+.+...|..+...+.+.|++++|..+|+.....  .|+.  ..|..+...+.+.|+.++|..+|
T Consensus       302 ~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  379 (530)
T 2ooe_A          302 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIF  379 (530)
T ss_dssp             HHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHH
Confidence              66666666553222224556666666666667777777777666653  3432  35666666666667777777777


Q ss_pred             HHHHHCCCCCC-hhhHHHHHH-HHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011378          369 SKMVSEGVDPD-SISYNTLIN-GFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKG  445 (487)
Q Consensus       369 ~~m~~~g~~p~-~~~~~~li~-~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  445 (487)
                      +...+.  .|+ ...|..... .+...|+.++|..+|++..+.  .| +...|..++..+.+.|+.++|..+|++....+
T Consensus       380 ~~Al~~--~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~--~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          380 KKARED--ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             HHHHTC--TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             HHHHhc--cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            666543  222 111211111 122466777777777655442  23 35566666666677777777777777766542


Q ss_pred             -CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          446 -LNPD--RSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       446 -~~p~--~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                       ..|+  ...|...+......|+.+.+.++..++.
T Consensus       456 ~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~  490 (530)
T 2ooe_A          456 SLPPEKSGEIWARFLAFESNIGDLASILKVEKRRF  490 (530)
T ss_dssp             CSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             2222  3366666666666677777776666654

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

Probab=99.71  E-value=3.5e-13  Score=134.74  Aligned_cols=381  Identities=9%  Similarity=0.044  Sum_probs=254.5

Q ss_pred             CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 011378           64 GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIG  143 (487)
Q Consensus        64 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  143 (487)
                      +...|..++. +.+.|+++.|..+|+++.+. .+-+...|..++..+.+.|+++.|.++|++..+.  .|+...|...+.
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~-~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw~~~~~   87 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQ-FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLWKCYLS   87 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTT-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHHHHHHH
Confidence            5567888887 47788999999999998764 2345667888888888899999999999988765  367776766664


Q ss_pred             H-HHhCCCHHHHHH----HHHHHHH-CCCCCC-hhhHHHHHHHHHh---------cCCHHHHHHHHHHHHHcCCcCCh--
Q 011378          144 I-FSRNGQLDRALM----YFREMKS-AGLVPD-NVLYTIIINGYCR---------NGFVLEALKMRDEMLEKGCVMDV--  205 (487)
Q Consensus       144 ~-~~~~g~~~~a~~----~~~~m~~-~g~~~~-~~~~~~ll~~~~~---------~~~~~~a~~~~~~m~~~g~~~~~--  205 (487)
                      . ....|+.+.|.+    +|+.... .|..|+ ...|...+....+         .|+.+.|..++++..+.   |+.  
T Consensus        88 ~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~---P~~~~  164 (530)
T 2ooe_A           88 YVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVN---PMINI  164 (530)
T ss_dssp             HHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTS---CCTTH
T ss_pred             HHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhc---hhhhH
Confidence            3 345677666554    6665543 455543 4566666665544         56777777777776652   221  


Q ss_pred             -hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH------HCC---CCCCe
Q 011378          206 -VTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMT------QKS---IKPDI  275 (487)
Q Consensus       206 -~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~------~~~---~~~~~  275 (487)
                       ..|..........+                    ..+...++.  .+.++++.|..+++...      +..   ++|+.
T Consensus       165 ~~~~~~~~~~e~~~~--------------------~~~~~~~l~--~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~  222 (530)
T 2ooe_A          165 EQLWRDYNKYEEGIN--------------------IHLAKKMIE--DRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQN  222 (530)
T ss_dssp             HHHHHHHHHHHHHHC--------------------HHHHHHHHH--TTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC-
T ss_pred             HHHHHHHHHHHHhhc--------------------hhHHHHHHH--HhhHHHHHHHHHHHHHHHHHHHhccccccCCCCC
Confidence             12211111000000                    011111111  12345667776665532      121   34442


Q ss_pred             --------eehHHHHHHHHcc----CCH----HHHHHHHHHHHhCCCCCChhhHHHHHHHHHh-------cCCHH-----
Q 011378          276 --------VTYNTLIDGFCKV----GEM----EKANKLWADMISRKISPNYISYGILINGYCS-------MGHVT-----  327 (487)
Q Consensus       276 --------~~~~~li~~~~~~----g~~----~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~-------~~~~~-----  327 (487)
                              ..|...+......    ++.    +.+..+|++.... .+-+...|..+...+..       .|+++     
T Consensus       223 ~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~  301 (530)
T 2ooe_A          223 TPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLF  301 (530)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhh
Confidence                    3555555443322    233    4677788877654 23356778777777765       78887     


Q ss_pred             --HHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh--hhHHHHHHHHhccCCHHHHHHHH
Q 011378          328 --EAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS--ISYNTLINGFVREENMDKAFALV  403 (487)
Q Consensus       328 --~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~--~~~~~li~~~~~~~~~~~a~~~~  403 (487)
                        +|..+++.-...-.+.+...|..+...+.+.|+.++|..++++..+.  .|+.  ..|..+...+.+.|++++|.++|
T Consensus       302 ~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  379 (530)
T 2ooe_A          302 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIF  379 (530)
T ss_dssp             HHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHH
Confidence              89999998875323445778999999999999999999999999874  5642  47888888888999999999999


Q ss_pred             HHHHhCCCCCC-HhhHHHHHH-HHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 011378          404 SKMENQGLVPD-VITYNVILT-GFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNLKEAFRFHDEMLQRG  480 (487)
Q Consensus       404 ~~m~~~g~~p~-~~~~~~li~-~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g  480 (487)
                      ++..+.  .|+ ...|-.... .+...|+.++|..+|++..+.  .| +...|..++..+.+.|+.++|..++++.+..+
T Consensus       380 ~~Al~~--~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~--~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          380 KKARED--ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             HHHHTC--TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             HHHHhc--cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            988764  232 222222222 234689999999999998764  35 57788999999999999999999999998763

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

Probab=99.70  E-value=3.7e-13  Score=126.85  Aligned_cols=326  Identities=12%  Similarity=0.053  Sum_probs=171.0

Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHH
Q 011378          101 ATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGY  180 (487)
Q Consensus       101 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~  180 (487)
                      ..+..+-..+...|++++|...|++..+.. +.+...+..+...+.+.|++++|...+++..+.. +.+...|..+...+
T Consensus         4 ~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~   81 (359)
T 3ieg_A            4 EKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLL   81 (359)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHH
Confidence            344445555555666666666666555432 1234455555555566666666666665554431 11234455555555


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCc--CChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHH
Q 011378          181 CRNGFVLEALKMRDEMLEKGCV--MDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNK  258 (487)
Q Consensus       181 ~~~~~~~~a~~~~~~m~~~g~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~  258 (487)
                      .+.|+.++|...+++..+....  .+...+..+...+       .                ...+..+...+...|++++
T Consensus        82 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~-------~----------------~~~~~~~a~~~~~~~~~~~  138 (359)
T 3ieg_A           82 LKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKAD-------E----------------MQRLRSQALDAFDGADYTA  138 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHH-------H----------------HHHHHHHHHHHHHTTCHHH
T ss_pred             HHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHH-------H----------------HHHHHHHHHHHHHccCHHH
Confidence            5555555555555555432110  0111222220000       0                0001112345555666666


Q ss_pred             HHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011378          259 ALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVG  338 (487)
Q Consensus       259 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  338 (487)
                      |+..++.+.+.. +.+...+..+...+...|++++|...+.+..... +.+..++..+...+...|++++|...++...+
T Consensus       139 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~  216 (359)
T 3ieg_A          139 AITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLK  216 (359)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            666665554321 1233455555566666666666666666554431 22445556666666666666666666665554


Q ss_pred             CCCCCChhhHH------------HHHHHHHhcCChHHHHHHHHHHHHCCCCCCh-----hhHHHHHHHHhccCCHHHHHH
Q 011378          339 KGIKPTLVSCN------------TIIKGYCRSGDASKADEFLSKMVSEGVDPDS-----ISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       339 ~~~~~~~~~~~------------~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-----~~~~~li~~~~~~~~~~~a~~  401 (487)
                      .. +.+...+.            .+...+.+.|+.++|...+++..+..  |+.     ..+..+...|.+.|++++|..
T Consensus       217 ~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          217 LD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSVAEYTVRSKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSSHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hC-ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            32 11122221            22445667777777777777766533  322     224445667777788888887


Q ss_pred             HHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHH
Q 011378          402 LVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLING  459 (487)
Q Consensus       402 ~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~  459 (487)
                      .+++..+.. ..+...|..+...+.+.|++++|...+++..+.  .|+ ...+..+..+
T Consensus       294 ~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~~~  349 (359)
T 3ieg_A          294 ICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH--NENDQQIREGLEKA  349 (359)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChHHHHHHHHH
Confidence            777776531 225667777777777888888888777777653  344 3334443333

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.70  E-value=4.9e-12  Score=125.07  Aligned_cols=338  Identities=13%  Similarity=0.079  Sum_probs=179.6

Q ss_pred             cCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----CC
Q 011378           78 KGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCR----KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR----NG  149 (487)
Q Consensus        78 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g  149 (487)
                      .++++.|...|....+.|   +...+..|-..|..    .++.++|.+.|++..+.|   +...+..+-..|..    .+
T Consensus        56 ~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~  129 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKV  129 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCC
T ss_pred             CcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCC
Confidence            455555555555554432   23344444444444    555555555555555543   33344444444544    45


Q ss_pred             CHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHh----cCCH
Q 011378          150 QLDRALMYFREMKSAGLVPDNVLYTIIINGYCR----NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCR----AKML  221 (487)
Q Consensus       150 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~~~  221 (487)
                      ++++|...|++....|   +...+..|-..|..    .++.++|.+.+++..+.|   +...+..+-..|.+    .++.
T Consensus       130 ~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~  203 (490)
T 2xm6_A          130 DKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERND  203 (490)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCH
T ss_pred             CHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCH
Confidence            5555655555555443   23344444444444    455556665555555543   34445555555554    5566


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHc----cCCHHH
Q 011378          222 TEADDLFNEMLERGVFPDFYTFTTLIHGHCK----DGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCK----VGEMEK  293 (487)
Q Consensus       222 ~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~g~~~~  293 (487)
                      +.|.+.|++..+.|   +...+..+-..|..    .++.++|...|+...+.+   +...+..+-..|..    .++.++
T Consensus       204 ~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~  277 (490)
T 2xm6_A          204 AISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLK  277 (490)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHH
T ss_pred             HHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHH
Confidence            66666666555543   34444445445543    555666666665554432   22233344444444    556666


Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHhc-----CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC---ChHHHH
Q 011378          294 ANKLWADMISRKISPNYISYGILINGYCSM-----GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG---DASKAD  365 (487)
Q Consensus       294 a~~~~~~m~~~~~~p~~~t~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~---~~~~a~  365 (487)
                      |...|+.....+   +...+..|-..|...     ++.++|...++.....|   +...+..+-..|...|   +.++|.
T Consensus       278 A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~  351 (490)
T 2xm6_A          278 ALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAV  351 (490)
T ss_dssp             HHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHH
T ss_pred             HHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHH
Confidence            666666555432   333444555555554     56666666666665543   2334444444454434   566666


Q ss_pred             HHHHHHHHCCCCCChhhHHHHHHHHhc----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh----cCChHHHHHH
Q 011378          366 EFLSKMVSEGVDPDSISYNTLINGFVR----EENMDKAFALVSKMENQGLVPDVITYNVILTGFCR----QGRMHDSELI  437 (487)
Q Consensus       366 ~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~  437 (487)
                      +.+++..+.|   +...+..|-..|..    .++.++|...+++..+.|   +...+..|-..|.+    .++.++|...
T Consensus       352 ~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~  425 (490)
T 2xm6_A          352 EWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERDYVQAWAW  425 (490)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHH
T ss_pred             HHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            6666666543   34455555555555    566667776666666544   34455555555555    6667777776


Q ss_pred             HHHHHHcC
Q 011378          438 LWRMIEKG  445 (487)
Q Consensus       438 ~~~m~~~g  445 (487)
                      |++..+.|
T Consensus       426 ~~~A~~~~  433 (490)
T 2xm6_A          426 FDTASTND  433 (490)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHCC
Confidence            66666554

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.70  E-value=6.8e-12  Score=124.07  Aligned_cols=364  Identities=14%  Similarity=0.060  Sum_probs=285.8

Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHh----cCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHh----cCChhhHH
Q 011378           14 AKMFLCEMEQKGVYPDTVTYNTLINAYCR----EGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCK----KGRCDRAK   85 (487)
Q Consensus        14 a~~~~~~~~~~g~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~   85 (487)
                      +...+....+.|   +...+..+-..|..    .++++.|..+|+...+.|   ++..+..+-..+..    .+++++|.
T Consensus        26 ~~~~~~~~a~~g---~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~   99 (490)
T 2xm6_A           26 NLEQLKQKAESG---EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAV   99 (490)
T ss_dssp             CHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence            344455544443   66777778888887    899999999999887764   45567777777777    88999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHc----cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----CCCHHHHHHH
Q 011378           86 EVLDEMLQMGLSPDTATYNTLLVESCR----KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR----NGQLDRALMY  157 (487)
Q Consensus        86 ~~~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~  157 (487)
                      +.|.+..+.|   +...+..|-..|..    .++.++|.+.|++..+.|   +...+..+-..|..    .++.++|.+.
T Consensus       100 ~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~  173 (490)
T 2xm6_A          100 IWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREW  173 (490)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHH
T ss_pred             HHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            9999988765   55566667677776    789999999999988876   45667777777877    7899999999


Q ss_pred             HHHHHHCCCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHh----cCCHHHHHHHHH
Q 011378          158 FREMKSAGLVPDNVLYTIIINGYCR----NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCR----AKMLTEADDLFN  229 (487)
Q Consensus       158 ~~~m~~~g~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~~~~~a~~~~~  229 (487)
                      |++..+.|   +...+..|-..|.+    .++.++|.+.+++..+.|   +...+..+-..|..    .++++.|.+.|+
T Consensus       174 ~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~  247 (490)
T 2xm6_A          174 YSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFS  247 (490)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            99988764   56677788888887    789999999999888765   45677777777776    789999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc-----CCHHHHHHHHHH
Q 011378          230 EMLERGVFPDFYTFTTLIHGHCK----DGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV-----GEMEKANKLWAD  300 (487)
Q Consensus       230 ~m~~~~~~~~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~-----g~~~~a~~~~~~  300 (487)
                      +..+.|   +...+..+-..|..    .++.++|+..|+...+.+   +...+..|-..|...     ++.++|...|..
T Consensus       248 ~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~  321 (490)
T 2xm6_A          248 QSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTK  321 (490)
T ss_dssp             HHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHH
Confidence            988764   45566667677777    889999999999887654   344666677777776     899999999998


Q ss_pred             HHhCCCCCChhhHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh----cCChHHHHHHHHHHHH
Q 011378          301 MISRKISPNYISYGILINGYCSMG---HVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCR----SGDASKADEFLSKMVS  373 (487)
Q Consensus       301 m~~~~~~p~~~t~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~  373 (487)
                      ..+.+   +...+..|-..|...|   +.++|...|+.....|   +...+..|-..|..    .++.++|...+++..+
T Consensus       322 a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~  395 (490)
T 2xm6_A          322 SAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAE  395 (490)
T ss_dssp             HHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             HHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHh
Confidence            87764   4456677777777766   7889999999888764   56777778888887    7899999999999888


Q ss_pred             CCCCCChhhHHHHHHHHhc----cCCHHHHHHHHHHHHhCC
Q 011378          374 EGVDPDSISYNTLINGFVR----EENMDKAFALVSKMENQG  410 (487)
Q Consensus       374 ~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g  410 (487)
                      .|   +...+..|-..|.+    .++.++|...+++..+.+
T Consensus       396 ~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          396 QG---LSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTND  433 (490)
T ss_dssp             TT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHH
T ss_pred             CC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC
Confidence            66   45667777788877    799999999999887765

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

Probab=99.69  E-value=2.6e-13  Score=127.92  Aligned_cols=311  Identities=12%  Similarity=0.053  Sum_probs=156.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011378           30 TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVE  109 (487)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  109 (487)
                      +..+..+...+.+.|++++|...|+...... +.+..+|..+...+.+.|++++|...+++..+.. +-+...|..+...
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~   80 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHH
Confidence            3445566666677777777777777665431 1234556666666666777777777777665532 1244556666666


Q ss_pred             HHccCChhHHHHHHHHHHHCCCCC----CHhHHHHH------------HHHHHhCCCHHHHHHHHHHHHHCCCCCChhhH
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAP----DIVSFSTL------------IGIFSRNGQLDRALMYFREMKSAGLVPDNVLY  173 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p----~~~~~~~l------------i~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~  173 (487)
                      +...|++++|...+++..+.  .|    +...+..+            ...+...|++++|.+.+++..+.. +.+...+
T Consensus        81 ~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  157 (359)
T 3ieg_A           81 LLKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELR  157 (359)
T ss_dssp             HHHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHcCChHHHHHHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHH
Confidence            66667777777776666543  23    22222222            344555555555555555554422 1233444


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 011378          174 TIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD  253 (487)
Q Consensus       174 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~  253 (487)
                      ..+...+.+.|+.++|...+++..+.. +.+...|..+...+...|+++.|...|++..+.. +.+...+..+...    
T Consensus       158 ~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~----  231 (359)
T 3ieg_A          158 ELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQV----  231 (359)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH----
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHHH----
Confidence            455555555555555555555544332 2233444555555555555555555555544321 1111111111000    


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-----hhHHHHHHHHHhcCCHHH
Q 011378          254 GNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-----ISYGILINGYCSMGHVTE  328 (487)
Q Consensus       254 g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-----~t~~~li~~~~~~~~~~~  328 (487)
                                   .      .......+...+.+.|++++|...+.+.....  |+.     ..+..+...+...|++++
T Consensus       232 -------------~------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~la~~~~~~~~~~~  290 (359)
T 3ieg_A          232 -------------K------KLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSVAEYTVRSKERICHCFSKDEKPVE  290 (359)
T ss_dssp             -------------H------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSSHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             -------------H------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHHHHHHccCHHH
Confidence                         0      00000112334555555555555555554432  221     123334555566666666


Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          329 AFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       329 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      |...++...... +.+..++..+-..|...|+.++|...+++..+
T Consensus       291 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~  334 (359)
T 3ieg_A          291 AIRICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQE  334 (359)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            666666555431 22445555666666666666666666666554

>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=99.69  E-value=9.1e-14  Score=129.59  Aligned_cols=280  Identities=11%  Similarity=-0.008  Sum_probs=130.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 011378          173 YTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCK  252 (487)
Q Consensus       173 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~  252 (487)
                      +..+...+...|+.++|.++++++.+.. +.+...+..+...+.+.|++++|..+++++.+.. +.+...+..+...+..
T Consensus        25 ~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  102 (330)
T 3hym_B           25 VVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYYLM  102 (330)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHH
Confidence            3333333444444444444444433321 1122233333444444444444444444444321 1123344444444444


Q ss_pred             cC-CHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011378          253 DG-NMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFR  331 (487)
Q Consensus       253 ~g-~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~  331 (487)
                      .| +.++|...|+...+.. +.+...|..+...+...|++++|...+.+...... .+...+..+...|...|++++|..
T Consensus       103 ~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~  180 (330)
T 3hym_B          103 VGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYGLTNNSKLAER  180 (330)
T ss_dssp             SCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhHHHHHH
Confidence            44 4444444444443221 11223344444445555555555555544433211 122334445555555555555555


Q ss_pred             HHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCC--------CCCChhhHHHHHHHHhccCCHHHHHHHH
Q 011378          332 LWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEG--------VDPDSISYNTLINGFVREENMDKAFALV  403 (487)
Q Consensus       332 ~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g--------~~p~~~~~~~li~~~~~~~~~~~a~~~~  403 (487)
                      .++...... +.+...+..+...+...|+.++|...+++..+..        .+.+..++..+...|...|++++|...+
T Consensus       181 ~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  259 (330)
T 3hym_B          181 FFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYH  259 (330)
T ss_dssp             HHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            555554332 2234455555555555566666655555554321        1222345666666666666666666666


Q ss_pred             HHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHH
Q 011378          404 SKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGH  460 (487)
Q Consensus       404 ~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~  460 (487)
                      ++..+.. ..+...|..+...+.+.|++++|...+++..+  +.| +...+..+..++
T Consensus       260 ~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~l~~~~  314 (330)
T 3hym_B          260 RQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALG--LRRDDTFSVTMLGHCI  314 (330)
T ss_dssp             HHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTT--TCSCCHHHHHHHHHHH
T ss_pred             HHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHc--cCCCchHHHHHHHHHH
Confidence            6554431 22345566666666666666666666666543  234 334444444444

>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=99.69  E-value=1e-13  Score=129.27  Aligned_cols=267  Identities=10%  Similarity=-0.027  Sum_probs=130.2

Q ss_pred             CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 011378           64 GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIG  143 (487)
Q Consensus        64 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  143 (487)
                      +...+..+...+...|++++|.++|+++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+..
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   98 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGC   98 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHH
Confidence            33344444444444555555555555544321 1122333334444445555555555555554421 113334455555


Q ss_pred             HHHhCC-CHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHH
Q 011378          144 IFSRNG-QLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLT  222 (487)
Q Consensus       144 ~~~~~g-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~  222 (487)
                      .+...| ++++|...|++..+.. +.+...|..+...+...|+.++|...+++..+..- .+...+..+...|...|+++
T Consensus        99 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~  176 (330)
T 3hym_B           99 YYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYGLTNNSK  176 (330)
T ss_dssp             HHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhHH
Confidence            555555 5666666665554432 11234455555555555555555555555544321 12334445556666666666


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC--------CCCCeeehHHHHHHHHccCCHHHH
Q 011378          223 EADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKS--------IKPDIVTYNTLIDGFCKVGEMEKA  294 (487)
Q Consensus       223 ~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~--------~~~~~~~~~~li~~~~~~g~~~~a  294 (487)
                      .|.+.+++..+.. +.+...+..+...+...|++++|...++...+..        .+.+..++..+...|.+.|++++|
T Consensus       177 ~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  255 (330)
T 3hym_B          177 LAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEA  255 (330)
T ss_dssp             HHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHH
Confidence            6666666655432 2345556666666666666666666665544311        011233445555555555555555


Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          295 NKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEM  336 (487)
Q Consensus       295 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m  336 (487)
                      ...+++..... +.+...+..+...+...|++++|...++..
T Consensus       256 ~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  296 (330)
T 3hym_B          256 LDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTA  296 (330)
T ss_dssp             HHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTT
T ss_pred             HHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            55555444321 113344444455555555555555555444

>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=99.67  E-value=1e-11  Score=130.19  Aligned_cols=413  Identities=11%  Similarity=0.085  Sum_probs=273.3

Q ss_pred             hhhHHhcCChhhHHHHHHHHHhCCC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcC
Q 011378            2 VNALCKDHKIDSAKMFLCEMEQKGV--YPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKG   79 (487)
Q Consensus         2 i~~~~~~~~~~~a~~~~~~~~~~g~--~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~   79 (487)
                      ++.|...|.+..|.++++++...+-  .-+....+.++.+..+. +.....+..+....       ....-+-..+...|
T Consensus       992 vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~-------~d~~eIA~Iai~lg 1063 (1630)
T 1xi4_A          992 VKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDN-------YDAPDIANIAISNE 1063 (1630)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhh-------ccHHHHHHHHHhCC
Confidence            4556666777777777776653321  11234455555555555 44555544444331       11223445556677


Q ss_pred             ChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHH
Q 011378           80 RCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFR  159 (487)
Q Consensus        80 ~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  159 (487)
                      .+++|..+|++..     ......+.++.   ..+++++|.++.++..      +..+|..+-.++.+.|++++|.+.|.
T Consensus      1064 lyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aervn------~p~vWsqLAKAql~~G~~kEAIdsYi 1129 (1630)
T 1xi4_A         1064 LFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYI 1129 (1630)
T ss_pred             CHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhcC------CHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            7777777777642     12222233332   5566777777776441      35568888888888888998888886


Q ss_pred             HHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011378          160 EMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD  239 (487)
Q Consensus       160 ~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~  239 (487)
                      +.      -|...|..++..+.+.|+.+++.+.+..-++..  +++...+.+..+|++.++++....+.+       .++
T Consensus      1130 KA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI~-------~~n 1194 (1630)
T 1xi4_A         1130 KA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFIN-------GPN 1194 (1630)
T ss_pred             hc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHHh-------CCC
Confidence            53      456677888888888899988888887666544  333334458888888888876554431       346


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011378          240 FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILING  319 (487)
Q Consensus       240 ~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~  319 (487)
                      ...|..+-..|...|++++|...|...         ..|..+...|.+.|++++|.+.+++.      -+..+|.-+-.+
T Consensus      1195 ~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~a 1259 (1630)
T 1xi4_A         1195 NAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFA 1259 (1630)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHH
Confidence            667777888888899999999888864         38889999999999999999988765      366888888888


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc--cCCHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR--EENMD  397 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~--~~~~~  397 (487)
                      |...|++..|......     +..+...+..++..|.+.|.+++|..+++.-.... .-....|.-|-..|++  .+++.
T Consensus      1260 cve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELaiLyaKy~peklm 1333 (1630)
T 1xi4_A         1260 CVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMR 1333 (1630)
T ss_pred             HhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHHHHHHhCCHHHHH
Confidence            8888888888775542     45566777789999999999999999997665332 2233355555555554  34555


Q ss_pred             HHHHHHHHHHhCCCCC------CHhhHHHHHHHHHhcCChHHHHHHHHHHHH-----------cCCCCCHHHHHHHHHHH
Q 011378          398 KAFALVSKMENQGLVP------DVITYNVILTGFCRQGRMHDSELILWRMIE-----------KGLNPDRSTYTTLINGH  460 (487)
Q Consensus       398 ~a~~~~~~m~~~g~~p------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----------~g~~p~~~ty~~l~~~~  460 (487)
                      ++.++|..  ..++.|      +...|.-++-.|.+.|+++.|....-+-..           ..-..+...|...+.-|
T Consensus      1334 Ehlk~f~~--rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~~~~~Fk~~i~kv~n~elyykai~Fy 1411 (1630)
T 1xi4_A         1334 EHLELFWS--RVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFY 1411 (1630)
T ss_pred             HHHHHHHH--hcccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhhhhHHHHHHhcccccHHHHHHHHHHH
Confidence            55555542  122333      456799999999999999988632211100           01135677777778777


Q ss_pred             HhcC---------------CHHHHHHHHH
Q 011378          461 VSQN---------------NLKEAFRFHD  474 (487)
Q Consensus       461 ~~~~---------------~~~~a~~~~~  474 (487)
                      ....               +++.+.+++.
T Consensus      1412 l~~~P~~lndLl~~l~~rlD~~R~V~l~~ 1440 (1630)
T 1xi4_A         1412 LEFKPLLLNDLLMVLSPRLDHTRAVNYFS 1440 (1630)
T ss_pred             HhhChHHHHHHHHHhhhcCChHHHHHHHH
Confidence            7776               7777766665

>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=99.67  E-value=2.3e-14  Score=135.98  Aligned_cols=231  Identities=7%  Similarity=-0.070  Sum_probs=116.4

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011378          171 VLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGH  250 (487)
Q Consensus       171 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~  250 (487)
                      ..+..+-..+.+.|+.++|...+++..+.. +.+...|..+...+.+.|+++.|.+.|+++.+.. +.+..++..+...|
T Consensus        65 ~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~  142 (368)
T 1fch_A           65 PQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSF  142 (368)
T ss_dssp             SSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            345556666666666666666666665542 2344566666666777777777777777666543 23556666777777


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCCCeeehHH---------------HHHHHHccCCHHHHHHHHHHHHhCCCC-CChhhHH
Q 011378          251 CKDGNMNKALNLFDIMTQKSIKPDIVTYNT---------------LIDGFCKVGEMEKANKLWADMISRKIS-PNYISYG  314 (487)
Q Consensus       251 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~---------------li~~~~~~g~~~~a~~~~~~m~~~~~~-p~~~t~~  314 (487)
                      ...|+.++|...|+.+.+..... ...+..               .+..+...|++++|...+.++...... ++..++.
T Consensus       143 ~~~g~~~~A~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~  221 (368)
T 1fch_A          143 TNESLQRQACEILRDWLRYTPAY-AHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQC  221 (368)
T ss_dssp             HHTTCHHHHHHHHHHHHHTSTTT-GGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCcCc-HHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHH
Confidence            77777777777776665532111 111110               122222445555555555544432211 1234444


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccC
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREE  394 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~  394 (487)
                      .+...+...|++++|...++...... +.+..++..+...|...|+.++|...+++..+.. +.+...+..+...|.+.|
T Consensus       222 ~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g  299 (368)
T 1fch_A          222 GLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLG  299 (368)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCC
Confidence            55555555555555555555444321 2223344444444444555555555444444321 112334444444444444


Q ss_pred             CHHHHHHHHHHH
Q 011378          395 NMDKAFALVSKM  406 (487)
Q Consensus       395 ~~~~a~~~~~~m  406 (487)
                      ++++|...+++.
T Consensus       300 ~~~~A~~~~~~a  311 (368)
T 1fch_A          300 AHREAVEHFLEA  311 (368)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            444444444443

>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=99.66  E-value=4.1e-14  Score=134.32  Aligned_cols=302  Identities=13%  Similarity=0.026  Sum_probs=166.0

Q ss_pred             hcCChhHHHH-HHHHHhhCC-CCC--CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChh
Q 011378           42 REGFLEEAFQ-LMNSMSGKG-LKP--GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMS  117 (487)
Q Consensus        42 ~~~~~~~a~~-~~~~m~~~~-~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  117 (487)
                      -.|+++.|.+ .++...... -.|  +...|..+-..+.+.|++++|...|+++.+.. +.+...|..+...+...|+++
T Consensus        37 ~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~  115 (368)
T 1fch_A           37 WLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQEL  115 (368)
T ss_dssp             ---------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHH
Confidence            3467777776 666433211 111  34567777778888888888888888887653 335667777777888888888


Q ss_pred             HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChh-hHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          118 EAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNV-LYTIIINGYCRNGFVLEALKMRDEM  196 (487)
Q Consensus       118 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~m  196 (487)
                      +|.+.|++..+.. +.+..++..+...+.+.|++++|...++++....  |+.. .+..+-..       ...       
T Consensus       116 ~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~-------~~~-------  178 (368)
T 1fch_A          116 LAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYT--PAYAHLVTPAEEG-------AGG-------  178 (368)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--TTTGGGCC----------------------
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHH-------hhh-------
Confidence            8888888877653 2356677778888888888888888888877643  2211 11111000       000       


Q ss_pred             HHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCe
Q 011378          197 LEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVF-PDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI  275 (487)
Q Consensus       197 ~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~  275 (487)
                          ..+ ...+. .+..+...|+++.|...|+++.+..-. ++..++..+...|...|++++|+..|+...+.. +.+.
T Consensus       179 ----~~~-~~~~~-~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~  251 (368)
T 1fch_A          179 ----AGL-GPSKR-ILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDY  251 (368)
T ss_dssp             ------------C-TTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH
T ss_pred             ----hcc-cHHHH-HHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCH
Confidence                000 00001 112222555566666666555543211 135555556666666666666666665544331 1123


Q ss_pred             eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC----------CCCh
Q 011378          276 VTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGI----------KPTL  345 (487)
Q Consensus       276 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~----------~~~~  345 (487)
                      .++..+...+.+.|++++|...|.+..... +.+...+..+...|...|++++|...|+......-          ....
T Consensus       252 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  330 (368)
T 1fch_A          252 LLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSE  330 (368)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhh
Confidence            455556666666666666666666554431 22345566666666666666666666665543210          0114


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHH
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLS  369 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~  369 (487)
                      .+|..+..+|...|+.++|..+++
T Consensus       331 ~~~~~l~~~~~~~g~~~~A~~~~~  354 (368)
T 1fch_A          331 NIWSTLRLALSMLGQSDAYGAADA  354 (368)
T ss_dssp             HHHHHHHHHHHHHTCGGGHHHHHT
T ss_pred             HHHHHHHHHHHHhCChHhHHHhHH
Confidence            566667777777777777666655

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

Probab=99.62  E-value=1.5e-13  Score=130.33  Aligned_cols=262  Identities=7%  Similarity=-0.088  Sum_probs=137.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          172 LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHC  251 (487)
Q Consensus       172 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~  251 (487)
                      .|..+...+.+.|+.++|...+++..+.. +.+...|..+...|.+.|+++.|...|++..+.. +.+..++..+...|.
T Consensus        67 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~  144 (365)
T 4eqf_A           67 GAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYT  144 (365)
T ss_dssp             THHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            34455555555555555555555554432 2234456666666666666666666666665532 224556666666666


Q ss_pred             hcCCHHHHHHHHHHHHHCCCC---------CCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCC-CChhhHHHHHHHHH
Q 011378          252 KDGNMNKALNLFDIMTQKSIK---------PDIVTYNTLIDGFCKVGEMEKANKLWADMISRKIS-PNYISYGILINGYC  321 (487)
Q Consensus       252 ~~g~~~~a~~~~~~m~~~~~~---------~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-p~~~t~~~li~~~~  321 (487)
                      ..|++++|+..|+.+.+....         ....++..+...+.+.|++++|...+.+....... ++..++..+...|.
T Consensus       145 ~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~  224 (365)
T 4eqf_A          145 NTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFH  224 (365)
T ss_dssp             HTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHH
Confidence            666666666666655442100         01223334456666677777777777666554211 14556666666666


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHH
Q 011378          322 SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  401 (487)
                      ..|++++|...++...... +.+..+|..+..+|...|+.++|...+++..+.. +.+..++..+...|.+.|++++|..
T Consensus       225 ~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~  302 (365)
T 4eqf_A          225 LSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAVS  302 (365)
T ss_dssp             HHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHH
Confidence            6677777776666665432 2345556666666666666666666666655432 1124455556666666666666666


Q ss_pred             HHHHHHhCC---CCC--------CHhhHHHHHHHHHhcCChHHHHHH
Q 011378          402 LVSKMENQG---LVP--------DVITYNVILTGFCRQGRMHDSELI  437 (487)
Q Consensus       402 ~~~~m~~~g---~~p--------~~~~~~~li~~~~~~g~~~~a~~~  437 (487)
                      .+++..+..   ..|        +...|..+...+...|+.+.+..+
T Consensus       303 ~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  349 (365)
T 4eqf_A          303 NFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAA  349 (365)
T ss_dssp             HHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHH
Confidence            665543210   000        134455555555555555555443

>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=99.61  E-value=3.7e-11  Score=126.12  Aligned_cols=379  Identities=13%  Similarity=0.157  Sum_probs=245.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCC--CCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011378           32 TYNTLINAYCREGFLEEAFQLMNSMSGKG--LKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVE  109 (487)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  109 (487)
                      -....+++|+..|.+.+++++++...-.+  +.-+...-+.++.+..+. +.....++.++...    .+   ...+-..
T Consensus       987 eVs~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~----~d---~~eIA~I 1058 (1630)
T 1xi4_A          987 EVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDN----YD---APDIANI 1058 (1630)
T ss_pred             HhHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhh----cc---HHHHHHH
Confidence            34566777777788888888887766321  111223344455555555 55666666665542    11   2224455


Q ss_pred             HHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHH-hCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHH
Q 011378          110 SCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFS-RNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLE  188 (487)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~-~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~  188 (487)
                      +...|.+++|..+|++..         .+...+..+. ..+++++|.++.++.      -+..+|..+-.++-+.|++++
T Consensus      1059 ai~lglyEEAf~IYkKa~---------~~~~A~~VLie~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~~kE 1123 (1630)
T 1xi4_A         1059 AISNELFEEAFAIFRKFD---------VNTSAVQVLIEHIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKE 1123 (1630)
T ss_pred             HHhCCCHHHHHHHHHHcC---------CHHHHHHHHHHHHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCCHHH
Confidence            666788888888887742         1122223333 667788888777754      235677788888888888888


Q ss_pred             HHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          189 ALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       189 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      |.+.+.+-      -|...|..++.+|.+.|++++|.+.+...++..  +++...+.+..+|++.+++++...+.    +
T Consensus      1124 AIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~ 1191 (1630)
T 1xi4_A         1124 AIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N 1191 (1630)
T ss_pred             HHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h
Confidence            88777542      456677778888888888888888887665543  33333334777788887777544332    1


Q ss_pred             CCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhH
Q 011378          269 KSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSC  348 (487)
Q Consensus       269 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  348 (487)
                         .++...|..+-..|-..|++++|...|...         ..|..+..+|.+.|++++|.+.++.-      .+..+|
T Consensus      1192 ---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aW 1253 (1630)
T 1xi4_A         1192 ---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTW 1253 (1630)
T ss_pred             ---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHH
Confidence               234455666777778888888888888753         47788888888888888888877654      355777


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHH-
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFC-  426 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~-  426 (487)
                      .-+-.+|...|++..|..+...     +..+...+..++..|-+.|.+++|..+++.--  |+.| ....|+-+-..++ 
T Consensus      1254 kev~~acve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL--~LeraH~gmftELaiLyaK 1326 (1630)
T 1xi4_A         1254 KEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAAL--GLERAHMGMFTELAILYSK 1326 (1630)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh--ccChhHhHHHHHHHHHHHh
Confidence            7777788888887777666543     33455667788888999999999999886543  2222 2234444444444 


Q ss_pred             -hcCChHHHHHHHHHHHHcCCCC------CHHHHHHHHHHHHhcCCHHHHHHH
Q 011378          427 -RQGRMHDSELILWRMIEKGLNP------DRSTYTTLINGHVSQNNLKEAFRF  472 (487)
Q Consensus       427 -~~g~~~~a~~~~~~m~~~g~~p------~~~ty~~l~~~~~~~~~~~~a~~~  472 (487)
                       +-+++-++.++|..=  ..+.|      +...|..++..|.+.|+++.|..+
T Consensus      1327 y~peklmEhlk~f~~r--ini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~t 1377 (1630)
T 1xi4_A         1327 FKPQKMREHLELFWSR--VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIIT 1377 (1630)
T ss_pred             CCHHHHHHHHHHHHHh--cccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHH
Confidence             455555555555531  22222      456899999999999999999743

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

Probab=99.61  E-value=2.1e-13  Score=124.79  Aligned_cols=249  Identities=6%  Similarity=-0.009  Sum_probs=151.1

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCcCCh--hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 011378          179 GYCRNGFVLEALKMRDEMLEKGCVMDV--VTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM  256 (487)
Q Consensus       179 ~~~~~~~~~~a~~~~~~m~~~g~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~  256 (487)
                      -....|....|....+....  ..|+.  ...-.+..+|...|+++.|...++.    .-.|+..++..+...+...++.
T Consensus         8 ~~~~~g~y~~ai~~~~~~~~--~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~   81 (291)
T 3mkr_A            8 NAFYIGSYQQCINEAQRVKP--SSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRR   81 (291)
T ss_dssp             HHHHTTCHHHHHHHHHHSCC--CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHHHhccc--CCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcH
Confidence            34455667776666554422  22322  2334455677777777777665543    1345566666677777777777


Q ss_pred             HHHHHHHHHHHHCCCCCCee-ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          257 NKALNLFDIMTQKSIKPDIV-TYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYE  335 (487)
Q Consensus       257 ~~a~~~~~~m~~~~~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  335 (487)
                      ++|+..++.+...+..|+.. .+..+-..+...|++++|.+.++.      +.+...+..+...+.+.|++++|...++.
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            77777777776665555433 334444666777777777777754      34566667777777777777777777777


Q ss_pred             HHhCCCCCChhhH---HHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCC
Q 011378          336 MVGKGIKPTLVSC---NTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLV  412 (487)
Q Consensus       336 m~~~~~~~~~~~~---~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  412 (487)
                      +....  |+....   ..++..+...|+.++|..+++++.+. .+.+...++.+..++.+.|++++|...+++..+.. .
T Consensus       156 ~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p  231 (291)
T 3mkr_A          156 MQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-S  231 (291)
T ss_dssp             HHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-C
Confidence            76542  443211   12233334446777777777777654 33456667777777777777777777777655431 1


Q ss_pred             CCHhhHHHHHHHHHhcCChHH-HHHHHHHHHH
Q 011378          413 PDVITYNVILTGFCRQGRMHD-SELILWRMIE  443 (487)
Q Consensus       413 p~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~  443 (487)
                      -+..++..++..+...|+.++ +..+++++.+
T Consensus       232 ~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          232 GHPETLINLVVLSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            245566667777777777655 4566666654

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

Probab=99.60  E-value=1.9e-13  Score=129.68  Aligned_cols=265  Identities=9%  Similarity=-0.028  Sum_probs=212.4

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHH
Q 011378          204 DVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLID  283 (487)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~  283 (487)
                      +...|..+...+.+.|+++.|.+.|+++.+.. +.+..+|..+...|...|++++|+..|+...+.. +.+..++..+..
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            45568889999999999999999999998764 3478899999999999999999999999887643 234678999999


Q ss_pred             HHHccCCHHHHHHHHHHHHhCCCCCC-----------hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CChhhHHHH
Q 011378          284 GFCKVGEMEKANKLWADMISRKISPN-----------YISYGILINGYCSMGHVTEAFRLWYEMVGKGIK-PTLVSCNTI  351 (487)
Q Consensus       284 ~~~~~g~~~~a~~~~~~m~~~~~~p~-----------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~~~~l  351 (487)
                      .|...|++++|...+.+.....  |+           ...+..+...+...|++++|...++......-. ++..++..+
T Consensus       142 ~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  219 (365)
T 4eqf_A          142 SYTNTSHQQDACEALKNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGL  219 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC--HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHH
T ss_pred             HHHccccHHHHHHHHHHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHH
Confidence            9999999999999999987632  22           223445678899999999999999998875322 267889999


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCC
Q 011378          352 IKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGR  430 (487)
Q Consensus       352 i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~  430 (487)
                      ...|...|+.++|...+++..+.. +.+..+|..+...|...|++++|...+++..+.  .| +...|..+...|.+.|+
T Consensus       220 ~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~  296 (365)
T 4eqf_A          220 GVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEI--QPGFIRSRYNLGISCINLGA  296 (365)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHCCC
Confidence            999999999999999999988653 235778999999999999999999999988764  34 47789999999999999


Q ss_pred             hHHHHHHHHHHHHcCC---C--------CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          431 MHDSELILWRMIEKGL---N--------PDRSTYTTLINGHVSQNNLKEAFRFHDE  475 (487)
Q Consensus       431 ~~~a~~~~~~m~~~g~---~--------p~~~ty~~l~~~~~~~~~~~~a~~~~~~  475 (487)
                      +++|...+++..+..-   .        .+...|..+..++...|+.+.+.+..++
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            9999999999875321   1        1367899999999999999988877653

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

Probab=99.59  E-value=3e-13  Score=123.79  Aligned_cols=246  Identities=13%  Similarity=0.080  Sum_probs=131.4

Q ss_pred             HhcCChhhHHHHHHHHHhCCCCCCh--hhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhh
Q 011378            6 CKDHKIDSAKMFLCEMEQKGVYPDT--VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDR   83 (487)
Q Consensus         6 ~~~~~~~~a~~~~~~~~~~g~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~   83 (487)
                      .-.|.+..|....+....  ..|+.  ...-.+.+++...|+++.|...++.    .-+|+..++..+...+.+.++.++
T Consensus        10 ~~~g~y~~ai~~~~~~~~--~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~~   83 (291)
T 3mkr_A           10 FYIGSYQQCINEAQRVKP--SSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRDA   83 (291)
T ss_dssp             HHTTCHHHHHHHHHHSCC--CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHHH
T ss_pred             HHHHHHHHHHHHHHhccc--CCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHHH
Confidence            345566666665554432  12332  2334455666666666666654432    123444555555566666666666


Q ss_pred             HHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHH
Q 011378           84 AKEVLDEMLQMGLSPDT-ATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMK  162 (487)
Q Consensus        84 a~~~~~~m~~~g~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  162 (487)
                      |.+.++++...+..|+. ..+..+-..+...|++++|.+.+++      +.+...+..+...+.+.|++++|.+.|+.+.
T Consensus        84 A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~  157 (291)
T 3mkr_A           84 IVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQ  157 (291)
T ss_dssp             HHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            66666666655544433 3333333555666666666666654      3455556666666666666666666666665


Q ss_pred             HCCCCCChhhH---HHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011378          163 SAGLVPDNVLY---TIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPD  239 (487)
Q Consensus       163 ~~g~~~~~~~~---~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~  239 (487)
                      +..  |+....   ...+..+...|+.++|..+++++.+. .+.+...|+.+..++.+.|++++|...|++..+.. +-+
T Consensus       158 ~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~  233 (291)
T 3mkr_A          158 DQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGH  233 (291)
T ss_dssp             HHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC
T ss_pred             hhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCC
Confidence            542  432211   11222333345666666666666554 33455556666666666666666666666655432 224


Q ss_pred             HHHHHHHHHHHHhcCCHHH-HHHHHHHHH
Q 011378          240 FYTFTTLIHGHCKDGNMNK-ALNLFDIMT  267 (487)
Q Consensus       240 ~~t~~~li~~~~~~g~~~~-a~~~~~~m~  267 (487)
                      +.++..++..+...|+.++ +.++++.+.
T Consensus       234 ~~~l~~l~~~~~~~g~~~eaa~~~~~~~~  262 (291)
T 3mkr_A          234 PETLINLVVLSQHLGKPPEVTNRYLSQLK  262 (291)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            5556666666666665543 345555444

>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=99.59  E-value=5.9e-13  Score=123.87  Aligned_cols=276  Identities=11%  Similarity=-0.055  Sum_probs=163.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          172 LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHC  251 (487)
Q Consensus       172 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~  251 (487)
                      .+..+...+.+.|+.++|..++++..+.. +-+...|..+...+.+.|+++.|...|+++.+.. +.+..++..+...|.
T Consensus        23 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~  100 (327)
T 3cv0_A           23 NPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHT  100 (327)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHH
Confidence            34444555555556666655555554432 1234445555555555555555555555554432 223445555555555


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHH--HHHhcCCHHHH
Q 011378          252 KDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILIN--GYCSMGHVTEA  329 (487)
Q Consensus       252 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~--~~~~~~~~~~a  329 (487)
                      ..|++++|...++...+.... +...+..+...                      .|+......+..  .+...|++++|
T Consensus       101 ~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~A  157 (327)
T 3cv0_A          101 NEHNANAALASLRAWLLSQPQ-YEQLGSVNLQA----------------------DVDIDDLNVQSEDFFFAAPNEYREC  157 (327)
T ss_dssp             HTTCHHHHHHHHHHHHHTSTT-TTTC------------------------------------------CCTTSHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHH----------------------HHHHHHHHHHHHhHHHHHcccHHHH
Confidence            555555555555554433111 11111111000                      000000011102  25566677777


Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          330 FRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       330 ~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      ...++...... +.+...+..+...|...|+.++|...+++..+.. +.+...+..+...|...|++++|...+++..+.
T Consensus       158 ~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  235 (327)
T 3cv0_A          158 RTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDI  235 (327)
T ss_dssp             HHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            77777766543 3356677777777788888888888887776542 234567778888888888888888888877653


Q ss_pred             CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-----------CHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          410 GLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-----------DRSTYTTLINGHVSQNNLKEAFRFHDE  475 (487)
Q Consensus       410 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-----------~~~ty~~l~~~~~~~~~~~~a~~~~~~  475 (487)
                      . ..+...|..+...+.+.|++++|...+++.....-..           +...|..+...+...|++++|..++++
T Consensus       236 ~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  311 (327)
T 3cv0_A          236 N-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQ  311 (327)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTC
T ss_pred             C-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            2 2346678888888889999999998888877543221           367888888999999999999888764

>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=99.58  E-value=1.4e-12  Score=121.26  Aligned_cols=277  Identities=9%  Similarity=-0.082  Sum_probs=198.3

Q ss_pred             CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHH
Q 011378          134 DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILN  213 (487)
Q Consensus       134 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~  213 (487)
                      +...+-.....+.+.|++++|..+|+++.+.. +.+...+..+...+.+.|+.++|...+++..+.. +.+...+..+..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~   97 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAV   97 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHH
Confidence            33456677888999999999999999987753 2356788889999999999999999999988753 346678889999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHH--HHHccCCH
Q 011378          214 GLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLID--GFCKVGEM  291 (487)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~--~~~~~g~~  291 (487)
                      .+...|+++.|.+.++++.+... .+...+..+...                      .|+......+-.  .+...|++
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~  154 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQP-QYEQLGSVNLQA----------------------DVDIDDLNVQSEDFFFAAPNEY  154 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTST-TTTTC------------------------------------------CCTTSHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCC-ccHHHHHHHhHH----------------------HHHHHHHHHHHHhHHHHHcccH
Confidence            99999999999999999987531 122222222110                      011111112212  25566777


Q ss_pred             HHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          292 EKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       292 ~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  371 (487)
                      ++|...+.+..... +.+...+..+...+...|++++|...++...... +.+...+..+...+...|+.++|...+++.
T Consensus       155 ~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  232 (327)
T 3cv0_A          155 RECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRA  232 (327)
T ss_dssp             HHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            77777777765432 2256677777778888888888888888776542 335667778888888888888888888887


Q ss_pred             HHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-------------CHhhHHHHHHHHHhcCChHHHHHHH
Q 011378          372 VSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-------------DVITYNVILTGFCRQGRMHDSELIL  438 (487)
Q Consensus       372 ~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-------------~~~~~~~li~~~~~~g~~~~a~~~~  438 (487)
                      .+.. +.+...+..+...|.+.|++++|.+.+++..+.  .|             +...|..+...+.+.|+.++|..++
T Consensus       233 ~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  309 (327)
T 3cv0_A          233 LDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYM--QVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTY  309 (327)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHT
T ss_pred             HHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            6643 234667888888888999999999888877653  23             3678888999999999999998877


Q ss_pred             HH
Q 011378          439 WR  440 (487)
Q Consensus       439 ~~  440 (487)
                      ++
T Consensus       310 ~~  311 (327)
T 3cv0_A          310 AQ  311 (327)
T ss_dssp             TC
T ss_pred             HH
Confidence            64

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

Probab=99.41  E-value=4.4e-11  Score=106.93  Aligned_cols=121  Identities=12%  Similarity=0.002  Sum_probs=64.5

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKA  399 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a  399 (487)
                      +...|++++|...++...... +.+...+..+...+...|+.++|...+++..+.. +.+...+..+...|.+.|++++|
T Consensus       115 ~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A  192 (258)
T 3uq3_A          115 LTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEA  192 (258)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHH
Confidence            333444555555555544321 1123344555555555666666666665555432 12344555666666666666666


Q ss_pred             HHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          400 FALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       400 ~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ...+++..+.. ..+...|..+...+.+.|++++|...+++..+
T Consensus       193 ~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  235 (258)
T 3uq3_A          193 IADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDAART  235 (258)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            66666554431 22345566666666666666666666666543

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

Probab=99.41  E-value=7.5e-11  Score=105.41  Aligned_cols=224  Identities=12%  Similarity=0.100  Sum_probs=164.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCC--CCCC----hhhHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRK--ISPN----YISYGI  315 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~--~~p~----~~t~~~  315 (487)
                      .+..+-..+...|++++|+..|+...+..  .+...+..+...+...|++++|...+.+.....  ..|+    ...+..
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            44555555666666666666666555544  445556666666666666666666666554321  1112    467777


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCC
Q 011378          316 LINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREEN  395 (487)
Q Consensus       316 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~  395 (487)
                      +...+...|++++|...|+.....  .|+.       ..+...|+.++|...++...... +.+...+..+...|...|+
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            888888888888888888887664  3442       34667788999999999988742 1235578888899999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          396 MDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDE  475 (487)
Q Consensus       396 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~  475 (487)
                      +++|...+++..+.. ..+...|..+...|.+.|++++|...+++..+.. ..+...|..+...|...|++++|...+++
T Consensus       155 ~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  232 (258)
T 3uq3_A          155 WPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDA  232 (258)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            999999999887643 3357789999999999999999999999988753 23477889999999999999999999998


Q ss_pred             HHHC
Q 011378          476 MLQR  479 (487)
Q Consensus       476 m~~~  479 (487)
                      ..+.
T Consensus       233 a~~~  236 (258)
T 3uq3_A          233 ARTK  236 (258)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            7653

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.38  E-value=1.4e-09  Score=106.65  Aligned_cols=199  Identities=13%  Similarity=-0.000  Sum_probs=90.2

Q ss_pred             cchHHHHHHHHhcCChhhHHHHHHHHHHC-----C---CCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHC----C--C
Q 011378           66 FTYNSLINGLCKKGRCDRAKEVLDEMLQM-----G---LSPDTATYNTLLVESCRKENMSEAEEIFCEMSRR----G--V  131 (487)
Q Consensus        66 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----g---~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----g--~  131 (487)
                      ..||.+-..+...|++++|++.|++..+.     +   ......+|+.+-..|...|++++|...+++..+.    .  .
T Consensus        52 ~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~  131 (472)
T 4g1t_A           52 TMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPY  131 (472)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSS
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccccc
Confidence            34555555555556666665555543321     0   1112345555555666666666666555544321    0  0


Q ss_pred             CC-CHhHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCCCCh-hhHHHHHHH---HHhcCCHHHHHHHHHHHHHcCCcCC
Q 011378          132 AP-DIVSFSTLIGIFSR--NGQLDRALMYFREMKSAGLVPDN-VLYTIIING---YCRNGFVLEALKMRDEMLEKGCVMD  204 (487)
Q Consensus       132 ~p-~~~~~~~li~~~~~--~g~~~~a~~~~~~m~~~g~~~~~-~~~~~ll~~---~~~~~~~~~a~~~~~~m~~~g~~~~  204 (487)
                      .+ ...+++..-.++.+  .+++++|.+.|++..+.  .|+. ..+..+..+   +...+..++|++.+++..+.. +.+
T Consensus       132 ~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~--~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~  208 (472)
T 4g1t_A          132 RIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK--KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDN  208 (472)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSC
T ss_pred             chhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-Ccc
Confidence            11 12233333333332  23456666666655542  2332 222222222   223344455555555444321 112


Q ss_pred             hhhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          205 VVTYNTILNGLCR----AKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       205 ~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      ...+..+...+..    .++++.|.+.+++..... +.+...+..+-..|...|+.++|+..|+...+
T Consensus       209 ~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  275 (472)
T 4g1t_A          209 QYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALE  275 (472)
T ss_dssp             HHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence            2333333333322    345556666666555432 23445566666666666666666666665543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.37  E-value=2.5e-09  Score=104.88  Aligned_cols=391  Identities=14%  Similarity=0.018  Sum_probs=228.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHhh-----CC--CCC-CccchHHHHHHHHhcCChhhHHHHHHHHHHC----C
Q 011378           28 PDTVTYNTLINAYCREGFLEEAFQLMNSMSG-----KG--LKP-GVFTYNSLINGLCKKGRCDRAKEVLDEMLQM----G   95 (487)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-----~~--~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g   95 (487)
                      .....||.+-..+...|+.++|++.|+.-.+     .+  ..| ...+|+.+-..|...|++++|...+++..+.    .
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            3456789999999999999999999976432     11  123 3467889999999999999999999876542    1


Q ss_pred             --CCC-CHHHHHHHHHHHHc--cCChhHHHHHHHHHHHCCCCCC-HhHHHHHHHH---HHhCCCHHHHHHHHHHHHHCCC
Q 011378           96 --LSP-DTATYNTLLVESCR--KENMSEAEEIFCEMSRRGVAPD-IVSFSTLIGI---FSRNGQLDRALMYFREMKSAGL  166 (487)
Q Consensus        96 --~~~-~~~~~~~ll~~~~~--~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~---~~~~g~~~~a~~~~~~m~~~g~  166 (487)
                        ..+ ...+++..-.++.+  .+++++|.+.|++..+.  .|+ ...+..+..+   +...++.++|++.+++..+.  
T Consensus       129 ~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~--~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l--  204 (472)
T 4g1t_A          129 SPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK--KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRL--  204 (472)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHH--
T ss_pred             cccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhc--
Confidence              112 24455555444443  45799999999998764  343 3344444333   45567888899888887664  


Q ss_pred             CCC-hhhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH
Q 011378          167 VPD-NVLYTIIINGYCR----NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFY  241 (487)
Q Consensus       167 ~~~-~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  241 (487)
                      .|+ ...+..+...+.+    .+..++|.+.+++..... +.+...+..+...|.+.|+++.|...+++..+.. +-+..
T Consensus       205 ~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~  282 (472)
T 4g1t_A          205 NPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAY  282 (472)
T ss_dssp             CSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHH
T ss_pred             CCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHH
Confidence            343 4455555555554    456778888888776643 3456678899999999999999999999988753 22455


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYC  321 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~  321 (487)
                      ++..+-..|...+....         ... .......      ....+..+.|...+....... +.+..++..+-..+.
T Consensus       283 ~~~~lg~~y~~~~~~~~---------~~~-~~~~~~~------~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~  345 (472)
T 4g1t_A          283 LHCQIGCCYRAKVFQVM---------NLR-ENGMYGK------RKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHA  345 (472)
T ss_dssp             HHHHHHHHHHHHHHHHH---------HC-------CH------HHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhh---------hHH-HHHHHHH------HHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHH
Confidence            66665554432211100         000 0000011      111223566777776655432 234456777778888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCChh--hHHHHHH-HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHH
Q 011378          322 SMGHVTEAFRLWYEMVGKGIKPTLV--SCNTIIK-GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDK  398 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~~~~~~~~--~~~~li~-~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~  398 (487)
                      ..|++++|...|+........+...  .+..+-. .....|+.++|...+++..+  +.|+.......         .+.
T Consensus       346 ~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~--i~~~~~~~~~~---------~~~  414 (472)
T 4g1t_A          346 LADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK--INQKSREKEKM---------KDK  414 (472)
T ss_dssp             HTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH--SCCCCHHHHHH---------HHH
T ss_pred             HhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh--cCcccHHHHHH---------HHH
Confidence            8888888888888776654333221  1222211 23456888888888887765  34554332222         233


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCCHHHH
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKG-LNPDRSTY  453 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~ty  453 (487)
                      +.+++++..+.. ..+..+|+.+-..|...|++++|...|++..+.| ..|+..+|
T Consensus       415 l~~~~~~~l~~~-p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          415 LQKIAKMRLSKN-GADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHHHHHHHHHHC-C-CTTHHHHHHHHHHHHHHCC----------------------
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence            344444433321 3456788888888999999999999999887653 34665554

>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=99.37  E-value=1.7e-09  Score=97.77  Aligned_cols=223  Identities=13%  Similarity=0.001  Sum_probs=153.3

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCeeehH
Q 011378          204 DVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCK----DGNMNKALNLFDIMTQKSIKPDIVTYN  279 (487)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~  279 (487)
                      +...+..+-..+.+.|+++.|.+.|++..+.   -+...+..+-..|..    .++.++|+..|+...+.+   +...+.
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            4456667777777888888888888887763   245667777777777    888888888887776654   455666


Q ss_pred             HHHHHHHc----cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCChhhHHHH
Q 011378          280 TLIDGFCK----VGEMEKANKLWADMISRKISPNYISYGILINGYCS----MGHVTEAFRLWYEMVGKGIKPTLVSCNTI  351 (487)
Q Consensus       280 ~li~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~l  351 (487)
                      .+-..|..    .+++++|...|+.....+   +...+..+-..|..    .+++++|...|+.....+   +...+..+
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            67777777    778888888877776654   55666777777777    777777777777776655   44555566


Q ss_pred             HHHHHh----cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          352 IKGYCR----SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR----EENMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       352 i~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                      -..|..    .++.++|...+++..+.+   +...+..|-..|..    .+++++|...+++..+.+   +...+..+-.
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            666666    677777777777766653   34555566666666    777777777777666543   2455566666


Q ss_pred             HHHh----cCChHHHHHHHHHHHHc
Q 011378          424 GFCR----QGRMHDSELILWRMIEK  444 (487)
Q Consensus       424 ~~~~----~g~~~~a~~~~~~m~~~  444 (487)
                      .|.+    .+++++|...+++..+.
T Consensus       227 ~~~~g~~~~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHHH
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHHc
Confidence            6666    67777777777766554

>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=99.36  E-value=2.2e-09  Score=97.09  Aligned_cols=222  Identities=14%  Similarity=0.034  Sum_probs=138.9

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHh----cCChhhHHHHHHHHHHCCCCCCHHHHH
Q 011378           29 DTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCK----KGRCDRAKEVLDEMLQMGLSPDTATYN  104 (487)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~  104 (487)
                      +..++..+-..+.+.|++++|.+.|+...+.   -+...+..+-..+.+    .+++++|.+.|++..+.+   +...+.
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            4455666667777777777777777776652   234456666666666    777777777777776654   555666


Q ss_pred             HHHHHHHc----cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----CCCHHHHHHHHHHHHHCCCCCChhhHHHH
Q 011378          105 TLLVESCR----KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR----NGQLDRALMYFREMKSAGLVPDNVLYTII  176 (487)
Q Consensus       105 ~ll~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~~~~~~~~~l  176 (487)
                      .+-..+..    .+++++|.+.|++..+.+   +...+..+-..|.+    .+++++|...|++..+.+   +...+..+
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    777777777777776654   45566666666666    777777777777766654   34455555


Q ss_pred             HHHHHh----cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011378          177 INGYCR----NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCR----AKMLTEADDLFNEMLERGVFPDFYTFTTLIH  248 (487)
Q Consensus       177 l~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~  248 (487)
                      -..|.+    .++.++|...+++..+.+   +...+..+-..|..    .++++.|.+.|++..+.+   +...+..+-.
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    666666666666665543   23455555556666    666666666666665543   2444555555


Q ss_pred             HHHh----cCCHHHHHHHHHHHHH
Q 011378          249 GHCK----DGNMNKALNLFDIMTQ  268 (487)
Q Consensus       249 ~~~~----~g~~~~a~~~~~~m~~  268 (487)
                      .|..    .++.++|...|+...+
T Consensus       227 ~~~~g~~~~~~~~~A~~~~~~a~~  250 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQAIENFKKGCK  250 (273)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHH
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHH
Confidence            5555    5666666666655443

>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=99.35  E-value=5.5e-10  Score=99.57  Aligned_cols=197  Identities=11%  Similarity=-0.007  Sum_probs=102.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          243 FTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCS  322 (487)
Q Consensus       243 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~  322 (487)
                      +..+...+...|++++|...|+.+.+.. +.+...+..+...|.+.|++++|.+.+.+..... +.+...+..+...|..
T Consensus        40 ~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~  117 (252)
T 2ho1_A           40 YIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYE  117 (252)
T ss_dssp             HHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHH
Confidence            3444444444455555554444443321 1123344444444555555555555554443321 1234445555555556


Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHH
Q 011378          323 MGHVTEAFRLWYEMVGKGIKP-TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  401 (487)
                      .|++++|...++.....+..| +...+..+...|...|+.++|...+++..+.. +.+...+..+...|...|++++|..
T Consensus       118 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~  196 (252)
T 2ho1_A          118 QKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQ  196 (252)
T ss_dssp             TTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHH
Confidence            666666666666555422333 23445555556666666666666666655432 1234455666666666666666666


Q ss_pred             HHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          402 LVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       402 ~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      .+++..+.. ..+...+..+...+.+.|+.++|...++++.+
T Consensus       197 ~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          197 YYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             HHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            666655431 23444556666666666666666666666654

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

Probab=99.34  E-value=5.3e-10  Score=97.53  Aligned_cols=128  Identities=10%  Similarity=-0.044  Sum_probs=52.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFC  286 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  286 (487)
                      .|..+...+...|+++.|.+.|++..+.. +.+...+..+...|...|+.++|...++...+.. +.+..++..+...+.
T Consensus        10 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~   87 (225)
T 2vq2_A           10 IKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLC   87 (225)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHH
Confidence            34444444445555555555555444321 1233444444444455555555555444443321 112223334444444


Q ss_pred             cc-CCHHHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          287 KV-GEMEKANKLWADMISRKISPN-YISYGILINGYCSMGHVTEAFRLWYEM  336 (487)
Q Consensus       287 ~~-g~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m  336 (487)
                      .. |++++|...+.+....+..|+ ...+..+...+...|++++|...++..
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  139 (225)
T 2vq2_A           88 GRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRS  139 (225)
T ss_dssp             TTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            44 444444444444433111121 233333444444444444444444443

>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=99.33  E-value=4.7e-10  Score=100.03  Aligned_cols=201  Identities=9%  Similarity=-0.047  Sum_probs=169.0

Q ss_pred             eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011378          275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKG  354 (487)
Q Consensus       275 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  354 (487)
                      ...+..+...+...|++++|...|.+..... +.+...+..+...+...|++++|...++...... +.+...+..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH
Confidence            3456777888999999999999999887643 3356788899999999999999999999987653 3467788889999


Q ss_pred             HHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHH
Q 011378          355 YCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHD  433 (487)
Q Consensus       355 ~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~  433 (487)
                      |...|+.++|.+.++++.+.+..| +...+..+...|...|++++|.+.+++..+.. ..+...+..+...+.+.|++++
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHH
Confidence            999999999999999998754556 45678888899999999999999999887643 2357788999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          434 SELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       434 a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      |...+++..+.. ..+...+..+...+...|++++|.++++++.+.
T Consensus       194 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          194 ARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            999999987642 246677888889999999999999999998764

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.33  E-value=1e-09  Score=107.05  Aligned_cols=346  Identities=13%  Similarity=0.051  Sum_probs=185.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCCh---hhHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 011378           36 LINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRC---DRAKEVLDEMLQMGLSPDTATYNTLLVESCR  112 (487)
Q Consensus        36 ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~---~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~  112 (487)
                      +...+.+.|++++|.++|+...+.|.   +..+..+-..+...|+.   ++|.+.|.+..+.    +...+..|-..+..
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g~---~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~~   81 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELGY---SEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLAA   81 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTC---CTGGGTCC--------------------------------CHHHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHHh
Confidence            45566677888888888887766552   22333344444556666   7788887776643    33334444443333


Q ss_pred             cC-----ChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHH---HHHHHHHHHHCCCCCChhhHHHHHHHHHhcC
Q 011378          113 KE-----NMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDR---ALMYFREMKSAGLVPDNVLYTIIINGYCRNG  184 (487)
Q Consensus       113 ~~-----~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~---a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~  184 (487)
                      .+     +.++|...|++..+.|...   .+..|-..|...+..+.   +.+.+......|.   ...+..|-..|...+
T Consensus        82 ~~~~~~~~~~~A~~~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~Lg~~y~~~~  155 (452)
T 3e4b_A           82 KPGATEAEHHEAESLLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGY---PEAGLAQVLLYRTQG  155 (452)
T ss_dssp             C--CCHHHHHHHHHHHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTC---TTHHHHHHHHHHHHT
T ss_pred             CCCCCCcCHHHHHHHHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCC
Confidence            33     6778888888877765432   45556666665554333   3344444333332   334555556666666


Q ss_pred             CHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc----CCHH
Q 011378          185 FVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAK---MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD----GNMN  257 (487)
Q Consensus       185 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~----g~~~  257 (487)
                      .++++......+.+.-...++..+..+-..|.+.|   +.++|.+.|++..+.| .++...+..+-..|...    ++.+
T Consensus       156 ~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~~  234 (452)
T 3e4b_A          156 TYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDEK  234 (452)
T ss_dssp             CGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCHH
T ss_pred             CcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCHH
Confidence            55444444333333222233447777777777777   7778888888777766 34444445555555444    6788


Q ss_pred             HHHHHHHHHHHCCCCCCeeehHHHHHH-H--HccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC-----CHHHH
Q 011378          258 KALNLFDIMTQKSIKPDIVTYNTLIDG-F--CKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMG-----HVTEA  329 (487)
Q Consensus       258 ~a~~~~~~m~~~~~~~~~~~~~~li~~-~--~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~-----~~~~a  329 (487)
                      +|+..|+...    +-+...+..|-.. |  ...++.++|.+.|++....|   +...+..|-..|. .|     ++++|
T Consensus       235 ~A~~~~~~aa----~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A  306 (452)
T 3e4b_A          235 TAQALLEKIA----PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAA  306 (452)
T ss_dssp             HHHHHHHHHG----GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHH
T ss_pred             HHHHHHHHHc----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHH
Confidence            8888887765    2233444444444 2  45777888888887776655   4555555555555 44     77777


Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHh----cCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc----cCCHHHHHH
Q 011378          330 FRLWYEMVGKGIKPTLVSCNTIIKGYCR----SGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR----EENMDKAFA  401 (487)
Q Consensus       330 ~~~~~~m~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~  401 (487)
                      ...|+.-.    .-+......|-..|..    ..+.++|...+++..+.|.   ......|-..|..    ..+.++|..
T Consensus       307 ~~~~~~Aa----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~---~~A~~~Lg~~y~~G~g~~~d~~~A~~  379 (452)
T 3e4b_A          307 EAHFEKAV----GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ---NSADFAIAQLFSQGKGTKPDPLNAYV  379 (452)
T ss_dssp             HHHHHTTT----TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC---TTHHHHHHHHHHSCTTBCCCHHHHHH
T ss_pred             HHHHHHHh----CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh---HHHHHHHHHHHHhCCCCCCCHHHHHH
Confidence            77776654    3344455555545544    2377777777777776653   2223334444432    456777777


Q ss_pred             HHHHHHhCC
Q 011378          402 LVSKMENQG  410 (487)
Q Consensus       402 ~~~~m~~~g  410 (487)
                      .+++-.+.|
T Consensus       380 ~~~~A~~~g  388 (452)
T 3e4b_A          380 FSQLAKAQD  388 (452)
T ss_dssp             HHHHHHTTC
T ss_pred             HHHHHHHCC
Confidence            777766655

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

Probab=99.32  E-value=1.2e-09  Score=95.29  Aligned_cols=211  Identities=9%  Similarity=-0.001  Sum_probs=140.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          239 DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILIN  318 (487)
Q Consensus       239 ~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~  318 (487)
                      +...+..+...+...|++++|...|+...+.. +.+...+..+...|...|++++|...+.+..... +.+..++..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            45667777788888888888888887766532 2235567777777888888888888887766532 234566777777


Q ss_pred             HHHhc-CCHHHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCH
Q 011378          319 GYCSM-GHVTEAFRLWYEMVGKGIKPT-LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENM  396 (487)
Q Consensus       319 ~~~~~-~~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~  396 (487)
                      .+... |++++|...++.....+..|+ ...+..+...+...|+.++|...++++.+.. +.+...+..+...|.+.|++
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            77777 888888888877766333333 4556667777777777777777777766532 12355666777777777777


Q ss_pred             HHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHH
Q 011378          397 DKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYT  454 (487)
Q Consensus       397 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~  454 (487)
                      ++|...+++..+..-..+...+..+...+...|+.+++..+++.+...  .|+...+.
T Consensus       164 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~  219 (225)
T 2vq2_A          164 GDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--FPYSEELQ  219 (225)
T ss_dssp             HHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHH
Confidence            777777776655321134555666666667777777777777766543  34444333

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

Probab=99.31  E-value=1e-10  Score=105.67  Aligned_cols=244  Identities=9%  Similarity=-0.047  Sum_probs=138.7

Q ss_pred             cCCHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHH
Q 011378          218 AKMLTEADDLFNEMLERGVF---PDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKA  294 (487)
Q Consensus       218 ~~~~~~a~~~~~~m~~~~~~---~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a  294 (487)
                      .|+++.|...|+++.+....   .+..++..+...+...|++++|...|+...+.. +.+..++..+...|...|++++|
T Consensus        18 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A   96 (275)
T 1xnf_A           18 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAA   96 (275)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHH
Confidence            34555666666655543211   123455555556666666666666665554432 11344555566666666666666


Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 011378          295 NKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSE  374 (487)
Q Consensus       295 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  374 (487)
                      .+.|.+..... +.+...+..+...|...|++++|...++.....  .|+.......+..+...|+.++|...+++....
T Consensus        97 ~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  173 (275)
T 1xnf_A           97 YEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  173 (275)
T ss_dssp             HHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            66666555431 123456666666677777777777777666543  344333444444445567777777777665543


Q ss_pred             CCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC-----HhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 011378          375 GVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPD-----VITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD  449 (487)
Q Consensus       375 g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  449 (487)
                      . +++...+ .+...+...++.++|...+++..+.  .|+     ...|..+...|.+.|++++|...+++....  .|+
T Consensus       174 ~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~  247 (275)
T 1xnf_A          174 S-DKEQWGW-NIVEFYLGNISEQTLMERLKADATD--NTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVH  247 (275)
T ss_dssp             S-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCS--HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCT
T ss_pred             C-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcc--cccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--Cch
Confidence            2 2333333 3566666677777777777665432  221     466777778888888888888888887654  342


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHH
Q 011378          450 RSTYTTLINGHVSQNNLKEAFRFH  473 (487)
Q Consensus       450 ~~ty~~l~~~~~~~~~~~~a~~~~  473 (487)
                      .  +.....++...|++++|++-+
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            2  233344566667777776654

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

Probab=99.29  E-value=1.9e-10  Score=103.88  Aligned_cols=119  Identities=9%  Similarity=-0.116  Sum_probs=54.5

Q ss_pred             cCChhHHHHHHHHHHHCCCCC---CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHH
Q 011378          113 KENMSEAEEIFCEMSRRGVAP---DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEA  189 (487)
Q Consensus       113 ~~~~~~a~~~~~~m~~~g~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  189 (487)
                      .+++++|...++++.+.....   +...+..+...+...|++++|...|++..+.. +.+...|..+...+.+.|+.++|
T Consensus        18 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A   96 (275)
T 1xnf_A           18 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAA   96 (275)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHH
Confidence            345555555555555432111   23344445555555555555555555554421 11234444444445555555555


Q ss_pred             HHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          190 LKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       190 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (487)
                      .+.+++..+.. +.+...|..+...|.+.|++++|.+.|+++.+
T Consensus        97 ~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  139 (275)
T 1xnf_A           97 YEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  139 (275)
T ss_dssp             HHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            55544444321 11233444444444444444444444444443

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

Probab=99.27  E-value=7.7e-10  Score=96.39  Aligned_cols=111  Identities=16%  Similarity=0.040  Sum_probs=47.0

Q ss_pred             CCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          149 GQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDL  227 (487)
Q Consensus       149 g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~  227 (487)
                      |++++|...|++..+.  .|+ ...|..+-..+...|+.++|...+++..+..  .+...+..+-..|...|++++|...
T Consensus        98 g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~  173 (217)
T 2pl2_A           98 GYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQ  173 (217)
T ss_dssp             HHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHH
Confidence            5555555555554432  222 3344444444555555555555555544443  3444445555555555555555555


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          228 FNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFD  264 (487)
Q Consensus       228 ~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~  264 (487)
                      |++..+.. +-+...+..+...+...|+.++|+..|+
T Consensus       174 ~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~  209 (217)
T 2pl2_A          174 YAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAA  209 (217)
T ss_dssp             HHHHHHHS-TTCHHHHHHHHHHHTC------------
T ss_pred             HHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHH
Confidence            55544421 1234444445555555555555554444

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

Probab=99.27  E-value=1.6e-09  Score=97.78  Aligned_cols=128  Identities=13%  Similarity=0.119  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCe--eehHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDI--VTYNTLIDGF  285 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~--~~~~~li~~~  285 (487)
                      +-.....+.+.|+++.|...|++..+.. +.+...+..+...|...|++++|+..++...+..-.|+.  ..|..+-..+
T Consensus         6 ~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~   84 (272)
T 3u4t_A            6 EFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKIL   84 (272)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHH
Confidence            3344445555566666666665555432 112334555555555555555555555555442211111  1144455555


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          286 CKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMV  337 (487)
Q Consensus       286 ~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~  337 (487)
                      ...|++++|...|....... +.+...+..+...|...|++++|...++...
T Consensus        85 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al  135 (272)
T 3u4t_A           85 MKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQI  135 (272)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGC
T ss_pred             HHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            55555555555555544321 1123344445555555555555555554443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.25  E-value=4e-09  Score=102.77  Aligned_cols=378  Identities=12%  Similarity=0.051  Sum_probs=234.5

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh---hHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh
Q 011378           71 LINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENM---SEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR  147 (487)
Q Consensus        71 li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~---~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  147 (487)
                      +-..+.+.|++++|.+.|.+..+.|. ++.  +..|-..+...|+.   ++|.+.|++..+.    +...+..+-..+..
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g~-~~A--~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~~   81 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELGY-SEA--QVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLAA   81 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTC-CTG--GGTCC--------------------------------CHHHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCC-HHH--HHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHHh
Confidence            45566788999999999999887763 222  22333334445666   8999999888754    44455566664555


Q ss_pred             CC-----CHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHH---HHHHHHHHHHHcCCcCChhhHHHHHHHHHhcC
Q 011378          148 NG-----QLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVL---EALKMRDEMLEKGCVMDVVTYNTILNGLCRAK  219 (487)
Q Consensus       148 ~g-----~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~---~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~  219 (487)
                      .+     ++++|...|++....|...   .+..|-..|...+...   ++.+.+....+.|.   ...+..+-..|...+
T Consensus        82 ~~~~~~~~~~~A~~~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~Lg~~y~~~~  155 (452)
T 3e4b_A           82 KPGATEAEHHEAESLLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGY---PEAGLAQVLLYRTQG  155 (452)
T ss_dssp             C--CCHHHHHHHHHHHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTC---TTHHHHHHHHHHHHT
T ss_pred             CCCCCCcCHHHHHHHHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCC
Confidence            55     7889999999998866432   5666666666655433   44555555555544   456667777777777


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc----CCHH
Q 011378          220 MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDG---NMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV----GEME  292 (487)
Q Consensus       220 ~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g---~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~----g~~~  292 (487)
                      .++.+..-.....+.-...++..+..+-..|...|   +.++|+..|+...+.|-. +...+..|-..|...    ++.+
T Consensus       156 ~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~-~a~~~~~Lg~~y~~g~~~~~d~~  234 (452)
T 3e4b_A          156 TYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTV-TAQRVDSVARVLGDATLGTPDEK  234 (452)
T ss_dssp             CGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCS-CHHHHHHHHHHHTCGGGSSCCHH
T ss_pred             CcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHhCCCCCCCCHH
Confidence            55544444333322212223347788888888899   899999999988776632 333334566666544    7999


Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHH-H--HhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC-----ChHHH
Q 011378          293 KANKLWADMISRKISPNYISYGILING-Y--CSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG-----DASKA  364 (487)
Q Consensus       293 ~a~~~~~~m~~~~~~p~~~t~~~li~~-~--~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~-----~~~~a  364 (487)
                      +|.+.|+... .   -+...+..|-.. +  ...+++++|...|+.-...|   +...+..|-..|. .|     +.++|
T Consensus       235 ~A~~~~~~aa-~---g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A  306 (452)
T 3e4b_A          235 TAQALLEKIA-P---GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAA  306 (452)
T ss_dssp             HHHHHHHHHG-G---GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHH
T ss_pred             HHHHHHHHHc-C---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHH
Confidence            9999999876 3   344555555555 3  45899999999999988877   5566666666665 45     99999


Q ss_pred             HHHHHHHHHCCCCCChhhHHHHHHHHhc----cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh----cCChHHHHH
Q 011378          365 DEFLSKMVSEGVDPDSISYNTLINGFVR----EENMDKAFALVSKMENQGLVPDVITYNVILTGFCR----QGRMHDSEL  436 (487)
Q Consensus       365 ~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~  436 (487)
                      ...+++.. .   -+...+..|-..|..    ..+.++|...+++-.+.|.   ......|-..|..    ..+..+|..
T Consensus       307 ~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~---~~A~~~Lg~~y~~G~g~~~d~~~A~~  379 (452)
T 3e4b_A          307 EAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ---NSADFAIAQLFSQGKGTKPDPLNAYV  379 (452)
T ss_dssp             HHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC---TTHHHHHHHHHHSCTTBCCCHHHHHH
T ss_pred             HHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh---HHHHHHHHHHHHhCCCCCCCHHHHHH
Confidence            99999877 3   345556666666655    4599999999999888763   3344445445542    568999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          437 ILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       437 ~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      .++...+.|........ ..+......++.++|.++.++.++
T Consensus       380 ~~~~A~~~g~~~a~~~l-~~l~~~~~~~~~~~a~~~~~~~~~  420 (452)
T 3e4b_A          380 FSQLAKAQDTPEANDLA-TQLEAPLTPAQRAEGQRLVQQELA  420 (452)
T ss_dssp             HHHHHHTTCCHHHHHHH-HHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHH-HHHHHhCCHHHHHHHHHHHHHHHH
Confidence            99998887753322222 223333445567788888777654

>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=99.25  E-value=2.1e-07  Score=94.24  Aligned_cols=217  Identities=11%  Similarity=0.001  Sum_probs=135.2

Q ss_pred             HHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHH-HHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          259 ALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKAN-KLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMV  337 (487)
Q Consensus       259 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~-~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~  337 (487)
                      ...+|+..... .+-+...|-.....+...|+.++|. +++..... .++.+...|-..+...-+.|++++|..+|+...
T Consensus       328 v~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~-~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l  405 (679)
T 4e6h_A          328 MTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQ-CIPNSAVLAFSLSEQYELNTKIPEIETTILSCI  405 (679)
T ss_dssp             HHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHH-HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-hCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            34455544432 1223445555556666667777775 77777654 333455556666677777788888888887766


Q ss_pred             hCC---------CCCC------------hhhHHHHHHHHHhcCChHHHHHHHHHHHHC-C-CCCChhhHHHHHHHHhccC
Q 011378          338 GKG---------IKPT------------LVSCNTIIKGYCRSGDASKADEFLSKMVSE-G-VDPDSISYNTLINGFVREE  394 (487)
Q Consensus       338 ~~~---------~~~~------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g-~~p~~~~~~~li~~~~~~~  394 (487)
                      ...         -.|+            ..+|...++...+.|+.+.|..+|....+. + ..+......+.+.-.. .+
T Consensus       406 ~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~  484 (679)
T 4e6h_A          406 DRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SK  484 (679)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TS
T ss_pred             HHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CC
Confidence            431         0131            235767777777778888888888887765 2 2233333333333221 34


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCCHHHHHHH
Q 011378          395 NMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP--DRSTYTTLINGHVSQNNLKEAFRF  472 (487)
Q Consensus       395 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~ty~~l~~~~~~~~~~~~a~~~  472 (487)
                      +.+.|.++|+...+. ..-+...|...+......|+.+.|+.+|++.......|  ....|..+++.-...|+.+.+.++
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            578888888776554 22344556677777777888888888888776543322  235777778877888888888888


Q ss_pred             HHHHHHC
Q 011378          473 HDEMLQR  479 (487)
Q Consensus       473 ~~~m~~~  479 (487)
                      .+++.+.
T Consensus       564 ~~R~~~~  570 (679)
T 4e6h_A          564 EKRFFEK  570 (679)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            8887653

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

Probab=99.25  E-value=7.2e-10  Score=96.56  Aligned_cols=90  Identities=13%  Similarity=0.018  Sum_probs=33.9

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGH  460 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~  460 (487)
                      .+..+-..|...|++++|...+++..+..  .+...+..+...+...|++++|...+++..+.  .| +...+..+...+
T Consensus       120 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~la~~~  195 (217)
T 2pl2_A          120 LHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQ--APKDLDLRVRYASAL  195 (217)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHH
Confidence            34444444444444444444444443333  33444444444444444444444444444432  12 233444444444


Q ss_pred             HhcCCHHHHHHHHHH
Q 011378          461 VSQNNLKEAFRFHDE  475 (487)
Q Consensus       461 ~~~~~~~~a~~~~~~  475 (487)
                      ...|++++|...+++
T Consensus       196 ~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          196 LLKGKAEEAARAAAL  210 (217)
T ss_dssp             TC-------------
T ss_pred             HHccCHHHHHHHHHH
Confidence            444555555444443

>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=99.24  E-value=3.3e-07  Score=92.78  Aligned_cols=438  Identities=10%  Similarity=0.087  Sum_probs=283.5

Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCC---hhhHHHHHHH
Q 011378           14 AKMFLCEMEQKGVYPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGR---CDRAKEVLDE   90 (487)
Q Consensus        14 a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~---~~~a~~~~~~   90 (487)
                      ...+-..+.+..  -|..+|..++..+.+.+.++.+..+|+.+... ++.+...|...+..-.+.++   ++.+.++|++
T Consensus        52 i~~lE~~l~~np--~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeR  128 (679)
T 4e6h_A           52 IGKLNDMIEEQP--TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLAR  128 (679)
T ss_dssp             HHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCc--CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHH
Confidence            334444455542  48889999999999999999999999998764 34455678888888888888   9999999999


Q ss_pred             HHHCC-CCCCHHHHHHHHHHHHccCCh--------hHHHHHHHHHHH-CCC-CCC-HhHHHHHHHHHHh---------CC
Q 011378           91 MLQMG-LSPDTATYNTLLVESCRKENM--------SEAEEIFCEMSR-RGV-APD-IVSFSTLIGIFSR---------NG  149 (487)
Q Consensus        91 m~~~g-~~~~~~~~~~ll~~~~~~~~~--------~~a~~~~~~m~~-~g~-~p~-~~~~~~li~~~~~---------~g  149 (487)
                      ..... ..|+...|...+.-..+.++.        +.+.++|+.... .|. .|+ ...|...+....+         .+
T Consensus       129 al~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~  208 (679)
T 4e6h_A          129 CLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQ  208 (679)
T ss_dssp             HTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHH
T ss_pred             HHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHh
Confidence            87653 248888888887766555543        334477776543 466 553 4567777665432         34


Q ss_pred             CHHHHHHHHHHHHHCCCCCChhhH---HHHHHHHHh----------cCCHHHHHHHHHHHHH--cCCc---CC-------
Q 011378          150 QLDRALMYFREMKSAGLVPDNVLY---TIIINGYCR----------NGFVLEALKMRDEMLE--KGCV---MD-------  204 (487)
Q Consensus       150 ~~~~a~~~~~~m~~~g~~~~~~~~---~~ll~~~~~----------~~~~~~a~~~~~~m~~--~g~~---~~-------  204 (487)
                      +++.+..+|..........-..+|   ..+.+....          ...++.|...+.++..  .++.   |.       
T Consensus       209 ~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~  288 (679)
T 4e6h_A          209 RVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATE  288 (679)
T ss_dssp             HHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCT
T ss_pred             HHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchh
Confidence            577888999988753221112233   222222100          0112223333333321  1211   10       


Q ss_pred             -------------hhhHHHHHHHHHhcC-------CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHH-HHH
Q 011378          205 -------------VVTYNTILNGLCRAK-------MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKAL-NLF  263 (487)
Q Consensus       205 -------------~~~~~~li~~~~~~~-------~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~-~~~  263 (487)
                                   ...|...+.---..+       ..+.+..+|++.... ++-+...|-....-+...|+.++|. .+|
T Consensus       289 ~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il  367 (679)
T 4e6h_A          289 SNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYL  367 (679)
T ss_dssp             TTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHH
T ss_pred             ccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence                         123444444322222       123455677777654 3346777888888888889999997 999


Q ss_pred             HHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCC---------CCCC------------hhhHHHHHHHHHh
Q 011378          264 DIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRK---------ISPN------------YISYGILINGYCS  322 (487)
Q Consensus       264 ~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~---------~~p~------------~~t~~~li~~~~~  322 (487)
                      +.... .++.+...|-..+...-+.|+++.|.++|.......         ..|+            ...|...+....+
T Consensus       368 ~rAi~-~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR  446 (679)
T 4e6h_A          368 KLGQQ-CIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKR  446 (679)
T ss_dssp             HHHHH-HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH-hCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHH
Confidence            88765 233455556777888888999999999999887531         0132            2357777887788


Q ss_pred             cCCHHHHHHHHHHHHhC-C-CCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHH
Q 011378          323 MGHVTEAFRLWYEMVGK-G-IKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAF  400 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~-~-~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~  400 (487)
                      .|..+.|..+|....+. + ..+......+.+.-. ..++.+.|..+|+...+. .+-+...+...+.-....|+.+.|.
T Consensus       447 ~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~-~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR  524 (679)
T 4e6h_A          447 IQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYH-ISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVK  524 (679)
T ss_dssp             HHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHT-TTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHH
Confidence            89999999999998765 2 222233322333221 235589999999988765 3334556667777777889999999


Q ss_pred             HHHHHHHhCCCCC--CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011378          401 ALVSKMENQGLVP--DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGH  460 (487)
Q Consensus       401 ~~~~~m~~~g~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~  460 (487)
                      .+|++.....-.+  ....|...+..=.+.|..+.+.++.+++.+.  .|+......+++-|
T Consensus       525 ~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~--~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          525 SLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK--FPEVNKLEEFTNKY  584 (679)
T ss_dssp             HHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--STTCCHHHHHHHHT
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCcHHHHHHHHh
Confidence            9999886653211  3457888888889999999999999999875  34444444444443

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

Probab=99.23  E-value=1.1e-09  Score=96.84  Aligned_cols=200  Identities=15%  Similarity=0.108  Sum_probs=113.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          239 DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILIN  318 (487)
Q Consensus       239 ~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~  318 (487)
                      ...+|..+...+...|++++|...|+...+.. +.+...+..+...+.+.|++++|...+.+..... +.+...+..+..
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   99 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGN   99 (243)
T ss_dssp             --------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHH
Confidence            44556666667777777777777777665422 2234566666677777777777777777665432 224556666677


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHH
Q 011378          319 GYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDK  398 (487)
Q Consensus       319 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~  398 (487)
                      .+...|++++|...++...+.. +.+...+..+...+...|+.++|...+++..+.. +.+...+..+...|.+.|++++
T Consensus       100 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A          100 VYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHH
Confidence            7777777777777777665543 3345566666666777777777777777665432 1245566666666777777777


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      |...+++..+.. ..+...|..+...|.+.|++++|...+++..+
T Consensus       178 A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  221 (243)
T 2q7f_A          178 ALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAID  221 (243)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHc
Confidence            777776665432 22355666666677777777777777776655

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

Probab=99.21  E-value=4.1e-09  Score=95.01  Aligned_cols=159  Identities=12%  Similarity=0.056  Sum_probs=75.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHh
Q 011378          175 IIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFP--DFYTFTTLIHGHCK  252 (487)
Q Consensus       175 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~--~~~t~~~li~~~~~  252 (487)
                      ..-..+.+.|+.++|...+++..+.. +-+...|..+...|.+.|++++|...+++..+..-.|  ....|..+-..+..
T Consensus         8 ~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~   86 (272)
T 3u4t_A            8 RYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMK   86 (272)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHH
Confidence            34444555556666665555555432 1123355555555555566666666655555422111  12235555555555


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHH
Q 011378          253 DGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFR  331 (487)
Q Consensus       253 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~  331 (487)
                      .|++++|+..|+...+.. +.+..++..+-..|...|++++|...|.+....  .| +...|..+...+...+++++|..
T Consensus        87 ~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~~A~~  163 (272)
T 3u4t_A           87 KGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP--TTTDPKVFYELGQAYYYNKEYVKADS  163 (272)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS--SCCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc--CCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence            566666665555544321 112345555555555566666665555544332  22 22333333312222334555555


Q ss_pred             HHHHHH
Q 011378          332 LWYEMV  337 (487)
Q Consensus       332 ~~~~m~  337 (487)
                      .|+...
T Consensus       164 ~~~~a~  169 (272)
T 3u4t_A          164 SFVKVL  169 (272)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.19  E-value=3.6e-10  Score=108.74  Aligned_cols=276  Identities=13%  Similarity=0.081  Sum_probs=140.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CCCHHHH
Q 011378          173 YTIIINGYCRNGFVLEALKMRDEMLEKGCVMDV----VTYNTILNGLCRAKMLTEADDLFNEMLER----GV-FPDFYTF  243 (487)
Q Consensus       173 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~-~~~~~t~  243 (487)
                      +..+-..+...|+.++|...+++..+.+.. +.    ..|..+...|...|+++.|.+.+++..+.    +- .....++
T Consensus        51 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  129 (411)
T 4a1s_A           51 LALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSS  129 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHH
Confidence            334455566677777777777766654211 11    34566666666677777777776665432    11 1123445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHC----CCCC-CeeehHHHHHHHHccCC----------HHHHHHHHHHHHhCCCCC
Q 011378          244 TTLIHGHCKDGNMNKALNLFDIMTQK----SIKP-DIVTYNTLIDGFCKVGE----------MEKANKLWADMISRKISP  308 (487)
Q Consensus       244 ~~li~~~~~~g~~~~a~~~~~~m~~~----~~~~-~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~~~p  308 (487)
                      ..+-..|...|++++|...++...+.    +-.| ...++..+-..|...|+          .++|...           
T Consensus       130 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~-----------  198 (411)
T 4a1s_A          130 GNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEA-----------  198 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHH-----------
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHH-----------
Confidence            55556666666666666666544321    1001 12234444444444444          0000000           


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCC-CCC---
Q 011378          309 NYISYGILINGYCSMGHVTEAFRLWYEMVGK----GIKP-TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGV-DPD---  379 (487)
Q Consensus       309 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~---  379 (487)
                                       +++|...+++....    +-.+ ...++..+-..|...|++++|...+++..+..- .++   
T Consensus       199 -----------------~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  261 (411)
T 4a1s_A          199 -----------------LTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAA  261 (411)
T ss_dssp             -----------------HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             -----------------HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHH
Confidence                             44444444332210    1111 122444555555566666666666655443110 011   


Q ss_pred             -hhhHHHHHHHHhccCCHHHHHHHHHHHHhC----CCC-CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-
Q 011378          380 -SISYNTLINGFVREENMDKAFALVSKMENQ----GLV-PDVITYNVILTGFCRQGRMHDSELILWRMIEK----GLNP-  448 (487)
Q Consensus       380 -~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-  448 (487)
                       ..++..+...|...|++++|...+++..+.    +-. ....++..+...|...|++++|...+++....    +-.+ 
T Consensus       262 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  341 (411)
T 4a1s_A          262 ERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIG  341 (411)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHH
Confidence             125556666666677777777666554321    100 01345666666777777777777777765532    1111 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          449 DRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       449 ~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      ...+|..+...|...|++++|...+++..
T Consensus       342 ~~~~~~~la~~~~~~g~~~~A~~~~~~al  370 (411)
T 4a1s_A          342 EARACWSLGNAHSAIGGHERALKYAEQHL  370 (411)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            12366666677777777777777777654

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

Probab=99.18  E-value=2.7e-09  Score=94.31  Aligned_cols=195  Identities=14%  Similarity=0.091  Sum_probs=78.6

Q ss_pred             hHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh
Q 011378           68 YNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR  147 (487)
Q Consensus        68 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  147 (487)
                      |..+-..+.+.|++++|...|++..+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..+...+.+
T Consensus        26 ~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~  103 (243)
T 2q7f_A           26 GGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVV  103 (243)
T ss_dssp             ----------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHH
Confidence            3334444444455555555554444321 1223344444444444455555555554444331 1133444444455555


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          148 NGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDL  227 (487)
Q Consensus       148 ~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~  227 (487)
                      .|++++|.+.+++..+.. ..+...+..+...+.+.|+.++|...+++..+.. +.+...+..+...+.+.|+++.|.+.
T Consensus       104 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~  181 (243)
T 2q7f_A          104 KEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEALSQ  181 (243)
T ss_dssp             TTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            555555555555544322 1123344444444444444444444444443321 11233444444444555555555555


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          228 FNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMT  267 (487)
Q Consensus       228 ~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~  267 (487)
                      |++..+.. +.+..++..+...|...|+.++|...++...
T Consensus       182 ~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  220 (243)
T 2q7f_A          182 FAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAI  220 (243)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHH
T ss_pred             HHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            55444331 1233444444444555555555555544443

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.16  E-value=9e-10  Score=105.96  Aligned_cols=60  Identities=13%  Similarity=0.092  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CC----eeehHHHHHHHHccCCHHHHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIK-PD----IVTYNTLIDGFCKVGEMEKANKLWADM  301 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-~~----~~~~~~li~~~~~~g~~~~a~~~~~~m  301 (487)
                      ++..+-..|...|++++|+..++...+.... ++    ..++..+...|...|++++|...+.+.
T Consensus       225 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  289 (411)
T 4a1s_A          225 ACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRT  289 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555555666666666666666544321100 00    113444445555555555555555443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.16  E-value=2e-09  Score=103.04  Aligned_cols=91  Identities=19%  Similarity=0.234  Sum_probs=43.4

Q ss_pred             HHHHHHHHhcCChhhHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHccCChhHHHHHHHHHHHC----CCCC-CHhHH
Q 011378           69 NSLINGLCKKGRCDRAKEVLDEMLQMGLSPD-----TATYNTLLVESCRKENMSEAEEIFCEMSRR----GVAP-DIVSF  138 (487)
Q Consensus        69 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~-----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~  138 (487)
                      ...-..+.+.|++++|...|++..+..  |+     ...|..+-..+...|++++|...+++..+.    +-.| ....+
T Consensus        13 ~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   90 (406)
T 3sf4_A           13 ALEGERLCKSGDCRAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKAS   90 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHH
Confidence            333444555666666666666655432  22     234444555555555555555555544321    1111 12234


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHH
Q 011378          139 STLIGIFSRNGQLDRALMYFREM  161 (487)
Q Consensus       139 ~~li~~~~~~g~~~~a~~~~~~m  161 (487)
                      ..+...+...|++++|...+++.
T Consensus        91 ~~la~~~~~~g~~~~A~~~~~~a  113 (406)
T 3sf4_A           91 GNLGNTLKVLGNFDEAIVCCQRH  113 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHH
Confidence            44444555555555555555444

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.16  E-value=9.3e-10  Score=102.18  Aligned_cols=133  Identities=11%  Similarity=0.018  Sum_probs=89.9

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHC----CCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhC----CCCC-CHh
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSE----GVDP-DSISYNTLINGFVREENMDKAFALVSKMENQ----GLVP-DVI  416 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~  416 (487)
                      ++..+-..|...|+.++|...+++..+.    +..+ ...++..+...|...|++++|.+.+++..+.    +-.+ ...
T Consensus       185 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  264 (338)
T 3ro2_A          185 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ  264 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHH
Confidence            5566666777777777777777765532    1111 1236777777788888888888887765431    1111 145


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEK----GLNP-DRSTYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                      ++..+...+...|++++|...+++....    +-.+ ...++..+...|...|++++|...+++..+.
T Consensus       265 ~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          265 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            6777788888899999998888887542    1111 1347777888899999999999999887753

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.14  E-value=1.4e-09  Score=101.04  Aligned_cols=61  Identities=20%  Similarity=0.183  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHC----CCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          348 CNTIIKGYCRSGDASKADEFLSKMVSE----GVDP-DSISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       348 ~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      +..+-..|...|+.++|...+++..+.    +-.+ ...++..+...|.+.|++++|...+++..+
T Consensus       266 ~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  331 (338)
T 3ro2_A          266 CYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  331 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            334444444455555555544443321    1101 122445555556666666666666655543

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.14  E-value=1.6e-09  Score=103.76  Aligned_cols=130  Identities=17%  Similarity=0.142  Sum_probs=70.8

Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhCCC-CCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC-hh
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISRKI-SPN----YISYGILINGYCSMGHVTEAFRLWYEMVGK----GIKPT-LV  346 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~~-~~  346 (487)
                      ++..+-..|...|++++|...+.+...... .++    ..++..+...|...|++++|...++.....    +-.+. ..
T Consensus       189 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  268 (406)
T 3sf4_A          189 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ  268 (406)
T ss_dssp             HHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHH
Confidence            344555555555666666555554432100 011    225556666666667777766666654421    11111 33


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHC----CCCCC-hhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSE----GVDPD-SISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      ++..+-..|...|++++|...+++....    +-.+. ..++..+-..|...|++++|.+.+++.
T Consensus       269 ~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  333 (406)
T 3sf4_A          269 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  333 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            5556666677777777777777665432    11111 345666667777777777777776654

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

Probab=99.13  E-value=5.3e-08  Score=89.69  Aligned_cols=233  Identities=10%  Similarity=-0.012  Sum_probs=139.8

Q ss_pred             hhHHHHHHHHHhc----CCH----HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh-------cCCH-------HHHHHHH
Q 011378          206 VTYNTILNGLCRA----KML----TEADDLFNEMLERGVFPDFYTFTTLIHGHCK-------DGNM-------NKALNLF  263 (487)
Q Consensus       206 ~~~~~li~~~~~~----~~~----~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~-------~g~~-------~~a~~~~  263 (487)
                      ..|...+.---+.    ++.    +.|..+|++..+.. +-++..|..+...+..       .|+.       ++|..+|
T Consensus         9 ~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~   87 (308)
T 2ond_A            9 DMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIY   87 (308)
T ss_dssp             HHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHH
Confidence            4566666554333    132    56667777776532 3355667666666653       4664       7777777


Q ss_pred             HHHHHCCCCCC-eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-h-hHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 011378          264 DIMTQKSIKPD-IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-I-SYGILINGYCSMGHVTEAFRLWYEMVGKG  340 (487)
Q Consensus       264 ~~m~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~-t~~~li~~~~~~~~~~~a~~~~~~m~~~~  340 (487)
                      +...+. +.|+ ...|..+...+.+.|++++|..+|++..+  +.|+. . .|..+...+.+.|++++|..+|+...+..
T Consensus        88 ~rAl~~-~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~  164 (308)
T 2ond_A           88 ERAIST-LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA  164 (308)
T ss_dssp             HHHHTT-TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST
T ss_pred             HHHHHH-hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            766542 2343 34677777777777777777777777665  33432 2 56777777777777777777777766543


Q ss_pred             CCCChhhHHHHHHHH-HhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC-CCCCC--Hh
Q 011378          341 IKPTLVSCNTIIKGY-CRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ-GLVPD--VI  416 (487)
Q Consensus       341 ~~~~~~~~~~li~~~-~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~--~~  416 (487)
                       +++...|....... ...|+.++|..+|+...+.. +-+...|..++..+.+.|+.++|..+|++.... .+.|+  ..
T Consensus       165 -p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~  242 (308)
T 2ond_A          165 -RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGE  242 (308)
T ss_dssp             -TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHH
T ss_pred             -CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHH
Confidence             22333333222221 12577777777777665431 123456666666677777777777777776664 23442  45


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      .|..++....+.|+.++|..+++++.+.
T Consensus       243 l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          243 IWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6666666667777777777777776653

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.12  E-value=1.2e-08  Score=97.11  Aligned_cols=228  Identities=11%  Similarity=-0.010  Sum_probs=115.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc--CCC--C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC----CC-CC-CeeehHH
Q 011378          212 LNGLCRAKMLTEADDLFNEMLER--GVF--P-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQK----SI-KP-DIVTYNT  280 (487)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~--~~~--~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~----~~-~~-~~~~~~~  280 (487)
                      -..+...|+++.|...|++..+.  ...  + ...++..+-..|...|+.+.|+..++...+.    +- .+ ...+++.
T Consensus       110 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  189 (383)
T 3ulq_A          110 GMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSL  189 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHH
Confidence            34456677777777777776542  111  1 2345666777777777777777777654431    10 01 1234555


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhC----CCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CC-CCChhhHHH
Q 011378          281 LIDGFCKVGEMEKANKLWADMISR----KISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGK----GI-KPTLVSCNT  350 (487)
Q Consensus       281 li~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----~~-~~~~~~~~~  350 (487)
                      +-..|...|++++|...+.+....    +-.+ ...++..+-..|...|++++|...+++....    +. +....++..
T Consensus       190 lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  269 (383)
T 3ulq_A          190 FATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFL  269 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHH
Confidence            566666667777766666654421    1011 1124555666666666666666666654431    22 222344555


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHC----CCCCChhhHHHHHHHHhccCC---HHHHHHHHHHHHhCCCCCCH-hhHHHHH
Q 011378          351 IIKGYCRSGDASKADEFLSKMVSE----GVDPDSISYNTLINGFVREEN---MDKAFALVSKMENQGLVPDV-ITYNVIL  422 (487)
Q Consensus       351 li~~~~~~~~~~~a~~~~~~m~~~----g~~p~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~g~~p~~-~~~~~li  422 (487)
                      +-..|.+.|+.++|...+++..+.    +-+.....+..|-..|...|+   +++|..++++.   +..|+. ..+..+.
T Consensus       270 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~la  346 (383)
T 3ulq_A          270 ITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLEDFAIDVA  346 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHHHH
Confidence            556666666666666666554421    111111223444445555555   34444433332   222221 2334444


Q ss_pred             HHHHhcCChHHHHHHHHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~  442 (487)
                      ..|.+.|++++|...+++..
T Consensus       347 ~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          347 KYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHH
Confidence            45555555555555555443

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

Probab=99.11  E-value=8e-08  Score=88.45  Aligned_cols=233  Identities=7%  Similarity=0.026  Sum_probs=164.2

Q ss_pred             hhHHHHHHHHHhc----CCH----HHHHHHHHHHHHcCCcCChhhHHHHHHHHHh-------cCCH-------HHHHHHH
Q 011378          171 VLYTIIINGYCRN----GFV----LEALKMRDEMLEKGCVMDVVTYNTILNGLCR-------AKML-------TEADDLF  228 (487)
Q Consensus       171 ~~~~~ll~~~~~~----~~~----~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~-------~~~~-------~~a~~~~  228 (487)
                      ..|...++.--+.    ++.    .+|...+++.... .+-+...|..+...+..       .|++       ++|..+|
T Consensus         9 ~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~-~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~   87 (308)
T 2ond_A            9 DMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIY   87 (308)
T ss_dssp             HHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHH
Confidence            4566666654443    122    5677777777664 23455677777776653       4775       8888888


Q ss_pred             HHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCee--ehHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 011378          229 NEMLERGVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIV--TYNTLIDGFCKVGEMEKANKLWADMISRK  305 (487)
Q Consensus       229 ~~m~~~~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--~~~~li~~~~~~g~~~~a~~~~~~m~~~~  305 (487)
                      ++..+. +.| +...|..+...+.+.|++++|..+|+...+  +.|+..  .|..+...+.+.|++++|..+|.+.....
T Consensus        88 ~rAl~~-~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~  164 (308)
T 2ond_A           88 ERAIST-LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA  164 (308)
T ss_dssp             HHHHTT-TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST
T ss_pred             HHHHHH-hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            887763 234 556788888888888999999999988776  345432  68888888888889999999988877543


Q ss_pred             CCCChhhHHHHHHHHH-hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCC-CCCC--hh
Q 011378          306 ISPNYISYGILINGYC-SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEG-VDPD--SI  381 (487)
Q Consensus       306 ~~p~~~t~~~li~~~~-~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~--~~  381 (487)
                       +++...|........ ..|+.++|..+|+...+.. +-+...|..+...+.+.|+.++|..+|+...... ..|+  ..
T Consensus       165 -p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~  242 (308)
T 2ond_A          165 -RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGE  242 (308)
T ss_dssp             -TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHH
T ss_pred             -CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHH
Confidence             223344433322222 3688999999888876542 3356778888888888899999999998888763 4553  45


Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      .|..++....+.|+.+.|..++++..+.
T Consensus       243 l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          243 IWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7888888888889999998888887653

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.10  E-value=9.3e-09  Score=97.94  Aligned_cols=160  Identities=11%  Similarity=0.043  Sum_probs=86.0

Q ss_pred             HHHHhCCCHHHHHHHHHHHHHC----CCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----C--CcCChhhHHHH
Q 011378          143 GIFSRNGQLDRALMYFREMKSA----GLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEK----G--CVMDVVTYNTI  211 (487)
Q Consensus       143 ~~~~~~g~~~~a~~~~~~m~~~----g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----g--~~~~~~~~~~l  211 (487)
                      ..+...|++++|...|++..+.    +-.+ ...+|..+-..|...|+.++|...+.+..+.    +  ......+++.+
T Consensus       111 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  190 (383)
T 3ulq_A          111 MYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLF  190 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHH
Confidence            4456667777777777766542    1111 1235566666666666666666666554431    1  01112355666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH----CCC-CCCeeehHHH
Q 011378          212 LNGLCRAKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQ----KSI-KPDIVTYNTL  281 (487)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~----~~~-~~~~~~~~~l  281 (487)
                      -..|...|+++.|.+.|++..+.    +-.+ ...++..+-..|...|++++|+..|+...+    .+- +....++..+
T Consensus       191 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l  270 (383)
T 3ulq_A          191 ATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLI  270 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHH
Confidence            66666777777777766665432    1000 113555666666666666666666655443    122 1223345555


Q ss_pred             HHHHHccCCHHHHHHHHHHHH
Q 011378          282 IDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       282 i~~~~~~g~~~~a~~~~~~m~  302 (487)
                      -..|.+.|++++|...+.+..
T Consensus       271 ~~~~~~~g~~~~A~~~~~~al  291 (383)
T 3ulq_A          271 TQIHYKLGKIDKAHEYHSKGM  291 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHH
Confidence            556666666666666655443

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

Probab=99.09  E-value=2.8e-09  Score=97.94  Aligned_cols=168  Identities=16%  Similarity=0.104  Sum_probs=95.7

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHHc-------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC------CC
Q 011378          205 VVTYNTILNGLCRAKMLTEADDLFNEMLER-------GVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQK------SI  271 (487)
Q Consensus       205 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-------~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~------~~  271 (487)
                      ..++..+...+...|+++.|..+|+++.+.       .......++..+...|...|++++|...++...+.      +-
T Consensus        27 ~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  106 (311)
T 3nf1_A           27 LRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKD  106 (311)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            456777777788888888888888877652       22223456677777777788888888777765432      11


Q ss_pred             CC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhC------CCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----
Q 011378          272 KP-DIVTYNTLIDGFCKVGEMEKANKLWADMISR------KISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGK----  339 (487)
Q Consensus       272 ~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----  339 (487)
                      .| ...++..+...|...|++++|...+.+....      +..| ....+..+...+...|++++|...++.....    
T Consensus       107 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~  186 (311)
T 3nf1_A          107 HPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTK  186 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            11 2345566666666666777766666655432      1112 2234555555555566666666655554432    


Q ss_pred             --CCCC-ChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          340 --GIKP-TLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       340 --~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                        +-.| ...++..+...|...|+.++|...+++..
T Consensus       187 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  222 (311)
T 3nf1_A          187 LGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEIL  222 (311)
T ss_dssp             SCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence              1111 12234444555555555555555555544

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

Probab=99.08  E-value=4.2e-09  Score=96.77  Aligned_cols=169  Identities=17%  Similarity=0.109  Sum_probs=136.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHHc-------CCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc------CC
Q 011378          170 NVLYTIIINGYCRNGFVLEALKMRDEMLEK-------GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLER------GV  236 (487)
Q Consensus       170 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-------g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~  236 (487)
                      ..++..+...+...|+.++|...+++..+.       ..+.....+..+...|...|++++|...+++..+.      +-
T Consensus        27 ~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  106 (311)
T 3nf1_A           27 LRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKD  106 (311)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            457888999999999999999999988763       33445567888999999999999999999998764      22


Q ss_pred             CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC------CCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhC----
Q 011378          237 FP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQK------SIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISR----  304 (487)
Q Consensus       237 ~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~------~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----  304 (487)
                      .| ...++..+...|...|++++|...|+...+.      +-.| ....+..+-..+...|++++|...+.+....    
T Consensus       107 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~  186 (311)
T 3nf1_A          107 HPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTK  186 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            22 4567888999999999999999999877653      2222 3456788889999999999999999988754    


Q ss_pred             --CCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011378          305 --KISP-NYISYGILINGYCSMGHVTEAFRLWYEMVG  338 (487)
Q Consensus       305 --~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  338 (487)
                        +..| ...++..+...|...|++++|...+++...
T Consensus       187 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          187 LGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             SCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              2233 345788899999999999999999998764

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.03  E-value=1.8e-07  Score=88.64  Aligned_cols=297  Identities=12%  Similarity=0.067  Sum_probs=187.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCcCChh----hHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCCH----HHHHH
Q 011378          175 IIINGYCRNGFVLEALKMRDEMLEKGCVMDVV----TYNTILNGLCRAKMLTEADDLFNEMLERGV-FPDF----YTFTT  245 (487)
Q Consensus       175 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~----~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~~~----~t~~~  245 (487)
                      ..-..+...|+.++|...+++.....-..+..    .++.+-..+...|+++.|.+.+++..+..- ..+.    .++..
T Consensus        19 ~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~   98 (373)
T 1hz4_A           19 LRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQ   98 (373)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            33445567899999999888877643222221    455666778888999999999888764210 1122    33566


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHC----CCC--CC-eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCC--C--ChhhHH
Q 011378          246 LIHGHCKDGNMNKALNLFDIMTQK----SIK--PD-IVTYNTLIDGFCKVGEMEKANKLWADMISRKIS--P--NYISYG  314 (487)
Q Consensus       246 li~~~~~~g~~~~a~~~~~~m~~~----~~~--~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~--p--~~~t~~  314 (487)
                      +-..+...|++++|...++...+.    +-.  |. ...+..+-..+...|++++|...+.+.......  +  ...++.
T Consensus        99 la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  178 (373)
T 1hz4_A           99 QSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLA  178 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHH
Confidence            777788899999999888766432    222  22 234566677788889999999988876643221  1  234567


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCh-hhHH-----HHHHHHHhcCChHHHHHHHHHHHHCCCCCC---hhhHHH
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVGKGIKPTL-VSCN-----TIIKGYCRSGDASKADEFLSKMVSEGVDPD---SISYNT  385 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~  385 (487)
                      .+...+...|++++|...+++.....-.++. ..+.     .....+...|+.++|...++........++   ...+..
T Consensus       179 ~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~  258 (373)
T 1hz4_A          179 MLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRN  258 (373)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHH
Confidence            7777888889999999888876543211111 1121     223446788899999888887665332111   224566


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHh----CCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011378          386 LINGFVREENMDKAFALVSKMEN----QGLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGH  460 (487)
Q Consensus       386 li~~~~~~~~~~~a~~~~~~m~~----~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~  460 (487)
                      +...+...|++++|...+++...    .|..++. ..+..+...+...|+.++|...+++.....-  .    ...+..+
T Consensus       259 la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~~--~----~g~~~~~  332 (373)
T 1hz4_A          259 IARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLAN--R----TGFISHF  332 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH--H----HCCCHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhc--c----ccHHHHH
Confidence            67778888899888888876642    2322233 2556666777888888888888888764210  0    1123344


Q ss_pred             HhcCCHHHHHHHHHHHHHC
Q 011378          461 VSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       461 ~~~~~~~~a~~~~~~m~~~  479 (487)
                      ...|  +....+++.+...
T Consensus       333 ~~~g--~~~~~ll~~~~~~  349 (373)
T 1hz4_A          333 VIEG--EAMAQQLRQLIQL  349 (373)
T ss_dssp             HTTH--HHHHHHHHHHHHT
T ss_pred             HHcc--HHHHHHHHHHHhC
Confidence            4455  4556666666543

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.00  E-value=3.7e-07  Score=86.36  Aligned_cols=200  Identities=10%  Similarity=-0.004  Sum_probs=109.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC--C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC--C--Cee
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLER----GVF--P-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIK--P--DIV  276 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~--~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~--~--~~~  276 (487)
                      +..+-..+...|++++|...+++..+.    +-.  | ....+..+-..+...|++++|...++........  +  ...
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            344555556666666666666655432    111  2 2234445556666667777777666654432111  1  123


Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh-hhHH-----HHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---hhh
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISRKISPNY-ISYG-----ILINGYCSMGHVTEAFRLWYEMVGKGIKPT---LVS  347 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~t~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~~~~---~~~  347 (487)
                      ++..+-..+...|++++|...+.+.......++. ..+.     .....+...|++++|...++........++   ...
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            4555556666677777777777665432111111 1111     222335677777777777766544321111   123


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHH----CCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHH
Q 011378          348 CNTIIKGYCRSGDASKADEFLSKMVS----EGVDPDSI-SYNTLINGFVREENMDKAFALVSKME  407 (487)
Q Consensus       348 ~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~  407 (487)
                      +..+...+...|+.++|...++....    .|..++.. .+..+-.++...|+.++|...+++..
T Consensus       256 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al  320 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  320 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            45566777777888888777776643    22222222 55556677778888888888777654

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.99  E-value=1.7e-07  Score=88.68  Aligned_cols=220  Identities=11%  Similarity=0.066  Sum_probs=95.4

Q ss_pred             HHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCC-HHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHHhcCC
Q 011378          108 VESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQ-LDRALMYFREMKSAGLVP-DNVLYTIIINGYCRNGF  185 (487)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~  185 (487)
                      ..+.+.|++++|.+.+++..+.. +-+...|+.+-.++.+.|+ +++|+..|++.....  | +...|..+-.++.+.|+
T Consensus       105 ~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g~~~~~~g~  181 (382)
T 2h6f_A          105 AVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRRVLVEWLRD  181 (382)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHccC
Confidence            33344444444444444443321 1123334444444444443 444444444444321  2 23344444444444444


Q ss_pred             HHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh-cCCHHHH-----
Q 011378          186 VLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCK-DGNMNKA-----  259 (487)
Q Consensus       186 ~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~-~g~~~~a-----  259 (487)
                      .++|...+++..+.. +-+...|..+-.++.+.|++++|...|+++.+.. +-+...|+.+-.++.+ .|..++|     
T Consensus       182 ~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~eA~~~~e  259 (382)
T 2h6f_A          182 PSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLERE  259 (382)
T ss_dssp             CTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcchHHHHHHH
Confidence            444444444444321 1133344444455555555555555555554432 1234444444444544 3333444     


Q ss_pred             HHHHHHHHHCCCCC-CeeehHHHHHHHHccC--CHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC---------CHH
Q 011378          260 LNLFDIMTQKSIKP-DIVTYNTLIDGFCKVG--EMEKANKLWADMISRKISPNYISYGILINGYCSMG---------HVT  327 (487)
Q Consensus       260 ~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g--~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~---------~~~  327 (487)
                      +..|+...+.  .| +...|+.+-..+.+.|  +.++|.+.+.++  .....+...+..+...|...|         .++
T Consensus       260 l~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~--~~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~  335 (382)
T 2h6f_A          260 VQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL--QPSHSSPYLIAFLVDIYEDMLENQCDNKEDILN  335 (382)
T ss_dssp             HHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH--TTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHH
T ss_pred             HHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHHHHh--ccCCCCHHHHHHHHHHHHHHhcccccchHHHHH
Confidence            2444433321  22 2234444444454444  355555555444  112223344455555555442         235


Q ss_pred             HHHHHHHHH
Q 011378          328 EAFRLWYEM  336 (487)
Q Consensus       328 ~a~~~~~~m  336 (487)
                      +|..+++.+
T Consensus       336 ~A~~~~~~l  344 (382)
T 2h6f_A          336 KALELCEIL  344 (382)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            566665555

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.98  E-value=2.2e-07  Score=87.85  Aligned_cols=226  Identities=10%  Similarity=0.065  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCC-HHHHHHHHHHHHHcCCcCChhhHHHHHHH
Q 011378          137 SFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGF-VLEALKMRDEMLEKGCVMDVVTYNTILNG  214 (487)
Q Consensus       137 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~~li~~  214 (487)
                      .|..+-..+.+.|++++|+..+++....  .|+ ...|+.+-..+.+.|+ .++|+..+++..+..- -+...|+.+-.+
T Consensus        99 a~~~lg~~~~~~g~~~~Al~~~~~al~l--~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P-~~~~a~~~~g~~  175 (382)
T 2h6f_A           99 VYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRVL  175 (382)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCC-CCHHHHHHHHHH
Confidence            3445555566666666666666666553  233 4456666666666664 6666666666655321 234456666666


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHc-cCCHHH
Q 011378          215 LCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCK-VGEMEK  293 (487)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~-~g~~~~  293 (487)
                      +.+.|++++|...|+++.+.. +-+...|..+-.++.+.|++++|+..|+.+.+... -+...|+.+-..+.+ .|..++
T Consensus       176 ~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~~~~e  253 (382)
T 2h6f_A          176 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGYNDR  253 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCcchH
Confidence            666666666666666666542 22455666666666666666666666666554321 134455566666665 444355


Q ss_pred             H-----HHHHHHHHhCCCCC-ChhhHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC------
Q 011378          294 A-----NKLWADMISRKISP-NYISYGILINGYCSMG--HVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG------  359 (487)
Q Consensus       294 a-----~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~------  359 (487)
                      |     ...+.+....  .| +...|..+...+...|  ++++|...+.++  ..-..+...+..+...|.+.|      
T Consensus       254 A~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~--~~~p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          254 AVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL--QPSHSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             HHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH--TTTCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHHHHh--ccCCCCHHHHHHHHHHHHHHhcccccc
Confidence            5     3555544432  23 3445666666666555  466666666655  222334455556666665543      


Q ss_pred             ---ChHHHHHHHHHH
Q 011378          360 ---DASKADEFLSKM  371 (487)
Q Consensus       360 ---~~~~a~~~~~~m  371 (487)
                         ..++|.++++++
T Consensus       330 ~~~~~~~A~~~~~~l  344 (382)
T 2h6f_A          330 KEDILNKALELCEIL  344 (382)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHH
Confidence               235666666665

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.96  E-value=2.1e-07  Score=88.40  Aligned_cols=227  Identities=10%  Similarity=0.009  Sum_probs=124.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHC----CC-CC-CeeehHHH
Q 011378          213 NGLCRAKMLTEADDLFNEMLERGV-FPD----FYTFTTLIHGHCKDGNMNKALNLFDIMTQK----SI-KP-DIVTYNTL  281 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~-~~~----~~t~~~li~~~~~~g~~~~a~~~~~~m~~~----~~-~~-~~~~~~~l  281 (487)
                      ..+...|+++.|...|++..+... .++    ..++..+-..|...|+.+.|...++...+.    +- .+ ...+++.+
T Consensus       109 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  188 (378)
T 3q15_A          109 MYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVI  188 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHH
Confidence            344567788888888877654311 122    345666777777778877777777654431    10 11 13355666


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhC----CCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCChhhHHHHH
Q 011378          282 IDGFCKVGEMEKANKLWADMISR----KISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGK----GIKPTLVSCNTII  352 (487)
Q Consensus       282 i~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~~~~~~~~li  352 (487)
                      -..|...|++++|...+.+....    +-.+ ...++..+-..|...|++++|...+++....    +.+....++..+-
T Consensus       189 g~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la  268 (378)
T 3q15_A          189 AGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLS  268 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHH
Confidence            66677777777777777655431    1111 1234566666677777777777777665431    2122244556666


Q ss_pred             HHHHhcCChHHHHHHHHHHHHCC----CCCChhhHHHHHHHHhccCC---HHHHHHHHHHHHhCCCCCCH-hhHHHHHHH
Q 011378          353 KGYCRSGDASKADEFLSKMVSEG----VDPDSISYNTLINGFVREEN---MDKAFALVSKMENQGLVPDV-ITYNVILTG  424 (487)
Q Consensus       353 ~~~~~~~~~~~a~~~~~~m~~~g----~~p~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~g~~p~~-~~~~~li~~  424 (487)
                      ..|.+.|+.++|...+++..+..    -+.....+..+-..|...++   +++|...+++   .+..|+. ..+..+...
T Consensus       269 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~~~~~~~~~~~la~~  345 (378)
T 3q15_A          269 WTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNLHAYIEACARSAAAV  345 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCChhHHHHHHHHHHHH
Confidence            66667777777777776655421    11112234455555555555   4444444443   2222222 234445555


Q ss_pred             HHhcCChHHHHHHHHHHH
Q 011378          425 FCRQGRMHDSELILWRMI  442 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~  442 (487)
                      |.+.|++++|...|++..
T Consensus       346 y~~~g~~~~A~~~~~~al  363 (378)
T 3q15_A          346 FESSCHFEQAAAFYRKVL  363 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHH
Confidence            666666666666655543

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.96  E-value=1e-07  Score=79.82  Aligned_cols=163  Identities=11%  Similarity=0.068  Sum_probs=99.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHh
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFV  391 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  391 (487)
                      .+..+...+...|++++|...++...... +.+...+..+...+...|+.++|...+++..+.. +.+...+..+...|.
T Consensus        10 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~   87 (186)
T 3as5_A           10 YYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYV   87 (186)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            34445555666666666666665554321 2344555666666666666666666666665432 223455666666666


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 011378          392 REENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFR  471 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~  471 (487)
                      ..|++++|.+.+++..+.. ..+...+..+...+...|++++|...+++..... ..+...+..+...+...|++++|..
T Consensus        88 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  165 (186)
T 3as5_A           88 QVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALP  165 (186)
T ss_dssp             HHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHH
Confidence            7777777777776665431 2345566666667777777777777777766542 2345666667777777777777777


Q ss_pred             HHHHHHH
Q 011378          472 FHDEMLQ  478 (487)
Q Consensus       472 ~~~~m~~  478 (487)
                      .+++..+
T Consensus       166 ~~~~~~~  172 (186)
T 3as5_A          166 HFKKANE  172 (186)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.95  E-value=1.1e-07  Score=90.29  Aligned_cols=159  Identities=14%  Similarity=0.061  Sum_probs=82.6

Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCC-CCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----C-CcC-ChhhHHHHH
Q 011378          144 IFSRNGQLDRALMYFREMKSAGL-VPD----NVLYTIIINGYCRNGFVLEALKMRDEMLEK----G-CVM-DVVTYNTIL  212 (487)
Q Consensus       144 ~~~~~g~~~~a~~~~~~m~~~g~-~~~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----g-~~~-~~~~~~~li  212 (487)
                      .+...|++++|...|++..+.-- .++    ..++..+-..|...|+.+.|...+.+..+.    + ..+ ...+++.+-
T Consensus       110 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg  189 (378)
T 3q15_A          110 YEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIA  189 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHH
Confidence            34566777777777766654210 111    234555556666666666666665554331    1 011 133455666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC----CCCCCeeehHHHHH
Q 011378          213 NGLCRAKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQK----SIKPDIVTYNTLID  283 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~~~~~li~  283 (487)
                      ..|...|+++.|.+.|++..+.    +-.+ ...++..+-..|...|++++|+..|+...+.    +-+....++..+-.
T Consensus       190 ~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  269 (378)
T 3q15_A          190 GNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSW  269 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHH
Confidence            6666677777777666665432    1111 1234555566666666666666666554430    11111334455555


Q ss_pred             HHHccCCHHHHHHHHHHHH
Q 011378          284 GFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       284 ~~~~~g~~~~a~~~~~~m~  302 (487)
                      .|.+.|++++|...+.+..
T Consensus       270 ~~~~~g~~~~A~~~~~~al  288 (378)
T 3q15_A          270 TLCKAGQTQKAFQFIEEGL  288 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHH
Confidence            5555566666655555544

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

Probab=98.89  E-value=5.6e-07  Score=75.62  Aligned_cols=164  Identities=13%  Similarity=0.087  Sum_probs=82.5

Q ss_pred             eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011378          276 VTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGY  355 (487)
Q Consensus       276 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  355 (487)
                      .+|..+=..|.+.|++++|.+.|++..+.. +-+...+..+...|...|++++|...+....... +.+...+..+-..+
T Consensus         6 ~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~   83 (184)
T 3vtx_A            6 TIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGSAN   83 (184)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHHHH
Confidence            345555555666666666666665554321 1134455555555556666666665555544332 22333444444455


Q ss_pred             HhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHH
Q 011378          356 CRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSE  435 (487)
Q Consensus       356 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  435 (487)
                      ...++.+.+...+++..... +-+...+..+-..|.+.|++++|.+.+++..+.. .-+...|..+...|.+.|++++|.
T Consensus        84 ~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~  161 (184)
T 3vtx_A           84 FMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAV  161 (184)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHH
Confidence            55555555555555544321 1123445555555555555555555555544321 113344555555555555555555


Q ss_pred             HHHHHHHH
Q 011378          436 LILWRMIE  443 (487)
Q Consensus       436 ~~~~~m~~  443 (487)
                      ..|++..+
T Consensus       162 ~~~~~al~  169 (184)
T 3vtx_A          162 KYFKKALE  169 (184)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            55555443

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

Probab=98.88  E-value=1.1e-07  Score=93.23  Aligned_cols=211  Identities=10%  Similarity=0.047  Sum_probs=109.6

Q ss_pred             hhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh-hHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHH
Q 011378           81 CDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENM-SEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFR  159 (487)
Q Consensus        81 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~-~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  159 (487)
                      ++.+.+.+++..... ..+...|..+-..+...|++ ++|.+.|++..+.. +-+...|..+-..|.+.|++++|.+.|+
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~  161 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFS  161 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            344444444433221 12444555555555555665 66666655554432 1134455555555666666666666666


Q ss_pred             HHHHCCCCCChhhHHHHHHHHHhc---------CCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhc--------CCHH
Q 011378          160 EMKSAGLVPDNVLYTIIINGYCRN---------GFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRA--------KMLT  222 (487)
Q Consensus       160 ~m~~~g~~~~~~~~~~ll~~~~~~---------~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~--------~~~~  222 (487)
                      +..+.  .|+...+..+-..+...         |+.++|.+.+++..+.. +-+...|..+..+|...        |+++
T Consensus       162 ~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~  238 (474)
T 4abn_A          162 GALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQ  238 (474)
T ss_dssp             HHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHH
Confidence            55543  24445555555555555         56666666665555432 12344555555555555        5566


Q ss_pred             HHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHH
Q 011378          223 EADDLFNEMLERGVF--PDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLW  298 (487)
Q Consensus       223 ~a~~~~~~m~~~~~~--~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~  298 (487)
                      +|.+.|++..+..-.  -+...|..+-..|...|++++|+..|+...+.  .| +...+..+-..+...|++++|...+
T Consensus       239 ~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          239 QALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL--DPAWPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            666666665543200  24555666666666666666666666555432  12 2234555555555556666655544

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.88  E-value=3.1e-08  Score=89.36  Aligned_cols=227  Identities=15%  Similarity=0.087  Sum_probs=152.9

Q ss_pred             HhcCCHHHHHHHHHHHHHC-------CCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhC------CCCC-ChhhHHHH
Q 011378          251 CKDGNMNKALNLFDIMTQK-------SIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISR------KISP-NYISYGIL  316 (487)
Q Consensus       251 ~~~g~~~~a~~~~~~m~~~-------~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~t~~~l  316 (487)
                      ...|++++|+..|+...+.       .-+....++..+-..|...|++++|...+.+....      +-.| ...++..+
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            4567777887777655431       11223567888889999999999999999987754      2223 35678889


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhC------CC-CCChhhHHHHHHHHHhcCChHHHHHHHHHHHHC------CCCCC-hhh
Q 011378          317 INGYCSMGHVTEAFRLWYEMVGK------GI-KPTLVSCNTIIKGYCRSGDASKADEFLSKMVSE------GVDPD-SIS  382 (487)
Q Consensus       317 i~~~~~~~~~~~a~~~~~~m~~~------~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p~-~~~  382 (487)
                      ...|...|++++|...+......      .- +....++..+-..|...|++++|...+++..+.      +-.|+ ..+
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            99999999999999999987653      11 223567888888999999999999999988764      22332 457


Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHhC-------CCCCCHhh-HHHHHHHHHhcCChHHHHHHHHHHHH--cCCC---C-
Q 011378          383 YNTLINGFVREENMDKAFALVSKMENQ-------GLVPDVIT-YNVILTGFCRQGRMHDSELILWRMIE--KGLN---P-  448 (487)
Q Consensus       383 ~~~li~~~~~~~~~~~a~~~~~~m~~~-------g~~p~~~~-~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~---p-  448 (487)
                      +..+...|...|++++|...+++..+.       ...+.... |..+...+...+....+.. +.+...  ....   | 
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAP-YGEYGSWYKACKVDSPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC-------------CCCCCCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHH-HHHHHHHHHhcCCCCHH
Confidence            888889999999999999999877542       12333333 3333333333333222222 222211  1111   2 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          449 DRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       449 ~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      ...+|..+...|...|++++|..++++.++
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            234788888999999999999999998764

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.87  E-value=3.3e-07  Score=76.68  Aligned_cols=160  Identities=14%  Similarity=0.040  Sum_probs=77.8

Q ss_pred             HHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhc
Q 011378          104 NTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRN  183 (487)
Q Consensus       104 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  183 (487)
                      ..+...+...|++++|.+.++++.+.. +.+...+..+...+.+.|++++|...+++..+.. ..+...+..+...+...
T Consensus        12 ~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~   89 (186)
T 3as5_A           12 RDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQV   89 (186)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHh
Confidence            334444444555555555554443321 1234444455555555555555555555544321 12233444445555555


Q ss_pred             CCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 011378          184 GFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLF  263 (487)
Q Consensus       184 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~  263 (487)
                      |+.++|.+.+++..+.. +.+...+..+...+...|+++.|.+.+++..+.. +.+...+..+...+...|+.++|...+
T Consensus        90 ~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~  167 (186)
T 3as5_A           90 QKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALPHF  167 (186)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            55555555555444331 1233445555555555555555555555554432 223445555555555555555555555


Q ss_pred             HHHH
Q 011378          264 DIMT  267 (487)
Q Consensus       264 ~~m~  267 (487)
                      +...
T Consensus       168 ~~~~  171 (186)
T 3as5_A          168 KKAN  171 (186)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

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

Probab=98.86  E-value=9e-07  Score=74.32  Aligned_cols=57  Identities=9%  Similarity=0.004  Sum_probs=22.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      +..+-..|.+.|++++|.+.|++..+.. +.+..+|..+-..|.+.|+.++|+..|+.
T Consensus       110 ~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  166 (184)
T 3vtx_A          110 YYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKK  166 (184)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            3333344444444444444444433321 11233344444444444444444444443

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

Probab=98.85  E-value=1.3e-07  Score=92.64  Aligned_cols=206  Identities=13%  Similarity=-0.005  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH-HHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHH
Q 011378          221 LTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM-NKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWA  299 (487)
Q Consensus       221 ~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~-~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  299 (487)
                      ++.+...+++.... -+.+...+..+-..+...|++ ++|+..|+...+.. +-+...|..+-..|.+.|++++|...|.
T Consensus        84 ~~~al~~l~~~~~~-~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~  161 (474)
T 4abn_A           84 MEKTLQQMEEVLGS-AQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFS  161 (474)
T ss_dssp             HHHHHHHHHHHHTT-CCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc-CchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            44444444443321 123455555666666666666 66666665554331 1123455555555555666666666555


Q ss_pred             HHHhCCCCCChhhHHHHHHHHHhc---------CCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc--------CChH
Q 011378          300 DMISRKISPNYISYGILINGYCSM---------GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRS--------GDAS  362 (487)
Q Consensus       300 ~m~~~~~~p~~~t~~~li~~~~~~---------~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~--------~~~~  362 (487)
                      .....  .|+...+..+-..+...         |++++|...+++..... +.+...|..+-.+|...        |+++
T Consensus       162 ~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~  238 (474)
T 4abn_A          162 GALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQ  238 (474)
T ss_dssp             HHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHH
Confidence            55433  24445555555555555         55555555555544331 22334444444444444        4455


Q ss_pred             HHHHHHHHHHHCCCCC----ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHH
Q 011378          363 KADEFLSKMVSEGVDP----DSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSE  435 (487)
Q Consensus       363 ~a~~~~~~m~~~g~~p----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~  435 (487)
                      +|...+++..+.  .|    +...|..+-..|...|++++|.+.+++..+.  .| +...+..+...+...|++++|.
T Consensus       239 ~A~~~~~~al~~--~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~a~~~l~~~~~~lg~~~eAi  312 (474)
T 4abn_A          239 QALSAYAQAEKV--DRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL--DPAWPEPQQREQQLLEFLSRLTSLL  312 (474)
T ss_dssp             HHHHHHHHHHHH--CGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            555555544432  12    3334444444444455555555444444332  12 2223444444444444444443

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.85  E-value=7.2e-08  Score=86.95  Aligned_cols=133  Identities=15%  Similarity=0.060  Sum_probs=72.8

Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHHC------CCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc------C-C
Q 011378          136 VSFSTLIGIFSRNGQLDRALMYFREMKSA------GLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEK------G-C  201 (487)
Q Consensus       136 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~------g-~  201 (487)
                      .++..+...+...|++++|...+++....      +-.| ...++..+-..|...|+.++|...+++..+.      . .
T Consensus        44 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  123 (283)
T 3edt_B           44 TMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFH  123 (283)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCC
Confidence            34444555555555555555555554332      1111 1234555555555555555555555444332      1 1


Q ss_pred             cCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc------CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          202 VMDVVTYNTILNGLCRAKMLTEADDLFNEMLER------GVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       202 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      +.....|..+...|...|++++|...|++..+.      +-.| ...++..+...|...|+.++|...++...+
T Consensus       124 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          124 PDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            223445666667777777777777777776543      1122 245666777777777777777777765543

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

Probab=98.70  E-value=3.5e-06  Score=75.87  Aligned_cols=178  Identities=10%  Similarity=0.084  Sum_probs=84.2

Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          294 ANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGI-KPTLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       294 a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      |...|++....+ .++..+...+..++...|++++|++++......+- .-+...+..++..+.+.|+.+.|.+.+++|.
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            344444443332 23333334555555556666666666655443332 1233445555566666666666666666654


Q ss_pred             HCCCCC-----ChhhHHHHHHHHh--ccC--CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          373 SEGVDP-----DSISYNTLINGFV--REE--NMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       373 ~~g~~p-----~~~~~~~li~~~~--~~~--~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +.  .|     +..+...|..+++  ..|  +..+|..+|+++.+.  .|+..+-..++.++.+.|++++|+..++.+.+
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            42  34     2334444444422  122  566666666665443  23322223333355566666666666654432


Q ss_pred             c-----CC---CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          444 K-----GL---NP-DRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       444 ~-----g~---~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      .     +-   .| ++.++..++......|+  +|.++++++.+
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            1     00   12 33344344444444454  55555555553

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.70  E-value=1.4e-06  Score=68.42  Aligned_cols=94  Identities=15%  Similarity=0.223  Sum_probs=41.7

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHV  461 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~  461 (487)
                      .+..+...+...|++++|...++++...+ ..+...+..+...+.+.|++++|...++++.... ..+...+..+...+.
T Consensus        37 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~  114 (136)
T 2fo7_A           37 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY  114 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHH
Confidence            33334444444444444444444443321 1123344444444455555555555555444321 112344444555555


Q ss_pred             hcCCHHHHHHHHHHHH
Q 011378          462 SQNNLKEAFRFHDEML  477 (487)
Q Consensus       462 ~~~~~~~a~~~~~~m~  477 (487)
                      ..|++++|...++++.
T Consensus       115 ~~~~~~~A~~~~~~~~  130 (136)
T 2fo7_A          115 KQGDYDEAIEYYQKAL  130 (136)
T ss_dssp             TTTCHHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHH
Confidence            5555555555555544

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.70  E-value=1.5e-06  Score=68.16  Aligned_cols=130  Identities=15%  Similarity=0.222  Sum_probs=110.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHh
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFV  391 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  391 (487)
                      .|..+...+...|++++|..+++.+.... +.+...+..+...+...|+.++|...++++...+ +.+...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            56788889999999999999999987654 3466788888999999999999999999988654 235667888999999


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          392 REENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      ..|++++|.+.++++.+.. ..+...+..+...+.+.|++++|...+.++...
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            9999999999999987643 335778889999999999999999999998764

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

Probab=98.67  E-value=3.1e-06  Score=76.25  Aligned_cols=179  Identities=10%  Similarity=0.037  Sum_probs=108.4

Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CCeeehHHHHHHHHccCCHHHHHHHHHHHH
Q 011378          224 ADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIK-PDIVTYNTLIDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       224 a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  302 (487)
                      +...|++..+.+ .++..++..+-.++...|++++|++++......+-. -+...+..++..+.+.|+.+.|.+.+++|.
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            455666655544 445555556667777788888888887765443321 234566677777888888888888887776


Q ss_pred             hCCCCC-----ChhhHHHHHHH--HHhcC--CHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          303 SRKISP-----NYISYGILING--YCSMG--HVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       303 ~~~~~p-----~~~t~~~li~~--~~~~~--~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      +.  .|     +..+...|..+  ....|  +..+|+.+|+++...  .|+..+-..++.++.+.|++++|.+.++.+.+
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  34     34555556655  23333  777888888877543  34433334445567777777777777775543


Q ss_pred             C-----CC---CC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          374 E-----GV---DP-DSISYNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       374 ~-----g~---~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      .     ..   .| |..+...+|......|+  +|.++++++++.
T Consensus       240 ~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          240 DYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             HHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             hcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence            2     11   13 34455344444444555  667777777664

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.60  E-value=0.00011  Score=72.07  Aligned_cols=365  Identities=10%  Similarity=0.029  Sum_probs=163.9

Q ss_pred             CChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCC-hhhHHHHHHHHHH-CCCCC-CHHHHHHHHHHHHc----cCCh
Q 011378           44 GFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGR-CDRAKEVLDEMLQ-MGLSP-DTATYNTLLVESCR----KENM  116 (487)
Q Consensus        44 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~-~g~~~-~~~~~~~ll~~~~~----~~~~  116 (487)
                      ++++.+..+|+.....  .|+...|...++-..+.++ .+....+|+.... .|..| +...|...+.-+-.    .+++
T Consensus        28 ~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~  105 (493)
T 2uy1_A           28 KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRI  105 (493)
T ss_dssp             TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHH
T ss_pred             CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHH
Confidence            7778888888776553  4677777777776666553 3556666766543 24333 45566666554321    2456


Q ss_pred             hHHHHHHHHHHHCCCCCCHhHHHHHHHHHH---hCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHH
Q 011378          117 SEAEEIFCEMSRRGVAPDIVSFSTLIGIFS---RNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMR  193 (487)
Q Consensus       117 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~---~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~  193 (487)
                      +.+.++|+.....   |.. ....+-..|.   +..+...+..+..+.                   .  +....|..++
T Consensus       106 ~~vR~iy~rAL~~---P~~-~~~~lw~~Y~~fE~~~~~~~~~~~~~~~-------------------~--~~y~~ar~~y  160 (493)
T 2uy1_A          106 EKIRNGYMRALQT---PMG-SLSELWKDFENFELELNKITGKKIVGDT-------------------L--PIFQSSFQRY  160 (493)
T ss_dssp             HHHHHHHHHHHTS---CCT-THHHHHHHHHHHHHHHCHHHHHHHHHHH-------------------H--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC---hhh-hHHHHHHHHHHHHHHhccccHHHHHHHH-------------------h--HHHHHHHHHH
Confidence            6666677666652   211 1111111111   111112222222111                   0  1122233333


Q ss_pred             HHHHHcCCcCChhhHHHHHHHHHhcC--C-----HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          194 DEMLEKGCVMDVVTYNTILNGLCRAK--M-----LTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       194 ~~m~~~g~~~~~~~~~~li~~~~~~~--~-----~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      ++....--..+...|...+.--...+  .     .+.+..+|+++... .+.++..|...+.-+.+.|+++.|..+|+..
T Consensus       161 ~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~erA  239 (493)
T 2uy1_A          161 QQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVERG  239 (493)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            32221000012234444333322111  0     23455667766653 2344566666666667777777777777766


Q ss_pred             HHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChh
Q 011378          267 TQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLV  346 (487)
Q Consensus       267 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  346 (487)
                      ...   |.......   .|......++.   +..+...-.               . ...+.+     ...  .......
T Consensus       240 i~~---P~~~~l~~---~y~~~~e~~~~---~~~l~~~~~---------------~-~~~~~~-----~~~--~~~~~~~  287 (493)
T 2uy1_A          240 IEM---SDGMFLSL---YYGLVMDEEAV---YGDLKRKYS---------------M-GEAESA-----EKV--FSKELDL  287 (493)
T ss_dssp             HHH---CCSSHHHH---HHHHHTTCTHH---HHHHHHHTC---------------------------------CHHHHHH
T ss_pred             HhC---CCcHHHHH---HHHhhcchhHH---HHHHHHHHH---------------h-hccchh-----hhh--cccccHH
Confidence            655   33221111   12221111111   111111000               0 000000     000  0000113


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHH--HHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYN--TLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTG  424 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  424 (487)
                      .|...++...+.++.+.|..+|+.....+  ++...|.  +.+.... .++.+.|..+|+...+.. .-+...|...++.
T Consensus       288 lw~~y~~~~~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~-~~~~~~~~~yid~  363 (493)
T 2uy1_A          288 LRINHLNYVLKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH-PDSTLLKEEFFLF  363 (493)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            34445555555566666777766661111  1222222  2222211 224666777776654431 1122334555565


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          425 FCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      ..+.|+.+.|+.+|++.     ......|...+..-...|+.+.+.+++++..
T Consensus       364 e~~~~~~~~aR~l~er~-----~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~  411 (493)
T 2uy1_A          364 LLRIGDEENARALFKRL-----EKTSRMWDSMIEYEFMVGSMELFRELVDQKM  411 (493)
T ss_dssp             HHHHTCHHHHHHHHHHS-----CCBHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56667777777777664     1245566666666666677777766666655

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.56  E-value=9.3e-06  Score=70.68  Aligned_cols=130  Identities=16%  Similarity=0.038  Sum_probs=76.2

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHH
Q 011378          204 DVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLI  282 (487)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li  282 (487)
                      |+..|...-..+.+.|++++|.+.|++..+..-.++...+..+-..+...|++++|+..|+...+.  .| +...+..+-
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~   83 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKS   83 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHH
Confidence            445666666667777777777777777766543356666666666677777777777777665543  22 234555666


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCC-h-------hhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          283 DGFCKVGEMEKANKLWADMISRKISPN-Y-------ISYGILINGYCSMGHVTEAFRLWYEMV  337 (487)
Q Consensus       283 ~~~~~~g~~~~a~~~~~~m~~~~~~p~-~-------~t~~~li~~~~~~~~~~~a~~~~~~m~  337 (487)
                      ..|...|++++|...+++.....  |+ .       ..|..+-..+...|++++|...|+...
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al  144 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHAT  144 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHH
Confidence            66666666666666666655432  22 2       224444444445555555555555543

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

Probab=98.56  E-value=4.3e-06  Score=76.08  Aligned_cols=97  Identities=14%  Similarity=0.087  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHCC----CCCC-e
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKD-GNMNKALNLFDIMTQKS----IKPD-I  275 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~-g~~~~a~~~~~~m~~~~----~~~~-~  275 (487)
                      +|+.+-..|.+.|++++|...|++..+.    |-.. -..+++.+-..|... |++++|+..|+...+..    -.+. .
T Consensus        79 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~  158 (292)
T 1qqe_A           79 TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSN  158 (292)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHH
Confidence            4455555555555555555555544321    1000 022444455555553 55555555554433210    0000 1


Q ss_pred             eehHHHHHHHHccCCHHHHHHHHHHHHh
Q 011378          276 VTYNTLIDGFCKVGEMEKANKLWADMIS  303 (487)
Q Consensus       276 ~~~~~li~~~~~~g~~~~a~~~~~~m~~  303 (487)
                      .+++.+-..+.+.|++++|...|.+...
T Consensus       159 ~~~~~lg~~~~~~g~~~~A~~~~~~al~  186 (292)
T 1qqe_A          159 KCFIKCADLKALDGQYIEASDIYSKLIK  186 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            2344444444455555555555544443

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.56  E-value=4.1e-06  Score=85.72  Aligned_cols=159  Identities=14%  Similarity=0.098  Sum_probs=77.6

Q ss_pred             eehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011378          276 VTYNTLIDGFCKVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKG  354 (487)
Q Consensus       276 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  354 (487)
                      ..|+.|-..|.+.|++++|.+.|++..+.  .| +...|..+-.+|.+.|++++|...|++..+.. +-+...|..+-.+
T Consensus        10 ~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~~   86 (723)
T 4gyw_A           10 DSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNT   86 (723)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34555555555555555555555554432  22 23445555555555555555555555544321 1123445555555


Q ss_pred             HHhcCChHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChH
Q 011378          355 YCRSGDASKADEFLSKMVSEGVDPD-SISYNTLINGFVREENMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMH  432 (487)
Q Consensus       355 ~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~  432 (487)
                      |...|+.++|.+.+++..+.  .|+ ...|+.|-..|...|++++|.+.+++..+.  .|+ ...|..+...+...|+++
T Consensus        87 l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~~~  162 (723)
T 4gyw_A           87 LKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCDWT  162 (723)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCCT
T ss_pred             HHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhcccHH
Confidence            55555555555555554432  232 334555555555555555555555544332  232 334445555555555555


Q ss_pred             HHHHHHHHH
Q 011378          433 DSELILWRM  441 (487)
Q Consensus       433 ~a~~~~~~m  441 (487)
                      +|...+++.
T Consensus       163 ~A~~~~~ka  171 (723)
T 4gyw_A          163 DYDERMKKL  171 (723)
T ss_dssp             THHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555544444

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

Probab=98.54  E-value=7e-06  Score=74.71  Aligned_cols=204  Identities=13%  Similarity=0.075  Sum_probs=130.6

Q ss_pred             hhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHC----CCCCC-hhhHHHHHHHHHhcCCHHHHH
Q 011378          116 MSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSA----GLVPD-NVLYTIIINGYCRNGFVLEAL  190 (487)
Q Consensus       116 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~~~-~~~~~~ll~~~~~~~~~~~a~  190 (487)
                      +++|...+++.               ...|...|++++|...|++....    |-.++ ..+|+.+-..|.+.|+.++|.
T Consensus        33 ~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~   97 (292)
T 1qqe_A           33 FEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAV   97 (292)
T ss_dssp             HHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHH
Confidence            66666666554               34566777777777777765432    21122 346777777777888888887


Q ss_pred             HHHHHHHHc----CCcC-ChhhHHHHHHHHHhc-CCHHHHHHHHHHHHHcC----CCCC-HHHHHHHHHHHHhcCCHHHH
Q 011378          191 KMRDEMLEK----GCVM-DVVTYNTILNGLCRA-KMLTEADDLFNEMLERG----VFPD-FYTFTTLIHGHCKDGNMNKA  259 (487)
Q Consensus       191 ~~~~~m~~~----g~~~-~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~----~~~~-~~t~~~li~~~~~~g~~~~a  259 (487)
                      ..+++..+.    |-.. -..+|+.+-..|... |+++.|...|++..+..    -.+. ..++..+...+.+.|++++|
T Consensus        98 ~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A  177 (292)
T 1qqe_A           98 DSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEA  177 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHH
Confidence            777665432    2111 134677888888886 99999999998876531    1111 35688888999999999999


Q ss_pred             HHHHHHHHHCCCCCCee------ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh------hhHHHHHHHHH--hcCC
Q 011378          260 LNLFDIMTQKSIKPDIV------TYNTLIDGFCKVGEMEKANKLWADMISRKISPNY------ISYGILINGYC--SMGH  325 (487)
Q Consensus       260 ~~~~~~m~~~~~~~~~~------~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~------~t~~~li~~~~--~~~~  325 (487)
                      +..|+...+........      .|..+..++...|++++|...|++...  +.|+.      ..+..++.+|.  ..++
T Consensus       178 ~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--l~p~~~~~~~~~~l~~l~~~~~~~~~~~  255 (292)
T 1qqe_A          178 SDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS--EDPNFADSRESNFLKSLIDAVNEGDSEQ  255 (292)
T ss_dssp             HHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC--C---------HHHHHHHHHHHHTTCTTT
T ss_pred             HHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCCCCcHHHHHHHHHHHHHHcCCHHH
Confidence            99999887654332221      456667778888999999988887653  23332      12344555554  3456


Q ss_pred             HHHHHHHHHHH
Q 011378          326 VTEAFRLWYEM  336 (487)
Q Consensus       326 ~~~a~~~~~~m  336 (487)
                      +++|...|+.+
T Consensus       256 ~~~A~~~~~~~  266 (292)
T 1qqe_A          256 LSEHCKEFDNF  266 (292)
T ss_dssp             HHHHHHHHTTS
T ss_pred             HHHHHHHhccC
Confidence            67777666544

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.53  E-value=1e-05  Score=70.40  Aligned_cols=192  Identities=11%  Similarity=0.045  Sum_probs=140.9

Q ss_pred             CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          274 DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIK  353 (487)
Q Consensus       274 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  353 (487)
                      |...+...-..+.+.|++++|...|.........++...+..+..++...|++++|...++...... +.+...|..+-.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHHH
Confidence            3456677778888999999999999988876544677777778899999999999999999887643 234567888888


Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCC-h-------hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC---HhhHHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPD-S-------ISYNTLINGFVREENMDKAFALVSKMENQGLVPD---VITYNVIL  422 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~-~-------~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~li  422 (487)
                      .|...|+.++|...+++..+..  |+ .       ..|..+-..+...|++++|.+.+++..+.  .|+   ...|..+-
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l~  160 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSLG  160 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHHH
Confidence            9999999999999999887643  43 3       34677777788899999999999987653  565   45566666


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      ..|...|     ..+++++...+ ..+...|......  ..+.+++|...+++-.+
T Consensus       161 ~~~~~~~-----~~~~~~a~~~~-~~~~~~~~~~~~~--~~~~~~~A~~~~~~a~~  208 (228)
T 4i17_A          161 VLFYNNG-----ADVLRKATPLA-SSNKEKYASEKAK--ADAAFKKAVDYLGEAVT  208 (228)
T ss_dssp             HHHHHHH-----HHHHHHHGGGT-TTCHHHHHHHHHH--HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-----HHHHHHHHhcc-cCCHHHHHHHHHH--HHHHHHHHHHHHHHHhh
Confidence            6665443     34445554432 2345556555433  34668999999988875

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.50  E-value=8.2e-06  Score=83.55  Aligned_cols=159  Identities=16%  Similarity=0.122  Sum_probs=75.8

Q ss_pred             cchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCC-CHhHHHHHHH
Q 011378           66 FTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPD-TATYNTLLVESCRKENMSEAEEIFCEMSRRGVAP-DIVSFSTLIG  143 (487)
Q Consensus        66 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~  143 (487)
                      ..|+.+-..+.+.|++++|.+.|++..+.  .|+ ...|+.+-..+.+.|++++|.+.|++..+.  .| +...|..+-.
T Consensus        10 ~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~   85 (723)
T 4gyw_A           10 DSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            44555555555555666555555555442  232 344555555555555555555555555442  22 2344555555


Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHH
Q 011378          144 IFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLT  222 (487)
Q Consensus       144 ~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~  222 (487)
                      ++.+.|++++|++.|++..+.  .|+ ...|+.+-..|.+.|+.++|.+.+++..+.. +-+...|..+...+...|+++
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~~~  162 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCDWT  162 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCCT
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhcccHH
Confidence            555555555555555554432  222 3344444444444455555444444443321 112233444444444444444


Q ss_pred             HHHHHHHHH
Q 011378          223 EADDLFNEM  231 (487)
Q Consensus       223 ~a~~~~~~m  231 (487)
                      +|.+.+++.
T Consensus       163 ~A~~~~~ka  171 (723)
T 4gyw_A          163 DYDERMKKL  171 (723)
T ss_dssp             THHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            444444443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.49  E-value=0.0004  Score=67.92  Aligned_cols=368  Identities=11%  Similarity=0.028  Sum_probs=207.3

Q ss_pred             CChhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCC-hhHHHHHHHHHhh-CCCCC-CccchHHHHHHHH----hcCCh
Q 011378            9 HKIDSAKMFLCEMEQKGVYPDTVTYNTLINAYCREGF-LEEAFQLMNSMSG-KGLKP-GVFTYNSLINGLC----KKGRC   81 (487)
Q Consensus         9 ~~~~~a~~~~~~~~~~g~~p~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~-~~~~p-~~~~~~~li~~~~----~~~~~   81 (487)
                      +.++.+..+|++....  .|+...|..-++-..+.++ .+....+|+.... -|..| +...|...+.-+.    ..++.
T Consensus        28 ~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~  105 (493)
T 2uy1_A           28 KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRI  105 (493)
T ss_dssp             TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHH
T ss_pred             CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHH
Confidence            6788888999887763  4899999998888877764 4567778887655 35434 4566776666543    34678


Q ss_pred             hhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHH
Q 011378           82 DRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREM  161 (487)
Q Consensus        82 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  161 (487)
                      +.+.++|++.......--...|..... +-+..+...+.++..+.                   .  +.+..|..+++..
T Consensus       106 ~~vR~iy~rAL~~P~~~~~~lw~~Y~~-fE~~~~~~~~~~~~~~~-------------------~--~~y~~ar~~y~~~  163 (493)
T 2uy1_A          106 EKIRNGYMRALQTPMGSLSELWKDFEN-FELELNKITGKKIVGDT-------------------L--PIFQSSFQRYQQI  163 (493)
T ss_dssp             HHHHHHHHHHHTSCCTTHHHHHHHHHH-HHHHHCHHHHHHHHHHH-------------------H--HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhChhhhHHHHHHHHHH-HHHHhccccHHHHHHHH-------------------h--HHHHHHHHHHHHH
Confidence            899999999887321111122222211 11111222333332221                   1  1233344444444


Q ss_pred             HHCCCCCChhhHHHHHHHHHhcC--C-----HHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011378          162 KSAGLVPDNVLYTIIINGYCRNG--F-----VLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLER  234 (487)
Q Consensus       162 ~~~g~~~~~~~~~~ll~~~~~~~--~-----~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (487)
                      ...--..+...|...++---..+  .     ...+..++++.... ++.+...|-..+.-+.+.|+++.|..++++....
T Consensus       164 ~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~  242 (493)
T 2uy1_A          164 QPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM  242 (493)
T ss_dssp             HHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            32100013345665555433221  1     23456678877764 3455677888888888999999999999999887


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHH
Q 011378          235 GVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYG  314 (487)
Q Consensus       235 ~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~  314 (487)
                        +.+...|.    .|+...+.++   +++.+.+               .+... ..+.+..     . . .......|.
T Consensus       243 --P~~~~l~~----~y~~~~e~~~---~~~~l~~---------------~~~~~-~~~~~~~-----~-~-~~~~~~lw~  290 (493)
T 2uy1_A          243 --SDGMFLSL----YYGLVMDEEA---VYGDLKR---------------KYSMG-EAESAEK-----V-F-SKELDLLRI  290 (493)
T ss_dssp             --CCSSHHHH----HHHHHTTCTH---HHHHHHH---------------HTC-----------------C-HHHHHHHHH
T ss_pred             --CCcHHHHH----HHHhhcchhH---HHHHHHH---------------HHHhh-ccchhhh-----h-c-ccccHHHHH
Confidence              33332222    2222211111   1222221               11000 0000000     0 0 001123455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHH--HHHHHHHhcCChHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHh
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCN--TIIKGYCRSGDASKADEFLSKMVSEGVDPD-SISYNTLINGFV  391 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~  391 (487)
                      ..+....+.+..+.|..+|+.. +.. ..+...|.  +.+.... .++.+.|..+++...+.-  |+ ...+...++-..
T Consensus       291 ~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~~~~yid~e~  365 (493)
T 2uy1_A          291 NHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLLKEEFFLFLL  365 (493)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHHHHHHHHHHH
Confidence            5566666677788888888877 211 12333332  2222222 346889999998877642  32 334555666667


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          392 REENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +.|+.+.|..++++..     .....|...+..=.+.|+.+.+..++++...
T Consensus       366 ~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          366 RIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999998862     2567788888877888999999998888763

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.41  E-value=6.3e-06  Score=75.60  Aligned_cols=95  Identities=13%  Similarity=-0.022  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHC----CCCCC-hhhHHHHHHHHhccCCHHHHHHHHHHHHh----CCCCCCH-h
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSE----GVDPD-SISYNTLINGFVREENMDKAFALVSKMEN----QGLVPDV-I  416 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p~~-~  416 (487)
                      +++.+-..|.. |++++|...+++..+.    |-.+. ..++..+-..|.+.|++++|...+++..+    .+..+.. .
T Consensus       118 ~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (307)
T 2ifu_A          118 ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYK  196 (307)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHH
Confidence            34444444444 5555555555544321    10000 23444555555555555555555554432    1111111 1


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      .+..+...+...|++++|...|++..
T Consensus       197 ~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          197 KCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            34444444455556666655555544

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.34  E-value=2.2e-05  Score=71.94  Aligned_cols=199  Identities=10%  Similarity=-0.020  Sum_probs=102.5

Q ss_pred             cCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          113 KENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKM  192 (487)
Q Consensus       113 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~  192 (487)
                      .|++++|.+++++..+.-- .+         .+...++++.|...|++.               ...|...|+.++|...
T Consensus         4 ~~~~~eA~~~~~~a~k~~~-~~---------~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~   58 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLK-TS---------FMKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAKDA   58 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-CC---------SSSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHcc-cc---------ccCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHHHH
Confidence            4667788888876654211 00         011135566666555543               2345566666666666


Q ss_pred             HHHHHHc----CCcC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHH
Q 011378          193 RDEMLEK----GCVM-DVVTYNTILNGLCRAKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKDGNMNKALNL  262 (487)
Q Consensus       193 ~~~m~~~----g~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~g~~~~a~~~  262 (487)
                      +.+..+.    |-.. -..+|+.+...|.+.|++++|...|++..+.    |-.. -..++..+-..|.. |++++|+..
T Consensus        59 ~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~  137 (307)
T 2ifu_A           59 YLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHL  137 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHH
Confidence            5554321    1111 1235666666677777777777777665432    1111 12455566666666 777777776


Q ss_pred             HHHHHHC----CCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhC----CCCCCh-hhHHHHHHHHHhcCCHHHHHHH
Q 011378          263 FDIMTQK----SIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISR----KISPNY-ISYGILINGYCSMGHVTEAFRL  332 (487)
Q Consensus       263 ~~~m~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p~~-~t~~~li~~~~~~~~~~~a~~~  332 (487)
                      |+...+.    +-.+ ...+++.+-..|.+.|++++|...|.+....    +..+.. ..+..+...+...|++++|...
T Consensus       138 ~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~  217 (307)
T 2ifu_A          138 YQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKC  217 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            6654321    1100 0234555556666666666666666554431    111111 1344444455555666666666


Q ss_pred             HHHHH
Q 011378          333 WYEMV  337 (487)
Q Consensus       333 ~~~m~  337 (487)
                      |++..
T Consensus       218 ~~~al  222 (307)
T 2ifu_A          218 VRESY  222 (307)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            66554

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.32  E-value=0.00021  Score=64.78  Aligned_cols=161  Identities=11%  Similarity=-0.007  Sum_probs=83.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCC-CCCCh----hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC-CC----hhhHHHH
Q 011378          317 INGYCSMGHVTEAFRLWYEMVGKG-IKPTL----VSCNTIIKGYCRSGDASKADEFLSKMVSEGVD-PD----SISYNTL  386 (487)
Q Consensus       317 i~~~~~~~~~~~a~~~~~~m~~~~-~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~----~~~~~~l  386 (487)
                      +..+...|++++|..+++...... ..|+.    ..+..+...+...++.++|...+++....... ++    ..+++.+
T Consensus        82 i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~l  161 (293)
T 3u3w_A           82 VIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAI  161 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence            444555555666655555554321 11121    11223334444555666666666665542211 22    1245666


Q ss_pred             HHHHhccCCHHHHHHHHHHHHh----C-CCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHH----cCCCCC-HHHHHH
Q 011378          387 INGFVREENMDKAFALVSKMEN----Q-GLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIE----KGLNPD-RSTYTT  455 (487)
Q Consensus       387 i~~~~~~~~~~~a~~~~~~m~~----~-g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~-~~ty~~  455 (487)
                      -..|...|++++|...+++..+    . +..+.. .+|..+...|.+.|++++|...+++..+    .+-.+. ..+|..
T Consensus       162 g~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~  241 (293)
T 3u3w_A          162 ANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQ  241 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            6666666666666666655542    1 111221 2566666667777777777766666542    222222 446666


Q ss_pred             HHHHHHhcC-CHHHHHHHHHHHH
Q 011378          456 LINGHVSQN-NLKEAFRFHDEML  477 (487)
Q Consensus       456 l~~~~~~~~-~~~~a~~~~~~m~  477 (487)
                      +-..|...| ++++|.+.+++-.
T Consensus       242 lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          242 RGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHH
Confidence            666777777 3577766666544

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.29  E-value=0.00018  Score=65.28  Aligned_cols=160  Identities=9%  Similarity=0.001  Sum_probs=81.7

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC-CCCChh----hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCc-CC----hhhHHH
Q 011378          141 LIGIFSRNGQLDRALMYFREMKSAG-LVPDNV----LYTIIINGYCRNGFVLEALKMRDEMLEKGCV-MD----VVTYNT  210 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~~g-~~~~~~----~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~----~~~~~~  210 (487)
                      .+..+.+.|++++|..++++..... ..|+..    .+..+...+...++.++|...+++..+.... .+    ..+|+.
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            3556667777777777777765522 122211    2223444444555666666666666552221 12    124666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHH----CCCCCC-eeehH
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLER-----GVFPD-FYTFTTLIHGHCKDGNMNKALNLFDIMTQ----KSIKPD-IVTYN  279 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~----~~~~~~-~~~~~  279 (487)
                      +...|...|+++.|...|++..+.     +..+. ..++..+...|.+.|++++|+..++...+    .+..+. ..+|.
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            666666667777776666666531     11111 23555666666666666666666654332    111111 23444


Q ss_pred             HHHHHHHccCC-HHHHHHHHHH
Q 011378          280 TLIDGFCKVGE-MEKANKLWAD  300 (487)
Q Consensus       280 ~li~~~~~~g~-~~~a~~~~~~  300 (487)
                      .+-..|.+.|+ .++|.+.+.+
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~  262 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKK  262 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHH
Confidence            45555555553 3555555543

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

Probab=98.24  E-value=8.1e-05  Score=66.20  Aligned_cols=182  Identities=10%  Similarity=0.064  Sum_probs=97.5

Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-C-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CC-ChhhHHHHH
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISRKISP-N-YISYGILINGYCSMGHVTEAFRLWYEMVGKGI-KP-TLVSCNTII  352 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~-~~~~~~~li  352 (487)
                      .+-.+-..+.+.|++++|...|.......... . ...+..+..+|...|++++|...|+...+..- .| ....+..+-
T Consensus        17 ~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg   96 (261)
T 3qky_A           17 EAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERA   96 (261)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHH
Confidence            34445555666777777777777766542111 0 34556666667777777777777776665321 11 123444455


Q ss_pred             HHHHh--------cCChHHHHHHHHHHHHCCCCCCh-hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          353 KGYCR--------SGDASKADEFLSKMVSEGVDPDS-ISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       353 ~~~~~--------~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                      .++..        .|+.++|...+++..+..  |+. .....+.              .+......    -...+-.+..
T Consensus        97 ~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~--------------~~~~~~~~----~~~~~~~la~  156 (261)
T 3qky_A           97 MCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQ--------------KIRELRAK----LARKQYEAAR  156 (261)
T ss_dssp             HHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHH--------------HHHHHHHH----HHHHHHHHHH
T ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHH--------------HHHHHHHH----HHHHHHHHHH
Confidence            55555        666777777776665432  322 1111110              00000000    0001244455


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCC-C-CHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHH
Q 011378          424 GFCRQGRMHDSELILWRMIEKGLN-P-DRSTYTTLINGHVSQ----------NNLKEAFRFHDEMLQ  478 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~~g~~-p-~~~ty~~l~~~~~~~----------~~~~~a~~~~~~m~~  478 (487)
                      .|.+.|++++|...|++.....-. | ....+..+..+|...          |++++|...+++.++
T Consensus       157 ~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~  223 (261)
T 3qky_A          157 LYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQ  223 (261)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHH
Confidence            677777777777777777654211 1 234555566666644          777778777777764

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.23  E-value=0.00011  Score=63.21  Aligned_cols=126  Identities=13%  Similarity=0.065  Sum_probs=54.4

Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcC----CHHHHHHHHHHHHHcCCcCChhhHHHH
Q 011378          136 VSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG----FVLEALKMRDEMLEKGCVMDVVTYNTI  211 (487)
Q Consensus       136 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~----~~~~a~~~~~~m~~~g~~~~~~~~~~l  211 (487)
                      ..+..+-..|...+++++|.+.|++..+.|   +...+..|-..|.. +    +.++|.+.+++..+.|   +...+..|
T Consensus        19 ~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~~~L   91 (212)
T 3rjv_A           19 RAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGEIVL   91 (212)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHHHHH
Confidence            334444444444445555555544444432   22233333333333 3    4444444444444333   22333444


Q ss_pred             HHHHHh----cCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHH
Q 011378          212 LNGLCR----AKMLTEADDLFNEMLERGVF-PDFYTFTTLIHGHCK----DGNMNKALNLFDIMTQ  268 (487)
Q Consensus       212 i~~~~~----~~~~~~a~~~~~~m~~~~~~-~~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~  268 (487)
                      -..|..    .++++.|.+.|++..+.|.. .++..+..|-..|..    .++.++|+..|+...+
T Consensus        92 g~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~  157 (212)
T 3rjv_A           92 ARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSS  157 (212)
T ss_dssp             HHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            444443    44555555555555443311 013444444444444    4455555555554443

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.22  E-value=0.00035  Score=59.90  Aligned_cols=164  Identities=12%  Similarity=0.026  Sum_probs=87.8

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC----ChHHHHHHHHHHHHCCCCCChhhHH
Q 011378          309 NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG----DASKADEFLSKMVSEGVDPDSISYN  384 (487)
Q Consensus       309 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~----~~~~a~~~~~~m~~~g~~p~~~~~~  384 (487)
                      +...+..|-..|...+++++|+..|+.....|   +...+..|-..|.. +    +.++|.+.+++..+.|   +...+.
T Consensus        17 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~~   89 (212)
T 3rjv_A           17 DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGEI   89 (212)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            44445555555555566666666666555543   33444444444444 4    5666666666665543   334444


Q ss_pred             HHHHHHhc----cCCHHHHHHHHHHHHhCCCC-CCHhhHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCCHHHHHH
Q 011378          385 TLINGFVR----EENMDKAFALVSKMENQGLV-PDVITYNVILTGFCR----QGRMHDSELILWRMIEKGLNPDRSTYTT  455 (487)
Q Consensus       385 ~li~~~~~----~~~~~~a~~~~~~m~~~g~~-p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~  455 (487)
                      .|-..|..    .+++++|.+.+++..+.|-. ..+..+..|-..|..    .+++++|...|++..+.  ..+...+..
T Consensus        90 ~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~a~~~  167 (212)
T 3rjv_A           90 VLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTGYAEYW  167 (212)
T ss_dssp             HHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTTHHHHH
T ss_pred             HHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCHHHHHH
Confidence            55555554    56666666666665554311 014455555555555    56666666666666554  123334455


Q ss_pred             HHHHHHhc-C-----CHHHHHHHHHHHHHCCC
Q 011378          456 LINGHVSQ-N-----NLKEAFRFHDEMLQRGF  481 (487)
Q Consensus       456 l~~~~~~~-~-----~~~~a~~~~~~m~~~g~  481 (487)
                      |-..|... |     ++++|...+++-.+.|.
T Consensus       168 Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          168 AGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            55555432 2     66667666666655553

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

Probab=98.21  E-value=6.5e-05  Score=66.82  Aligned_cols=97  Identities=11%  Similarity=-0.020  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCC----HhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC-CCC-hhhH
Q 011378          100 TATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPD----IVSFSTLIGIFSRNGQLDRALMYFREMKSAGL-VPD-NVLY  173 (487)
Q Consensus       100 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~~~-~~~~  173 (487)
                      ...+-.+-..+.+.|++++|...|+++.+..  |+    ...+..+..++.+.|++++|...|++..+... .|. ...+
T Consensus        15 ~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           15 PQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            3444444455556666666666666665532  21    34455555666666666666666666655321 111 2234


Q ss_pred             HHHHHHHHh--------cCCHHHHHHHHHHHHH
Q 011378          174 TIIINGYCR--------NGFVLEALKMRDEMLE  198 (487)
Q Consensus       174 ~~ll~~~~~--------~~~~~~a~~~~~~m~~  198 (487)
                      ..+-.++.+        .|+.++|...+++..+
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~  125 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFID  125 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHH
Confidence            444444444        5555555555555544

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.15  E-value=0.00031  Score=60.82  Aligned_cols=178  Identities=13%  Similarity=0.007  Sum_probs=107.0

Q ss_pred             hHHHHHHHHccCCHHHHHHHHHHHHhCCCC-CC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChh----hHHHH
Q 011378          278 YNTLIDGFCKVGEMEKANKLWADMISRKIS-PN-YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLV----SCNTI  351 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~----~~~~l  351 (487)
                      +..+...+.+.|++++|...|.++...... |. ...+..+..++...|++++|...|+...+..  |+..    .+-.+
T Consensus         7 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~--P~~~~~~~a~~~~   84 (225)
T 2yhc_A            7 IYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN--PTHPNIDYVMYMR   84 (225)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCcHHHHHHHH
Confidence            344556677788888888888887764321 21 2456677788888888888888888876542  3221    22223


Q ss_pred             HHHHHh------------------cCChHHHHHHHHHHHHCCCCCChh-hHHHHHHHHhccCCHHHHHHHHHHHHhCCCC
Q 011378          352 IKGYCR------------------SGDASKADEFLSKMVSEGVDPDSI-SYNTLINGFVREENMDKAFALVSKMENQGLV  412 (487)
Q Consensus       352 i~~~~~------------------~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  412 (487)
                      -.++..                  .|+.++|...+++..+.  .|+.. .+..+..          ...+...+.     
T Consensus        85 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~----------l~~~~~~~~-----  147 (225)
T 2yhc_A           85 GLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKR----------LVFLKDRLA-----  147 (225)
T ss_dssp             HHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHH----------HHHHHHHHH-----
T ss_pred             HHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHH----------HHHHHHHHH-----
Confidence            333332                  34555566666555542  23321 1111100          000000000     


Q ss_pred             CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          413 PDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR----STYTTLINGHVSQNNLKEAFRFHDEMLQR  479 (487)
Q Consensus       413 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~ty~~l~~~~~~~~~~~~a~~~~~~m~~~  479 (487)
                         ...-.+...|.+.|++++|...|+++.+.  .|+.    ..+..+..+|.+.|++++|.+.++.+...
T Consensus       148 ---~~~~~~a~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          148 ---KYEYSVAEYYTERGAWVAVVNRVEGMLRD--YPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             ---HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             ---HHHHHHHHHHHHcCcHHHHHHHHHHHHHH--CcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence               01123455778899999999999998764  3432    46778889999999999999999988765

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.14  E-value=0.00037  Score=63.12  Aligned_cols=121  Identities=12%  Similarity=-0.031  Sum_probs=55.8

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCC---CCC--hhhHHHHHHHHhccCCHHHHHHHHHHHHh----CCCCC--CHhhHHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEGV---DPD--SISYNTLINGFVREENMDKAFALVSKMEN----QGLVP--DVITYNVIL  422 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~---~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p--~~~~~~~li  422 (487)
                      .+...|+.++|...+++......   .+.  ..+|+.+-..|...|++++|...+++..+    .+-.+  ...+|..+.
T Consensus       124 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg  203 (293)
T 2qfc_A          124 YVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHA  203 (293)
T ss_dssp             HHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHH
T ss_pred             HHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHH
Confidence            34444555555555555443211   111  22455555555555555555555554431    11111  113455555


Q ss_pred             HHHHhcCChHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHhcCCHHHH-HHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMIEK----GLNPD-RSTYTTLINGHVSQNNLKEA-FRFHD  474 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~ty~~l~~~~~~~~~~~~a-~~~~~  474 (487)
                      ..|.+.|++++|...+++..+.    +.... ..+|..+-..|...|++++| ...++
T Consensus       204 ~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~  261 (293)
T 2qfc_A          204 KALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYK  261 (293)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence            5555666666665555554321    11111 34555555555556666555 44343

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.12  E-value=0.00052  Score=62.16  Aligned_cols=125  Identities=11%  Similarity=0.058  Sum_probs=62.0

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCC---CC--hhhHHHHHHHHHhcCCHHHHHHHHHHHHH----cCCcC--ChhhHH
Q 011378          141 LIGIFSRNGQLDRALMYFREMKSAGLV---PD--NVLYTIIINGYCRNGFVLEALKMRDEMLE----KGCVM--DVVTYN  209 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~~g~~---~~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~g~~~--~~~~~~  209 (487)
                      +...+...|++++|+..+++.......   +.  ..+|+.+-..|...|+.++|...+++..+    .+..+  ...+|+
T Consensus       121 ~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~  200 (293)
T 2qfc_A          121 VAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRY  200 (293)
T ss_dssp             HHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHH
T ss_pred             HHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHH
Confidence            333444555555555555554432111   11  22455555555555555555555555431    11111  113555


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHH-HHHHHH
Q 011378          210 TILNGLCRAKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKDGNMNKA-LNLFDI  265 (487)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~g~~~~a-~~~~~~  265 (487)
                      .+...|.+.|++++|...+++..+.    +... -..+|..+-..|.+.|+.++| ...++.
T Consensus       201 nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~  262 (293)
T 2qfc_A          201 NHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKK  262 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             hHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            6666666666666666666655432    1111 144566666666666666666 554543

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

Probab=98.10  E-value=9.6e-05  Score=66.90  Aligned_cols=166  Identities=10%  Similarity=0.030  Sum_probs=117.0

Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHH
Q 011378          307 SPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTL  386 (487)
Q Consensus       307 ~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  386 (487)
                      +.+...+..+-..+...|++++|...++...... +-+...+..+-..+.+.|+.++|...++.....  .|+.......
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~  190 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLV  190 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHH
Confidence            3344566677777888888888888888876542 335567777888888889999988888876543  3554432222


Q ss_pred             H-HHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhc
Q 011378          387 I-NGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKGLN-PDRSTYTTLINGHVSQ  463 (487)
Q Consensus       387 i-~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~ty~~l~~~~~~~  463 (487)
                      . ..+...++.+.|...+++....  .| +...+..+...+.+.|++++|...+.+.....-. .+...+..+...+...
T Consensus       191 ~~~~l~~~~~~~~a~~~l~~al~~--~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~  268 (287)
T 3qou_A          191 AQIELLXQAADTPEIQQLQQQVAE--NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAAL  268 (287)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcccCccHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHc
Confidence            2 2355667777777777766553  34 4667788888888999999999888888765321 1256788888888888


Q ss_pred             CCHHHHHHHHHHHH
Q 011378          464 NNLKEAFRFHDEML  477 (487)
Q Consensus       464 ~~~~~a~~~~~~m~  477 (487)
                      |+.++|...+++-+
T Consensus       269 g~~~~a~~~~r~al  282 (287)
T 3qou_A          269 GTGDALASXYRRQL  282 (287)
T ss_dssp             CTTCHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHH
Confidence            88888887776644

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.10  E-value=0.00077  Score=58.31  Aligned_cols=62  Identities=11%  Similarity=0.069  Sum_probs=36.4

Q ss_pred             hHHHHHHHHhcCChhhHHHHHHHHHHCCC-CCC-HHHHHHHHHHHHccCChhHHHHHHHHHHHC
Q 011378           68 YNSLINGLCKKGRCDRAKEVLDEMLQMGL-SPD-TATYNTLLVESCRKENMSEAEEIFCEMSRR  129 (487)
Q Consensus        68 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  129 (487)
                      +-.+-..+.+.|++++|...|+++.+..- .|. ...+..+..++.+.|++++|...|++..+.
T Consensus         7 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   70 (225)
T 2yhc_A            7 IYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   70 (225)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            33444556667777777777777665321 111 234555566666777777777777766543

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.09  E-value=4e-05  Score=63.63  Aligned_cols=62  Identities=11%  Similarity=0.127  Sum_probs=31.2

Q ss_pred             HhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          415 VITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       415 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      ...+..+...+.+.|++++|...|++.....-.+ +...+..+...+...|+.++|...+++.
T Consensus       108 ~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A          108 FELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHH
Confidence            4445555555555555555555555554432211 1334555555555555555555555543

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.09  E-value=0.00025  Score=60.59  Aligned_cols=124  Identities=11%  Similarity=-0.038  Sum_probs=70.6

Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC
Q 011378          280 TLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG  359 (487)
Q Consensus       280 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  359 (487)
                      .+-..+...|++++|...|.+.    +.|+...|..+...+...|++++|...++...... +.+...+..+-..|...|
T Consensus        11 ~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~   85 (213)
T 1hh8_A           11 NEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTE   85 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcc
Confidence            3444555666666666666544    24555666666666666666666666666655432 234455666666666666


Q ss_pred             ChHHHHHHHHHHHHCCCC--------------CC-hhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          360 DASKADEFLSKMVSEGVD--------------PD-SISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g~~--------------p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      +.++|...+++..+..-.              |+ ...+..+-..|.+.|++++|.+.+++..+
T Consensus        86 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  149 (213)
T 1hh8_A           86 KYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  149 (213)
T ss_dssp             CHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            666666666666543211              11 13445555555566666666666655544

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.08  E-value=0.00012  Score=73.36  Aligned_cols=153  Identities=8%  Similarity=0.000  Sum_probs=110.6

Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHH
Q 011378          288 VGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADE  366 (487)
Q Consensus       288 ~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  366 (487)
                      .|++++|...+++....  .| +...+..+-..+...|++++|...+++..+.. +.+...+..+-..|...|+.++|.+
T Consensus         2 ~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH--RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            47889999999877543  34 46788889999999999999999999987653 3356788888899999999999999


Q ss_pred             HHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhc---CChHHHHHHHHHHHH
Q 011378          367 FLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQ---GRMHDSELILWRMIE  443 (487)
Q Consensus       367 ~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~---g~~~~a~~~~~~m~~  443 (487)
                      .+++..+.. +.+...+..+-..|.+.|++++|.+.+++..+.. ..+...+..+...+...   |+.++|...+++..+
T Consensus        79 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           79 LLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            999987643 2246688888999999999999999999886642 22467788888899999   999999999999877


Q ss_pred             cC
Q 011378          444 KG  445 (487)
Q Consensus       444 ~g  445 (487)
                      .+
T Consensus       157 ~~  158 (568)
T 2vsy_A          157 QG  158 (568)
T ss_dssp             HT
T ss_pred             cC
Confidence            54

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

Probab=98.04  E-value=0.00011  Score=66.57  Aligned_cols=161  Identities=11%  Similarity=-0.017  Sum_probs=86.8

Q ss_pred             HhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHH-H
Q 011378          135 IVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTI-L  212 (487)
Q Consensus       135 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l-i  212 (487)
                      ...+..+...+.+.|++++|...|++....  .| +...+..+...+.+.|+.++|...+++....  .|+....... .
T Consensus       117 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~  192 (287)
T 3qou_A          117 EELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQ  192 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHH
Confidence            334445555666666777776666666543  23 2345555666666666666666666655432  2332222111 1


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCH
Q 011378          213 NGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEM  291 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~  291 (487)
                      ..+.+.+..+.|...+++..+.. +.+...+..+-..+...|+.++|+..|+...+..-.. +...+..+...|...|+.
T Consensus       193 ~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~  271 (287)
T 3qou_A          193 IELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTG  271 (287)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTT
T ss_pred             HHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCC
Confidence            22444555555666666655432 2345566666666666666666666666555432111 133556666666666666


Q ss_pred             HHHHHHHHH
Q 011378          292 EKANKLWAD  300 (487)
Q Consensus       292 ~~a~~~~~~  300 (487)
                      ++|...+++
T Consensus       272 ~~a~~~~r~  280 (287)
T 3qou_A          272 DALASXYRR  280 (287)
T ss_dssp             CHHHHHHHH
T ss_pred             CcHHHHHHH
Confidence            666555544

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.04  E-value=0.0004  Score=59.31  Aligned_cols=124  Identities=15%  Similarity=-0.039  Sum_probs=65.9

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC
Q 011378          141 LIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM  220 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~  220 (487)
                      +...+.+.|++++|...|++.    +.|+...|..+-..+.+.|+.++|...+++..+.. +.+...|..+..+|.+.|+
T Consensus        12 ~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~   86 (213)
T 1hh8_A           12 EGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   86 (213)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHccc
Confidence            334444555555555555543    23444555555555555555555555555544432 2234455555556666666


Q ss_pred             HHHHHHHHHHHHHcC--------------CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          221 LTEADDLFNEMLERG--------------VFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQK  269 (487)
Q Consensus       221 ~~~a~~~~~~m~~~~--------------~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~  269 (487)
                      +++|.+.|++..+..              ..| ....+..+-..|...|+.++|...|+...+.
T Consensus        87 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           87 YDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            666666666555421              111 1245566666666777777777776665543

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.03  E-value=0.00017  Score=72.34  Aligned_cols=152  Identities=14%  Similarity=0.024  Sum_probs=111.5

Q ss_pred             cCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011378          253 DGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFR  331 (487)
Q Consensus       253 ~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~  331 (487)
                      .|+.++|+..|+...+.  .| +...+..+-..+.+.|++++|...+++..+.. +.+...+..+...|...|++++|..
T Consensus         2 ~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH--RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            47889999999876543  34 35678888899999999999999999887642 2356788899999999999999999


Q ss_pred             HHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhcc---CCHHHHHHHHHHHHh
Q 011378          332 LWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVRE---ENMDKAFALVSKMEN  408 (487)
Q Consensus       332 ~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~---~~~~~a~~~~~~m~~  408 (487)
                      .++...+.. +.+...+..+-..|.+.|+.++|.+.+++..+.. +.+...+..+...+...   |+.++|.+.+++..+
T Consensus        79 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           79 LLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            999987653 3456788889999999999999999999987653 22466788889999999   999999999998876


Q ss_pred             C
Q 011378          409 Q  409 (487)
Q Consensus       409 ~  409 (487)
                      .
T Consensus       157 ~  157 (568)
T 2vsy_A          157 Q  157 (568)
T ss_dssp             H
T ss_pred             c
Confidence            4

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.00  E-value=6.4e-05  Score=62.38  Aligned_cols=60  Identities=17%  Similarity=0.133  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHH
Q 011378          240 FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWA  299 (487)
Q Consensus       240 ~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~  299 (487)
                      ...+..+-..+...|+.++|...|+...+....+ +...+..+...+...|+.++|...|+
T Consensus       108 ~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~  168 (176)
T 2r5s_A          108 FELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYR  168 (176)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHH
Confidence            3444444444555555555555554444332211 12234444444444444444444444

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.00  E-value=0.00012  Score=74.94  Aligned_cols=150  Identities=9%  Similarity=-0.047  Sum_probs=73.5

Q ss_pred             HccCCHHHHHHHHHHHHh------CCC-CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc
Q 011378          286 CKVGEMEKANKLWADMIS------RKI-SPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRS  358 (487)
Q Consensus       286 ~~~g~~~~a~~~~~~m~~------~~~-~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  358 (487)
                      ...|++++|.+.+++...      ... +.+...+..+..++...|++++|...++...+.. +.+...|..+-.+|...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHc
Confidence            445555555555555441      011 2233445555555555555555555555554321 22334454555555555


Q ss_pred             CChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHH
Q 011378          359 GDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       359 ~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~  436 (487)
                      |++++|...|++..+..  | +...+..+-.+|.+.|++++ .+.+++..+.  .| +...|..+-..+.+.|++++|..
T Consensus       481 g~~~~A~~~~~~al~l~--P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTF--PGELAPKLALAATAELAGNTDE-HKFYQTVWST--NDGVISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             TCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHh--CCchHHHHHHHHHHHHHcCCHHHHHH
Confidence            55555555555554322  2 23344555555555555555 5555544332  22 23445555555555555555555


Q ss_pred             HHHHH
Q 011378          437 ILWRM  441 (487)
Q Consensus       437 ~~~~m  441 (487)
                      .|++.
T Consensus       556 ~~~~a  560 (681)
T 2pzi_A          556 TLDEV  560 (681)
T ss_dssp             HHHTS
T ss_pred             HHHhh
Confidence            55543

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

Probab=98.00  E-value=0.00021  Score=61.11  Aligned_cols=162  Identities=14%  Similarity=0.067  Sum_probs=101.3

Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCC-hhhHHH----------------HHHHHHhcCCHHHHHHHHHHHHhCCCCCCh
Q 011378          283 DGFCKVGEMEKANKLWADMISRKISPN-YISYGI----------------LINGYCSMGHVTEAFRLWYEMVGKGIKPTL  345 (487)
Q Consensus       283 ~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~t~~~----------------li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  345 (487)
                      ..+...|++++|...|.+....  .|+ ...|..                +-.+|...|++++|...|+...+.. +-+.
T Consensus        12 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~   88 (208)
T 3urz_A           12 SAAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA-PNNV   88 (208)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCH
Confidence            4567789999999999887654  343 334555                7777788888888888888776543 3356


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHhccCC--HHHHHHHHHHHHhCCCCCCHhh--HHH
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD-SISYNTLINGFVREEN--MDKAFALVSKMENQGLVPDVIT--YNV  420 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~g~~p~~~~--~~~  420 (487)
                      ..+..+-..|...|+.++|...+++..+.  .|+ ...+..+-..|...++  .+.+...+...    +.|+...  +..
T Consensus        89 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~a~~~  162 (208)
T 3urz_A           89 DCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKL----SSPTKMQYARYR  162 (208)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHH----hCCCchhHHHHH
Confidence            67777777888888888888888887763  343 4566666666654443  23333333332    2344332  222


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHH
Q 011378          421 ILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTT  455 (487)
Q Consensus       421 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~  455 (487)
                      .-.++...|++++|...|++..+  +.|+......
T Consensus       163 ~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~  195 (208)
T 3urz_A          163 DGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKT  195 (208)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHH
Confidence            33344557788888888887653  4676544333

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.99  E-value=8.9e-05  Score=62.78  Aligned_cols=156  Identities=10%  Similarity=-0.051  Sum_probs=92.4

Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh----CCCCC-ChhhHHHHHHHHHhcCC
Q 011378          286 CKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVG----KGIKP-TLVSCNTIIKGYCRSGD  360 (487)
Q Consensus       286 ~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~~-~~~~~~~li~~~~~~~~  360 (487)
                      ...|++++|.+.++.... ........+..+-..+...|++++|...+++...    .+..| ...++..+-..|...|+
T Consensus         3 ~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ----CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            456788888884444332 1123456677777788888888888888877654    22222 23456666677777888


Q ss_pred             hHHHHHHHHHHHHC----CCCC--ChhhHHHHHHHHhccCCHHHHHHHHHHHHh----CCCCC-CHhhHHHHHHHHHhcC
Q 011378          361 ASKADEFLSKMVSE----GVDP--DSISYNTLINGFVREENMDKAFALVSKMEN----QGLVP-DVITYNVILTGFCRQG  429 (487)
Q Consensus       361 ~~~a~~~~~~m~~~----g~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p-~~~~~~~li~~~~~~g  429 (487)
                      +++|...+++..+.    +-.|  ....+..+-..+...|++++|...+++..+    .+-.+ -..++..+...+...|
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            88887777765532    2111  123466666777777777777777766542    11111 1123456666677777


Q ss_pred             ChHHHHHHHHHHH
Q 011378          430 RMHDSELILWRMI  442 (487)
Q Consensus       430 ~~~~a~~~~~~m~  442 (487)
                      ++++|...+++..
T Consensus       162 ~~~~A~~~~~~al  174 (203)
T 3gw4_A          162 NLLEAQQHWLRAR  174 (203)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH
Confidence            7777776666543

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

Probab=97.97  E-value=0.00035  Score=59.67  Aligned_cols=57  Identities=14%  Similarity=0.209  Sum_probs=28.7

Q ss_pred             HHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 011378          106 LLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKS  163 (487)
Q Consensus       106 ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  163 (487)
                      +-..+.+.|++++|...|++..+.. +-+...+..+-.++.+.|++++|...|++..+
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  116 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQ  116 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4444455555555555555554431 11344455555555555555555555555544

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

Probab=97.94  E-value=0.00032  Score=53.56  Aligned_cols=59  Identities=20%  Similarity=0.285  Sum_probs=23.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      +..+...+...|++++|...++...... +.+..++..+...+.+.|+.++|...++++.
T Consensus        12 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~   70 (125)
T 1na0_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKAL   70 (125)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3334444444444444444444443321 1223333334444444444444444444433

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.94  E-value=0.00016  Score=61.19  Aligned_cols=131  Identities=12%  Similarity=-0.079  Sum_probs=58.8

Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHH----CCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCc--CC
Q 011378          136 VSFSTLIGIFSRNGQLDRALMYFREMKS----AGLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEK----GCV--MD  204 (487)
Q Consensus       136 ~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~--~~  204 (487)
                      ..+..+-..+...|++++|...+++...    .+..| ....+..+-..+...|+.++|.+.+++..+.    +-.  ..
T Consensus        27 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  106 (203)
T 3gw4_A           27 GARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAA  106 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHH
Confidence            3444444455555555555555544432    11111 1223444444444555555554444433321    101  11


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          205 VVTYNTILNGLCRAKMLTEADDLFNEMLER----GVF-PDFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       205 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~-~~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      ...+..+-..+...|++++|.+.+++..+.    +-. .-..++..+-..+...|++++|...++..
T Consensus       107 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  173 (203)
T 3gw4_A          107 SANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRA  173 (203)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            223455555556666666666666555421    100 01123445555566666666666555443

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

Probab=97.93  E-value=0.00042  Score=52.91  Aligned_cols=98  Identities=14%  Similarity=0.224  Sum_probs=77.9

Q ss_pred             hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH
Q 011378          345 LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTG  424 (487)
Q Consensus       345 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  424 (487)
                      ...+..+...+...|++++|...++++.+.. +.+...+..+...+.+.|++++|...++++.+.. ..+...+..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            4567777888888999999999998887643 2356678888888889999999999998886642 3356778888888


Q ss_pred             HHhcCChHHHHHHHHHHHHc
Q 011378          425 FCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~  444 (487)
                      +.+.|++++|...++++...
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHh
Confidence            99999999999999888764

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.91  E-value=0.00036  Score=71.43  Aligned_cols=173  Identities=9%  Similarity=-0.089  Sum_probs=108.4

Q ss_pred             HccCChhHHHHHHHHHHH------CCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhc
Q 011378          111 CRKENMSEAEEIFCEMSR------RGVAP-DIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRN  183 (487)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~------~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~  183 (487)
                      ...+++++|.+.+++..+      ....| +...+..+...+.+.|++++|...|++..+.. .-+...|..+-.++.+.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHc
Confidence            566777777777776651      01223 34456666677777777777777777766532 12345666677777777


Q ss_pred             CCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 011378          184 GFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLF  263 (487)
Q Consensus       184 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~  263 (487)
                      |+.++|...|++..+.. +-+...|..+-.++.+.|++++ .+.|++..+.. +-+...|..+-.++.+.|+.++|+..|
T Consensus       481 g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~  557 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRTL  557 (681)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            77777777777766542 1244566777777777788877 77777776543 235567777777788888888888777


Q ss_pred             HHHHHCCCCCC-eeehHHHHHHHHccC
Q 011378          264 DIMTQKSIKPD-IVTYNTLIDGFCKVG  289 (487)
Q Consensus       264 ~~m~~~~~~~~-~~~~~~li~~~~~~g  289 (487)
                      +...+  +.|+ ...+..+..++...+
T Consensus       558 ~~al~--l~P~~~~a~~~~~~~~~~~~  582 (681)
T 2pzi_A          558 DEVPP--TSRHFTTARLTSAVTLLSGR  582 (681)
T ss_dssp             HTSCT--TSTTHHHHHHHHHHHTC---
T ss_pred             Hhhcc--cCcccHHHHHHHHHHHHccC
Confidence            65543  2343 344555555554433

>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=97.83  E-value=0.0007  Score=54.90  Aligned_cols=127  Identities=14%  Similarity=0.111  Sum_probs=69.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh
Q 011378          348 CNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCR  427 (487)
Q Consensus       348 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  427 (487)
                      +..+-..+...|++++|...+++..+.. +.+...+..+...|...|++++|...+++..+.. ..+...|..+...+.+
T Consensus        16 ~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~   93 (166)
T 1a17_A           16 LKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMA   93 (166)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHH
Confidence            3344445555566666666665554422 1234455556666666666666666666554431 2234556666666667


Q ss_pred             cCChHHHHHHHHHHHHcCCCCCHHHH--HHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          428 QGRMHDSELILWRMIEKGLNPDRSTY--TTLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       428 ~g~~~~a~~~~~~m~~~g~~p~~~ty--~~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      .|++++|...+++..+..- .+...+  -.....+...|++++|.+.++...
T Consensus        94 ~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           94 LGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             TTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            7777777777766654321 122233  223333556677777777766543

>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=97.80  E-value=0.00093  Score=54.13  Aligned_cols=127  Identities=8%  Similarity=-0.051  Sum_probs=69.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHh
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFV  391 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  391 (487)
                      .+..+...+...|++++|...|+...... +.+...+..+-..+...|++++|...+++..+.. +.+...+..+-..|.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            34445555556666666666666554432 2244555556666666666666666666655432 123445666666666


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCHhhH--HHHHHHHHhcCChHHHHHHHHHH
Q 011378          392 REENMDKAFALVSKMENQGLVPDVITY--NVILTGFCRQGRMHDSELILWRM  441 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~~g~~p~~~~~--~~li~~~~~~g~~~~a~~~~~~m  441 (487)
                      ..|++++|...+++..+.. ..+...+  -.....+.+.|++++|...+.+.
T Consensus        93 ~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            6777777777766655431 1122233  22223355666777776666554

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.76  E-value=0.014  Score=52.74  Aligned_cols=216  Identities=11%  Similarity=0.061  Sum_probs=102.5

Q ss_pred             ChhHHHHHHHHHhhCCCCCCc-cchHHHHHHHHhcC--ChhhHHHHHHHHHHCCCCCCHHHHHHHHHHH----Hcc---C
Q 011378           45 FLEEAFQLMNSMSGKGLKPGV-FTYNSLINGLCKKG--RCDRAKEVLDEMLQMGLSPDTATYNTLLVES----CRK---E  114 (487)
Q Consensus        45 ~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~--~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~----~~~---~  114 (487)
                      ..++|+++.+.+...  .|+- ..|+.--..+...+  +++++++.++.+.... +-+...|+---..+    ...   +
T Consensus        48 ~s~~aL~~t~~~L~~--nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l~~~~  124 (306)
T 3dra_A           48 YSERALHITELGINE--LASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELNNNDF  124 (306)
T ss_dssp             CSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCHHHHHHHHHHHHH--CcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhccccC
Confidence            345788877777653  3443 23554444555556  7777777777776532 11223333222222    223   5


Q ss_pred             ChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHH--HHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCC------H
Q 011378          115 NMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLD--RALMYFREMKSAGLVPDNVLYTIIINGYCRNGF------V  186 (487)
Q Consensus       115 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~--~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~------~  186 (487)
                      ++++++++++.+.+.. +-|...|+.--.+..+.|.++  +++++++++.+... -|...|+.--..+.+.+.      .
T Consensus       125 ~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~~~  202 (306)
T 3dra_A          125 DPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDNTI  202 (306)
T ss_dssp             CTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhhhH
Confidence            6677777777776542 225556665555555666666  66666666665331 233344433333333333      4


Q ss_pred             HHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCH-HHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 011378          187 LEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKML-TEADDLFNEMLERG--VFPDFYTFTTLIHGHCKDGNMNKALNLF  263 (487)
Q Consensus       187 ~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~m~~~~--~~~~~~t~~~li~~~~~~g~~~~a~~~~  263 (487)
                      +++++.++.+.... +-|...|+-+-..+.+.|.. +.+..+..+..+.+  -..++..+..+...|.+.|+.++|.+++
T Consensus       203 ~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~  281 (306)
T 3dra_A          203 DEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVY  281 (306)
T ss_dssp             HHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            44444444444332 12333444444444444332 22223333322211  1123344444444444444444444444


Q ss_pred             HHH
Q 011378          264 DIM  266 (487)
Q Consensus       264 ~~m  266 (487)
                      +.+
T Consensus       282 ~~l  284 (306)
T 3dra_A          282 DLL  284 (306)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

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

Probab=97.76  E-value=0.00083  Score=51.69  Aligned_cols=92  Identities=12%  Similarity=0.050  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhc
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVR  392 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  392 (487)
                      +..+...+...|++++|...++...... +.+...+..+...+...|+.++|...+++..+.. +.+...+..+...|.+
T Consensus        15 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~   92 (131)
T 2vyi_A           15 LKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSS   92 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHH
Confidence            3334444444444444444444443321 1223333444444444444444444444433321 1122333333344444


Q ss_pred             cCCHHHHHHHHHHH
Q 011378          393 EENMDKAFALVSKM  406 (487)
Q Consensus       393 ~~~~~~a~~~~~~m  406 (487)
                      .|++++|...+++.
T Consensus        93 ~~~~~~A~~~~~~~  106 (131)
T 2vyi_A           93 LNKHVEAVAYYKKA  106 (131)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHH
Confidence            44444444444433

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.73  E-value=0.0032  Score=60.26  Aligned_cols=194  Identities=7%  Similarity=-0.034  Sum_probs=94.8

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCC-Cee---------------ehHHHHHHHHccCCHHHHHHHHHHHHhC-CCCCCh
Q 011378          248 HGHCKDGNMNKALNLFDIMTQKSIKP-DIV---------------TYNTLIDGFCKVGEMEKANKLWADMISR-KISPNY  310 (487)
Q Consensus       248 ~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~---------------~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~p~~  310 (487)
                      ..+.+.|++++|++.|....+..... +..               .+..|...|.+.|++++|.+.+...... +..++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            45667788888888887776543222 111               1455666667777777777666654421 111111


Q ss_pred             h----hHHHHHHHHHhcCCHHHHHHHHHHHHh----CCCCCC-hhhHHHHHHHHHhcCChHHHHHHHHHHHHC--CCC--
Q 011378          311 I----SYGILINGYCSMGHVTEAFRLWYEMVG----KGIKPT-LVSCNTIIKGYCRSGDASKADEFLSKMVSE--GVD--  377 (487)
Q Consensus       311 ~----t~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~--  377 (487)
                      .    ..+.+-..+...|+.+++..++.....    .+..+. ..++..+...|...|++++|..++++....  +..  
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~  171 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDK  171 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCS
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccc
Confidence            1    111122222334566666666654432    222222 234455555666666666666666554422  111  


Q ss_pred             CC-hhhHHHHHHHHhccCCHHHHHHHHHHHHh----CCCCCC--HhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          378 PD-SISYNTLINGFVREENMDKAFALVSKMEN----QGLVPD--VITYNVILTGFCRQGRMHDSELILWRM  441 (487)
Q Consensus       378 p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m  441 (487)
                      |. ..++..+...|...|++++|...+++...    .+..|.  ...+..+...+...|++++|...|.+.
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a  242 (434)
T 4b4t_Q          172 PSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFES  242 (434)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            11 23455555556666666666665554332    111111  123444444555555666665555554

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

Probab=97.69  E-value=0.0013  Score=50.57  Aligned_cols=120  Identities=8%  Similarity=0.013  Sum_probs=92.7

Q ss_pred             ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          344 TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                      +...+..+...+...|++++|...+++..... +.+...+..+...|...|++++|.+.+++..+.. ..+...+..+..
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~   88 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHH
Confidence            34566777788889999999999999987643 2356778888899999999999999998887642 234677888888


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 011378          424 GFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNL  466 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~  466 (487)
                      .+.+.|++++|...+++.....- .+...+..+...+...|++
T Consensus        89 ~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           89 ALSSLNKHVEAVAYYKKALELDP-DNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHHhcC
Confidence            99999999999999999876521 2456666677777666653

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

Probab=97.67  E-value=0.0012  Score=51.09  Aligned_cols=60  Identities=5%  Similarity=-0.022  Sum_probs=24.5

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      .+..+...|...|++++|.+.+++..+.. ..+...+..+...+.+.|++++|...+++..
T Consensus        52 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  111 (133)
T 2lni_A           52 LYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKAL  111 (133)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            33334444444444444444444333221 1123334444444444444444444444443

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

Probab=97.62  E-value=0.0018  Score=50.07  Aligned_cols=95  Identities=19%  Similarity=0.130  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHH
Q 011378          137 SFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLC  216 (487)
Q Consensus       137 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~  216 (487)
                      .+..+...+.+.|++++|...|++..... ..+...+..+...+...|+.++|.+.+++..+.. +.+...|..+...+.
T Consensus        18 ~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~   95 (133)
T 2lni_A           18 MVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALE   95 (133)
T ss_dssp             HHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHH
Confidence            34444444445555555555544443321 1123334444444444444444444444443321 112334444444455


Q ss_pred             hcCCHHHHHHHHHHHHH
Q 011378          217 RAKMLTEADDLFNEMLE  233 (487)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (487)
                      +.|++++|.+.|++..+
T Consensus        96 ~~~~~~~A~~~~~~~~~  112 (133)
T 2lni_A           96 AMKDYTKAMDVYQKALD  112 (133)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHH
Confidence            55555555555554443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.58  E-value=0.00044  Score=55.56  Aligned_cols=82  Identities=17%  Similarity=0.143  Sum_probs=39.1

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHh
Q 011378          350 TIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCR  427 (487)
Q Consensus       350 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~  427 (487)
                      .+-..|.+.|++++|.+.+++..+.  .| +...|..+-..|.+.|++++|...+++..+.  .| +...|..+...|.+
T Consensus        36 ~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~  111 (150)
T 4ga2_A           36 YFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCK  111 (150)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            3444444555555555555544432  12 2334555555555555555555555544432  23 23445555555555


Q ss_pred             cCChHHHH
Q 011378          428 QGRMHDSE  435 (487)
Q Consensus       428 ~g~~~~a~  435 (487)
                      .|+.+++.
T Consensus       112 ~~~~~~aa  119 (150)
T 4ga2_A          112 NDVTDGRA  119 (150)
T ss_dssp             HCSSSSHH
T ss_pred             cCChHHHH
Confidence            55554433

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.56  E-value=0.0048  Score=59.06  Aligned_cols=196  Identities=12%  Similarity=0.012  Sum_probs=139.9

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCC-CH---------------HHHHHHHHHHHhcCCHHHHHHHHHHHHHCC-CCCCe
Q 011378          213 NGLCRAKMLTEADDLFNEMLERGVFP-DF---------------YTFTTLIHGHCKDGNMNKALNLFDIMTQKS-IKPDI  275 (487)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~~-~~---------------~t~~~li~~~~~~g~~~~a~~~~~~m~~~~-~~~~~  275 (487)
                      ..+.+.|++++|.+.|.+..+..-.. +.               ..+..+...|...|++++|.+.+......- -.++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            55678899999999999998754322 11               237788999999999999999998765421 11121


Q ss_pred             ---eehHHHH-HHHHccCCHHHHHHHHHHHHh----CCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCC
Q 011378          276 ---VTYNTLI-DGFCKVGEMEKANKLWADMIS----RKISPN-YISYGILINGYCSMGHVTEAFRLWYEMVGK----GIK  342 (487)
Q Consensus       276 ---~~~~~li-~~~~~~g~~~~a~~~~~~m~~----~~~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~  342 (487)
                         .....++ ..+...|+.++|..++.....    .+..+. ..++..+...+...|++++|..++.+....    +-+
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~  171 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDK  171 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCS
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccc
Confidence               1222233 334557889999999987653    333333 456788999999999999999999887642    222


Q ss_pred             CC-hhhHHHHHHHHHhcCChHHHHHHHHHHHHC--CC--CCC--hhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          343 PT-LVSCNTIIKGYCRSGDASKADEFLSKMVSE--GV--DPD--SISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       343 ~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--g~--~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      +. ..++..+...|...|++++|..++++....  .+  +|.  ...+..+...+...+++++|...+.+.-+
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          172 PSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            22 347888899999999999999999887532  22  222  24567777888899999999998876644

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.55  E-value=0.0021  Score=59.46  Aligned_cols=131  Identities=14%  Similarity=-0.005  Sum_probs=76.5

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--------------hhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 011378          309 NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT--------------LVSCNTIIKGYCRSGDASKADEFLSKMVSE  374 (487)
Q Consensus       309 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  374 (487)
                      +...+..+-..|...|++++|...|+......-...              ...|..+-.+|.+.|++++|...+++..+.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            345667777777778888888888777665421111              355666666666666666666666666543


Q ss_pred             CCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHH-HHHHHHH
Q 011378          375 GVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSE-LILWRMI  442 (487)
Q Consensus       375 g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~-~~~~~m~  442 (487)
                      . +.+...|..+-.+|...|++++|...|++..+.  .| +...+..+...+.+.|+.+++. ..++.|.
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2 123445566666666666666666666655442  23 3445555555666666666652 3444443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.55  E-value=0.0016  Score=60.22  Aligned_cols=129  Identities=12%  Similarity=-0.042  Sum_probs=90.7

Q ss_pred             eeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC--------------hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 011378          275 IVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN--------------YISYGILINGYCSMGHVTEAFRLWYEMVGKG  340 (487)
Q Consensus       275 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~--------------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~  340 (487)
                      ...+..+-..|.+.|++++|...|.+.....-...              ...|..+-.+|...|++++|...++......
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  226 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD  226 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            44566677778888888888888887765432211              3677788888888888888888888776643


Q ss_pred             CCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHH-HHHHHH
Q 011378          341 IKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAF-ALVSKM  406 (487)
Q Consensus       341 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~-~~~~~m  406 (487)
                       +.+...|..+-.+|...|++++|...+++..+.  .| +...+..+-..+.+.++.++|. ..+++|
T Consensus       227 -p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  291 (336)
T 1p5q_A          227 -SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLAREKKLYANM  291 (336)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             335667777778888888888888888887754  24 3456777777777777777773 344444

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.54  E-value=0.00048  Score=55.31  Aligned_cols=19  Identities=21%  Similarity=0.342  Sum_probs=7.1

Q ss_pred             HHHHHHhCCCHHHHHHHHH
Q 011378          141 LIGIFSRNGQLDRALMYFR  159 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~  159 (487)
                      +-.++.+.|++++|...|+
T Consensus        71 lg~~~~~~~~~~~A~~~~~   89 (150)
T 4ga2_A           71 LGLLYELEENTDKAVECYR   89 (150)
T ss_dssp             HHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHcCchHHHHHHHH
Confidence            3333333333333333333

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.53  E-value=0.00078  Score=55.59  Aligned_cols=119  Identities=11%  Similarity=0.110  Sum_probs=58.8

Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHH-HHhcCCh--HH
Q 011378          287 KVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKG-YCRSGDA--SK  363 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~-~~~~~~~--~~  363 (487)
                      ..|++++|...+....... +.+...|..+...|...|++++|...|+...... +.+...+..+-.. +...|+.  ++
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHH
Confidence            3445555555555443321 1234455555666666666666666666554332 2233444444444 4455555  66


Q ss_pred             HHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          364 ADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       364 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      |...+++..+.. +.+...+..+...|...|++++|...+++..+
T Consensus       100 A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          100 TRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            666666555432 11234455555555666666666666655544

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

Probab=97.52  E-value=0.0034  Score=50.30  Aligned_cols=95  Identities=11%  Similarity=-0.050  Sum_probs=55.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGF  425 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~  425 (487)
                      .+..+-..+.+.|++++|...|+...... +-+...|..|-.+|...|++++|...+++..+.  .| +...|..+-..|
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l--~P~~~~~~~~lg~~~  114 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL--GKNDYTPVFHTGQCQ  114 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CCCCcHHHHHHHHHH
Confidence            34445555666666666666666665432 123445666666666666666666666665542  23 344556666666


Q ss_pred             HhcCChHHHHHHHHHHHHc
Q 011378          426 CRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       426 ~~~g~~~~a~~~~~~m~~~  444 (487)
                      .+.|++++|...|++..+.
T Consensus       115 ~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          115 LRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            6666666666666665543

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.49  E-value=0.0011  Score=54.74  Aligned_cols=120  Identities=8%  Similarity=0.052  Sum_probs=89.3

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHH-HhccCCH--HH
Q 011378          322 SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLING-FVREENM--DK  398 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~-~~~~~~~--~~  398 (487)
                      ..|++++|...++...... +.+...|..+-..|...|++++|...+++..... +.+...+..+... |...|++  ++
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHH
Confidence            4577888888888766543 3466788888889999999999999999887643 1245567777777 7788888  99


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      |...+++..+.. ..+...+..+...+...|++++|...+++....
T Consensus       100 A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A          100 TRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            999998886642 224667788888899999999999999998764

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

Probab=97.47  E-value=0.002  Score=47.90  Aligned_cols=96  Identities=8%  Similarity=-0.087  Sum_probs=52.9

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-CCHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLN-PDRSTYTTLINGH  460 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~ty~~l~~~~  460 (487)
                      .+..+...+...|++++|...+++..+.. ..+...|..+...+.+.|++++|...+++..+..-. .+...+..+...|
T Consensus         8 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~   86 (112)
T 2kck_A            8 EYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADAL   86 (112)
T ss_dssp             GGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHH
Confidence            34444555555666666666665554321 123445555556666666666666666665543210 0345566666666


Q ss_pred             Hhc-CCHHHHHHHHHHHHH
Q 011378          461 VSQ-NNLKEAFRFHDEMLQ  478 (487)
Q Consensus       461 ~~~-~~~~~a~~~~~~m~~  478 (487)
                      ... |++++|.+.+++..+
T Consensus        87 ~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           87 RYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             TTCSSCSHHHHHHHHHHGG
T ss_pred             HHHhCCHHHHHHHHHHHhh
Confidence            666 666666666666553

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.45  E-value=0.06  Score=48.60  Aligned_cols=219  Identities=8%  Similarity=-0.006  Sum_probs=157.9

Q ss_pred             CChhhHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcC--ChhHHHHHHHHHhhCCCCCC-ccchHHHHHHH----Hhc--
Q 011378            9 HKIDSAKMFLCEMEQKGVYPD-TVTYNTLINAYCREG--FLEEAFQLMNSMSGKGLKPG-VFTYNSLINGL----CKK--   78 (487)
Q Consensus         9 ~~~~~a~~~~~~~~~~g~~p~-~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~----~~~--   78 (487)
                      ...++|....+.+....  |+ ...|+.--..+...+  ++++++++++.+...  .|. ..+|+.--..+    ...  
T Consensus        47 e~s~~aL~~t~~~L~~n--P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~--nPk~y~aW~~R~~iL~~~~~~l~~  122 (306)
T 3dra_A           47 EYSERALHITELGINEL--ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALD--NEKNYQIWNYRQLIIGQIMELNNN  122 (306)
T ss_dssp             CCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHH--CTTCCHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCHHHHHHHHHHHHHC--cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHH--CcccHHHHHHHHHHHHHHHHhccc
Confidence            34468888888876643  53 456787777777777  999999999998764  243 34455433333    344  


Q ss_pred             -CChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChh--HHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCC-----
Q 011378           79 -GRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMS--EAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQ-----  150 (487)
Q Consensus        79 -~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~--~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~-----  150 (487)
                       +++++++++++.+.+.. +-|...|+---..+.+.+..+  ++++.++.+.+... -|...|+.--.+..+.+.     
T Consensus       123 ~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~  200 (306)
T 3dra_A          123 DFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDN  200 (306)
T ss_dssp             CCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhh
Confidence             78999999999998743 346777776666677778777  99999999987653 367778776666666666     


Q ss_pred             -HHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHH-HHHHHHHHHHcC--CcCChhhHHHHHHHHHhcCCHHHHHH
Q 011378          151 -LDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLE-ALKMRDEMLEKG--CVMDVVTYNTILNGLCRAKMLTEADD  226 (487)
Q Consensus       151 -~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~-a~~~~~~m~~~g--~~~~~~~~~~li~~~~~~~~~~~a~~  226 (487)
                       ++++++.++++.... .-|...|+-+-..+.+.|...+ +..+.++..+.+  -+.+...+..+...|.+.|+.++|.+
T Consensus       201 ~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~  279 (306)
T 3dra_A          201 TIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRT  279 (306)
T ss_dssp             HHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHH
Confidence             888999988877643 2356678888777878777444 445665554432  23466778889999999999999999


Q ss_pred             HHHHHHHc
Q 011378          227 LFNEMLER  234 (487)
Q Consensus       227 ~~~~m~~~  234 (487)
                      +++.+.++
T Consensus       280 ~~~~l~~~  287 (306)
T 3dra_A          280 VYDLLKSK  287 (306)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhc
Confidence            99998763

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

Probab=97.44  E-value=0.0029  Score=48.86  Aligned_cols=95  Identities=9%  Similarity=0.060  Sum_probs=64.2

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFC  426 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  426 (487)
                      .+...=..|.+.|++++|.+.|++..+.. +.+...|..+-.+|.+.|++++|...+++..+.. ..+...|..+-..+.
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~   92 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLV   92 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHH
Confidence            45555666777778888877777766532 2245567777777777777777777777665432 223556777777777


Q ss_pred             hcCChHHHHHHHHHHHH
Q 011378          427 RQGRMHDSELILWRMIE  443 (487)
Q Consensus       427 ~~g~~~~a~~~~~~m~~  443 (487)
                      ..|++++|...|++..+
T Consensus        93 ~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           93 AMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHH
Confidence            77777777777777665

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

Probab=97.44  E-value=0.0021  Score=47.81  Aligned_cols=94  Identities=13%  Similarity=0.016  Sum_probs=40.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CCeeehHHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIK-PDIVTYNTLIDGFC  286 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-~~~~~~~~li~~~~  286 (487)
                      |..+...+.+.|++++|...|++..+.. +.+...+..+-..+...|++++|...|+...+..-. .+...+..+...+.
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~   87 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALR   87 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHH
Confidence            3344444444455555555554444321 123334444444444455555555544444332110 02233444444444


Q ss_pred             cc-CCHHHHHHHHHHHH
Q 011378          287 KV-GEMEKANKLWADMI  302 (487)
Q Consensus       287 ~~-g~~~~a~~~~~~m~  302 (487)
                      +. |++++|.+.+....
T Consensus        88 ~~~~~~~~A~~~~~~~~  104 (112)
T 2kck_A           88 YIEGKEVEAEIAEARAK  104 (112)
T ss_dssp             TCSSCSHHHHHHHHHHG
T ss_pred             HHhCCHHHHHHHHHHHh
Confidence            44 44444444444443

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

Probab=97.43  E-value=0.006  Score=48.82  Aligned_cols=95  Identities=14%  Similarity=0.073  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHH
Q 011378          137 SFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLC  216 (487)
Q Consensus       137 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~  216 (487)
                      .+..+-..+.+.|++++|...|++..... +.+...|..+-.+|.+.|+.++|...+++..+.. +-++..|..+-.+|.
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~  115 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHH
Confidence            34444455566666666666666655432 1123445555555555555555555555554432 113344555555555


Q ss_pred             hcCCHHHHHHHHHHHHH
Q 011378          217 RAKMLTEADDLFNEMLE  233 (487)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (487)
                      +.|++++|...|++..+
T Consensus       116 ~lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          116 RLKAPLKAKECFELVIQ  132 (151)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            55555555555555554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.43  E-value=0.0028  Score=56.28  Aligned_cols=186  Identities=9%  Similarity=-0.086  Sum_probs=91.5

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHH-------HHHHHhcCCHHHHHHHHHHHHHCCCCCCee-------------
Q 011378          217 RAKMLTEADDLFNEMLERGVFPDFYTFTTL-------IHGHCKDGNMNKALNLFDIMTQKSIKPDIV-------------  276 (487)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~~~~~~~~t~~~l-------i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------------  276 (487)
                      ..++...|.+.|.+..+.. +-....|..+       ...+.+.++..+++..+.  +..++.|+..             
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-ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLS--GSVQISMSTLNARIAIGGLYGDI   94 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHH--HTTTCCGGGGCCEEECCTTTCCC
T ss_pred             cCCCHHHHHHHHHHHHHhC-hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHH--HHhcCChhhhhhhhccCCccccc
Confidence            5678888888888877642 1133455544       223333222333332222  2234344311             


Q ss_pred             ---------ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--h
Q 011378          277 ---------TYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT--L  345 (487)
Q Consensus       277 ---------~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--~  345 (487)
                               ..-.+...+...|++++|.++|..+...+  |+....-.+-..+.+.+++++|+..|+...... .|.  .
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                     01223455566677777777776554332  433233344445666677777776665332211 110  1


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC--hhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD--SISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      ..+..+=.++.+.|+.++|...+++.......|.  ......+-.++.+.|+.++|...|+++..
T Consensus       172 ~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a  236 (282)
T 4f3v_A          172 AAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQT  236 (282)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            2344445556666666666666666553332233  11233333445556666666666666554

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.43  E-value=0.0042  Score=48.37  Aligned_cols=99  Identities=8%  Similarity=0.008  Sum_probs=76.8

Q ss_pred             CChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHH
Q 011378          343 PTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVIL  422 (487)
Q Consensus       343 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  422 (487)
                      .+...+..+-..+...|++++|...++...... +.+...+..+-..|...|++++|...+++..+.. ..+...|..+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            456677788888888999999999998877643 2246678888888888999999998888876642 22466788888


Q ss_pred             HHHHhcCChHHHHHHHHHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ..+...|++++|...|.+...
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHH
Confidence            888889999999888888764

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.42  E-value=0.0023  Score=56.72  Aligned_cols=126  Identities=7%  Similarity=-0.105  Sum_probs=71.2

Q ss_pred             HHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC--hhhHHHHHHHHHhc
Q 011378          106 LLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD--NVLYTIIINGYCRN  183 (487)
Q Consensus       106 ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~--~~~~~~ll~~~~~~  183 (487)
                      +...+...|++++|.++|+.+...+  |+....-.+-..+.+.+++++|+..|+...... .|.  ...+..+=.++.+.
T Consensus       108 yA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~L  184 (282)
T 4f3v_A          108 FAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAANL  184 (282)
T ss_dssp             HHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHHC
Confidence            3445556667777777776665432  433233344446667777777777776433211 110  22455566666777


Q ss_pred             CCHHHHHHHHHHHHHcCCcCC--hhhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011378          184 GFVLEALKMRDEMLEKGCVMD--VVTYNTILNGLCRAKMLTEADDLFNEMLER  234 (487)
Q Consensus       184 ~~~~~a~~~~~~m~~~g~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (487)
                      |+.++|+..+++.......|.  .......-.++.+.|+.++|..+|+++...
T Consensus       185 G~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          185 ALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             TCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            777777777776653322132  223444555566677777777777777664

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.40  E-value=0.0083  Score=44.83  Aligned_cols=56  Identities=23%  Similarity=0.194  Sum_probs=21.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  371 (487)
                      .+...+...|++++|...++...... +.+...+..+-..+...|+.++|...+++.
T Consensus         9 ~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~   64 (118)
T 1elw_A            9 EKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKT   64 (118)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence            33333444444444444444433221 112333333333344444444444444433

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.37  E-value=0.0083  Score=53.77  Aligned_cols=91  Identities=12%  Similarity=-0.053  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFC  286 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~  286 (487)
                      +..+...+.+.|++++|...|++..+.. +-+...|..+-..|.+.|++++|+..++...+.  .| +...+..+-.+|.
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            7 LKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            3334444444555555555555444321 113444444445555555555555555444322  22 2233444444555


Q ss_pred             ccCCHHHHHHHHHHH
Q 011378          287 KVGEMEKANKLWADM  301 (487)
Q Consensus       287 ~~g~~~~a~~~~~~m  301 (487)
                      ..|++++|...|...
T Consensus        84 ~~g~~~~A~~~~~~a   98 (281)
T 2c2l_A           84 EMESYDEAIANLQRA   98 (281)
T ss_dssp             HTTCHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHH
Confidence            555555555555443

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.37  E-value=0.0039  Score=46.70  Aligned_cols=98  Identities=9%  Similarity=0.041  Sum_probs=71.0

Q ss_pred             hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHH
Q 011378          345 LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTG  424 (487)
Q Consensus       345 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  424 (487)
                      ...+..+...+...|++++|...++...... +.+...+..+...|...|++++|...+++..+.. ..+...+..+...
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   81 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            4556667777888888888888888876542 2255667777778888888888888887776542 2245667777778


Q ss_pred             HHhcCChHHHHHHHHHHHHc
Q 011378          425 FCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~  444 (487)
                      +.+.|++++|...+++..+.
T Consensus        82 ~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHhhHHHHHHHHHHHHHc
Confidence            88888888888888877643

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

Probab=97.37  E-value=0.0069  Score=46.72  Aligned_cols=96  Identities=13%  Similarity=0.001  Sum_probs=62.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGF  390 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  390 (487)
                      ..+...-..|.+.|++++|...|++..+.. +.+...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.+|
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~   91 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHH
Confidence            445666666777777777777777665432 3345566666677777777777777777766532 12345666666777


Q ss_pred             hccCCHHHHHHHHHHHHh
Q 011378          391 VREENMDKAFALVSKMEN  408 (487)
Q Consensus       391 ~~~~~~~~a~~~~~~m~~  408 (487)
                      ...|++++|.+.|++..+
T Consensus        92 ~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           92 VAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            777777777777766654

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.36  E-value=0.0055  Score=54.97  Aligned_cols=95  Identities=11%  Similarity=-0.080  Sum_probs=53.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011378          172 LYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHC  251 (487)
Q Consensus       172 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~  251 (487)
                      .+..+-..+.+.|+.++|...+.+..+.. +-+...|..+-.+|.+.|++++|...+++..+.. +-+...+..+-.+|.
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            33444444455555555555555444321 1244455666666666666666666666665432 224556666666777


Q ss_pred             hcCCHHHHHHHHHHHHH
Q 011378          252 KDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       252 ~~g~~~~a~~~~~~m~~  268 (487)
                      ..|++++|+..|+...+
T Consensus        84 ~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           84 EMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            77777777777765543

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.36  E-value=0.0038  Score=47.86  Aligned_cols=94  Identities=12%  Similarity=0.110  Sum_probs=45.5

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCC--CCCC----HhhHHHHH
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQG--LVPD----VITYNVIL  422 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g--~~p~----~~~~~~li  422 (487)
                      ..+-..+...|++++|...+++..... +.+...+..+...|...|++++|...+++..+..  ..++    ...|..+.
T Consensus         8 ~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la   86 (131)
T 1elr_A            8 KELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHH
Confidence            334444444455555555554444322 1233344444555555555555555555443321  0111    34455555


Q ss_pred             HHHHhcCChHHHHHHHHHHHH
Q 011378          423 TGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ..+.+.|++++|...+++..+
T Consensus        87 ~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           87 NSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHH
Confidence            566666666666666666554

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.36  E-value=0.0018  Score=51.93  Aligned_cols=60  Identities=13%  Similarity=-0.022  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      .+..+...+...|++++|.+.+++..+.    +..+ ...++..+-..+...|+.++|...++..
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  155 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  155 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            3444555555666666666666554421    1100 1234445555555666666666555543

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.35  E-value=0.0015  Score=52.38  Aligned_cols=97  Identities=11%  Similarity=0.055  Sum_probs=57.3

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHh----CCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-CHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMEN----QGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEK----GLNP-DRS  451 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~  451 (487)
                      ++..+-..|...|++++|.+.+++..+    .+-.+ ....+..+...+...|++++|...+++..+.    +-.+ ...
T Consensus        51 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  130 (164)
T 3ro3_A           51 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  130 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHH
Confidence            445555555666666666666554432    11111 1334566666777777777777777765532    1111 123


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          452 TYTTLINGHVSQNNLKEAFRFHDEMLQ  478 (487)
Q Consensus       452 ty~~l~~~~~~~~~~~~a~~~~~~m~~  478 (487)
                      .+..+...|...|++++|.+.+++-.+
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            566677788888888888888877654

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.32  E-value=0.004  Score=49.68  Aligned_cols=98  Identities=15%  Similarity=-0.020  Sum_probs=78.1

Q ss_pred             ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHH
Q 011378          344 TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVIL  422 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li  422 (487)
                      +...+..+-..+.+.|++++|...++...... +.+...|..+-.+|...|++++|...+++....  .| +...|..+-
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg   96 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM--DIXEPRFPFHAA   96 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCTHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCCchHHHHHH
Confidence            34456667778889999999999999887643 235667888888899999999999999888654  34 456788888


Q ss_pred             HHHHhcCChHHHHHHHHHHHHc
Q 011378          423 TGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       423 ~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      ..|...|++++|...|++..+.
T Consensus        97 ~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           97 ECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            8999999999999999987653

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.30  E-value=0.0032  Score=48.27  Aligned_cols=96  Identities=18%  Similarity=0.170  Sum_probs=47.6

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--cCC----hhhHHHH
Q 011378          138 FSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGC--VMD----VVTYNTI  211 (487)
Q Consensus       138 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~----~~~~~~l  211 (487)
                      +..+...+.+.|+++.|...|++..... ..+...+..+...+...|+.++|...+++..+...  .++    ...|..+
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l   85 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHH
Confidence            3444445555555555555555544322 12233444455555555555555555554443211  111    3345555


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc
Q 011378          212 LNGLCRAKMLTEADDLFNEMLER  234 (487)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~  234 (487)
                      ...+.+.|+++.|.+.|++..+.
T Consensus        86 a~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           86 GNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHh
Confidence            55666666666666666665553

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

Probab=97.30  E-value=0.0045  Score=48.86  Aligned_cols=97  Identities=8%  Similarity=-0.071  Sum_probs=74.0

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHH
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGF  425 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  425 (487)
                      ..+..+-..+.+.|++++|...++...... +.+...|..+-.+|.+.|++++|...+++..... .-+...|..+...|
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   96 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHH
Confidence            345556667788899999999998887643 2256677788888889999999999998876642 22456677788888


Q ss_pred             HhcCChHHHHHHHHHHHHc
Q 011378          426 CRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       426 ~~~g~~~~a~~~~~~m~~~  444 (487)
                      ...|++++|...|++..+.
T Consensus        97 ~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            8999999999998887653

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.25  E-value=0.0058  Score=51.36  Aligned_cols=26  Identities=15%  Similarity=0.109  Sum_probs=13.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVG  338 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~  338 (487)
                      +..+-..+...|++++|...|+....
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~   66 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALD   66 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44444455555555655555555443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.25  E-value=0.0068  Score=46.46  Aligned_cols=96  Identities=17%  Similarity=0.070  Sum_probs=71.3

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHH
Q 011378          346 VSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTG  424 (487)
Q Consensus       346 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~  424 (487)
                      ..|..+-..+.+.|++++|...+++..+.. +.+...|..+-.+|.+.|++++|...+++..+.  .| +...|..+...
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~   81 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEK--DPNFVRAYIRKATA   81 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCcHHHHHHHHHH
Confidence            445566677788888888888888877643 224567778888888888888888888877654  34 45677777788


Q ss_pred             HHhcCChHHHHHHHHHHHHc
Q 011378          425 FCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~  444 (487)
                      +...|++++|...|++..+.
T Consensus        82 ~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           82 QIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhCHHHHHHHHHHHHHh
Confidence            88888888888888877653

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.25  E-value=0.0077  Score=46.80  Aligned_cols=99  Identities=12%  Similarity=-0.022  Sum_probs=78.4

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHH
Q 011378          308 PNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLI  387 (487)
Q Consensus       308 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  387 (487)
                      .+...+..+...+...|++++|...|....... +.+...|..+-..+...|++++|...++...+.. +.+...+..+-
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            456778888888899999999999998876653 3356778888888889999999999998887643 22456788888


Q ss_pred             HHHhccCCHHHHHHHHHHHHh
Q 011378          388 NGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       388 ~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      ..|...|++++|...+++..+
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHH
Confidence            888899999999988887654

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

Probab=97.24  E-value=0.018  Score=45.14  Aligned_cols=95  Identities=14%  Similarity=-0.037  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHH
Q 011378          136 VSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD----NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTI  211 (487)
Q Consensus       136 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  211 (487)
                      ..+..+...+.+.|++++|...|++..+.  .|+    ...|..+-..|.+.|+.++|...+++..+.. +.+...|..+
T Consensus        29 ~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~  105 (148)
T 2dba_A           29 EQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRR  105 (148)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHH
Confidence            34444444555555555555555554432  233    2344444444445555555555444443321 1123344445


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHH
Q 011378          212 LNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~  233 (487)
                      ..++...|++++|...|++..+
T Consensus       106 a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            5555555555555555555544

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

Probab=97.23  E-value=0.015  Score=45.66  Aligned_cols=93  Identities=18%  Similarity=0.125  Sum_probs=44.9

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC----hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD----SISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVI  421 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~l  421 (487)
                      .+..+-..+...|++++|...+++..+.  .|+    ...+..+-..|...|++++|...+++..+.  .| +...|..+
T Consensus        30 ~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~  105 (148)
T 2dba_A           30 QLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK--DGGDVKALYRR  105 (148)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TSCCHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CccCHHHHHHH
Confidence            3344444444445555555555444432  233    334444445555555555555555544332  12 33444555


Q ss_pred             HHHHHhcCChHHHHHHHHHHHH
Q 011378          422 LTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       422 i~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ...+...|++++|...+++..+
T Consensus       106 a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            5555555566666555555543

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

Probab=97.20  E-value=0.0065  Score=49.24  Aligned_cols=99  Identities=9%  Similarity=-0.037  Sum_probs=82.2

Q ss_pred             ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 011378          344 TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILT  423 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  423 (487)
                      +...+..+-..+.+.|++++|...+++..+.. +-+...|..+-.+|.+.|++++|...+++..+.. .-+...|..+-.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            45567778888999999999999999988643 2256788889999999999999999999887642 224678888999


Q ss_pred             HHHhcCChHHHHHHHHHHHHc
Q 011378          424 GFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       424 ~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      .|.+.|++++|...|++..+.
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999998764

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.20  E-value=0.009  Score=46.10  Aligned_cols=101  Identities=16%  Similarity=0.164  Sum_probs=52.9

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CcCC----hhhHHH
Q 011378          138 FSTLIGIFSRNGQLDRALMYFREMKSAGLVP-DNVLYTIIINGYCRNGFVLEALKMRDEMLEKG--CVMD----VVTYNT  210 (487)
Q Consensus       138 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~----~~~~~~  210 (487)
                      +..+-..+.+.|++++|++.|++..+.  .| +...|..+-.+|.+.|+.++|.+.+++..+..  ...+    ..+|..
T Consensus        11 ~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A           11 EKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            444555566666666666666655442  22 23445555555666666666655555544321  1111    123445


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFPDFYT  242 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t  242 (487)
                      +-.++...|+++.|.+.|++..+.  .||+.+
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~  118 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLSE--FRDPEL  118 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--SCCHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhh--CcCHHH
Confidence            555566666777777776665542  344443

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.18  E-value=0.0066  Score=48.39  Aligned_cols=95  Identities=7%  Similarity=-0.136  Sum_probs=53.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHh
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFV  391 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  391 (487)
                      .+..+-..+...|++++|...|+...... +.+...|..+-.+|...|++++|...+++..... +.+...+..+-.+|.
T Consensus        23 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~  100 (148)
T 2vgx_A           23 QLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLL  100 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHH
Confidence            44445555566666666666666554432 2244555555556666666666666666655432 113345555666666


Q ss_pred             ccCCHHHHHHHHHHHHh
Q 011378          392 REENMDKAFALVSKMEN  408 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~  408 (487)
                      ..|++++|.+.+++..+
T Consensus       101 ~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A          101 QXGELAEAESGLFLAQE  117 (148)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            66666666666665543

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.18  E-value=0.011  Score=49.51  Aligned_cols=26  Identities=12%  Similarity=0.263  Sum_probs=13.6

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHH
Q 011378          138 FSTLIGIFSRNGQLDRALMYFREMKS  163 (487)
Q Consensus       138 ~~~li~~~~~~g~~~~a~~~~~~m~~  163 (487)
                      +..+-..+.+.|++++|...|++...
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~   66 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALD   66 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33344455555555555555555544

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

Probab=97.17  E-value=0.0072  Score=47.65  Aligned_cols=95  Identities=8%  Similarity=-0.155  Sum_probs=56.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHh
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFV  391 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  391 (487)
                      .+..+-..+...|++++|...|+...... +.+...|..+-.+|.+.|++++|...++...... +.+...+..+-.+|.
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~   97 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHH
Confidence            34444555666666666666666655432 2344555566666666677777777766665532 123345555666666


Q ss_pred             ccCCHHHHHHHHHHHHh
Q 011378          392 REENMDKAFALVSKMEN  408 (487)
Q Consensus       392 ~~~~~~~a~~~~~~m~~  408 (487)
                      ..|++++|.+.+++..+
T Consensus        98 ~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARA  114 (142)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            77777777776666543

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.16  E-value=0.013  Score=44.85  Aligned_cols=96  Identities=8%  Similarity=0.026  Sum_probs=70.3

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGF  390 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  390 (487)
                      ..|..+-..+...|++++|...|+...... +.+...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.+|
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            456666777788888888888888776543 3356677777888888888888888888877643 12355677777888


Q ss_pred             hccCCHHHHHHHHHHHHh
Q 011378          391 VREENMDKAFALVSKMEN  408 (487)
Q Consensus       391 ~~~~~~~~a~~~~~~m~~  408 (487)
                      ...|++++|...+++..+
T Consensus        83 ~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           83 IAVKEYASALETLDAART  100 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHH
Confidence            888888888888877654

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.12  E-value=0.0037  Score=48.35  Aligned_cols=59  Identities=7%  Similarity=0.098  Sum_probs=33.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMT  267 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~  267 (487)
                      +..+-..+.+.|++++|.+.|++..+.. +-+...|..+-.+|...|++++|+..|+...
T Consensus        11 ~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al   69 (127)
T 4gcn_A           11 EKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAV   69 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHH
Confidence            4445555666666666666666655432 2244556666666666666666666665443

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

Probab=97.08  E-value=0.0078  Score=48.73  Aligned_cols=99  Identities=13%  Similarity=-0.007  Sum_probs=83.4

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHH
Q 011378          309 NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLIN  388 (487)
Q Consensus       309 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  388 (487)
                      +...+..+-..+...|++++|...|+...... +.+...|..+-.+|.+.|++++|...+++..+.. +-+...|..+-.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            45678888899999999999999999987653 3367788889999999999999999999988753 224678888999


Q ss_pred             HHhccCCHHHHHHHHHHHHhC
Q 011378          389 GFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       389 ~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      .|...|++++|...+++..+.
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999987653

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

Probab=97.07  E-value=0.011  Score=45.27  Aligned_cols=91  Identities=11%  Similarity=0.114  Sum_probs=67.4

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHCCCCCCh----hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC----HhhHHHH
Q 011378          350 TIIKGYCRSGDASKADEFLSKMVSEGVDPDS----ISYNTLINGFVREENMDKAFALVSKMENQGLVPD----VITYNVI  421 (487)
Q Consensus       350 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~l  421 (487)
                      .+-..+...|++++|...++...+..  |+.    ..+..+-..|.+.|++++|...+++..+.  .|+    ...+..+
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~~~~l   82 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSR--YPTHDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTSTTHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHH--CCCCcccHHHHHHH
Confidence            34556778889999999888887643  332    36666777888888999998888887653  243    4556777


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHc
Q 011378          422 LTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       422 i~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      ...+.+.|++++|...|++....
T Consensus        83 a~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           83 GLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH
Confidence            77888888888888888887764

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

Probab=96.96  E-value=0.0048  Score=59.93  Aligned_cols=97  Identities=11%  Similarity=0.019  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHH-----CCC-CCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHH-------cCCc
Q 011378          137 SFSTLIGIFSRNGQLDRALMYFREMKS-----AGL-VPD-NVLYTIIINGYCRNGFVLEALKMRDEMLE-------KGCV  202 (487)
Q Consensus       137 ~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~-~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~-------~g~~  202 (487)
                      +++.|..+|...|++++|..++++...     .|- -|+ ..+++.|-..|...|+.++|..++++..+       ...+
T Consensus       353 ~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp  432 (490)
T 3n71_A          353 LLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHP  432 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCCh
Confidence            444455555555555555555444321     111 122 22455555555555555555554443321       1222


Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          203 MDVVTYNTILNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       203 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (487)
                      ....+.+.+-.++...+.+++|+.++..+++
T Consensus       433 ~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          433 ITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2223445555666666777777777777764

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

Probab=96.88  E-value=0.0061  Score=59.19  Aligned_cols=87  Identities=13%  Similarity=0.012  Sum_probs=41.5

Q ss_pred             HHccCCHHHHHHHHHHHHhC---CCC---C-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHh---CCCC---CC-hhhHHH
Q 011378          285 FCKVGEMEKANKLWADMISR---KIS---P-NYISYGILINGYCSMGHVTEAFRLWYEMVG---KGIK---PT-LVSCNT  350 (487)
Q Consensus       285 ~~~~g~~~~a~~~~~~m~~~---~~~---p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~---~~-~~~~~~  350 (487)
                      +...|++++|..++.+....   -+.   | ...+++.|...|...|++++|..+++....   .-+.   |+ ..+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            34456666666665544321   111   1 123455666666666666666655554321   1111   11 234555


Q ss_pred             HHHHHHhcCChHHHHHHHHHH
Q 011378          351 IIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       351 li~~~~~~~~~~~a~~~~~~m  371 (487)
                      |-..|...|++++|..++++.
T Consensus       399 La~~~~~~G~~~eA~~~~~~A  419 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKA  419 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHH
Confidence            555555555555555555443

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

Probab=96.88  E-value=0.0023  Score=48.55  Aligned_cols=83  Identities=14%  Similarity=0.040  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHH
Q 011378          289 GEMEKANKLWADMISRKI--SPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADE  366 (487)
Q Consensus       289 g~~~~a~~~~~~m~~~~~--~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  366 (487)
                      |++++|...|.+....+.  +.+...+..+-..|...|++++|...|+...... +-+...+..+-.++...|+.++|..
T Consensus         4 g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHHH
Confidence            344444444444443220  1122334444444555555555555555444331 1223344444444555555555555


Q ss_pred             HHHHHH
Q 011378          367 FLSKMV  372 (487)
Q Consensus       367 ~~~~m~  372 (487)
                      .+++..
T Consensus        83 ~~~~al   88 (117)
T 3k9i_A           83 LLLKII   88 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            554443

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

Probab=96.83  E-value=0.0024  Score=48.46  Aligned_cols=84  Identities=18%  Similarity=0.137  Sum_probs=42.4

Q ss_pred             CChHHHHHHHHHHHHCCC-CC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHH
Q 011378          359 GDASKADEFLSKMVSEGV-DP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       359 ~~~~~a~~~~~~m~~~g~-~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  436 (487)
                      |+.++|...+++..+.+. .| +...+..|-..|...|++++|...+++..+.. .-+...+..+...+.+.|++++|..
T Consensus         4 g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHHH
Confidence            455555555555554321 12 23345555555666666666666665554431 1124455555556666666666666


Q ss_pred             HHHHHHH
Q 011378          437 ILWRMIE  443 (487)
Q Consensus       437 ~~~~m~~  443 (487)
                      .+++...
T Consensus        83 ~~~~al~   89 (117)
T 3k9i_A           83 LLLKIIA   89 (117)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6665543

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

Probab=96.79  E-value=0.014  Score=44.44  Aligned_cols=88  Identities=13%  Similarity=0.061  Sum_probs=46.6

Q ss_pred             HHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhc
Q 011378          386 LINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQ  463 (487)
Q Consensus       386 li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~  463 (487)
                      +-..+.+.|++++|...+++..+.  .| +...|..+-..+.+.|++++|...+++..+.  .| +...+..+...|...
T Consensus        23 ~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           23 EGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHc
Confidence            334445555555555555555432  23 3444555555555666666666666555443  23 334555555556666


Q ss_pred             CCHHHHHHHHHHHH
Q 011378          464 NNLKEAFRFHDEML  477 (487)
Q Consensus       464 ~~~~~a~~~~~~m~  477 (487)
                      |++++|...+++.+
T Consensus        99 g~~~~A~~~~~~al  112 (121)
T 1hxi_A           99 HNANAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            66666666665554

>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=96.75  E-value=0.0075  Score=58.68  Aligned_cols=114  Identities=14%  Similarity=0.162  Sum_probs=55.0

Q ss_pred             HhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHH
Q 011378          356 CRSGDASKADEFLSKMVSEGVDP-DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDS  434 (487)
Q Consensus       356 ~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a  434 (487)
                      .+.|++++|.+.+++..+.  .| +...|..+-.+|.+.|++++|.+.+++..+.. .-+...|..+...|.+.|++++|
T Consensus        17 ~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           17 FKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             TTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            3445555555555555442  22 24455555555566666666666655554431 11344555555566666666666


Q ss_pred             HHHHHHHHHcCCCCC-HHHHHHHHHH--HHhcCCHHHHHHHHH
Q 011378          435 ELILWRMIEKGLNPD-RSTYTTLING--HVSQNNLKEAFRFHD  474 (487)
Q Consensus       435 ~~~~~~m~~~g~~p~-~~ty~~l~~~--~~~~~~~~~a~~~~~  474 (487)
                      ...+++..+.  .|+ ...+..+-.+  +...|++++|.+.++
T Consensus        94 ~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKV--KPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHH--STTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            6666665543  121 1222223222  555566666666554

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

Probab=96.75  E-value=0.035  Score=42.33  Aligned_cols=23  Identities=17%  Similarity=0.166  Sum_probs=10.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHH
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMV  337 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~  337 (487)
                      .+..++...|++++|...|+...
T Consensus        44 ~lg~~~~~~~~~~~A~~~~~~~~   66 (129)
T 2xev_A           44 WLGESYYATRNFQLAEAQFRDLV   66 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHH
Confidence            33444444444444444444443

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

Probab=96.63  E-value=0.018  Score=43.83  Aligned_cols=89  Identities=13%  Similarity=0.064  Sum_probs=41.7

Q ss_pred             HHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCH
Q 011378           72 INGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQL  151 (487)
Q Consensus        72 i~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~  151 (487)
                      -..+.+.|++++|...|++..+.. +-+...|..+-..+...|++++|...|++..+.. +-+...+..+..++.+.|++
T Consensus        24 g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~~g~~  101 (121)
T 1hxi_A           24 GLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNA  101 (121)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence            334445555555555555544321 1133444444444555555555555555544331 11333444455555555555


Q ss_pred             HHHHHHHHHHH
Q 011378          152 DRALMYFREMK  162 (487)
Q Consensus       152 ~~a~~~~~~m~  162 (487)
                      ++|...+++..
T Consensus       102 ~~A~~~~~~al  112 (121)
T 1hxi_A          102 NAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555555443

>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=96.60  E-value=0.0093  Score=58.02  Aligned_cols=116  Identities=16%  Similarity=0.102  Sum_probs=66.7

Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHH
Q 011378          285 FCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKA  364 (487)
Q Consensus       285 ~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a  364 (487)
                      +.+.|++++|.+.+++..+.. +.+...|..+..+|...|++++|...++...+.. +.+...+..+-.+|...|+.++|
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            445666666666666655431 1235566667777777777777777777666542 23455666666777777777777


Q ss_pred             HHHHHHHHHCCCCCC-hhhHHHHHHH--HhccCCHHHHHHHHH
Q 011378          365 DEFLSKMVSEGVDPD-SISYNTLING--FVREENMDKAFALVS  404 (487)
Q Consensus       365 ~~~~~~m~~~g~~p~-~~~~~~li~~--~~~~~~~~~a~~~~~  404 (487)
                      .+.+++..+..  |+ ...+..+-.+  +.+.|++++|.+.++
T Consensus        94 ~~~~~~al~~~--p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKVK--PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHS--TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            77777766532  22 2233333333  666677777777665

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.55  E-value=0.15  Score=39.64  Aligned_cols=111  Identities=14%  Similarity=0.040  Sum_probs=54.7

Q ss_pred             ChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh----cCChHHHH
Q 011378          360 DASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCR----QGRMHDSE  435 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~  435 (487)
                      +.++|.+.+++..+.| .|+..    |-..|...+.+++|.+.+++--+.|   +...+..|-..|..    .+++++|.
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-EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            3445555555555544 12221    3344444445555555555554443   33444444444444    55555555


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCC
Q 011378          436 LILWRMIEKGLNPDRSTYTTLINGHVS----QNNLKEAFRFHDEMLQRGF  481 (487)
Q Consensus       436 ~~~~~m~~~g~~p~~~ty~~l~~~~~~----~~~~~~a~~~~~~m~~~g~  481 (487)
                      ..|++..+.|   +...+..|-..|..    .+++++|.+.+++-.+.|.
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            5555555442   34444455555555    5556666666655555443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.50  E-value=0.042  Score=53.06  Aligned_cols=128  Identities=13%  Similarity=-0.002  Sum_probs=75.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--------------hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT--------------LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVD  377 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  377 (487)
                      .|..+-..+.+.|++++|...|+......-...              ...|..+-.+|.+.|++++|...+++..+.. +
T Consensus       270 ~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p  348 (457)
T 1kt0_A          270 IVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-S  348 (457)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-T
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-C
Confidence            455555666666666666666665544211100              3556666667777777777777777766532 1


Q ss_pred             CChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHH-HHHHHH
Q 011378          378 PDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSEL-ILWRMI  442 (487)
Q Consensus       378 p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~-~~~~m~  442 (487)
                      .+...|..+-.+|...|++++|...|++..+.  .| +...+..+...+.+.|+.+++.+ .+..|.
T Consensus       349 ~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          349 ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            23556666777777777777777777776543  34 33456666666666666666653 344443

>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=96.46  E-value=0.52  Score=43.16  Aligned_cols=32  Identities=13%  Similarity=0.307  Sum_probs=24.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          237 FPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       237 ~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      .+.+..+..+...|...|+.++|.++++.+.+
T Consensus       299 ~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          299 LPVPLALEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            35667777788888888888888888877754

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.43  E-value=0.046  Score=56.99  Aligned_cols=75  Identities=16%  Similarity=0.081  Sum_probs=37.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhc
Q 011378          244 TTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSM  323 (487)
Q Consensus       244 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~  323 (487)
                      ..++..+.+.|..+.|+++.+.-            ..-.......|+++.|.++.+.+      .+...|..|-..+.+.
T Consensus       633 ~~~~~~l~~~~~~~~a~~~~~~~------------~~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~  694 (814)
T 3mkq_A          633 TKIARFLEGQEYYEEALNISPDQ------------DQKFELALKVGQLTLARDLLTDE------SAEMKWRALGDASLQR  694 (814)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCCCH------------HHHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCChHHheecCCCc------------chheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHc
Confidence            55555555566666655443210            01122334455666665554322      3445566666666666


Q ss_pred             CCHHHHHHHHHHH
Q 011378          324 GHVTEAFRLWYEM  336 (487)
Q Consensus       324 ~~~~~a~~~~~~m  336 (487)
                      ++++.|.+.|..+
T Consensus       695 ~~~~~A~~~y~~~  707 (814)
T 3mkq_A          695 FNFKLAIEAFTNA  707 (814)
T ss_dssp             TCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHc
Confidence            6666665555544

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.41  E-value=0.041  Score=53.12  Aligned_cols=89  Identities=9%  Similarity=0.009  Sum_probs=61.8

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-ChhhHHHHHH
Q 011378          310 YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP-DSISYNTLIN  388 (487)
Q Consensus       310 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~  388 (487)
                      ...|..+-.+|.+.|++++|+..++...... +.+...|..+-.+|...|++++|...|++..+.  .| +...+..+-.
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~  393 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISM  393 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            3567777778888888888888888776543 335667777777888888888888888877753  34 3446667777


Q ss_pred             HHhccCCHHHHHH
Q 011378          389 GFVREENMDKAFA  401 (487)
Q Consensus       389 ~~~~~~~~~~a~~  401 (487)
                      .+.+.++.+++.+
T Consensus       394 ~~~~~~~~~~a~~  406 (457)
T 1kt0_A          394 CQKKAKEHNERDR  406 (457)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777766653

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.40  E-value=0.042  Score=51.35  Aligned_cols=88  Identities=10%  Similarity=0.010  Sum_probs=57.0

Q ss_pred             hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHH
Q 011378          380 SISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLI  457 (487)
Q Consensus       380 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~  457 (487)
                      ...|..+-.+|.+.|++++|.+.+++..+.  .| +...|..+-.+|.+.|++++|...|++..+.  .| +...+..+-
T Consensus       273 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~  348 (370)
T 1ihg_A          273 LSCVLNIGACKLKMSDWQGAVDSCLEALEI--DPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELL  348 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            345666777777777777777777776653  34 4556677777777788888887777776654  34 344555555


Q ss_pred             HHHHhcCCHHHHHH
Q 011378          458 NGHVSQNNLKEAFR  471 (487)
Q Consensus       458 ~~~~~~~~~~~a~~  471 (487)
                      ..+...++.+++.+
T Consensus       349 ~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          349 KVKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            55555565555543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.37  E-value=0.052  Score=56.56  Aligned_cols=150  Identities=12%  Similarity=0.125  Sum_probs=77.5

Q ss_pred             HccCChhHHHH-HHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHH
Q 011378          111 CRKENMSEAEE-IFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEA  189 (487)
Q Consensus       111 ~~~~~~~~a~~-~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  189 (487)
                      ...+++++|.+ ++..+      |+......++..+.+.|.++.|+++.+.-.            .-.......|++++|
T Consensus       610 ~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~~~~~~a~~~~~~~~------------~~f~~~l~~~~~~~A  671 (814)
T 3mkq_A          610 TLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQEYYEEALNISPDQD------------QKFELALKVGQLTLA  671 (814)
T ss_dssp             HHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHTTCHHHHHHHCCCHH------------HHHHHHHHHTCHHHH
T ss_pred             HHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhCCChHHheecCCCcc------------hheehhhhcCCHHHH
Confidence            34666777665 44221      101123566667777777777776543111            112233456677776


Q ss_pred             HHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          190 LKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQK  269 (487)
Q Consensus       190 ~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~  269 (487)
                      .++.+.+      .+...|..+-..+.+.++++.|++.|..+.+         |..+...|...|+.+....+-+.....
T Consensus       672 ~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~  736 (814)
T 3mkq_A          672 RDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETT  736 (814)
T ss_dssp             HHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHc
Confidence            6664332      3455677777777777777777777766542         334444444455555544444333332


Q ss_pred             CCCCCeeehHHHHHHHHccCCHHHHHHHHH
Q 011378          270 SIKPDIVTYNTLIDGFCKVGEMEKANKLWA  299 (487)
Q Consensus       270 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  299 (487)
                      |      -++.-..+|.+.|++++|.+++.
T Consensus       737 ~------~~~~A~~~~~~~g~~~~a~~~~~  760 (814)
T 3mkq_A          737 G------KFNLAFNAYWIAGDIQGAKDLLI  760 (814)
T ss_dssp             T------CHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             C------chHHHHHHHHHcCCHHHHHHHHH
Confidence            2      22333334444555555555443

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.29  E-value=0.17  Score=39.39  Aligned_cols=16  Identities=6%  Similarity=0.237  Sum_probs=7.7

Q ss_pred             ChhHHHHHHHHHHHCC
Q 011378          115 NMSEAEEIFCEMSRRG  130 (487)
Q Consensus       115 ~~~~a~~~~~~m~~~g  130 (487)
                      +.++|.+.|++..+.|
T Consensus        10 d~~~A~~~~~~aa~~g   25 (138)
T 1klx_A           10 DLKKAIQYYVKACELN   25 (138)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHcCC
Confidence            4444555555444444

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.27  E-value=0.043  Score=51.29  Aligned_cols=120  Identities=16%  Similarity=0.132  Sum_probs=76.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhC--------------CCCC-ChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC
Q 011378          313 YGILINGYCSMGHVTEAFRLWYEMVGK--------------GIKP-TLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVD  377 (487)
Q Consensus       313 ~~~li~~~~~~~~~~~a~~~~~~m~~~--------------~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  377 (487)
                      +..+-..+.+.|++++|...|+.....              ...| +...|..+-.+|.+.|++++|...+++..+.  .
T Consensus       226 ~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--~  303 (370)
T 1ihg_A          226 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI--D  303 (370)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh--C
Confidence            444555555666666666666554430              0122 3456677777788888888888888877753  3


Q ss_pred             C-ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHH
Q 011378          378 P-DSISYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       378 p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~  436 (487)
                      | +...+..+-.+|...|++++|.+.+++..+.  .| +...+..+...+.+.++.+++.+
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4 4556777778888888888888888777653  34 44555666666666666665543

>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=96.21  E-value=0.72  Score=42.22  Aligned_cols=168  Identities=9%  Similarity=0.008  Sum_probs=80.4

Q ss_pred             hhHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccC-ChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhC-C-CHHHHHHH
Q 011378           82 DRAKEVLDEMLQMGLSPD-TATYNTLLVESCRKE-NMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRN-G-QLDRALMY  157 (487)
Q Consensus        82 ~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~-g-~~~~a~~~  157 (487)
                      ++|+++++.+....  |+ ...|+.--..+...+ ++++++++++.+....- -+..+|+.--.++.+. + ++++++++
T Consensus        71 e~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nP-Kny~aW~hR~wlL~~l~~~~~~~EL~~  147 (349)
T 3q7a_A           71 ERALELTEIIVRMN--PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNL-KSYQVWHHRLLLLDRISPQDPVSEIEY  147 (349)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHHHCCSCCHHHHHH
T ss_pred             HHHHHHHHHHHHhC--chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHhcCCChHHHHHH
Confidence            35555555555422  22 233443333333344 36666666666654321 1334444433333333 3 55666666


Q ss_pred             HHHHHHCCCCCChhhHHHHHHHHHhcCCHH--------HHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC-------HH
Q 011378          158 FREMKSAGLVPDNVLYTIIINGYCRNGFVL--------EALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM-------LT  222 (487)
Q Consensus       158 ~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~--------~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~-------~~  222 (487)
                      ++++.+.. .-|...|+----.+.+.|..+        ++++..+++.+... -|-..|+..-..+.+.+.       ++
T Consensus       148 ~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~~l~~~~~~~~~~~  225 (349)
T 3q7a_A          148 IHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRVSRPGAETSSRSLQ  225 (349)
T ss_dssp             HHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHTTSTTCCCCHHHHH
T ss_pred             HHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccccchHHHH
Confidence            66665432 123334443333333322222        56666666665432 345556655555555554       45


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 011378          223 EADDLFNEMLERGVFPDFYTFTTLIHGHCKDGN  255 (487)
Q Consensus       223 ~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~  255 (487)
                      ++.+.++++.... +-|...|+-+-..+.+.|+
T Consensus       226 eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          226 DELIYILKSIHLI-PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC
Confidence            6666666665532 2355566555444444443

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

Probab=96.07  E-value=0.095  Score=41.98  Aligned_cols=60  Identities=13%  Similarity=0.128  Sum_probs=26.9

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKME  407 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  407 (487)
                      .|..+-.+|.+.|++++|...++...+.. +.+...|..+-.+|...|++++|...+++..
T Consensus        65 ~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al  124 (162)
T 3rkv_A           65 LYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLL  124 (162)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHH
Confidence            34444444445555555555554444321 1123344444444455555555555444443

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

Probab=96.01  E-value=0.22  Score=39.76  Aligned_cols=69  Identities=9%  Similarity=0.060  Sum_probs=55.7

Q ss_pred             hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHH
Q 011378          380 SISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRS  451 (487)
Q Consensus       380 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  451 (487)
                      ...|..+-.+|.+.|++++|...+++..+.. ..+...|..+-.+|...|++++|...|++....  .|+-.
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~  131 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAA  131 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCH
Confidence            3578888899999999999999998886642 235677888889999999999999999988764  45543

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

Probab=95.93  E-value=0.022  Score=52.60  Aligned_cols=145  Identities=8%  Similarity=-0.018  Sum_probs=71.1

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHH
Q 011378          310 YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLING  389 (487)
Q Consensus       310 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  389 (487)
                      ...+..+-..+.+.|++++|...|+.....  .|+...       +...++.+++...+.          ...|..+-.+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l~----------~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAVK----------NPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHHH----------THHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHHH----------HHHHHHHHHH
Confidence            345666666777778888888888776543  233221       111222222222111          1256677777


Q ss_pred             HhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHH-HHHHHHHH-HHhcCCH
Q 011378          390 FVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRS-TYTTLING-HVSQNNL  466 (487)
Q Consensus       390 ~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-ty~~l~~~-~~~~~~~  466 (487)
                      |.+.|++++|...+++..+.  .| +...|..+-.+|...|++++|...|++..+  +.|+.. .+..+... ....+..
T Consensus       240 ~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~--l~p~~~~a~~~L~~l~~~~~~~~  315 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTE--EEKNPKALFRRGKAKAELGQMDSARDDFRKAQK--YAPDDKAIRRELRALAEQEKALY  315 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHH
Confidence            88888888888888776553  34 566777788888888888888888887643  344332 33333333 2334566


Q ss_pred             HHHHHHHHHHH
Q 011378          467 KEAFRFHDEML  477 (487)
Q Consensus       467 ~~a~~~~~~m~  477 (487)
                      +.+.+++..|.
T Consensus       316 ~~a~~~~~~~l  326 (338)
T 2if4_A          316 QKQKEMYKGIF  326 (338)
T ss_dssp             -----------
T ss_pred             HHHHHHHHHhh
Confidence            67777777776

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

Probab=95.57  E-value=0.048  Score=40.13  Aligned_cols=61  Identities=7%  Similarity=0.059  Sum_probs=30.2

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      .+..+-..+...|++++|.+.+++..+.. ..+...|..+-..+.+.|++++|...+++..+
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            6 KQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            34444445555555555555555443321 11334455555555555555555555555543

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=95.49  E-value=0.29  Score=39.01  Aligned_cols=61  Identities=13%  Similarity=0.019  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC-HHHH----HHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLER-----GVFPD-FYTF----TTLIHGHCKDGNMNKALNLFDIMT  267 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~-~~t~----~~li~~~~~~g~~~~a~~~~~~m~  267 (487)
                      .|+.+-.++.+.|++++|...+++..+.     .+.|+ ...|    ...-.++...|++++|+..|+...
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAl  129 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  129 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHH
Confidence            6667777777777777777777766653     12453 3456    666777777777777777776554

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

Probab=95.45  E-value=0.12  Score=38.38  Aligned_cols=79  Identities=14%  Similarity=0.124  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          363 KADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       363 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      .|...+++..+.. +.+...+..+-..|...|++++|...+++..+.. ..+...|..+...|.+.|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4566777766532 2356678888889999999999999998886642 2345678888889999999999999998876


Q ss_pred             H
Q 011378          443 E  443 (487)
Q Consensus       443 ~  443 (487)
                      +
T Consensus        81 ~   81 (115)
T 2kat_A           81 A   81 (115)
T ss_dssp             H
T ss_pred             H
Confidence            5

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

Probab=95.43  E-value=0.063  Score=39.46  Aligned_cols=62  Identities=11%  Similarity=0.064  Sum_probs=31.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      ..+..+-..+...|++++|...|+...... +.+...+..+-.+|.+.|++++|...+++..+
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            344445555555555555555555544331 22344455555555555555555555555543

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=95.41  E-value=0.21  Score=39.86  Aligned_cols=61  Identities=11%  Similarity=-0.006  Sum_probs=36.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCCh-hhH----HHHHHHHHhcCChHHHHHHHHHHH
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGK-----GIKPTL-VSC----NTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~~-~~~----~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      .|+.+-.++...|++++|+..++.-...     .+.|+. ..|    ...-.++...|++++|...|++..
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAl  129 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  129 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHH
Confidence            6666777777777777777766655432     124432 244    555556666666666666666654

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

Probab=95.38  E-value=0.06  Score=49.58  Aligned_cols=112  Identities=10%  Similarity=-0.028  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011378          241 YTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGY  320 (487)
Q Consensus       241 ~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~  320 (487)
                      ..+..+-..+.+.|++++|+..|+...+.  .|+..       .+...|+.+++...+.          ...|..+-.+|
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~-------~~~~~~~~~~~~~~l~----------~~~~~nla~~~  240 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDF-------MFQLYGKYQDMALAVK----------NPCHLNIAACL  240 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHH-------HHTCCHHHHHHHHHHH----------THHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccch-------hhhhcccHHHHHHHHH----------HHHHHHHHHHH
Confidence            34555556666666677776666654432  12111       1112222222222111          12445555555


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          321 CSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       321 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      .+.|++++|...++...... +.+...|..+-.+|...|++++|...+++..
T Consensus       241 ~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al  291 (338)
T 2if4_A          241 IKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQ  291 (338)
T ss_dssp             HTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTT
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            55555555555555544321 2233444455555555555555555555443

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=95.32  E-value=0.11  Score=49.35  Aligned_cols=60  Identities=7%  Similarity=-0.110  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc-----CCC-CC-HHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          417 TYNVILTGFCRQGRMHDSELILWRMIEK-----GLN-PD-RSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       417 ~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~-p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      +++.|...|..+|++++|..++++..+.     |-. |+ ..+|+.|-..|..+|++++|..++++-
T Consensus       342 ~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          342 MMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHH
Confidence            4555555555555555555555554321     110 11 124555555555555555555555443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.12  E-value=0.74  Score=37.24  Aligned_cols=97  Identities=12%  Similarity=0.178  Sum_probs=43.4

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHH
Q 011378          322 SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFA  401 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  401 (487)
                      ..|+++.|.++.+++      .+...|..|-+...+.|+++-|+++|+....         +..|.-.|.-.|+.+...+
T Consensus        17 ~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~k   81 (177)
T 3mkq_B           17 EYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSK   81 (177)
T ss_dssp             HTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHH
T ss_pred             hcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHH
Confidence            345555555544443      2344455555555555555555555554331         3333334444454444333


Q ss_pred             HHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHH
Q 011378          402 LVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILW  439 (487)
Q Consensus       402 ~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  439 (487)
                      +-+.-...|      -+++-...+-..|+++++.+++.
T Consensus        82 la~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~  113 (177)
T 3mkq_B           82 MQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFA  113 (177)
T ss_dssp             HHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHH
Confidence            322222222      24444444444555555554443

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

Probab=95.12  E-value=0.27  Score=34.26  Aligned_cols=61  Identities=13%  Similarity=0.233  Sum_probs=30.5

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      .+..+-..|...|++++|...+++..+.. ..+...+..+...+.+.|++++|...+++..+
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            34444444555555555555555443321 11334455555555566666666665555544

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

Probab=95.05  E-value=0.14  Score=48.75  Aligned_cols=91  Identities=8%  Similarity=-0.041  Sum_probs=55.7

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCC---CCCC----hhhHHHHHHHHhccCCHHHHHHHHHHHHh-----CC-CCCCH-hh
Q 011378          352 IKGYCRSGDASKADEFLSKMVSEG---VDPD----SISYNTLINGFVREENMDKAFALVSKMEN-----QG-LVPDV-IT  417 (487)
Q Consensus       352 i~~~~~~~~~~~a~~~~~~m~~~g---~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~g-~~p~~-~~  417 (487)
                      +..+.+.|++++|..++++..+..   ..|+    ..+++.|...|...|++++|+.++++..+     .| -.|++ .+
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            445556677777777777766431   2222    24667777777777777777777665532     11 12332 35


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          418 YNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       418 ~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      ++.|-..|..+|++++|..++++..
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            6777777777777777777776654

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

Probab=95.00  E-value=0.26  Score=34.39  Aligned_cols=60  Identities=18%  Similarity=0.300  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHh
Q 011378          348 CNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       348 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      +..+-..+...|++++|...+++..+.. +.+...+..+-..|.+.|++++|...+++..+
T Consensus        12 ~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            3334444444455555555554444321 11233444455555555555555555555443

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

Probab=94.94  E-value=0.27  Score=36.47  Aligned_cols=59  Identities=14%  Similarity=-0.040  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHH
Q 011378          102 TYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREM  161 (487)
Q Consensus       102 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  161 (487)
                      .+..+-..+...|++++|...|++..+.. +.+...|..+..++.+.|++++|...|++.
T Consensus        21 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A           21 LRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            33334444444444444444444443321 112333444444444444444444444443

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

Probab=94.89  E-value=0.19  Score=36.38  Aligned_cols=64  Identities=22%  Similarity=0.215  Sum_probs=52.1

Q ss_pred             ChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          379 DSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       379 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +...+..+-..|...|++++|...|++..+.. .-+...|..+-..|.+.|++++|...+++..+
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            45678888889999999999999999887642 22456788888899999999999999888654

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

Probab=94.73  E-value=0.19  Score=36.42  Aligned_cols=58  Identities=16%  Similarity=0.091  Sum_probs=25.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      .|..+-..|.+.|++++|.+.|++..+.. +-+...|..+-.+|...|+.++|...|+.
T Consensus         9 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~   66 (100)
T 3ma5_A            9 TRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQ   66 (100)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34444444444444444444444444322 11233444444444444444444444443

>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=94.62  E-value=0.24  Score=47.12  Aligned_cols=58  Identities=12%  Similarity=0.048  Sum_probs=25.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc-----C-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLER-----G-VFPD-FYTFTTLIHGHCKDGNMNKALNLFD  264 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~-~~~~-~~t~~~li~~~~~~g~~~~a~~~~~  264 (487)
                      +++.+...|...|++++|..++++..+-     | -.|+ ..+++.|-..|...|++++|+.+++
T Consensus       331 ~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~  395 (429)
T 3qwp_A          331 VLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLR  395 (429)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            3444444444444444444444443321     1 1121 2334445555555555555555444

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=94.49  E-value=0.21  Score=47.47  Aligned_cols=61  Identities=5%  Similarity=-0.189  Sum_probs=35.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----C-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          206 VTYNTILNGLCRAKMLTEADDLFNEMLER-----G-VFPD-FYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~-~~~~-~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      .+++.|...|...|++++|..++++..+-     | -.|+ ..+++.|-..|...|+.++|+.+++..
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHH
Confidence            45666666666666666666666655431     1 1232 235666666666666666666666543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=93.74  E-value=2.1  Score=34.55  Aligned_cols=44  Identities=27%  Similarity=0.346  Sum_probs=20.0

Q ss_pred             hcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHH
Q 011378           77 KKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEM  126 (487)
Q Consensus        77 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  126 (487)
                      +.|+++.|.++.+++      -+...|..|-......|+++-|++.|...
T Consensus        17 ~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~   60 (177)
T 3mkq_B           17 EYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQ   60 (177)
T ss_dssp             HTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             hcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHh
Confidence            344444444444433      23444444444444444444444444443

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

Probab=93.19  E-value=1.8  Score=39.74  Aligned_cols=73  Identities=11%  Similarity=0.102  Sum_probs=41.4

Q ss_pred             CChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHH
Q 011378          378 PDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYT  454 (487)
Q Consensus       378 p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~  454 (487)
                      .+..+|.++-..+...|++++|...+++....+  |+...|..+-..+.-.|+.++|...+.+....  .|...||.
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~  347 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLY  347 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHH
Confidence            345556555555555566666666666665543  55555544445555666666666666655442  45555543

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

Probab=93.18  E-value=2.3  Score=39.03  Aligned_cols=62  Identities=15%  Similarity=-0.016  Sum_probs=35.8

Q ss_pred             CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          413 PDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       413 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      .+...|.++...+...|++++|...+++....+  |+...|..+-..+...|++++|...+++-
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~A  336 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTA  336 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            345555555555555566666666666665543  55555555555666666666666665543

>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=92.78  E-value=5.5  Score=36.09  Aligned_cols=220  Identities=12%  Similarity=0.113  Sum_probs=134.6

Q ss_pred             HhcCChh-HHHHHHHHHhhCCCCCCcc-chHH---HHHHHHhcC-------ChhhHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011378           41 CREGFLE-EAFQLMNSMSGKGLKPGVF-TYNS---LINGLCKKG-------RCDRAKEVLDEMLQMGLSPDTATYNTLLV  108 (487)
Q Consensus        41 ~~~~~~~-~a~~~~~~m~~~~~~p~~~-~~~~---li~~~~~~~-------~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  108 (487)
                      .+.|.++ +|+++++.+...  .|+.. +|+.   ++....+..       .+++++.+++.+.... +-+..+|+---.
T Consensus        40 ~~~~e~s~eaL~~t~~~L~~--nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-PKny~aW~hR~w  116 (331)
T 3dss_A           40 RQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCW  116 (331)
T ss_dssp             HHTTCCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            4556554 788888887763  34432 2442   233333211       1577888888877642 235566665555


Q ss_pred             HHHccC--ChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCC-HHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhc--
Q 011378          109 ESCRKE--NMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQ-LDRALMYFREMKSAGLVPDNVLYTIIINGYCRN--  183 (487)
Q Consensus       109 ~~~~~~--~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~--  183 (487)
                      .+.+.+  ++++++++++.+.+.. +-|...|+.--.+..+.|. ++++++.++.+.+... -|...|+..-..+.+.  
T Consensus       117 lL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~SAW~~R~~ll~~l~~  194 (331)
T 3dss_A          117 LLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHP  194 (331)
T ss_dssp             HHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHHSC
T ss_pred             HHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHhhh
Confidence            555555  4788888888887754 2366777776666677777 5888888888876542 2444555554444443  


Q ss_pred             ------------CCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhc-----------CCHHHHHHHHHHHHHcCCCCC-
Q 011378          184 ------------GFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRA-----------KMLTEADDLFNEMLERGVFPD-  239 (487)
Q Consensus       184 ------------~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~~~~~-  239 (487)
                                  +.++++++.+....... +-|...|+-+--.+.+.           +.++++.+.++++.+..  || 
T Consensus       195 ~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~--pd~  271 (331)
T 3dss_A          195 QPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELE--PEN  271 (331)
T ss_dssp             CC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHC--TTC
T ss_pred             ccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhC--ccc
Confidence                        34677888877776543 23555666444444444           45788888888888743  43 


Q ss_pred             HHHHHHHH---HHHHhcCCHHHHHHHHHHHHH
Q 011378          240 FYTFTTLI---HGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       240 ~~t~~~li---~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      ...+..++   ...-..+..+++...+..+.+
T Consensus       272 ~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          272 KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            33333332   233346777888888887764

>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=92.55  E-value=5.9  Score=35.89  Aligned_cols=220  Identities=11%  Similarity=0.065  Sum_probs=138.2

Q ss_pred             HhcCChh-hHHHHHHHHHHCCCCCCH-HHHHH---HHHHHHccC-------ChhHHHHHHHHHHHCCCCCCHhHHHHHHH
Q 011378           76 CKKGRCD-RAKEVLDEMLQMGLSPDT-ATYNT---LLVESCRKE-------NMSEAEEIFCEMSRRGVAPDIVSFSTLIG  143 (487)
Q Consensus        76 ~~~~~~~-~a~~~~~~m~~~g~~~~~-~~~~~---ll~~~~~~~-------~~~~a~~~~~~m~~~g~~p~~~~~~~li~  143 (487)
                      .+.|.++ +|++..+.+...  .|+. ..|+.   ++....+..       .+++++.+++.+.... +-+..+|+.--.
T Consensus        40 ~~~~e~s~eaL~~t~~~L~~--nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-PKny~aW~hR~w  116 (331)
T 3dss_A           40 RQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCW  116 (331)
T ss_dssp             HHTTCCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            3456655 788888888764  3443 33443   233222211       2678888998887653 236667777666


Q ss_pred             HHHhCC--CHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCC-HHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhc--
Q 011378          144 IFSRNG--QLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGF-VLEALKMRDEMLEKGCVMDVVTYNTILNGLCRA--  218 (487)
Q Consensus       144 ~~~~~g--~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~--  218 (487)
                      ++.+.|  .+++++.+++.+.+.. .-|...|+.---.+.+.|. .+++++.++.+.+... -|...|+.....+.+.  
T Consensus       117 lL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~SAW~~R~~ll~~l~~  194 (331)
T 3dss_A          117 LLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHP  194 (331)
T ss_dssp             HHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHHSC
T ss_pred             HHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHhhh
Confidence            666666  4889999999988743 2355667666666667777 5888899888887643 4566676655554443  


Q ss_pred             ------------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-----------CCHHHHHHHHHHHHHCCCCCCe
Q 011378          219 ------------KMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD-----------GNMNKALNLFDIMTQKSIKPDI  275 (487)
Q Consensus       219 ------------~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~-----------g~~~~a~~~~~~m~~~~~~~~~  275 (487)
                                  +.++++.+.+....... +-|...|+-+--.+.+.           +.++++++.++.+.+.  .||.
T Consensus       195 ~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~--~pd~  271 (331)
T 3dss_A          195 QPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQEL--EPEN  271 (331)
T ss_dssp             CC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHH--CTTC
T ss_pred             ccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhh--Cccc
Confidence                        45778888888877643 33566666444444443           3578888888877754  3443


Q ss_pred             -eehHH---HHHHHHccCCHHHHHHHHHHHHh
Q 011378          276 -VTYNT---LIDGFCKVGEMEKANKLWADMIS  303 (487)
Q Consensus       276 -~~~~~---li~~~~~~g~~~~a~~~~~~m~~  303 (487)
                       .++-+   ++......|..+++...+.++..
T Consensus       272 ~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          272 KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence             22222   22333346677788888887764

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.54  E-value=2.8  Score=32.08  Aligned_cols=67  Identities=13%  Similarity=0.089  Sum_probs=38.4

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC
Q 011378          310 YISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVD  377 (487)
Q Consensus       310 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  377 (487)
                      ......-++.....|.-+.-.++..++.. ..+|+....-.+-.+|.+.|+..++.+++.+.-++|++
T Consensus        91 se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           91 NEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            33444555555566666666666666433 33555555556666666666666666666666666653

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

Probab=92.05  E-value=0.56  Score=33.40  Aligned_cols=52  Identities=12%  Similarity=0.232  Sum_probs=25.7

Q ss_pred             HhccCCHHHHHHHHHHHHhCCCCC-CHh-hHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          390 FVREENMDKAFALVSKMENQGLVP-DVI-TYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       390 ~~~~~~~~~a~~~~~~m~~~g~~p-~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +.+.|++++|.+.+++..+.  .| +.. .|..+-..|...|++++|...|++..+
T Consensus        10 ~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A           10 LINQGDIENALQALEEFLQT--EPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH--CSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44455555555555544432  22 223 444455555555555555555555544

>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=91.35  E-value=0.69  Score=36.77  Aligned_cols=60  Identities=20%  Similarity=0.195  Sum_probs=37.7

Q ss_pred             hhHHHHHHHHHHHCCCCC-CHhHHHHHHHHHHhC-----------CCHHHHHHHHHHHHHCCCCCChhhHHHHHHH
Q 011378          116 MSEAEEIFCEMSRRGVAP-DIVSFSTLIGIFSRN-----------GQLDRALMYFREMKSAGLVPDNVLYTIIING  179 (487)
Q Consensus       116 ~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~-----------g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~  179 (487)
                      +++|...|++..+.  .| +...|..+-.+|...           |++++|.+.|++..+  +.|+...|...+..
T Consensus        62 ~~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~  133 (158)
T 1zu2_A           62 IQEAITKFEEALLI--DPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHH
Confidence            44666666666553  23 345566666666654           478888888887776  35766666555554

>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=91.18  E-value=0.53  Score=37.43  Aligned_cols=30  Identities=13%  Similarity=0.073  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHCCCCCC-hhhHHHHHHHHhcc
Q 011378          362 SKADEFLSKMVSEGVDPD-SISYNTLINGFVRE  393 (487)
Q Consensus       362 ~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~  393 (487)
                      ++|+..|++.++.  .|+ ...|..|-.+|...
T Consensus        63 ~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~l   93 (158)
T 1zu2_A           63 QEAITKFEEALLI--DPKKDEAVWCIGNAYTSF   93 (158)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHh
Confidence            3455555544432  232 23444444444433

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=90.85  E-value=1.8  Score=31.39  Aligned_cols=70  Identities=14%  Similarity=0.177  Sum_probs=50.5

Q ss_pred             ChhhHHHHHHHHhccCCHHHHHHHHHHHHhC------CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCH
Q 011378          379 DSISYNTLINGFVREENMDKAFALVSKMENQ------GLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDR  450 (487)
Q Consensus       379 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  450 (487)
                      +..-+-.|-..+.+.++++.|...++...+.      +-.+....+..+..++.+.|++++|...+++...  +.|+-
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~--l~P~~   79 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE--LDPEH   79 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTC
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh--cCCCC
Confidence            3444556777788889999999888765432      1123456788888888999999999998888765  35654

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1

Probab=90.81  E-value=4.3  Score=38.34  Aligned_cols=356  Identities=17%  Similarity=0.154  Sum_probs=162.2

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHHCCCCCCHHH--HHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHh--HHHHHHHHHH
Q 011378           71 LINGLCKKGRCDRAKEVLDEMLQMGLSPDTAT--YNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIV--SFSTLIGIFS  146 (487)
Q Consensus        71 li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~--~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~--~~~~li~~~~  146 (487)
                      .+...++.|+.+-+..    +.+.|..|+...  ..+.|...+..|+.+-+..++    +.|..++..  .-.+.+...+
T Consensus        17 ~L~~Aa~~g~~~~v~~----Ll~~g~~~~~~~~~~~t~L~~A~~~g~~~~v~~Ll----~~g~~~~~~~~~g~t~L~~A~   88 (437)
T 1n11_A           17 PLHVASFMGHLPIVKN----LLQRGASPNVSNVKVETPLHMAARAGHTEVAKYLL----QNKAKVNAKAKDDQTPLHCAA   88 (437)
T ss_dssp             HHHHHHHHTCHHHHHH----HHHTTCCSCCSSSCCCCHHHHHHHHTCHHHHHHHH----HHTCCSSCCCTTSCCHHHHHH
T ss_pred             HHHHHHHCCCHHHHHH----HHHcCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHH----hCCCCCCCCCCCCCCHHHHHH
Confidence            3444456777654444    444566655321  223455566677766555444    345444321  1123455556


Q ss_pred             hCCCHHHHHHHHHHHHHCCCCCChhh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCCh---hhHHHHHHHHHhcCCH
Q 011378          147 RNGQLDRALMYFREMKSAGLVPDNVL--YTIIINGYCRNGFVLEALKMRDEMLEKGCVMDV---VTYNTILNGLCRAKML  221 (487)
Q Consensus       147 ~~g~~~~a~~~~~~m~~~g~~~~~~~--~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~---~~~~~li~~~~~~~~~  221 (487)
                      +.|+.+-+..+++    .|..|+...  -.+.+...++.|+.+-+..    +.+.+..++.   ..++ .+...++.|+.
T Consensus        89 ~~g~~~~v~~Ll~----~ga~~~~~~~~g~t~L~~A~~~g~~~~v~~----Ll~~~~~~~~~~~~g~t-~L~~A~~~g~~  159 (437)
T 1n11_A           89 RIGHTNMVKLLLE----NNANPNLATTAGHTPLHIAAREGHVETVLA----LLEKEASQACMTKKGFT-PLHVAAKYGKV  159 (437)
T ss_dssp             HHTCHHHHHHHHH----HTCCTTCCCTTCCCHHHHHHHHTCHHHHHH----HHHTTCCSCCCCTTSCC-HHHHHHHTTCH
T ss_pred             HCCCHHHHHHHHh----CCCCCCCCCCCCCcHHHHHHHcCCHHHHHH----HHhCCCCCcCCCCCCCC-HHHHHHHcCCH
Confidence            7777765554444    354443221  1123334455666654443    3344443322   2222 33444566666


Q ss_pred             HHHHHHHHHHHHcCCCCCHHH--HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeeh--HHHHHHHHccCCHHHHHHH
Q 011378          222 TEADDLFNEMLERGVFPDFYT--FTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTY--NTLIDGFCKVGEMEKANKL  297 (487)
Q Consensus       222 ~~a~~~~~~m~~~~~~~~~~t--~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~--~~li~~~~~~g~~~~a~~~  297 (487)
                      +-+..    +.+.|..++...  -.+.+...+..|+.+    +++.+.+.|..++...+  .+.+...++.|+.+-+..+
T Consensus       160 ~~v~~----Ll~~g~~~~~~~~~g~t~L~~A~~~~~~~----~v~~Ll~~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~L  231 (437)
T 1n11_A          160 RVAEL----LLERDAHPNAAGKNGLTPLHVAVHHNNLD----IVKLLLPRGGSPHSPAWNGYTPLHIAAKQNQVEVARSL  231 (437)
T ss_dssp             HHHHH----HHHTTCCTTCCCSSCCCHHHHHHHTTCHH----HHHHHGGGTCCSCCCCTTCCCHHHHHHHTTCHHHHHHH
T ss_pred             HHHHH----HHhCCCCCCCCCCCCCCHHHHHHHcCCHH----HHHHHHhCCCCCCCcCCCCCCHHHHHHHcCCHHHHHHH
Confidence            54443    344555443211  112344455666654    44455556655544321  2334444566776555444


Q ss_pred             HHHHHhCCCCCChh---hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChh---hHHHHHHHHHhcCChHHHHHHHHHH
Q 011378          298 WADMISRKISPNYI---SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLV---SCNTIIKGYCRSGDASKADEFLSKM  371 (487)
Q Consensus       298 ~~~m~~~~~~p~~~---t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m  371 (487)
                      +    +.|..++..   -.+.|. ..+..|+.+    +.+.+.+.|..++..   -.+.|. ..++.|+.+-+    +.+
T Consensus       232 l----~~g~~~~~~~~~g~t~L~-~A~~~g~~~----~v~~Ll~~~~~~~~~~~~g~t~L~-~A~~~~~~~~~----~~L  297 (437)
T 1n11_A          232 L----QYGGSANAESVQGVTPLH-LAAQEGHAE----MVALLLSKQANGNLGNKSGLTPLH-LVAQEGHVPVA----DVL  297 (437)
T ss_dssp             H----HTTCCTTCCCTTCCCHHH-HHHHTTCHH----HHHHHHTTTCCTTCCCTTCCCHHH-HHHHHTCHHHH----HHH
T ss_pred             H----HcCCCCCCCCCCCCCHHH-HHHHCCCHH----HHHHHHhcCCCCCCCCCCCCCHHH-HHHHcCCHHHH----HHH
Confidence            4    344433322   223333 334556654    333444555554432   223333 34455665543    333


Q ss_pred             HHCCCCCChh---hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhh---HHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011378          372 VSEGVDPDSI---SYNTLINGFVREENMDKAFALVSKMENQGLVPDVIT---YNVILTGFCRQGRMHDSELILWRMIEKG  445 (487)
Q Consensus       372 ~~~g~~p~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~---~~~li~~~~~~g~~~~a~~~~~~m~~~g  445 (487)
                      .+.|..++..   -.+. +...+..|+.+-+..++    +.|..++...   ++. +...++.|..+-+    +-+.+.|
T Consensus       298 l~~g~~~~~~~~~g~t~-L~~A~~~g~~~~v~~Ll----~~gad~n~~~~~g~t~-L~~A~~~g~~~iv----~~Ll~~g  367 (437)
T 1n11_A          298 IKHGVMVDATTRMGYTP-LHVASHYGNIKLVKFLL----QHQADVNAKTKLGYSP-LHQAAQQGHTDIV----TLLLKNG  367 (437)
T ss_dssp             HHHTCCTTCCCSSCCCH-HHHHHHSSCSHHHHHHH----HTTCCTTCCCTTSCCH-HHHHHHTTCHHHH----HHHHHTT
T ss_pred             HhCCccCCCCCCCCCCH-HHHHHHcCcHHHHHHHH----hcCCCCCCCCCCCCCH-HHHHHHCChHHHH----HHHHHCc
Confidence            4445554432   2223 33444566665444333    3455544322   233 3334456665433    4455567


Q ss_pred             CCCCHHH--HHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          446 LNPDRST--YTTLINGHVSQNNLKEAFRFHDEM  476 (487)
Q Consensus       446 ~~p~~~t--y~~l~~~~~~~~~~~~a~~~~~~m  476 (487)
                      ..|+...  -.+-+....+.|.. +..+++...
T Consensus       368 a~~~~~~~~g~t~l~~A~~~g~~-~~~~~l~~~  399 (437)
T 1n11_A          368 ASPNEVSSDGTTPLAIAKRLGYI-SVTDVLKVV  399 (437)
T ss_dssp             CCSCCCCSSSCCHHHHHHHTTCH-HHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHcCcH-HHHHHHHhc
Confidence            7776431  11122333444543 444555444

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=90.46  E-value=3.7  Score=32.22  Aligned_cols=85  Identities=15%  Similarity=0.107  Sum_probs=55.0

Q ss_pred             hhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC---ChhHHHHHHHHHHHCCCCC-C-HhHHHHHHHHHHhCCCHHHHHH
Q 011378           82 DRAKEVLDEMLQMGLSPDTATYNTLLVESCRKE---NMSEAEEIFCEMSRRGVAP-D-IVSFSTLIGIFSRNGQLDRALM  156 (487)
Q Consensus        82 ~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~---~~~~a~~~~~~m~~~g~~p-~-~~~~~~li~~~~~~g~~~~a~~  156 (487)
                      ..+.+-|.+..+.|. ++..+.-.+-.++++.+   +++++..+|++..+.. .| + ...+=.+--+|.+.|++++|.+
T Consensus        15 ~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHH
Confidence            344555555555443 56666666677777777   5668888888877754 23 1 2223335556788899999998


Q ss_pred             HHHHHHHCCCCCCh
Q 011378          157 YFREMKSAGLVPDN  170 (487)
Q Consensus       157 ~~~~m~~~g~~~~~  170 (487)
                      +++.+.+  +.|+.
T Consensus        93 y~~~lL~--ieP~n  104 (152)
T 1pc2_A           93 YVRGLLQ--TEPQN  104 (152)
T ss_dssp             HHHHHHH--HCTTC
T ss_pred             HHHHHHh--cCCCC
Confidence            8888876  35654

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=90.37  E-value=4.4  Score=35.28  Aligned_cols=19  Identities=16%  Similarity=0.123  Sum_probs=10.6

Q ss_pred             HHHHHHHhcCChhHHHHHH
Q 011378           35 TLINAYCREGFLEEAFQLM   53 (487)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~~   53 (487)
                      +.+...++.|+++....++
T Consensus         7 ~~L~~A~~~g~~~~v~~Ll   25 (285)
T 1wdy_A            7 HLLIKAVQNEDVDLVQQLL   25 (285)
T ss_dssp             HHHHHHHHTTCHHHHHHHH
T ss_pred             hHHHHHHHcCCHHHHHHHH
Confidence            4455556667665554444

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

Probab=89.93  E-value=2  Score=30.30  Aligned_cols=52  Identities=15%  Similarity=0.138  Sum_probs=22.1

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLV-SCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      +...|++++|...++...... +.+.. .+..+-.+|...|+.++|...+++..
T Consensus        10 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al   62 (99)
T 2kc7_A           10 LINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAI   62 (99)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334444444444444443321 11223 34444444444445555544444444

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=89.87  E-value=2.9  Score=32.80  Aligned_cols=65  Identities=11%  Similarity=0.105  Sum_probs=29.2

Q ss_pred             CChhhHHHHHHHHhccC---CHHHHHHHHHHHHhCCCCC-C-HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          378 PDSISYNTLINGFVREE---NMDKAFALVSKMENQGLVP-D-VITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       378 p~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~g~~p-~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ++..+.-.+--++++.+   +.+++..+++..-+.. .| + ...+=.|--+|.+.|++++|.+.++.+.+
T Consensus        30 ~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~   99 (152)
T 1pc2_A           30 VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQ   99 (152)
T ss_dssp             CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            34433334444444444   3445555555444332 23 1 22222233344555666666665555544

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=89.36  E-value=4.5  Score=35.21  Aligned_cols=15  Identities=13%  Similarity=0.388  Sum_probs=6.8

Q ss_pred             HHHHHHHHHCCCCCC
Q 011378          365 DEFLSKMVSEGVDPD  379 (487)
Q Consensus       365 ~~~~~~m~~~g~~p~  379 (487)
                      .++++.+.+.|..++
T Consensus       199 ~~i~~~Ll~~g~~~~  213 (285)
T 1wdy_A          199 EAITHLLLDHGADVN  213 (285)
T ss_dssp             HHHHHHHHHTTCCSS
T ss_pred             HHHHHHHHHcCCCCC
Confidence            344444444454443

>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=88.84  E-value=19  Score=35.42  Aligned_cols=136  Identities=10%  Similarity=-0.016  Sum_probs=60.5

Q ss_pred             hhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCC--CHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcC-CHHHHHHH
Q 011378          116 MSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNG--QLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG-FVLEALKM  192 (487)
Q Consensus       116 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g--~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~-~~~~a~~~  192 (487)
                      ++++.+.++.+.+.. +-+..+|+.=-.++.+.|  +++++++.++++.+.. .-+...|+.--..+.+.| ..+++++.
T Consensus        89 ~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~  166 (567)
T 1dce_A           89 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAF  166 (567)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHH
Confidence            444444444444322 113334444334444444  3455555555554422 112334444333344444 44444444


Q ss_pred             HHHHHHcCCcCChhhHHHHHHHHHhc--------------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 011378          193 RDEMLEKGCVMDVVTYNTILNGLCRA--------------KMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGN  255 (487)
Q Consensus       193 ~~~m~~~g~~~~~~~~~~li~~~~~~--------------~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~  255 (487)
                      ++++.+... -|...|+.....+.+.              +.++++.+.+++..... +-|...|.-.-..+.+.++
T Consensus       167 ~~~~I~~~p-~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          167 TDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             HHTTTTTTC-CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHCC-CCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCC
Confidence            444443221 2333444333333321              34567777777766532 2245566665555555554

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=88.66  E-value=3.1  Score=35.32  Aligned_cols=21  Identities=24%  Similarity=0.313  Sum_probs=9.0

Q ss_pred             HHhcCChhHHHHHHHHHhhCC
Q 011378           40 YCREGFLEEAFQLMNSMSGKG   60 (487)
Q Consensus        40 ~~~~~~~~~a~~~~~~m~~~~   60 (487)
                      .++.|+.+.+..+++.+...|
T Consensus        16 A~~~g~~~~v~~Ll~~~~~~~   36 (241)
T 1k1a_A           16 AVVQGNLPAVHRLVNLFQQGG   36 (241)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHcCCHHHHHHHHHHHHhcC
Confidence            334444444444444433333

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens}

Probab=88.42  E-value=2.4  Score=35.95  Aligned_cols=50  Identities=18%  Similarity=-0.029  Sum_probs=22.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH--HHHHHHHHHhcCCHHHHHHHHHH
Q 011378          212 LNGLCRAKMLTEADDLFNEMLERGVFPDFYT--FTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t--~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      +...++.|+.+-+..++    +.|..++...  -.+.+....+.|+.+-+.-+++.
T Consensus       181 L~~A~~~~~~~~v~~Ll----~~g~~~~~~~~~g~t~l~~A~~~~~~~~v~~L~~~  232 (240)
T 3eu9_A          181 LHWAVLAGNTTVISLLL----EAGANVDAQNIKGESALDLAKQRKNVWMINHLQEA  232 (240)
T ss_dssp             HHHHHHHTCHHHHHHHH----HHTCCTTCBCTTSCBHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHH----HcCCCCCCcCCCCCCHHHHHHHcCcHHHHHHHHHh
Confidence            44445556655443333    3344333211  11234445566666655555443

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=88.28  E-value=5.2  Score=28.25  Aligned_cols=46  Identities=11%  Similarity=0.074  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          396 MDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       396 ~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      .++|..++++....  .|+ +.....+-..+.+.|++++|...++++.+
T Consensus        25 ~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A           25 TDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             CHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            45555555544432  232 23333333444555555555555555543

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=88.01  E-value=7.5  Score=29.75  Aligned_cols=63  Identities=17%  Similarity=0.143  Sum_probs=32.0

Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 011378          383 YNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGL  446 (487)
Q Consensus       383 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  446 (487)
                      .+.-++..+..|+-|+-.++...+.. +-+|++...--+..+|.+-|+..++..++.+.-++|+
T Consensus        94 vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A           94 VNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence            34444555555555555555554311 1234444445555555555555555555555555554

>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=87.94  E-value=2.5  Score=30.27  Aligned_cols=62  Identities=18%  Similarity=0.204  Sum_probs=38.3

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011378          395 NMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLI  457 (487)
Q Consensus       395 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~  457 (487)
                      +.-+..+-+..+-...+.|++......+.+|.+-+++..|.++|+-.+.+- .+...+|..++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~l   86 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   86 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHH
Confidence            444555555555566667777777777777777777777777777666442 22233455544

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=87.87  E-value=22  Score=34.98  Aligned_cols=174  Identities=11%  Similarity=0.071  Sum_probs=116.8

Q ss_pred             HhcC-ChhHHHHHHHHHhhCCCCCCc-cchHHHHHHHHhcCC----------hhhHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011378           41 CREG-FLEEAFQLMNSMSGKGLKPGV-FTYNSLINGLCKKGR----------CDRAKEVLDEMLQMGLSPDTATYNTLLV  108 (487)
Q Consensus        41 ~~~~-~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~----------~~~a~~~~~~m~~~g~~~~~~~~~~ll~  108 (487)
                      .+.| ..++|++.++.+...  .|+- ..|+.-=..+.+.++          ++++++.++.+.+.. +-+...|+---.
T Consensus        39 ~~~~~~~eeal~~~~~~l~~--nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w  115 (567)
T 1dce_A           39 RQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCW  115 (567)
T ss_dssp             HHTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            3444 446789999888763  3443 345543334444444          889999999988643 235667777677


Q ss_pred             HHHccC--ChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCC-CHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhc--
Q 011378          109 ESCRKE--NMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNG-QLDRALMYFREMKSAGLVPDNVLYTIIINGYCRN--  183 (487)
Q Consensus       109 ~~~~~~--~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~--  183 (487)
                      .+.+.+  +++++.+.++.+.+... -|...|+.--.+..+.| ..+++++.++++.+.. .-|...|+..-..+.+.  
T Consensus       116 ~l~~l~~~~~~~el~~~~k~l~~d~-~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~  193 (567)
T 1dce_A          116 LLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHP  193 (567)
T ss_dssp             HHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSC
T ss_pred             HHHHcccccHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhcc
Confidence            777778  67999999999988653 37778888777778888 8899999988886543 22455666666655552  


Q ss_pred             ------------CCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC
Q 011378          184 ------------GFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM  220 (487)
Q Consensus       184 ------------~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~  220 (487)
                                  +.++++.+.+.+..... +-|...|+-.-..+.+.+.
T Consensus       194 ~~~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          194 QPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             CCCSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCC
T ss_pred             cccccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCC
Confidence                        44677777777766533 2355567666666655555

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=87.86  E-value=3.9  Score=29.51  Aligned_cols=57  Identities=12%  Similarity=0.093  Sum_probs=23.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcC------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          210 TILNGLCRAKMLTEADDLFNEMLERG------VFPDFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~~------~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      .|-..+.+.+++..|...|+...+.-      -.+....+..+-.++.+.|+.+.|+..++..
T Consensus        10 ~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~a   72 (104)
T 2v5f_A           10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKL   72 (104)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            34444444444444444444433210      0122333444444444444444444444433

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=86.75  E-value=6.5  Score=27.75  Aligned_cols=48  Identities=10%  Similarity=0.135  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 011378          221 LTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQK  269 (487)
Q Consensus       221 ~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~  269 (487)
                      .++|..++++..+.. +-++.....+-..+...|++++|+..|+.+.+.
T Consensus        25 ~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A           25 TDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            456666666655432 123444455555566666666666666655543

>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=86.11  E-value=7.4  Score=27.90  Aligned_cols=62  Identities=13%  Similarity=0.180  Sum_probs=41.1

Q ss_pred             hhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHH
Q 011378          116 MSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIIN  178 (487)
Q Consensus       116 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  178 (487)
                      .=++.+-++.+....+.|++....+.+++|-|.+++..|.++|+-.+.+ +.+...+|..+++
T Consensus        26 ~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lq   87 (109)
T 1v54_E           26 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ   87 (109)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHH
Confidence            3355566666667777777777777888888888888888887777653 2222345555554

>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=85.66  E-value=9.4  Score=29.80  Aligned_cols=112  Identities=12%  Similarity=0.049  Sum_probs=64.4

Q ss_pred             ChhhHHHHHHHHHhcCCh------HHHHHHHHHHHHCCCCCChh-hHHHHHHHH------hccCCHHHHHHHHHHHHhCC
Q 011378          344 TLVSCNTIIKGYCRSGDA------SKADEFLSKMVSEGVDPDSI-SYNTLINGF------VREENMDKAFALVSKMENQG  410 (487)
Q Consensus       344 ~~~~~~~li~~~~~~~~~------~~a~~~~~~m~~~g~~p~~~-~~~~li~~~------~~~~~~~~a~~~~~~m~~~g  410 (487)
                      |..+|-..++-.-+.|+.      ++..++|+.... .++|+.. .|..-|..+      ...++.++|.++|+.+...+
T Consensus        12 ~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia-~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~h   90 (161)
T 4h7y_A           12 NPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIE-ALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANC   90 (161)
T ss_dssp             SHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHH-HSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHH-cCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence            344555555555555555      555566665543 3444421 111111111      23378888888888885433


Q ss_pred             CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011378          411 LVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLIN  458 (487)
Q Consensus       411 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~~  458 (487)
                      -+- ...|-.....=.++|++..|++++.+....+.+|.. ..+..+.
T Consensus        91 KkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~-~le~a~~  136 (161)
T 4h7y_A           91 KKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLE-MLEIALR  136 (161)
T ss_dssp             TTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHH-HHHHHHH
T ss_pred             HHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHH-HHHHHHH
Confidence            233 555666666667899999999999988877665543 3333333

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=85.61  E-value=8.2  Score=29.10  Aligned_cols=86  Identities=13%  Similarity=0.134  Sum_probs=51.6

Q ss_pred             hcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHH---HHHHHHHHHhCCCCC-CHhhHHH-HHHHHHhcCCh
Q 011378          357 RSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDK---AFALVSKMENQGLVP-DVITYNV-ILTGFCRQGRM  431 (487)
Q Consensus       357 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~---a~~~~~~m~~~g~~p-~~~~~~~-li~~~~~~g~~  431 (487)
                      ....+..+.+-+......|. |+..+--.+-.++++....++   +..+++..-..+ .| ....+.- |.-++.+.|++
T Consensus        13 ~~~~l~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y   90 (126)
T 1nzn_A           13 SVEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEY   90 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCH
T ss_pred             CHHHHHHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhH
Confidence            33444555555655554444 555555555666777776555   667776665542 23 2333333 33477888888


Q ss_pred             HHHHHHHHHHHHc
Q 011378          432 HDSELILWRMIEK  444 (487)
Q Consensus       432 ~~a~~~~~~m~~~  444 (487)
                      ++|.+.++.+++.
T Consensus        91 ~~A~~~~~~lL~~  103 (126)
T 1nzn_A           91 EKALKYVRGLLQT  103 (126)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            8888888888764

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens}

Probab=84.68  E-value=3.2  Score=35.10  Aligned_cols=52  Identities=15%  Similarity=0.138  Sum_probs=21.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHhcCCHHHHHHHHHHHH
Q 011378          422 LTGFCRQGRMHDSELILWRMIEKGLNPDRSTYT--TLINGHVSQNNLKEAFRFHDEML  477 (487)
Q Consensus       422 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~--~l~~~~~~~~~~~~a~~~~~~m~  477 (487)
                      +...++.|..+-+..+    .+.|..|+.....  +-+....+.|+.+-+..+++...
T Consensus       181 L~~A~~~~~~~~v~~L----l~~g~~~~~~~~~g~t~l~~A~~~~~~~~v~~L~~~~~  234 (240)
T 3eu9_A          181 LHWAVLAGNTTVISLL----LEAGANVDAQNIKGESALDLAKQRKNVWMINHLQEARQ  234 (240)
T ss_dssp             HHHHHHHTCHHHHHHH----HHHTCCTTCBCTTSCBHHHHHHHTTCHHHHHHHHHHC-
T ss_pred             HHHHHHcCCHHHHHHH----HHcCCCCCCcCCCCCCHHHHHHHcCcHHHHHHHHHhhh
Confidence            3444455555443333    3335544432111  12333345565555544444333

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1

Probab=84.51  E-value=19  Score=33.84  Aligned_cols=357  Identities=17%  Similarity=0.155  Sum_probs=163.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCCCCCccc--hHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHH--HHHHHHHHH
Q 011378           35 TLINAYCREGFLEEAFQLMNSMSGKGLKPGVFT--YNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTA--TYNTLLVES  110 (487)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~--~~~~ll~~~  110 (487)
                      +.+...+..|+.+-+..++    ++|..|+...  ....+...++.|+.+-+.-+++    .|..++..  .-.+.|...
T Consensus        16 t~L~~Aa~~g~~~~v~~Ll----~~g~~~~~~~~~~~t~L~~A~~~g~~~~v~~Ll~----~g~~~~~~~~~g~t~L~~A   87 (437)
T 1n11_A           16 TPLHVASFMGHLPIVKNLL----QRGASPNVSNVKVETPLHMAARAGHTEVAKYLLQ----NKAKVNAKAKDDQTPLHCA   87 (437)
T ss_dssp             CHHHHHHHHTCHHHHHHHH----HTTCCSCCSSSCCCCHHHHHHHHTCHHHHHHHHH----HTCCSSCCCTTSCCHHHHH
T ss_pred             CHHHHHHHCCCHHHHHHHH----HcCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHh----CCCCCCCCCCCCCCHHHHH
Confidence            3456666777776555444    3455554322  1233444456676654444443    34333221  112234445


Q ss_pred             HccCChhHHHHHHHHHHHCCCCCCHhH--HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC---hhhHHHHHHHHHhcCC
Q 011378          111 CRKENMSEAEEIFCEMSRRGVAPDIVS--FSTLIGIFSRNGQLDRALMYFREMKSAGLVPD---NVLYTIIINGYCRNGF  185 (487)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~g~~p~~~~--~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~---~~~~~~ll~~~~~~~~  185 (487)
                      +..|+.+-+.    .+.+.|..|+...  -.+.+...++.|+.+.+..+++.    +..++   ..-++ .+...++.|+
T Consensus        88 ~~~g~~~~v~----~Ll~~ga~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~~----~~~~~~~~~~g~t-~L~~A~~~g~  158 (437)
T 1n11_A           88 ARIGHTNMVK----LLLENNANPNLATTAGHTPLHIAAREGHVETVLALLEK----EASQACMTKKGFT-PLHVAAKYGK  158 (437)
T ss_dssp             HHHTCHHHHH----HHHHHTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHHT----TCCSCCCCTTSCC-HHHHHHHTTC
T ss_pred             HHCCCHHHHH----HHHhCCCCCCCCCCCCCcHHHHHHHcCCHHHHHHHHhC----CCCCcCCCCCCCC-HHHHHHHcCC
Confidence            5666665443    3444455443221  12344555667777766655543    32221   11122 3333455566


Q ss_pred             HHHHHHHHHHHHHcCCcCChhh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH--HHHHHHHHHhcCCHHHHHH
Q 011378          186 VLEALKMRDEMLEKGCVMDVVT--YNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYT--FTTLIHGHCKDGNMNKALN  261 (487)
Q Consensus       186 ~~~a~~~~~~m~~~g~~~~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t--~~~li~~~~~~g~~~~a~~  261 (487)
                      .+    +++.+.+.|..++...  -.+.+...+..|+.+-    .+.+.+.|..|+...  -.+.+...+..|+.+.+..
T Consensus       159 ~~----~v~~Ll~~g~~~~~~~~~g~t~L~~A~~~~~~~~----v~~Ll~~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~  230 (437)
T 1n11_A          159 VR----VAELLLERDAHPNAAGKNGLTPLHVAVHHNNLDI----VKLLLPRGGSPHSPAWNGYTPLHIAAKQNQVEVARS  230 (437)
T ss_dssp             HH----HHHHHHHTTCCTTCCCSSCCCHHHHHHHTTCHHH----HHHHGGGTCCSCCCCTTCCCHHHHHHHTTCHHHHHH
T ss_pred             HH----HHHHHHhCCCCCCCCCCCCCCHHHHHHHcCCHHH----HHHHHhCCCCCCCcCCCCCCHHHHHHHcCCHHHHHH
Confidence            54    3444555665554321  1123344455666543    344445554443221  1223445556677655443


Q ss_pred             HHHHHHHCCCCCCee---ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCh---hhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          262 LFDIMTQKSIKPDIV---TYNTLIDGFCKVGEMEKANKLWADMISRKISPNY---ISYGILINGYCSMGHVTEAFRLWYE  335 (487)
Q Consensus       262 ~~~~m~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~---~t~~~li~~~~~~~~~~~a~~~~~~  335 (487)
                          +.+.|..++..   ..+. +...+..|..+-+..++    +.+..++.   .-.+.|. ..+..|+.+-+    +.
T Consensus       231 ----Ll~~g~~~~~~~~~g~t~-L~~A~~~g~~~~v~~Ll----~~~~~~~~~~~~g~t~L~-~A~~~~~~~~~----~~  296 (437)
T 1n11_A          231 ----LLQYGGSANAESVQGVTP-LHLAAQEGHAEMVALLL----SKQANGNLGNKSGLTPLH-LVAQEGHVPVA----DV  296 (437)
T ss_dssp             ----HHHTTCCTTCCCTTCCCH-HHHHHHTTCHHHHHHHH----TTTCCTTCCCTTCCCHHH-HHHHHTCHHHH----HH
T ss_pred             ----HHHcCCCCCCCCCCCCCH-HHHHHHCCCHHHHHHHH----hcCCCCCCCCCCCCCHHH-HHHHcCCHHHH----HH
Confidence                44455444332   2223 33445667765544443    34433332   1222333 33455666533    33


Q ss_pred             HHhCCCCCChh---hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhh---HHHHHHHHhccCCHHHHHHHHHHHHhC
Q 011378          336 MVGKGIKPTLV---SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSIS---YNTLINGFVREENMDKAFALVSKMENQ  409 (487)
Q Consensus       336 m~~~~~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~---~~~li~~~~~~~~~~~a~~~~~~m~~~  409 (487)
                      +.+.|..++..   -.+.|. ..+..|+.+-    ++.+.+.|..++...   ++.| ...+..|+.+-+    +.+.+.
T Consensus       297 Ll~~g~~~~~~~~~g~t~L~-~A~~~g~~~~----v~~Ll~~gad~n~~~~~g~t~L-~~A~~~g~~~iv----~~Ll~~  366 (437)
T 1n11_A          297 LIKHGVMVDATTRMGYTPLH-VASHYGNIKL----VKFLLQHQADVNAKTKLGYSPL-HQAAQQGHTDIV----TLLLKN  366 (437)
T ss_dssp             HHHHTCCTTCCCSSCCCHHH-HHHHSSCSHH----HHHHHHTTCCTTCCCTTSCCHH-HHHHHTTCHHHH----HHHHHT
T ss_pred             HHhCCccCCCCCCCCCCHHH-HHHHcCcHHH----HHHHHhcCCCCCCCCCCCCCHH-HHHHHCChHHHH----HHHHHC
Confidence            44445544432   223333 3445677654    444455666654322   2333 334456766544    344455


Q ss_pred             CCCCCHhh--HHHHHHHHHhcCChHHHHHHHHHH
Q 011378          410 GLVPDVIT--YNVILTGFCRQGRMHDSELILWRM  441 (487)
Q Consensus       410 g~~p~~~~--~~~li~~~~~~g~~~~a~~~~~~m  441 (487)
                      |..|+...  -.+-+....+.|.. +..++++..
T Consensus       367 ga~~~~~~~~g~t~l~~A~~~g~~-~~~~~l~~~  399 (437)
T 1n11_A          367 GASPNEVSSDGTTPLAIAKRLGYI-SVTDVLKVV  399 (437)
T ss_dssp             TCCSCCCCSSSCCHHHHHHHTTCH-HHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHcCcH-HHHHHHHhc
Confidence            66665421  12233334555553 333444443

>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=84.33  E-value=11  Score=33.27  Aligned_cols=93  Identities=11%  Similarity=0.047  Sum_probs=66.4

Q ss_pred             hHHHHHHHHHHHCCCCCC---HhHHHHHHHHHHhC-----CCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhc-CCHH
Q 011378          117 SEAEEIFCEMSRRGVAPD---IVSFSTLIGIFSRN-----GQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRN-GFVL  187 (487)
Q Consensus       117 ~~a~~~~~~m~~~g~~p~---~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~-~~~~  187 (487)
                      ..|...+++..+  +.|+   ...|..+...|.+.     |+.++|.+.|++....+..-+..++...-+.+++. |+.+
T Consensus       180 ~~A~a~lerAle--LDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~  257 (301)
T 3u64_A          180 HAAVMMLERACD--LWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRA  257 (301)
T ss_dssp             HHHHHHHHHHHH--HCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHH
T ss_pred             HHHHHHHHHHHH--hCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHH
Confidence            344455555544  3455   55788888889984     99999999999988754322366777777888885 8899


Q ss_pred             HHHHHHHHHHHcCCc--CChhhHHHH
Q 011378          188 EALKMRDEMLEKGCV--MDVVTYNTI  211 (487)
Q Consensus       188 ~a~~~~~~m~~~g~~--~~~~~~~~l  211 (487)
                      ++.+.+++-......  |+....|.+
T Consensus       258 ~a~~~L~kAL~a~p~~~P~~~lan~~  283 (301)
T 3u64_A          258 GFDEALDRALAIDPESVPHNKLLVIL  283 (301)
T ss_dssp             HHHHHHHHHHHCCGGGCSSCHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCChhHHHHH
Confidence            999999998887666  665555443

>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=84.02  E-value=4.7  Score=37.55  Aligned_cols=67  Identities=10%  Similarity=0.111  Sum_probs=41.8

Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH-----HcCCCCCHHH
Q 011378          385 TLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMI-----EKGLNPDRST  452 (487)
Q Consensus       385 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t  452 (487)
                      .++.++...|+.++|...+..+... -..+...|..++.++.+.|+..+|...|+++.     +.|+.|+..+
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            4455566667777776666655432 12355567777777777777777777666654     3477777654

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.96  E-value=29  Score=32.81  Aligned_cols=92  Identities=15%  Similarity=0.092  Sum_probs=48.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC--CCCCC---hhhHHHHHHHHHhcCChHHHHHHHHHHHH----CCCCCC--hhhH
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVGK--GIKPT---LVSCNTIIKGYCRSGDASKADEFLSKMVS----EGVDPD--SISY  383 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~~--~~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p~--~~~~  383 (487)
                      .|...+-..|++.+|.++..++...  |.-..   ...+...++.|...+++.+|..++++...    ....|+  ...|
T Consensus       142 ~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~  221 (445)
T 4b4t_P          142 DLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYY  221 (445)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHH
Confidence            4455555566666666666655422  21111   12445556666677777777776666531    222222  1245


Q ss_pred             HHHHHHHhccCCHHHHHHHHHHH
Q 011378          384 NTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       384 ~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      ...+..+...+++.+|...|-+.
T Consensus       222 ~~~~~~~~~e~~y~~a~~~y~e~  244 (445)
T 4b4t_P          222 NLLVKISLHKREYLEVAQYLQEI  244 (445)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHH
Confidence            55556666667776666655444

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.70  E-value=33  Score=32.46  Aligned_cols=187  Identities=11%  Similarity=0.071  Sum_probs=92.4

Q ss_pred             CCHHHHHHHHHHHHHC-----CCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhC-CCCCChhhHHHHHHHHH----hc
Q 011378          254 GNMNKALNLFDIMTQK-----SIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISR-KISPNYISYGILINGYC----SM  323 (487)
Q Consensus       254 g~~~~a~~~~~~m~~~-----~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~----~~  323 (487)
                      |+++.|++.+-.+.+.     ...........++..|.+.|+++...+.+.-+... |..+...  ..++..+.    ..
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai--~~~V~~~~~~l~~~  107 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSI--QYMIQKVMEYLKSS  107 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHH--HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHH--HHHHHHHHHHHhcC
Confidence            6788888777555432     12223345677788888888888877766554432 3333222  23333322    12


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCh--------hhHHHHHHHHHhcCChHHHHHHHHHHHHC--CCCCC---hhhHHHHHHHH
Q 011378          324 GHVTEAFRLWYEMVGKGIKPTL--------VSCNTIIKGYCRSGDASKADEFLSKMVSE--GVDPD---SISYNTLINGF  390 (487)
Q Consensus       324 ~~~~~a~~~~~~m~~~~~~~~~--------~~~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p~---~~~~~~li~~~  390 (487)
                      ...+.-..+.-.-.-..+....        .....|.+.|...|++.+|..++..+...  |..+.   ...+-.-+..|
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            2222111110000001111111        12234566666777777777777766532  22221   23455555666


Q ss_pred             hccCCHHHHHHHHHHHHh----CCCCCCH--hhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          391 VREENMDKAFALVSKMEN----QGLVPDV--ITYNVILTGFCRQGRMHDSELILWRMI  442 (487)
Q Consensus       391 ~~~~~~~~a~~~~~~m~~----~g~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~m~  442 (487)
                      ...+++.+|..++.+...    ..-.|+.  .-|...+..+...+++.+|.+.|.+..
T Consensus       188 l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~  245 (445)
T 4b4t_P          188 ILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIY  245 (445)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            666777777766665431    1111211  234555555556666666666555543

>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=82.48  E-value=12  Score=33.10  Aligned_cols=68  Identities=16%  Similarity=0.120  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHh-----cCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHcc-CCHHHHHHHHHHHHhCCCC
Q 011378          240 FYTFTTLIHGHCK-----DGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKV-GEMEKANKLWADMISRKIS  307 (487)
Q Consensus       240 ~~t~~~li~~~~~-----~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~~~~  307 (487)
                      ...|..+...|..     .|+.++|.+.|+...+.+-.-+..++...-+.++.. |+.+++.+.+.+.......
T Consensus       199 GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          199 GAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGG
T ss_pred             CHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCC
Confidence            3455566666666     366666666666555433222244555555556553 6666666666666655444

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=82.04  E-value=9  Score=32.30  Aligned_cols=21  Identities=14%  Similarity=0.186  Sum_probs=9.5

Q ss_pred             HhcCChhhHHHHHHHHHHCCC
Q 011378           76 CKKGRCDRAKEVLDEMLQMGL   96 (487)
Q Consensus        76 ~~~~~~~~a~~~~~~m~~~g~   96 (487)
                      ++.|+.+.+..+++.+.+.|.
T Consensus        17 ~~~g~~~~v~~Ll~~~~~~~~   37 (241)
T 1k1a_A           17 VVQGNLPAVHRLVNLFQQGGR   37 (241)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHcCCHHHHHHHHHHHHhcCC
Confidence            334455444444444444443

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=81.98  E-value=4.1e-05  Score=71.72  Aligned_cols=202  Identities=10%  Similarity=0.099  Sum_probs=102.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHH
Q 011378          239 DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILIN  318 (487)
Q Consensus       239 ~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~  318 (487)
                      |+..|..+|.+..+.|.+++-+..+...++..-.|  .+=+.|+-+|++.+++.+.++++.       .||..-...+-+
T Consensus        82 Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~--~IDteLi~ayAk~~rL~elEefl~-------~~N~A~iq~VGD  152 (624)
T 3lvg_A           82 DPSSYMEVVQAANTSGNWEELVKYLQMARKKARES--YVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGD  152 (624)
T ss_dssp             CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCST--TTTHHHHHHHHTSCSSSTTTSTTS-------CCSSSCTHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccc--ccHHHHHHHHHhhCcHHHHHHHHc-------CCCcccHHHHHH
Confidence            34445555555555555555555554444332222  223355555555555444333321       244444444444


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHH
Q 011378          319 GYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDK  398 (487)
Q Consensus       319 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~  398 (487)
                      -|...|.++.|.-+|..+         ..|..|-..+.+.|+++.|.+.-+      -.-++.||.-.-.+|+..+.+.-
T Consensus       153 rcf~e~lYeAAKilys~i---------sN~akLAstLV~L~~yq~AVdaAr------KAns~ktWKeV~~ACvd~~EfrL  217 (624)
T 3lvg_A          153 RCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGAR------KANSTRTWKEVCFACVDGKEFRL  217 (624)
T ss_dssp             HHHHSCCSTTSSTTGGGS---------CCCTTTSSSSSSCSGGGSSTTTTT------TCCSSCSHHHHTHHHHHSCTTTT
T ss_pred             HHHHccCHHHHHHHHHhC---------ccHHHHHHHHHHHHHHHHHHHHHH------hcCChhHHHHHHHHHhCchHHHH
Confidence            444555544444444322         122233334444555555433222      12356678888888888887766


Q ss_pred             HHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcCCHHHHHHH
Q 011378          399 AFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGL-NPDRSTYTTLINGHVSQNNLKEAFRF  472 (487)
Q Consensus       399 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~ty~~l~~~~~~~~~~~~a~~~  472 (487)
                      |.-.--.+.     .......-++..|-..|.+++-..+++.-.  |+ +....+|+.|-=.|++- +++..++-
T Consensus       218 AqicGLniI-----vhadeL~elv~~YE~~G~f~ELIsLlEagl--glErAHmGmFTELaILYsKY-~PeKlmEH  284 (624)
T 3lvg_A          218 AQMCGLHIV-----VHADELEELINYYQDRGYFEELITMLEAAL--GLERAHMGMFTELAILYSKF-KPQKMREH  284 (624)
T ss_dssp             TTHHHHHHH-----CCSSCCSGGGSSSSTTCCCTTSTTTHHHHT--TSTTCCHHHHHHHHHHHHSS-CTTHHHHH
T ss_pred             HHHhcchhc-----ccHHHHHHHHHHHHhCCCHHHHHHHHHHHh--CCCchhHHHHHHHHHHHHhc-CHHHHHHH
Confidence            544332222     112233456667888888888777766532  33 35667888887777765 34444433

>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=81.07  E-value=10  Score=28.83  Aligned_cols=62  Identities=18%  Similarity=0.204  Sum_probs=33.5

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011378          395 NMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLI  457 (487)
Q Consensus       395 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~  457 (487)
                      +.-+..+-+..+-...+.|++.....-+.+|.+-+++..|.++|+-.+.+- .+....|.-++
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~l  129 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI  129 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHH
Confidence            333344444444455566666666666666666666666666666655432 22233454443

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A 4dx1_A 4dx2_A*

Probab=80.38  E-value=2.4  Score=36.63  Aligned_cols=55  Identities=16%  Similarity=0.062  Sum_probs=31.8

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCCcc-------chHHHHHHHH--hcCChhhHHHHHHHH
Q 011378           37 INAYCREGFLEEAFQLMNSMSGKGLKPGVF-------TYNSLINGLC--KKGRCDRAKEVLDEM   91 (487)
Q Consensus        37 l~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-------~~~~li~~~~--~~~~~~~a~~~~~~m   91 (487)
                      +...++.|+.+....+++.+.+.|..++..       -++.|..+..  +.|..+-+..+++.-
T Consensus         9 L~~A~~~g~~~~v~~ll~~l~~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~g~~~~v~~Ll~~g   72 (260)
T 3jxi_A            9 LFDIVSRGSPDGLEGLLSFLLTHKKRLTDEEFREPSTGKTCLPKALLNLSAGRNDTIPILLDIA   72 (260)
T ss_dssp             HHHHHHHTCGGGGTTHHHHHHHHTCCTTSGGGSCTTTCCCHHHHHHTSCBTTBCTHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCcchhhhhccCCCCcHHHHHHHHhhcCCHHHHHHHHHhc
Confidence            444556777777777777666666555532       3344544442  456666666555543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	487
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.78
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.77
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.17
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.17
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.85
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.83
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.75
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.73
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.19
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.18
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.08
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.03
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.98
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.94
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.92
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.9
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.83
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.76
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.74
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.7
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.33
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.33
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.29
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.25
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.18
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.17
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.16
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.14
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.91
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.89
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	96.85
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.84
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.44
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.37
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.28
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.26
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.25
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.24
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.76
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	95.32
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.32
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.2
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.1
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.01
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	94.84
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	94.76
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	94.48
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	93.83
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	93.82
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	92.67
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	90.37
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	89.8
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	89.55
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	87.54
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	86.73
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	84.97
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	84.81
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	83.65
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	80.94

>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=99.78  E-value=3.5e-14  Score=132.92  Aligned_cols=376  Identities=14%  Similarity=0.115  Sum_probs=216.9

Q ss_pred             HhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHH
Q 011378           76 CKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRAL  155 (487)
Q Consensus        76 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  155 (487)
                      .+.|++++|.+.+++..+.. +-+...+..+-..+.+.|++++|...+++..+.. +-+..++..+..++.+.|++++|+
T Consensus        10 ~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~   87 (388)
T d1w3ba_          10 YQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAI   87 (388)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccccccc
Confidence            34455555555555544321 1123444444455555555555555555554431 113445555556666666666666


Q ss_pred             HHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011378          156 MYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERG  235 (487)
Q Consensus       156 ~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (487)
                      ..+......... +...+..........+....+............ ................+....+...+.......
T Consensus        88 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (388)
T d1w3ba_          88 EHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ  165 (388)
T ss_dssp             HHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC
T ss_pred             cccccccccccc-ccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhhhHHHHHHhhccC
Confidence            666655543211 122222222223333333333333322222221 222233344444455556666666555554432


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHH
Q 011378          236 VFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYG  314 (487)
Q Consensus       236 ~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~  314 (487)
                       +-+...+..+...+...|+.++|...++...+.  .| +...+..+...+...|++++|...+....... ..+...+.
T Consensus       166 -~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  241 (388)
T d1w3ba_         166 -PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL--DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHG  241 (388)
T ss_dssp             -TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             -cchhHHHHhhcccccccCcHHHHHHHHHHHHHh--CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHH
Confidence             224455666666667777777777777655442  23 23456666677777777777777776665432 23445566


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccC
Q 011378          315 ILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREE  394 (487)
Q Consensus       315 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~  394 (487)
                      .+...+...|++++|...|+...... +-+..++..+-..+...|+.++|.+.++..... .+.+...+..+...+.+.|
T Consensus       242 ~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~  319 (388)
T d1w3ba_         242 NLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQG  319 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHHHCC
Confidence            67777777788888877777765532 234556777777788888888888888776543 2345567777777888888


Q ss_pred             CHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCC
Q 011378          395 NMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIEKGLNPD-RSTYTTLINGHVSQNN  465 (487)
Q Consensus       395 ~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l~~~~~~~~~  465 (487)
                      ++++|.+.+++..+.  .|+ ...|..+...|.+.|++++|...|++..+  +.|+ ...|..+...|.+.||
T Consensus       320 ~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         320 NIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR--ISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             CHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT--TCTTCHHHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCC
Confidence            888888888776543  454 45677777788888888888888887654  4564 4567777777766554

>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=99.77  E-value=5.8e-14  Score=131.43  Aligned_cols=376  Identities=14%  Similarity=0.050  Sum_probs=178.9

Q ss_pred             HhcCChhHHHHHHHHHhhCCCCC-CccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHH
Q 011378           41 CREGFLEEAFQLMNSMSGKGLKP-GVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEA  119 (487)
Q Consensus        41 ~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a  119 (487)
                      -+.|++++|.+.++.+.+.  .| ++..+..+-..+.+.|++++|...+++..+.. +-+...|..+...+.+.|++++|
T Consensus        10 ~~~G~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A   86 (388)
T d1w3ba_          10 YQAGDFEAAERHCMQLWRQ--EPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEA   86 (388)
T ss_dssp             HHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcccccc
Confidence            3444444444444444332  12 22333444444444444444444444443321 11233444444444444555555


Q ss_pred             HHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011378          120 EEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEK  199 (487)
Q Consensus       120 ~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  199 (487)
                      .+.+....+.... +..............+....+........... .................+....+...+......
T Consensus        87 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (388)
T d1w3ba_          87 IEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACYLKAIET  164 (388)
T ss_dssp             HHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             ccccccccccccc-cccccccccccccccccccccccccccccccc-cccccccccccccccccchhhhhHHHHHHhhcc
Confidence            5444444433211 11122222222222333333332222222211 111222222333333344444444444333322


Q ss_pred             CCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehH
Q 011378          200 GCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYN  279 (487)
Q Consensus       200 g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~  279 (487)
                      . +-+...+..+...+...|+++.|...+++..+.. +-+...+..+...+...|++++|+..++....... .+...+.
T Consensus       165 ~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~  241 (388)
T d1w3ba_         165 Q-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NHAVVHG  241 (388)
T ss_dssp             C-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TCHHHHH
T ss_pred             C-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh-hHHHHHH
Confidence            1 1123344444555555556666665555554432 12344555555556666666666666655443221 1233444


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC
Q 011378          280 TLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSG  359 (487)
Q Consensus       280 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  359 (487)
                      .+-..+.+.|++++|...|++..... +-+..++..+...+...|++++|...++..... .+.+...+..+...+...|
T Consensus       242 ~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~  319 (388)
T d1w3ba_         242 NLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQG  319 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHHHCC
Confidence            55555666666666666665554321 123445566666666666666666666655433 2445556666666666777


Q ss_pred             ChHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCC
Q 011378          360 DASKADEFLSKMVSEGVDPD-SISYNTLINGFVREENMDKAFALVSKMENQGLVPD-VITYNVILTGFCRQGR  430 (487)
Q Consensus       360 ~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~  430 (487)
                      +.++|...+++..+  +.|+ ..++..+-..|.+.|++++|.+.+++..+  +.|+ ...|..+...|.+.|+
T Consensus       320 ~~~~A~~~~~~al~--~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         320 NIEEAVRLYRKALE--VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR--ISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             CHHHHHHHHHHHTT--SCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT--TCTTCHHHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCC
Confidence            77777777766554  2343 44566666677777777777777766544  3453 4456666666655543

>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=99.17  E-value=1.6e-08  Score=91.51  Aligned_cols=267  Identities=10%  Similarity=0.010  Sum_probs=147.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 011378          177 INGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNM  256 (487)
Q Consensus       177 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~  256 (487)
                      -..+.+.|+.++|...|++..+.. +-+...|..+..++...|+++.|...|.+..+.. +-+...|..+...|...|+.
T Consensus        26 g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~  103 (323)
T d1fcha_          26 GLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQ  103 (323)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccc
Confidence            334667777777777777776643 2245567777777777777777777777766542 22456667777777777777


Q ss_pred             HHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          257 NKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEM  336 (487)
Q Consensus       257 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m  336 (487)
                      ++|.+.++......  |+.............                   ..+.......+..+...+.+.++...+...
T Consensus       104 ~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a  162 (323)
T d1fcha_         104 RQACEILRDWLRYT--PAYAHLVTPAEEGAG-------------------GAGLGPSKRILGSLLSDSLFLEVKELFLAA  162 (323)
T ss_dssp             HHHHHHHHHHHHTS--TTTGGGCC----------------------------------CTTHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccchhhHHHhc--cchHHHHHhhhhhhh-------------------hcccccchhhHHHHHHhhHHHHHHHHHHHH
Confidence            77777777665432  211000000000000                   000000001111222334455566655554


Q ss_pred             HhC-CCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-C
Q 011378          337 VGK-GIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVP-D  414 (487)
Q Consensus       337 ~~~-~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~  414 (487)
                      ... .-.++..++..+-..+...|+.++|...+++..... +-+...|..+-..|.+.|++++|.+.+++..+.  .| +
T Consensus       163 l~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~  239 (323)
T d1fcha_         163 VRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGY  239 (323)
T ss_dssp             HHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHH--hhcc
Confidence            432 122344556666666777777777777777665432 113456666777777777777777777766542  33 3


Q ss_pred             HhhHHHHHHHHHhcCChHHHHHHHHHHHHc----------CCCCCHHHHHHHHHHHHhcCCHHHH
Q 011378          415 VITYNVILTGFCRQGRMHDSELILWRMIEK----------GLNPDRSTYTTLINGHVSQNNLKEA  469 (487)
Q Consensus       415 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----------g~~p~~~ty~~l~~~~~~~~~~~~a  469 (487)
                      ...|..+...|.+.|++++|...|++..+.          ........|..+-.++...|+.+.+
T Consensus       240 ~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~  304 (323)
T d1fcha_         240 IRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY  304 (323)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            455667777777777777777777776531          1112233455555555555555433

>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=99.17  E-value=2.5e-08  Score=90.17  Aligned_cols=240  Identities=10%  Similarity=0.031  Sum_probs=158.1

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcC
Q 011378          141 LIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAK  219 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~  219 (487)
                      .-..+.+.|++++|...|++..+..  |+ ...|..+-..+...|+.++|...+.+..+.. +-+...|..+...|...|
T Consensus        25 ~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          25 EGLRRLQEGDLPNAVLLFEAAVQQD--PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccc
Confidence            4456789999999999999998753  54 6688999999999999999999999887643 235667888889999999


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHH
Q 011378          220 MLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWA  299 (487)
Q Consensus       220 ~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  299 (487)
                      +++.|.+.+++.....  |+............                   ...+.......+..+.+.+..+++...+.
T Consensus       102 ~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  160 (323)
T d1fcha_         102 LQRQACEILRDWLRYT--PAYAHLVTPAEEGA-------------------GGAGLGPSKRILGSLLSDSLFLEVKELFL  160 (323)
T ss_dssp             CHHHHHHHHHHHHHTS--TTTGGGCC----------------------------------CTTHHHHHHHHHHHHHHHHH
T ss_pred             cccccccchhhHHHhc--cchHHHHHhhhhhh-------------------hhcccccchhhHHHHHHhhHHHHHHHHHH
Confidence            9999999999987642  32111000000000                   00001111112222333445566666665


Q ss_pred             HHHhCC-CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC
Q 011378          300 DMISRK-ISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDP  378 (487)
Q Consensus       300 ~m~~~~-~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  378 (487)
                      +..... -.++...+..+...+...|++++|...++...... +-+...|..+-..|...|+.++|.+.+++..+.  .|
T Consensus       161 ~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p  237 (323)
T d1fcha_         161 AAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QP  237 (323)
T ss_dssp             HHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT
T ss_pred             HHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHH--hh
Confidence            544322 22345566667777777788888888877765432 234556777777777888888888888777653  34


Q ss_pred             C-hhhHHHHHHHHhccCCHHHHHHHHHHHH
Q 011378          379 D-SISYNTLINGFVREENMDKAFALVSKME  407 (487)
Q Consensus       379 ~-~~~~~~li~~~~~~~~~~~a~~~~~~m~  407 (487)
                      + ...+..|-.+|.+.|++++|.+.|++..
T Consensus       238 ~~~~a~~~lg~~~~~~g~~~~A~~~~~~al  267 (323)
T d1fcha_         238 GYIRSRYNLGISCINLGAHREAVEHFLEAL  267 (323)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3 4567777778888888888888877654

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.85  E-value=6.4e-07  Score=80.14  Aligned_cols=183  Identities=12%  Similarity=0.106  Sum_probs=78.2

Q ss_pred             hhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHH
Q 011378           81 CDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFRE  160 (487)
Q Consensus        81 ~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  160 (487)
                      .+++..++++..+...+.+...|.......-+.|+.+.|..+|+.+.+..-......|...+....+.|+++.|.++|+.
T Consensus        80 ~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~  159 (308)
T d2onda1          80 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  159 (308)
T ss_dssp             HHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            34455555555443323333444445555555555555555555554432222223455555555555555555555555


Q ss_pred             HHHCCCCCChhhHHHHHH-HHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCC
Q 011378          161 MKSAGLVPDNVLYTIIIN-GYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERG-VFP  238 (487)
Q Consensus       161 m~~~g~~~~~~~~~~ll~-~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~~  238 (487)
                      ..+.+.. +...|..... -+...|+.+.|..+++...+. .+.+...|...++...+.|+++.|..+|++..+.. ..|
T Consensus       160 al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~  237 (308)
T d2onda1         160 AREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPP  237 (308)
T ss_dssp             HHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCG
T ss_pred             HHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCh
Confidence            5443211 1111111111 112234444444444444432 22233344444444444444444444444443322 122


Q ss_pred             C--HHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          239 D--FYTFTTLIHGHCKDGNMNKALNLFDI  265 (487)
Q Consensus       239 ~--~~t~~~li~~~~~~g~~~~a~~~~~~  265 (487)
                      +  ...|...+..-...|+.+.+..+++.
T Consensus       238 ~~~~~iw~~~~~fE~~~G~~~~~~~~~~r  266 (308)
T d2onda1         238 EKSGEIWARFLAFESNIGDLASILKVEKR  266 (308)
T ss_dssp             GGCHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            1  12344444443444444444444443

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.83  E-value=9e-07  Score=79.14  Aligned_cols=186  Identities=11%  Similarity=0.041  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011378          256 MNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYE  335 (487)
Q Consensus       256 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  335 (487)
                      .++|..+|+...+...+.+...|...+..+-+.|+++.|..+|..+...........|...+..+.+.|.++.|..+|..
T Consensus        80 ~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~  159 (308)
T d2onda1          80 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  159 (308)
T ss_dssp             HHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            35555555555443333333445555555566666666666666655432222233455566666666666666666665


Q ss_pred             HHhCCCCCChhhHHHHHH-HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhC-CCCC
Q 011378          336 MVGKGIKPTLVSCNTIIK-GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQ-GLVP  413 (487)
Q Consensus       336 m~~~~~~~~~~~~~~li~-~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p  413 (487)
                      ..+.+- .+...|..... -+...|+.+.|..+++.+.+. .+.+...|...++...+.|+.+.|..+|++.... +..|
T Consensus       160 al~~~~-~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~  237 (308)
T d2onda1         160 AREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPP  237 (308)
T ss_dssp             HHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCG
T ss_pred             HHHhCC-CcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCh
Confidence            544331 12222222111 122345566666666655543 2223445555566666666666666666654432 2333


Q ss_pred             C--HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          414 D--VITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       414 ~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +  ...|...+..-.+.|+++.+..+.+++.+
T Consensus       238 ~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         238 EKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             GGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2  23455555555556666666666665543

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.75  E-value=2.6e-05  Score=70.21  Aligned_cols=197  Identities=10%  Similarity=-0.018  Sum_probs=83.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHH----cCCC--CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC----CCCeee
Q 011378          209 NTILNGLCRAKMLTEADDLFNEMLE----RGVF--PD-FYTFTTLIHGHCKDGNMNKALNLFDIMTQKSI----KPDIVT  277 (487)
Q Consensus       209 ~~li~~~~~~~~~~~a~~~~~~m~~----~~~~--~~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~~~~~~  277 (487)
                      ..+...+...|++..+...+.+...    .+..  +. ...+..+-..+...|+++.+...+........    ......
T Consensus        95 ~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  174 (366)
T d1hz4a_          95 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  174 (366)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHH
Confidence            3344445555566655555554432    1111  11 12333344455556666666665554433211    111222


Q ss_pred             hHHHHHHHHccCCHHHHHHHHHHHHhC----CCCC--ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---hhhH
Q 011378          278 YNTLIDGFCKVGEMEKANKLWADMISR----KISP--NYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPT---LVSC  348 (487)
Q Consensus       278 ~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~---~~~~  348 (487)
                      +..+...+...+....+...+.+....    +..+  ....+..+...+...|+.++|...+..........+   ...+
T Consensus       175 ~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  254 (366)
T d1hz4a_         175 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQW  254 (366)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHH
Confidence            333334444555555555544433221    1001  011233334444555555555555544332211111   1223


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHH----CCCCCCh-hhHHHHHHHHhccCCHHHHHHHHHH
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVS----EGVDPDS-ISYNTLINGFVREENMDKAFALVSK  405 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~  405 (487)
                      ..+-.++...|+.++|...++....    .+..|+. ..+..+-..|.+.|++++|.+.+++
T Consensus       255 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~  316 (366)
T d1hz4a_         255 RNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLD  316 (366)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            3344455555555555555554431    2333322 2344444555555555555555543

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.73  E-value=5.4e-06  Score=74.88  Aligned_cols=268  Identities=12%  Similarity=0.054  Sum_probs=176.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCcCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHH
Q 011378          176 IINGYCRNGFVLEALKMRDEMLEKGCVMD----VVTYNTILNGLCRAKMLTEADDLFNEMLERGV-FPD----FYTFTTL  246 (487)
Q Consensus       176 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~~----~~t~~~l  246 (487)
                      .-..+...|+.++|.+++++..+..-..+    ...++.+-..|...|++++|...|++..+..- .++    ..++..+
T Consensus        18 rA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   97 (366)
T d1hz4a_          18 RAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQ   97 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            34556788999999999988776421111    23566677888889999999999988765211 111    2355667


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHH----CCCCCC---eeehHHHHHHHHccCCHHHHHHHHHHHHhCC----CCCChhhHHH
Q 011378          247 IHGHCKDGNMNKALNLFDIMTQ----KSIKPD---IVTYNTLIDGFCKVGEMEKANKLWADMISRK----ISPNYISYGI  315 (487)
Q Consensus       247 i~~~~~~g~~~~a~~~~~~m~~----~~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~----~~p~~~t~~~  315 (487)
                      ...+...|++..+...+.....    .+....   ...+..+-..+...|+++.+...+.......    .......+..
T Consensus        98 ~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  177 (366)
T d1hz4a_          98 SEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAM  177 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence            7788888999999888875442    222221   1244555677788899999988887766432    2223345556


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC--CCCCC----hhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC---hhhHHHH
Q 011378          316 LINGYCSMGHVTEAFRLWYEMVGK--GIKPT----LVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD---SISYNTL  386 (487)
Q Consensus       316 li~~~~~~~~~~~a~~~~~~m~~~--~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~l  386 (487)
                      +...+...+...++...+.+....  .....    ...+..+...+...|+.+.|...++.........+   ...+..+
T Consensus       178 ~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l  257 (366)
T d1hz4a_         178 LIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNI  257 (366)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHH
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHH
Confidence            666777888888888887765431  11111    12345556667788888888888877654332222   3345567


Q ss_pred             HHHHhccCCHHHHHHHHHHHH----hCCCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          387 INGFVREENMDKAFALVSKME----NQGLVPDV-ITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       387 i~~~~~~~~~~~a~~~~~~m~----~~g~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      ...+...|++++|...+++..    ..+..|+. ..+..+-..|.+.|++++|...+++..+
T Consensus       258 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         258 ARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            778888899999988887664    33545543 4566677788888999999888888654

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.19  E-value=0.00035  Score=61.88  Aligned_cols=195  Identities=12%  Similarity=0.091  Sum_probs=122.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCc-cchHHHHHHHHhcC-ChhhHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011378           31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGV-FTYNSLINGLCKKG-RCDRAKEVLDEMLQMGLSPDTATYNTLLV  108 (487)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  108 (487)
                      ..|+.+-..+.+.+.+++|+++++...+.  .|+- ..|+..-..+...+ ++++|...++...+.. +-+..+|+.+-.
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~  120 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhH
Confidence            34556666677788888898888888763  4544 34666666666655 5888888888776542 234677777777


Q ss_pred             HHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC-ChhhHHHHHHHHHhcCC--
Q 011378          109 ESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVP-DNVLYTIIINGYCRNGF--  185 (487)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~~~~ll~~~~~~~~--  185 (487)
                      .+.+.|++++|.+.++.+.+.. +-+...|..+...+.+.|++++|++.+++..+.+  | +...|+.+-..+.+.+.  
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~--p~n~~a~~~r~~~l~~~~~~~  197 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFVISNTTGYN  197 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCSC
T ss_pred             HHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC--CccHHHHHHHHHHHHHccccc
Confidence            7888888888888888887642 2256778888888888888888888888887643  3 34455555444444433  


Q ss_pred             ----HHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          186 ----VLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       186 ----~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (487)
                          .++|.+.+....+.. +-+...|+.+...+. ....+++.+.++...+
T Consensus       198 ~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~-~~~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         198 DRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQ-DRGLSKYPNLLNQLLD  247 (315)
T ss_dssp             SHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHT-TTCGGGCHHHHHHHHH
T ss_pred             hhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHH-hcChHHHHHHHHHHHH
Confidence                345555555544432 123444544444333 2334555555555443

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=0.00057  Score=60.45  Aligned_cols=195  Identities=10%  Similarity=0.058  Sum_probs=134.2

Q ss_pred             chHHHHHHHHhcCChhhHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccC-ChhHHHHHHHHHHHCCCCCCHhHHHHHHHH
Q 011378           67 TYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPD-TATYNTLLVESCRKE-NMSEAEEIFCEMSRRGVAPDIVSFSTLIGI  144 (487)
Q Consensus        67 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  144 (487)
                      .|+.+-..+.+.+.+++|++.+++..+.  .|+ ...|+..-..+...+ ++++|.+.++...+.. +-+..+|...-..
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~  121 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHH
Confidence            3444545566788889999999988774  454 456666666666655 5889998888876653 2256778888888


Q ss_pred             HHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCC----
Q 011378          145 FSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKM----  220 (487)
Q Consensus       145 ~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~----  220 (487)
                      +.+.|++++|++.++++.+.. +.+...|..+...+.+.|+.++|.+.++...+... -+...|+.+...+.+.+.    
T Consensus       122 ~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~~~~~~~~  199 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGYNDR  199 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHHccccchh
Confidence            888999999999998887642 22467888888888888999999888888877532 245567666555555444    


Q ss_pred             --HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          221 --LTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       221 --~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                        ++.|.+.+.+..+.. +-+...|+.+...+... ..+++...++...+
T Consensus       200 ~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         200 AVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDR-GLSKYPNLLNQLLD  247 (315)
T ss_dssp             HHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTT-CGGGCHHHHHHHHH
T ss_pred             hhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHhc-ChHHHHHHHHHHHH
Confidence              566777777766543 23566676665555443 35666777765554

>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=98.08  E-value=0.003  Score=55.64  Aligned_cols=293  Identities=14%  Similarity=0.130  Sum_probs=158.7

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHH
Q 011378           27 YPDTVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTL  106 (487)
Q Consensus        27 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  106 (487)
                      .|+..--..+..-|-+.|.++.|..++..+..         |..++..+.+.+++..|.+++...      -+..+|..+
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            35555556678888899999999999986543         788889999999999888887654      367788888


Q ss_pred             HHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCH
Q 011378          107 LVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFV  186 (487)
Q Consensus       107 l~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  186 (487)
                      ...+.+......+     ++...+...+......++..|-..|.++....+++..... -.++...++-++..|++.+. 
T Consensus        76 ~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~-  148 (336)
T d1b89a_          76 CFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP-  148 (336)
T ss_dssp             HHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH-
T ss_pred             HHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh-
Confidence            8888877655443     3333444456666778999999999999999888876432 24566678889999888643 


Q ss_pred             HHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          187 LEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       187 ~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      +   ++.+.+...+...   ....++..|-+.+.++                      -++..|.+.|+++.|..+.   
T Consensus       149 ~---kl~e~l~~~s~~y---~~~k~~~~c~~~~l~~----------------------elv~Ly~~~~~~~~A~~~~---  197 (336)
T d1b89a_         149 Q---KMREHLELFWSRV---NIPKVLRAAEQAHLWA----------------------ELVFLYDKYEEYDNAIITM---  197 (336)
T ss_dssp             H---HHHHHHHHHSTTS---CHHHHHHHHHTTTCHH----------------------HHHHHHHHTTCHHHHHHHH---
T ss_pred             H---HHHHHHHhccccC---CHHHHHHHHHHcCChH----------------------HHHHHHHhcCCHHHHHHHH---
Confidence            2   2333333321111   1222333333333333                      3344455555556554432   


Q ss_pred             HHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChh
Q 011378          267 TQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLV  346 (487)
Q Consensus       267 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  346 (487)
                      .++  .++..-...++..+.+..+.+...++.......  .|+  ..+.|+......-+..+..+.+             
T Consensus       198 i~~--~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~--~p~--~i~~lL~~v~~~~d~~r~V~~~-------------  258 (336)
T d1b89a_         198 MNH--PTDAWKEGQFKDIITKVANVELYYRAIQFYLEF--KPL--LLNDLLMVLSPRLDHTRAVNYF-------------  258 (336)
T ss_dssp             HHS--TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH--CGG--GHHHHHHHHGGGCCHHHHHHHH-------------
T ss_pred             HHc--chhhhhHHHHHHHHHccCChHHHHHHHHHHHHc--CHH--HHHHHHHHhccCCCHHHHHHHH-------------
Confidence            221  223334455566666666666555555443332  232  2344554444444443333322             


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHH
Q 011378          347 SCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALV  403 (487)
Q Consensus       347 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~  403 (487)
                               .+.+++......++.....|.   ..+.++|...|...++++.-...+
T Consensus       259 ---------~k~~~l~li~p~Le~v~~~n~---~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         259 ---------SKVKQLPLVKPYLRSVQNHNN---KSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             ---------HHTTCTTTTHHHHHHHHTTCC---HHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ---------HhcCCcHHHHHHHHHHHHcCh---HHHHHHHHHHHhCcchhHHHHHHH
Confidence                     233444444455554444332   245666666666666655444433

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.03  E-value=0.00028  Score=60.27  Aligned_cols=193  Identities=8%  Similarity=-0.035  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKP-DIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGY  320 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~  320 (487)
                      +|..+-..|.+.|++++|+..|+...+.  .| +..+|+.+-.+|.+.|++++|.+.|.+..... +-+..++..+..++
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~  115 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIAL  115 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-hhhhhhHHHHHHHH
Confidence            3444445555556666666555554432  22 23445555555666666666666665554421 11233455555666


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCH----
Q 011378          321 CSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENM----  396 (487)
Q Consensus       321 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~----  396 (487)
                      ...|++++|...|+...+.. +.+......+..++.+.+..+.+..+........  ++...++ ++..+......    
T Consensus       116 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~~~~~~~~~~~  191 (259)
T d1xnfa_         116 YYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSD--KEQWGWN-IVEFYLGNISEQTLM  191 (259)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSC--CCSTHHH-HHHHHTTSSCHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccc--hhhhhhh-HHHHHHHHHHHHHHH
Confidence            66666666666666554432 1122222222233333344444444434333321  1111121 22222221111    


Q ss_pred             HHHHHHHHHHHhCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          397 DKAFALVSKMENQGLVPD-VITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       397 ~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +.+...+..-.  ...|+ ..+|..+-..+...|++++|...|++...
T Consensus       192 ~~~~~~~~~~~--~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  237 (259)
T d1xnfa_         192 ERLKADATDNT--SLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  237 (259)
T ss_dssp             HHHHHHCCSHH--HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhh--hcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            11111111000  00121 23455666777788888888888887654

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.98  E-value=9.5e-06  Score=73.13  Aligned_cols=216  Identities=7%  Similarity=-0.010  Sum_probs=101.6

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCcCChhhHH-HHHHHHHhcCCHHHH
Q 011378          148 NGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG--FVLEALKMRDEMLEKGCVMDVVTYN-TILNGLCRAKMLTEA  224 (487)
Q Consensus       148 ~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~g~~~~~~~~~-~li~~~~~~~~~~~a  224 (487)
                      .|++++|+.+++...+.. +-+...|..+..++...+  +.+++...+....+... .+...|. ..-..+...+..+.|
T Consensus        86 ~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~A  163 (334)
T d1dcea1          86 AALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEE  163 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHH
T ss_pred             HHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHH
Confidence            344556666666655432 113334555555555444  35666666666554321 2233332 233445556667777


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhC
Q 011378          225 DDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISR  304 (487)
Q Consensus       225 ~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  304 (487)
                      ...++.+.+.. +-+...|+.+-..+.+.|+.++|...+....+.  .|   ....+...+...+..+++...+......
T Consensus       164 l~~~~~~i~~~-p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~---~~~~~~~~~~~l~~~~~a~~~~~~~l~~  237 (334)
T d1dcea1         164 LAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENV--LL---KELELVQNAFFTDPNDQSAWFYHRWLLG  237 (334)
T ss_dssp             HHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHH--HH---HHHHHHHHHHHHCSSCSHHHHHHHHHHS
T ss_pred             HHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHh--HH---HHHHHHHHHHHhcchhHHHHHHHHHHHh
Confidence            77666665443 224556666666666666665553322211100  00   0111222233334444444444443332


Q ss_pred             CCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          305 KISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       305 ~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      . +++...+..+...+...++.++|...+.+..... +.+...+..+-..|...|+.++|.+.+++..+
T Consensus       238 ~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~  304 (334)
T d1dcea1         238 R-AEPLFRCELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  304 (334)
T ss_dssp             C-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHH
T ss_pred             C-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2 2233334444445555556666666555543221 11233444455555566666666666665554

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.94  E-value=0.00066  Score=57.79  Aligned_cols=198  Identities=11%  Similarity=0.016  Sum_probs=129.9

Q ss_pred             ehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011378          277 TYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYC  356 (487)
Q Consensus       277 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  356 (487)
                      +|..+=..|.+.|++++|...|.+..... +-+..+|..+-.+|...|++++|...|+...+.. +-+..++..+-.+|.
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~  116 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALY  116 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-hhhhhhHHHHHHHHH
Confidence            55566678899999999999999887542 2356789999999999999999999999988753 234567888888999


Q ss_pred             hcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHH
Q 011378          357 RSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSEL  436 (487)
Q Consensus       357 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  436 (487)
                      ..|+.++|...++...+.. +.+......+..++.+.+..+.+..+.......  .++...++ ++..+...  ..... 
T Consensus       117 ~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~-~~~~~~~~--~~~~~-  189 (259)
T d1xnfa_         117 YGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS--DKEQWGWN-IVEFYLGN--ISEQT-  189 (259)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS--CCCSTHHH-HHHHHTTS--SCHHH-
T ss_pred             HHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhcc--chhhhhhh-HHHHHHHH--HHHHH-
Confidence            9999999999999987643 123333333344445556555555555555543  22222222 22233222  12211 


Q ss_pred             HHHHHHHcC-----CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCC
Q 011378          437 ILWRMIEKG-----LNPD-RSTYTTLINGHVSQNNLKEAFRFHDEMLQRGFVPDD  485 (487)
Q Consensus       437 ~~~~m~~~g-----~~p~-~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~~p~~  485 (487)
                      .+.......     ..|+ ..+|..+-..|...|++++|.+.+++-++  ..|++
T Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--~~p~~  242 (259)
T d1xnfa_         190 LMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA--NNVHN  242 (259)
T ss_dssp             HHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--TCCTT
T ss_pred             HHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--cCCCC
Confidence            122222111     1122 23666778899999999999999998774  44553

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.92  E-value=2.1e-05  Score=70.76  Aligned_cols=143  Identities=12%  Similarity=0.076  Sum_probs=68.9

Q ss_pred             hCCCHHHHHHHHHHHHHCCCCCChh-hHHH---HHHHHHh-------cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHH
Q 011378          147 RNGQLDRALMYFREMKSAGLVPDNV-LYTI---IINGYCR-------NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGL  215 (487)
Q Consensus       147 ~~g~~~~a~~~~~~m~~~g~~~~~~-~~~~---ll~~~~~-------~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~  215 (487)
                      +.+..++|++++++..+.  .|+.. .|+.   ++..+..       .|..++++.+++...+.. +-+...|..+..++
T Consensus        41 ~~~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~  117 (334)
T d1dcea1          41 AGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLL  117 (334)
T ss_dssp             TTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHH
Confidence            333446777777777653  35543 2322   2222222       233455666666555432 22334454444444


Q ss_pred             HhcC--CHHHHHHHHHHHHHcCCCCCHHHHHH-HHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHH
Q 011378          216 CRAK--MLTEADDLFNEMLERGVFPDFYTFTT-LIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME  292 (487)
Q Consensus       216 ~~~~--~~~~a~~~~~~m~~~~~~~~~~t~~~-li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~  292 (487)
                      ...+  +.+++...+.+..+.. +++...+.. .-..+...+..++|+..++...+... -+...|+.+-..+.+.|+++
T Consensus       118 ~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~~~~~~~~  195 (334)
T d1dcea1         118 SRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQP  195 (334)
T ss_dssp             HTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCC
T ss_pred             HHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCHH
Confidence            4443  3566666666665542 223343332 23445556666666666654443321 12334444555555555544


Q ss_pred             HH
Q 011378          293 KA  294 (487)
Q Consensus       293 ~a  294 (487)
                      +|
T Consensus       196 ~A  197 (334)
T d1dcea1         196 DS  197 (334)
T ss_dssp             CS
T ss_pred             HH
Confidence            44

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.90  E-value=0.0005  Score=59.99  Aligned_cols=162  Identities=12%  Similarity=0.038  Sum_probs=78.8

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHC----CCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHH----cCCc-CChhhHHH
Q 011378          141 LIGIFSRNGQLDRALMYFREMKSA----GLVPD-NVLYTIIINGYCRNGFVLEALKMRDEMLE----KGCV-MDVVTYNT  210 (487)
Q Consensus       141 li~~~~~~g~~~~a~~~~~~m~~~----g~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~g~~-~~~~~~~~  210 (487)
                      ..+.|...|++++|.+.|.+....    +-.++ ..+|..+-..|.+.|++++|.+.+++..+    .|.. ....++..
T Consensus        43 aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  122 (290)
T d1qqea_          43 AATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFE  122 (290)
T ss_dssp             HHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHH
Confidence            345666777777777777665431    11111 23555566666666666666665554332    1111 11223344


Q ss_pred             HHHHHHh-cCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCee------eh
Q 011378          211 ILNGLCR-AKMLTEADDLFNEMLER----GVFP-DFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIV------TY  278 (487)
Q Consensus       211 li~~~~~-~~~~~~a~~~~~~m~~~----~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~------~~  278 (487)
                      +...|.. .|+++.|.+.+++..+.    +..+ -..++..+...+...|++++|+..|+............      .+
T Consensus       123 l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~  202 (290)
T d1qqea_         123 LGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYF  202 (290)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHH
T ss_pred             HHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHH
Confidence            4444433 46666666666655321    1111 12345555666666666666666666554432111111      11


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHH
Q 011378          279 NTLIDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       279 ~~li~~~~~~g~~~~a~~~~~~m~  302 (487)
                      ......+...|+++.|...+....
T Consensus       203 ~~~~~~~l~~~d~~~A~~~~~~~~  226 (290)
T d1qqea_         203 LKKGLCQLAATDAVAAARTLQEGQ  226 (290)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHGGG
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHH
Confidence            222333444556666665555443

>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=97.83  E-value=0.0084  Score=52.67  Aligned_cols=293  Identities=12%  Similarity=0.072  Sum_probs=152.5

Q ss_pred             CCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHH
Q 011378           63 PGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLI  142 (487)
Q Consensus        63 p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  142 (487)
                      ||..--..+.+-|.+.|.++.|..++..+.         -|..++..+.+.++++.|.+++....      +..+|..+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~---------d~~rl~~~~v~l~~~~~avd~~~k~~------~~~~~k~~~   76 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS---------NFGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVC   76 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT---------CHHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC---------CHHHHHHHHHhhccHHHHHHHHHHcC------CHHHHHHHH
Confidence            444444455666777777777777777543         24556666677777777766665431      445666666


Q ss_pred             HHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHH
Q 011378          143 GIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLT  222 (487)
Q Consensus       143 ~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~  222 (487)
                      ..|.+......+     ++...+...+......++..|-..|..++...+++..... -..+...++-++..|++.+. +
T Consensus        77 ~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~-~  149 (336)
T d1b89a_          77 FACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP-Q  149 (336)
T ss_dssp             HHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH-H
T ss_pred             HHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh-H
Confidence            777666555443     1222223334444456666666667666666666654322 13344556666666666432 2


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHH
Q 011378          223 EADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       223 ~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  302 (487)
                      ...+.++..   .-..                +++++.++.   .+      ...|.-++-.|.+.|.++.|..+.-.  
T Consensus       150 kl~e~l~~~---s~~y----------------~~~k~~~~c---~~------~~l~~elv~Ly~~~~~~~~A~~~~i~--  199 (336)
T d1b89a_         150 KMREHLELF---WSRV----------------NIPKVLRAA---EQ------AHLWAELVFLYDKYEEYDNAIITMMN--  199 (336)
T ss_dssp             HHHHHHHHH---STTS----------------CHHHHHHHH---HT------TTCHHHHHHHHHHTTCHHHHHHHHHH--
T ss_pred             HHHHHHHhc---cccC----------------CHHHHHHHH---HH------cCChHHHHHHHHhcCCHHHHHHHHHH--
Confidence            222222111   0000                122222221   11      12345566677778888888765432  


Q ss_pred             hCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhh
Q 011378          303 SRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSIS  382 (487)
Q Consensus       303 ~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~  382 (487)
                         ..++..-....+..+.+..+.+...++.....+.  .|  ...+.++......-+..++.+.++   +         
T Consensus       200 ---~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~--~p--~~i~~lL~~v~~~~d~~r~V~~~~---k---------  260 (336)
T d1b89a_         200 ---HPTDAWKEGQFKDIITKVANVELYYRAIQFYLEF--KP--LLLNDLLMVLSPRLDHTRAVNYFS---K---------  260 (336)
T ss_dssp             ---STTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH--CG--GGHHHHHHHHGGGCCHHHHHHHHH---H---------
T ss_pred             ---cchhhhhHHHHHHHHHccCChHHHHHHHHHHHHc--CH--HHHHHHHHHhccCCCHHHHHHHHH---h---------
Confidence               1234444455677788888888776666655442  23  445677777766666666555443   3         


Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHH
Q 011378          383 YNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILW  439 (487)
Q Consensus       383 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  439 (487)
                                .+++.-...+++...+.|   +....+++...|...++++.-++.++
T Consensus       261 ----------~~~l~li~p~Le~v~~~n---~~~vn~al~~lyie~~d~~~l~~~i~  304 (336)
T d1b89a_         261 ----------VKQLPLVKPYLRSVQNHN---NKSVNESLNNLFITEEDYQALRTSID  304 (336)
T ss_dssp             ----------TTCTTTTHHHHHHHHTTC---CHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ----------cCCcHHHHHHHHHHHHcC---hHHHHHHHHHHHhCcchhHHHHHHHH
Confidence                      333333445555544444   34578888888888888766555443

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.76  E-value=0.00062  Score=59.39  Aligned_cols=126  Identities=13%  Similarity=-0.008  Sum_probs=60.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc----CCcC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-CCHHHHHHH
Q 011378          177 INGYCRNGFVLEALKMRDEMLEK----GCVM-DVVTYNTILNGLCRAKMLTEADDLFNEMLER----GVF-PDFYTFTTL  246 (487)
Q Consensus       177 l~~~~~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~-~~~~t~~~l  246 (487)
                      -+.|...+++++|.+.|.+..+.    +..+ -..+|+.+..+|.+.|++++|.+.+++..+.    |.. ....++..+
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            34566677777777776655431    2211 1245666667777777777777776655431    110 012233444


Q ss_pred             HHHHHh-cCCHHHHHHHHHHHHH----CCCCCC-eeehHHHHHHHHccCCHHHHHHHHHHHH
Q 011378          247 IHGHCK-DGNMNKALNLFDIMTQ----KSIKPD-IVTYNTLIDGFCKVGEMEKANKLWADMI  302 (487)
Q Consensus       247 i~~~~~-~g~~~~a~~~~~~m~~----~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~  302 (487)
                      ...|.. .|++++|+..|+...+    .+-.+. ..++..+...|.+.|++++|...|.+..
T Consensus       124 ~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~  185 (290)
T d1qqea_         124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLI  185 (290)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHH
Confidence            444433 3666666665554321    111110 1233444444444444555544444433

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.74  E-value=0.0011  Score=53.58  Aligned_cols=82  Identities=12%  Similarity=-0.085  Sum_probs=44.1

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 011378          181 CRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKAL  260 (487)
Q Consensus       181 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~  260 (487)
                      ...|+++.|++.|.+.    .+++..+|..+-.+|.+.|+++.|.+.|++..+.. +-++..|..+-.+|.+.|+.++|+
T Consensus        16 ~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          16 ADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             HHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHH
Confidence            3445555555544432    22444455555566666666666666666655432 223455555666666666666666


Q ss_pred             HHHHHHH
Q 011378          261 NLFDIMT  267 (487)
Q Consensus       261 ~~~~~m~  267 (487)
                      ..|+...
T Consensus        91 ~~~~kAl   97 (192)
T d1hh8a_          91 KDLKEAL   97 (192)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6665543

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.70  E-value=0.0012  Score=53.47  Aligned_cols=126  Identities=9%  Similarity=-0.018  Sum_probs=86.6

Q ss_pred             HHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChh
Q 011378           38 NAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMS  117 (487)
Q Consensus        38 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~  117 (487)
                      ..+...|+++.|++.|+.+.    .|++.+|..+-..+...|++++|.+.|++..+.. +-+...|..+-.++.+.|+++
T Consensus        13 ~~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~   87 (192)
T d1hh8a_          13 VLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYD   87 (192)
T ss_dssp             HHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHH
Confidence            34467788888888887542    3566777777778888888888888888877643 234567777777788888888


Q ss_pred             HHHHHHHHHHHC------------CCC--CC-HhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC
Q 011378          118 EAEEIFCEMSRR------------GVA--PD-IVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVP  168 (487)
Q Consensus       118 ~a~~~~~~m~~~------------g~~--p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~  168 (487)
                      +|.+-|++....            |..  ++ ..++..+-.++.+.|++++|.+.++...+....+
T Consensus        88 ~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~  153 (192)
T d1hh8a_          88 LAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  153 (192)
T ss_dssp             HHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            888888776532            111  11 2344556667888888888888888776654443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.33  E-value=0.0024  Score=49.78  Aligned_cols=89  Identities=13%  Similarity=0.141  Sum_probs=52.7

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHD  433 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~  433 (487)
                      .|.+.|++++|...|++..+.. +-+...|..+-..|...|++++|...+++..+.. .-+...|..+...|...|++++
T Consensus        19 ~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~e   96 (159)
T d1a17a_          19 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRA   96 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHH
Confidence            4456666666666666655432 1234456666666666666666666666665432 1233566666666666777777


Q ss_pred             HHHHHHHHHHc
Q 011378          434 SELILWRMIEK  444 (487)
Q Consensus       434 a~~~~~~m~~~  444 (487)
                      |...+++....
T Consensus        97 A~~~~~~a~~~  107 (159)
T d1a17a_          97 ALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHc
Confidence            76666666553

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.33  E-value=0.00043  Score=51.41  Aligned_cols=102  Identities=11%  Similarity=0.121  Sum_probs=71.9

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCC---HHHHHHHHHHHHhCCCCCC-HhhHHHHHHH
Q 011378          349 NTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREEN---MDKAFALVSKMENQGLVPD-VITYNVILTG  424 (487)
Q Consensus       349 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~g~~p~-~~~~~~li~~  424 (487)
                      ..++..+...+++++|++.|++....+ +.+..++..+-.++.+.++   +++|..++++.-...-.|+ ..+|..+-.+
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            467788888889999999998887643 2345667777777776554   4468888887755432233 2356777788


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCCHHHH
Q 011378          425 FCRQGRMHDSELILWRMIEKGLNPDRSTY  453 (487)
Q Consensus       425 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty  453 (487)
                      |.+.|++++|...|++..+.  .|+-.-.
T Consensus        82 y~~~g~~~~A~~~~~~aL~~--~P~~~~A  108 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQT--EPQNNQA  108 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CTTCHHH
T ss_pred             HHHHhhhHHHHHHHHHHHHh--CcCCHHH
Confidence            88999999999999988763  5664433

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.29  E-value=0.0034  Score=48.80  Aligned_cols=87  Identities=17%  Similarity=0.095  Sum_probs=43.8

Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHH
Q 011378          285 FCKVGEMEKANKLWADMISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKA  364 (487)
Q Consensus       285 ~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a  364 (487)
                      |.+.|++++|...|.+..... +-+...|..+-.+|...|++++|...|+...+.. +-+...|..+..+|...|++++|
T Consensus        20 ~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~eA   97 (159)
T d1a17a_          20 YFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   97 (159)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHHH
Confidence            344555555555555444322 1234445555555555555555555555554332 22334555555555555555555


Q ss_pred             HHHHHHHHH
Q 011378          365 DEFLSKMVS  373 (487)
Q Consensus       365 ~~~~~~m~~  373 (487)
                      ...+++...
T Consensus        98 ~~~~~~a~~  106 (159)
T d1a17a_          98 LRDYETVVK  106 (159)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.25  E-value=0.0039  Score=45.53  Aligned_cols=88  Identities=10%  Similarity=0.068  Sum_probs=48.2

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHD  433 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~  433 (487)
                      .+...|++++|..+|++.++.. +-+...|..+-.+|.+.|++++|...+++..+.. ..+...|..+...+...|++++
T Consensus        12 ~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~   89 (117)
T d1elwa_          12 KALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEE   89 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHH
Confidence            3445566666666665555421 1233455555566666666666666665554432 2344555666666666666666


Q ss_pred             HHHHHHHHHH
Q 011378          434 SELILWRMIE  443 (487)
Q Consensus       434 a~~~~~~m~~  443 (487)
                      |...+++..+
T Consensus        90 A~~~~~~a~~   99 (117)
T d1elwa_          90 AKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHH
Confidence            6666666543

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.18  E-value=0.0054  Score=44.76  Aligned_cols=87  Identities=14%  Similarity=0.110  Sum_probs=43.1

Q ss_pred             HHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHH
Q 011378           75 LCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRA  154 (487)
Q Consensus        75 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a  154 (487)
                      +.+.|++++|...|.+..+.. +-+...|..+-.++.+.|++++|...++...+.. +.+...|..+..++...|++++|
T Consensus        13 ~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~A   90 (117)
T d1elwa_          13 ALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEA   90 (117)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHHH
Confidence            344455555555555544321 1233445555555555555555555555554432 22444455555555555555555


Q ss_pred             HHHHHHHHH
Q 011378          155 LMYFREMKS  163 (487)
Q Consensus       155 ~~~~~~m~~  163 (487)
                      +..|++..+
T Consensus        91 ~~~~~~a~~   99 (117)
T d1elwa_          91 KRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            555555543

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.17  E-value=0.0037  Score=50.51  Aligned_cols=55  Identities=11%  Similarity=-0.043  Sum_probs=21.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHH
Q 011378          208 YNTILNGLCRAKMLTEADDLFNEMLERGVFP-DFYTFTTLIHGHCKDGNMNKALNLFD  264 (487)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~t~~~li~~~~~~g~~~~a~~~~~  264 (487)
                      |+.+-.+|.+.|+++.|...|++..+.  .| +..+|..+-.+|.+.|++++|+..|+
T Consensus        41 ~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~lg~~~~~l~~~~~A~~~~~   96 (201)
T d2c2la1          41 YTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQLEMESYDEAIANLQ   96 (201)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            333333444444444444444433321  12 23334444444444444444444443

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.0019  Score=47.67  Aligned_cols=98  Identities=16%  Similarity=0.120  Sum_probs=56.2

Q ss_pred             HHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC---hhHHHHHHHHHHHCCCCCC-HhHHHHHHHHH
Q 011378           70 SLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKEN---MSEAEEIFCEMSRRGVAPD-IVSFSTLIGIF  145 (487)
Q Consensus        70 ~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~---~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~  145 (487)
                      .+++.+...+++++|.+.|+.....+ +.+..++..+-.++.+.++   .++|..+|++..+..-.|+ ..++..+-.+|
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            45556666666666777666665533 2344555555555555433   3346666666655432232 22455566667


Q ss_pred             HhCCCHHHHHHHHHHHHHCCCCCCh
Q 011378          146 SRNGQLDRALMYFREMKSAGLVPDN  170 (487)
Q Consensus       146 ~~~g~~~~a~~~~~~m~~~g~~~~~  170 (487)
                      .+.|++++|.+.|++..+.  .|+.
T Consensus        83 ~~~g~~~~A~~~~~~aL~~--~P~~  105 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQT--EPQN  105 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHhhhHHHHHHHHHHHHh--CcCC
Confidence            7777777777777776653  3543

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.14  E-value=0.0039  Score=50.38  Aligned_cols=99  Identities=14%  Similarity=0.013  Sum_probs=82.2

Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC-hhhHHH
Q 011378          307 SPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPD-SISYNT  385 (487)
Q Consensus       307 ~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~  385 (487)
                      .|+...+...-..|...|++++|+..|....... +.+...|..+-.+|.+.|++++|...+++..+  +.|+ ...|..
T Consensus         1 ~~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~   77 (201)
T d2c2la1           1 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFF   77 (201)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHH
Confidence            3677777778888999999999999999877653 44667788888999999999999999998875  4564 567888


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHh
Q 011378          386 LINGFVREENMDKAFALVSKMEN  408 (487)
Q Consensus       386 li~~~~~~~~~~~a~~~~~~m~~  408 (487)
                      +-.+|.+.|++++|...+++..+
T Consensus        78 lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          78 LGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999999999999987654

>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=96.91  E-value=0.004  Score=45.06  Aligned_cols=83  Identities=12%  Similarity=0.088  Sum_probs=42.6

Q ss_pred             HhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHH
Q 011378          390 FVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIEKGLNP-DRSTYTTLINGHVSQNNLK  467 (487)
Q Consensus       390 ~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~l~~~~~~~~~~~  467 (487)
                      +.+.|++++|...+++....  .| +...|..+-..+.+.|++++|...+++..+.  .| +...|..+...|...|+++
T Consensus        26 ~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~a~~~la~~y~~~g~~~  101 (112)
T d1hxia_          26 MLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTNEHNAN  101 (112)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHhhhccc--ccccchhhhhhhhhhhhhhhHHHhhccccccccc--ccccccchHHHHHHHHHCCCHH
Confidence            44455555555555554432  23 2444555555555555555555555554442  22 2445555555555556666


Q ss_pred             HHHHHHHHH
Q 011378          468 EAFRFHDEM  476 (487)
Q Consensus       468 ~a~~~~~~m  476 (487)
                      +|.+.+++.
T Consensus       102 ~A~~~l~~~  110 (112)
T d1hxia_         102 AALASLRAW  110 (112)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            665555543

>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=96.89  E-value=0.004  Score=45.10  Aligned_cols=84  Identities=13%  Similarity=0.022  Sum_probs=34.5

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHH
Q 011378          320 YCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKA  399 (487)
Q Consensus       320 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a  399 (487)
                      +.+.|++++|...|+...... +-+...|..+-.++.+.|+.++|...+++..+.. +.+...+..|-..|...|++++|
T Consensus        26 ~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~A  103 (112)
T d1hxia_          26 MLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAA  103 (112)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHHH
Confidence            334444444444444443321 1123334444444444444444444444443321 11233444444444444444444


Q ss_pred             HHHHHH
Q 011378          400 FALVSK  405 (487)
Q Consensus       400 ~~~~~~  405 (487)
                      .+.+++
T Consensus       104 ~~~l~~  109 (112)
T d1hxia_         104 LASLRA  109 (112)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>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=96.85  E-value=0.1  Score=43.76  Aligned_cols=51  Identities=12%  Similarity=-0.096  Sum_probs=27.4

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHh----cCChHHHHHHHHHHHHcCC
Q 011378          393 EENMDKAFALVSKMENQGLVPDVITYNVILTGFCR----QGRMHDSELILWRMIEKGL  446 (487)
Q Consensus       393 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~  446 (487)
                      ..+.++|...|.+-.+.|   ++..+..|-..|.+    ..+.++|.+.|++....|-
T Consensus       195 ~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~  249 (265)
T d1ouva_         195 TKNFKEALARYSKACELE---NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGA  249 (265)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTC
T ss_pred             ccchhhhhhhHhhhhccc---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCcC
Confidence            456777777777666655   23333333333332    2356666666666555543

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.84  E-value=0.013  Score=46.36  Aligned_cols=71  Identities=10%  Similarity=0.117  Sum_probs=55.7

Q ss_pred             hhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH-----HcCCCCCHHH
Q 011378          381 ISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMI-----EKGLNPDRST  452 (487)
Q Consensus       381 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t  452 (487)
                      ..+..+...+.+.|++++|...+++..+.. .-+...|..++.+|.+.|+..+|...|+++.     +.|+.|+..|
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            346677888888899999998888886532 2366778888999999999999988888874     4688888765

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.44  E-value=0.052  Score=42.70  Aligned_cols=121  Identities=12%  Similarity=0.049  Sum_probs=71.3

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh
Q 011378           37 INAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENM  116 (487)
Q Consensus        37 l~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~  116 (487)
                      -......|++++|.+.|..-....  +....        ......+.+...-..+..    .....+..+...+.+.|++
T Consensus        18 g~~~~~~g~~e~A~~~~~~AL~l~--rG~~l--------~~~~~~~w~~~~r~~l~~----~~~~a~~~la~~~~~~g~~   83 (179)
T d2ff4a2          18 GVHAAAAGRFEQASRHLSAALREW--RGPVL--------DDLRDFQFVEPFATALVE----DKVLAHTAKAEAEIACGRA   83 (179)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTC--CSSTT--------GGGTTSTTHHHHHHHHHH----HHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhC--ccccc--------ccCcchHHHHHHHHHHHH----HHHHHHHHHHHHHHHCCCc
Confidence            345677888888888887765521  11100        000011111111111111    1134556677777778888


Q ss_pred             hHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHH-----HCCCCCChhh
Q 011378          117 SEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMK-----SAGLVPDNVL  172 (487)
Q Consensus       117 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~~~~~~  172 (487)
                      ++|...++.+.+.. +-+...|..++.++.+.|+.++|++.|+++.     +.|+.|+..+
T Consensus        84 ~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          84 SAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             hHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            88888888776642 2366777888888888888888888888763     3577776543

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.37  E-value=0.05  Score=42.34  Aligned_cols=110  Identities=9%  Similarity=-0.049  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYC  321 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~  321 (487)
                      .+...-+.+.+.|++++|+..|....+.-  |....+            .+........+       -..+|+.+..+|.
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~--~~~~~~------------~~~~~~~~~~~-------~~~~~~nla~~y~   73 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSF------------SNEEAQKAQAL-------RLASHLNLAMCHL   73 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCC------------CSHHHHHHHHH-------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHh--hhcccc------------chHHHhhhchh-------HHHHHHHHHHHHH
Confidence            34444567788888888888887655421  100000            00000001111       1235666777777


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          322 SMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       322 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      +.|++++|+..++...... +.+...|..+-.+|...|++++|...|++..+
T Consensus        74 k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          74 KLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhhhcccccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            8888888888777766543 33566677777777777888888888777765

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.28  E-value=0.013  Score=43.46  Aligned_cols=91  Identities=13%  Similarity=0.155  Sum_probs=48.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CC-----eeehHHHHHH
Q 011378          211 ILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIK-PD-----IVTYNTLIDG  284 (487)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-~~-----~~~~~~li~~  284 (487)
                      +-..+.+.|++++|.+.|.+..+.+ +.+...+..+-.+|.+.|++++|+..++.+.+..-. +.     ..+|..+-..
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~   88 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNS   88 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHH
Confidence            3445666666666666666666542 234556666666666666666666666654431100 00     0133334444


Q ss_pred             HHccCCHHHHHHHHHHHH
Q 011378          285 FCKVGEMEKANKLWADMI  302 (487)
Q Consensus       285 ~~~~g~~~~a~~~~~~m~  302 (487)
                      +...+++++|...|....
T Consensus        89 ~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          89 YFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHH
Confidence            455555555555555443

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.26  E-value=0.074  Score=41.30  Aligned_cols=60  Identities=7%  Similarity=-0.061  Sum_probs=41.2

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVP-DVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +|+.+-.+|.+.|++++|...+++..+.  .| ++..|..+..+|...|++++|...|++..+
T Consensus        64 ~~~nla~~y~k~~~~~~A~~~~~~al~~--~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          64 SHLNLAMCHLKLQAFSAAIESCNKALEL--DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcccccchhhhhhhc--cccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4555666677777777777777666553  34 556667777777777777777777777665

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.25  E-value=0.016  Score=42.83  Aligned_cols=52  Identities=12%  Similarity=0.065  Sum_probs=23.1

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCChhhHHHHHHHHhccCCHHHHHHHHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKM  406 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  406 (487)
                      .|.+.|++++|...|++.++.. +.+...+..+-.+|.+.|++++|...+++.
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~a   64 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKA   64 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHH
Confidence            3444455555555554444321 112334444444444444444444444443

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=96.24  E-value=0.059  Score=41.05  Aligned_cols=110  Identities=13%  Similarity=-0.032  Sum_probs=64.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCeeehHHHHHHHHccCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011378          243 FTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPNYISYGILINGYCS  322 (487)
Q Consensus       243 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~  322 (487)
                      +..--+.+.+.|++++|+..|....+.-.....             ..-.....-...       ....+|+.+..+|.+
T Consensus        20 ~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~-------------~~~~~~~~~~~~-------~~~~~~~Nla~~~~~   79 (153)
T d2fbna1          20 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEE-------------WDDQILLDKKKN-------IEISCNLNLATCYNK   79 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTT-------------CCCHHHHHHHHH-------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhh-------------hhhHHHHHhhhh-------HHHHHHhhHHHHHHH
Confidence            444456777888888888887766542110000             000000000000       123456677777777


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          323 MGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      .|++++|+..+....... +.+...|..+-.+|...|++++|...|+...+
T Consensus        80 l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          80 NKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            888888888777766543 44566777777777777777777777777665

>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=95.76  E-value=0.22  Score=37.67  Aligned_cols=61  Identities=11%  Similarity=-0.020  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQ  268 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~~~~g~~~~a~~~~~~m~~  268 (487)
                      +|+.+..+|.+.|+++.|.+.+++..+.. +.++.+|..+..++...|++++|+..|+...+
T Consensus        69 ~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          69 CNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            55566666666667777766666665542 33556666666666777777777766665544

>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=95.32  E-value=0.61  Score=38.56  Aligned_cols=222  Identities=14%  Similarity=0.020  Sum_probs=102.6

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHh----cCChhhHHHHHHHHHHCCCCCCHHHHHHH
Q 011378           31 VTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCK----KGRCDRAKEVLDEMLQMGLSPDTATYNTL  106 (487)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  106 (487)
                      ..+..|-..+-+.+++++|+++|+...+.|   +...+-.|-..+..    ..++..+...+..-...+.   ......+
T Consensus         3 ~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~---~~a~~~l   76 (265)
T d1ouva_           3 KELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNY---SNGCHLL   76 (265)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccc---cchhhcc
Confidence            344555555566777777777777776654   22333333333333    3456666666666555442   1222222


Q ss_pred             HHHHH----ccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----CCCHHHHHHHHHHHHHCCCCCChhhHHHHHH
Q 011378          107 LVESC----RKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR----NGQLDRALMYFREMKSAGLVPDNVLYTIIIN  178 (487)
Q Consensus       107 l~~~~----~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  178 (487)
                      ...+.    ...+.+.|...++...+.|...   ....+...+..    ......+...+......   .+...+..|..
T Consensus        77 ~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~---a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~L~~  150 (265)
T d1ouva_          77 GNLYYSGQGVSQNTNKALQYYSKACDLKYAE---GCASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDGDGCTILGS  150 (265)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTTCHH---HHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCHHHHHHHHH
T ss_pred             ccccccccccchhhHHHHHHHhhhhhhhhhh---HHHhhcccccCCCcccchhHHHHHHhhhhhcc---cccchhhhhhh
Confidence            22221    2455666666666666555321   12222222221    23344555555544432   23344445555


Q ss_pred             HHHh----cCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011378          179 GYCR----NGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCR----AKMLTEADDLFNEMLERGVFPDFYTFTTLIHGH  250 (487)
Q Consensus       179 ~~~~----~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~t~~~li~~~  250 (487)
                      .|..    ..+...+...+....+.|.   ......+-..|..    ..+++.|...|....+.|   ++..+..|-..|
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~a~~~g~---~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y  224 (265)
T d1ouva_         151 LYDAGRGTPKDLKKALASYDKACDLKD---SPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQ  224 (265)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHH
T ss_pred             hhccCCCcccccccchhhhhccccccc---cccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHHH
Confidence            4443    2234444444444444332   2222223223322    345666666666665554   233333444444


Q ss_pred             Hh----cCCHHHHHHHHHHHHHCC
Q 011378          251 CK----DGNMNKALNLFDIMTQKS  270 (487)
Q Consensus       251 ~~----~g~~~~a~~~~~~m~~~~  270 (487)
                      .+    ..+.++|.+.|+.....|
T Consensus       225 ~~G~g~~~n~~~A~~~~~kAa~~g  248 (265)
T d1ouva_         225 YNGEGVTRNEKQAIENFKKGCKLG  248 (265)
T ss_dssp             HTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HcCCCCccCHHHHHHHHHHHHHCc
Confidence            33    224555555555544433

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.32  E-value=0.14  Score=39.61  Aligned_cols=62  Identities=11%  Similarity=-0.080  Sum_probs=40.2

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      ..|..+-.++.+.|++++|+..++...+.. +.+...|..+-.+|.+.|+++.|.+.|++..+
T Consensus        78 ~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          78 SCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            445556666677777777777777665432 33445666666677777777777777776665

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.20  E-value=0.21  Score=38.40  Aligned_cols=64  Identities=6%  Similarity=-0.116  Sum_probs=47.9

Q ss_pred             hhhHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011378          380 SISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEK  444 (487)
Q Consensus       380 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  444 (487)
                      ...|..+-.+|.+.|++++|+..+.+..+.. ..++..|..+-.++.+.|++++|...|++..+.
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3456666777888888888888888776542 235567888888888888888888888887764

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=95.10  E-value=0.38  Score=36.83  Aligned_cols=61  Identities=11%  Similarity=0.019  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          312 SYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       312 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  373 (487)
                      .|+.+-.+|.+.|++++|+..++...... +.+...|..+-.+|...|++++|...++...+
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~  126 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLE  126 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45556666777777777777777665532 34555666666777777777777777777664

>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=95.01  E-value=0.026  Score=47.69  Aligned_cols=52  Identities=17%  Similarity=0.231  Sum_probs=33.9

Q ss_pred             HccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 011378          111 CRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKS  163 (487)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  163 (487)
                      .+.|++++|...+++..+.. +-|...+..+...++..|++++|...++...+
T Consensus         7 L~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~   58 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIK   58 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            35567777777776665542 22556666777777777777777777776655

>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=94.84  E-value=0.022  Score=48.10  Aligned_cols=49  Identities=24%  Similarity=0.365  Sum_probs=23.2

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011378          323 MGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMV  372 (487)
Q Consensus       323 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  372 (487)
                      .|++++|...+++-.+.. +-|...+..+...|+..|++++|...++...
T Consensus         9 ~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~   57 (264)
T d1zbpa1           9 EGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSI   57 (264)
T ss_dssp             TTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            445555555555444332 2333444445555555555555555554444

>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=94.76  E-value=0.61  Score=35.60  Aligned_cols=61  Identities=8%  Similarity=-0.003  Sum_probs=40.4

Q ss_pred             hHHHHHHHHhccCCHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011378          382 SYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIE  443 (487)
Q Consensus       382 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  443 (487)
                      +|+.+-.+|.+.|++++|...+++..+.. +.+...|..+..++...|++++|...|.+...
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~  126 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLE  126 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34455566677777777777776665432 23455666677777777777777777777665

>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=94.48  E-value=0.47  Score=35.76  Aligned_cols=20  Identities=10%  Similarity=0.082  Sum_probs=11.4

Q ss_pred             HHHhcCChHHHHHHHHHHHH
Q 011378          354 GYCRSGDASKADEFLSKMVS  373 (487)
Q Consensus       354 ~~~~~~~~~~a~~~~~~m~~  373 (487)
                      .+...|++++|...+++..+
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~   37 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAME   37 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            34455666666666666543

>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=93.83  E-value=0.61  Score=35.04  Aligned_cols=62  Identities=13%  Similarity=0.045  Sum_probs=34.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011378          206 VTYNTILNGLCRAKMLTEADDLFNEMLER-----GVFPD-----FYTFTTLIHGHCKDGNMNKALNLFDIMT  267 (487)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~-----~~t~~~li~~~~~~g~~~~a~~~~~~m~  267 (487)
                      ..|+.+-.+|.+.|+++.|...+++..+.     ...++     ...++.+-.+|...|++++|+..|+...
T Consensus        56 ~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          56 FCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            34556666666667776666666665431     11111     1234555566666777777766665543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=93.82  E-value=0.22  Score=37.29  Aligned_cols=43  Identities=16%  Similarity=0.339  Sum_probs=29.8

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 011378          431 MHDSELILWRMIEKGLNPDRSTYTTLINGHVSQNNLKEAFRFHDEMLQRGF  481 (487)
Q Consensus       431 ~~~a~~~~~~m~~~g~~p~~~ty~~l~~~~~~~~~~~~a~~~~~~m~~~g~  481 (487)
                      +++|...|++..+  +.|+-.+|..-+..+      ..|.+++.+..+.|+
T Consensus       102 ~~~A~~~~~kal~--l~P~~~~~~~~L~~~------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         102 FDLATQFFQQAVD--EQPDNTHYLKSLEMT------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHHHHHHHHH--HCTTCHHHHHHHHHH------HTHHHHHHHHHHSSS
T ss_pred             HHHhhhhhhcccc--cCCCHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence            5677777777665  468877777666555      356778888777775

>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=92.67  E-value=0.37  Score=35.92  Aligned_cols=14  Identities=7%  Similarity=-0.145  Sum_probs=7.2

Q ss_pred             CCHHHHHHHHHHHH
Q 011378          289 GEMEKANKLWADMI  302 (487)
Q Consensus       289 g~~~~a~~~~~~m~  302 (487)
                      +.+++|.+.|+...
T Consensus        11 ~~fe~A~~~~e~al   24 (145)
T d1zu2a1          11 LLFEQIRQDAENTY   24 (145)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH
Confidence            34555555555544

>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=90.37  E-value=2.1  Score=30.37  Aligned_cols=66  Identities=14%  Similarity=0.115  Sum_probs=40.3

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC
Q 011378          311 ISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVD  377 (487)
Q Consensus       311 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  377 (487)
                      ...+.-++.....|.-+.-.++++++.+.+ +|++...-.+-.+|.+.|+..++-+++++.-+.|++
T Consensus        87 e~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          87 EHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            334455555666666666666666655533 556666666666777777777777777766666653

>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=89.80  E-value=1.2  Score=30.05  Aligned_cols=25  Identities=24%  Similarity=0.320  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHH
Q 011378          242 TFTTLIHGHCKDGNMNKALNLFDIM  266 (487)
Q Consensus       242 t~~~li~~~~~~g~~~~a~~~~~~m  266 (487)
                      ++..+-.++.+.|++++|+..++..
T Consensus        48 ~l~~Lg~~~~~~g~~~~A~~~y~~a   72 (95)
T d1tjca_          48 VLDYLSYAVYQQGDLDKALLLTKKL   72 (95)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhhHHHhcCChHHHHHHHHHH
Confidence            3444444444444444444444443

>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=89.55  E-value=1.3  Score=40.69  Aligned_cols=166  Identities=7%  Similarity=-0.036  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCeeehHHHHHHHH--ccCCHHHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHhcCCHHHHHHH
Q 011378          256 MNKALNLFDIMTQKSIKPDIVTYNTLIDGFC--KVGEMEKANKLWADMISRKISP-NYISYGILINGYCSMGHVTEAFRL  332 (487)
Q Consensus       256 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~--~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~  332 (487)
                      +..+.+.++...+..-.++..-....+..+.  ..+.++.+...+...  -++.| +...+..+-..+.+.|+.++|...
T Consensus        65 y~~~ie~~r~~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~--~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~  142 (497)
T d1ya0a1          65 FKNQITTLQGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTV--FNVDLPCRVKSSQLGIISNKQTHTSAIVKP  142 (497)
T ss_dssp             THHHHHHHHHHHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC---------------------------------
T ss_pred             HHHHHHHHHHhcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCChhhHHHHHHhHHHHHhCCCHHHHHHH
Confidence            4455666665554443444332222222221  122333333332221  12333 445566677777778888888776


Q ss_pred             HHHHHhCCCCCChhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCh-hhHHHHHHHHhccCCHHHHHHHHHHHHhCCC
Q 011378          333 WYEMVGKGIKPTLVSCNTIIKGYCRSGDASKADEFLSKMVSEGVDPDS-ISYNTLINGFVREENMDKAFALVSKMENQGL  411 (487)
Q Consensus       333 ~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  411 (487)
                      +..-....   ...++..+-..+...|++++|...+++..+.  .|+. ..|+.|-..|...|+..+|...+.+-.... 
T Consensus       143 ~~~al~~~---~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-  216 (497)
T d1ya0a1         143 QSSSCSYI---CQHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-  216 (497)
T ss_dssp             CCHHHHHH---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-
T ss_pred             HHHHhCCC---HHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-
Confidence            65443211   1235666777788889999999999887753  4554 588888888999999999988888776543 


Q ss_pred             CCCHhhHHHHHHHHHhcC
Q 011378          412 VPDVITYNVILTGFCRQG  429 (487)
Q Consensus       412 ~p~~~~~~~li~~~~~~g  429 (487)
                      .|-...+..|...|.+..
T Consensus       217 ~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         217 FPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             BCCHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHhh
Confidence            456677888877776543

>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=87.54  E-value=2.8  Score=28.01  Aligned_cols=27  Identities=19%  Similarity=0.155  Sum_probs=15.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011378          207 TYNTILNGLCRAKMLTEADDLFNEMLE  233 (487)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (487)
                      +++.+-.++.+.|++++|...+++..+
T Consensus        48 ~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_          48 VLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            445555555555555555555555554

>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=86.73  E-value=2.5  Score=28.37  Aligned_cols=62  Identities=18%  Similarity=0.204  Sum_probs=37.4

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011378          395 NMDKAFALVSKMENQGLVPDVITYNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLI  457 (487)
Q Consensus       395 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l~  457 (487)
                      +.-++.+-+..+-...+.|++....+-+.+|.+-+++..|.++|+-.+.+. .++...|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHH
Confidence            444444555555556667777777777777777777777777777665432 22344555443

>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=84.97  E-value=4.9  Score=28.46  Aligned_cols=140  Identities=19%  Similarity=0.152  Sum_probs=69.7

Q ss_pred             HhcCChhHHHHHHHHHhhCCCCCCccchHHHHHHHHhcCChhhHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChhHHH
Q 011378           41 CREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTATYNTLLVESCRKENMSEAE  120 (487)
Q Consensus        41 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~  120 (487)
                      ...|.+++..++......+   .+..-||.+|=-....-+.+...++++..-.   -.|.          .+++++..+.
T Consensus        13 ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~---~FDl----------s~C~Nlk~vv   76 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGS---YFDL----------DKCQNLKSVV   76 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGG---GSCG----------GGCSCTHHHH
T ss_pred             HHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhh---hcCc----------hhhhcHHHHH
Confidence            4456666666666665542   2334455555555555555555555444321   1111          1233333333


Q ss_pred             HHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011378          121 EIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVLEALKMRDEMLEKG  200 (487)
Q Consensus       121 ~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g  200 (487)
                      .-+-.+-     -+...++..+....+.|.-|.-.++++.+.+ +-+|++...-.+-++|.+.|...++.+++.+.-+.|
T Consensus        77 ~C~~~~n-----~~se~vdlALd~lv~~~kkd~Ld~i~~~l~k-n~~i~~~~llkia~A~kkig~~re~nell~~ACe~G  150 (161)
T d1wy6a1          77 ECGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKG  150 (161)
T ss_dssp             HHHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHhc-----chHHHHHHHHHHHHHhccHHHHHHHHHHHHh-cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHh
Confidence            3222221     1222345555666666666666666666443 234555555556666666666666666666666655


Q ss_pred             Cc
Q 011378          201 CV  202 (487)
Q Consensus       201 ~~  202 (487)
                      ..
T Consensus       151 ~K  152 (161)
T d1wy6a1         151 EK  152 (161)
T ss_dssp             CH
T ss_pred             HH
Confidence            53

>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=84.81  E-value=2.9  Score=38.15  Aligned_cols=112  Identities=14%  Similarity=0.039  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHccCChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC-hhhHHHHHHH
Q 011378          101 ATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPD-NVLYTIIING  179 (487)
Q Consensus       101 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~~~~ll~~  179 (487)
                      ..+..+-..+.+.++.+.|...+....+..  | ..++..+-..+...|++++|...|.+..+.  .|+ ...|+.|-..
T Consensus       121 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~  195 (497)
T d1ya0a1         121 VKSSQLGIISNKQTHTSAIVKPQSSSCSYI--C-QHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAIL  195 (497)
T ss_dssp             ----------------------CCHHHHHH--H-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHH
T ss_pred             HHHHHhHHHHHhCCCHHHHHHHHHHHhCCC--H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHH
Confidence            344444444555555555554443332210  1 123444555566666666666666665543  343 3456666666


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCcCChhhHHHHHHHHHhc
Q 011378          180 YCRNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRA  218 (487)
Q Consensus       180 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  218 (487)
                      +...|+..+|...+.+-.... +|-..++..|...+.+.
T Consensus       196 ~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~~  233 (497)
T d1ya0a1         196 ASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSKA  233 (497)
T ss_dssp             HHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHh
Confidence            666666666666655554432 23444555555555543

>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=83.65  E-value=5.8  Score=28.24  Aligned_cols=49  Identities=10%  Similarity=-0.005  Sum_probs=22.0

Q ss_pred             CChhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHh----CCCHHHHHHHHHHHHHCC
Q 011378          114 ENMSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSR----NGQLDRALMYFREMKSAG  165 (487)
Q Consensus       114 ~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  165 (487)
                      .+.+.|.+.|+...+.|.   +..+..|-..|.+    ..+.++|.++|+...+.|
T Consensus        73 ~d~~~A~~~~~~aa~~g~---~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          73 KDLRKAAQYYSKACGLND---QDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             CCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHhhhhccCc---chHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            445555555555555442   2222333333332    234555555555544433

>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=80.94  E-value=5.9  Score=26.48  Aligned_cols=62  Identities=13%  Similarity=0.180  Sum_probs=42.6

Q ss_pred             hhHHHHHHHHHHHCCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCChhhHHHHHH
Q 011378          116 MSEAEEIFCEMSRRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIIN  178 (487)
Q Consensus       116 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~~~~ll~  178 (487)
                      .=++.+-++.+....+.|++....+.+++|-|.+++..|.++|+-.+.+ ..++...|.-+++
T Consensus        22 ~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilq   83 (105)
T d1v54e_          22 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHH
Confidence            3355566667777777888888888888888888888888888877653 2233445555554