Citrus Sinensis ID: 041561

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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------
Protein Sequence
VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccccccHHHHHHHHcccccHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHHHHHHHHcHHHccccccccccccccHHHHHHHHHHHHHHccHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHHccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHcccHHHHHHcc
Coil and Loop (DISEMBL)
vyptqfpfttVLSSCAKLSSLFLGRQILTRIVKdgygndifvgsapiniycncgvtwNEMIHGYAENEYVEQAISLYKDIIAsgvkhdgvTFVAILTpcshsglvYAEVEIFNSmehdhevkpkclmpykddlVVWGDLVSSCQVHSNVRLAKKAA
Flexible Loop (DISEMBL)
vyptqfpfttVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSScqvhsnvrlakkaa
Low Complexity Region (SEG)
VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA
Disordered region (IsUnstruct)
*****FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSN********
Disordered Region (DISOPRED)
VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA
Disordered Region (DISEMBL)
VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA
Disordered Region (DISPRO)
VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA
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	156	2.2.26 [Sep-21-2011]
Q9SVH0	774	Pentatricopeptide repeat-	yes	no	0.987	0.198	0.410	8e-35
Q9SIT7	697	Pentatricopeptide repeat-	no	no	1.0	0.223	0.320	9e-26
Q9SY02	781	Pentatricopeptide repeat-	no	no	0.955	0.190	0.331	1e-24
Q9M4P3	656	Pentatricopeptide repeat-	no	no	1.0	0.237	0.314	2e-23
Q9FWA6	903	Pentatricopeptide repeat-	no	no	0.993	0.171	0.304	1e-22
Q5G1T1	850	Pentatricopeptide repeat-	no	no	0.980	0.18	0.324	2e-22
Q9FNN7	511	Pentatricopeptide repeat-	no	no	1.0	0.305	0.308	3e-22
Q9CAY1	623	Putative pentatricopeptid	no	no	0.993	0.248	0.301	5e-22
Q9LW63	715	Putative pentatricopeptid	no	no	1.0	0.218	0.324	7e-22
Q1PFQ9	520	Pentatricopeptide repeat-	no	no	0.993	0.298	0.316	1e-21

>sp|Q9SVH0|PP329_ARATH Pentatricopeptide repeat-containing protein At4g20770 OS=Arabidopsis thaliana GN=PCMP-E35 PE=3 SV=2

 Score =  145 bits (367), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 109/195 (55%), Gaps = 41/195 (21%)

Query: 3   PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------- 54
           P +  F TVLSSC++L SL  GRQ    +VK GY +D FV +A  ++YC CG        
Sbjct: 517 PNETSFATVLSSCSRLCSLLHGRQFHGLVVKSGYVSDSFVETALTDMYCKCGEIDSARQF 576

Query: 55  ---------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLV 105
                    V WNEMIHGY  N   ++A+ LY+ +I+SG K DG+TFV++LT CSHSGLV
Sbjct: 577 FDAVLRKNTVIWNEMIHGYGHNGRGDEAVGLYRKMISSGEKPDGITFVSVLTACSHSGLV 636

Query: 106 YAEVEIFNSMEHDHEVKPK---------CL---------------MPYKDDLVVWGDLVS 141
              +EI +SM+  H ++P+         CL                PYK   V+W  L+S
Sbjct: 637 ETGLEILSSMQRIHGIEPELDHYICIVDCLGRAGRLEDAEKLAEATPYKSSSVLWEILLS 696

Query: 142 SCQVHSNVRLAKKAA 156
           SC+VH +V LA++ A
Sbjct: 697 SCRVHGDVSLARRVA 711

Arabidopsis thaliana (taxid: 3702)

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

 Score =  115 bits (289), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 65/203 (32%), Positives = 101/203 (49%), Gaps = 47/203 (23%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYG------NDIFVGSAPINIYCNCG 54
           V PT + F  +L +CA L+ L LG Q    ++K G+       +DIFVG++ I++Y  CG
Sbjct: 382 VCPTHYSFANILKACADLAELHLGMQAHVHVLKHGFKFQSGEEDDIFVGNSLIDMYVKCG 441

Query: 55  -----------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILT 97
                            V+WN MI G+A+N Y  +A+ L+++++ SG K D +T + +L+
Sbjct: 442 CVEEGYLVFRKMMERDCVSWNAMIIGFAQNGYGNEALELFREMLESGEKPDHITMIGVLS 501

Query: 98  PCSHSGLVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDL 133
            C H+G V      F+SM  D  V P      C+                   MP + D 
Sbjct: 502 ACGHAGFVEEGRHYFSSMTRDFGVAPLRDHYTCMVDLLGRAGFLEEAKSMIEEMPMQPDS 561

Query: 134 VVWGDLVSSCQVHSNVRLAKKAA 156
           V+WG L+++C+VH N+ L K  A
Sbjct: 562 VIWGSLLAACKVHRNITLGKYVA 584

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SY02|PP301_ARATH Pentatricopeptide repeat-containing protein At4g02750 OS=Arabidopsis thaliana GN=PCMP-H24 PE=3 SV=1

 Score =  112 bits (279), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 63/190 (33%), Positives = 97/190 (51%), Gaps = 41/190 (21%)

Query: 8   FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------------- 54
           F++ LS+CA + +L LG+Q+  R+VK GY    FVG+A + +YC CG             
Sbjct: 412 FSSALSTCADVVALELGKQLHGRLVKGGYETGCFVGNALLLMYCKCGSIEEANDLFKEMA 471

Query: 55  ----VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVE 110
               V+WN MI GY+ + + E A+  ++ +   G+K D  T VA+L+ CSH+GLV    +
Sbjct: 472 GKDIVSWNTMIAGYSRHGFGEVALRFFESMKREGLKPDDATMVAVLSACSHTGLVDKGRQ 531

Query: 111 IFNSMEHDHEVKPK-----CL-------------------MPYKDDLVVWGDLVSSCQVH 146
            F +M  D+ V P      C+                   MP++ D  +WG L+ + +VH
Sbjct: 532 YFYTMTQDYGVMPNSQHYACMVDLLGRAGLLEDAHNLMKNMPFEPDAAIWGTLLGASRVH 591

Query: 147 SNVRLAKKAA 156
            N  LA+ AA
Sbjct: 592 GNTELAETAA 601

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M4P3|PP316_ARATH Pentatricopeptide repeat-containing protein At4g16835, mitochondrial OS=Arabidopsis thaliana GN=DYW10 PE=2 SV=3

 Score =  108 bits (269), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 62/197 (31%), Positives = 103/197 (52%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           + P     ++ L  C++LS+L LGRQI   + K    ND+   ++ I++YC CG      
Sbjct: 280 IRPNSSGLSSALLGCSELSALQLGRQIHQIVSKSTLCNDVTALTSLISMYCKCGELGDAW 339

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V WN MI GYA++   ++A+ L++++I + ++ D +TFVA+L  C+H+G
Sbjct: 340 KLFEVMKKKDVVAWNAMISGYAQHGNADKALCLFREMIDNKIRPDWITFVAVLLACNHAG 399

Query: 104 LVYAEVEIFNSMEHDHEVKPK-----CL-------------------MPYKDDLVVWGDL 139
           LV   +  F SM  D++V+P+     C+                   MP++    V+G L
Sbjct: 400 LVNIGMAYFESMVRDYKVEPQPDHYTCMVDLLGRAGKLEEALKLIRSMPFRPHAAVFGTL 459

Query: 140 VSSCQVHSNVRLAKKAA 156
           + +C+VH NV LA+ AA
Sbjct: 460 LGACRVHKNVELAEFAA 476

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FWA6|PP207_ARATH Pentatricopeptide repeat-containing protein At3g02330 OS=Arabidopsis thaliana GN=PCMP-E90 PE=2 SV=2

 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 60/197 (30%), Positives = 101/197 (51%), Gaps = 42/197 (21%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           + P +F + TVL +CA L+S  LG+QI  +++K    +D+++ S  +++Y  CG      
Sbjct: 599 ITPDKFTYATVLDTCANLASAGLGKQIHAQVIKKELQSDVYICSTLVDMYSKCGDLHDSR 658

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      VTWN MI GYA +   E+AI L++ +I   +K + VTF++IL  C+H G
Sbjct: 659 LMFEKSLRRDFVTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHVTFISILRACAHMG 718

Query: 104 LVYAEVEIFNSMEHDHEVKPKC------------------------LMPYKDDLVVWGDL 139
           L+   +E F  M+ D+ + P+                          MP++ D V+W  L
Sbjct: 719 LIDKGLEYFYMMKRDYGLDPQLPHYSNMVDILGKSGKVKRALELIREMPFEADDVIWRTL 778

Query: 140 VSSCQVH-SNVRLAKKA 155
           +  C +H +NV +A++A
Sbjct: 779 LGVCTIHRNNVEVAEEA 795

Arabidopsis thaliana (taxid: 3702)

>sp|Q5G1T1|PP272_ARATH Pentatricopeptide repeat-containing protein At3g49170, chloroplastic OS=Arabidopsis thaliana GN=EMB2261 PE=2 SV=1

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/194 (32%), Positives = 98/194 (50%), Gaps = 41/194 (21%)

Query: 4   TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------- 54
           + F F ++LS  A + S+  G QI +++VK G   +  V +A I++Y  CG         
Sbjct: 473 SAFTFASLLSGVANVGSIRKGEQIHSQVVKLGLSCNQPVCNALISMYSKCGSIDTASRVF 532

Query: 55  --------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVY 106
                   ++W  MI G+A++ +  + +  +  +I  GVK + VT+VAIL+ CSH GLV 
Sbjct: 533 NFMENRNVISWTSMITGFAKHGFAIRVLETFNQMIEEGVKPNEVTYVAILSACSHVGLVS 592

Query: 107 AEVEIFNSMEHDHEVKPK-----CL-------------------MPYKDDLVVWGDLVSS 142
                FNSM  DH++KPK     C+                   MP++ D++VW   + +
Sbjct: 593 EGWRHFNSMYEDHKIKPKMEHYACMVDLLCRAGLLTDAFEFINTMPFQADVLVWRTFLGA 652

Query: 143 CQVHSNVRLAKKAA 156
           C+VHSN  L K AA
Sbjct: 653 CRVHSNTELGKLAA 666

May play a role in embryogenesis.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FNN7|PP371_ARATH Pentatricopeptide repeat-containing protein At5g08510 OS=Arabidopsis thaliana GN=PCMP-E20 PE=2 SV=1

 Score =  103 bits (258), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 61/198 (30%), Positives = 95/198 (47%), Gaps = 42/198 (21%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGV----- 55
           V P      +VL +CA L  L +GR++     ++G+ ++I+V +A I +Y  CG+     
Sbjct: 211 VKPNHITVVSVLPACANLGELEIGRRLEGYARENGFFDNIYVCNATIEMYSKCGMIDVAK 270

Query: 56  -------------TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHS 102
                        +WN MI   A +   ++A++L+  ++  G K D VTFV +L  C H 
Sbjct: 271 RLFEELGNQRNLCSWNSMIGSLATHGKHDEALTLFAQMLREGEKPDAVTFVGLLLACVHG 330

Query: 103 GLVYAEVEIFNSMEHDHEVKPK-----CL-------------------MPYKDDLVVWGD 138
           G+V    E+F SME  H++ PK     C+                   MP K D VVWG 
Sbjct: 331 GMVVKGQELFKSMEEVHKISPKLEHYGCMIDLLGRVGKLQEAYDLIKTMPMKPDAVVWGT 390

Query: 139 LVSSCQVHSNVRLAKKAA 156
           L+ +C  H NV +A+ A+
Sbjct: 391 LLGACSFHGNVEIAEIAS 408

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAY1|PP223_ARATH Putative pentatricopeptide repeat-containing protein At3g11460 OS=Arabidopsis thaliana GN=PCMP-H52 PE=3 SV=1

 Score =  103 bits (257), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 59/196 (30%), Positives = 97/196 (49%), Gaps = 41/196 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           V P  F   +VLSSCA L +  +G ++   +  +G+  ++FV +A I++Y  CG      
Sbjct: 253 VCPDPFTLVSVLSSCAHLGAKKIGHEVGKLVESNGFVPNVFVSNASISMYARCGNLAKAR 312

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V+W  MI  Y  +   E  + L+ D+I  G++ DG  FV +L+ CSHSG
Sbjct: 313 AVFDIMPVKSLVSWTAMIGCYGMHGMGEIGLMLFDDMIKRGIRPDGAVFVMVLSACSHSG 372

Query: 104 LVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDLVVWGDL 139
           L    +E+F +M+ +++++P      CL                   MP + D  VWG L
Sbjct: 373 LTDKGLELFRAMKREYKLEPGPEHYSCLVDLLGRAGRLDEAMEFIESMPVEPDGAVWGAL 432

Query: 140 VSSCQVHSNVRLAKKA 155
           + +C++H NV +A+ A
Sbjct: 433 LGACKIHKNVDMAELA 448

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LW63|PP251_ARATH Putative pentatricopeptide repeat-containing protein At3g23330 OS=Arabidopsis thaliana GN=PCMP-H32 PE=3 SV=1

 Score =  102 bits (255), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 64/197 (32%), Positives = 100/197 (50%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           V P    F++V+ +CA L++L LG+Q+   +++ G+G++IF+ SA +++Y  CG      
Sbjct: 339 VKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSKCGNIKAAR 398

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V+W  +I G+A + +  +A+SL++++   GVK + V FVA+LT CSH G
Sbjct: 399 KIFDRMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVG 458

Query: 104 LVYAEVEIFNSM--------EHDHEVKPKCLMPYKDDL----------------VVWGDL 139
           LV      FNSM        E +H      L+     L                 VW  L
Sbjct: 459 LVDEAWGYFNSMTKVYGLNQELEHYAAVADLLGRAGKLEEAYNFISKMCVEPTGSVWSTL 518

Query: 140 VSSCQVHSNVRLAKKAA 156
           +SSC VH N+ LA+K A
Sbjct: 519 LSSCSVHKNLELAEKVA 535

Arabidopsis thaliana (taxid: 3702)

>sp|Q1PFQ9|PPR62_ARATH Pentatricopeptide repeat-containing protein At1g28690, mitochondrial OS=Arabidopsis thaliana GN=PCMP-E34 PE=2 SV=2

 Score =  102 bits (254), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 97/196 (49%), Gaps = 41/196 (20%)

Query: 2   YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------- 54
           +P    F +V+ +C+ L+S  +G+Q+  +I+K G    I +GS+ +++Y  CG       
Sbjct: 270 HPNISTFASVIGACSVLTSHEVGQQVHAQIMKSGVYTHIKMGSSLLDMYAKCGGINDARR 329

Query: 55  ----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGL 104
                      +W  MI GY +N   E+A+ L+  +    ++ + VTF+  L+ CSHSGL
Sbjct: 330 VFDQMQEKNVFSWTSMIDGYGKNGNPEEALELFTRMKEFRIEPNYVTFLGALSACSHSGL 389

Query: 105 VYAEVEIFNSMEHDHEVKPK-----CL-------------------MPYKDDLVVWGDLV 140
           V    EIF SM+ D+ +KPK     C+                   MP + D  +W  L+
Sbjct: 390 VDKGYEIFESMQRDYSMKPKMEHYACIVDLMGRAGDLNKAFEFARAMPERPDSDIWAALL 449

Query: 141 SSCQVHSNVRLAKKAA 156
           SSC +H NV LA  AA
Sbjct: 450 SSCNLHGNVELASIAA 465

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	156
357481329	831	Pentatricopeptide repeat-containing prot	0.993	0.186	0.5	3e-44
356495733	770	PREDICTED: pentatricopeptide repeat-cont	0.993	0.201	0.474	2e-40
297740913	768	unnamed protein product [Vitis vinifera]	1.0	0.203	0.456	2e-40
359483750	847	PREDICTED: pentatricopeptide repeat-cont	1.0	0.184	0.456	3e-40
242064134	807	hypothetical protein SORBIDRAFT_04g00450	1.0	0.193	0.380	2e-33
334186756	774	pentatricopeptide repeat-containing prot	0.987	0.198	0.410	4e-33
5262217	740	putative protein [Arabidopsis thaliana]	0.987	0.208	0.410	5e-33
357136755	805	PREDICTED: pentatricopeptide repeat-cont	1.0	0.193	0.395	7e-33
297799986	760	predicted protein [Arabidopsis lyrata su	1.0	0.205	0.390	3e-32
49387750	803	putative pentatricopeptide (PPR) repeat-	1.0	0.194	0.375	1e-30

>gi|357481329|ref|XP_003610950.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355512285|gb|AES93908.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  182 bits (463), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 98/196 (50%), Positives = 124/196 (63%), Gaps = 41/196 (20%)

Query: 2   YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------- 54
           +P++F F T+ SSCAKLSSLF G+QI  +I+KDGY +++FVGS+ + +YC CG       
Sbjct: 516 FPSEFSFATIASSCAKLSSLFQGQQIHAQIIKDGYVDNVFVGSSLVEMYCKCGDVGAARY 575

Query: 55  ----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGL 104
                     VTWNEMIHGYA N Y  +A+SLYKD+I+SG K D +TFVA+LT CSHS L
Sbjct: 576 YFDMMPGKNIVTWNEMIHGYAHNGYGLEAVSLYKDMISSGEKPDDITFVAVLTACSHSAL 635

Query: 105 VYAEVEIFNSMEHDHEVKPK---------CL---------------MPYKDDLVVWGDLV 140
           V   VEIF+SM    EV PK         CL               MPYKDD +VW  ++
Sbjct: 636 VDEGVEIFSSMLQKFEVVPKLDHYTCIIDCLGRVGRFNEVEVILDTMPYKDDTIVWEVVL 695

Query: 141 SSCQVHSNVRLAKKAA 156
           SSC+VH+NV LAK+AA
Sbjct: 696 SSCRVHANVSLAKRAA 711

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356495733|ref|XP_003516728.1| PREDICTED: pentatricopeptide repeat-containing protein At4g20770-like [Glycine max]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 93/196 (47%), Positives = 120/196 (61%), Gaps = 41/196 (20%)

Query: 2   YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------- 54
           +P++F F TV+SSCAKLSSLF G+Q   +IVKDG+ +DIFVGS+ I +YC CG       
Sbjct: 514 FPSEFSFATVVSSCAKLSSLFQGQQFHAQIVKDGFLDDIFVGSSLIEMYCKCGDVNGARC 573

Query: 55  ----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGL 104
                     VTWNEMIHGYA+N     A+ LY D+I+SG K D +T+VA+LT CSHS L
Sbjct: 574 FFDVMPGRNTVTWNEMIHGYAQNGDGHNALCLYNDMISSGEKPDDITYVAVLTACSHSAL 633

Query: 105 VYAEVEIFNSMEHDHEVKPK---------CL---------------MPYKDDLVVWGDLV 140
           V   +EIFN+M   + V PK         CL               MP KDD VVW  ++
Sbjct: 634 VDEGLEIFNAMLQKYGVVPKVAHYTCIIDCLSRAGRFNEVEVILDAMPCKDDAVVWEVVL 693

Query: 141 SSCQVHSNVRLAKKAA 156
           SSC++H+N+ LAK+AA
Sbjct: 694 SSCRIHANLSLAKRAA 709

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740913|emb|CBI31095.3| unnamed protein product [Vitis vinifera]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 90/197 (45%), Positives = 124/197 (62%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           ++P+QF + TVLS CAKLSSL  GRQ+ ++I ++GY ND FVGSA I++Y  CG      
Sbjct: 487 MFPSQFSYATVLSCCAKLSSLSQGRQVHSQIAREGYMNDAFVGSALIDMYSKCGDVDAAR 546

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      VTWNEMIHGYA+N   ++A+ LY+D+I SG K DG+TFVA+LT CSHSG
Sbjct: 547 WVFDMMLGKNTVTWNEMIHGYAQNGCGDEAVLLYEDMIGSGEKPDGITFVAVLTACSHSG 606

Query: 104 LVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDLVVWGDL 139
           LV   ++IFNSM+ +H V+P      C+                   MP K D ++W  L
Sbjct: 607 LVDTGIKIFNSMQQEHGVEPLVDHYTCIIDSLGRAGRLHEAEVLIDKMPCKYDPIIWEVL 666

Query: 140 VSSCQVHSNVRLAKKAA 156
           +SSC+V+++V LA++AA
Sbjct: 667 LSSCRVYADVSLARRAA 683

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483750|ref|XP_002269533.2| PREDICTED: pentatricopeptide repeat-containing protein At4g20770-like [Vitis vinifera]

 Score =  169 bits (429), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 90/197 (45%), Positives = 124/197 (62%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           ++P+QF + TVLS CAKLSSL  GRQ+ ++I ++GY ND FVGSA I++Y  CG      
Sbjct: 516 MFPSQFSYATVLSCCAKLSSLSQGRQVHSQIAREGYMNDAFVGSALIDMYSKCGDVDAAR 575

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      VTWNEMIHGYA+N   ++A+ LY+D+I SG K DG+TFVA+LT CSHSG
Sbjct: 576 WVFDMMLGKNTVTWNEMIHGYAQNGCGDEAVLLYEDMIGSGEKPDGITFVAVLTACSHSG 635

Query: 104 LVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDLVVWGDL 139
           LV   ++IFNSM+ +H V+P      C+                   MP K D ++W  L
Sbjct: 636 LVDTGIKIFNSMQQEHGVEPLVDHYTCIIDSLGRAGRLHEAEVLIDKMPCKYDPIIWEVL 695

Query: 140 VSSCQVHSNVRLAKKAA 156
           +SSC+V+++V LA++AA
Sbjct: 696 LSSCRVYADVSLARRAA 712

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242064134|ref|XP_002453356.1| hypothetical protein SORBIDRAFT_04g004500 [Sorghum bicolor] gi|241933187|gb|EES06332.1| hypothetical protein SORBIDRAFT_04g004500 [Sorghum bicolor]

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 75/197 (38%), Positives = 116/197 (58%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           ++PT+  + ++++SCA+LSS+  GRQI  +++KDGY  +++VGS+ I++Y  CG      
Sbjct: 515 MFPTESSYASMINSCARLSSIPQGRQIHAQVLKDGYDQNVYVGSSLIDMYAKCGNMDDAR 574

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V WNEMIHGYA+N + E+A+ L++ ++ +  K D VTF+A+LT CSHSG
Sbjct: 575 LFFNCMIVKNIVAWNEMIHGYAQNGFGEKAVELFEYMLTTKQKPDSVTFIAVLTGCSHSG 634

Query: 104 LVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDLVVWGDL 139
           LV   +  FNSME ++ ++P      CL                   MPYKDD ++W  L
Sbjct: 635 LVDEAIAYFNSMESNYGIRPLVEHYTCLIDALGRAGRFAEVVAVIDKMPYKDDAILWEVL 694

Query: 140 VSSCQVHSNVRLAKKAA 156
           +++C VH N  L + AA
Sbjct: 695 LAACVVHHNAELGEFAA 711

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334186756|ref|NP_193809.2| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|223635629|sp|Q9SVH0.2|PP329_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At4g20770 gi|332658959|gb|AEE84359.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 109/195 (55%), Gaps = 41/195 (21%)

Query: 3   PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------- 54
           P +  F TVLSSC++L SL  GRQ    +VK GY +D FV +A  ++YC CG        
Sbjct: 517 PNETSFATVLSSCSRLCSLLHGRQFHGLVVKSGYVSDSFVETALTDMYCKCGEIDSARQF 576

Query: 55  ---------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLV 105
                    V WNEMIHGY  N   ++A+ LY+ +I+SG K DG+TFV++LT CSHSGLV
Sbjct: 577 FDAVLRKNTVIWNEMIHGYGHNGRGDEAVGLYRKMISSGEKPDGITFVSVLTACSHSGLV 636

Query: 106 YAEVEIFNSMEHDHEVKPK---------CL---------------MPYKDDLVVWGDLVS 141
              +EI +SM+  H ++P+         CL                PYK   V+W  L+S
Sbjct: 637 ETGLEILSSMQRIHGIEPELDHYICIVDCLGRAGRLEDAEKLAEATPYKSSSVLWEILLS 696

Query: 142 SCQVHSNVRLAKKAA 156
           SC+VH +V LA++ A
Sbjct: 697 SCRVHGDVSLARRVA 711

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5262217|emb|CAB45843.1| putative protein [Arabidopsis thaliana] gi|7268873|emb|CAB79077.1| putative protein [Arabidopsis thaliana]

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 109/195 (55%), Gaps = 41/195 (21%)

Query: 3   PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------- 54
           P +  F TVLSSC++L SL  GRQ    +VK GY +D FV +A  ++YC CG        
Sbjct: 483 PNETSFATVLSSCSRLCSLLHGRQFHGLVVKSGYVSDSFVETALTDMYCKCGEIDSARQF 542

Query: 55  ---------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLV 105
                    V WNEMIHGY  N   ++A+ LY+ +I+SG K DG+TFV++LT CSHSGLV
Sbjct: 543 FDAVLRKNTVIWNEMIHGYGHNGRGDEAVGLYRKMISSGEKPDGITFVSVLTACSHSGLV 602

Query: 106 YAEVEIFNSMEHDHEVKPK---------CL---------------MPYKDDLVVWGDLVS 141
              +EI +SM+  H ++P+         CL                PYK   V+W  L+S
Sbjct: 603 ETGLEILSSMQRIHGIEPELDHYICIVDCLGRAGRLEDAEKLAEATPYKSSSVLWEILLS 662

Query: 142 SCQVHSNVRLAKKAA 156
           SC+VH +V LA++ A
Sbjct: 663 SCRVHGDVSLARRVA 677

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357136755|ref|XP_003569969.1| PREDICTED: pentatricopeptide repeat-containing protein At4g20770-like [Brachypodium distachyon]

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 78/197 (39%), Positives = 113/197 (57%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           + PT+  + ++++SCA+LSS+  GRQI  +IVKDGY  +++VGSA I++Y  CG      
Sbjct: 513 MMPTESSYASMINSCARLSSVPQGRQIHAQIVKDGYDQNVYVGSALIDMYAKCGNMDDAR 572

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V WNEMIHGYA+N + E+A+ L++ ++ +  + DGVTF+A+LT CSHSG
Sbjct: 573 VFFDCMVTKNIVAWNEMIHGYAQNGFGEKAVDLFEYMLTTEQRPDGVTFIAVLTGCSHSG 632

Query: 104 LVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDLVVWGDL 139
           LV   +  FNSME  + + P      CL                   MP KDD +VW  L
Sbjct: 633 LVDEAIAFFNSMESTYGITPLAEHYTCLIDGLGRAGRLVEVEALIDNMPCKDDPIVWEVL 692

Query: 140 VSSCQVHSNVRLAKKAA 156
           +++C VH N  L + AA
Sbjct: 693 LAACAVHHNAELGECAA 709

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799986|ref|XP_002867877.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297313713|gb|EFH44136.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 77/197 (39%), Positives = 112/197 (56%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           + P +  +  VL SC++L SL  GRQ   ++VK GY +D FV +A  ++YC CG      
Sbjct: 501 LLPNETTYAIVLGSCSRLCSLVHGRQFHGQVVKSGYVSDSFVETAVTDMYCKCGEIESAR 560

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V WNEMIHGYA N   ++A+ LY+++I++G K DG+TFV++LT CSHSG
Sbjct: 561 QFFDTVSRKNTVIWNEMIHGYAHNGRGDEAVDLYREMISAGEKPDGITFVSVLTACSHSG 620

Query: 104 LVYAEVEIFNSMEHDHEVKPK---------CL---------------MPYKDDLVVWGDL 139
           LV   +EI +SM+ DH ++P+         CL                PYK   V+W  L
Sbjct: 621 LVDTGLEILSSMQRDHGIEPELDHYICIVDCLGRAGRLEDAETLAEATPYKSSSVLWEIL 680

Query: 140 VSSCQVHSNVRLAKKAA 156
           +SSC+V+ +V LA++ A
Sbjct: 681 LSSCRVYGDVSLARRVA 697

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|49387750|dbj|BAD26238.1| putative pentatricopeptide (PPR) repeat-containing protein [Oryza sativa Japonica Group] gi|218190136|gb|EEC72563.1| hypothetical protein OsI_05996 [Oryza sativa Indica Group]

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 74/197 (37%), Positives = 112/197 (56%), Gaps = 41/197 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           + PT+  + ++++SC++LSS+  GRQI  +++KDGY  +++VGSA I++Y  CG      
Sbjct: 514 IMPTESSYASMINSCSRLSSIPHGRQIHAQVMKDGYDQNVYVGSALIDMYAKCGNMDDAR 573

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V WNEMIHGYA+N   ++A+ L++ ++ +  K D VTF+A+LT CSHSG
Sbjct: 574 LFFDTMMMKNIVAWNEMIHGYAQNGLGDKAVELFEYMLTTEQKPDAVTFIAVLTGCSHSG 633

Query: 104 LVYAEVEIFNSMEHDHEVKP-----KCL-------------------MPYKDDLVVWGDL 139
           LV   +  FNSME+ + + P      CL                   MP KDD ++W  L
Sbjct: 634 LVDKAMAFFNSMENSYGIIPLAEHYTCLIDALGRAGRFVEVEALIHKMPCKDDPIIWEVL 693

Query: 140 VSSCQVHSNVRLAKKAA 156
           +++C VH N  L K AA
Sbjct: 694 LAACVVHHNAELGKCAA 710

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	156
TAIR|locus:2159602	511	AT5G08510 "AT5G08510" [Arabido	0.442	0.135	0.391	3.6e-23
TAIR|locus:2045580	559	AT2G42920 [Arabidopsis thalian	0.429	0.119	0.388	2.8e-22
TAIR|locus:2080727	623	MEF10 "mitochondrial RNA editi	0.442	0.110	0.362	3.1e-22
TAIR|locus:2082886	850	EMB2261 "embryo defective 2261	0.448	0.082	0.428	3.6e-22
TAIR|locus:2083961	768	AT3G53360 "AT3G53360" [Arabido	0.442	0.089	0.376	1e-21
TAIR|locus:2027589	611	PGN "AT1G56570" [Arabidopsis t	0.442	0.112	0.347	1.1e-21
TAIR|locus:2055919	786	AT2G22070 "AT2G22070" [Arabido	0.442	0.087	0.289	1.4e-21
TAIR|locus:2119440	1064	AT4G13650 [Arabidopsis thalian	0.448	0.065	0.342	1.9e-21
TAIR|locus:2049736	500	AT2G37320 "AT2G37320" [Arabido	0.442	0.138	0.408	2.4e-21
TAIR|locus:2007888	731	AT1G17630 [Arabidopsis thalian	0.448	0.095	0.4	3.5e-21

TAIR|locus:2159602 AT5G08510 "AT5G08510" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 3.6e-23, Sum P(3) = 3.6e-23
 Identities = 27/69 (39%), Positives = 41/69 (59%)

Query:    56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM 115
             +WN MI   A +   ++A++L+  ++  G K D VTFV +L  C H G+V    E+F SM
Sbjct:   284 SWNSMIGSLATHGKHDEALTLFAQMLREGEKPDAVTFVGLLLACVHGGMVVKGQELFKSM 343

Query:   116 EHDHEVKPK 124
             E  H++ PK
Sbjct:   344 EEVHKISPK 352

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 147 (56.8 bits), Expect = 2.8e-22, Sum P(3) = 2.8e-22
 Identities = 26/67 (38%), Positives = 43/67 (64%)

Query:    57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME 116
             WN MI G A N + E+A+ L+ ++  SG++ D V+F+ +LT C+HSG V+   E F  M+
Sbjct:   327 WNSMILGLANNGFEERAMDLFSELERSGLEPDSVSFIGVLTACAHSGEVHRADEFFRLMK 386

Query:   117 HDHEVKP 123
               + ++P
Sbjct:   387 EKYMIEP 393

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2080727 MEF10 "mitochondrial RNA editing factor 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 3.1e-22, Sum P(3) = 3.1e-22
 Identities = 25/69 (36%), Positives = 43/69 (62%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             V+W  MI  Y  +   E  + L+ D+I  G++ DG  FV +L+ CSHSGL    +E+F +
Sbjct:   324 VSWTAMIGCYGMHGMGEIGLMLFDDMIKRGIRPDGAVFVMVLSACSHSGLTDKGLELFRA 383

Query:   115 MEHDHEVKP 123
             M+ +++++P
Sbjct:   384 MKREYKLEP 392

GO:0005739 "mitochondrion" evidence=ISM

GO:0016554 "cytidine to uridine editing" evidence=IMP

TAIR|locus:2082886 EMB2261 "embryo defective 2261" [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 3.6e-22, Sum P(3) = 3.6e-22
 Identities = 30/70 (42%), Positives = 45/70 (64%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             ++W  MI G+A++ +  + +  +  +I  GVK + VT+VAIL+ CSH GLV      FNS
Sbjct:   541 ISWTSMITGFAKHGFAIRVLETFNQMIEEGVKPNEVTYVAILSACSHVGLVSEGWRHFNS 600

Query:   115 MEHDHEVKPK 124
             M  DH++KPK
Sbjct:   601 MYEDHKIKPK 610

GO:0009507 "chloroplast" evidence=ISM

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP;NAS

TAIR|locus:2083961 AT3G53360 "AT3G53360" [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 1.0e-21, Sum P(3) = 1.0e-21
 Identities = 26/69 (37%), Positives = 51/69 (73%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             V+W+ +I GYA++ + E+A+ L+K++ ++G++ + VTFV +LT CSH GLV   ++++ +
Sbjct:   540 VSWSTLIVGYAQSGFGEEALILFKEMKSAGIEPNHVTFVGVLTACSHVGLVEEGLKLYAT 599

Query:   115 MEHDHEVKP 123
             M+ +H + P
Sbjct:   600 MQTEHGISP 608

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2027589 PGN "AT1G56570" [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 1.1e-21, Sum P(3) = 1.1e-21
 Identities = 24/69 (34%), Positives = 45/69 (65%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             V+W  M+ GY  + Y  +A+ L+  +++SG++ D + F+A+L+ C H+GLV   ++ FN 
Sbjct:   381 VSWTSMMIGYGSHGYGAEAVELFDKMVSSGIRPDRIVFMAVLSACRHAGLVEKGLKYFNV 440

Query:   115 MEHDHEVKP 123
             ME ++ + P
Sbjct:   441 MESEYGINP 449

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009651 "response to salt stress" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0009749 "response to glucose stimulus" evidence=IMP

GO:0050832 "defense response to fungus" evidence=IMP

TAIR|locus:2055919 AT2G22070 "AT2G22070" [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 1.4e-21, Sum P(3) = 1.4e-21
 Identities = 20/69 (28%), Positives = 43/69 (62%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             V+W  MI   A++ + E+A+ L++ ++  G++ D +T+V + + C+H+GLV    + F+ 
Sbjct:   481 VSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVFSACTHAGLVNQGRQYFDM 540

Query:   115 MEHDHEVKP 123
             M+   ++ P
Sbjct:   541 MKDVDKIIP 549

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2119440 AT4G13650 [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 1.9e-21, Sum P(3) = 1.9e-21
 Identities = 24/70 (34%), Positives = 43/70 (61%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             V+WN +I+ Y+++ +  +A+  +  +I S V+ + VT V +L+ CSH GLV   +  F S
Sbjct:   759 VSWNAIINAYSKHGFGSEALDSFDQMIHSNVRPNHVTLVGVLSACSHIGLVDKGIAYFES 818

Query:   115 MEHDHEVKPK 124
             M  ++ + PK
Sbjct:   819 MNSEYGLSPK 828

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2049736 AT2G37320 "AT2G37320" [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 2.4e-21, Sum P(3) = 2.4e-21
 Identities = 29/71 (40%), Positives = 46/71 (64%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIA-SGVKHDGVTFVAILTPCSHSGLVYAEVEIFN 113
             V+WN MI GYA++    QAI L++ ++  SG K D +T++ +L+ C H+GLV    + FN
Sbjct:   288 VSWNSMIAGYAQHGLAMQAIELFELMMPKSGTKPDAITYLGVLSSCRHAGLVKEGRKFFN 347

Query:   114 SMEHDHEVKPK 124
              M  +H +KP+
Sbjct:   348 LMA-EHGLKPE 357

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2007888 AT1G17630 [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 3.5e-21, Sum P(3) = 3.5e-21
 Identities = 28/70 (40%), Positives = 46/70 (65%)

Query:    55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNS 114
             ++WN +I GY  + + E+A+S++  +I+SG   DG+  VA+L+ CSH+GLV    EIF S
Sbjct:   501 ISWNSIIKGYGMHGFAEKALSMFDRMISSGFHPDGIALVAVLSACSHAGLVEKGREIFYS 560

Query:   115 MEHDHEVKPK 124
             M     ++P+
Sbjct:   561 MSKRFGLEPQ 570

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00029872001 RecName- Full=Non-specific lipid-transfer protein;; Plant non-specific lipid-transfer proteins transfer phospholipids as well as galactolipids across membranes. May play a role in wax or cutin deposition in the cell walls of expanding epidermal cells and certain secretory tissues (By similarity) (897 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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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	156
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-28
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-27
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-14
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-11
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	7e-10
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-08
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	8e-06
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-05
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	8e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-04
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04

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

 Score =  108 bits (270), Expect = 5e-28
 Identities = 56/196 (28%), Positives = 95/196 (48%), Gaps = 40/196 (20%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           + P        LS+CA++ +L  G++I   +++ G G D F+ +A +++Y  CG      
Sbjct: 485 LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAW 544

Query: 55  ----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGL 104
                     V+WN ++ GY  +     A+ L+  ++ SGV  D VTF+++L  CS SG+
Sbjct: 545 NQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGM 604

Query: 105 VYAEVEIFNSMEHDHEVKPK-----CL-------------------MPYKDDLVVWGDLV 140
           V   +E F+SME  + + P      C+                   MP   D  VWG L+
Sbjct: 605 VTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALL 664

Query: 141 SSCQVHSNVRLAKKAA 156
           ++C++H +V L + AA
Sbjct: 665 NACRIHRHVELGELAA 680

Length = 857

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

 Score =  104 bits (261), Expect = 8e-27
 Identities = 50/193 (25%), Positives = 95/193 (49%), Gaps = 41/193 (21%)

Query: 5   QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------- 54
           QF F+ ++   ++L+ L   +Q    +++ G+  DI   +A +++Y   G          
Sbjct: 325 QFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFD 384

Query: 55  -------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYA 107
                  ++WN +I GY  +    +A+ +++ +IA GV  + VTF+A+L+ C +SGL   
Sbjct: 385 RMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQ 444

Query: 108 EVEIFNSMEHDHEVKPK-----CLM-------------------PYKDDLVVWGDLVSSC 143
             EIF SM  +H +KP+     C++                   P+K  + +W  L+++C
Sbjct: 445 GWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTAC 504

Query: 144 QVHSNVRLAKKAA 156
           ++H N+ L + AA
Sbjct: 505 RIHKNLELGRLAA 517

Length = 697

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

 Score = 68.7 bits (168), Expect = 2e-14
 Identities = 37/115 (32%), Positives = 54/115 (46%), Gaps = 17/115 (14%)

Query: 8   FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------------- 54
           F  +L + A L S   G+Q+   ++K G   D FV  A I++Y  CG             
Sbjct: 227 FVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP 286

Query: 55  ----VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLV 105
               V WN M+ GYA + Y E+A+ LY ++  SGV  D  TF  ++   S   L+
Sbjct: 287 EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALL 341

Length = 697

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

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 34/128 (26%), Positives = 60/128 (46%), Gaps = 17/128 (13%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           V P     T+V+S+C  L    LGR++   +VK G+  D+ V ++ I +Y + G      
Sbjct: 284 VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAE 343

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      V+W  MI GY +N   ++A+  Y  +    V  D +T  ++L+ C+  G
Sbjct: 344 KVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLG 403

Query: 104 LVYAEVEI 111
            +   V++
Sbjct: 404 DLDVGVKL 411

Length = 857

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

 Score = 56.0 bits (135), Expect = 7e-10
 Identities = 31/116 (26%), Positives = 53/116 (45%), Gaps = 17/116 (14%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           V P  + F  VL +C  +  L  GR++   +V+ G+  D+ V +A I +Y  CG      
Sbjct: 183 VRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSAR 242

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPC 99
                      ++WN MI GY EN    + + L+  +    V  D +T  ++++ C
Sbjct: 243 LVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISAC 298

Length = 857

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

 Score = 45.9 bits (110), Expect = 9e-08
 Identities = 13/42 (30%), Positives = 26/42 (61%)

Query: 55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAIL 96
          VT+N +I GY +   VE+A+ L+ ++   G+K +  T+  ++
Sbjct: 4  VTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILI 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|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 44.5 bits (105), Expect = 8e-06
 Identities = 30/128 (23%), Positives = 57/128 (44%), Gaps = 18/128 (14%)

Query: 1   VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------ 54
           V P +    +VLS+CA L  L +G ++     + G  + + V +A I +Y  C       
Sbjct: 385 VSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKAL 444

Query: 55  -----------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG 103
                      ++W  +I G   N    +A+  ++ ++ + +K + VT +A L+ C+  G
Sbjct: 445 EVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIG 503

Query: 104 LVYAEVEI 111
            +    EI
Sbjct: 504 ALMCGKEI 511

Length = 857

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

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 34/142 (23%), Positives = 58/142 (40%), Gaps = 33/142 (23%)

Query: 8   FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGV-----TWNEMIH 62
           +TT++S+CAK   +    ++   +V                   N GV     T+  +I 
Sbjct: 475 YTTLISTCAKSGKVDAMFEVFHEMV-------------------NAGVEANVHTFGALID 515

Query: 63  GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD-HEV 121
           G A    V +A   Y  + +  VK D V F A+++ C  SG V    ++   M+ + H +
Sbjct: 516 GCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPI 575

Query: 122 KPKCLMPYKDDLVVWGDLVSSC 143
            P        D +  G L+ +C
Sbjct: 576 DP--------DHITVGALMKAC 589

Length = 1060

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

 Score = 41.4 bits (97), Expect = 8e-05
 Identities = 16/44 (36%), Positives = 28/44 (63%)

Query: 56  TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPC 99
           +WN ++ GYA+  Y ++A+ LY  ++ +GV+ D  TF  +L  C
Sbjct: 154 SWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTC 197

Length = 857

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

 Score = 37.1 bits (87), Expect = 1e-04
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD 88
          VT+N +I G  +   VE+A+ L+K++   G++ D
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 = 36.7 bits (86), Expect = 2e-04
 Identities = 12/31 (38%), Positives = 21/31 (67%)

Query: 55 VTWNEMIHGYAENEYVEQAISLYKDIIASGV 85
          VT+N +I GY +   +E+A+ L+K++   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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	156
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	99.97
PLN03077	857	Protein ECB2; Provisional	99.97
PLN03218	1060	maturation of RBCL 1; Provisional	99.97
PLN03077	857	Protein ECB2; Provisional	99.96
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.96
PF13041	50	PPR_2: PPR repeat family	99.7
PF13041	50	PPR_2: PPR repeat family	99.69
PF12854	34	PPR_1: PPR repeat	99.25
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.2
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.19
PF12854	34	PPR_1: PPR repeat	99.17
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.15
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.05
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.98
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.94
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.84
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.81
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.81
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.79
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.75
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.74
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.55
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.46
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.44
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.4
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.39
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.36
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.21
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.2
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.18
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.1
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.04
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.98
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.93
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	97.91
PRK12370	553	invasion protein regulator; Provisional	97.89
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.87
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	97.86
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.78
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.76
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	97.71
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.7
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	97.66
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	97.66
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.64
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.64
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	97.62
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.59
KOG3941	406	consensus Intermediate in Toll signal transduction	97.58
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.55
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.55
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.55
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.49
PRK12370	553	invasion protein regulator; Provisional	97.46
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.44
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.38
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.32
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.31
KOG1126	638	consensus DNA-binding cell division cycle control	97.3
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.3
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.28
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.25
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.23
PRK14574	822	hmsH outer membrane protein; Provisional	97.22
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.2
PRK15359	144	type III secretion system chaperone protein SscB;	97.19
PRK15359	144	type III secretion system chaperone protein SscB;	97.16
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.14
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.11
PRK11189	296	lipoprotein NlpI; Provisional	97.03
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.03
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.0
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.99
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.98
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.95
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.89
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.89
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.89
PRK14574	822	hmsH outer membrane protein; Provisional	96.87
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.84
KOG2003	840	consensus TPR repeat-containing protein [General f	96.83
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.62
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.6
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	96.6
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.53
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.52
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	96.49
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.46
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.41
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.41
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.41
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.37
PF12688	120	TPR_5: Tetratrico peptide repeat	96.36
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.36
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	96.35
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.34
KOG0495	913	consensus HAT repeat protein [RNA processing and m	96.31
PRK11189	296	lipoprotein NlpI; Provisional	96.27
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.23
KOG1126	638	consensus DNA-binding cell division cycle control	96.19
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.17
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.15
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.06
PF12688	120	TPR_5: Tetratrico peptide repeat	96.0
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	95.94
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	95.89
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.88
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.87
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.84
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	95.82
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.81
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.8
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.7
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.7
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.61
KOG2003	840	consensus TPR repeat-containing protein [General f	95.56
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.55
KOG3941	406	consensus Intermediate in Toll signal transduction	95.52
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	95.47
KOG1129	478	consensus TPR repeat-containing protein [General f	95.46
PRK10803	263	tol-pal system protein YbgF; Provisional	95.42
KOG1915	677	consensus Cell cycle control protein (crooked neck	95.41
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.39
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	95.29
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	95.23
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	95.2
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	95.17
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	95.16
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	95.03
PF13371	73	TPR_9: Tetratricopeptide repeat	94.8
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	94.79
KOG2047	835	consensus mRNA splicing factor [RNA processing and	94.71
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	94.68
KOG2076	895	consensus RNA polymerase III transcription factor	94.61
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	94.6
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	94.37
KOG3616	1636	consensus Selective LIM binding factor [Transcript	94.21
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	94.2
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	94.05
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	93.99
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.93
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.85
PRK10803	263	tol-pal system protein YbgF; Provisional	93.71
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.71
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	93.62
KOG2047	835	consensus mRNA splicing factor [RNA processing and	93.47
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.25
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	93.21
KOG2376	652	consensus Signal recognition particle, subunit Srp	93.13
KOG1128	777	consensus Uncharacterized conserved protein, conta	93.11
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	93.06
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	92.86
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	92.84
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	92.84
PRK14720	906	transcript cleavage factor/unknown domain fusion p	92.83
KOG3785	557	consensus Uncharacterized conserved protein [Funct	92.5
PF13762	145	MNE1: Mitochondrial splicing apparatus component	92.4
PF13371	73	TPR_9: Tetratricopeptide repeat	92.37
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	92.34
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	92.09
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	91.98
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	91.94
PF13762	145	MNE1: Mitochondrial splicing apparatus component	91.87
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	91.75
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	91.32
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	91.17
KOG3785	557	consensus Uncharacterized conserved protein [Funct	91.16
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	91.03
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	90.86
COG3898	531	Uncharacterized membrane-bound protein [Function u	90.74
KOG1129	478	consensus TPR repeat-containing protein [General f	90.71
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	90.69
PF13428	44	TPR_14: Tetratricopeptide repeat	90.65
COG3629	280	DnrI DNA-binding transcriptional activator of the	90.64
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	90.59
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	90.59
KOG2376	652	consensus Signal recognition particle, subunit Srp	90.59
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	90.57
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	90.55
KOG4570	418	consensus Uncharacterized conserved protein [Funct	90.29
COG4783	484	Putative Zn-dependent protease, contains TPR repea	90.02
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	89.67
PF13512	142	TPR_18: Tetratricopeptide repeat	89.64
KOG1128	777	consensus Uncharacterized conserved protein, conta	89.3
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	89.26
KOG0547	606	consensus Translocase of outer mitochondrial membr	89.04
smart00299	140	CLH Clathrin heavy chain repeat homology.	89.03
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	89.03
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	88.8
PF13929	292	mRNA_stabil: mRNA stabilisation	88.58
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	88.25
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	87.77
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	87.73
PF13428	44	TPR_14: Tetratricopeptide repeat	87.55
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	87.33
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.96
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	86.79
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	86.77
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	86.7
KOG2076	895	consensus RNA polymerase III transcription factor	86.66
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	86.53
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	86.39
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	86.25
PF13929	292	mRNA_stabil: mRNA stabilisation	86.18
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	85.93
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	85.65
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	85.31
COG4700	251	Uncharacterized protein conserved in bacteria cont	85.2
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	85.08
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	84.39
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	84.16
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	84.11
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	83.96
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	83.96
KOG1125	579	consensus TPR repeat-containing protein [General f	83.94
PRK15331	165	chaperone protein SicA; Provisional	83.77
KOG4570	418	consensus Uncharacterized conserved protein [Funct	83.67
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	83.29
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	82.63
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	82.62
KOG0547	606	consensus Translocase of outer mitochondrial membr	82.62
PRK10564	303	maltose regulon periplasmic protein; Provisional	82.34
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	82.02
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	81.58
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	81.54
KOG0553	304	consensus TPR repeat-containing protein [General f	81.53
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	81.45
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	81.06
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	80.88
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	80.12

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

Probab=100.00  E-value=1.3e-32  Score=222.72  Aligned_cols=155  Identities=32%  Similarity=0.690  Sum_probs=133.2

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-----------------chHHHHHHH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-----------------VTWNEMIHG   63 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-----------------~~~~~li~~   63 (156)
                      ++||..||+++|++|++.|++++|+++|++|.+.|+.||..+||+||++|+++|                 .+||+||.+
T Consensus       321 ~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~  400 (697)
T PLN03081        321 VSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAG  400 (697)
T ss_pred             CCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHH
Confidence            357777777777777777777777777777777777777777777777777777                 899999999


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-----c-------------
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-----C-------------  125 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-----c-------------  125 (156)
                      |+++|+.++|.++|++|.+.|+.||..||+++|++|++.|++++|.++|+.|.+++|+.|+     |             
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            9999999999999999999999999999999999999999999999999999878898887     2             


Q ss_pred             ------CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          126 ------LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       126 ------~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                            ++++.||..+|++||.+|+.+|+++.|+++
T Consensus       481 A~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~  516 (697)
T PLN03081        481 AYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLA  516 (697)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHH
Confidence                  677888888899998888888888888765

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.97  E-value=2.5e-30  Score=214.65  Aligned_cols=152  Identities=24%  Similarity=0.380  Sum_probs=116.7

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc---------------------chHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------------------VTWNEMI   61 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---------------------~~~~~li   61 (156)
                      ||..||+.+|.+|++.|+++.|.++|++|.+.|+.||..+||+||.+|++.|                     .+||+||
T Consensus       435 pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI  514 (1060)
T PLN03218        435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI  514 (1060)
T ss_pred             CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            7888888888888888888888888888888888888888888888888888                     7888888


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccc-cccCCC-----------c----
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD-HEVKPK-----------C----  125 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-~~~~~~-----------c----  125 (156)
                      .+|++.|++++|.++|++|.+.|+.||..||+.+|++|++.|++++|.++|++|..+ .|+.|+           |    
T Consensus       515 ~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~  594 (1060)
T PLN03218        515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQ  594 (1060)
T ss_pred             HHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCC
Confidence            888888888888888888888888888888888888888888888888888888533 454333           0    


Q ss_pred             ------------CCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          126 ------------LMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       126 ------------~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                                  ..++.||..+||+||.+|++.|++++|.+
T Consensus       595 ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~  635 (1060)
T PLN03218        595 VDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALS  635 (1060)
T ss_pred             HHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHH
Confidence                        23345555555555555555555555554

>PLN03077 Protein ECB2; Provisional

Probab=99.97  E-value=1.3e-30  Score=215.05  Aligned_cols=155  Identities=35%  Similarity=0.770  Sum_probs=139.4

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----------------chHHHHHHHH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----------------VTWNEMIHGY   64 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----------------~~~~~li~~~   64 (156)
                      ++||..||+++|.+|++.|+++.++++|..+.+.|+.+|..++|+||++|+++|                .+||+||.+|
T Consensus       485 ~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~  564 (857)
T PLN03077        485 LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGY  564 (857)
T ss_pred             CCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHH
Confidence            468888888888888888888889999998888999999999999999999998                6899999999


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-----c--------------
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-----C--------------  125 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-----c--------------  125 (156)
                      +++|+.++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|+.|.+++|+.|+     |              
T Consensus       565 ~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA  644 (857)
T PLN03077        565 VAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEA  644 (857)
T ss_pred             HHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHH
Confidence            999999999999999999999999999999999999999999999999999778998886     2              


Q ss_pred             -----CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          126 -----LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       126 -----~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                           +++++||..+|++||.+|..+|+.+.|+++
T Consensus       645 ~~~~~~m~~~pd~~~~~aLl~ac~~~~~~e~~e~~  679 (857)
T PLN03077        645 YNFINKMPITPDPAVWGALLNACRIHRHVELGELA  679 (857)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHcCChHHHHHH
Confidence                 667788888888888888888888777654

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.97  E-value=5.9e-30  Score=212.38  Aligned_cols=154  Identities=18%  Similarity=0.291  Sum_probs=120.8

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHH--hCCCCchHHHhHHHHHhhhcc---------------------chH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVK--DGYGNDIFVGSAPINIYCNCG---------------------VTW   57 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~--~g~~~~~~~~~~li~~~~~~~---------------------~~~   57 (156)
                      ++||..||+++|.+|++.|++++|.++|++|.+  .|+.||..+|++||.+|++.|                     .+|
T Consensus       538 v~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~ty  617 (1060)
T PLN03218        538 VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVY  617 (1060)
T ss_pred             CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHH
Confidence            468888888888888888888888888888865  567888888888888888877                     578


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-----------c-
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-----------C-  125 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-----------c-  125 (156)
                      |++|.+|++.|++++|.++|++|.+.|+.||..||+++|++|++.|++++|.++|+.| .+.|+.|+           | 
T Consensus       618 nsLI~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        618 TIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDA-RKQGIKLGTVSYSSLMGACSN  696 (1060)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHH-HHcCCCCCHHHHHHHHHHHHh
Confidence            8888888888888888888888888888888888888888888888888888888888 55666665           1 


Q ss_pred             ---------------CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          126 ---------------LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       126 ---------------~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                                     ..++.||..+||+||.+|++.|++++|.++
T Consensus       697 ~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlel  741 (1060)
T PLN03218        697 AKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEV  741 (1060)
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence                           345677888888888888888888777664

>PLN03077 Protein ECB2; Provisional

Probab=99.96  E-value=7e-29  Score=204.80  Aligned_cols=145  Identities=26%  Similarity=0.442  Sum_probs=118.7

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-----------------chHHHHHHH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-----------------VTWNEMIHG   63 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-----------------~~~~~li~~   63 (156)
                      ++||..||+.+|.+|++.|+++.++++|..|.+.|+.||..+||+||++|++.|                 .+||+||.+
T Consensus       284 ~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~  363 (857)
T PLN03077        284 VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG  363 (857)
T ss_pred             CCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHH
Confidence            367777777777777777777777777777777788888888888888888888                 799999999


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      |++.|++++|+++|++|++.|+.||..||+.+|.+|++.|++++|.++++.| .+.|+        .||..+||+||.+|
T Consensus       364 ~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~-~~~g~--------~~~~~~~n~Li~~y  434 (857)
T PLN03077        364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELA-ERKGL--------ISYVVVANALIEMY  434 (857)
T ss_pred             HHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHH-HHhCC--------CcchHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999 56664        45555555555555


Q ss_pred             hhcCCHhHHhh
Q 041561          144 QVHSNVRLAKK  154 (156)
Q Consensus       144 ~~~g~~~~a~~  154 (156)
                      ++.|++++|++
T Consensus       435 ~k~g~~~~A~~  445 (857)
T PLN03077        435 SKCKCIDKALE  445 (857)
T ss_pred             HHcCCHHHHHH
Confidence            55555555544

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

Probab=99.96  E-value=1.2e-28  Score=199.70  Aligned_cols=152  Identities=24%  Similarity=0.432  Sum_probs=130.6

Q ss_pred             CCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc-----------------------------------hHHHhHH
Q 041561            2 YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND-----------------------------------IFVGSAP   46 (156)
Q Consensus         2 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-----------------------------------~~~~~~l   46 (156)
                      .||..+|+++|.+|++.|++++|.++|++|.+.|+.||                                   ..+||+|
T Consensus       186 ~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~L  265 (697)
T PLN03081        186 ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCAL  265 (697)
T ss_pred             CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHH
Confidence            47888888888888888888888888888876665554                                   5556777


Q ss_pred             HHHhhhcc-----------------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHH
Q 041561           47 INIYCNCG-----------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEV  109 (156)
Q Consensus        47 i~~~~~~~-----------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  109 (156)
                      |++|+++|                 ++||+||.+|++.|++++|+++|++|.+.|+.||..||++++++|++.|++++|.
T Consensus       266 i~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~  345 (697)
T PLN03081        266 IDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAK  345 (697)
T ss_pred             HHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHH
Confidence            78888887                 7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccccccCCC-------------c-----------CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          110 EIFNSMEHDHEVKPK-------------C-----------LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       110 ~~~~~m~~~~~~~~~-------------c-----------~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ++|+.| .+.|+.++             |           .+. +||..+||+||.+|+++|+.++|.++
T Consensus       346 ~i~~~m-~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~-~~d~~t~n~lI~~y~~~G~~~~A~~l  413 (697)
T PLN03081        346 QAHAGL-IRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-RKNLISWNALIAGYGNHGRGTKAVEM  413 (697)
T ss_pred             HHHHHH-HHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC-CCCeeeHHHHHHHHHHcCCHHHHHHH
Confidence            999999 67787776             1           443 68888888888888888888888764

>PF13041 PPR_2: PPR repeat family

Probab=99.70  E-value=5.8e-17  Score=88.68  Aligned_cols=47  Identities=30%  Similarity=0.588  Sum_probs=45.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSH  101 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  101 (156)
                      .+||++|.+|++.|++++|+++|++|++.|+.||..||+.+|++|++
T Consensus         4 ~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    4 VTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999999999999999999999999999999986

>PF13041 PPR_2: PPR repeat family

Probab=99.69  E-value=4.9e-17  Score=88.97  Aligned_cols=50  Identities=20%  Similarity=0.331  Sum_probs=48.2

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhh
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCN   52 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~   52 (156)
                      ||+.+||++|++|++.|++++|.++|++|.+.|++||..||++||++||+
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            89999999999999999999999999999999999999999999998875

>PF12854 PPR_1: PPR repeat

Probab=99.25  E-value=7.3e-12  Score=62.59  Aligned_cols=33  Identities=27%  Similarity=0.484  Sum_probs=31.9

Q ss_pred             CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           83 SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        83 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +|+.||.+|||+||+++++.|++++|.++|++|
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            589999999999999999999999999999998

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.20  E-value=2.6e-10  Score=86.22  Aligned_cols=136  Identities=18%  Similarity=0.110  Sum_probs=98.4

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-------------------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------------------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-------------------------------   54 (156)
                      .|=|.+++. ...|.+..+--+++.|.+.|+..+..+--.|++..+-.+                               
T Consensus       117 ~~E~nL~km-IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~v  195 (625)
T KOG4422|consen  117 ETENNLLKM-ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAV  195 (625)
T ss_pred             cchhHHHHH-HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccH
Confidence            344555554 567888899999999999998888888777776665444                               


Q ss_pred             ------------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccC
Q 041561           55 ------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVK  122 (156)
Q Consensus        55 ------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~  122 (156)
                                  .++.+||.+.|+--..+.|.+++++-.....+.+..+||.+|.+-+-..+    +++..+|....   
T Consensus       196 AdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqk---  268 (625)
T KOG4422|consen  196 ADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQK---  268 (625)
T ss_pred             HHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhh---
Confidence                        78999999999999999999998887776666777777777766543333    55666663331   


Q ss_pred             CCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          123 PKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       123 ~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                            ++||..|+|+++++.++.|+++.|++.
T Consensus       269 ------m~Pnl~TfNalL~c~akfg~F~~ar~a  295 (625)
T KOG4422|consen  269 ------MTPNLFTFNALLSCAAKFGKFEDARKA  295 (625)
T ss_pred             ------cCCchHhHHHHHHHHHHhcchHHHHHH
Confidence                  567777777777777777777666543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.19  E-value=1.7e-10  Score=87.10  Aligned_cols=122  Identities=16%  Similarity=0.137  Sum_probs=100.8

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      -+..||.++|.++++--..+.|.+++.+-.....+.+..+||.+|.+            ..|..      ..++..+|..
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~------------~S~~~------~K~Lv~EMis  266 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGA------------SSYSV------GKKLVAEMIS  266 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhH------------HHhhc------cHHHHHHHHH
Confidence            45689999999999999999999999998887788888666666542            22322      2788999999


Q ss_pred             CCCCccHHHHHHHHHhhcCCCchHHHH----HHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhH
Q 041561           83 SGVKHDGVTFVAILTPCSHSGLVYAEV----EIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRL  151 (156)
Q Consensus        83 ~g~~p~~~t~~~ll~~~~~~~~~~~a~----~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~  151 (156)
                      ..+.||..|||+++++.++.|+++.++    +++.+| ++.|        +.|...+|-.+|..+.+.+++.+
T Consensus       267 qkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~Em-KeiG--------VePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  267 QKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEM-KEIG--------VEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             hhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHH-HHhC--------CCcchhhHHHHHHHhcccCCchh
Confidence            999999999999999999999887755    677788 6666        79999999999999999998865

>PF12854 PPR_1: PPR repeat

Probab=99.17  E-value=3.8e-11  Score=59.98  Aligned_cols=34  Identities=32%  Similarity=0.687  Sum_probs=31.4

Q ss_pred             hCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561           34 DGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus        34 ~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      .|+.||.              .|||+||.+||+.|++++|.++|++|+
T Consensus         1 ~G~~Pd~--------------~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDV--------------VTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcH--------------hHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            4889999              888999999999999999999999984

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.15  E-value=1.5e-09  Score=82.67  Aligned_cols=139  Identities=8%  Similarity=-0.097  Sum_probs=74.9

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCch----HHHhHHHHHhhhcc--------------------chHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDI----FVGSAPINIYCNCG--------------------VTWNEM   60 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~~--------------------~~~~~l   60 (156)
                      ..++..+...+.+.|+.++|.+.++.+.+.+..++.    ..+..+...+.+.|                    ..+..+
T Consensus       141 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l  220 (389)
T PRK11788        141 EGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAADPQCVRASILL  220 (389)
T ss_pred             HHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHCcCCHHHHHHH
Confidence            345556666666666666666666666554322211    12233333444443                    344455


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHH
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLV  140 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li  140 (156)
                      ...|.+.|++++|.++|+++.+.+......+++.+..++.+.|+.++|...++.+..           ..|+...++.+.
T Consensus       221 a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~-----------~~p~~~~~~~la  289 (389)
T PRK11788        221 GDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALE-----------EYPGADLLLALA  289 (389)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----------hCCCchHHHHHH
Confidence            566666666666666666665433222234555666666666666666666666522           234545555666


Q ss_pred             HHHhhcCCHhHHhh
Q 041561          141 SSCQVHSNVRLAKK  154 (156)
Q Consensus       141 ~~~~~~g~~~~a~~  154 (156)
                      ..+.+.|++++|.+
T Consensus       290 ~~~~~~g~~~~A~~  303 (389)
T PRK11788        290 QLLEEQEGPEAAQA  303 (389)
T ss_pred             HHHHHhCCHHHHHH
Confidence            66666666666654

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.05  E-value=3.6e-10  Score=56.43  Aligned_cols=35  Identities=34%  Similarity=0.683  Sum_probs=33.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG   89 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   89 (156)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999984

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.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.98  E-value=3.4e-08  Score=75.14  Aligned_cols=109  Identities=8%  Similarity=0.035  Sum_probs=55.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc---hHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND---IFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~---~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      ++..+...+.+.|++++|..+++.+...+-.++   ...+..+...|.+.|                    .+++.+...
T Consensus        71 ~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~  150 (389)
T PRK11788         71 LHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEI  150 (389)
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHH
Confidence            455555555666666666666666555432111   234455555555544                    345555555


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccH----HHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDG----VTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +.+.|++++|.+.|+.+.+.+..++.    ..+..+...+.+.|++++|...|+++
T Consensus       151 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  206 (389)
T PRK11788        151 YQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKA  206 (389)
T ss_pred             HHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            55666666666666655544322211    12333444445555555555555555

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.94  E-value=2e-09  Score=53.51  Aligned_cols=33  Identities=24%  Similarity=0.460  Sum_probs=31.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      ++||++|.+|++.|+++.|.++|++|++.|++|
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            589999999999999999999999999999988

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.84  E-value=5.1e-09  Score=52.13  Aligned_cols=35  Identities=11%  Similarity=0.312  Sum_probs=33.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCch
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDI   40 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~   40 (156)
                      .|||++|++|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            48999999999999999999999999999999984

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

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.81  E-value=7.7e-09  Score=51.33  Aligned_cols=34  Identities=18%  Similarity=0.323  Sum_probs=32.4

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN   38 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~   38 (156)
                      +.||+++|.+|++.|+++.|.++|++|++.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            4689999999999999999999999999999988

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

Probab=98.81  E-value=7.7e-09  Score=50.19  Aligned_cols=31  Identities=29%  Similarity=0.672  Sum_probs=28.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ++||+||++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4799999999999999999999999998874

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.

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

Probab=98.79  E-value=3.2e-07  Score=75.68  Aligned_cols=58  Identities=9%  Similarity=-0.034  Sum_probs=23.4

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      |..+...+...|++++|.++++.+.+.+ .++...+..+...+.+.|++++|...+..+
T Consensus       672 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~  729 (899)
T TIGR02917       672 QIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKA  729 (899)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3344444444444444444444443332 122333333334444444444444444443

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

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

Probab=98.75  E-value=5.3e-08  Score=79.21  Aligned_cols=151  Identities=10%  Similarity=0.069  Sum_probs=116.5

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----------chHHHHHHHHHcCCCH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----------VTWNEMIHGYAENEYV   70 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----------~~~~~li~~~~~~g~~   70 (156)
                      +.|+-+||..+|..|+..|+++.|- +|..|.....+.+-..++.++.++.+.+          .+|++|+.+|..+||+
T Consensus        21 i~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll~ayr~hGDl   99 (1088)
T KOG4318|consen   21 ILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLLKAYRIHGDL   99 (1088)
T ss_pred             CCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHHHHHHHhccch
Confidence            4699999999999999999999999 9999988777777777888888877776          6788888888887774


Q ss_pred             H---HHHHHHHH--------------------------------------------------------------------
Q 041561           71 E---QAISLYKD--------------------------------------------------------------------   79 (156)
Q Consensus        71 ~---~a~~~~~~--------------------------------------------------------------------   79 (156)
                      .   .+.+.+..                                                                    
T Consensus       100 i~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa~~~p~~vfLr  179 (1088)
T KOG4318|consen  100 ILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLR  179 (1088)
T ss_pred             HHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCcccccchHHHHHH
Confidence            3   22221111                                                                    


Q ss_pred             --------------HHHCCC-CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC--------c-----------
Q 041561           80 --------------IIASGV-KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK--------C-----------  125 (156)
Q Consensus        80 --------------m~~~g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~--------c-----------  125 (156)
                                    |-+++. .||..+|.++++.-..+|+.+.|..++..| ++.|++-.        |           
T Consensus       180 qnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~em-ke~gfpir~HyFwpLl~g~~~~q~~e~v  258 (1088)
T KOG4318|consen  180 QNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEM-KEKGFPIRAHYFWPLLLGINAAQVFEFV  258 (1088)
T ss_pred             HhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHH-HHcCCCcccccchhhhhcCccchHHHHH
Confidence                          111112 489999999999999999999999999999 66666655        2           


Q ss_pred             -----CCCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561          126 -----LMPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus       126 -----~~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                           ..++.||..|+...+-.+..+|....+.
T Consensus       259 lrgmqe~gv~p~seT~adyvip~l~N~~t~~~~  291 (1088)
T KOG4318|consen  259 LRGMQEKGVQPGSETQADYVIPQLSNGQTKYGE  291 (1088)
T ss_pred             HHHHHHhcCCCCcchhHHHHHhhhcchhhhhcc
Confidence                 6678899999999888888877765543

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

Probab=98.74  E-value=7.6e-07  Score=73.49  Aligned_cols=136  Identities=10%  Similarity=-0.028  Sum_probs=79.4

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYA   65 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~   65 (156)
                      ..+..+...+.+.|+.++|..+++.+.+. .+.+...|..+...|.+.|                    ..|..+...+.
T Consensus       568 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  646 (899)
T TIGR02917       568 EPALALAQYYLGKGQLKKALAILNEAADA-APDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYA  646 (899)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            34445555666666666666666666543 2345556666666666555                    34556666666


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      +.|++++|.+.|+++.+.. ..+..++..+...+...|++++|.++++.+....          .++...|..+...+..
T Consensus       647 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~----------~~~~~~~~~~~~~~~~  715 (899)
T TIGR02917       647 VMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH----------PKAALGFELEGDLYLR  715 (899)
T ss_pred             HcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC----------cCChHHHHHHHHHHHH
Confidence            6777777777776665532 2235566666777777777777777777774331          2344445555555555


Q ss_pred             cCCHhHHh
Q 041561          146 HSNVRLAK  153 (156)
Q Consensus       146 ~g~~~~a~  153 (156)
                      .|++++|.
T Consensus       716 ~g~~~~A~  723 (899)
T TIGR02917       716 QKDYPAAI  723 (899)
T ss_pred             CCCHHHHH
Confidence            55555554

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.

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

Probab=98.55  E-value=1.1e-07  Score=45.99  Aligned_cols=31  Identities=10%  Similarity=0.315  Sum_probs=29.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGY   36 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~   36 (156)
                      +||+++|++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            5899999999999999999999999999875

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.

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

Probab=98.46  E-value=1.1e-06  Score=64.31  Aligned_cols=142  Identities=12%  Similarity=0.024  Sum_probs=71.3

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhC-CCCchHHHhHHHHHhhhcc--------------------chHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDG-YGNDIFVGSAPINIYCNCG--------------------VTWNEMI   61 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~~--------------------~~~~~li   61 (156)
                      +++..+...+..+.+.++.+.+..+++.+.+.. .++|...|..+-..+.+.|                    ...+.++
T Consensus       108 ~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~  187 (280)
T PF13429_consen  108 GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALA  187 (280)
T ss_dssp             ----------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHH
T ss_pred             cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            445566677777788888888888888876533 4566766666666666665                    3455666


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVS  141 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~  141 (156)
                      ..+...|+.+++.++++...+.. ..|...+..+-.++...|+.++|...++...+.          .+.|......+-.
T Consensus       188 ~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~----------~p~d~~~~~~~a~  256 (280)
T PF13429_consen  188 WLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKL----------NPDDPLWLLAYAD  256 (280)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH----------STT-HHHHHHHHH
T ss_pred             HHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccccccccccc----------ccccccccccccc
Confidence            66666666666666666655443 334445555666666666677777666666332          1235666666667


Q ss_pred             HHhhcCCHhHHhhh
Q 041561          142 SCQVHSNVRLAKKA  155 (156)
Q Consensus       142 ~~~~~g~~~~a~~~  155 (156)
                      ++...|+.++|.++
T Consensus       257 ~l~~~g~~~~A~~~  270 (280)
T PF13429_consen  257 ALEQAGRKDEALRL  270 (280)
T ss_dssp             HHT-----------
T ss_pred             cccccccccccccc
Confidence            77777777777654

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

Probab=98.44  E-value=3e-06  Score=59.26  Aligned_cols=104  Identities=14%  Similarity=0.100  Sum_probs=82.1

Q ss_pred             CcccHHHHHHHhc-----CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcC--CCHHHHHHH
Q 041561            4 TQFPFTTVLSSCA-----KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAEN--EYVEQAISL   76 (156)
Q Consensus         4 ~~~t~~~ll~~~~-----~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~--g~~~~a~~~   76 (156)
                      |-.+|..+++.+.     +.|.++-....+..|.+.|+.-|..+|+.||+.+=+....=.+++.+-..+  .+.+-|.++
T Consensus        46 ~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~l  125 (228)
T PF06239_consen   46 DKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDL  125 (228)
T ss_pred             cHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHH
Confidence            4456777777775     447788899999999999999999999999999998763222233332222  246779999


Q ss_pred             HHHHHHCCCCccHHHHHHHHHhhcCCCchHH
Q 041561           77 YKDIIASGVKHDGVTFVAILTPCSHSGLVYA  107 (156)
Q Consensus        77 ~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  107 (156)
                      +++|..+|+.||..|+..+++.+.+.+..-.
T Consensus       126 L~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~  156 (228)
T PF06239_consen  126 LEQMENNGVMPDKETEQMLLNIFGRKSHPMK  156 (228)
T ss_pred             HHHHHHcCCCCcHHHHHHHHHHhccccHHHH
Confidence            9999999999999999999999998775543

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.40  E-value=3.8e-05  Score=53.44  Aligned_cols=137  Identities=10%  Similarity=0.001  Sum_probs=71.8

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      .+..+-..+.+.|+.++|...+++..+.. +.+...+..+-..|...|                    ..+..+-..+..
T Consensus        33 ~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  111 (234)
T TIGR02521        33 IRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQ  111 (234)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHH
Confidence            34445555666666677776666665432 223444455555554444                    334445555666


Q ss_pred             CCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           67 NEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      .|++++|.+.|++.......| +...+..+-..+.+.|+.++|.+.++.....          ...+...|..+-..+..
T Consensus       112 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----------~~~~~~~~~~la~~~~~  181 (234)
T TIGR02521       112 QGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQI----------DPQRPESLLELAELYYL  181 (234)
T ss_pred             cccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CcCChHHHHHHHHHHHH
Confidence            666666666666665432111 2233444455555666666666666655322          11233445555555555


Q ss_pred             cCCHhHHhh
Q 041561          146 HSNVRLAKK  154 (156)
Q Consensus       146 ~g~~~~a~~  154 (156)
                      .|++++|.+
T Consensus       182 ~~~~~~A~~  190 (234)
T TIGR02521       182 RGQYKDARA  190 (234)
T ss_pred             cCCHHHHHH
Confidence            666655543

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.

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

Probab=98.39  E-value=2.6e-06  Score=53.55  Aligned_cols=87  Identities=10%  Similarity=0.190  Sum_probs=67.9

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      ..-|..|...++......+|..+++.|+ .|+..+|+.++.+-++...      +...-.+.+-+.+.+|+.|..++++|
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~l------D~~~ie~kl~~LLtvYqDiL~~~lKP  102 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKREL------DSEDIENKLTNLLTVYQDILSNKLKP  102 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccc------cchhHHHHHHHHHHHHHHHHHhccCC
Confidence            4456677777999999999999999999 8999777777766655441      00122223556889999999999999


Q ss_pred             cHHHHHHHHHhhcC
Q 041561           88 DGVTFVAILTPCSH  101 (156)
Q Consensus        88 ~~~t~~~ll~~~~~  101 (156)
                      +..||+.++..+.+
T Consensus       103 ~~etYnivl~~Llk  116 (120)
T PF08579_consen  103 NDETYNIVLGSLLK  116 (120)
T ss_pred             cHHHHHHHHHHHHH
Confidence            99999999998764

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 [, , ].

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.36  E-value=5.6e-05  Score=52.56  Aligned_cols=139  Identities=9%  Similarity=0.013  Sum_probs=105.6

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----------------------chHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----------------------VTWNEMIH   62 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----------------------~~~~~li~   62 (156)
                      ...+..+-..+...|+.++|.+.++...+..- .+...+..+-..|...|                      ..+..+-.
T Consensus        65 ~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~  143 (234)
T TIGR02521        65 YLAYLALALYYQQLGELEKAEDSFRRALTLNP-NNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGL  143 (234)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHH
Confidence            45566777788889999999999998877542 34455666666666655                      24556677


Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      .+...|++++|.+.|++..+... .+...+..+...+.+.|+.++|...+++....          ...+...+..+...
T Consensus       144 ~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~~~~~  212 (234)
T TIGR02521       144 CALKAGDFDKAEKYLTRALQIDP-QRPESLLELAELYYLRGQYKDARAYLERYQQT----------YNQTAESLWLGIRI  212 (234)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCc-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHH
Confidence            88899999999999999876532 24557778888889999999999999988433          13466777788899


Q ss_pred             HhhcCCHhHHhhh
Q 041561          143 CQVHSNVRLAKKA  155 (156)
Q Consensus       143 ~~~~g~~~~a~~~  155 (156)
                      +...|+.++|++.
T Consensus       213 ~~~~~~~~~a~~~  225 (234)
T TIGR02521       213 ARALGDVAAAQRY  225 (234)
T ss_pred             HHHHhhHHHHHHH
Confidence            9999999998764

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.

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

Probab=98.21  E-value=2e-05  Score=49.65  Aligned_cols=81  Identities=14%  Similarity=0.158  Sum_probs=65.8

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-CccHHHHHHHHHhhcCCC--------chHHHHHHHHhcccccccCCCcC
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGV-KHDGVTFVAILTPCSHSG--------LVYAEVEIFNSMEHDHEVKPKCL  126 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~m~~~~~~~~~c~  126 (156)
                      |-...|..+...+++.....+|+.++++|+ .|+..+|+.++++.++..        .+-+...+++.|... +      
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~-~------   99 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSN-K------   99 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHh-c------
Confidence            445567777778999999999999999999 999999999999988533        344566778888433 2      


Q ss_pred             CCCCCChhhHHHHHHHHhh
Q 041561          127 MPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus       127 ~~~~pd~~~~~~li~~~~~  145 (156)
                        ++|+..|||.+|....+
T Consensus       100 --lKP~~etYnivl~~Llk  116 (120)
T PF08579_consen  100 --LKPNDETYNIVLGSLLK  116 (120)
T ss_pred             --cCCcHHHHHHHHHHHHH
Confidence              89999999999988654

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

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

Probab=98.20  E-value=2e-05  Score=60.90  Aligned_cols=119  Identities=12%  Similarity=0.082  Sum_probs=90.3

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhC--CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDG--YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      ......++..+...-+++.++.++-..+...  ...-.              .|..++|+.|-+.|..++++++++.=..
T Consensus        66 ~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~--------------~t~ha~vR~~l~~~~~~~~l~~L~n~~~  131 (429)
T PF10037_consen   66 SLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLP--------------STHHALVRQCLELGAEDELLELLKNRLQ  131 (429)
T ss_pred             HHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccC--------------ccHHHHHHHHHhcCCHHHHHHHHhChhh
Confidence            3455666666666667777777777665431  11111              5667999999999999999999999888


Q ss_pred             CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc
Q 041561           83 SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH  146 (156)
Q Consensus        83 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~  146 (156)
                      -|+-||.+|||.+++.+.+.|++..|.++...|..+-         ...+..|+.--+.+|.+.
T Consensus       132 yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe---------~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  132 YGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQE---------EFDNPSTQALALYSCYKY  186 (429)
T ss_pred             cccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhh---------ccCCchHHHHHHHHHHHh
Confidence            9999999999999999999999999999999885442         234556666666666554

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 [].

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

Probab=98.18  E-value=7.2e-06  Score=60.06  Aligned_cols=87  Identities=15%  Similarity=0.124  Sum_probs=47.7

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      .|..+-..+.+.|+.++|.+.|++..+.  .| |....+.++..+...|+.+++.+++....+.          ...|..
T Consensus       148 ~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~----------~~~~~~  215 (280)
T PF13429_consen  148 FWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKA----------APDDPD  215 (280)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-----------HTSCC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHH----------CcCHHH
Confidence            3444455555566666666666665542  33 2444555566666666666666666655333          234555


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                      .|..+-.+|...|+.++|..
T Consensus       216 ~~~~la~~~~~lg~~~~Al~  235 (280)
T PF13429_consen  216 LWDALAAAYLQLGRYEEALE  235 (280)
T ss_dssp             HCHHHHHHHHHHT-HHHHHH
T ss_pred             HHHHHHHHhccccccccccc
Confidence            66666666666666666654

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

Probab=98.10  E-value=4.4e-05  Score=56.17  Aligned_cols=126  Identities=11%  Similarity=0.161  Sum_probs=93.9

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhC-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDG-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      .+|..+|+..-|.+.++.|+++|.+..+.+ ....++...++|.               |...++.+.|.++|+...+. 
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E---------------~~~~~d~~~A~~Ife~glk~-   65 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALME---------------YYCNKDPKRARKIFERGLKK-   65 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHH---------------HHTCS-HHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHH---------------HHhCCCHHHHHHHHHHHHHH-
Confidence            578899999999999999999999998654 3456655555543               23356777799999998765 


Q ss_pred             CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           85 VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        85 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +..+...|...++.+.+.++.+.++.+|+.......        -.. -...|..+|+--.+.|+.+...+|
T Consensus        66 f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~--------~~~~~~~iw~~~i~fE~~~Gdl~~v~~v  129 (280)
T PF05843_consen   66 FPSDPDFWLEYLDFLIKLNDINNARALFERAISSLP--------KEKQSKKIWKKFIEFESKYGDLESVRKV  129 (280)
T ss_dssp             HTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSS--------CHHHCHHHHHHHHHHHHHHS-HHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcC--------chhHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            455677888999999999999999999999854411        122 335999999999999999877664

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.04  E-value=0.00036  Score=57.22  Aligned_cols=58  Identities=14%  Similarity=0.050  Sum_probs=24.1

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +..+-..+...|++++|...+++..+.... +...+..+-..+.+.|++++|.+.++.+
T Consensus       287 ~~~lg~~l~~~g~~~eA~~~l~~al~l~P~-~~~a~~~La~~l~~~G~~~eA~~~l~~a  344 (656)
T PRK15174        287 VTLYADALIRTGQNEKAIPLLQQSLATHPD-LPYVRAMYARALRQVGQYTAASDEFVQL  344 (656)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            334444444444444444444444432111 1222333344444445555555444444

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

Probab=97.98  E-value=3.9e-05  Score=59.30  Aligned_cols=83  Identities=12%  Similarity=0.145  Sum_probs=76.9

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      .|..++++.|.+.|..+.+..++..=.+.|+=||.              .+||.||+.+.+.|++..|.++..+|...+.
T Consensus       104 ~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~--------------~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~  169 (429)
T PF10037_consen  104 STHHALVRQCLELGAEDELLELLKNRLQYGIFPDN--------------FSFNLLMDHFLKKGNYKSAAKVATEMMLQEE  169 (429)
T ss_pred             ccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCCh--------------hhHHHHHHHHhhcccHHHHHHHHHHHHHhhc
Confidence            46689999999999999999999999999999999              8888889999999999999999999999888


Q ss_pred             CccHHHHHHHHHhhcCC
Q 041561           86 KHDGVTFVAILTPCSHS  102 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~  102 (156)
                      ..+..|+...+.+|.+-
T Consensus       170 ~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  170 FDNPSTQALALYSCYKY  186 (429)
T ss_pred             cCCchHHHHHHHHHHHh
Confidence            88889998888888776

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

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

Probab=97.93  E-value=0.00015  Score=50.95  Aligned_cols=88  Identities=16%  Similarity=0.126  Sum_probs=71.4

Q ss_pred             chHHHHHHHHH-----cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCC----------------chHHHHHHHH
Q 041561           55 VTWNEMIHGYA-----ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG----------------LVYAEVEIFN  113 (156)
Q Consensus        55 ~~~~~li~~~~-----~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~----------------~~~~a~~~~~  113 (156)
                      .+|..+++.|.     ++|.++=...-++.|.+-|+.-|..+|+.||+.+=+..                +-+-|.++++
T Consensus        48 ~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~  127 (228)
T PF06239_consen   48 ATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLE  127 (228)
T ss_pred             HHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHH
Confidence            34444444444     56788888889999999999999999999999886633                5667889999


Q ss_pred             hcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhH
Q 041561          114 SMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRL  151 (156)
Q Consensus       114 ~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~  151 (156)
                      +| +++|        +-||..|+..+++.|.+.+.+-+
T Consensus       128 qM-E~~g--------V~Pd~Et~~~ll~iFG~~s~p~~  156 (228)
T PF06239_consen  128 QM-ENNG--------VMPDKETEQMLLNIFGRKSHPMK  156 (228)
T ss_pred             HH-HHcC--------CCCcHHHHHHHHHHhccccHHHH
Confidence            99 7887        68999999999999999887643

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

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=97.91  E-value=0.00084  Score=55.11  Aligned_cols=100  Identities=8%  Similarity=-0.087  Sum_probs=45.7

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQ   72 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~   72 (156)
                      .+....|+.+.|...++.+.+.. +.+...+..+-..+.+.|                    ..|..+...+...|++++
T Consensus        84 ~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~e  162 (656)
T PRK15174         84 ISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQ  162 (656)
T ss_pred             hhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHH
Confidence            33344555555555555554431 112333444444444444                    344555555555566666


Q ss_pred             HHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           73 AISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        73 a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      |...++.+......+....++ + ..+.+.|++++|..+++.+
T Consensus       163 A~~~~~~~~~~~P~~~~a~~~-~-~~l~~~g~~~eA~~~~~~~  203 (656)
T PRK15174        163 AISLARTQAQEVPPRGDMIAT-C-LSFLNKSRLPEDHDLARAL  203 (656)
T ss_pred             HHHHHHHHHHhCCCCHHHHHH-H-HHHHHcCCHHHHHHHHHHH
Confidence            655555554432222222111 1 1234455555555555554

>PRK12370 invasion protein regulator; Provisional

Probab=97.89  E-value=0.00083  Score=54.04  Aligned_cols=108  Identities=8%  Similarity=-0.092  Sum_probs=58.2

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYA   65 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~   65 (156)
                      ..+..+-..+...|+.++|...+++..+.. +.+...+..+-..|...|                    ..+..+...+.
T Consensus       339 ~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~  417 (553)
T PRK12370        339 QALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITY  417 (553)
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHH
Confidence            344455555667788888888888877653 223444444444455544                    11222333344


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           66 ENEYVEQAISLYKDIIASGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ..|++++|.+.+++..+.. .|+ ...+..+-.++...|+.++|.+.+..+
T Consensus       418 ~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~  467 (553)
T PRK12370        418 YHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEI  467 (553)
T ss_pred             hccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHh
Confidence            5566666666666654432 222 223344444555666666666666655

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

Probab=97.87  E-value=4.8e-05  Score=62.63  Aligned_cols=90  Identities=13%  Similarity=0.135  Sum_probs=79.4

Q ss_pred             CCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561            2 YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus         2 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      .||+.+|..++++-.-+|+++.|..++.+|++.|++-+.              +-|.-||-+   .+....+..+.+.|.
T Consensus       201 ~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~--------------HyFwpLl~g---~~~~q~~e~vlrgmq  263 (1088)
T KOG4318|consen  201 APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRA--------------HYFWPLLLG---INAAQVFEFVLRGMQ  263 (1088)
T ss_pred             CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCccc--------------ccchhhhhc---CccchHHHHHHHHHH
Confidence            389999999999999999999999999999999998888              666666655   888899999999999


Q ss_pred             HCCCCccHHHHHHHHHhhcCCCchHHH
Q 041561           82 ASGVKHDGVTFVAILTPCSHSGLVYAE  108 (156)
Q Consensus        82 ~~g~~p~~~t~~~ll~~~~~~~~~~~a  108 (156)
                      +.|+.|+..|+.-.+-.+..+|....+
T Consensus       264 e~gv~p~seT~adyvip~l~N~~t~~~  290 (1088)
T KOG4318|consen  264 EKGVQPGSETQADYVIPQLSNGQTKYG  290 (1088)
T ss_pred             HhcCCCCcchhHHHHHhhhcchhhhhc
Confidence            999999999999999988886664433

>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=97.86  E-value=0.0011  Score=53.94  Aligned_cols=135  Identities=7%  Similarity=-0.062  Sum_probs=93.6

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc-hHHHhHHHHHhhhcc--------------------chHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND-IFVGSAPINIYCNCG--------------------VTWNEMIHGYA   65 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~~--------------------~~~~~li~~~~   65 (156)
                      .|..+-..+...|+.++|...++...+.  .|+ ...|..+-..|...|                    ..|..+-..+.
T Consensus       333 a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~  410 (615)
T TIGR00990       333 ALNLRGTFKCLKGKHLEALADLSKSIEL--DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHF  410 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            3444555556678888888888877654  243 335555555555444                    56677777888


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      ..|++++|.+.|++..+... .+...+..+-..+.+.|++++|...|+.....          ...+...|+.+-..+..
T Consensus       411 ~~g~~~~A~~~~~kal~l~P-~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~----------~P~~~~~~~~lg~~~~~  479 (615)
T TIGR00990       411 IKGEFAQAGKDYQKSIDLDP-DFIFSHIQLGVTQYKEGSIASSMATFRRCKKN----------FPEAPDVYNYYGELLLD  479 (615)
T ss_pred             HcCCHHHHHHHHHHHHHcCc-cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----------CCCChHHHHHHHHHHHH
Confidence            88888888888888776431 23455666667777888999999888887433          22356778888888999


Q ss_pred             cCCHhHHhh
Q 041561          146 HSNVRLAKK  154 (156)
Q Consensus       146 ~g~~~~a~~  154 (156)
                      .|++++|.+
T Consensus       480 ~g~~~~A~~  488 (615)
T TIGR00990       480 QNKFDEAIE  488 (615)
T ss_pred             ccCHHHHHH
Confidence            999998865

>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=97.78  E-value=0.0011  Score=51.04  Aligned_cols=116  Identities=11%  Similarity=0.029  Sum_probs=89.0

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      .++++.+...++++.|..+++++.+..  |++                .-.|.+.+...++-.+|.++.++..+.. .-|
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev----------------~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d  233 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRERD--PEV----------------AVLLARVYLLMNEEVEAIRLLNEALKEN-PQD  233 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhcC--CcH----------------HHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCC
Confidence            456777778899999999999998865  443                2335566666777888999888887542 224


Q ss_pred             HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh-hhHHHHHHHHhhcCCHhHHhh
Q 041561           89 GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL-VVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        89 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~-~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ......-.+.|.+.++.+.|..+.++.. +          +.|+. .+|..|..+|...|+++.|..
T Consensus       234 ~~LL~~Qa~fLl~k~~~~lAL~iAk~av-~----------lsP~~f~~W~~La~~Yi~~~d~e~ALl  289 (395)
T PF09295_consen  234 SELLNLQAEFLLSKKKYELALEIAKKAV-E----------LSPSEFETWYQLAECYIQLGDFENALL  289 (395)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH-H----------hCchhHHHHHHHHHHHHhcCCHHHHHH
Confidence            5566666677889999999999999884 3          45655 599999999999999999974

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

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.76  E-value=0.0011  Score=51.24  Aligned_cols=119  Identities=11%  Similarity=-0.029  Sum_probs=84.8

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      .........+.+.|+.++|.++++...+.  .||..                -.++.+....++++++.+..+...+.  
T Consensus       264 ~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~----------------l~~l~~~l~~~~~~~al~~~e~~lk~--  323 (398)
T PRK10747        264 ALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER----------------LVLLIPRLKTNNPEQLEKVLRQQIKQ--  323 (398)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH----------------HHHHHhhccCCChHHHHHHHHHHHhh--
Confidence            34444555555666666666666555442  22221                11234444568999999999998864  


Q ss_pred             CccHH-HHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           86 KHDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        86 ~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|+.. ...++=+.|.+.+++++|++.|+...+           ..|+..+|..|-..+.+.|+.++|.+.
T Consensus       324 ~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~-----------~~P~~~~~~~La~~~~~~g~~~~A~~~  383 (398)
T PRK10747        324 HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALK-----------QRPDAYDYAWLADALDRLHKPEEAAAM  383 (398)
T ss_pred             CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-----------cCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            44444 566777888899999999999999843           479999999999999999999999763

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

Probab=97.71  E-value=0.0028  Score=48.10  Aligned_cols=141  Identities=9%  Similarity=0.002  Sum_probs=100.7

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCch-------HHHhHHHHHhhhcc--------------------ch
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDI-------FVGSAPINIYCNCG--------------------VT   56 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~-------~~~~~li~~~~~~~--------------------~~   56 (156)
                      ++.......++|.+.|++..+..+...|.+.|+-.|.       .+|+.+++-....+                    ..
T Consensus       186 ~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l  265 (400)
T COG3071         186 HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPEL  265 (400)
T ss_pred             ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhH
Confidence            3456677889999999999999999999999976655       56777776655544                    23


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH------------------------------HHHHHHHHhhcCCCchH
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDG------------------------------VTFVAILTPCSHSGLVY  106 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~------------------------------~t~~~ll~~~~~~~~~~  106 (156)
                      -.+++.-+.++|+.++|.++..+-.+++..|+.                              -.+.++=.-|.+.+.+.
T Consensus       266 ~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~  345 (400)
T COG3071         266 VVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWG  345 (400)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHH
Confidence            355677778888888888887776655544431                              23333444444555555


Q ss_pred             HHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          107 AEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       107 ~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +|...|+.-           ...+|+..+|+-+=.+|.+.|++++|.++
T Consensus       346 kA~~~leaA-----------l~~~~s~~~~~~la~~~~~~g~~~~A~~~  383 (400)
T COG3071         346 KASEALEAA-----------LKLRPSASDYAELADALDQLGEPEEAEQV  383 (400)
T ss_pred             HHHHHHHHH-----------HhcCCChhhHHHHHHHHHHcCChHHHHHH
Confidence            555555533           34689999999999999999999998764

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=97.70  E-value=0.00024  Score=46.03  Aligned_cols=65  Identities=15%  Similarity=0.083  Sum_probs=53.2

Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC---------cCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK---------CLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~---------c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      |+.++.++|-++++.|+++....+.+..   .||..+         .+++..|+..+..+++.+|+.+|++..|.++
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~---WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~   74 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSV---WGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKL   74 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHh---cCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHH
Confidence            5677888888889999988888887644   444433         2677899999999999999999999999886

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

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=97.66  E-value=0.0032  Score=53.92  Aligned_cols=46  Identities=17%  Similarity=0.036  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           68 EYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      |++++|...|++..+.  .|+...+..+-..+.+.|+.++|...++..
T Consensus       590 Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~A  635 (987)
T PRK09782        590 GQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAA  635 (987)
T ss_pred             CCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            5555555555555442  234445555555555555555555555554

>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=97.66  E-value=0.0036  Score=50.98  Aligned_cols=146  Identities=10%  Similarity=0.014  Sum_probs=73.3

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      +|..+-..+...|++++|...|+...+.. +.+..+|..+-..|...|                    ..|..+-..+.+
T Consensus       367 ~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~  445 (615)
T TIGR00990       367 SYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYK  445 (615)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHH
Confidence            44444555556666666666666654432 223445555555555544                    233444445555


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccc-cccCC---C------------------
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD-HEVKP---K------------------  124 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-~~~~~---~------------------  124 (156)
                      .|++++|...|++..+.. .-+...++.+-..+...|++++|...|+.-... ....+   +                  
T Consensus       446 ~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~  524 (615)
T TIGR00990       446 EGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDF  524 (615)
T ss_pred             CCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhH
Confidence            555555555555554321 112334444444555555555555554442111 00000   0                  


Q ss_pred             ------c--CCCCCC-ChhhHHHHHHHHhhcCCHhHHhh
Q 041561          125 ------C--LMPYKD-DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       125 ------c--~~~~~p-d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                            |  .....| +...+..+-..+...|++++|.+
T Consensus       525 ~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~  563 (615)
T TIGR00990       525 IEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALK  563 (615)
T ss_pred             HHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHH
Confidence                  0  011223 44568888889999999988865

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.64  E-value=0.0041  Score=48.07  Aligned_cols=129  Identities=5%  Similarity=0.019  Sum_probs=78.2

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHh--HHHHHhhhcc--------------------chHHHHHHHHHcCCCHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGS--APINIYCNCG--------------------VTWNEMIHGYAENEYVEQ   72 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~--~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~   72 (156)
                      ..+.|+.+.+...+.++.+.  .|+....-  .....+...|                    .....+...|.+.|++++
T Consensus       128 A~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~  205 (398)
T PRK10747        128 AQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSS  205 (398)
T ss_pred             HHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHH
Confidence            35667777777777777553  34443222  2223344344                    455667777777777777


Q ss_pred             HHHHHHHHHHCCCCccH-------HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           73 AISLYKDIIASGVKHDG-------VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        73 a~~~~~~m~~~g~~p~~-------~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      +.+++..+.+.+..++.       .+|..++....+..+.+...++++.+.++          .+.+......+..++..
T Consensus       206 a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~----------~~~~~~~~~~~A~~l~~  275 (398)
T PRK10747        206 LLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRK----------TRHQVALQVAMAEHLIE  275 (398)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHH----------HhCCHHHHHHHHHHHHH
Confidence            77777777776544322       13333344434444555566666666443          34577778888888888


Q ss_pred             cCCHhHHhhh
Q 041561          146 HSNVRLAKKA  155 (156)
Q Consensus       146 ~g~~~~a~~~  155 (156)
                      .|+.++|.++
T Consensus       276 ~g~~~~A~~~  285 (398)
T PRK10747        276 CDDHDTAQQI  285 (398)
T ss_pred             CCCHHHHHHH
Confidence            8888888764

>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=97.64  E-value=0.0017  Score=48.12  Aligned_cols=88  Identities=8%  Similarity=0.033  Sum_probs=63.1

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHH----HHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAI----LTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l----l~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      +.....+..|.+.++++.|.+.++.|.+..  .|. +...+    ++.......+.+|..+|+++..+          ..
T Consensus       132 E~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~-~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~----------~~  198 (290)
T PF04733_consen  132 ELLALAVQILLKMNRPDLAEKELKNMQQID--EDS-ILTQLAEAWVNLATGGEKYQDAFYIFEELSDK----------FG  198 (290)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCH-HHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC----------S-
T ss_pred             cHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcH-HHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc----------cC
Confidence            555667888999999999999999998642  333 33333    33333345799999999999554          45


Q ss_pred             CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          131 DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       131 pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ++..+.|.+..+....|++++|+++
T Consensus       199 ~t~~~lng~A~~~l~~~~~~eAe~~  223 (290)
T PF04733_consen  199 STPKLLNGLAVCHLQLGHYEEAEEL  223 (290)
T ss_dssp             -SHHHHHHHHHHHHHCT-HHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            7888899999999999999999864

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.

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=97.62  E-value=0.0049  Score=52.83  Aligned_cols=139  Identities=12%  Similarity=0.005  Sum_probs=97.0

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-------------------chHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------------------VTWNEMIHGY   64 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-------------------~~~~~li~~~   64 (156)
                      +...+..+-..+.+.|+.+.|.+.+....+.. +++...+..+.....+.|                   ..|..+-..+
T Consensus       541 ~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l  619 (987)
T PRK09782        541 SNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIY  619 (987)
T ss_pred             CcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            33344445556677788888888888776654 122222222222221123                   4677778889


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccH-HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      .+.|++++|.+.|++..+.  .|+. ..++.+-.++...|+.++|...++...+.          ..-+...+..+=.++
T Consensus       620 ~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l----------~P~~~~a~~nLA~al  687 (987)
T PRK09782        620 RQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREMLERAHKG----------LPDDPALIRQLAYVN  687 (987)
T ss_pred             HHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHHH
Confidence            9999999999999998874  4444 45666667888999999999999988443          123667888999999


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ...|++++|++.
T Consensus       688 ~~lGd~~eA~~~  699 (987)
T PRK09782        688 QRLDDMAATQHY  699 (987)
T ss_pred             HHCCCHHHHHHH
Confidence            999999998753

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=97.59  E-value=0.00049  Score=44.60  Aligned_cols=99  Identities=8%  Similarity=0.063  Sum_probs=62.8

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      |..++..+|-++++.|+++..+.+.+..  .|+.++..                       ...+.         --..+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~--WgI~~~~~-----------------------~~~~~---------~~~~s   46 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSV--WGIDVNGK-----------------------KKEGD---------YPPSS   46 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHh--cCCCCCCc-----------------------cccCc---------cCCCC
Confidence            3456677777777777777766666432  34333320                       01111         11124


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHh
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQ  144 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~  144 (156)
                      ...|+..+..+++.+++..+++..|.++.+.+.+.++        +.-+..+|..|++=.-
T Consensus        47 pl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~--------I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   47 PLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYP--------IPIPKEFWRRLLEWAY   99 (126)
T ss_pred             CCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcC--------CCCCHHHHHHHHHHHH
Confidence            5778888888888888888888888888888877776        3445777777775443

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

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

Probab=97.58  E-value=0.00093  Score=48.97  Aligned_cols=87  Identities=13%  Similarity=0.072  Sum_probs=72.4

Q ss_pred             CchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-chHHHHHHHHHcCCC-HHHHHHHHHHHHHCCCCccHHHHHHHH
Q 041561           19 SSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-VTWNEMIHGYAENEY-VEQAISLYKDIIASGVKHDGVTFVAIL   96 (156)
Q Consensus        19 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~t~~~ll   96 (156)
                      +.++-....+..|.+.|+..|..+|+.||+.+=+.. ..-|.+-..|.+.-+ -+=+.+++++|...|+.||..+--.++
T Consensus        86 ~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lv  165 (406)
T KOG3941|consen   86 THVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILV  165 (406)
T ss_pred             chHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHH
Confidence            557777788889999999999999999999999988 445555555665543 345789999999999999999999999


Q ss_pred             HhhcCCCch
Q 041561           97 TPCSHSGLV  105 (156)
Q Consensus        97 ~~~~~~~~~  105 (156)
                      +++.+.+-.
T Consensus       166 n~FGr~~~p  174 (406)
T KOG3941|consen  166 NAFGRWNFP  174 (406)
T ss_pred             HHhcccccc
Confidence            999987744

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

Probab=97.55  E-value=0.00084  Score=39.25  Aligned_cols=89  Identities=10%  Similarity=0.049  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .|..+...+...|++++|.+.|++..+... .+...+..+...+...++.++|.+.++.....          ...+..+
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~----------~~~~~~~   70 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDP-DNADAYYNLAAAYYKLGKYEEALEDYEKALEL----------DPDNAKA   70 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC----------CCcchhH
Confidence            355667778889999999999999876532 23366777888888899999999999987433          2335568


Q ss_pred             HHHHHHHHhhcCCHhHHhhh
Q 041561          136 WGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~~  155 (156)
                      +..+...+...|+.++|.+.
T Consensus        71 ~~~~~~~~~~~~~~~~a~~~   90 (100)
T cd00189          71 YYNLGLAYYKLGKYEEALEA   90 (100)
T ss_pred             HHHHHHHHHHHHhHHHHHHH
Confidence            88888999999999988753

>TIGR00540 hemY_coli hemY protein

Probab=97.55  E-value=0.005  Score=47.72  Aligned_cols=143  Identities=9%  Similarity=-0.043  Sum_probs=88.6

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHH-------HhHHHHHhhhc-c-------------------ch
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFV-------GSAPINIYCNC-G-------------------VT   56 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~-------~~~li~~~~~~-~-------------------~~   56 (156)
                      ++.....+...+.+.|+++.|.+++..+.+.++.+....       +..++..-... +                   ..
T Consensus       186 ~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l  265 (409)
T TIGR00540       186 HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIAL  265 (409)
T ss_pred             CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHH
Confidence            345677888889999999999999999998876443322       22222111110 1                   34


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCC----------------------------------CCccHH---HHHHHHHhh
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASG----------------------------------VKHDGV---TFVAILTPC   99 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g----------------------------------~~p~~~---t~~~ll~~~   99 (156)
                      +-.+...+...|+.++|.+++++..+..                                  ..|+..   ...++=..+
T Consensus       266 ~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~  345 (409)
T TIGR00540       266 KIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLL  345 (409)
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHH
Confidence            5556667777777777777776655431                                  123332   222444555


Q ss_pred             cCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          100 SHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       100 ~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+.|++++|++.|+... ..        ...||...+..+-..+-+.|+.++|.++
T Consensus       346 ~~~~~~~~A~~~le~a~-a~--------~~~p~~~~~~~La~ll~~~g~~~~A~~~  392 (409)
T TIGR00540       346 MKHGEFIEAADAFKNVA-AC--------KEQLDANDLAMAADAFDQAGDKAEAAAM  392 (409)
T ss_pred             HHcccHHHHHHHHHHhH-Hh--------hcCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            56777777777777310 00        1367888888888888888888888754

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.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.55  E-value=0.0016  Score=51.71  Aligned_cols=146  Identities=12%  Similarity=0.117  Sum_probs=99.9

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHH---h--CC-CCchHHHhH-HHHHhhhcc------------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVK---D--GY-GNDIFVGSA-PINIYCNCG------------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~---~--g~-~~~~~~~~~-li~~~~~~~------------------------   54 (156)
                      .+++-|-.+|.+.|++++|+..++...+   .  |. .|.+..... +...++.-+                        
T Consensus       284 ~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~  363 (508)
T KOG1840|consen  284 ATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDN  363 (508)
T ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccc
Confidence            3555556678899999999888887543   1  21 233322222 222222222                        


Q ss_pred             ----chHHHHHHHHHcCCCHHHHHHHHHHHHHC----C--CCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCC
Q 041561           55 ----VTWNEMIHGYAENEYVEQAISLYKDIIAS----G--VKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKP  123 (156)
Q Consensus        55 ----~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g--~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~  123 (156)
                          .+++.|-..|-+.|++++|.++|++....    +  ..+. ...++-|-.+|.+.++.++|.++|.+-. .  |..
T Consensus       364 ~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~-~--i~~  440 (508)
T KOG1840|consen  364 VNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAK-D--IMK  440 (508)
T ss_pred             hHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHH-H--HHH
Confidence                68899999999999999999999987531    1  2222 4567778888899999999999988652 1  112


Q ss_pred             CcCCCCCCC-hhhHHHHHHHHhhcCCHhHHhhh
Q 041561          124 KCLMPYKDD-LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       124 ~c~~~~~pd-~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|+.. .|| ..+|.-|...|.+.|++|.|.++
T Consensus       441 ~~g~~-~~~~~~~~~nL~~~Y~~~g~~e~a~~~  472 (508)
T KOG1840|consen  441 LCGPD-HPDVTYTYLNLAALYRAQGNYEAAEEL  472 (508)
T ss_pred             HhCCC-CCchHHHHHHHHHHHHHcccHHHHHHH
Confidence            22232 344 47799999999999999999886

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

Probab=97.49  E-value=0.012  Score=38.91  Aligned_cols=125  Identities=9%  Similarity=0.023  Sum_probs=86.3

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .|..++... ..++...+...++.+.+..- .+.+  ..+         ..=.+-..+...|++++|...|+........
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~-~s~y--a~~---------A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d   80 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDYP-SSPY--AAL---------AALQLAKAAYEQGDYDEAKAALEKALANAPD   80 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHCC-CChH--HHH---------HHHHHHHHHHHCCCHHHHHHHHHHHHhhCCC
Confidence            455666666 47788888888888877532 1211  111         1123457788899999999999999987644


Q ss_pred             ccHH--HHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           87 HDGV--TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        87 p~~~--t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      |+..  ..-.+-..+...|++++|...++.....           ......+...=..|.+.|+.++|+..
T Consensus        81 ~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~-----------~~~~~~~~~~Gdi~~~~g~~~~A~~~  140 (145)
T PF09976_consen   81 PELKPLARLRLARILLQQGQYDEALATLQQIPDE-----------AFKALAAELLGDIYLAQGDYDEARAA  140 (145)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCc-----------chHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4322  3444667788899999999999876321           23445566666899999999999863

>PRK12370 invasion protein regulator; Provisional

Probab=97.46  E-value=0.007  Score=48.80  Aligned_cols=127  Identities=9%  Similarity=-0.051  Sum_probs=86.7

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQAISL   76 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a~~~   76 (156)
                      ..++.++|...++...+.. +-+...+..+-..+...|                    ..|..+-..+...|++++|.+.
T Consensus       316 ~~~~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~  394 (553)
T PRK12370        316 KQNAMIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQT  394 (553)
T ss_pred             cchHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            3456788999999887753 225555665555555555                    4677788889999999999999


Q ss_pred             HHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-hhhHHHHHHHHhhcCCHhHHhhh
Q 041561           77 YKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        77 ~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +++..+-...+.. .+..+...+...|++++|...+++....          ..|+ ...+..+-..+...|+.++|++.
T Consensus       395 ~~~Al~l~P~~~~-~~~~~~~~~~~~g~~eeA~~~~~~~l~~----------~~p~~~~~~~~la~~l~~~G~~~eA~~~  463 (553)
T PRK12370        395 INECLKLDPTRAA-AGITKLWITYYHTGIDDAIRLGDELRSQ----------HLQDNPILLSMQVMFLSLKGKHELARKL  463 (553)
T ss_pred             HHHHHhcCCCChh-hHHHHHHHHHhccCHHHHHHHHHHHHHh----------ccccCHHHHHHHHHHHHhCCCHHHHHHH
Confidence            9998875333212 2223344455678899999999887433          1343 34466666778889999999864

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

Probab=97.44  E-value=0.001  Score=37.79  Aligned_cols=64  Identities=11%  Similarity=0.128  Sum_probs=49.9

Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHH
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLV  140 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li  140 (156)
                      ...|++++|.++|++....... |......+..+|.+.|++++|..+++.+...           .||...|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~-----------~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPD-NPEARLLLAQCYLKQGQYDEAEELLERLLKQ-----------DPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTT-SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG-----------GTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-----------CcCHHHHHHHH
Confidence            4678999999999999876433 5566668999999999999999999999544           57755555554

...

>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=97.38  E-value=0.0051  Score=45.58  Aligned_cols=120  Identities=8%  Similarity=0.051  Sum_probs=79.5

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ......+..+.+.++++.|.+.++.|.+.  ..|....+..           .+.+..+.-.+.+.+|..+|+++.+. .
T Consensus       132 E~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~eD~~l~qLa-----------~awv~l~~g~e~~~~A~y~f~El~~~-~  197 (290)
T PF04733_consen  132 ELLALAVQILLKMNRPDLAEKELKNMQQI--DEDSILTQLA-----------EAWVNLATGGEKYQDAFYIFEELSDK-F  197 (290)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHCC--SCCHHHHHHH-----------HHHHHHHHTTTCCCHHHHHHHHHHCC-S
T ss_pred             cHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHHHHHHH-----------HHHHHHHhCchhHHHHHHHHHHHHhc-c
Confidence            34456778888889999999999998764  3454332221           22233333345689999999998654 5


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                      .++..+.|.+.-++...|++++|.+++.+-....          .-|..+..-+|-.....|+.
T Consensus       198 ~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~----------~~~~d~LaNliv~~~~~gk~  251 (290)
T PF04733_consen  198 GSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD----------PNDPDTLANLIVCSLHLGKP  251 (290)
T ss_dssp             --SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-----------CCHHHHHHHHHHHHHHTT-T
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc----------cCCHHHHHHHHHHHHHhCCC
Confidence            6788889999999999999999999988763331          23455555567666677766

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.

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

Probab=97.32  E-value=0.01  Score=42.83  Aligned_cols=121  Identities=11%  Similarity=0.024  Sum_probs=91.4

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS-GVKH   87 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p   87 (156)
                      +.......+.|++..|...+.+...- -++|+              ..||.+=.+|.+.|++++|..-|.+..+- +-. 
T Consensus       104 ~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~--------------~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~-  167 (257)
T COG5010         104 AAQGKNQIRNGNFGEAVSVLRKAARL-APTDW--------------EAWNLLGAALDQLGRFDEARRAYRQALELAPNE-  167 (257)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHhcc-CCCCh--------------hhhhHHHHHHHHccChhHHHHHHHHHHHhccCC-
Confidence            44677788899999999999988653 35677              77888888899999999999888887662 222 


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhhC
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~~  156 (156)
                       ....|.+--.+.-.|+.+.|+.++..-...          -.-|...=.-+.......|++++|+.++
T Consensus       168 -p~~~nNlgms~~L~gd~~~A~~lll~a~l~----------~~ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         168 -PSIANNLGMSLLLRGDLEDAETLLLPAYLS----------PAADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             -chhhhhHHHHHHHcCCHHHHHHHHHHHHhC----------CCCchHHHHHHHHHHhhcCChHHHHhhc
Confidence             234555555666789999999998877332          2347777777888889999999998875

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.31  E-value=0.012  Score=49.25  Aligned_cols=130  Identities=10%  Similarity=-0.058  Sum_probs=81.3

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCC-Cc-hHHHhHHHHHhhhcc------------------------chHHHHHHHHHcC
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYG-ND-IFVGSAPINIYCNCG------------------------VTWNEMIHGYAEN   67 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~-~~-~~~~~~li~~~~~~~------------------------~~~~~li~~~~~~   67 (156)
                      ++...|+.++|...|+.+.+.+-. |+ ...+  +-..|...|                        .....+..++...
T Consensus       246 ~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~--la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~  323 (765)
T PRK10049        246 ALLARDRYKDVISEYQRLKAEGQIIPPWAQRW--VASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLES  323 (765)
T ss_pred             HHHHhhhHHHHHHHHHHhhccCCCCCHHHHHH--HHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhc
Confidence            344567888888888888776531 32 2222  233444444                        0133345567788


Q ss_pred             CCHHHHHHHHHHHHHCC-----------CCccH---HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh
Q 041561           68 EYVEQAISLYKDIIASG-----------VKHDG---VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL  133 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g-----------~~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~  133 (156)
                      |++++|.++++.+....           -.|+.   ..+..+...+...|++++|.++++.+...          .+-+.
T Consensus       324 g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~----------~P~n~  393 (765)
T PRK10049        324 ENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYN----------APGNQ  393 (765)
T ss_pred             ccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCH
Confidence            88888888888887642           12332   23445566777788888888888887443          23355


Q ss_pred             hhHHHHHHHHhhcCCHhHHhhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ..+..+...+...|++++|+++
T Consensus       394 ~l~~~lA~l~~~~g~~~~A~~~  415 (765)
T PRK10049        394 GLRIDYASVLQARGWPRAAENE  415 (765)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHH
Confidence            6777777777777777777653

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

Probab=97.30  E-value=0.001  Score=53.28  Aligned_cols=128  Identities=9%  Similarity=0.072  Sum_probs=92.2

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhC-C-CCchHHHhHHHHHhhhcc-----------------chHHHHHHHHHcCCCHH
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDG-Y-GNDIFVGSAPINIYCNCG-----------------VTWNEMIHGYAENEYVE   71 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g-~-~~~~~~~~~li~~~~~~~-----------------~~~~~li~~~~~~g~~~   71 (156)
                      +=++|-..++.++++++|+.+.+.. . .-+..+|++.+=-.-+.=                 .+|.++=++|+-.++.+
T Consensus       359 ~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~~sPesWca~GNcfSLQkdh~  438 (638)
T KOG1126|consen  359 LGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDPNSPESWCALGNCFSLQKDHD  438 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCCCCcHHHHHhcchhhhhhHHH
Confidence            3456777889999999999997643 3 346677776653222111                 89999999999999999


Q ss_pred             HHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHH---HHHhhcC
Q 041561           72 QAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLV---SSCQVHS  147 (156)
Q Consensus        72 ~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li---~~~~~~g  147 (156)
                      .|++.|++-.+  +.| ..++|+.+=.=+.....+|.|...|+.-             +..|.+.||++-   ..|.+.+
T Consensus       439 ~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~A-------------l~~~~rhYnAwYGlG~vy~Kqe  503 (638)
T KOG1126|consen  439 TAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRKA-------------LGVDPRHYNAWYGLGTVYLKQE  503 (638)
T ss_pred             HHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHhh-------------hcCCchhhHHHHhhhhheeccc
Confidence            99999998765  445 5667776666666677888888888755             566777777765   4566666


Q ss_pred             CHhHHh
Q 041561          148 NVRLAK  153 (156)
Q Consensus       148 ~~~~a~  153 (156)
                      ++|.|+
T Consensus       504 k~e~Ae  509 (638)
T KOG1126|consen  504 KLEFAE  509 (638)
T ss_pred             hhhHHH
Confidence            666554

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.30  E-value=0.017  Score=48.49  Aligned_cols=131  Identities=11%  Similarity=-0.032  Sum_probs=84.4

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCC
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEY   69 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~   69 (156)
                      -.+......|+.++|.+++....... +.+...+..+-..+.+.|                    ..+..+...+...|+
T Consensus        20 d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~   98 (765)
T PRK10049         20 DWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQ   98 (765)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCC
Confidence            34455555666666666666654411 223333444444444444                    345567777888899


Q ss_pred             HHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCC
Q 041561           70 VEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSN  148 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~  148 (156)
                      +++|...+++..+.  .|+...+..+-..+.+.|+.++|...+++..+.           .| +...+..+..++...|+
T Consensus        99 ~~eA~~~l~~~l~~--~P~~~~~~~la~~l~~~g~~~~Al~~l~~al~~-----------~P~~~~~~~~la~~l~~~~~  165 (765)
T PRK10049         99 YDEALVKAKQLVSG--APDKANLLALAYVYKRAGRHWDELRAMTQALPR-----------APQTQQYPTEYVQALRNNRL  165 (765)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----------CCCCHHHHHHHHHHHHHCCC
Confidence            99999999988765  333222667777778889999999999888443           34 44556667777778888


Q ss_pred             HhHHhh
Q 041561          149 VRLAKK  154 (156)
Q Consensus       149 ~~~a~~  154 (156)
                      .++|.+
T Consensus       166 ~e~Al~  171 (765)
T PRK10049        166 SAPALG  171 (765)
T ss_pred             hHHHHH
Confidence            887764

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

Probab=97.28  E-value=0.0079  Score=38.78  Aligned_cols=96  Identities=8%  Similarity=-0.032  Sum_probs=73.1

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      .....+...+.+.|+.++|...++...+.+ +.+.              ..|..+-..+...|++++|.+.|++..+.+ 
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~--------------~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-   81 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNS--------------RYWLGLAACCQMLKEYEEAIDAYALAAALD-   81 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-
Confidence            334555566778899999999999987754 2244              556677788888999999999999887654 


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      ..+..++..+-..+...|+.++|...|+...+
T Consensus        82 p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        82 PDDPRPYFHAAECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33455566666788899999999999998843

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

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.25  E-value=0.011  Score=51.73  Aligned_cols=92  Identities=13%  Similarity=-0.003  Sum_probs=66.9

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC--
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD--  131 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p--  131 (156)
                      ..+..+...|...|+.++|.+.++...+.  .|+ ..+...+-.++.+.|+.++|.++++.......       .-.|  
T Consensus       638 ~a~~~la~~~~~~g~~~eA~~~l~~ll~~--~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~-------~~~~~~  708 (1157)
T PRK11447        638 DARLGLIEVDIAQGDLAAARAQLAKLPAT--ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAK-------SQPPSM  708 (1157)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCc-------cCCcch
Confidence            56778888999999999999999987653  333 34455566777789999999999999854321       0112  


Q ss_pred             -ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          132 -DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       132 -d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       +...+..+-..+...|++++|.+.
T Consensus       709 ~~a~~~~~~a~~~~~~G~~~~A~~~  733 (1157)
T PRK11447        709 ESALVLRDAARFEAQTGQPQQALET  733 (1157)
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHH
Confidence             224555566788899999999764

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.23  E-value=0.015  Score=36.24  Aligned_cols=99  Identities=7%  Similarity=-0.048  Sum_probs=73.4

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchH-HHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIF-VGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ++......+.+.|+.++|...++.+.+..  |+.. .-           ..+..+-..+.+.|++++|.+.|+.......
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~-----------~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p   70 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKY--PKSTYAP-----------NAHYWLGEAYYAQGKYADAAKAFLAVVKKYP   70 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccH-----------HHHHHHHHHHHhhccHHHHHHHHHHHHHHCC
Confidence            45566677788999999999999997643  2210 00           2344577888999999999999999886432


Q ss_pred             C--ccHHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           86 K--HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        86 ~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      .  ....++..+-..+.+.++.++|...++.....
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        71 KSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             CCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            2  12455677777888999999999999998544

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.22  E-value=0.021  Score=48.21  Aligned_cols=123  Identities=11%  Similarity=0.035  Sum_probs=82.2

Q ss_pred             cCCCchHHHHHHHHHHHHhCCCCch--HHHhHHHHHhhhcc------------------chHHHH--HHHHHcCCCHHHH
Q 041561           16 AKLSSLFLGRQILTRIVKDGYGNDI--FVGSAPINIYCNCG------------------VTWNEM--IHGYAENEYVEQA   73 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~~g~~~~~--~~~~~li~~~~~~~------------------~~~~~l--i~~~~~~g~~~~a   73 (156)
                      .+.|+.+.|...|.+..+..  |+.  .++ .++..+...|                  ..+..+  ...|...|++++|
T Consensus        45 ~r~Gd~~~Al~~L~qaL~~~--P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~A  121 (822)
T PRK14574         45 ARAGDTAPVLDYLQEESKAG--PLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQA  121 (822)
T ss_pred             HhCCCHHHHHHHHHHHHhhC--ccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            58888889999888887643  442  233 6677776666                  122333  4477778999999


Q ss_pred             HHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561           74 ISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus        74 ~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                      .++|+++.+.... |...+..+...+...++.++|.+.++.....           .|+...+..++..+...++..+|.
T Consensus       122 iely~kaL~~dP~-n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~-----------dp~~~~~l~layL~~~~~~~~~AL  189 (822)
T PRK14574        122 LALWQSSLKKDPT-NPDLISGMIMTQADAGRGGVVLKQATELAER-----------DPTVQNYMTLSYLNRATDRNYDAL  189 (822)
T ss_pred             HHHHHHHHhhCCC-CHHHHHHHHHHHhhcCCHHHHHHHHHHhccc-----------CcchHHHHHHHHHHHhcchHHHHH
Confidence            9999999875433 2344457778888899999999999988443           566666644444443344443343

>TIGR00540 hemY_coli hemY protein

Probab=97.20  E-value=0.036  Score=43.03  Aligned_cols=25  Identities=8%  Similarity=-0.023  Sum_probs=22.2

Q ss_pred             CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          131 DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       131 pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+...+-.+...+...|+.++|.++
T Consensus       261 ~~~~l~~~~a~~l~~~g~~~~A~~~  285 (409)
T TIGR00540       261 HNIALKIALAEHLIDCDDHDSAQEI  285 (409)
T ss_pred             CCHHHHHHHHHHHHHCCChHHHHHH
Confidence            4888999999999999999999875

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

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.19  E-value=0.0068  Score=40.09  Aligned_cols=85  Identities=6%  Similarity=-0.105  Sum_probs=65.0

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHH
Q 041561           60 MIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDL  139 (156)
Q Consensus        60 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~l  139 (156)
                      .-..+...|++++|.+.|+...... ..+...|..+-..+.+.|++++|...|+.....          -..+...|..+
T Consensus        30 ~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l----------~p~~~~a~~~l   98 (144)
T PRK15359         30 SGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALML----------DASHPEPVYQT   98 (144)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc----------CCCCcHHHHHH
Confidence            4456678899999999999887643 235667777778888899999999999988432          23477788888


Q ss_pred             HHHHhhcCCHhHHhhh
Q 041561          140 VSSCQVHSNVRLAKKA  155 (156)
Q Consensus       140 i~~~~~~g~~~~a~~~  155 (156)
                      =.++...|++++|.+.
T Consensus        99 g~~l~~~g~~~eAi~~  114 (144)
T PRK15359         99 GVCLKMMGEPGLAREA  114 (144)
T ss_pred             HHHHHHcCCHHHHHHH
Confidence            8888899999988753

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.16  E-value=0.01  Score=39.24  Aligned_cols=93  Identities=8%  Similarity=-0.105  Sum_probs=75.0

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      +...-..+...|++++|...|....+.  .|+..             ..|..+-.++...|++++|...|+...+-. ..
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~-------------~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~   90 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMA--QPWSW-------------RAHIALAGTWMMLKEYTTAINFYGHALMLD-AS   90 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcH-------------HHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CC
Confidence            445566778899999999999998764  34332             667788888999999999999999998743 34


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      +..++..+-.++.+.|+.++|...|+...
T Consensus        91 ~~~a~~~lg~~l~~~g~~~eAi~~~~~Al  119 (144)
T PRK15359         91 HPEPVYQTGVCLKMMGEPGLAREAFQTAI  119 (144)
T ss_pred             CcHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            66677778888889999999999999883

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.14  E-value=0.023  Score=49.72  Aligned_cols=140  Identities=7%  Similarity=-0.061  Sum_probs=89.6

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhh---ccchHHHHHHHHHcCCCHHHHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCN---CGVTWNEMIHGYAENEYVEQAISLYKDI   80 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m   80 (156)
                      |+..+..+...+.+.|+.++|.+.++.+.+..  |+...+..+-..+..   .+...-.+...+.+.|++++|.+.|+.+
T Consensus        61 ~p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~--P~~~~~~~~~~~~~~~~~~~~~~l~~A~ll~~~g~~~eA~~~~~~~  138 (1157)
T PRK11447         61 NPDVIAARFRLLLRQGDSDGAQKLLDRLSQLA--PDSNAYRSSRTTMLLSTPEGRQALQQARLLATTGRTEEALASYDKL  138 (1157)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC--CCChHHHHHHHHHHhcCCchhhHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            44566777777788888888888888887754  443322221111111   1122344455788999999999999998


Q ss_pred             HHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           81 IASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        81 ~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+............+.......|+.++|.+.++.+...+          .-+...+..+-..+...|+.++|.+.
T Consensus       139 l~~~p~~~~la~~y~~~~~~~~g~~~~A~~~L~~ll~~~----------P~~~~~~~~LA~ll~~~g~~~eAl~~  203 (1157)
T PRK11447        139 FNGAPPELDLAVEYWRLVAKLPAQRPEAINQLQRLNADY----------PGNTGLRNTLALLLFSSGRRDEGFAV  203 (1157)
T ss_pred             ccCCCCChHHHHHHHHHHhhCCccHHHHHHHHHHHHHhC----------CCCHHHHHHHHHHHHccCCHHHHHHH
Confidence            765322211111111222235689999999999995542          33566777888888899999988763

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.11  E-value=0.011  Score=36.88  Aligned_cols=93  Identities=10%  Similarity=-0.056  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCC--CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGV--KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL  133 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~--~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~  133 (156)
                      ++-.+...+.+.|++++|.+.|..+.....  ......+..+-..+.+.|++++|.+.++.......       ......
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-------~~~~~~   76 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYP-------KSPKAP   76 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCC-------CCCccc
Confidence            345566778889999999999999986431  11234566688889999999999999999854321       001124


Q ss_pred             hhHHHHHHHHhhcCCHhHHhhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ..+..+-..+...|+.++|.+.
T Consensus        77 ~~~~~~~~~~~~~~~~~~A~~~   98 (119)
T TIGR02795        77 DALLKLGMSLQELGDKEKAKAT   98 (119)
T ss_pred             HHHHHHHHHHHHhCChHHHHHH
Confidence            5677777888999999988763

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.03  E-value=0.04  Score=40.85  Aligned_cols=74  Identities=8%  Similarity=-0.184  Sum_probs=42.3

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcC
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAEN   67 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~   67 (156)
                      |...=..+.+.|+.++|...|+...+.. +.+...|+.+=..|.+.|                    ..|..+-.++...
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~  145 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYG  145 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC
Confidence            3334445667788888888888877643 224545555544444444                    3444444455555


Q ss_pred             CCHHHHHHHHHHHHH
Q 041561           68 EYVEQAISLYKDIIA   82 (156)
Q Consensus        68 g~~~~a~~~~~~m~~   82 (156)
                      |++++|.+.|+...+
T Consensus       146 g~~~eA~~~~~~al~  160 (296)
T PRK11189        146 GRYELAQDDLLAFYQ  160 (296)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            566666666555544

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.03  E-value=0.024  Score=46.94  Aligned_cols=122  Identities=9%  Similarity=-0.027  Sum_probs=83.8

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      +..+-.|-....+.|..++|+.+++...+.  .||..             ..+-.+...+.+.+++++|....++.... 
T Consensus        86 ~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~-------------~a~~~~a~~L~~~~~~eeA~~~~~~~l~~-  149 (694)
T PRK15179         86 ELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSS-------------EAFILMLRGVKRQQGIEAGRAEIELYFSG-  149 (694)
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcH-------------HHHHHHHHHHHHhccHHHHHHHHHHHhhc-
Confidence            555666667777888899999999888774  56654             44555667777888888888888777653 


Q ss_pred             CCccHHHH-HHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhh
Q 041561           85 VKHDGVTF-VAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        85 ~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                       .|+..+. ..+-.++.+.|+.++|..+|++....           .| +..+|.++=.++...|+.++|..
T Consensus       150 -~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~-----------~p~~~~~~~~~a~~l~~~G~~~~A~~  209 (694)
T PRK15179        150 -GSSSAREILLEAKSWDEIGQSEQADACFERLSRQ-----------HPEFENGYVGWAQSLTRRGALWRARD  209 (694)
T ss_pred             -CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhc-----------CCCcHHHHHHHHHHHHHcCCHHHHHH
Confidence             4555443 33445555788888888888877432           23 36667777777777788777754

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

Probab=97.00  E-value=0.058  Score=40.56  Aligned_cols=131  Identities=13%  Similarity=0.071  Sum_probs=87.2

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhh----cc--------------------chHHHHHHHHHcCCC
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCN----CG--------------------VTWNEMIHGYAENEY   69 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~--------------------~~~~~li~~~~~~g~   69 (156)
                      .+...|+.+.|.++++...+.. +.|...++. ...+..    .+                    .....+-..+...|+
T Consensus        52 ~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~  129 (355)
T cd05804          52 SAWIAGDLPKALALLEQLLDDY-PRDLLALKL-HLGAFGLGDFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQ  129 (355)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHH-hHHHHHhcccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCC
Confidence            3456789999999999887652 223333331 111111    11                    222334457788999


Q ss_pred             HHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh--hhHHHHHHHHhhcC
Q 041561           70 VEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL--VVWGDLVSSCQVHS  147 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~--~~~~~li~~~~~~g  147 (156)
                      +++|.+.+++..+.. ..+...+..+-..+...|++++|...++.......        ..|+.  ..|-.+-..+...|
T Consensus       130 ~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~--------~~~~~~~~~~~~la~~~~~~G  200 (355)
T cd05804         130 YDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWD--------CSSMLRGHNWWHLALFYLERG  200 (355)
T ss_pred             HHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccC--------CCcchhHHHHHHHHHHHHHCC
Confidence            999999999998753 22345667777888899999999999998743311        12333  34667888899999


Q ss_pred             CHhHHhhh
Q 041561          148 NVRLAKKA  155 (156)
Q Consensus       148 ~~~~a~~~  155 (156)
                      +.++|.++
T Consensus       201 ~~~~A~~~  208 (355)
T cd05804         201 DYEAALAI  208 (355)
T ss_pred             CHHHHHHH
Confidence            99999764

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.

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

Probab=96.99  E-value=0.021  Score=44.58  Aligned_cols=112  Identities=13%  Similarity=0.034  Sum_probs=88.4

Q ss_pred             cCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc-HHHHHH
Q 041561           16 AKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD-GVTFVA   94 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~   94 (156)
                      -..|..++|+..+..+.+.  .||-.             ..+.....-+.+.++.++|.+.|+.+...  .|+ ....-.
T Consensus       317 ~~~~~~d~A~~~l~~L~~~--~P~N~-------------~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~  379 (484)
T COG4783         317 YLAGQYDEALKLLQPLIAA--QPDNP-------------YYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLN  379 (484)
T ss_pred             HHhcccchHHHHHHHHHHh--CCCCH-------------HHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHH
Confidence            3567889999999998664  35443             44455567788999999999999999874  555 445555


Q ss_pred             HHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           95 ILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        95 ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +-+++.+.|+.++|..+++....+          .+-|...|..|=++|...|+..+|..
T Consensus       380 ~a~all~~g~~~eai~~L~~~~~~----------~p~dp~~w~~LAqay~~~g~~~~a~~  429 (484)
T COG4783         380 LAQALLKGGKPQEAIRILNRYLFN----------DPEDPNGWDLLAQAYAELGNRAEALL  429 (484)
T ss_pred             HHHHHHhcCChHHHHHHHHHHhhc----------CCCCchHHHHHHHHHHHhCchHHHHH
Confidence            678899999999999999988554          45688999999999999999988764

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

Probab=96.98  E-value=0.0026  Score=37.88  Aligned_cols=77  Identities=13%  Similarity=0.096  Sum_probs=55.7

Q ss_pred             CCCHHHHHHHHHHHHHCCC-CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHh
Q 041561           67 NEYVEQAISLYKDIIASGV-KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQ  144 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~  144 (156)
                      .|++++|..+|+++.+... .|+...+-.+-.++.+.|+.++|..+++.. ..           .| +....-.+-.+|.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~-~~-----------~~~~~~~~~l~a~~~~   69 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKL-KL-----------DPSNPDIHYLLARCLL   69 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCH-TH-----------HHCHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHh-CC-----------CCCCHHHHHHHHHHHH
Confidence            5789999999999988654 335555656889999999999999999983 22           22 2233334468899


Q ss_pred             hcCCHhHHhhh
Q 041561          145 VHSNVRLAKKA  155 (156)
Q Consensus       145 ~~g~~~~a~~~  155 (156)
                      ..|++++|.++
T Consensus        70 ~l~~y~eAi~~   80 (84)
T PF12895_consen   70 KLGKYEEAIKA   80 (84)
T ss_dssp             HTT-HHHHHHH
T ss_pred             HhCCHHHHHHH
Confidence            99999999864

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

Probab=96.95  E-value=0.0021  Score=38.25  Aligned_cols=80  Identities=8%  Similarity=0.052  Sum_probs=56.4

Q ss_pred             CCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH-HHHHHH
Q 041561           18 LSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG-VTFVAI   95 (156)
Q Consensus        18 ~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~l   95 (156)
                      .|+.+.|..+++.+.+..- .|+.              ..|-.+-.+|.+.|++++|.++++. .+  ..|+. ...-.+
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~--------------~~~~~la~~~~~~~~y~~A~~~~~~-~~--~~~~~~~~~~l~   64 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNS--------------AYLYNLAQCYFQQGKYEEAIELLQK-LK--LDPSNPDIHYLL   64 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHH--------------HHHHHHHHHHHHTTHHHHHHHHHHC-HT--HHHCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhH--------------HHHHHHHHHHHHCCCHHHHHHHHHH-hC--CCCCCHHHHHHH
Confidence            5789999999999987543 2233              3344578899999999999999988 22  22222 222234


Q ss_pred             HHhhcCCCchHHHHHHHHh
Q 041561           96 LTPCSHSGLVYAEVEIFNS  114 (156)
Q Consensus        96 l~~~~~~~~~~~a~~~~~~  114 (156)
                      -++|.+.|++++|..+++.
T Consensus        65 a~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   65 ARCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             HHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHhc
Confidence            6777799999999999874

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

Probab=96.89  E-value=0.039  Score=38.55  Aligned_cols=100  Identities=4%  Similarity=-0.036  Sum_probs=72.4

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHH-HHcCCC--HHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHG-YAENEY--VEQAISLYKD   79 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~-~~~~g~--~~~a~~~~~~   79 (156)
                      .|...|..+-..+...|+.+.|...++...+..- -|.              ..+..+-.+ +...|+  .++|.+++++
T Consensus        71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P-~~~--------------~~~~~lA~aL~~~~g~~~~~~A~~~l~~  135 (198)
T PRK10370         71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQLRG-ENA--------------ELYAALATVLYYQAGQHMTPQTREMIDK  135 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCH--------------HHHHHHHHHHHHhcCCCCcHHHHHHHHH
Confidence            3456677777778888888888888888776431 233              444555554 356666  5999999999


Q ss_pred             HHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           80 IIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        80 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      ..+.... +...+..+-..+.+.|++++|...++.+.+.
T Consensus       136 al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        136 ALALDAN-EVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHhCCC-ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            9886533 4556666777778999999999999999544

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

Probab=96.89  E-value=0.016  Score=37.34  Aligned_cols=86  Identities=9%  Similarity=0.052  Sum_probs=66.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHH
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWG  137 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~  137 (156)
                      ..+...+...|+.++|.+.|+.....+ ..+...+..+-..+.+.|+.++|...++.....          ...+...|.
T Consensus        21 ~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------~p~~~~~~~   89 (135)
T TIGR02552        21 YALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAAL----------DPDDPRPYF   89 (135)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----------CCCChHHHH
Confidence            345566778899999999999987754 235667777888888999999999999987332          234567777


Q ss_pred             HHHHHHhhcCCHhHHhh
Q 041561          138 DLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       138 ~li~~~~~~g~~~~a~~  154 (156)
                      .+=..|...|+.++|.+
T Consensus        90 ~la~~~~~~g~~~~A~~  106 (135)
T TIGR02552        90 HAAECLLALGEPESALK  106 (135)
T ss_pred             HHHHHHHHcCCHHHHHH
Confidence            77788999999999865

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

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

Probab=96.89  E-value=0.014  Score=33.83  Aligned_cols=92  Identities=10%  Similarity=0.084  Sum_probs=69.4

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      +..+...+.+.|++++|...++...+..  |+..             ..+..+-..+...+++++|.+.|+...... ..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~-------------~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~   66 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD--PDNA-------------DAYYNLAAAYYKLGKYEEALEDYEKALELD-PD   66 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC--CccH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-Cc
Confidence            4556667778899999999999987653  3221             344556667777899999999999987654 22


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +..++..+...+...|+.++|...+...
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~   94 (100)
T cd00189          67 NAKAYYNLGLAYYKLGKYEEALEAYEKA   94 (100)
T ss_pred             chhHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            3357778888888999999999999876

>PRK14574 hmsH outer membrane protein; Provisional

Probab=96.87  E-value=0.049  Score=46.05  Aligned_cols=90  Identities=10%  Similarity=0.020  Sum_probs=45.4

Q ss_pred             HHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC-----CC
Q 041561           12 LSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG-----VK   86 (156)
Q Consensus        12 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-----~~   86 (156)
                      +-++...|+..++.+.++.|...|.+.-.++-              -.+.++|...+++++|..+|++.....     ..
T Consensus       299 l~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~--------------~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~  364 (822)
T PRK14574        299 LGALLVRHQTADLIKEYEAMEAEGYKMPDYAR--------------RWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNS  364 (822)
T ss_pred             HHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHH--------------HHHHHHHHhcCCcHHHHHHHHHHhhccccccCCC
Confidence            44556667777888888888777754222222              233444445555555555555543321     01


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ++......|+.++...+++++|.++++.+
T Consensus       365 ~~~~~~~~L~yA~ld~e~~~~A~~~l~~~  393 (822)
T PRK14574        365 DDLLDADDLYYSLNESEQLDKAYQFAVNY  393 (822)
T ss_pred             cchHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            11222344455555555555555555555

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

Probab=96.84  E-value=0.024  Score=45.12  Aligned_cols=113  Identities=14%  Similarity=0.206  Sum_probs=91.6

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhcc--chHHH-----------------HHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCG--VTWNE-----------------MIHGYA   65 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~--~~~~~-----------------li~~~~   65 (156)
                      .+|...|+.--|..-++.|+.+|....+.+..+ .+++++++|..||...  ..|+.                 -++-+.
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD~~~AfrIFeLGLkkf~d~p~yv~~YldfL~  446 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKDKETAFRIFELGLKKFGDSPEYVLKYLDFLS  446 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            467788888888888999999999999999888 9999999999999887  33333                 444455


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccH--HHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDG--VTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      +.++-..+..+|+....+++.||.  ..|..+|+--+.-|++..+..+-+++...
T Consensus       447 ~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~a  501 (656)
T KOG1914|consen  447 HLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTA  501 (656)
T ss_pred             HhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            566667788999999888666665  58999999999999999998887766443

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

Probab=96.83  E-value=0.044  Score=43.00  Aligned_cols=103  Identities=17%  Similarity=0.256  Sum_probs=78.4

Q ss_pred             CCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHH
Q 041561           36 YGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAI   95 (156)
Q Consensus        36 ~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l   95 (156)
                      ++.|+.+.+-|-+.|-+.|                    ++-.=|-.-|....-.+++...|+.-..  +.|+..-|-.|
T Consensus       588 ip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlm  665 (840)
T KOG2003|consen  588 IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLM  665 (840)
T ss_pred             CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHH
Confidence            4557888888888998888                    2222344555566667889999887543  79999999999


Q ss_pred             HHhhc-CCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHh
Q 041561           96 LTPCS-HSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVR  150 (156)
Q Consensus        96 l~~~~-~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~  150 (156)
                      |..|. |.|++++|++++.+.-++          +.-|.....-|+..+.-.|..+
T Consensus       666 iasc~rrsgnyqka~d~yk~~hrk----------fpedldclkflvri~~dlgl~d  711 (840)
T KOG2003|consen  666 IASCFRRSGNYQKAFDLYKDIHRK----------FPEDLDCLKFLVRIAGDLGLKD  711 (840)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHHh----------CccchHHHHHHHHHhccccchh
Confidence            98887 799999999999988544          4567788888888877776543

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

Probab=96.62  E-value=0.034  Score=36.51  Aligned_cols=100  Identities=12%  Similarity=0.109  Sum_probs=72.4

Q ss_pred             cCCCchHHHHHHHHHHHH--hC-CCCchH--HHhHHHHHhhhcc--chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561           16 AKLSSLFLGRQILTRIVK--DG-YGNDIF--VGSAPINIYCNCG--VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~--~g-~~~~~~--~~~~li~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      ...++.+.+...+.....  .| +-|+..  -|..-...+.+..  .....++..+...|++++|.++.+.+.... ..|
T Consensus        17 ~~~~~~~~~~~~~~~al~ly~G~~l~~~~~~~W~~~~r~~l~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~   95 (146)
T PF03704_consen   17 ARAGDPEEAIELLEEALALYRGDFLPDLDDEEWVEPERERLRELYLDALERLAEALLEAGDYEEALRLLQRALALD-PYD   95 (146)
T ss_dssp             HHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-
T ss_pred             HHCCCHHHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCC
Confidence            456788888888888765  34 444432  3444444444333  667778888889999999999999998754 447


Q ss_pred             HHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           89 GVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        89 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      ...|..+|.++.+.|+..+|.++|+.+.
T Consensus        96 E~~~~~lm~~~~~~g~~~~A~~~Y~~~~  123 (146)
T PF03704_consen   96 EEAYRLLMRALAAQGRRAEALRVYERYR  123 (146)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            8899999999999999999999998874

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

>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=96.60  E-value=0.15  Score=40.90  Aligned_cols=26  Identities=12%  Similarity=0.054  Sum_probs=17.4

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHHhC
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVKDG   35 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~~g   35 (156)
                      ..-+.+.+.|+.++|+.++..+.+.+
T Consensus        43 ~rA~ll~kLg~~~eA~~~y~~Li~rN   68 (517)
T PF12569_consen   43 KRAELLLKLGRKEEAEKIYRELIDRN   68 (517)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            33455667777777777777777654

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 [], [].

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

Probab=96.60  E-value=0.036  Score=41.51  Aligned_cols=113  Identities=13%  Similarity=0.103  Sum_probs=78.5

Q ss_pred             CchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCccHHHH--HHH
Q 041561           19 SSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS-GVKHDGVTF--VAI   95 (156)
Q Consensus        19 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~--~~l   95 (156)
                      ...++|..+|-+|.+    .|+.++.+           -=+|=+-|.+.|..|.|+++.+.+.++ +...+...+  -.+
T Consensus        49 ~Q~dKAvdlF~e~l~----~d~~t~e~-----------~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL  113 (389)
T COG2956          49 NQPDKAVDLFLEMLQ----EDPETFEA-----------HLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQL  113 (389)
T ss_pred             cCcchHHHHHHHHHh----cCchhhHH-----------HHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHH
Confidence            456888889988876    34433322           234556677899999999999998864 333333322  235


Q ss_pred             HHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhhC
Q 041561           96 LTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus        96 l~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~~  156 (156)
                      -+-|..+|-+|.|+++|..+..+.          .--....-.|+..|-...++++|..+|
T Consensus       114 ~~Dym~aGl~DRAE~~f~~L~de~----------efa~~AlqqLl~IYQ~treW~KAId~A  164 (389)
T COG2956         114 GRDYMAAGLLDRAEDIFNQLVDEG----------EFAEGALQQLLNIYQATREWEKAIDVA  164 (389)
T ss_pred             HHHHHHhhhhhHHHHHHHHHhcch----------hhhHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            566778999999999999985432          123455677888999999999888765

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

Probab=96.53  E-value=0.012  Score=33.07  Aligned_cols=56  Identities=5%  Similarity=0.078  Sum_probs=45.9

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      -..+...|++++|.+.|++..+.... +...+..+-..+.+.|++++|...|+...+
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQDPD-NPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45678899999999999999987622 666777788888899999999999998843

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.52  E-value=0.1  Score=35.35  Aligned_cols=116  Identities=9%  Similarity=-0.043  Sum_probs=77.0

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .+..+-..+.+.|+.++|...|++..+....++..            ...|..+-..+.+.|++++|.+.+++....  .
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~------------~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~  102 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDR------------SYILYNMGIIYASNGEHDKALEYYHQALEL--N  102 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchH------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--C
Confidence            45556667778899999999999987654322210            045677788889999999999999998764  3


Q ss_pred             c-cHHHHHHHHHhhcCCCc--------------hHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           87 H-DGVTFVAILTPCSHSGL--------------VYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        87 p-~~~t~~~ll~~~~~~~~--------------~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                      | +...+..+-..+...|+              +++|.++++...             ..+...|..++.-+...|+.
T Consensus       103 p~~~~~~~~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~-------------~~~p~~~~~~~~~~~~~~~~  167 (172)
T PRK02603        103 PKQPSALNNIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAI-------------RLAPNNYIEAQNWLKTTGRS  167 (172)
T ss_pred             cccHHHHHHHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHH-------------hhCchhHHHHHHHHHhcCcc
Confidence            3 34445555555655555              456666666652             23334477777777666654

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

Probab=96.49  E-value=0.26  Score=37.80  Aligned_cols=91  Identities=7%  Similarity=0.042  Sum_probs=76.7

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH-------HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG-------VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-------~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                      ..-.....+|.+.|++.+..++...|.+.|+-.|+       .+|+.+++=+...++.+.-.+.++....+         
T Consensus       188 ~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~---------  258 (400)
T COG3071         188 EVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK---------  258 (400)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH---------
Confidence            56777888999999999999999999998875554       46888888888888888888888888655         


Q ss_pred             CCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          128 PYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       128 ~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       .+-|+..-.+++.-+.+.|+.++|.++
T Consensus       259 -lr~~p~l~~~~a~~li~l~~~~~A~~~  285 (400)
T COG3071         259 -LRNDPELVVAYAERLIRLGDHDEAQEI  285 (400)
T ss_pred             -hhcChhHHHHHHHHHHHcCChHHHHHH
Confidence             577888889999999999999999876

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

Probab=96.46  E-value=0.078  Score=41.84  Aligned_cols=124  Identities=11%  Similarity=0.098  Sum_probs=86.1

Q ss_pred             CCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHHHHHH
Q 041561           18 LSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQAISLY   77 (156)
Q Consensus        18 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a~~~~   77 (156)
                      .+++..|.++|+...... ..+...|--.+.+=-+.+                    ..|---+-.=-..|.+..|.++|
T Consensus        86 q~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqif  164 (677)
T KOG1915|consen   86 QKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIF  164 (677)
T ss_pred             HHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHH
Confidence            456677888888776533 244445544444433333                    22322333333466777788888


Q ss_pred             HHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           78 KDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        78 ~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +.-.  ...|+...|.+.|+.-.+-..++.|+.+++.+..           +.|++.+|--...=--++|.+..|+.|
T Consensus       165 erW~--~w~P~eqaW~sfI~fElRykeieraR~IYerfV~-----------~HP~v~~wikyarFE~k~g~~~~aR~V  229 (677)
T KOG1915|consen  165 ERWM--EWEPDEQAWLSFIKFELRYKEIERARSIYERFVL-----------VHPKVSNWIKYARFEEKHGNVALARSV  229 (677)
T ss_pred             HHHH--cCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe-----------ecccHHHHHHHHHHHHhcCcHHHHHHH
Confidence            7643  3789999999999999999999999999998843           579999998888888888888877764

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

Probab=96.41  E-value=0.041  Score=41.38  Aligned_cols=107  Identities=12%  Similarity=0.145  Sum_probs=70.9

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      +.+..|.-|...|....|.++-.+..   + ||.              .-|...|.+++..+++++..++...      +
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk---v-~dk--------------rfw~lki~aLa~~~~w~eL~~fa~s------k  234 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK---V-PDK--------------RFWWLKIKALAENKDWDELEKFAKS------K  234 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC---C-cHH--------------HHHHHHHHHHHhcCCHHHHHHHHhC------C
Confidence            34445555666666666655544432   2 555              6677888888888888886665432      2


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhhC
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~~  156 (156)
                      -.+.-|-.++++|.+.|+.++|..+...+..                   ..=+..|.+.|++.+|-+.|
T Consensus       235 KsPIGyepFv~~~~~~~~~~eA~~yI~k~~~-------------------~~rv~~y~~~~~~~~A~~~A  285 (319)
T PF04840_consen  235 KSPIGYEPFVEACLKYGNKKEASKYIPKIPD-------------------EERVEMYLKCGDYKEAAQEA  285 (319)
T ss_pred             CCCCChHHHHHHHHHCCCHHHHHHHHHhCCh-------------------HHHHHHHHHCCCHHHHHHHH
Confidence            2346777888888888888888877776521                   33567788888888887654

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.41  E-value=0.071  Score=35.94  Aligned_cols=89  Identities=9%  Similarity=0.045  Sum_probs=65.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc--cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKH--DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD  132 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd  132 (156)
                      ..|..+...+...|++++|...|++.......|  ...++..+-..+.+.|+.++|...++.....          .+..
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~----------~~~~  105 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER----------NPFL  105 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CcCc
Confidence            566777788888999999999999987643233  2347788888888999999999999887432          1223


Q ss_pred             hhhHHHHHHHHh-------hcCCHhHHh
Q 041561          133 LVVWGDLVSSCQ-------VHSNVRLAK  153 (156)
Q Consensus       133 ~~~~~~li~~~~-------~~g~~~~a~  153 (156)
                      ..+++.+-..+.       ..|++++|.
T Consensus       106 ~~~~~~la~i~~~~~~~~~~~g~~~~A~  133 (168)
T CHL00033        106 PQALNNMAVICHYRGEQAIEQGDSEIAE  133 (168)
T ss_pred             HHHHHHHHHHHHHhhHHHHHcccHHHHH
Confidence            455677767777       777777554

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.41  E-value=0.2  Score=35.48  Aligned_cols=78  Identities=13%  Similarity=0.097  Sum_probs=54.3

Q ss_pred             CCHHHHHHHHHHHHHCCCCccHH-HH-----------------HHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           68 EYVEQAISLYKDIIASGVKHDGV-TF-----------------VAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p~~~-t~-----------------~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      |+.++|.+.|+......  |+.. .+                 ..+-+.+.+.|+.++|...+......+.        -
T Consensus       129 ~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p--------~  198 (235)
T TIGR03302       129 TAAREAFEAFQELIRRY--PNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYP--------D  198 (235)
T ss_pred             HHHHHHHHHHHHHHHHC--CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCC--------C
Confidence            66788888888887642  2221 11                 1234556678999999999998855421        1


Q ss_pred             CC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 KD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .| ....|..+..++...|+.++|...
T Consensus       199 ~~~~~~a~~~l~~~~~~lg~~~~A~~~  225 (235)
T TIGR03302       199 TPATEEALARLVEAYLKLGLKDLAQDA  225 (235)
T ss_pred             CcchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            22 357889999999999999999763

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).

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

Probab=96.37  E-value=0.05  Score=35.82  Aligned_cols=88  Identities=6%  Similarity=0.015  Sum_probs=64.7

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTF   92 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~   92 (156)
                      ..+...|++++|...|+......  ||.....          ...-.|-..+...|++++|+..++.......  ....+
T Consensus        56 ~~~~~~g~~~~A~~~l~~~~~~~--~d~~l~~----------~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~  121 (145)
T PF09976_consen   56 KAAYEQGDYDEAKAALEKALANA--PDPELKP----------LARLRLARILLQQGQYDEALATLQQIPDEAF--KALAA  121 (145)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC--CCHHHHH----------HHHHHHHHHHHHcCCHHHHHHHHHhccCcch--HHHHH
Confidence            56678899999999999998876  4432211          1233467788899999999999977443333  33455


Q ss_pred             HHHHHhhcCCCchHHHHHHHHh
Q 041561           93 VAILTPCSHSGLVYAEVEIFNS  114 (156)
Q Consensus        93 ~~ll~~~~~~~~~~~a~~~~~~  114 (156)
                      ...=+.+.+.|+.++|+..|+.
T Consensus       122 ~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  122 ELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHH
Confidence            5666888899999999999874

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.36  E-value=0.072  Score=34.21  Aligned_cols=88  Identities=11%  Similarity=0.069  Sum_probs=61.5

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccH--HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHH
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDG--VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGD  138 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~  138 (156)
                      -.++-..|+.++|..+|++-...|.....  ..+-.+-..+...|++++|..+++....++.     +.++  +......
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p-----~~~~--~~~l~~f   80 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFP-----DDEL--NAALRVF   80 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC-----Cccc--cHHHHHH
Confidence            34667889999999999999998876653  3455566778889999999999998855421     0001  1222222


Q ss_pred             HHHHHhhcCCHhHHhhh
Q 041561          139 LVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       139 li~~~~~~g~~~~a~~~  155 (156)
                      +-.++...|+.++|.+.
T Consensus        81 ~Al~L~~~gr~~eAl~~   97 (120)
T PF12688_consen   81 LALALYNLGRPKEALEW   97 (120)
T ss_pred             HHHHHHHCCCHHHHHHH
Confidence            33477788999998764

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

Probab=96.36  E-value=0.2  Score=35.00  Aligned_cols=89  Identities=12%  Similarity=0.112  Sum_probs=69.3

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhh-cCCCc--hHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPC-SHSGL--VYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~-~~~~~--~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      ..|..+-..|...|++++|.+.|++..+-.. -|...+..+-.++ .+.|+  .++|.+++++..+.          -.-
T Consensus        74 ~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P-~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~----------dP~  142 (198)
T PRK10370         74 EQWALLGEYYLWRNDYDNALLAYRQALQLRG-ENAELYAALATVLYYQAGQHMTPQTREMIDKALAL----------DAN  142 (198)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHh----------CCC
Confidence            7899999999999999999999999877432 2444555555554 56676  59999999999544          133


Q ss_pred             ChhhHHHHHHHHhhcCCHhHHhh
Q 041561          132 DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       132 d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +...+..+=..+...|++++|..
T Consensus       143 ~~~al~~LA~~~~~~g~~~~Ai~  165 (198)
T PRK10370        143 EVTALMLLASDAFMQADYAQAIE  165 (198)
T ss_pred             ChhHHHHHHHHHHHcCCHHHHHH
Confidence            66788888889999999999975

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

Probab=96.35  E-value=0.098  Score=41.05  Aligned_cols=133  Identities=14%  Similarity=0.150  Sum_probs=90.7

Q ss_pred             CCCchHHHHHHHHHHHHhC-C-CCchHHHhHHHHHhhhcc-----------------chHHHHHHHHHcCCCHHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDG-Y-GNDIFVGSAPINIYCNCG-----------------VTWNEMIHGYAENEYVEQAISLY   77 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g-~-~~~~~~~~~li~~~~~~~-----------------~~~~~li~~~~~~g~~~~a~~~~   77 (156)
                      ...|+++|+.+|+++.+.. . .-|..+|+.++-.--...                 +|...+-+-|+-.++.++|...|
T Consensus       274 ~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YF  353 (559)
T KOG1155|consen  274 NQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYF  353 (559)
T ss_pred             hhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHH
Confidence            5579999999999998764 2 347788887764433322                 77788888888899999999999


Q ss_pred             HHHHHCCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC--------------------c------CCCCC
Q 041561           78 KDIIASGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK--------------------C------LMPYK  130 (156)
Q Consensus        78 ~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~--------------------c------~~~~~  130 (156)
                      +.-.+-  .|. ...|+.|=.-|...++-..|.+-++.-.+   +-|.                    |      ...++
T Consensus       354 kRALkL--Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvd---i~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k  428 (559)
T KOG1155|consen  354 KRALKL--NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVD---INPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK  428 (559)
T ss_pred             HHHHhc--CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHh---cCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC
Confidence            987653  333 23455555555556666555555544311   1111                    0      22244


Q ss_pred             C-ChhhHHHHHHHHhhcCCHhHHhh
Q 041561          131 D-DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       131 p-d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      | |.+.|.+|=+.|.+.++.++|.+
T Consensus       429 PnDsRlw~aLG~CY~kl~~~~eAiK  453 (559)
T KOG1155|consen  429 PNDSRLWVALGECYEKLNRLEEAIK  453 (559)
T ss_pred             CCchHHHHHHHHHHHHhccHHHHHH
Confidence            4 88999999999999999999875

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

Probab=96.34  E-value=0.21  Score=36.18  Aligned_cols=90  Identities=9%  Similarity=-0.000  Sum_probs=74.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..-+.......+.|++.+|...|++...- -.+|..+|+.+=-+|.+.|+.++|+.-|.+-.+-          ..-+..
T Consensus       101 ~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L----------~~~~p~  169 (257)
T COG5010         101 ELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLGRFDEARRAYRQALEL----------APNEPS  169 (257)
T ss_pred             HHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHh----------ccCCch
Confidence            44555788889999999999999998653 3678889999999999999999999999888433          123667


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ..|-|--.|.-.|+.+.|+.+
T Consensus       170 ~~nNlgms~~L~gd~~~A~~l  190 (257)
T COG5010         170 IANNLGMSLLLRGDLEDAETL  190 (257)
T ss_pred             hhhhHHHHHHHcCCHHHHHHH
Confidence            788888889999999999864

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

Probab=96.31  E-value=0.34  Score=39.89  Aligned_cols=136  Identities=10%  Similarity=0.073  Sum_probs=98.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      ||..--+.|.+.+.++-|..+|....+. ++-+...|......=-..|                    ..|-...+.+..
T Consensus       518 tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~  596 (913)
T KOG0495|consen  518 TWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWK  596 (913)
T ss_pred             HHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHh
Confidence            4555556666777777777777776653 2334445554443322223                    567777777888


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH  146 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~  146 (156)
                      .|++.+|..++.+..+...+ +...|-+-++-...+..++.|+.+|.+-..           ..|..+.|.--++--...
T Consensus       597 agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~eraR~llakar~-----------~sgTeRv~mKs~~~er~l  664 (913)
T KOG0495|consen  597 AGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELERARDLLAKARS-----------ISGTERVWMKSANLERYL  664 (913)
T ss_pred             cCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHHHHHHHHHHhc-----------cCCcchhhHHHhHHHHHh
Confidence            89999999999888775544 677888899999999999999999997743           357888888888888888


Q ss_pred             CCHhHHhhh
Q 041561          147 SNVRLAKKA  155 (156)
Q Consensus       147 g~~~~a~~~  155 (156)
                      |+.++|.++
T Consensus       665 d~~eeA~rl  673 (913)
T KOG0495|consen  665 DNVEEALRL  673 (913)
T ss_pred             hhHHHHHHH
Confidence            888888775

>PRK11189 lipoprotein NlpI; Provisional

Probab=96.27  E-value=0.19  Score=37.25  Aligned_cols=140  Identities=6%  Similarity=-0.071  Sum_probs=83.7

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhcc------------------chH-HHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCG------------------VTW-NEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~------------------~~~-~~li~~   63 (156)
                      +...|+.+=..+...|+.++|...|+...+.  .| +...|..+-..+...|                  ..+ ......
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l  174 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYL  174 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            3467888888889999999999999998764  34 3456666655565555                  111 111122


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSS  142 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~  142 (156)
                      ....+++++|.+.|.+.... ..|+...+ .+...  ..|+++.+ +.+..+.+....    ...+.| ....|.-+=..
T Consensus       175 ~~~~~~~~~A~~~l~~~~~~-~~~~~~~~-~~~~~--~lg~~~~~-~~~~~~~~~~~~----~~~l~~~~~ea~~~Lg~~  245 (296)
T PRK11189        175 AESKLDPKQAKENLKQRYEK-LDKEQWGW-NIVEF--YLGKISEE-TLMERLKAGATD----NTELAERLCETYFYLAKY  245 (296)
T ss_pred             HHccCCHHHHHHHHHHHHhh-CCccccHH-HHHHH--HccCCCHH-HHHHHHHhcCCC----cHHHHHHHHHHHHHHHHH
Confidence            34567899999999775533 23333322 23322  34555443 344444322110    000111 33578888899


Q ss_pred             HhhcCCHhHHhh
Q 041561          143 CQVHSNVRLAKK  154 (156)
Q Consensus       143 ~~~~g~~~~a~~  154 (156)
                      +...|+.++|..
T Consensus       246 ~~~~g~~~~A~~  257 (296)
T PRK11189        246 YLSLGDLDEAAA  257 (296)
T ss_pred             HHHCCCHHHHHH
Confidence            999999999976

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

Probab=96.23  E-value=0.028  Score=41.41  Aligned_cols=89  Identities=12%  Similarity=0.114  Sum_probs=69.6

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASG-VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      .|-.+|+..-+.+.++.|.++|.+-++.+ ...+.+...+++.-+ ..++.+.|..||+...+.          +..+..
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~-~~~d~~~A~~Ife~glk~----------f~~~~~   71 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK----------FPSDPD   71 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH----------HTT-HH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH----------CCCCHH
Confidence            57788888889889999999999998653 566777777777654 357788899999999776          356888


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|...|.-....|+.+.|+.+
T Consensus        72 ~~~~Y~~~l~~~~d~~~aR~l   92 (280)
T PF05843_consen   72 FWLEYLDFLIKLNDINNARAL   92 (280)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHH
Confidence            999999999999999998864

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.

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

Probab=96.19  E-value=0.057  Score=43.70  Aligned_cols=137  Identities=10%  Similarity=0.010  Sum_probs=82.5

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHH----------------------------------
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPIN----------------------------------   48 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~----------------------------------   48 (156)
                      .+.||.++=..|+-.++.+.|.+-|+...+.  .| ..++|+.+=+                                  
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~  497 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGT  497 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhh
Confidence            4578888888888888888888888887663  23 3344432211                                  


Q ss_pred             Hhhhcc--------------------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHH
Q 041561           49 IYCNCG--------------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAE  108 (156)
Q Consensus        49 ~~~~~~--------------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a  108 (156)
                      .|.|.+                    +.-..+...+-+.|+-|+|+++|++-..-..+ |...---....+--.++.++|
T Consensus       498 vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~~~~~~il~~~~~~~ea  576 (638)
T KOG1126|consen  498 VYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCKYHRASILFSLGRYVEA  576 (638)
T ss_pred             heeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhHHHHHHHHHhhcchHHH
Confidence            111111                    22333444555667777777777776543322 111111222333456778888


Q ss_pred             HHHHHhcccccccCCCcCCCCCCChh-hHHHHHHHHhhcCCHhHHhh
Q 041561          109 VEIFNSMEHDHEVKPKCLMPYKDDLV-VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       109 ~~~~~~m~~~~~~~~~c~~~~~pd~~-~~~~li~~~~~~g~~~~a~~  154 (156)
                      .+.++++ ++          +.||.. .|-.+-..|.+.|+.+.|..
T Consensus       577 l~~LEeL-k~----------~vP~es~v~~llgki~k~~~~~~~Al~  612 (638)
T KOG1126|consen  577 LQELEEL-KE----------LVPQESSVFALLGKIYKRLGNTDLALL  612 (638)
T ss_pred             HHHHHHH-HH----------hCcchHHHHHHHHHHHHHHccchHHHH
Confidence            8888888 44          567664 46666799999999888863

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.17  E-value=0.19  Score=32.79  Aligned_cols=116  Identities=15%  Similarity=0.147  Sum_probs=80.7

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------chHHHHHHHHHcCCCHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------VTWNEMIHGYAENEYVE   71 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------~~~~~li~~~~~~g~~~   71 (156)
                      .....++..+.+.+....+...++.+...+ ..+...+|.+|..|++..              .....+++.|-+.+.++
T Consensus         8 ~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~~~ll~~l~~~~~~yd~~~~~~~c~~~~l~~   86 (140)
T smart00299        8 IDVSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDPQKEIERLDNKSNHYDIEKVGKLCEKAKLYE   86 (140)
T ss_pred             CCHHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCHHHHHHHHHhccccCCHHHHHHHHHHcCcHH
Confidence            445678888888899999999999998877 378889999999999876              22344777777777777


Q ss_pred             HHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           72 QAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        72 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      ++..++..+..     .......+++.   .++.+.|.+.+..-               -|...|..++..+..
T Consensus        87 ~~~~l~~k~~~-----~~~Al~~~l~~---~~d~~~a~~~~~~~---------------~~~~lw~~~~~~~l~  137 (140)
T smart00299       87 EAVELYKKDGN-----FKDAIVTLIEH---LGNYEKAIEYFVKQ---------------NNPELWAEVLKALLD  137 (140)
T ss_pred             HHHHHHHhhcC-----HHHHHHHHHHc---ccCHHHHHHHHHhC---------------CCHHHHHHHHHHHHc
Confidence            77777766532     12233333332   27777777777643               255678888776653

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

Probab=96.15  E-value=0.13  Score=39.30  Aligned_cols=87  Identities=7%  Similarity=-0.015  Sum_probs=68.7

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFV   93 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~   93 (156)
                      .+...|+++.|...+++..+..  |+..             ..|..+-.+|.+.|++++|...+++..+... .+...|.
T Consensus        11 ~a~~~~~~~~Ai~~~~~Al~~~--P~~~-------------~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P-~~~~a~~   74 (356)
T PLN03088         11 EAFVDDDFALAVDLYTQAIDLD--PNNA-------------ELYADRAQANIKLGNFTEAVADANKAIELDP-SLAKAYL   74 (356)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC--CCCH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCHHHHH
Confidence            4457799999999999998743  4322             4566677788899999999999999987432 2455777


Q ss_pred             HHHHhhcCCCchHHHHHHHHhcc
Q 041561           94 AILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        94 ~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .+-.+|.+.|++++|...|+...
T Consensus        75 ~lg~~~~~lg~~~eA~~~~~~al   97 (356)
T PLN03088         75 RKGTACMKLEEYQTAKAALEKGA   97 (356)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHH
Confidence            77888889999999999999884

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

Probab=96.06  E-value=0.053  Score=35.61  Aligned_cols=71  Identities=11%  Similarity=0.119  Sum_probs=48.3

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH-----
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA-----   82 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----   82 (156)
                      ...+...+...|+.+.|..+...+.... +-|.              ..|-.+|.+|...|+..+|.++|+.+..     
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E--------------~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~e  129 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALD-PYDE--------------EAYRLLMRALAAQGRRAEALRVYERYRRRLREE  129 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-H--------------HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCH--------------HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3445566667888888888888886642 1233              6788899999999999999999999853     


Q ss_pred             CCCCccHHHHH
Q 041561           83 SGVKHDGVTFV   93 (156)
Q Consensus        83 ~g~~p~~~t~~   93 (156)
                      -|+.|+..|-.
T Consensus       130 lg~~Ps~~~~~  140 (146)
T PF03704_consen  130 LGIEPSPETRA  140 (146)
T ss_dssp             HS----HHHHH
T ss_pred             hCcCcCHHHHH
Confidence            39999887643

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

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.00  E-value=0.21  Score=32.03  Aligned_cols=105  Identities=10%  Similarity=0.038  Sum_probs=72.8

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc---HH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD---GV   90 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~---~~   90 (156)
                      ++-..|+.++|..+++.....|...+.. -..           +=.+-..+...|++++|..+|++....-  |+   ..
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~-~~a-----------~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~   75 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADR-RRA-----------LIQLASTLRNLGRYDEALALLEEALEEF--PDDELNA   75 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHH-HHH-----------HHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccH
Confidence            4456799999999999999988755432 122           2346677889999999999999987642  33   11


Q ss_pred             HHH-HHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           91 TFV-AILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        91 t~~-~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      ... .+--++...|+.++|...+-..             +.++..-|.--|..|+.
T Consensus        76 ~l~~f~Al~L~~~gr~~eAl~~~l~~-------------la~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   76 ALRVFLALALYNLGRPKEALEWLLEA-------------LAETLPRYRRAIRFYAD  118 (120)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHh
Confidence            111 1223666889999999888765             24455577777777654

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

Probab=95.94  E-value=0.1  Score=38.17  Aligned_cols=48  Identities=6%  Similarity=0.071  Sum_probs=28.2

Q ss_pred             CCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           68 EYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      +.+.+|+-+|++|-++ ..|+..+.|...-++...+++++|..+++...
T Consensus       187 ek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL  234 (299)
T KOG3081|consen  187 EKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEAL  234 (299)
T ss_pred             hhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHH
Confidence            3456666666666432 45556666666666666666666666666553

>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=95.89  E-value=0.4  Score=38.59  Aligned_cols=125  Identities=9%  Similarity=0.075  Sum_probs=92.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      ++.-+-..|-..|+.++|....+...++-  |+..             ..|..--+.+-+.|++++|.+.++.-+.-. .
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~ht--Pt~~-------------ely~~KarilKh~G~~~~Aa~~~~~Ar~LD-~  259 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIEHT--PTLV-------------ELYMTKARILKHAGDLKEAAEAMDEARELD-L  259 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhcC--CCcH-------------HHHHHHHHHHHHCCCHHHHHHHHHHHHhCC-h
Confidence            45666777889999999999999988763  5432             566777788889999999999999988755 4


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh----hH--HHHHHHHhhcCCHhHHhh
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV----VW--GDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~----~~--~~li~~~~~~g~~~~a~~  154 (156)
                      -|.+.-+-....+.|+|++++|.+++..+-++ +..+      .-|..    .|  .--=.+|.+.|++..|.+
T Consensus       260 ~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~-~~~~------~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk  326 (517)
T PF12569_consen  260 ADRYINSKCAKYLLRAGRIEEAEKTASLFTRE-DVDP------LSNLNDMQCMWFETECAEAYLRQGDYGLALK  326 (517)
T ss_pred             hhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCC-CCCc------ccCHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            47888888999999999999999999999433 2111      11221    11  222367888888887764

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 [], [].

>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=95.88  E-value=0.04  Score=31.01  Aligned_cols=63  Identities=10%  Similarity=0.125  Sum_probs=46.2

Q ss_pred             cCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHH
Q 041561           16 AKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAI   95 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l   95 (156)
                      .+.|++++|.++|+.+.+..-. |.              ..+-.+..+|.+.|++++|.++++.+...  .|+...|..+
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~-~~--------------~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l   64 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPD-NP--------------EARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQL   64 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTT-SH--------------HHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCC-CH--------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHH
Confidence            3578999999999999775321 33              45566889999999999999999998874  4554444433

...

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.87  E-value=0.14  Score=34.62  Aligned_cols=84  Identities=5%  Similarity=0.008  Sum_probs=62.7

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc--HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD--GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-  131 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-  131 (156)
                      ..|..+-..+...|++++|.+.|++.......++  ...+..+-..+.+.|+.++|...+......           .| 
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-----------~p~  104 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL-----------NPK  104 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----------Ccc
Confidence            4566677788889999999999999876543332  357778888888999999999999987432           33 


Q ss_pred             ChhhHHHHHHHHhhcCCH
Q 041561          132 DLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus       132 d~~~~~~li~~~~~~g~~  149 (156)
                      +...+..+-..|...|+.
T Consensus       105 ~~~~~~~lg~~~~~~g~~  122 (172)
T PRK02603        105 QPSALNNIAVIYHKRGEK  122 (172)
T ss_pred             cHHHHHHHHHHHHHcCCh
Confidence            455566666677776663

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

Probab=95.84  E-value=0.1  Score=39.82  Aligned_cols=83  Identities=13%  Similarity=0.029  Sum_probs=65.5

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVS  141 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~  141 (156)
                      ......|++++|.+.|++..+... -+...|..+-.++.+.|++++|...++.....          -..+...|..+-.
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l----------~P~~~~a~~~lg~   78 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLDP-NNAELYADRAQANIKLGNFTEAVADANKAIEL----------DPSLAKAYLRKGT   78 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CcCCHHHHHHHHH
Confidence            345578999999999999987542 24556777778888999999999999988432          1236678888889


Q ss_pred             HHhhcCCHhHHhhh
Q 041561          142 SCQVHSNVRLAKKA  155 (156)
Q Consensus       142 ~~~~~g~~~~a~~~  155 (156)
                      +|...|++++|.+.
T Consensus        79 ~~~~lg~~~eA~~~   92 (356)
T PLN03088         79 ACMKLEEYQTAKAA   92 (356)
T ss_pred             HHHHhCCHHHHHHH
Confidence            99999999999763

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

Probab=95.82  E-value=0.32  Score=43.05  Aligned_cols=138  Identities=9%  Similarity=0.023  Sum_probs=87.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHH-hCCCCchHHHhHHHHHhhhcc----------------------chHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVK-DGYGNDIFVGSAPINIYCNCG----------------------VTWNEMIHG   63 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~-~g~~~~~~~~~~li~~~~~~~----------------------~~~~~li~~   63 (156)
                      .|..|..-|.+....++|.++++.|.+ .|  -....|....+.+.+..                      ..-.-.+..
T Consensus      1532 V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqL 1609 (1710)
T KOG1070|consen 1532 VHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQL 1609 (1710)
T ss_pred             HHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHH
Confidence            456677777777778888888888754 44  44556666666665554                      111222333


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      -.++|+.+++..+|+.....-.+ -.-.|+.+|++-.+.|+.+.++.+|++... .++      +.+-=...|.-++..-
T Consensus      1610 EFk~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~-l~l------~~kkmKfffKkwLeyE 1681 (1710)
T KOG1070|consen 1610 EFKYGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIE-LKL------SIKKMKFFFKKWLEYE 1681 (1710)
T ss_pred             HhhcCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHh-cCC------ChhHhHHHHHHHHHHH
Confidence            34577777777777777654322 244688888888888888888888888833 221      1122346677777777


Q ss_pred             hhcCCHhHHhh
Q 041561          144 QVHSNVRLAKK  154 (156)
Q Consensus       144 ~~~g~~~~a~~  154 (156)
                      -.+|+-+.++.
T Consensus      1682 k~~Gde~~vE~ 1692 (1710)
T KOG1070|consen 1682 KSHGDEKNVEY 1692 (1710)
T ss_pred             HhcCchhhHHH
Confidence            77777655543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.81  E-value=0.33  Score=32.64  Aligned_cols=93  Identities=9%  Similarity=-0.082  Sum_probs=61.4

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .|..+...+...|++++|...|.......-.|...     .       .+|..+-..+...|++++|.+.++...... .
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~-----~-------~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~  103 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDR-----S-------YILYNIGLIHTSNGEHTKALEYYFQALERN-P  103 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhh-----H-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-c
Confidence            44556666777899999999999887653222110     0       356777788899999999999999987642 1


Q ss_pred             ccHHHHHHHHHhhc-------CCCchHHHHHHH
Q 041561           87 HDGVTFVAILTPCS-------HSGLVYAEVEIF  112 (156)
Q Consensus        87 p~~~t~~~ll~~~~-------~~~~~~~a~~~~  112 (156)
                      ....++..+...+.       ..|+.+.|...+
T Consensus       104 ~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~  136 (168)
T CHL00033        104 FLPQALNNMAVICHYRGEQAIEQGDSEIAEAWF  136 (168)
T ss_pred             CcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHH
Confidence            12334555555555       677776554444

>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=95.80  E-value=0.11  Score=40.32  Aligned_cols=86  Identities=10%  Similarity=0.057  Sum_probs=65.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhH
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVW  136 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~  136 (156)
                      -.+|+..+...+++++|.++|+++.+..  |+..  ..+.+.+...++-.+|.+++.+...+          .+-|....
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev~--~~LA~v~l~~~~E~~AI~ll~~aL~~----------~p~d~~LL  237 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRERD--PEVA--VLLARVYLLMNEEVEAIRLLNEALKE----------NPQDSELL  237 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhcC--CcHH--HHHHHHHHhcCcHHHHHHHHHHHHHh----------CCCCHHHH
Confidence            3567888888999999999999999876  5543  34677777778888888888887544          23366666


Q ss_pred             HHHHHHHhhcCCHhHHhhhC
Q 041561          137 GDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus       137 ~~li~~~~~~g~~~~a~~~~  156 (156)
                      +.-..-+...++.+.|.++|
T Consensus       238 ~~Qa~fLl~k~~~~lAL~iA  257 (395)
T PF09295_consen  238 NLQAEFLLSKKKYELALEIA  257 (395)
T ss_pred             HHHHHHHHhcCCHHHHHHHH
Confidence            66667789999999999875

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

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

Probab=95.70  E-value=0.04  Score=31.99  Aligned_cols=61  Identities=16%  Similarity=0.211  Sum_probs=48.4

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC----C-CCcc-HHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS----G-VKHD-GVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g-~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .+|+.+-..|...|++++|++.|++..+-    | -.|+ ..++..+-..+.+.|+.++|.+.+++-
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            46788889999999999999999997642    2 2243 557788888899999999999998864

...

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

Probab=95.70  E-value=0.061  Score=30.03  Aligned_cols=55  Identities=9%  Similarity=0.091  Sum_probs=44.8

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      ..+.+.|++++|...|+...+..  |+..             ..|..+-.++...|++++|...|++..+
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~--P~~~-------------~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD--PDNP-------------EAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS--TTHH-------------HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC--CCCH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45678899999999999998865  4332             6677778888999999999999999875

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

Probab=95.61  E-value=0.14  Score=40.32  Aligned_cols=118  Identities=13%  Similarity=0.192  Sum_probs=71.1

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhC-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDG-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +.+|...|...-|..-++.|+.+|-.+.+.| +.+++++++++|..|+...               +.-|.++|+.=.. 
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d---------------~~ta~~ifelGl~-  460 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGD---------------RATAYNIFELGLL-  460 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCC---------------cchHHHHHHHHHH-
Confidence            3567888888888888999999999999999 6899988888877666544               3444444433111 


Q ss_pred             CCCccHHHH-HHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC--hhhHHHHHHHHhhcCCH
Q 041561           84 GVKHDGVTF-VAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD--LVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        84 g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd--~~~~~~li~~~~~~g~~  149 (156)
                       ..||...| +-.+.-+.+.++-+.|+.+|+.-..+          +..+  ...|..||.--...|+.
T Consensus       461 -~f~d~~~y~~kyl~fLi~inde~naraLFetsv~r----------~~~~q~k~iy~kmi~YEs~~G~l  518 (660)
T COG5107         461 -KFPDSTLYKEKYLLFLIRINDEENARALFETSVER----------LEKTQLKRIYDKMIEYESMVGSL  518 (660)
T ss_pred             -hCCCchHHHHHHHHHHHHhCcHHHHHHHHHHhHHH----------HHHhhhhHHHHHHHHHHHhhcch
Confidence             12232222 23444455555666666666533222          1222  34555555555555555

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

Probab=95.56  E-value=0.25  Score=38.94  Aligned_cols=134  Identities=11%  Similarity=0.024  Sum_probs=76.0

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-------------------chHHHHHHHHHcCCCHHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------------------VTWNEMIHGYAENEYVEQAISLY   77 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-------------------~~~~~li~~~~~~g~~~~a~~~~   77 (156)
                      .+|++++|...+.+.....-.-....||+=+.+=....                   ...-.+.+-|-...++.+|.+++
T Consensus       502 ~ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  502 ANGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             ecCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            35777777777777665433333333443332222222                   22223444555556666777666


Q ss_pred             HHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCC-C---------------c----------CCCCC
Q 041561           78 KDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKP-K---------------C----------LMPYK  130 (156)
Q Consensus        78 ~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~---------------c----------~~~~~  130 (156)
                      .+  ...+.| |......+-+.|-+.|+-.+|++.+=.-   +..-| +               .          ..-+.
T Consensus       582 ~q--~~slip~dp~ilskl~dlydqegdksqafq~~yds---yryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliq  656 (840)
T KOG2003|consen  582 MQ--ANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDS---YRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQ  656 (840)
T ss_pred             HH--hcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhc---ccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcC
Confidence            43  334444 3445666667777777777777654321   11111 1               0          22268


Q ss_pred             CChhhHHHHH-HHHhhcCCHhHHhhh
Q 041561          131 DDLVVWGDLV-SSCQVHSNVRLAKKA  155 (156)
Q Consensus       131 pd~~~~~~li-~~~~~~g~~~~a~~~  155 (156)
                      |+..-|..|| +++.+.|++++|..+
T Consensus       657 p~~~kwqlmiasc~rrsgnyqka~d~  682 (840)
T KOG2003|consen  657 PNQSKWQLMIASCFRRSGNYQKAFDL  682 (840)
T ss_pred             ccHHHHHHHHHHHHHhcccHHHHHHH
Confidence            9999999999 456789999999763

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.55  E-value=0.11  Score=43.29  Aligned_cols=25  Identities=12%  Similarity=0.072  Sum_probs=17.8

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhC
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDG   35 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g   35 (156)
                      .+.+..+.+.+.+|..+++.+....
T Consensus       738 aieaai~akew~kai~ildniqdqk  762 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQK  762 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhc
Confidence            3455567778888888888876643

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

Probab=95.52  E-value=0.16  Score=37.66  Aligned_cols=87  Identities=15%  Similarity=0.119  Sum_probs=66.7

Q ss_pred             chHHHHHHHHHc-----CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCC----------------chHHHHHHHH
Q 041561           55 VTWNEMIHGYAE-----NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG----------------LVYAEVEIFN  113 (156)
Q Consensus        55 ~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~----------------~~~~a~~~~~  113 (156)
                      -+|-+.+.-|..     .+.++-..--++.|++-|++-|..+|+.||+.+=+..                +-.=+..+++
T Consensus        68 ~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLe  147 (406)
T KOG3941|consen   68 DSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLE  147 (406)
T ss_pred             HHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHH
Confidence            344455555544     3567777788888999999999999999998876644                2233667899


Q ss_pred             hcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHh
Q 041561          114 SMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVR  150 (156)
Q Consensus       114 ~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~  150 (156)
                      +| +.+|        +-||-.+=-.||++|.+.+.+-
T Consensus       148 qM-E~hG--------VmPdkE~e~~lvn~FGr~~~p~  175 (406)
T KOG3941|consen  148 QM-EWHG--------VMPDKEIEDILVNAFGRWNFPT  175 (406)
T ss_pred             HH-HHcC--------CCCchHHHHHHHHHhccccccH
Confidence            99 7887        6899999999999999988654

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=95.47  E-value=0.55  Score=37.68  Aligned_cols=147  Identities=9%  Similarity=0.014  Sum_probs=89.2

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHh-----CC-CCchHHHhH-HHHHhhhcc------------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKD-----GY-GNDIFVGSA-PINIYCNCG------------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----g~-~~~~~~~~~-li~~~~~~~------------------------   54 (156)
                      .|...+-..|...|+++.|+.++.+..+.     |. .|.+.+..- +=..|..-+                        
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            34555778889999999999999987543     31 222221111 222222222                        


Q ss_pred             ----chHHHHHHHHHcCCCHHHHHHHHHHHHH---C--C-CCccHHH-HHHHHHhhcCCCchHHHHHHHHhcccccccCC
Q 041561           55 ----VTWNEMIHGYAENEYVEQAISLYKDIIA---S--G-VKHDGVT-FVAILTPCSHSGLVYAEVEIFNSMEHDHEVKP  123 (156)
Q Consensus        55 ----~~~~~li~~~~~~g~~~~a~~~~~~m~~---~--g-~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~  123 (156)
                          .+++.|-..|.+.|++++|...+++-.+   +  | ..|...+ ++.+...|...+++++|..++..-.+.+.-.+
T Consensus       280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~  359 (508)
T KOG1840|consen  280 PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAP  359 (508)
T ss_pred             HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhc
Confidence                6677777788888888777766665431   1  2 2333332 44555666678888888877665433221000


Q ss_pred             CcCCCCC-CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          124 KCLMPYK-DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       124 ~c~~~~~-pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                        . .-. --..+++.|=..|-..|++++|+++
T Consensus       360 --g-~~~~~~a~~~~nl~~l~~~~gk~~ea~~~  389 (508)
T KOG1840|consen  360 --G-EDNVNLAKIYANLAELYLKMGKYKEAEEL  389 (508)
T ss_pred             --c-ccchHHHHHHHHHHHHHHHhcchhHHHHH
Confidence              0 011 1247799999999999999999875

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

Probab=95.46  E-value=0.25  Score=37.41  Aligned_cols=151  Identities=13%  Similarity=0.113  Sum_probs=88.7

Q ss_pred             CCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHH
Q 041561            2 YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMI   61 (156)
Q Consensus         2 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li   61 (156)
                      +|.+.||-.+-++|-+...++.|+.++.+-.+. ++-|+..-.-+-+.+-.-+                    +.-..+-
T Consensus       253 ~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia  331 (478)
T KOG1129|consen  253 FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLHPINVEAIACIA  331 (478)
T ss_pred             CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcCCccceeeeeee
Confidence            366677777777777777777777777765443 2223322222222221111                    3334455


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccc---cccCCC--------------
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD---HEVKPK--------------  124 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~~~--------------  124 (156)
                      .+|.-.++++.|++.|+++.+.|+. +...|+.+--.|.-.+++|.+.--|+.-..-   .|...+              
T Consensus       332 ~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD  410 (478)
T KOG1129|consen  332 VGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGD  410 (478)
T ss_pred             eccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccc
Confidence            5667788899999999999988865 4455555555566677777666555543211   111111              


Q ss_pred             ------c----CCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          125 ------C----LMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       125 ------c----~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                            |    ...-.-....+|-|----.+.|++++|+-
T Consensus       411 ~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Ars  450 (478)
T KOG1129|consen  411 FNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARS  450 (478)
T ss_pred             hHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHH
Confidence                  2    22223355677777777788999998874

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.42  E-value=0.31  Score=35.72  Aligned_cols=94  Identities=12%  Similarity=0.008  Sum_probs=65.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc--HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD--GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD  132 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd  132 (156)
                      ..|+..+.-+.+.|++++|...|+.+.+.-....  ...+-.+-..+...|+.++|...|..+...+.-     .+..| 
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~-----s~~~~-  217 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPK-----SPKAA-  217 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-----Ccchh-
Confidence            5677777766778999999999999987532211  235566778888999999999999999665421     11222 


Q ss_pred             hhhHHHHHHHHhhcCCHhHHhhh
Q 041561          133 LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       133 ~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       ..+-.+...+...|+.++|.++
T Consensus       218 -dAl~klg~~~~~~g~~~~A~~~  239 (263)
T PRK10803        218 -DAMFKVGVIMQDKGDTAKAKAV  239 (263)
T ss_pred             -HHHHHHHHHHHHcCCHHHHHHH
Confidence             2333345567788999998764

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

Probab=95.41  E-value=0.2  Score=39.70  Aligned_cols=100  Identities=17%  Similarity=0.142  Sum_probs=74.6

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAIL   96 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll   96 (156)
                      ..|++.+|.++|+.-.+  +.||.              -.|++.|+-=.+-..++.|..+++..+.  ++|+..+|--..
T Consensus       153 ~LgNi~gaRqiferW~~--w~P~e--------------qaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikya  214 (677)
T KOG1915|consen  153 MLGNIAGARQIFERWME--WEPDE--------------QAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYA  214 (677)
T ss_pred             HhcccHHHHHHHHHHHc--CCCcH--------------HHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHH
Confidence            34777888888876554  46888              5566666666777889999999999886  679999999888


Q ss_pred             HhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           97 TPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        97 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      +--.+.|+...++.++..-....|           |...-..++.+|+.
T Consensus       215 rFE~k~g~~~~aR~VyerAie~~~-----------~d~~~e~lfvaFA~  252 (677)
T KOG1915|consen  215 RFEEKHGNVALARSVYERAIEFLG-----------DDEEAEILFVAFAE  252 (677)
T ss_pred             HHHHhcCcHHHHHHHHHHHHHHhh-----------hHHHHHHHHHHHHH
Confidence            888899999999999988754432           44444555555554

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

Probab=95.39  E-value=0.073  Score=30.86  Aligned_cols=66  Identities=14%  Similarity=0.155  Sum_probs=49.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhC--CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDG--YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g--~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      .+|+.+=..+.+.|+.++|...|++..+..  ..++.   ..++       .+++.+-..|...|++++|.+.|++-.
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~---~~~a-------~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDH---PDTA-------NTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHH---HHHH-------HHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCC---HHHH-------HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            467777888889999999999999986541  22221   1112       678889999999999999999998753

...

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

Probab=95.29  E-value=0.3  Score=36.72  Aligned_cols=88  Identities=8%  Similarity=-0.037  Sum_probs=61.1

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-CccHH-
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV-KHDGV-   90 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~-   90 (156)
                      ..+...|++++|...++...+..  |+..             ..+..+-..|...|++++|.+.+++...... .|+.. 
T Consensus       122 ~~~~~~G~~~~A~~~~~~al~~~--p~~~-------------~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~  186 (355)
T cd05804         122 FGLEEAGQYDRAEEAARRALELN--PDDA-------------WAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRG  186 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC--CCCc-------------HHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhH
Confidence            45566777777777777776643  3321             4556667788889999999999988765422 23332 


Q ss_pred             -HHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           91 -TFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        91 -t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                       .|..+-..+...|+.++|..+++..
T Consensus       187 ~~~~~la~~~~~~G~~~~A~~~~~~~  212 (355)
T cd05804         187 HNWWHLALFYLERGDYEAALAIYDTH  212 (355)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence             3445667778899999999999886

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.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=95.23  E-value=0.35  Score=40.34  Aligned_cols=96  Identities=11%  Similarity=0.129  Sum_probs=77.7

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      .....+...+.+.+.+++|....++.....  ||..             ...+.+-.++.+.|+.++|.++|++....  
T Consensus       121 ~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~--p~~~-------------~~~~~~a~~l~~~g~~~~A~~~y~~~~~~--  183 (694)
T PRK15179        121 EAFILMLRGVKRQQGIEAGRAEIELYFSGG--SSSA-------------REILLEAKSWDEIGQSEQADACFERLSRQ--  183 (694)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhhcC--CCCH-------------HHHHHHHHHHHHhcchHHHHHHHHHHHhc--
Confidence            445667788889999999999999987753  5443             34556677888999999999999999883  


Q ss_pred             Ccc-HHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           86 KHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        86 ~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      .|+ ..++..+=.++...|+.++|...|+.-...
T Consensus       184 ~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        184 HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            444 678888888999999999999999988554

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

Probab=95.20  E-value=1  Score=40.17  Aligned_cols=145  Identities=15%  Similarity=0.211  Sum_probs=101.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHH-hCCCC---chHHHhHHHHHhhhcc-------------------chHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVK-DGYGN---DIFVGSAPINIYCNCG-------------------VTWNEMIH   62 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~-~g~~~---~~~~~~~li~~~~~~~-------------------~~~~~li~   62 (156)
                      ..|-.-|......+++++|++++++... -++.-   -...|.++++.--..|                   ..|..|..
T Consensus      1459 i~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~V~~~L~~ 1538 (1710)
T KOG1070|consen 1459 ILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCDAYTVHLKLLG 1538 (1710)
T ss_pred             hHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHHHHHHHHH
Confidence            5678888889999999999999998754 33322   2345666665544444                   56788999


Q ss_pred             HHHcCCCHHHHHHHHHHHHHC-CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-----------------
Q 041561           63 GYAENEYVEQAISLYKDIIAS-GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-----------------  124 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-----------------  124 (156)
                      -|.+.+..++|-++|+.|.++ |  -....|....+.+.+..+-+.|..++.+-.+-   .|.                 
T Consensus      1539 iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~---lPk~eHv~~IskfAqLEFk~ 1613 (1710)
T KOG1070|consen 1539 IYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKS---LPKQEHVEFISKFAQLEFKY 1613 (1710)
T ss_pred             HHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhh---cchhhhHHHHHHHHHHHhhc
Confidence            999999999999999999875 4  35667888888888888877777766544221   111                 


Q ss_pred             c------------CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          125 C------------LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       125 c------------~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      |            -...+.-.-.|+..|..-.++|+.+.++.+
T Consensus      1614 GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~l 1656 (1710)
T KOG1070|consen 1614 GDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDL 1656 (1710)
T ss_pred             CCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHH
Confidence            1            111112235688888888888888877654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=95.17  E-value=0.11  Score=31.99  Aligned_cols=64  Identities=8%  Similarity=0.074  Sum_probs=50.0

Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      |.-++.+-++.+..-.+.|+.....+.++||-|.+|+..|.++|+..+.+.          ..+...|..+++-
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~----------~~~~~~y~~~lqe   85 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC----------GAHKEIYPYILQE   85 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc----------cCchhhHHHHHHH
Confidence            344556666666667899999999999999999999999999999996563          2345577777653

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.

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

Probab=95.16  E-value=0.087  Score=32.73  Aligned_cols=71  Identities=8%  Similarity=0.163  Sum_probs=47.1

Q ss_pred             HHHHcCCCHH--HHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHH
Q 041561           62 HGYAENEYVE--QAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDL  139 (156)
Q Consensus        62 ~~~~~~g~~~--~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~l  139 (156)
                      ..|....+.|  +..+-+..+....+.|+.....+.|+||-|..|+..|.++|+..+.+.|          +....|..+
T Consensus        16 ~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~----------~~~~~Y~~~   85 (108)
T PF02284_consen   16 EKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG----------NKKEIYPYI   85 (108)
T ss_dssp             HHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT----------T-TTHHHHH
T ss_pred             HHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc----------ChHHHHHHH
Confidence            3444444333  4555566666678999999999999999999999999999999976643          333378877


Q ss_pred             HHH
Q 041561          140 VSS  142 (156)
Q Consensus       140 i~~  142 (156)
                      ++-
T Consensus        86 lqE   88 (108)
T PF02284_consen   86 LQE   88 (108)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            753

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 ....

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

Probab=95.03  E-value=0.38  Score=36.29  Aligned_cols=80  Identities=15%  Similarity=0.005  Sum_probs=44.0

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHH-HhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAIL-TPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVS  141 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll-~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~  141 (156)
                      .+.-..+++.|..++..-.+.  .|+.+--++++ +-....|+.+.|.+.++...++.         ..--..+-..|..
T Consensus       189 ~~~~~~~~d~A~~~l~kAlqa--~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn---------~~yl~evl~~L~~  257 (389)
T COG2956         189 QALASSDVDRARELLKKALQA--DKKCVRASIILGRVELAKGDYQKAVEALERVLEQN---------PEYLSEVLEMLYE  257 (389)
T ss_pred             HHhhhhhHHHHHHHHHHHHhh--CccceehhhhhhHHHHhccchHHHHHHHHHHHHhC---------hHHHHHHHHHHHH
Confidence            333344555555555554432  33344333333 34446677777777777663331         1223355677778


Q ss_pred             HHhhcCCHhHHh
Q 041561          142 SCQVHSNVRLAK  153 (156)
Q Consensus       142 ~~~~~g~~~~a~  153 (156)
                      +|...|++++..
T Consensus       258 ~Y~~lg~~~~~~  269 (389)
T COG2956         258 CYAQLGKPAEGL  269 (389)
T ss_pred             HHHHhCCHHHHH
Confidence            888888887654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=94.80  E-value=0.19  Score=28.55  Aligned_cols=55  Identities=13%  Similarity=0.077  Sum_probs=44.4

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      ..|.+.+++++|.++++.+...... +...+...-..+.+.|++++|...|+...+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPD-DPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            5678999999999999999885422 444566666777899999999999999943

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

Probab=94.79  E-value=0.79  Score=33.66  Aligned_cols=108  Identities=6%  Similarity=-0.050  Sum_probs=70.0

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTF   92 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~   92 (156)
                      ..|...++.++|++.......    .+...-|                ...+-+..++|-|.+..+.|.+-   -+..|.
T Consensus       116 ~i~~~~~~~deAl~~~~~~~~----lE~~Al~----------------VqI~lk~~r~d~A~~~lk~mq~i---ded~tL  172 (299)
T KOG3081|consen  116 IIYMHDGDFDEALKALHLGEN----LEAAALN----------------VQILLKMHRFDLAEKELKKMQQI---DEDATL  172 (299)
T ss_pred             HHhhcCCChHHHHHHHhccch----HHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHcc---chHHHH
Confidence            346678888888887776211    2221111                12234555678888888888753   244555


Q ss_pred             HHHHHhh----cCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561           93 VAILTPC----SHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus        93 ~~ll~~~----~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                      +.|-.+.    ...+.+.+|+-+|++|..+          ..|+..+-|-+..++...|++++|+
T Consensus       173 tQLA~awv~la~ggek~qdAfyifeE~s~k----------~~~T~~llnG~Av~~l~~~~~eeAe  227 (299)
T KOG3081|consen  173 TQLAQAWVKLATGGEKIQDAFYIFEELSEK----------TPPTPLLLNGQAVCHLQLGRYEEAE  227 (299)
T ss_pred             HHHHHHHHHHhccchhhhhHHHHHHHHhcc----------cCCChHHHccHHHHHHHhcCHHHHH
Confidence            5444443    3455788888888888554          4678888888888888888888875

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

Probab=94.71  E-value=0.55  Score=38.56  Aligned_cols=46  Identities=4%  Similarity=0.026  Sum_probs=35.4

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG   54 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~   54 (156)
                      -|++|-+.|.+.|.+++|..++++-.+.  ...+.-|+.+.++|++-.
T Consensus       250 Lw~SLAdYYIr~g~~ekarDvyeeai~~--v~tvrDFt~ifd~Ya~FE  295 (835)
T KOG2047|consen  250 LWCSLADYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIFDAYAQFE  295 (835)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHHHHHHHHH
Confidence            4889999999999999999999987654  234555666677776554

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=94.68  E-value=1  Score=36.28  Aligned_cols=109  Identities=11%  Similarity=0.052  Sum_probs=76.0

Q ss_pred             CCcccHHHHHHHhcCC-----CchHHHHHHHHHHHHhCCCCch-HHHhHHHHHhhhcc----------------------
Q 041561            3 PTQFPFTTVLSSCAKL-----SSLFLGRQILTRIVKDGYGNDI-FVGSAPINIYCNCG----------------------   54 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~-----~~~~~a~~~~~~m~~~g~~~~~-~~~~~li~~~~~~~----------------------   54 (156)
                      .|...|...+++....     ++...|..+|++..+.  .||- ..|..+-.+|....                      
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            4567888888886533     2366788888888764  3442 23332222221110                      


Q ss_pred             --------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           55 --------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        55 --------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                              ..|..+--.....|++++|...|++...-.  |+...|..+-+.+...|+.++|.+.+.+-
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A  479 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTA  479 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                    345555455556799999999999988744  78889999999999999999999999876

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

Probab=94.61  E-value=0.87  Score=38.50  Aligned_cols=120  Identities=15%  Similarity=0.094  Sum_probs=87.6

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhCCCC--chHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDGYGN--DIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g~~~--~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      ++-++.+....+..+.+...+++..+.|  ++              ..|--+-++|-..|.+++|+++|..+.....--+
T Consensus       383 l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~--------------dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~  448 (895)
T KOG2076|consen  383 LMICLVHLKERELLEALLHFLVEDNVWVSDDV--------------DLYLDLADALTNIGKYKEALRLLSPITNREGYQN  448 (895)
T ss_pred             HhhhhhcccccchHHHHHHHHHHhcCChhhhH--------------HHHHHHHHHHHhcccHHHHHHHHHHHhcCccccc
Confidence            3344556666777777777777776433  33              5667788889999999999999999987655556


Q ss_pred             HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-hhhHHHHHHHHhhcCCHhHHhhh
Q 041561           89 GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        89 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ...|-.+-..|...|..++|.+.++.....           .|| .-.=-+|=..+-+.|+.|+|.++
T Consensus       449 ~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~-----------~p~~~D~Ri~Lasl~~~~g~~EkalEt  505 (895)
T KOG2076|consen  449 AFVWYKLARCYMELGEYEEAIEFYEKVLIL-----------APDNLDARITLASLYQQLGNHEKALET  505 (895)
T ss_pred             hhhhHHHHHHHHHHhhHHHHHHHHHHHHhc-----------CCCchhhhhhHHHHHHhcCCHHHHHHH
Confidence            778888888888999999999999988433           332 22233455667888999988764

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

Probab=94.60  E-value=0.31  Score=39.93  Aligned_cols=27  Identities=4%  Similarity=0.074  Sum_probs=14.0

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVK   33 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~   33 (156)
                      +|.-+-..+-..|++++|..+++.+.+
T Consensus       118 ~ysn~aN~~kerg~~~~al~~y~~aie  144 (966)
T KOG4626|consen  118 AYSNLANILKERGQLQDALALYRAAIE  144 (966)
T ss_pred             HHHHHHHHHHHhchHHHHHHHHHHHHh
Confidence            344444444455555555555555544

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=94.37  E-value=1.2  Score=31.39  Aligned_cols=112  Identities=8%  Similarity=-0.054  Sum_probs=75.1

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCC-CCch-HHHhHHHHHhhhc--------c--------------------ch
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGY-GNDI-FVGSAPINIYCNC--------G--------------------VT   56 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~-~~~~~li~~~~~~--------~--------------------~~   56 (156)
                      ++..+-..+.+.|+++.|...++.+.+..- .|.. ..+..+-..|.+.        |                    ..
T Consensus        72 a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~  151 (235)
T TIGR03302        72 AQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYA  151 (235)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhH
Confidence            455666777888999999999998876432 1211 1222222222221        1                    01


Q ss_pred             H-----------------HHHHHHHHcCCCHHHHHHHHHHHHHCCC-Cc-cHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           57 W-----------------NEMIHGYAENEYVEQAISLYKDIIASGV-KH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        57 ~-----------------~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +                 -.+-..|.+.|++++|...|++..+... .| ....+..+..++.+.|+.++|...++.+..
T Consensus       152 ~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~  231 (235)
T TIGR03302       152 PDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGA  231 (235)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            1                 1344567788999999999999887532 23 356888999999999999999999998855


Q ss_pred             c
Q 041561          118 D  118 (156)
Q Consensus       118 ~  118 (156)
                      +
T Consensus       232 ~  232 (235)
T TIGR03302       232 N  232 (235)
T ss_pred             h
Confidence            4

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).

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=94.21  E-value=0.33  Score=40.65  Aligned_cols=106  Identities=11%  Similarity=0.137  Sum_probs=71.7

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      -|..+-.-|+..|+++.|+++|-+.                       ..|+-.|..|.+.|++++|.++-.+.  .|..
T Consensus       767 yy~~iadhyan~~dfe~ae~lf~e~-----------------------~~~~dai~my~k~~kw~da~kla~e~--~~~e  821 (1636)
T KOG3616|consen  767 YYGEIADHYANKGDFEIAEELFTEA-----------------------DLFKDAIDMYGKAGKWEDAFKLAEEC--HGPE  821 (1636)
T ss_pred             cchHHHHHhccchhHHHHHHHHHhc-----------------------chhHHHHHHHhccccHHHHHHHHHHh--cCch
Confidence            3566778889999999999988765                       44566788888999998888876543  3555


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .....|-+--.-+-+.|++.+|.+++-.+             -.||.     -|+.|-++|..+...++
T Consensus       822 ~t~~~yiakaedldehgkf~eaeqlyiti-------------~~p~~-----aiqmydk~~~~ddmirl  872 (1636)
T KOG3616|consen  822 ATISLYIAKAEDLDEHGKFAEAEQLYITI-------------GEPDK-----AIQMYDKHGLDDDMIRL  872 (1636)
T ss_pred             hHHHHHHHhHHhHHhhcchhhhhheeEEc-------------cCchH-----HHHHHHhhCcchHHHHH
Confidence            55556655555566777777777776555             13443     35566666666655543

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

Probab=94.20  E-value=1.5  Score=31.59  Aligned_cols=104  Identities=10%  Similarity=0.040  Sum_probs=58.2

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCH
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYV   70 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~   70 (156)
                      +=-+|.+.|+...|+.-++...++. +.+..+|..+-..|-+.|                    ..-|.-=.=+|..|++
T Consensus        41 Lal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~  119 (250)
T COG3063          41 LALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRP  119 (250)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCCh
Confidence            3345667788888888888777653 124455666666666666                    1112222223556667


Q ss_pred             HHHHHHHHHHHHCC-CCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           71 EQAISLYKDIIASG-VKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        71 ~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ++|...|++-...- +.--..||..+--+-.+.|+.+.|+..|.+-
T Consensus       120 ~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~ra  165 (250)
T COG3063         120 EEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRA  165 (250)
T ss_pred             HHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHH
Confidence            77777776665531 1111234444444444666666666666654

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=94.05  E-value=0.58  Score=39.57  Aligned_cols=77  Identities=10%  Similarity=0.090  Sum_probs=42.0

Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      +.|..++|..+++....-+.. |..|.-.+-..|-+.+++|++..+++.....           -|+...-..+..+|.+
T Consensus        55 r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~-----------~P~eell~~lFmayvR  122 (932)
T KOG2053|consen   55 RLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK-----------YPSEELLYHLFMAYVR  122 (932)
T ss_pred             HhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-----------CCcHHHHHHHHHHHHH
Confidence            455556666555555443333 5555555555555666666666666655332           3455555555566666


Q ss_pred             cCCHhHHhh
Q 041561          146 HSNVRLAKK  154 (156)
Q Consensus       146 ~g~~~~a~~  154 (156)
                      .+++.+-++
T Consensus       123 ~~~yk~qQk  131 (932)
T KOG2053|consen  123 EKSYKKQQK  131 (932)
T ss_pred             HHHHHHHHH
Confidence            555554443

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

Probab=93.99  E-value=2  Score=35.47  Aligned_cols=27  Identities=4%  Similarity=0.127  Sum_probs=14.2

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVK   33 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~   33 (156)
                      .|+-+-.++-..|++.+|++.++....
T Consensus       322 Ay~NlanALkd~G~V~ea~~cYnkaL~  348 (966)
T KOG4626|consen  322 AYNNLANALKDKGSVTEAVDCYNKALR  348 (966)
T ss_pred             HHhHHHHHHHhccchHHHHHHHHHHHH
Confidence            445555555555555555555554443

>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=93.93  E-value=0.34  Score=27.15  Aligned_cols=59  Identities=15%  Similarity=0.234  Sum_probs=48.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCC-chHHHHHHHHhc
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG-LVYAEVEIFNSM  115 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~m  115 (156)
                      .|..+=..+...|++++|.+.|++..+.. .-+...|..+-.++.+.| +.++|...++.-
T Consensus         5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    5 AWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             HHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            56777788899999999999999988753 225557777778888898 799999988865

...

>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=93.85  E-value=0.095  Score=34.25  Aligned_cols=118  Identities=17%  Similarity=0.240  Sum_probs=65.9

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      ..+++.+.+.+.++.....++.+...+-..+....+.++              ..|++.+++++..++++       ..+
T Consensus        11 ~~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~--------------~ly~~~~~~~~l~~~L~-------~~~   69 (143)
T PF00637_consen   11 SEVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLL--------------ELYIKYDPYEKLLEFLK-------TSN   69 (143)
T ss_dssp             CCCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHH--------------HHHHCTTTCCHHHHTTT-------SSS
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHH--------------HHHHhcCCchHHHHHcc-------ccc
Confidence            346778888889999999999998776666675555554              45555554455555554       111


Q ss_pred             HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-------------cCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           89 GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-------------CLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        89 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-------------c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                      .+-...+++.|-+.+.++++.-++..+ ..+.---.             +-. -.+|..+|..++..|...+..
T Consensus        70 ~yd~~~~~~~c~~~~l~~~a~~Ly~~~-~~~~~al~i~~~~~~~~~a~e~~~-~~~~~~l~~~l~~~~l~~~~~  141 (143)
T PF00637_consen   70 NYDLDKALRLCEKHGLYEEAVYLYSKL-GNHDEALEILHKLKDYEEAIEYAK-KVDDPELWEQLLKYCLDSKPF  141 (143)
T ss_dssp             SS-CTHHHHHHHTTTSHHHHHHHHHCC-TTHTTCSSTSSSTHCSCCCTTTGG-GCSSSHHHHHHHHHHCTSTCT
T ss_pred             ccCHHHHHHHHHhcchHHHHHHHHHHc-ccHHHHHHHHHHHccHHHHHHHHH-hcCcHHHHHHHHHHHHhcCcc
Confidence            133334455555555555555555544 21110000             001 135688899999888776653

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=93.71  E-value=1.8  Score=31.73  Aligned_cols=99  Identities=7%  Similarity=-0.013  Sum_probs=65.1

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCch-HHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDI-FVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~-~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      .|...+....+.|+.++|...|+.+.+.-  |+. .+-           ..+--+-..|...|++++|...|+.+.+.-.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~-----------~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP  211 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQP-----------NANYWLGQLNYNKGKKDDAAYYFASVVKNYP  211 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchH-----------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC
Confidence            45555555566789999999999887642  222 000           1223455667889999999999999986421


Q ss_pred             C-c-cHHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           86 K-H-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        86 ~-p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      . | ....+-.+...+...|+.++|..+++.+.+.
T Consensus       212 ~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        212 KSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             CCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            1 1 1222333344555889999999999998655

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=93.71  E-value=1.3  Score=29.23  Aligned_cols=98  Identities=11%  Similarity=0.115  Sum_probs=66.1

Q ss_pred             CCCchHHHHHHHHHHHHhC-C-CCchHHHhHH------------------------------HHHhhhcc---chHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDG-Y-GNDIFVGSAP------------------------------INIYCNCG---VTWNEMI   61 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g-~-~~~~~~~~~l------------------------------i~~~~~~~---~~~~~li   61 (156)
                      -.|++++..++......+. . .-|++.+|.+                              +.+|++.+   ...+..+
T Consensus        14 ldG~V~qGveii~k~v~Ssni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n~~se~vD~AL   93 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNSSNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRNKLSEYVDLAL   93 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHHS-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT---HHHHHHH
T ss_pred             HhchHHHHHHHHHHHcCcCCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhcchHHHHHHHH
Confidence            3467777777777765543 2 3456666644                              33343333   6677788


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +.....|.-|+..++..++.+++ .|+....-.+-.||.+.|+..++-+++.+-
T Consensus        94 d~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~A  146 (161)
T PF09205_consen   94 DILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEA  146 (161)
T ss_dssp             HHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            88899999999999999987643 677888888999999999999999998876

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

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

Probab=93.62  E-value=0.85  Score=34.42  Aligned_cols=82  Identities=18%  Similarity=0.114  Sum_probs=65.3

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      .+-+..|.-+...|+...|.++-.+.+    .||..-|-.-|++++..+++++-.++-..               +.++.
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s---------------kKsPI  238 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS---------------KKSPI  238 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC---------------CCCCC
Confidence            455666777788899988888877774    68999999999999999999988776542               11346


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      =|..++.+|...|+.++|.+.
T Consensus       239 GyepFv~~~~~~~~~~eA~~y  259 (319)
T PF04840_consen  239 GYEPFVEACLKYGNKKEASKY  259 (319)
T ss_pred             ChHHHHHHHHHCCCHHHHHHH
Confidence            677799999999999998764

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

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

Probab=93.47  E-value=2.3  Score=35.16  Aligned_cols=97  Identities=13%  Similarity=0.184  Sum_probs=60.5

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC----------
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK----------  124 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~----------  124 (156)
                      ..|.-.|.=...++.++-+.++++.-.+  +.|  ..-+-.|.-++..+++++|.+.+.....+-.+...          
T Consensus       139 rIW~lyl~Fv~~~~lPets~rvyrRYLk--~~P--~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~  214 (835)
T KOG2047|consen  139 RIWDLYLKFVESHGLPETSIRVYRRYLK--VAP--EAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWL  214 (835)
T ss_pred             cchHHHHHHHHhCCChHHHHHHHHHHHh--cCH--HHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHH
Confidence            4555556655666666666666666543  222  23555566666777777777666665433222211          


Q ss_pred             --c---------------------CCCCCCCh--hhHHHHHHHHhhcCCHhHHhhh
Q 041561          125 --C---------------------LMPYKDDL--VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       125 --c---------------------~~~~~pd~--~~~~~li~~~~~~g~~~~a~~~  155 (156)
                        |                     +.+.-||-  ..|++|-.-|.+.|++|+|+.+
T Consensus       215 elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDv  270 (835)
T KOG2047|consen  215 ELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDV  270 (835)
T ss_pred             HHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence              3                     22233443  6799999999999999999864

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

Probab=93.25  E-value=2.6  Score=31.26  Aligned_cols=98  Identities=5%  Similarity=-0.035  Sum_probs=76.3

Q ss_pred             hHHHhHHHHHhhhcc--chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           40 IFVGSAPINIYCNCG--VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        40 ~~~~~~li~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      ...|-..++.+.+.-  .++..++..+...|+.+.+.+.++++.... .-|+..|..++.+|.+.|+...|.+.++++.+
T Consensus       137 f~~WV~~~R~~l~e~~~~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         137 FDEWVLEQRRALEELFIKALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence            555555555554443  678899999999999999999999998765 45788999999999999999999999998854


Q ss_pred             ccccCCCcCCCCCCChhhHHHHHHH
Q 041561          118 DHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus       118 ~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      ...-    ..++.|...++......
T Consensus       216 ~~~e----dlgi~P~~~~~~~y~~~  236 (280)
T COG3629         216 TLAE----ELGIDPAPELRALYEEI  236 (280)
T ss_pred             Hhhh----hcCCCccHHHHHHHHHH
Confidence            1111    22368888888777766

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=93.21  E-value=1.3  Score=29.79  Aligned_cols=88  Identities=8%  Similarity=-0.021  Sum_probs=65.3

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVA   94 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~   94 (156)
                      +-..|++++|+++|..+....  |...             .-|-.|=.++-..|++++|.+.|.....-.+ -|...+-.
T Consensus        45 ly~~G~l~~A~~~f~~L~~~D--p~~~-------------~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~  108 (157)
T PRK15363         45 LMEVKEFAGAARLFQLLTIYD--AWSF-------------DYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWA  108 (157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC--cccH-------------HHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHH
Confidence            457799999999999987643  3222             4466667777889999999999999877553 34445555


Q ss_pred             HHHhhcCCCchHHHHHHHHhcccc
Q 041561           95 ILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        95 ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      +=.++...|+.+.|++-|+.....
T Consensus       109 ag~c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        109 AAECYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            566777899999999999977443

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.13  E-value=2.4  Score=34.56  Aligned_cols=118  Identities=9%  Similarity=0.040  Sum_probs=70.9

Q ss_pred             HHHHHhcCCCchHHHHHHHH--------HHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561           10 TVLSSCAKLSSLFLGRQILT--------RIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~--------~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      +.+......|+++.|.+++.        .+.+.+..|-.+                ..+..-+.+.++-+.|..++++-.
T Consensus       381 ~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V----------------~aiv~l~~~~~~~~~a~~vl~~Ai  444 (652)
T KOG2376|consen  381 LRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTV----------------GAIVALYYKIKDNDSASAVLDSAI  444 (652)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHH----------------HHHHHHHHhccCCccHHHHHHHHH
Confidence            45666778899999999999        555555555443                344444555555555555555543


Q ss_pred             HC--CCCccHHHHHHHHH----hhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           82 AS--GVKHDGVTFVAILT----PCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        82 ~~--g~~p~~~t~~~ll~----~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ..  .-.+......+++.    .--+.|+.++|..+++++.+.          -.+|..+..-++.+|++. ++++|..
T Consensus       445 ~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~----------n~~d~~~l~~lV~a~~~~-d~eka~~  512 (652)
T KOG2376|consen  445 KWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKF----------NPNDTDLLVQLVTAYARL-DPEKAES  512 (652)
T ss_pred             HHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHh----------CCchHHHHHHHHHHHHhc-CHHHHHH
Confidence            21  11222233333332    223568888888888888443          256788888888888877 6666654

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

Probab=93.11  E-value=1.1  Score=37.21  Aligned_cols=117  Identities=14%  Similarity=0.153  Sum_probs=82.5

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTF   92 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~   92 (156)
                      ..+-+.|-...|..+|+.+                       ..|.-+|.+|...|+-++|..+..+-.+  -.||..-|
T Consensus       406 ell~slGitksAl~I~Erl-----------------------emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~ly  460 (777)
T KOG1128|consen  406 ELLLSLGITKSALVIFERL-----------------------EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLY  460 (777)
T ss_pred             HHHHHcchHHHHHHHHHhH-----------------------HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhH
Confidence            3444556666666666665                       6778888888888888888888877766  46778888


Q ss_pred             HHHHHhhcCCCchHHHHHHHHhcccc--cc----cCC--C--------------------------c-------------
Q 041561           93 VAILTPCSHSGLVYAEVEIFNSMEHD--HE----VKP--K--------------------------C-------------  125 (156)
Q Consensus        93 ~~ll~~~~~~~~~~~a~~~~~~m~~~--~~----~~~--~--------------------------c-------------  125 (156)
                      -.+-+..-...-+++|.+++++...+  ..    +..  +                          |             
T Consensus       461 c~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~  540 (777)
T KOG1128|consen  461 CLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVK  540 (777)
T ss_pred             HHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHH
Confidence            88888777777777787777766443  11    111  1                          1             


Q ss_pred             ----CCCCCCCh-hhHHHHHHHHhhcCCHhHHhh
Q 041561          126 ----LMPYKDDL-VVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       126 ----~~~~~pd~-~~~~~li~~~~~~g~~~~a~~  154 (156)
                          -....||. ..||.+=.+|.+.|+..+|.+
T Consensus       541 aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~  574 (777)
T KOG1128|consen  541 AFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFR  574 (777)
T ss_pred             HHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHH
Confidence                33356655 569999999999999988875

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

Probab=93.06  E-value=1.7  Score=37.87  Aligned_cols=126  Identities=12%  Similarity=0.139  Sum_probs=64.7

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      |+..|.-+++.+.+.|.+++..+.+-..++..-.|...                +.||-+|++.+++.+.+++.      
T Consensus      1132 Dps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id----------------~eLi~AyAkt~rl~elE~fi------ 1189 (1666)
T KOG0985|consen 1132 DPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID----------------SELIFAYAKTNRLTELEEFI------ 1189 (1666)
T ss_pred             CcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch----------------HHHHHHHHHhchHHHHHHHh------
Confidence            44555666666666666666555555444444444432                45666666666665544443      


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-------c-----CCCCCCChhhHHHHHHHHhhcCCHhH
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-------C-----LMPYKDDLVVWGDLVSSCQVHSNVRL  151 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-------c-----~~~~~pd~~~~~~li~~~~~~g~~~~  151 (156)
                       ..||..-.-.+=+-|-..+.++.|+-++... ..+.-...       .     ...-..+.+||.-+=-+|.-.+.+..
T Consensus      1190 -~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~v-SN~a~La~TLV~LgeyQ~AVD~aRKAns~ktWK~VcfaCvd~~EFrl 1267 (1666)
T KOG0985|consen 1190 -AGPNVANIQQVGDRCFEEKMYEAAKLLYSNV-SNFAKLASTLVYLGEYQGAVDAARKANSTKTWKEVCFACVDKEEFRL 1267 (1666)
T ss_pred             -cCCCchhHHHHhHHHhhhhhhHHHHHHHHHh-hhHHHHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHhchhhhhH
Confidence             3444444444444444555555554444433 11110000       0     00113466778777777777777766


Q ss_pred             Hh
Q 041561          152 AK  153 (156)
Q Consensus       152 a~  153 (156)
                      |.
T Consensus      1268 AQ 1269 (1666)
T KOG0985|consen 1268 AQ 1269 (1666)
T ss_pred             HH
Confidence            64

>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=92.86  E-value=0.83  Score=25.51  Aligned_cols=63  Identities=6%  Similarity=0.008  Sum_probs=49.8

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCC-CHHHHHHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENE-YVEQAISLYKDIIA   82 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~   82 (156)
                      +.+|..+=..+.+.|++++|...|+...+..  |+..             ..|..+-.+|.+.| ++++|.+.|++-.+
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~--p~~~-------------~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD--PNNA-------------EAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS--TTHH-------------HHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCH-------------HHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            4566777777889999999999999998863  4332             56777778888999 79999999987654

...

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=92.84  E-value=1.1  Score=30.19  Aligned_cols=82  Identities=12%  Similarity=-0.004  Sum_probs=59.5

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhc-CCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHH
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCS-HSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDL  139 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~-~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~l  139 (156)
                      -.-+...|++++|.++|+-+..  +.|+...|--=+-+|. ..|++++|.+.+..-. ...         +-|.+.+-.+
T Consensus        42 A~~ly~~G~l~~A~~~f~~L~~--~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~-~L~---------~ddp~~~~~a  109 (157)
T PRK15363         42 AMQLMEVKEFAGAARLFQLLTI--YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAA-QIK---------IDAPQAPWAA  109 (157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH--hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHH-hcC---------CCCchHHHHH
Confidence            3445689999999999999876  4555555444444444 6899999999999873 211         2366777777


Q ss_pred             HHHHhhcCCHhHHhh
Q 041561          140 VSSCQVHSNVRLAKK  154 (156)
Q Consensus       140 i~~~~~~g~~~~a~~  154 (156)
                      =.++...|+.+.|++
T Consensus       110 g~c~L~lG~~~~A~~  124 (157)
T PRK15363        110 AECYLACDNVCYAIK  124 (157)
T ss_pred             HHHHHHcCCHHHHHH
Confidence            788888888888875

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=92.84  E-value=0.43  Score=37.56  Aligned_cols=125  Identities=10%  Similarity=0.036  Sum_probs=82.1

Q ss_pred             CCCchHHHHHHHHHHHHhCC-CC----chHHHhHHHHHhhhcc-----------------chHHHHHHHHH--cCCCHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGY-GN----DIFVGSAPINIYCNCG-----------------VTWNEMIHGYA--ENEYVEQ   72 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~-~~----~~~~~~~li~~~~~~~-----------------~~~~~li~~~~--~~g~~~~   72 (156)
                      +.+++++++.+|...-+.-- .|    .-..-+.+|++|...+                 ..|-.+..+..  +.++.++
T Consensus        18 kq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~nld~Me~~l~~l~~~~~~s~~l~LF~~L~~Y~~k~~~k   97 (549)
T PF07079_consen   18 KQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNNLDLMEKQLMELRQQFGKSAYLPLFKALVAYKQKEYRK   97 (549)
T ss_pred             HHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhhHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhhhHHH
Confidence            66889999999999855321 11    1345668888988887                 44555554433  4566777


Q ss_pred             HHHHHHHHHHC--C------------CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHH
Q 041561           73 AISLYKDIIAS--G------------VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGD  138 (156)
Q Consensus        73 a~~~~~~m~~~--g------------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~  138 (156)
                      |.+.+..=..+  +            .-+|-+-=+...+++...|.+++++.+++++..+.=     +..+.+|..+||.
T Consensus        98 al~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~ll-----krE~~w~~d~yd~  172 (549)
T PF07079_consen   98 ALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLL-----KRECEWNSDMYDR  172 (549)
T ss_pred             HHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHh-----hhhhcccHHHHHH
Confidence            77776665443  2            233444445677888899999999999998854421     0013478999998


Q ss_pred             HHHHHhhc
Q 041561          139 LVSSCQVH  146 (156)
Q Consensus       139 li~~~~~~  146 (156)
                      .+-.+.++
T Consensus       173 ~vlmlsrS  180 (549)
T PF07079_consen  173 AVLMLSRS  180 (549)
T ss_pred             HHHHHhHH
Confidence            66665554

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

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

Probab=92.83  E-value=2.5  Score=36.40  Aligned_cols=109  Identities=6%  Similarity=0.026  Sum_probs=79.1

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhC-CCCchHHHhHHHHHhhhcc----------------------------
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDG-YGNDIFVGSAPINIYCNCG----------------------------   54 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~~----------------------------   54 (156)
                      +...+..|+..+-+.+++++|.++.+...+.. =.+....+..+  .|.+.+                            
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~--l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~~~  107 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGI--LSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHICD  107 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHH--HHHhhcchhhhhhhhhhhhcccccchhHHHHHHH
Confidence            34567788999999999999999999765542 23444444444  233332                            


Q ss_pred             ---------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           55 ---------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        55 ---------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                               ...-.+..+|-+.|+.+++.++|++..+-. .-|....|.+-..++.. ++++|.++...-.
T Consensus       108 ~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV  176 (906)
T PRK14720        108 KILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAI  176 (906)
T ss_pred             HHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHH
Confidence                     334457777778899999999999999866 44666788888888877 9999998766553

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.50  E-value=1.5  Score=33.73  Aligned_cols=85  Identities=9%  Similarity=0.099  Sum_probs=43.1

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHH
Q 041561           59 EMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGD  138 (156)
Q Consensus        59 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~  138 (156)
                      ++.+.+.-..++|+++-.+...+.-=..-|.+-|| +-+|.+.-|+..+|+++|-.+. ..         --.|..+|.+
T Consensus       364 smAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is-~~---------~ikn~~~Y~s  432 (557)
T KOG3785|consen  364 SMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRIS-GP---------EIKNKILYKS  432 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhc-Ch---------hhhhhHHHHH
Confidence            34444444445555555554444321222222222 4455666666777777766662 11         1245666666


Q ss_pred             HH-HHHhhcCCHhHHhh
Q 041561          139 LV-SSCQVHSNVRLAKK  154 (156)
Q Consensus       139 li-~~~~~~g~~~~a~~  154 (156)
                      |+ ..|.+++.++.|..
T Consensus       433 ~LArCyi~nkkP~lAW~  449 (557)
T KOG3785|consen  433 MLARCYIRNKKPQLAWD  449 (557)
T ss_pred             HHHHHHHhcCCchHHHH
Confidence            65 55666666666643

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=92.40  E-value=2.2  Score=28.36  Aligned_cols=84  Identities=13%  Similarity=0.161  Sum_probs=63.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC-C--C--CccHHHHHHHHHhhcCCCc-hHHHHHHHHhcccccccCCCcCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS-G--V--KHDGVTFVAILTPCSHSGL-VYAEVEIFNSMEHDHEVKPKCLMP  128 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g--~--~p~~~t~~~ll~~~~~~~~-~~~a~~~~~~m~~~~~~~~~c~~~  128 (156)
                      ...|.++.-.+..+.+....++++.+..- .  +  .-+..+|.+++++.+++.. ---+..+|+.|++ .+        
T Consensus        40 ~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~-~~--------  110 (145)
T PF13762_consen   40 IFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKK-ND--------  110 (145)
T ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHH-cC--------
Confidence            44688888888888888888888887531 0  1  3466789999999988777 4457789999954 43        


Q ss_pred             CCCChhhHHHHHHHHhhcC
Q 041561          129 YKDDLVVWGDLVSSCQVHS  147 (156)
Q Consensus       129 ~~pd~~~~~~li~~~~~~g  147 (156)
                      .+++..-|-.||+++.+.-
T Consensus       111 ~~~t~~dy~~li~~~l~g~  129 (145)
T PF13762_consen  111 IEFTPSDYSCLIKAALRGY  129 (145)
T ss_pred             CCCCHHHHHHHHHHHHcCC
Confidence            5789999999999987653

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.37  E-value=1.2  Score=25.15  Aligned_cols=57  Identities=11%  Similarity=0.021  Sum_probs=46.3

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      ..+.+.++++.|.++++.+.+.+  |+..             ..|...-..+.+.|++++|.+.|+...+.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~--p~~~-------------~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD--PDDP-------------ELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC--cccc-------------hhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            46788999999999999998863  4322             566667788899999999999999998643

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

Probab=92.34  E-value=4.7  Score=32.14  Aligned_cols=94  Identities=16%  Similarity=0.163  Sum_probs=68.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCC-CCCC-
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMP-YKDD-  132 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~-~~pd-  132 (156)
                      ..|.+|=++|.+.+++++|.+-|..-..-|-. +...+..+-+.+-+.++..+|.+.|+...+....     -+ ..|. 
T Consensus       433 Rlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~-----eg~~~~~t  506 (559)
T KOG1155|consen  433 RLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAKLYEELKDLNEAAQYYEKYVEVSEL-----EGEIDDET  506 (559)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHh-----hcccchHH
Confidence            78999999999999999999999998876533 5678889999999999999999998877543210     01 2221 


Q ss_pred             hhhHHHHHHHHhhcCCHhHHhh
Q 041561          133 LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       133 ~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ...-.-|-.-+-+.+++++|..
T Consensus       507 ~ka~~fLA~~f~k~~~~~~As~  528 (559)
T KOG1155|consen  507 IKARLFLAEYFKKMKDFDEASY  528 (559)
T ss_pred             HHHHHHHHHHHHhhcchHHHHH
Confidence            1222224466778888888765

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

Probab=92.09  E-value=6.2  Score=34.72  Aligned_cols=83  Identities=12%  Similarity=0.208  Sum_probs=60.7

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|+.+-.+--+.|.+.+|.+-|-.      .-|...|.-+|+.+++.|.+++-...+..-+++.         -+|.. 
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~---------~E~~i- 1168 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKV---------REPYI- 1168 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhh---------cCccc-
Confidence            5677777777777777777766643      2367789999999999999999988887654332         23433 


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                       =..||-+|++.+++.+-++
T Consensus      1169 -d~eLi~AyAkt~rl~elE~ 1187 (1666)
T KOG0985|consen 1169 -DSELIFAYAKTNRLTELEE 1187 (1666)
T ss_pred             -hHHHHHHHHHhchHHHHHH
Confidence             3568999999998876554

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

Probab=91.98  E-value=0.37  Score=23.60  Aligned_cols=26  Identities=23%  Similarity=0.354  Sum_probs=18.8

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      +|+.|-..|.+.|++++|.++|++..
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            46677778888888888888887743

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=91.94  E-value=3.8  Score=30.12  Aligned_cols=139  Identities=17%  Similarity=0.175  Sum_probs=79.7

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHH---hC-CCCchHHHhHHHHHhhhcc------chHHHHHHHHHcC-CCHHHHHHHHH
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVK---DG-YGNDIFVGSAPINIYCNCG------VTWNEMIHGYAEN-EYVEQAISLYK   78 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~---~g-~~~~~~~~~~li~~~~~~~------~~~~~li~~~~~~-g~~~~a~~~~~   78 (156)
                      .....+.+.++...+-..+.+...   .+ ..--...|..-+..|.+.|      ..+..+-..|-.. |++++|.+.|+
T Consensus        60 kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~  139 (282)
T PF14938_consen   60 KAADCYEKLGDKFEAAKAYEEAANCYKKGDPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQ  139 (282)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            333444445555554444444322   11 1112345566667777776      5677777888888 89999999888


Q ss_pred             HHHH----CCCCcc--HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCC-CCCChh-hHHHHHHHHhhcCCHh
Q 041561           79 DIIA----SGVKHD--GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMP-YKDDLV-VWGDLVSSCQVHSNVR  150 (156)
Q Consensus        79 ~m~~----~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~-~~pd~~-~~~~li~~~~~~g~~~  150 (156)
                      +-.+    .| .+.  ...+..+...+.+.|++++|.++|++.....-     ..+ .+++.. .|-..+-.+...||+.
T Consensus       140 ~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l-----~~~l~~~~~~~~~l~a~l~~L~~~D~v  213 (282)
T PF14938_consen  140 KAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCL-----ENNLLKYSAKEYFLKAILCHLAMGDYV  213 (282)
T ss_dssp             HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCC-----CHCTTGHHHHHHHHHHHHHHHHTT-HH
T ss_pred             HHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhh-----cccccchhHHHHHHHHHHHHHHcCCHH
Confidence            8653    33 222  33566677888899999999999998743311     001 233333 3344455777788888


Q ss_pred             HHhh
Q 041561          151 LAKK  154 (156)
Q Consensus       151 ~a~~  154 (156)
                      .|.+
T Consensus       214 ~A~~  217 (282)
T PF14938_consen  214 AARK  217 (282)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7765

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=91.87  E-value=2.6  Score=28.02  Aligned_cols=92  Identities=8%  Similarity=0.119  Sum_probs=60.4

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCC-HHHHHHHHHHHHHCCCC
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEY-VEQAISLYKDIIASGVK   86 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~   86 (156)
                      .|+++.-.+..++.....++++.+..  +.++      .+..+.. ..+|++++.+.+...- ---+..+|.-|++.+.+
T Consensus        42 iN~iL~hl~~~~nf~~~v~~L~~l~~--l~~~------~~~~~~~-~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~  112 (145)
T PF13762_consen   42 INCILNHLASYQNFSGVVSILEHLHF--LNTD------NIIGWLD-NSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIE  112 (145)
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHH--hhHH------HHhhhcc-cchHHHHHHHHccChHHHHHHHHHHHHHHHcCCC
Confidence            45556665666666666666666621  0011      0000000 0789999999977766 34567799999998999


Q ss_pred             ccHHHHHHHHHhhcCCCchHHH
Q 041561           87 HDGVTFVAILTPCSHSGLVYAE  108 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a  108 (156)
                      ++..-|..+|+++.+....+..
T Consensus       113 ~t~~dy~~li~~~l~g~~~~~~  134 (145)
T PF13762_consen  113 FTPSDYSCLIKAALRGYFHDSL  134 (145)
T ss_pred             CCHHHHHHHHHHHHcCCCCcch
Confidence            9999999999999877554443

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=91.75  E-value=1  Score=35.50  Aligned_cols=92  Identities=5%  Similarity=-0.009  Sum_probs=65.1

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH----HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG----VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      ..|+.+-.+|.+.|++++|...|++-.+  +.|+.    .+|..+-.+|++.|++++|.+.++...+.....-.+ +.-.
T Consensus        76 ~a~~NLG~AL~~lGryeEAIa~f~rALe--L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALelsn~~f~~-i~~D  152 (453)
T PLN03098         76 EDAVNLGLSLFSKGRVKDALAQFETALE--LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDYNLKFST-ILND  152 (453)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcchhHHH-HHhC
Confidence            7789999999999999999999999766  35553    468999999999999999999888774321000000 0011


Q ss_pred             C------ChhhHHHHHHHHhhcCCH
Q 041561          131 D------DLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus       131 p------d~~~~~~li~~~~~~g~~  149 (156)
                      |      +..-|..++....+.|..
T Consensus       153 pdL~plR~~pef~eLlee~rk~G~~  177 (453)
T PLN03098        153 PDLAPFRASPEFKELQEEARKGGED  177 (453)
T ss_pred             cchhhhcccHHHHHHHHHHHHhCCc
Confidence            2      223677777777777753

>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=91.32  E-value=3.3  Score=28.21  Aligned_cols=29  Identities=7%  Similarity=0.049  Sum_probs=19.9

Q ss_pred             HHHHHHHHhCCCCchHHHhHHHHHhhhcc
Q 041561           26 QILTRIVKDGYGNDIFVGSAPINIYCNCG   54 (156)
Q Consensus        26 ~~~~~m~~~g~~~~~~~~~~li~~~~~~~   54 (156)
                      +....+.+.|+.|+...+..+|+.+.+.|
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~   43 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNG   43 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcC
Confidence            34444556889999977777776666666

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=91.17  E-value=0.76  Score=34.30  Aligned_cols=67  Identities=15%  Similarity=0.324  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHHHCCCCccHHHHHHHHHh--hcCC----CchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           70 VEQAISLYKDIIASGVKHDGVTFVAILTP--CSHS----GLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~--~~~~----~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      +++..++++.|++.|+.-+.++|-+..-.  ....    ..+..+..+|+.|+++|.+..      .++...+.+|+..
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLT------s~~D~~~a~lLA~  150 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLT------SPEDYPFAALLAM  150 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCcccc------CccchhHHHHHhc
Confidence            56778899999999999999988773322  2222    356678999999988887644      3555556655544

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.16  E-value=0.62  Score=35.73  Aligned_cols=86  Identities=9%  Similarity=0.201  Sum_probs=54.5

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTF   92 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~   92 (156)
                      ++.+..|+..+|+++|-....-.+ .|..+|-             +.|.++|.+++.++-||++|-.+..   ..+.++.
T Consensus       401 QAk~atgny~eaEelf~~is~~~i-kn~~~Y~-------------s~LArCyi~nkkP~lAW~~~lk~~t---~~e~fsL  463 (557)
T KOG3785|consen  401 QAKLATGNYVEAEELFIRISGPEI-KNKILYK-------------SMLARCYIRNKKPQLAWDMMLKTNT---PSERFSL  463 (557)
T ss_pred             HHHHHhcChHHHHHHHhhhcChhh-hhhHHHH-------------HHHHHHHHhcCCchHHHHHHHhcCC---chhHHHH
Confidence            444555666666666644432211 2332222             3356788999999999888766542   3345554


Q ss_pred             HHHH-HhhcCCCchHHHHHHHHhc
Q 041561           93 VAIL-TPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        93 ~~ll-~~~~~~~~~~~a~~~~~~m  115 (156)
                      -.+| +-|-+.+.+--|..-|+.+
T Consensus       464 LqlIAn~CYk~~eFyyaaKAFd~l  487 (557)
T KOG3785|consen  464 LQLIANDCYKANEFYYAAKAFDEL  487 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHH
Confidence            4444 6677899998888888888

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

Probab=91.03  E-value=1.9  Score=34.87  Aligned_cols=77  Identities=21%  Similarity=0.242  Sum_probs=44.9

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      +++.|=.+|.+.+..++|...|+.-.... .-|..|+.++--.+...|+++.|.+.|..-.   .        ++||-.+
T Consensus       457 ~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL---~--------l~p~n~~  524 (611)
T KOG1173|consen  457 TLNNLGHAYRKLNKYEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKAL---A--------LKPDNIF  524 (611)
T ss_pred             HHHhHHHHHHHHhhHHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHH---h--------cCCccHH
Confidence            35566666666777777777776655432 2244455555445556677777777666441   1        4666666


Q ss_pred             HHHHHHHHh
Q 041561          136 WGDLVSSCQ  144 (156)
Q Consensus       136 ~~~li~~~~  144 (156)
                      -..|+..+.
T Consensus       525 ~~~lL~~ai  533 (611)
T KOG1173|consen  525 ISELLKLAI  533 (611)
T ss_pred             HHHHHHHHH
Confidence            666665443

>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=90.86  E-value=3.8  Score=27.97  Aligned_cols=109  Identities=12%  Similarity=0.064  Sum_probs=74.9

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhh-hc--------------cchHHHHHHHHH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYC-NC--------------GVTWNEMIHGYA   65 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~-~~--------------~~~~~~li~~~~   65 (156)
                      ++|+...|..+++.+.+.|....    +.++.+.++-+|...-...+-.+. +.              +..+..++..+-
T Consensus        25 i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~~~~~iievLL  100 (167)
T PF07035_consen   25 IPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGTAYEEIIEVLL  100 (167)
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            46778899999999999998544    455667777666544443333222 22              147888889999


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      ..|++-+|.++.+....    -+...-..++++-.+.+|...-..+|..+..
T Consensus       101 ~~g~vl~ALr~ar~~~~----~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen  101 SKGQVLEALRYARQYHK----VDSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             hCCCHHHHHHHHHHcCC----cccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999998877532    2233445568888888887777777766643

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=90.74  E-value=6.7  Score=30.74  Aligned_cols=94  Identities=13%  Similarity=0.073  Sum_probs=60.8

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHH-Hhhhc---c--------------------chHHHHHHHHHcCCCHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPIN-IYCNC---G--------------------VTWNEMIHGYAENEYVEQ   72 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~-~~~~~---~--------------------~~~~~li~~~~~~g~~~~   72 (156)
                      -.|+.+.|++-|+-|...     +.+--.=++ .|...   |                    -.+.+.+...|..|+++.
T Consensus       132 ~eG~~~~Ar~kfeAMl~d-----PEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~  206 (531)
T COG3898         132 LEGDYEDARKKFEAMLDD-----PETRLLGLRGLYLEAQRLGAREAARHYAERAAEKAPQLPWAARATLEARCAAGDWDG  206 (531)
T ss_pred             hcCchHHHHHHHHHHhcC-----hHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhccCCchHHHHHHHHHHhcCChHH
Confidence            358899999999998753     222111111 11111   1                    678899999999999999


Q ss_pred             HHHHHHHHHHC---------------------------------------CCCccHHHH-HHHHHhhcCCCchHHHHHHH
Q 041561           73 AISLYKDIIAS---------------------------------------GVKHDGVTF-VAILTPCSHSGLVYAEVEIF  112 (156)
Q Consensus        73 a~~~~~~m~~~---------------------------------------g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~  112 (156)
                      |+++.+.-+..                                       .+.||-+.- ..--+++.+.|++.++-.++
T Consensus       207 AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pdlvPaav~AAralf~d~~~rKg~~il  286 (531)
T COG3898         207 ALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVPAAVVAARALFRDGNLRKGSKIL  286 (531)
T ss_pred             HHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCccchHHHHHHHHHHhccchhhhhhHH
Confidence            99999874332                                       133443322 22346677788888888888


Q ss_pred             Hhc
Q 041561          113 NSM  115 (156)
Q Consensus       113 ~~m  115 (156)
                      +.+
T Consensus       287 E~a  289 (531)
T COG3898         287 ETA  289 (531)
T ss_pred             HHH
Confidence            877

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

Probab=90.71  E-value=2.8  Score=32.01  Aligned_cols=84  Identities=8%  Similarity=-0.098  Sum_probs=61.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHH
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWG  137 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~  137 (156)
                      +.|=++|-+.|.+++|.+.|+.-.+....|  .||-.+-+.|-+..+...|..++.+-...           .|-.+||-
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~~~~--dTfllLskvY~ridQP~~AL~~~~~gld~-----------fP~~VT~l  293 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQFPHP--DTFLLLSKVYQRIDQPERALLVIGEGLDS-----------FPFDVTYL  293 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcCCch--hHHHHHHHHHHHhccHHHHHHHHhhhhhc-----------CCchhhhh
Confidence            568889999999999999998877765444  46666788999999999999999877433           45555543


Q ss_pred             H-HHHHHhhcCCHhHHhh
Q 041561          138 D-LVSSCQVHSNVRLAKK  154 (156)
Q Consensus       138 ~-li~~~~~~g~~~~a~~  154 (156)
                      . +-..+-..++.++|.+
T Consensus       294 ~g~ARi~eam~~~~~a~~  311 (478)
T KOG1129|consen  294 LGQARIHEAMEQQEDALQ  311 (478)
T ss_pred             hhhHHHHHHHHhHHHHHH
Confidence            3 3355555666666654

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=90.69  E-value=0.18  Score=32.94  Aligned_cols=94  Identities=11%  Similarity=0.083  Sum_probs=64.8

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHH
Q 041561           59 EMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGD  138 (156)
Q Consensus        59 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~  138 (156)
                      .+|..+-+.+.++...++++.+...+..-+....+.++..|++.++.++..++++.. ..+  ...--...-.....|..
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~-~~y--d~~~~~~~c~~~~l~~~   88 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTS-NNY--DLDKALRLCEKHGLYEE   88 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS-SSS---CTHHHHHHHTTTSHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccc-ccc--CHHHHHHHHHhcchHHH
Confidence            357777788899999999999998777778899999999999999888888887744 221  11100000012235666


Q ss_pred             HHHHHhhcCCHhHHhhh
Q 041561          139 LVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       139 li~~~~~~g~~~~a~~~  155 (156)
                      .+-.|.+.|+.++|.++
T Consensus        89 a~~Ly~~~~~~~~al~i  105 (143)
T PF00637_consen   89 AVYLYSKLGNHDEALEI  105 (143)
T ss_dssp             HHHHHHCCTTHTTCSST
T ss_pred             HHHHHHHcccHHHHHHH
Confidence            77788888888887654

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.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=90.65  E-value=0.73  Score=23.56  Aligned_cols=28  Identities=18%  Similarity=0.332  Sum_probs=21.9

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +|..+-.+|.+.|++++|.++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4566777888888888888888888764

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

Probab=90.64  E-value=4.9  Score=29.80  Aligned_cols=80  Identities=13%  Similarity=0.075  Sum_probs=59.6

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH----
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA----   82 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----   82 (156)
                      ++..+.+.+...|+.+.+...++++..... -|.              ..|..+|.+|.+.|+...|.+.|+.+.+    
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp-~~E--------------~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~e  219 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDP-YDE--------------PAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAE  219 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCc-cch--------------HHHHHHHHHHHHcCCchHHHHHHHHHHHHhhh
Confidence            344566666677777777777777665321 122              6788999999999999999999998875    


Q ss_pred             -CCCCccHHHHHHHHHhhcC
Q 041561           83 -SGVKHDGVTFVAILTPCSH  101 (156)
Q Consensus        83 -~g~~p~~~t~~~ll~~~~~  101 (156)
                       -|+.|-..+.....+....
T Consensus       220 dlgi~P~~~~~~~y~~~~~~  239 (280)
T COG3629         220 ELGIDPAPELRALYEEILRQ  239 (280)
T ss_pred             hcCCCccHHHHHHHHHHhcc
Confidence             4999999998888887443

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=90.59  E-value=5.1  Score=31.59  Aligned_cols=136  Identities=11%  Similarity=0.080  Sum_probs=74.8

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCC--CCchHHHhHHHHHhhhcc-----------------chHHHHHHHHHc
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGY--GNDIFVGSAPINIYCNCG-----------------VTWNEMIHGYAE   66 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~--~~~~~~~~~li~~~~~~~-----------------~~~~~li~~~~~   66 (156)
                      .-...+-+.+...|+-+.+...|+.......  ...-..|..|+..=+.+.                 ..|=.-......
T Consensus       233 hLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~  312 (564)
T KOG1174|consen  233 HLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYD  312 (564)
T ss_pred             HHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhh
Confidence            3344555566667777777777776554221  011122233332222111                 122222333334


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHHHHHH---HhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHH
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTFVAIL---TPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSS  142 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll---~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~  142 (156)
                      .++++.|+.+-+.-.    ..|....-++|   +.+...++.++|.--|..-. .          +.| +...|.-|+.+
T Consensus       313 ~K~~~rAL~~~eK~I----~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq-~----------Lap~rL~~Y~GL~hs  377 (564)
T KOG1174|consen  313 EKKFERALNFVEKCI----DSEPRNHEALILKGRLLIALERHTQAVIAFRTAQ-M----------LAPYRLEIYRGLFHS  377 (564)
T ss_pred             hhhHHHHHHHHHHHh----ccCcccchHHHhccHHHHhccchHHHHHHHHHHH-h----------cchhhHHHHHHHHHH
Confidence            455555555554433    23333333333   34456788888888887662 2          343 78999999999


Q ss_pred             HhhcCCHhHHhhhC
Q 041561          143 CQVHSNVRLAKKAA  156 (156)
Q Consensus       143 ~~~~g~~~~a~~~~  156 (156)
                      |...|.+.+|.-.|
T Consensus       378 YLA~~~~kEA~~~A  391 (564)
T KOG1174|consen  378 YLAQKRFKEANALA  391 (564)
T ss_pred             HHhhchHHHHHHHH
Confidence            99999999997543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.59  E-value=2.5  Score=30.96  Aligned_cols=89  Identities=16%  Similarity=0.101  Sum_probs=64.8

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCC----CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASG----VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      .|+.-++.| +.|++.+|..-|....+..    +.||.  +-+|-.++...|+.++|..+|..+.++++-     ++..|
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA--~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~-----s~KAp  215 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNA--YYWLGESLYAQGDYEDAAYIFARVVKDYPK-----SPKAP  215 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchh--HHHHHHHHHhcccchHHHHHHHHHHHhCCC-----CCCCh
Confidence            488887766 5677999999999999864    34444  445789999999999999999999888762     23444


Q ss_pred             ChhhHHHHHHHHhhcCCHhHHhh
Q 041561          132 DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       132 d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      |.-.  -|-.+..+.|+.++|+.
T Consensus       216 dall--Klg~~~~~l~~~d~A~a  236 (262)
T COG1729         216 DALL--KLGVSLGRLGNTDEACA  236 (262)
T ss_pred             HHHH--HHHHHHHHhcCHHHHHH
Confidence            4332  33345567788888875

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.59  E-value=6.2  Score=32.31  Aligned_cols=138  Identities=11%  Similarity=0.019  Sum_probs=80.8

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc---------------chHHHH--HHHHHc--CCCH
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------------VTWNEM--IHGYAE--NEYV   70 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---------------~~~~~l--i~~~~~--~g~~   70 (156)
                      +=++-+...+++++|.+.-+.+...+ +-|...+..=+-+..+-+               .+++..  =.+||.  .+.+
T Consensus        17 t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~~~~~~~fEKAYc~Yrlnk~   95 (652)
T KOG2376|consen   17 TDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGALLVINSFFFEKAYCEYRLNKL   95 (652)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhhhcchhhHHHHHHHHHcccH
Confidence            34556677888999999888887765 222222222222222222               233333  455554  5678


Q ss_pred             HHHHHHHHHHHHCCCCccHH-HHHHHHHhhcCCCchHHHHHHHHhcccccccCCC-------c-------------CCCC
Q 041561           71 EQAISLYKDIIASGVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK-------C-------------LMPY  129 (156)
Q Consensus        71 ~~a~~~~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-------c-------------~~~~  129 (156)
                      |+|++.++     |..++.. +-..=-.-|-+.+++++|.++++.+ .+++....       |             ..+.
T Consensus        96 Dealk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L-~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~  169 (652)
T KOG2376|consen   96 DEALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHL-AKNNSDDQDEERRANLLAVAAALQVQLLQSVPE  169 (652)
T ss_pred             HHHHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHH-HhcCCchHHHHHHHHHHHHHHhhhHHHHHhccC
Confidence            88888776     3444433 4444445667899999999999999 44433322       2             4455


Q ss_pred             CCChhhHHHHHH---HHhhcCCHhHHhhh
Q 041561          130 KDDLVVWGDLVS---SCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~pd~~~~~~li~---~~~~~g~~~~a~~~  155 (156)
                      .| .-+|..+.+   .+...|++.+|.++
T Consensus       170 v~-e~syel~yN~Ac~~i~~gky~qA~el  197 (652)
T KOG2376|consen  170 VP-EDSYELLYNTACILIENGKYNQAIEL  197 (652)
T ss_pred             CC-cchHHHHHHHHHHHHhcccHHHHHHH
Confidence            55 445555554   24567888888764

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=90.57  E-value=1.8  Score=27.18  Aligned_cols=28  Identities=18%  Similarity=0.342  Sum_probs=26.1

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      .-|..|+.-|-.+|..++|++++.++..
T Consensus        40 ~~~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen   40 GKYQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             CCHHHHHHHHHccCccHHHHHHHHHHhc
Confidence            6799999999999999999999999987

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.

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

Probab=90.55  E-value=8.3  Score=31.40  Aligned_cols=100  Identities=10%  Similarity=0.064  Sum_probs=74.7

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC---c-----
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK---C-----  125 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~---c-----  125 (156)
                      .+|-..|+.--+..-++.|..+|.+.++.+..+ +.+..++++.-+| .+|...|.++|+.=.+.+|-.|.   |     
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d~p~yv~~YldfL  445 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGDSPEYVLKYLDFL  445 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            677788888888888888888898888887777 7778888888775 45667788888765566665554   1     


Q ss_pred             -----------------CCCCCC--ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          126 -----------------LMPYKD--DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       126 -----------------~~~~~p--d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                                       .+.+.|  ....|..||.--...|+..-+.++
T Consensus       446 ~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~l  494 (656)
T KOG1914|consen  446 SHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKL  494 (656)
T ss_pred             HHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHH
Confidence                             222333  458899999999999999877665

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.29  E-value=1.8  Score=32.77  Aligned_cols=53  Identities=13%  Similarity=0.092  Sum_probs=45.1

Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      -.-++++++.+...=..-|+-||.+|+..+++.+.+.+++.+|.++...|..+
T Consensus       112 lky~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  112 LKYDPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             HccChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            34577888888888888899999999999999999999999999887777544

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

Probab=90.02  E-value=5  Score=31.90  Aligned_cols=96  Identities=5%  Similarity=-0.051  Sum_probs=70.3

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      |++-+....+.+.+.++.++|.+.++.+...  .|+..             ..+-.+-.+|.+.|++.+|.++++.-..+
T Consensus       339 N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~-------------~l~~~~a~all~~g~~~eai~~L~~~~~~  403 (484)
T COG4783         339 NPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSP-------------LLQLNLAQALLKGGKPQEAIRILNRYLFN  403 (484)
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCcc-------------HHHHHHHHHHHhcCChHHHHHHHHHHhhc
Confidence            3444556667788999999999999998763  45532             34445567778899999999998887765


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      . .-|...|..+-++|...|+..++..-..+.
T Consensus       404 ~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         404 D-PEDPNGWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             C-CCCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence            3 457778888889888888777766554444

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

Probab=89.67  E-value=0.99  Score=22.21  Aligned_cols=27  Identities=19%  Similarity=0.410  Sum_probs=21.7

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      +++.|-..|...|++++|.+++++...
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            567888889999999999999988754

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=89.64  E-value=3.1  Score=27.59  Aligned_cols=78  Identities=13%  Similarity=0.045  Sum_probs=54.4

Q ss_pred             cCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHH
Q 041561           16 AKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAI   95 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l   95 (156)
                      .+.|+.+.|.+.|+.+..+- +-...+-.           .-=.|+.+|.+.+++++|...+++..+-...--.+-|...
T Consensus        21 l~~~~Y~~A~~~le~L~~ry-P~g~ya~q-----------AqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y   88 (142)
T PF13512_consen   21 LQKGNYEEAIKQLEALDTRY-PFGEYAEQ-----------AQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYY   88 (142)
T ss_pred             HHhCCHHHHHHHHHHHHhcC-CCCcccHH-----------HHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            46789999999999997642 11221112           2234788999999999999999999885443334667777


Q ss_pred             HHhhcCCCch
Q 041561           96 LTPCSHSGLV  105 (156)
Q Consensus        96 l~~~~~~~~~  105 (156)
                      +.+++.....
T Consensus        89 ~~gL~~~~~~   98 (142)
T PF13512_consen   89 MRGLSYYEQD   98 (142)
T ss_pred             HHHHHHHHHh
Confidence            7777755443

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

Probab=89.30  E-value=2.3  Score=35.47  Aligned_cols=61  Identities=11%  Similarity=0.228  Sum_probs=46.3

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      ..||.+-.+|.+.++-.+|...+.+-.+....|.. .|-..+-...+.|.+++|.+.+.++.
T Consensus       554 eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~-iWENymlvsvdvge~eda~~A~~rll  614 (777)
T KOG1128|consen  554 EAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQ-IWENYMLVSVDVGEFEDAIKAYHRLL  614 (777)
T ss_pred             hhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCe-eeechhhhhhhcccHHHHHHHHHHHH
Confidence            78899999999999999999988888876644443 34444445568888888888887774

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

Probab=89.26  E-value=1.3  Score=37.96  Aligned_cols=85  Identities=11%  Similarity=0.062  Sum_probs=52.3

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHH
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLV  140 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li  140 (156)
                      =-+++.+|++.+|.++|.+.++... -+.-+|-.+-..|...|++..|.++|+...+.+.        -+-+....+-|=
T Consensus       653 giVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~--------~~~~~~vl~~La  723 (1018)
T KOG2002|consen  653 GIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFY--------KKNRSEVLHYLA  723 (1018)
T ss_pred             hhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhc--------ccCCHHHHHHHH
Confidence            3345566677777777777666543 1233455566666667777777777766655543        234556666666


Q ss_pred             HHHhhcCCHhHHhh
Q 041561          141 SSCQVHSNVRLAKK  154 (156)
Q Consensus       141 ~~~~~~g~~~~a~~  154 (156)
                      .++-..|++.+|.+
T Consensus       724 ra~y~~~~~~eak~  737 (1018)
T KOG2002|consen  724 RAWYEAGKLQEAKE  737 (1018)
T ss_pred             HHHHHhhhHHHHHH
Confidence            77777777777655

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

Probab=89.04  E-value=5.6  Score=31.93  Aligned_cols=113  Identities=9%  Similarity=0.025  Sum_probs=72.5

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC-----CCC--ccH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS-----GVK--HDG   89 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~--p~~   89 (156)
                      |.+.+++++..|++.++. ++.-+              +.||-.-..+.-.+++++|.+.|+.-.+-     ++.  +..
T Consensus       440 r~~k~~~~m~~Fee~kkk-FP~~~--------------Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~p  504 (606)
T KOG0547|consen  440 RQHKIAESMKTFEEAKKK-FPNCP--------------EVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAP  504 (606)
T ss_pred             HHHHHHHHHHHHHHHHHh-CCCCc--------------hHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchh
Confidence            556667777777776543 22223              56677777778889999999999886541     222  222


Q ss_pred             HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           90 VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        90 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ...-+++-.- ..+++..|.+++..-.+-          -......|.+|=+.-.+.|+.++|.++
T Consensus       505 lV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~----------Dpkce~A~~tlaq~~lQ~~~i~eAiel  559 (606)
T KOG0547|consen  505 LVHKALLVLQ-WKEDINQAENLLRKAIEL----------DPKCEQAYETLAQFELQRGKIDEAIEL  559 (606)
T ss_pred             hhhhhHhhhc-hhhhHHHHHHHHHHHHcc----------CchHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            2222222221 458899999998877221          123557788888888888998888764

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=89.03  E-value=1.4  Score=28.51  Aligned_cols=54  Identities=17%  Similarity=0.265  Sum_probs=25.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ...|.+|..|++.. .++..+.+..      .++.+....+++-|.+.+-++++.-++..+
T Consensus        42 ~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~~l~~~~~~l~~k~   95 (140)
T smart00299       42 ALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKAKLYEEAVELYKKD   95 (140)
T ss_pred             hHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHcCcHHHHHHHHHhh
Confidence            34555555555442 2233333331      123344444555555555555555555554

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.03  E-value=2.2  Score=35.73  Aligned_cols=78  Identities=14%  Similarity=0.162  Sum_probs=57.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|.-=+.+++..+++++.+++-+.++.      ..-|.-.+.+|.+.|+.++|...+....               +..
T Consensus       716 r~~wLk~~aLa~~~kweeLekfAkskks------PIGy~PFVe~c~~~~n~~EA~KYiprv~---------------~l~  774 (829)
T KOG2280|consen  716 RLWWLKLTALADIKKWEELEKFAKSKKS------PIGYLPFVEACLKQGNKDEAKKYIPRVG---------------GLQ  774 (829)
T ss_pred             hhHHHHHHHHHhhhhHHHHHHHHhccCC------CCCchhHHHHHHhcccHHHHhhhhhccC---------------ChH
Confidence            5677778888888888887776655442      4456667888889999999988887661               111


Q ss_pred             hHHHHHHHHhhcCCHhHHhhhC
Q 041561          135 VWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~~  156 (156)
                         -.+.+|.+.|++.+|-++|
T Consensus       775 ---ekv~ay~~~~~~~eAad~A  793 (829)
T KOG2280|consen  775 ---EKVKAYLRVGDVKEAADLA  793 (829)
T ss_pred             ---HHHHHHHHhccHHHHHHHH
Confidence               4678899999999988765

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

Probab=88.80  E-value=2.1  Score=27.87  Aligned_cols=48  Identities=10%  Similarity=0.153  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccccc
Q 041561           72 QAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDH  119 (156)
Q Consensus        72 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~  119 (156)
                      +..+-+..+..-.+.|+.....+.++||-|.+|+..|.++|+..+.+.
T Consensus        67 EvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~  114 (149)
T KOG4077|consen   67 EVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDKC  114 (149)
T ss_pred             HHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHhc
Confidence            445556666666899999999999999999999999999999997663

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=88.58  E-value=3.6  Score=30.59  Aligned_cols=61  Identities=20%  Similarity=0.140  Sum_probs=31.2

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHh-CCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKD-GYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYK   78 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~   78 (156)
                      +..+..++|+.+++.+++....+.++..... +..-|.              ..|..+|+.-..+|+..-..++.+
T Consensus       201 ~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~--------------rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  201 TRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDP--------------RPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             ChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCC--------------chHHHHHHHHHHcCCHHHHHHHhh
Confidence            3344444555555555555555555544322 333344              556666666666666655544443

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=88.25  E-value=7.4  Score=29.11  Aligned_cols=27  Identities=11%  Similarity=0.186  Sum_probs=21.2

Q ss_pred             hHHHHHHHHHHHHhCCCCchHHHhHHH
Q 041561           21 LFLGRQILTRIVKDGYGNDIFVGSAPI   47 (156)
Q Consensus        21 ~~~a~~~~~~m~~~g~~~~~~~~~~li   47 (156)
                      ++....+++.|.+.|++.+.++|-+-.
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~  104 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAAL  104 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHH
Confidence            566788888999999988887777643

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=87.77  E-value=13  Score=30.08  Aligned_cols=58  Identities=12%  Similarity=0.048  Sum_probs=45.3

Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ..+...|.++--.....|++++|...+++.. +          +.|+...|..+-..+...|++++|.+
T Consensus       417 ~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl-~----------L~ps~~a~~~lG~~~~~~G~~~eA~~  474 (517)
T PRK10153        417 NVLPRIYEILAVQALVKGKTDEAYQAINKAI-D----------LEMSWLNYVLLGKVYELKGDNRLAAD  474 (517)
T ss_pred             cCChHHHHHHHHHHHhcCCHHHHHHHHHHHH-H----------cCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            3344566665444445799999999999883 3          57888899999999999999999875

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

Probab=87.73  E-value=5.5  Score=31.96  Aligned_cols=119  Identities=10%  Similarity=0.110  Sum_probs=77.8

Q ss_pred             CCCchHHHHHHHHHHHHhC---CCCchHHHhHHHHHhhhcc------------chHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDG---YGNDIFVGSAPINIYCNCG------------VTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g---~~~~~~~~~~li~~~~~~~------------~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      ....+.++++++.+..+.|   +..+...     +......            ..=-.+-.+..+.|+.++|.+.|++|.
T Consensus       212 eA~Ti~Eae~l~rqAvkAgE~~lg~s~~~-----~~~g~~~e~~~~Rdt~~~~y~KrRLAmCarklGr~~EAIk~~rdLl  286 (539)
T PF04184_consen  212 EASTIVEAEELLRQAVKAGEASLGKSQFL-----QHHGHFWEAWHRRDTNVLVYAKRRLAMCARKLGRLREAIKMFRDLL  286 (539)
T ss_pred             cccCHHHHHHHHHHHHHHHHHhhchhhhh-----hcccchhhhhhccccchhhhhHHHHHHHHHHhCChHHHHHHHHHHH
Confidence            3455788888888877654   2333211     1111111            111235566678899999999999997


Q ss_pred             HCC-CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCC
Q 041561           82 ASG-VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSN  148 (156)
Q Consensus        82 ~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~  148 (156)
                      +.- ..-+....-.+|.++-..+...++..++... .+...       -+--...|++.+..+...|+
T Consensus       287 ke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kY-dDi~l-------pkSAti~YTaALLkaRav~d  346 (539)
T PF04184_consen  287 KEFPNLDNLNIRENLIEALLELQAYADVQALLAKY-DDISL-------PKSATICYTAALLKARAVGD  346 (539)
T ss_pred             hhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHh-ccccC-------CchHHHHHHHHHHHHHhhcc
Confidence            643 2234457788999999999999999999998 43210       12345678888777666665

The molecular function of this protein is uncertain.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=87.55  E-value=1.2  Score=22.71  Aligned_cols=28  Identities=7%  Similarity=0.043  Sum_probs=24.3

Q ss_pred             HHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           91 TFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        91 t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      ++..+-+++.+.|++++|.++++...+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5667788999999999999999999654

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=87.33  E-value=7.2  Score=33.41  Aligned_cols=91  Identities=11%  Similarity=0.066  Sum_probs=64.0

Q ss_pred             HHHHHHHhc--CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            8 FTTVLSSCA--KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         8 ~~~ll~~~~--~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      |..++++++  |.|..++|..+++.....+.. |.              .|...+-.+|...++.+++..+|++...  .
T Consensus        44 ~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~--------------~tLq~l~~~y~d~~~~d~~~~~Ye~~~~--~  106 (932)
T KOG2053|consen   44 YAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DD--------------LTLQFLQNVYRDLGKLDEAVHLYERANQ--K  106 (932)
T ss_pred             HHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-ch--------------HHHHHHHHHHHHHhhhhHHHHHHHHHHh--h
Confidence            444444443  556666666555554332221 33              7788889999999999999999999765  4


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      -|+..-...++.+|+|-+++.+-.+.=-+|
T Consensus       107 ~P~eell~~lFmayvR~~~yk~qQkaa~~L  136 (932)
T KOG2053|consen  107 YPSEELLYHLFMAYVREKSYKKQQKAALQL  136 (932)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            677888888999999988887766555545

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

Probab=86.96  E-value=5.6  Score=24.88  Aligned_cols=63  Identities=13%  Similarity=0.063  Sum_probs=43.7

Q ss_pred             chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCccHHHHHHHHHh
Q 041561           20 SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS-GVKHDGVTFVAILTP   98 (156)
Q Consensus        20 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~ll~~   98 (156)
                      |.-+..+-++.+....+.|++              ....+.+++|.+-+++.-|.++|+-.+.+ |.+  ...|..+++-
T Consensus        25 D~we~rrglN~l~~~DlVP~P--------------~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~--~~~Y~~~lqE   88 (108)
T PF02284_consen   25 DGWELRRGLNNLFGYDLVPEP--------------KIIEAALRACRRVNDFALAVRILEGIKDKCGNK--KEIYPYILQE   88 (108)
T ss_dssp             -HHHHHHHHHHHTTSSB---H--------------HHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT---TTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCh--------------HHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCh--HHHHHHHHHH
Confidence            444677777777777888888              66778889999999999999999998753 433  2277777654

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 ....

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=86.79  E-value=10  Score=27.83  Aligned_cols=109  Identities=17%  Similarity=0.174  Sum_probs=68.5

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHH----h-C-CCCchHHHhHHHHHhhhcc------chHHHHHHHHHcCCCHHHHHH
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVK----D-G-YGNDIFVGSAPINIYCNCG------VTWNEMIHGYAENEYVEQAIS   75 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~----~-g-~~~~~~~~~~li~~~~~~~------~~~~~li~~~~~~g~~~~a~~   75 (156)
                      |.-.+..|...|+++.|-+.+..+-+    . | ..--...|..-+..|...+      ..+..+...+.+.|++++|.+
T Consensus        97 ~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~  176 (282)
T PF14938_consen   97 YEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIE  176 (282)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHH
Confidence            45556666777777776666666533    1 1 1122345555556666555      667788899999999999999


Q ss_pred             HHHHHHHCCC-----CccHH--HHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           76 LYKDIIASGV-----KHDGV--TFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        76 ~~~~m~~~g~-----~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +|++....-.     .++..  .+.++| .+...||+..|.+.++....
T Consensus       177 ~~e~~~~~~l~~~l~~~~~~~~~l~a~l-~~L~~~D~v~A~~~~~~~~~  224 (282)
T PF14938_consen  177 IYEEVAKKCLENNLLKYSAKEYFLKAIL-CHLAMGDYVAARKALERYCS  224 (282)
T ss_dssp             HHHHHHHTCCCHCTTGHHHHHHHHHHHH-HHHHTT-HHHHHHHHHHHGT
T ss_pred             HHHHHHHHhhcccccchhHHHHHHHHHH-HHHHcCCHHHHHHHHHHHHh
Confidence            9999876422     23332  234444 44457899999999998843

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=86.77  E-value=17  Score=30.22  Aligned_cols=89  Identities=11%  Similarity=0.080  Sum_probs=61.1

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHH-HHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ++--++..|-+.|+++.|....+.-..+  .|+.+ -|..=-+.+.+.|++++|..++++-. +.         -.||+.
T Consensus       373 t~y~laqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~-el---------D~aDR~  440 (700)
T KOG1156|consen  373 TLYFLAQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQ-EL---------DTADRA  440 (700)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHH-hc---------cchhHH
Confidence            3445778888899999999988876542  44444 23333377788999999999998873 32         256665


Q ss_pred             hHHHHHHHHhhcCCHhHHhhhC
Q 041561          135 VWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~~  156 (156)
                      .=.-=..-..+..+.++|.+++
T Consensus       441 INsKcAKYmLrAn~i~eA~~~~  462 (700)
T KOG1156|consen  441 INSKCAKYMLRANEIEEAEEVL  462 (700)
T ss_pred             HHHHHHHHHHHccccHHHHHHH
Confidence            5545555566777888887763

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

Probab=86.70  E-value=14  Score=32.10  Aligned_cols=62  Identities=13%  Similarity=0.204  Sum_probs=47.2

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH--HHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG--VTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      .+|=-+-++|-..|++++|...|.+-.+  ..||.  ..+-.+-+.+.+.|+++.+...|+.+-+.
T Consensus       308 es~Y~~gRs~Ha~Gd~ekA~~yY~~s~k--~~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~  371 (1018)
T KOG2002|consen  308 ESFYQLGRSYHAQGDFEKAFKYYMESLK--ADNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQ  371 (1018)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHc--cCCCCccccccchhHHHHHhchHHHHHHHHHHHHHh
Confidence            4466677788889999999999977554  34444  44556788889999999999999988544

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

Probab=86.66  E-value=20  Score=30.89  Aligned_cols=100  Identities=16%  Similarity=0.170  Sum_probs=64.7

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQA   73 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a   73 (156)
                      .+++ |+.+.|..++.+.++-. +.+...|-+|=..|-+.|                    ..|-.+-.-..+.|.+++|
T Consensus       149 lfar-g~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA  226 (895)
T KOG2076|consen  149 LFAR-GDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQA  226 (895)
T ss_pred             HHHh-CCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHH
Confidence            3455 99999999999987642 356777888888888877                    4455555555666666666


Q ss_pred             HHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           74 ISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        74 ~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .-.|.+-.+....-....| -=...|-+.|+...|.+-|.++-
T Consensus       227 ~~cy~rAI~~~p~n~~~~~-ers~L~~~~G~~~~Am~~f~~l~  268 (895)
T KOG2076|consen  227 RYCYSRAIQANPSNWELIY-ERSSLYQKTGDLKRAMETFLQLL  268 (895)
T ss_pred             HHHHHHHHhcCCcchHHHH-HHHHHHHHhChHHHHHHHHHHHH
Confidence            6666666553322122222 22345557788888877777773

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=86.53  E-value=2.9  Score=35.79  Aligned_cols=103  Identities=12%  Similarity=0.092  Sum_probs=68.4

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC-C--------C
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS-G--------V   85 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g--------~   85 (156)
                      |.-.|+++.|.+-...++..                    ..|..|.+.|.+..++|-|.--+..|... |        -
T Consensus       738 yvtiG~MD~AfksI~~IkS~--------------------~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q  797 (1416)
T KOG3617|consen  738 YVTIGSMDAAFKSIQFIKSD--------------------SVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQ  797 (1416)
T ss_pred             EEEeccHHHHHHHHHHHhhh--------------------HHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHh
Confidence            34557777777666666543                    67888888888888888888877777642 2        2


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhhC
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~~  156 (156)
                      .|+...-...+-| ...|.+++|..++.+- +++.                 .|=.-|-..|++++|.+||
T Consensus       798 ~~~e~eakvAvLA-ieLgMlEeA~~lYr~c-kR~D-----------------LlNKlyQs~g~w~eA~eiA  849 (1416)
T KOG3617|consen  798 NGEEDEAKVAVLA-IELGMLEEALILYRQC-KRYD-----------------LLNKLYQSQGMWSEAFEIA  849 (1416)
T ss_pred             CCcchhhHHHHHH-HHHhhHHHHHHHHHHH-HHHH-----------------HHHHHHHhcccHHHHHHHH
Confidence            3433322222222 2678999999999887 4432                 2445667788888888875

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=86.39  E-value=4.8  Score=31.88  Aligned_cols=68  Identities=7%  Similarity=-0.131  Sum_probs=52.8

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +...++.+=.+|.+.|++++|...|+...+.  .||....          ..+|..+-.+|...|++++|.+.+++..+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA----------~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEA----------QAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHH----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4467788888999999999999999998774  4654100          024778888899999999999999988764

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=86.25  E-value=10  Score=27.32  Aligned_cols=72  Identities=11%  Similarity=0.055  Sum_probs=41.8

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAIL   96 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll   96 (156)
                      +.|+.++|...|+.+...-..+ .....+.           =.+..+|.+.+++++|...|++..+.-..-...-+...+
T Consensus        44 ~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~-----------l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~  111 (243)
T PRK10866         44 QDGNWKQAITQLEALDNRYPFG-PYSQQVQ-----------LDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYM  111 (243)
T ss_pred             HCCCHHHHHHHHHHHHHhCCCC-hHHHHHH-----------HHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHH
Confidence            4566677777777765532111 1111111           235677788999999999999988754333333444445


Q ss_pred             Hhhc
Q 041561           97 TPCS  100 (156)
Q Consensus        97 ~~~~  100 (156)
                      .+.+
T Consensus       112 ~g~~  115 (243)
T PRK10866        112 RGLT  115 (243)
T ss_pred             HHHh
Confidence            5543

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=86.18  E-value=5.8  Score=29.51  Aligned_cols=77  Identities=8%  Similarity=0.076  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHH-CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           71 EQAISLYKDIIA-SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        71 ~~a~~~~~~m~~-~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                      .--.++.+-+.. .|-.++..+...+|+.++..+++.+-.++++.-....+        ..-|.+-|..+|..-..+|+.
T Consensus       183 ~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~--------~~~D~rpW~~FI~li~~sgD~  254 (292)
T PF13929_consen  183 NALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSV--------PGNDPRPWAEFIKLIVESGDQ  254 (292)
T ss_pred             hhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCC--------CCCCCchHHHHHHHHHHcCCH
Confidence            333444444443 35678888999999999999999999998887743322        356899999999999999999


Q ss_pred             hHHhhh
Q 041561          150 RLAKKA  155 (156)
Q Consensus       150 ~~a~~~  155 (156)
                      .-.+++
T Consensus       255 ~~~~ki  260 (292)
T PF13929_consen  255 EVMRKI  260 (292)
T ss_pred             HHHHHH
Confidence            887765

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=85.93  E-value=12  Score=27.83  Aligned_cols=113  Identities=9%  Similarity=-0.008  Sum_probs=73.0

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHH-hCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVK-DGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~-~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      |...|-.|=..|.+.|+.+.|...|....+ .|=.|+.  +..+           ...+-.-..-.+-.++.++|+++..
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~--~~g~-----------aeaL~~~a~~~~ta~a~~ll~~al~  221 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEI--LLGL-----------AEALYYQAGQQMTAKARALLRQALA  221 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHH--HHHH-----------HHHHHHhcCCcccHHHHHHHHHHHh
Confidence            567788888889999999999999988765 3333333  2222           2222222222245788999999987


Q ss_pred             CCCCccHH-HHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           83 SGVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        83 ~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      .  .|+.. +-.-+--.+...|++.+|...++.|...           -|....|..+|+.
T Consensus       222 ~--D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~-----------lp~~~~rr~~ie~  269 (287)
T COG4235         222 L--DPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDL-----------LPADDPRRSLIER  269 (287)
T ss_pred             c--CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc-----------CCCCCchHHHHHH
Confidence            4  34444 4444446667899999999999999543           3445555555543

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

Probab=85.65  E-value=2.6  Score=22.24  Aligned_cols=42  Identities=10%  Similarity=0.098  Sum_probs=32.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINI   49 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~   49 (156)
                      |...++.+ -+.|-+++++.+++.|.+.|+.-+...+..+++.
T Consensus         5 TlGiL~~A-k~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen    5 TLGILLLA-KRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             hHHHHHHH-HHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            44445544 5678888999999999999998888888777653

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

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=85.31  E-value=8.8  Score=27.03  Aligned_cols=77  Identities=10%  Similarity=-0.060  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           70 VEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                      -++|.+.|-.+...+..-+...-.++-.-| -..|.+++.+++.....-..      .+-.+|+..+.+|.+.|.+.|++
T Consensus       122 d~~A~~~fL~~E~~~~l~t~elq~aLAtyY-~krD~~Kt~~ll~~~L~l~~------~~~~~n~eil~sLas~~~~~~~~  194 (203)
T PF11207_consen  122 DQEALRRFLQLEGTPELETAELQYALATYY-TKRDPEKTIQLLLRALELSN------PDDNFNPEILKSLASIYQKLKNY  194 (203)
T ss_pred             cHHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HccCHHHHHHHHHHHHHhcC------CCCCCCHHHHHHHHHHHHHhcch
Confidence            366888888888887665555555555554 47788889888777644432      11267999999999999999999


Q ss_pred             hHHh
Q 041561          150 RLAK  153 (156)
Q Consensus       150 ~~a~  153 (156)
                      +.|-
T Consensus       195 e~AY  198 (203)
T PF11207_consen  195 EQAY  198 (203)
T ss_pred             hhhh
Confidence            9884

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=85.20  E-value=11  Score=26.60  Aligned_cols=97  Identities=11%  Similarity=0.047  Sum_probs=61.9

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      |++.---.+-.+..+.|+..+|...|++-...-+.-|..              ..-.+-++....+++.++...++.+-+
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a--------------~lLglA~Aqfa~~~~A~a~~tLe~l~e  152 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAA--------------MLLGLAQAQFAIQEFAAAQQTLEDLME  152 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHH--------------HHHHHHHHHHhhccHHHHHHHHHHHhh
Confidence            444444556677778888888888888876544555552              223344555667788888888877765


Q ss_pred             C---CCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           83 S---GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        83 ~---g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .   +-.||..  -.+-+.+...|...+|+.-|+..
T Consensus       153 ~~pa~r~pd~~--Ll~aR~laa~g~~a~Aesafe~a  186 (251)
T COG4700         153 YNPAFRSPDGH--LLFARTLAAQGKYADAESAFEVA  186 (251)
T ss_pred             cCCccCCCCch--HHHHHHHHhcCCchhHHHHHHHH
Confidence            3   3344433  33456666677777777777766

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

Probab=85.08  E-value=4  Score=21.50  Aligned_cols=35  Identities=11%  Similarity=0.153  Sum_probs=29.0

Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHh
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTP   98 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~   98 (156)
                      .-+.|.++++..++++|.++|+.-+...+..+++-
T Consensus        12 Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen   12 AKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            34677888999999999999999888888877754

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

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

Probab=84.39  E-value=13  Score=26.88  Aligned_cols=90  Identities=10%  Similarity=-0.027  Sum_probs=63.2

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH-HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL  133 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~  133 (156)
                      .+|..+-..|-+.|+.+.|.+-|+.-...  .|+. ...|..=--+|..|.+++|.+.|+.-..+...       -. -.
T Consensus        70 ~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y-------~~-~s  139 (250)
T COG3063          70 LAHLVRAHYYQKLGENDLADESYRKALSL--APNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAY-------GE-PS  139 (250)
T ss_pred             HHHHHHHHHHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCC-------CC-cc
Confidence            78899999999999999999999887652  2222 23444444567788999999999987554221       11 23


Q ss_pred             hhHHHHHHHHhhcCCHhHHhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~  154 (156)
                      .||.-+--+..+.|+++.|++
T Consensus       140 ~t~eN~G~Cal~~gq~~~A~~  160 (250)
T COG3063         140 DTLENLGLCALKAGQFDQAEE  160 (250)
T ss_pred             hhhhhhHHHHhhcCCchhHHH
Confidence            566666677778888887765

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

Probab=84.16  E-value=4.7  Score=27.81  Aligned_cols=56  Identities=5%  Similarity=-0.198  Sum_probs=42.9

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHH-CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           61 IHGYAENEYVEQAISLYKDIIA-SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      +.......+.+......+..++ -...|+..+|..++.++...|+.++|+++..++.
T Consensus       115 l~~~~~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~  171 (193)
T PF11846_consen  115 LLLARLPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARAR  171 (193)
T ss_pred             HHhhcCCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3333466666665555555544 3578999999999999999999999999999984

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

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=84.11  E-value=1.2  Score=29.13  Aligned_cols=30  Identities=13%  Similarity=0.102  Sum_probs=23.7

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPIN   48 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~   48 (156)
                      ..|+-..|-.+|..|.++|-+||.  |+.|+.
T Consensus       107 ~ygsk~DaY~VF~kML~~G~pPdd--W~~Ll~  136 (140)
T PF11663_consen  107 AYGSKTDAYAVFRKMLERGNPPDD--WDALLK  136 (140)
T ss_pred             hhccCCcHHHHHHHHHhCCCCCcc--HHHHHH
Confidence            346667799999999999999987  555554

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=83.96  E-value=7.9  Score=23.98  Aligned_cols=63  Identities=11%  Similarity=0.061  Sum_probs=50.3

Q ss_pred             chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH-CCCCccHHHHHHHHHh
Q 041561           20 SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA-SGVKHDGVTFVAILTP   98 (156)
Q Consensus        20 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~ll~~   98 (156)
                      |.-++.+-++.+....+.|++              ..-.+.+++|.+-+|+.-|.++|+-.+. .|.  +...|..+++-
T Consensus        22 D~we~rr~mN~l~~~DlVP~P--------------~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~--~~~~y~~~lqe   85 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEP--------------KVIEAALRACRRVNDFALAVRILEAIKDKCGA--HKEIYPYILQE   85 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCc--------------HHHHHHHHHHHHhhhHHHHHHHHHHHHHHccC--chhhHHHHHHH
Confidence            667788888898888899999              6667788999999999999999998874 343  44577777654

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.

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=83.96  E-value=15  Score=30.51  Aligned_cols=98  Identities=5%  Similarity=0.039  Sum_probs=73.2

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      .|+-.+...+-+.|+.+.|+...+....+  .|+.+             +.|-.=-+-+.+.|++++|...+++-++-. 
T Consensus       372 Wt~y~laqh~D~~g~~~~A~~yId~AIdH--TPTli-------------Ely~~KaRI~kH~G~l~eAa~~l~ea~elD-  435 (700)
T KOG1156|consen  372 WTLYFLAQHYDKLGDYEVALEYIDLAIDH--TPTLI-------------ELYLVKARIFKHAGLLDEAAAWLDEAQELD-  435 (700)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHhcc--CchHH-------------HHHHHHHHHHHhcCChHHHHHHHHHHHhcc-
Confidence            34556777788889999999999988765  34443             555555677889999999999999987643 


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccc
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHE  120 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  120 (156)
                      .||.+.-.--.+-..++..+++|..+...+ .+.|
T Consensus       436 ~aDR~INsKcAKYmLrAn~i~eA~~~~skF-Tr~~  469 (700)
T KOG1156|consen  436 TADRAINSKCAKYMLRANEIEEAEEVLSKF-TREG  469 (700)
T ss_pred             chhHHHHHHHHHHHHHccccHHHHHHHHHh-hhcc
Confidence            556665555666666889999999998888 4443

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=83.94  E-value=16  Score=29.88  Aligned_cols=106  Identities=13%  Similarity=0.047  Sum_probs=72.5

Q ss_pred             hHHHHHHHHHH-HHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc-HHHHHHHHHh
Q 041561           21 LFLGRQILTRI-VKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD-GVTFVAILTP   98 (156)
Q Consensus        21 ~~~a~~~~~~m-~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~   98 (156)
                      +.+..++|-++ .+.+-.+|+.+++.|              =--|--.|.+++|.+-|+....  ++|+ ..+||-|=-.
T Consensus       410 l~~i~~~fLeaa~~~~~~~DpdvQ~~L--------------GVLy~ls~efdraiDcf~~AL~--v~Pnd~~lWNRLGAt  473 (579)
T KOG1125|consen  410 LAHIQELFLEAARQLPTKIDPDVQSGL--------------GVLYNLSGEFDRAVDCFEAALQ--VKPNDYLLWNRLGAT  473 (579)
T ss_pred             HHHHHHHHHHHHHhCCCCCChhHHhhh--------------HHHHhcchHHHHHHHHHHHHHh--cCCchHHHHHHhhHH
Confidence            44555666655 456644555333333              2234578899999999999876  4555 4589999999


Q ss_pred             hcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh-hh-HHHHHHHHhhcCCHhHHhh
Q 041561           99 CSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL-VV-WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        99 ~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~-~~-~~~li~~~~~~g~~~~a~~  154 (156)
                      ++...+-.+|..-+.+-. +          ++|+- +. ||.= -+|...|.+++|.+
T Consensus       474 LAN~~~s~EAIsAY~rAL-q----------LqP~yVR~RyNlg-IS~mNlG~ykEA~~  519 (579)
T KOG1125|consen  474 LANGNRSEEAISAYNRAL-Q----------LQPGYVRVRYNLG-ISCMNLGAYKEAVK  519 (579)
T ss_pred             hcCCcccHHHHHHHHHHH-h----------cCCCeeeeehhhh-hhhhhhhhHHHHHH
Confidence            999999999999998773 3          45542 33 4443 45688888888864

>PRK15331 chaperone protein SicA; Provisional

Probab=83.77  E-value=7.4  Score=26.49  Aligned_cols=86  Identities=7%  Similarity=-0.127  Sum_probs=57.6

Q ss_pred             cCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHH
Q 041561           16 AKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAI   95 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l   95 (156)
                      -..|++++|+.+|..+...+.- |.              .-|..|-.++-..+++++|...|...-.-+. -|...+--.
T Consensus        48 y~~Gk~~eA~~~F~~L~~~d~~-n~--------------~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~a  111 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCIYDFY-NP--------------DYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFT  111 (165)
T ss_pred             HHCCCHHHHHHHHHHHHHhCcC-cH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchH
Confidence            3678999999999998775431 22              3345566666778889999998887654321 122223333


Q ss_pred             HHhhcCCCchHHHHHHHHhccc
Q 041561           96 LTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        96 l~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      =..+...|+.+.|+..|.....
T Consensus       112 gqC~l~l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        112 GQCQLLMRKAAKARQCFELVNE  133 (165)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHh
Confidence            4555678999999999987743

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.67  E-value=16  Score=27.94  Aligned_cols=91  Identities=10%  Similarity=-0.054  Sum_probs=64.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC---CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS---GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      .+-..++..-....+++.+...+-.++.+   -..|+...++. ++-|- .-+.+++.-+...= .++|        +-|
T Consensus        65 ~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~-irlll-ky~pq~~i~~l~np-IqYG--------iF~  133 (418)
T KOG4570|consen   65 LTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTW-IRLLL-KYDPQKAIYTLVNP-IQYG--------IFP  133 (418)
T ss_pred             eehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHH-HHHHH-ccChHHHHHHHhCc-chhc--------ccc
Confidence            45556666666778899999988888754   24444443332 33322 23556777766655 6777        679


Q ss_pred             ChhhHHHHHHHHhhcCCHhHHhhhC
Q 041561          132 DLVVWGDLVSSCQVHSNVRLAKKAA  156 (156)
Q Consensus       132 d~~~~~~li~~~~~~g~~~~a~~~~  156 (156)
                      |-.+++.+|..+.+.+++.+|.+|+
T Consensus       134 dqf~~c~l~D~flk~~n~~~aa~vv  158 (418)
T KOG4570|consen  134 DQFTFCLLMDSFLKKENYKDAASVV  158 (418)
T ss_pred             chhhHHHHHHHHHhcccHHHHHHHH
Confidence            9999999999999999999998774

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.29  E-value=13  Score=27.35  Aligned_cols=96  Identities=8%  Similarity=0.075  Sum_probs=70.0

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhC----CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDG----YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      -|+.-+.. .+.|++..|++.|...++..    +.||..-|                |-.++...|+.++|-.+|..+.+
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW----------------LGe~~y~qg~y~~Aa~~f~~~~k  206 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW----------------LGESLYAQGDYEDAAYIFARVVK  206 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHH----------------HHHHHHhcccchHHHHHHHHHHH
Confidence            36666665 46777999999999987743    33444221                56778899999999999999987


Q ss_pred             C-CCCccH-HHHHHHHHhhcCCCchHHHHHHHHhccccc
Q 041561           83 S-GVKHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEHDH  119 (156)
Q Consensus        83 ~-g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~  119 (156)
                      . +-.|.. -+.--+-....+.|+-++|+..++++.+++
T Consensus       207 ~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k~Y  245 (262)
T COG1729         207 DYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIKRY  245 (262)
T ss_pred             hCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHC
Confidence            4 323332 344455566679999999999999997774

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=82.63  E-value=1.6  Score=28.63  Aligned_cols=30  Identities=17%  Similarity=0.356  Sum_probs=24.1

Q ss_pred             CCHHHHHHHHHHHHHCCCCccHHHHHHHHHhh
Q 041561           68 EYVEQAISLYKDIIASGVKHDGVTFVAILTPC   99 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~   99 (156)
                      |.-.+|..+|+.|.++|-.||.  |+.|+..+
T Consensus       109 gsk~DaY~VF~kML~~G~pPdd--W~~Ll~~a  138 (140)
T PF11663_consen  109 GSKTDAYAVFRKMLERGNPPDD--WDALLKEA  138 (140)
T ss_pred             ccCCcHHHHHHHHHhCCCCCcc--HHHHHHHh
Confidence            3446789999999999999985  77777664

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=82.62  E-value=5  Score=20.83  Aligned_cols=26  Identities=27%  Similarity=0.404  Sum_probs=21.4

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561           60 MIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus        60 li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      +-.+|...|+.+.|.+++++....|-
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~~   30 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEGD   30 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcCC
Confidence            56788899999999999999886553

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

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

Probab=82.62  E-value=21  Score=28.93  Aligned_cols=75  Identities=11%  Similarity=0.186  Sum_probs=47.4

Q ss_pred             CCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc
Q 041561           68 EYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH  146 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~  146 (156)
                      +++++|..-|++-+.  +.| +.+.|..+--+.-|.+.++++...|++-+++          ++.-...||-.-+.+.-.
T Consensus       408 ~q~e~A~aDF~Kai~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk----------FP~~~Evy~~fAeiLtDq  475 (606)
T KOG0547|consen  408 QQYEEAIADFQKAIS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK----------FPNCPEVYNLFAEILTDQ  475 (606)
T ss_pred             HHHHHHHHHHHHHhh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----------CCCCchHHHHHHHHHhhH
Confidence            345566666655443  333 2335555555555777888888888888665          344566777777777777


Q ss_pred             CCHhHHhh
Q 041561          147 SNVRLAKK  154 (156)
Q Consensus       147 g~~~~a~~  154 (156)
                      +++++|.+
T Consensus       476 qqFd~A~k  483 (606)
T KOG0547|consen  476 QQFDKAVK  483 (606)
T ss_pred             HhHHHHHH
Confidence            77777764

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=82.34  E-value=4.2  Score=30.43  Aligned_cols=43  Identities=19%  Similarity=0.283  Sum_probs=36.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHH
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILT   97 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~   97 (156)
                      .-||..|+.-.+.||+++|+++.+|-++-|..--..||-.-++
T Consensus       258 ~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V~  300 (303)
T PRK10564        258 SYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSVK  300 (303)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHhh
Confidence            4589999999999999999999999999998877777755443

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

Probab=82.02  E-value=2.5  Score=18.90  Aligned_cols=20  Identities=10%  Similarity=0.132  Sum_probs=12.1

Q ss_pred             HHHHHHHcCCCHHHHHHHHH
Q 041561           59 EMIHGYAENEYVEQAISLYK   78 (156)
Q Consensus        59 ~li~~~~~~g~~~~a~~~~~   78 (156)
                      .+-.++...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34455666666666666654

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

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=81.58  E-value=3.7  Score=21.32  Aligned_cols=25  Identities=16%  Similarity=0.421  Sum_probs=21.9

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhC
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDG   35 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g   35 (156)
                      +-++|...|+.+.|+.++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5678999999999999999998654

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

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=81.54  E-value=16  Score=25.77  Aligned_cols=79  Identities=6%  Similarity=-0.030  Sum_probs=57.0

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH---CCCCccHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA---SGVKHDGVT   91 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t   91 (156)
                      .++.|| +.|.+.|-.+...|..-++...-.               +..|--..+.+++..++.+..+   .+-.+|...
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~a---------------LAtyY~krD~~Kt~~ll~~~L~l~~~~~~~n~ei  180 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYA---------------LATYYTKRDPEKTIQLLLRALELSNPDDNFNPEI  180 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHH---------------HHHHHHccCHHHHHHHHHHHHHhcCCCCCCCHHH
Confidence            355565 677777777877776666643333               3344456788999998888765   244889999


Q ss_pred             HHHHHHhhcCCCchHHHH
Q 041561           92 FVAILTPCSHSGLVYAEV  109 (156)
Q Consensus        92 ~~~ll~~~~~~~~~~~a~  109 (156)
                      +..|...+-+.++.+.|-
T Consensus       181 l~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  181 LKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHHHHHhcchhhhh
Confidence            999999999999988763

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

Probab=81.53  E-value=20  Score=26.88  Aligned_cols=75  Identities=9%  Similarity=0.100  Sum_probs=46.9

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL  133 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~  133 (156)
                      +-|..=-.+|++.|..+.|++--+.-..  +-|+ ..+|..|=.+|...|++.+|.+-|..- -+          +.|+-
T Consensus       116 VyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~~~A~~aykKa-Le----------ldP~N  182 (304)
T KOG0553|consen  116 VYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKYEEAIEAYKKA-LE----------LDPDN  182 (304)
T ss_pred             hHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcHHHHHHHHHhh-hc----------cCCCc
Confidence            5566666777777777777766555443  2333 236666777777777888777777655 22          46666


Q ss_pred             hhHHHHHHH
Q 041561          134 VVWGDLVSS  142 (156)
Q Consensus       134 ~~~~~li~~  142 (156)
                      .+|-.=|..
T Consensus       183 e~~K~nL~~  191 (304)
T KOG0553|consen  183 ESYKSNLKI  191 (304)
T ss_pred             HHHHHHHHH
Confidence            666554443

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

Probab=81.45  E-value=5  Score=27.68  Aligned_cols=47  Identities=9%  Similarity=-0.118  Sum_probs=33.7

Q ss_pred             CCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          101 HSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       101 ~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ...+.+......+...+-.        ...|+..+|..++.++...|+.++|++.
T Consensus       120 ~~~~~~~l~~~~~~a~~~l--------~~~P~~~~~~~~a~~l~~~G~~~eA~~~  166 (193)
T PF11846_consen  120 LPPDPEMLEAYIEWAERLL--------RRRPDPNVYQRYALALALLGDPEEARQW  166 (193)
T ss_pred             CCCCHHHHHHHHHHHHHHH--------HhCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            5555555554444442221        1579999999999999999999999875

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

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

Probab=81.06  E-value=10  Score=30.37  Aligned_cols=87  Identities=14%  Similarity=0.100  Sum_probs=64.9

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASG-VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL  133 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~  133 (156)
                      ..|...|+.--+..-++.|..+|-+..+.| +.++.+.+++++..++ .|+...|..+|+.=...           -||.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~-----------f~d~  465 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK-----------FPDS  465 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh-----------CCCc
Confidence            678889999989888999999999999988 7899999999999886 46777899998854333           3444


Q ss_pred             hhH-HHHHHHHhhcCCHhHHh
Q 041561          134 VVW-GDLVSSCQVHSNVRLAK  153 (156)
Q Consensus       134 ~~~-~~li~~~~~~g~~~~a~  153 (156)
                      ..| +-.+.-..+.++-+.|+
T Consensus       466 ~~y~~kyl~fLi~inde~nar  486 (660)
T COG5107         466 TLYKEKYLLFLIRINDEENAR  486 (660)
T ss_pred             hHHHHHHHHHHHHhCcHHHHH
Confidence            443 34444445555555544

>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=80.88  E-value=7.5  Score=26.65  Aligned_cols=62  Identities=10%  Similarity=0.078  Sum_probs=47.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH--HHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG--VTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      ..+..+-.-|++.|+.++|.+.|.++.+.-..|..  ..+-.+|+...-.++++.+.....+..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            56778888889999999999999998875444433  356677888888888888887776663

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.

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=80.12  E-value=20  Score=25.91  Aligned_cols=133  Identities=13%  Similarity=0.085  Sum_probs=82.7

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhh---c----------c-------------chHHHHHHH
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCN---C----------G-------------VTWNEMIHG   63 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~---~----------~-------------~~~~~li~~   63 (156)
                      +..++-+.++.++|...++...+.-. .|+. -+...+.+.+.   .          .             .++..+|+-
T Consensus        75 la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~-~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~  153 (243)
T PRK10866         75 LIYAYYKNADLPLAQAAIDRFIRLNPTHPNI-DYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRG  153 (243)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHhCcCCCch-HHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHH
Confidence            44666889999999999999876532 3333 23333333321   0          0             456666666


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      |-.+.-.++|.+....++..   .-..-+ .+-+-|-+.|.+..|..=++.+.+++.       +-.......-.|+.+|
T Consensus       154 yP~S~ya~~A~~rl~~l~~~---la~~e~-~ia~~Y~~~~~y~AA~~r~~~v~~~Yp-------~t~~~~eal~~l~~ay  222 (243)
T PRK10866        154 YPNSQYTTDATKRLVFLKDR---LAKYEL-SVAEYYTKRGAYVAVVNRVEQMLRDYP-------DTQATRDALPLMENAY  222 (243)
T ss_pred             CcCChhHHHHHHHHHHHHHH---HHHHHH-HHHHHHHHcCchHHHHHHHHHHHHHCC-------CCchHHHHHHHHHHHH
Confidence            66666666666555554321   001111 344557778888888888888866642       1223455666788999


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ...|..++|.++
T Consensus       223 ~~lg~~~~a~~~  234 (243)
T PRK10866        223 RQLQLNAQADKV  234 (243)
T ss_pred             HHcCChHHHHHH
Confidence            999999999764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	156
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-05

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 41.0 bits (94), Expect = 8e-05
 Identities = 13/134 (9%), Positives = 34/134 (25%), Gaps = 24/134 (17%)

Query: 3   PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-------- 54
           P +     +L       SL + +    +  +           A                 
Sbjct: 90  PWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHL 149

Query: 55  ----------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTP 98
                             +N ++ G+A     ++ + +   +  +G+  D +++ A L  
Sbjct: 150 LVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQC 209

Query: 99  CSHSGLVYAEVEIF 112
                     +E  
Sbjct: 210 MGRQDQDAGTIERC 223

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	156
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.92
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.8
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.54
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.52
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.06
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.04
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	98.99
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	98.94
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.93
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.92
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	98.92
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	98.91
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.88
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.82
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.81
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	98.8
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.78
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.71
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.68
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.67
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.67
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.66
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.66
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.66
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.66
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.66
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.64
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.63
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.63
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.6
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.59
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.58
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.57
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.48
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.48
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.47
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.44
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.41
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.4
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.38
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.36
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.35
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.33
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.33
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.33
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.3
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.29
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.27
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.27
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.22
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.19
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.18
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.16
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.14
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.14
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.12
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.12
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.07
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.06
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.06
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.04
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.04
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.03
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	97.97
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.92
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	97.88
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.85
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.85
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	97.84
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.83
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.82
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.82
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.8
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	97.79
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.78
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.74
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.73
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.73
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.68
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.67
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.67
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.66
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.63
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.63
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.63
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.61
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.58
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.58
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	97.57
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.56
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.56
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.56
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.55
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.53
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.52
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.51
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.5
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.5
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.49
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.49
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.46
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.45
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.44
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.43
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.42
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	97.4
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.4
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.39
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.38
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.37
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.37
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.37
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.36
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.34
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.34
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.34
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.34
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.33
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.32
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.3
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.29
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.28
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.28
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	97.27
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.27
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.25
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.25
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.24
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.22
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.22
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.19
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.18
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.17
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.14
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.14
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	97.14
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.13
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.13
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.1
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.08
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.08
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.08
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.06
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.04
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.0
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	96.99
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.97
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.96
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	96.96
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	96.96
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	96.93
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.91
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	96.89
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	96.84
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	96.83
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.8
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	96.8
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.76
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.72
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.69
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	96.68
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	96.56
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.49
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.47
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.44
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.43
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.39
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.36
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	96.24
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.23
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.19
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.18
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.18
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.15
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.12
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.04
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	95.98
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	95.94
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	95.94
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.87
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	95.82
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	95.67
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	95.59
4g1t_A	472	Interferon-induced protein with tetratricopeptide	95.42
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.4
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	95.39
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	95.22
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.21
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	95.17
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	95.17
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	95.13
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	94.89
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	94.75
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	94.68
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	94.53
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	94.39
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	93.87
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	93.8
1klx_A	138	Cysteine rich protein B; structural genomics, heli	93.62
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	93.46
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	93.29
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	93.08
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.39
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	92.29
1pc2_A	152	Mitochondria fission protein; unknown function; NM	91.68
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	90.39
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	90.14
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.95
1pc2_A	152	Mitochondria fission protein; unknown function; NM	89.12
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	88.72
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	88.68
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	88.65
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	88.39
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	87.92
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	87.66
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	87.45
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	87.32
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	85.6
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	85.48
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.2
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	85.02
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	83.59
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	81.4
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	80.46

>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=4.2e-33  Score=217.05  Aligned_cols=141  Identities=13%  Similarity=0.093  Sum_probs=134.2

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc------------------------------c
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------------------------------V   55 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~------------------------------~   55 (156)
                      ..++.+|.+|++.|++++|.++|++|.+.|++||..+||+||.+|++.+                              .
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~  106 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA  106 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHH
Confidence            3588899999999999999999999999999999999999999998764                              7


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      |||+||.+|++.|++++|.++|++|++.|+.||..|||++|.+|++.|++++|.++|++| .+.|        +.||..|
T Consensus       107 tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M-~~~G--------~~Pd~~t  177 (501)
T 4g26_A          107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM-VESE--------VVPEEPE  177 (501)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHTT--------CCCCHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHH-HhcC--------CCCCHHH
Confidence            999999999999999999999999999999999999999999999999999999999999 5555        7999999


Q ss_pred             HHHHHHHHhhcCCHhHHhhh
Q 041561          136 WGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~~  155 (156)
                      |++||.+|++.|++++|.++
T Consensus       178 y~~Li~~~~~~g~~d~A~~l  197 (501)
T 4g26_A          178 LAALLKVSMDTKNADKVYKT  197 (501)
T ss_dssp             HHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHhhCCCHHHHHHH
Confidence            99999999999999999875

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

Probab=99.97  E-value=2.4e-31  Score=207.15  Aligned_cols=139  Identities=11%  Similarity=0.135  Sum_probs=131.0

Q ss_pred             CCCCcccHHHHHHHhcCCCc---------hHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-----------------
Q 041561            1 VYPTQFPFTTVLSSCAKLSS---------LFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-----------------   54 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~---------~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-----------------   54 (156)
                      ++||..|||++|.+|++.+.         ++.|.++|++|.+.|+.||..+||+||++|++.|                 
T Consensus        57 v~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~  136 (501)
T 4g26_A           57 VQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGI  136 (501)
T ss_dssp             CCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTC
T ss_pred             CCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Confidence            58999999999999987654         6889999999999999999999999999999999                 


Q ss_pred             ----chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           55 ----VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        55 ----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                          .+||+||.+|++.|++++|.++|++|.+.|+.||..||++||++|++.|++++|.+++++| ++.|        ..
T Consensus       137 ~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~M-r~~g--------~~  207 (501)
T 4g26_A          137 QPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRL-RDLV--------RQ  207 (501)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHT--------SS
T ss_pred             CCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHH-HHhC--------CC
Confidence                8999999999999999999999999999999999999999999999999999999999999 5555        79


Q ss_pred             CChhhHHHHHHHHhhcCC
Q 041561          131 DDLVVWGDLVSSCQVHSN  148 (156)
Q Consensus       131 pd~~~~~~li~~~~~~g~  148 (156)
                      |+..||++++..|+..+.
T Consensus       208 ps~~T~~~l~~~F~s~~a  225 (501)
T 4g26_A          208 VSKSTFDMIEEWFKSEVA  225 (501)
T ss_dssp             BCHHHHHHHHHHHHSHHH
T ss_pred             cCHHHHHHHHHHHhcCcc
Confidence            999999999999987543

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

Probab=99.92  E-value=5.1e-26  Score=185.57  Aligned_cols=127  Identities=13%  Similarity=0.122  Sum_probs=115.9

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHH---HhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIV---KDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~---~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      .|||++|++|++.|++++|.++|++|.   +.|+.||+              +|||+||++||+.|++++|.++|++|.+
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~Pdv--------------vTYNtLI~Glck~G~~~eA~~Lf~eM~~  193 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTL--------------DMYNAVMLGWARQGAFKELVYVLFMVKD  193 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCH--------------HHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCH--------------hHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            589999999999999999999998876   46899999              8888999999999999999999999999


Q ss_pred             CCCCccHHHHHHHHHhhcCCCch-HHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           83 SGVKHDGVTFVAILTPCSHSGLV-YAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        83 ~g~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|+.||.+|||++|+++++.|+. ++|.++|++| .+.|        +.||..+|+++|+++.+.+-++..+++
T Consensus       194 ~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM-~~kG--------~~PD~vtY~~ll~~~eR~~vL~~Vrkv  258 (1134)
T 3spa_A          194 AGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM-SQEG--------LKLQALFTAVLLSEEDRATVLKAVHKV  258 (1134)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHH-HHHT--------CCSHHHHHHSCCCHHHHHHHHHHHGGG
T ss_pred             cCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHH-HHcC--------CCCChhhcccccChhhHHHHHHHHHHh
Confidence            99999999999999999999985 7899999999 5555        799999999999998888777766654

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

Probab=99.80  E-value=1e-19  Score=148.96  Aligned_cols=92  Identities=9%  Similarity=0.006  Sum_probs=84.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHH---CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIA---SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      .|||+||++||+.|++++|.++|++|.+   .|+.||.+|||+||++||+.|++++|.++|++| .+.|        +.|
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM-~~~G--------~~P  198 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMV-KDAG--------LTP  198 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHTT--------CCC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHH-HHcC--------CCC
Confidence            7999999999999999999999998874   589999999999999999999999999999999 5555        799


Q ss_pred             ChhhHHHHHHHHhhcCCH-hHHhhh
Q 041561          132 DLVVWGDLVSSCQVHSNV-RLAKKA  155 (156)
Q Consensus       132 d~~~~~~li~~~~~~g~~-~~a~~~  155 (156)
                      |.+|||+||.++++.|+. ++|.++
T Consensus       199 DvvTYntLI~glcK~G~~~e~A~~L  223 (1134)
T 3spa_A          199 DLLSYAAALQCMGRQDQDAGTIERC  223 (1134)
T ss_dssp             CHHHHHHHHHHHHHHTCCHHHHHHH
T ss_pred             cHHHHHHHHHHHHhCCCcHHHHHHH
Confidence            999999999999999985 677654

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

Probab=99.54  E-value=1.7e-13  Score=107.16  Aligned_cols=139  Identities=11%  Similarity=-0.066  Sum_probs=87.5

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      ..+|+.+...+.+.|+.++|.++|+.+.+.+ +.+..+|+.+..+|.+.|                    .+|+.+...|
T Consensus       407 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  485 (597)
T 2xpi_A          407 GPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVA  485 (597)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence            3455555555666666666666665555432 235555555655555555                    4566677777


Q ss_pred             HcCCCHHHHHHHHHHHHHC----CCCcc--HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHH
Q 041561           65 AENEYVEQAISLYKDIIAS----GVKHD--GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGD  138 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~----g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~  138 (156)
                      .+.|++++|.++|+++.+.    +..|+  ..+|..+..+|.+.|++++|.++|+.+.+.          ...+..+|..
T Consensus       486 ~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----------~p~~~~~~~~  555 (597)
T 2xpi_A          486 FNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLL----------STNDANVHTA  555 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------SSCCHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----------CCCChHHHHH
Confidence            7777777777777776554    55666  556777777777777777777777766332          1336677777


Q ss_pred             HHHHHhhcCCHhHHhh
Q 041561          139 LVSSCQVHSNVRLAKK  154 (156)
Q Consensus       139 li~~~~~~g~~~~a~~  154 (156)
                      +..+|.+.|++++|.+
T Consensus       556 l~~~~~~~g~~~~A~~  571 (597)
T 2xpi_A          556 IALVYLHKKIPGLAIT  571 (597)
T ss_dssp             HHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhCCHHHHHH
Confidence            7777777777777765

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

Probab=99.52  E-value=1.9e-13  Score=106.82  Aligned_cols=142  Identities=15%  Similarity=0.056  Sum_probs=91.5

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCC---------------------------------CCchHHHhHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGY---------------------------------GNDIFVGSAPINI   49 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~---------------------------------~~~~~~~~~li~~   49 (156)
                      +++.+|+.+...+.+.|++++|.++|+.+.+.+.                                 +.+..+|+.+...
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  382 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIY  382 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHH
Confidence            4555666666666666666666666666654331                                 2345566666666


Q ss_pred             hhhcc--------------------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHH
Q 041561           50 YCNCG--------------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEV  109 (156)
Q Consensus        50 ~~~~~--------------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  109 (156)
                      |.+.|                    .+|+.++.+|.+.|++++|.++|++|.+.+ ..+..+|+.+..+|.+.|++++|.
T Consensus       383 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~  461 (597)
T 2xpi_A          383 YLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLAN  461 (597)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHH
Confidence            66665                    466777777777777777777777766543 235666777777777777777777


Q ss_pred             HHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          110 EIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       110 ~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ++|+.+...          ...+..+|+.+...|.+.|++++|.++
T Consensus       462 ~~~~~~~~~----------~~~~~~~~~~l~~~~~~~g~~~~A~~~  497 (597)
T 2xpi_A          462 EYLQSSYAL----------FQYDPLLLNELGVVAFNKSDMQTAINH  497 (597)
T ss_dssp             HHHHHHHHH----------CCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHh----------CCCChHHHHHHHHHHHHhCCHHHHHHH
Confidence            777776432          234677788888888888888877653

>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=99.06  E-value=1.7e-10  Score=88.11  Aligned_cols=126  Identities=14%  Similarity=0.178  Sum_probs=35.1

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------chHHHHHHHHHcCC
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------VTWNEMIHGYAENE   68 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------~~~~~li~~~~~~g   68 (156)
                      ||..+|..+++++...|++++|...+...++.  .+++.+.+.|+.+|.+.|              .+|+.+-..|...|
T Consensus        59 ~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~pn~~a~~~IGd~~~~~g  136 (449)
T 1b89_A           59 DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEK  136 (449)
T ss_dssp             ----------------------------------------------------CHHHHTTTTTCC----------------
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHcCCcHHHHHHHHHHHHHcC
Confidence            56677888888888888888888877766653  456777888888888887              35555666666666


Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCC
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSN  148 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~  148 (156)
                      ++++|...|..+         ..|..+.+++.+.|++++|.+.+...               .++.+|..++.+|...|+
T Consensus       137 ~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA---------------~~~~~Wk~v~~aCv~~~e  192 (449)
T 1b89_A          137 MYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA---------------NSTRTWKEVCFACVDGKE  192 (449)
T ss_dssp             CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH---------------TCHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHc---------------CCchhHHHHHHHHHHcCc
Confidence            666666666544         25555555555666666555555544               145566666666666666


Q ss_pred             HhHHhh
Q 041561          149 VRLAKK  154 (156)
Q Consensus       149 ~~~a~~  154 (156)
                      +++|..
T Consensus       193 f~lA~~  198 (449)
T 1b89_A          193 FRLAQM  198 (449)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            655543

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

Probab=99.04  E-value=8.6e-09  Score=74.71  Aligned_cols=141  Identities=11%  Similarity=0.007  Sum_probs=109.7

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhcc---------------chHHHHHHHHHc
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCG---------------VTWNEMIHGYAE   66 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~---------------~~~~~li~~~~~   66 (156)
                      |+..++..+...+.+.++.++|.+.++.+...+..| +...+..+-..|.+.|               ..+..+...|.+
T Consensus        63 ~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~~~~~~~~~~l~~~~~~  142 (291)
T 3mkr_A           63 PELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQGDSLECMAMTVQILLK  142 (291)
T ss_dssp             HHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTTCCSHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            456678888889999999999999999998877656 4455555557777777               567888899999


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHH---HHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTF---VAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~---~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      .|++++|.+.|+++.+..  |+....   ...+..+...|++++|..+|+++...          ...+...|+.+-.++
T Consensus       143 ~g~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~----------~p~~~~~~~~la~~~  210 (291)
T 3mkr_A          143 LDRLDLARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK----------CSPTLLLLNGQAACH  210 (291)
T ss_dssp             TTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH----------SCCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh----------CCCcHHHHHHHHHHH
Confidence            999999999999998754  554311   23345455678999999999999655          245788899999999


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ...|++++|++.
T Consensus       211 ~~~g~~~eA~~~  222 (291)
T 3mkr_A          211 MAQGRWEAAEGV  222 (291)
T ss_dssp             HHTTCHHHHHHH
T ss_pred             HHcCCHHHHHHH
Confidence            999999998763

>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=98.99  E-value=2.8e-08  Score=73.78  Aligned_cols=59  Identities=17%  Similarity=0.252  Sum_probs=29.5

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +|..+...|.+.|++++|.+.|+++.+... .+..+|..+...+.+.|++++|...|+.+
T Consensus       239 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  297 (388)
T 1w3b_A          239 VHGNLACVYYEQGLIDLAIDTYRRAIELQP-HFPDAYCNLANALKEKGSVAEAEDCYNTA  297 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444555555555555555555555554321 12334445555555555555555555554

>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=98.94  E-value=5e-08  Score=72.44  Aligned_cols=130  Identities=11%  Similarity=0.083  Sum_probs=98.7

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVE   71 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~   71 (156)
                      ..+...|+.++|...++...+.  .| +..++..+...|.+.|                    .+|..+...+.+.|+++
T Consensus       211 ~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~  288 (388)
T 1w3b_A          211 NVLKEARIFDRAVAAYLRALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVA  288 (388)
T ss_dssp             HHHHTTTCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHH
Confidence            3333444444444444443332  23 4667777878887777                    57888999999999999


Q ss_pred             HHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhH
Q 041561           72 QAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRL  151 (156)
Q Consensus        72 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~  151 (156)
                      +|.+.|+++.+.. ..+..+++.+...+.+.|++++|...++.+.+.          .+.+..+|..+...|.+.|++++
T Consensus       289 ~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----------~p~~~~~~~~l~~~~~~~g~~~~  357 (388)
T 1w3b_A          289 EAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEV----------FPEFAAAHSNLASVLQQQGKLQE  357 (388)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS----------CTTCHHHHHHHHHHHHTTTCCHH
T ss_pred             HHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc----------CCCcHHHHHHHHHHHHHcCCHHH
Confidence            9999999998753 456778999999999999999999999998433          23467889999999999999999


Q ss_pred             Hhhh
Q 041561          152 AKKA  155 (156)
Q Consensus       152 a~~~  155 (156)
                      |.+.
T Consensus       358 A~~~  361 (388)
T 1w3b_A          358 ALMH  361 (388)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9763

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

Probab=98.93  E-value=6.6e-08  Score=65.84  Aligned_cols=140  Identities=6%  Similarity=-0.074  Sum_probs=105.9

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      +..|..+...+.+.|++++|...++...+.. +.+...+..+...|.+.|                    ..|..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~   86 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFL   86 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence            3456677777888889999999888887653 235667777777777776                    5677788888


Q ss_pred             HcC-CCHHHHHHHHHHHHHCCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           65 AEN-EYVEQAISLYKDIIASGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        65 ~~~-g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      ... |++++|.+.|+++.+.+..|+ ...+..+...+.+.|++++|...++.....          ...+...|..+...
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~la~~  156 (225)
T 2vq2_A           87 CGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAA----------QPQFPPAFKELART  156 (225)
T ss_dssp             HTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------STTCHHHHHHHHHH
T ss_pred             HHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCchHHHHHHHH
Confidence            888 999999999999887433343 567777888888899999999998888443          12357778888888


Q ss_pred             HhhcCCHhHHhhh
Q 041561          143 CQVHSNVRLAKKA  155 (156)
Q Consensus       143 ~~~~g~~~~a~~~  155 (156)
                      +...|++++|.+.
T Consensus       157 ~~~~~~~~~A~~~  169 (225)
T 2vq2_A          157 KMLAGQLGDADYY  169 (225)
T ss_dssp             HHHHTCHHHHHHH
T ss_pred             HHHcCCHHHHHHH
Confidence            8888888888753

>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=98.92  E-value=4.7e-08  Score=60.95  Aligned_cols=123  Identities=9%  Similarity=0.095  Sum_probs=100.0

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .|..+...+.+.|++++|..+++.+.+... .+.              ..|..+...+...|++++|.+.|+++...+ .
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~--------------~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~   66 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSA--------------EAWYNLGNAYYKQGDYDEAIEYYQKALELD-P   66 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCH--------------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCC-cch--------------hHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-C
Confidence            467778888899999999999999977532 233              456677788888999999999999998754 3


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+...+..+...+.+.|++++|.+.++.+...          ...+..+|..+...+...|++++|.+.
T Consensus        67 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~la~~~~~~~~~~~A~~~  125 (136)
T 2fo7_A           67 RSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL----------DPRSAEAWYNLGNAYYKQGDYDEAIEY  125 (136)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             CchHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----------CCCChHHHHHHHHHHHHHccHHHHHHH
Confidence            35667888889999999999999999998543          234678899999999999999999763

>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=98.92  E-value=3e-08  Score=74.76  Aligned_cols=139  Identities=9%  Similarity=-0.029  Sum_probs=106.3

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHH---
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEM---   60 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~l---   60 (156)
                      +..++..+...+.+.|+.++|...|+.+.+.. +.+..+|..+...|.+.|                    ..+..+   
T Consensus       176 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~  254 (450)
T 2y4t_A          176 DAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQV  254 (450)
T ss_dssp             CHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHHH
Confidence            45567777888888888888888888876642 345677888888888777                    223333   


Q ss_pred             ---------HHHHHcCCCHHHHHHHHHHHHHCCCCcc-----HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcC
Q 041561           61 ---------IHGYAENEYVEQAISLYKDIIASGVKHD-----GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCL  126 (156)
Q Consensus        61 ---------i~~~~~~g~~~~a~~~~~~m~~~g~~p~-----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~  126 (156)
                               ...+.+.|++++|.+.|+++.+.  .|+     ...+..+...+.+.|++++|...++.+...        
T Consensus       255 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--------  324 (450)
T 2y4t_A          255 KKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQM--------  324 (450)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--------
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------
Confidence                     77888889999999999998773  333     347788888899999999999999987433        


Q ss_pred             CCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          127 MPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       127 ~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                        .+.+..+|..+..+|...|++++|.+.
T Consensus       325 --~p~~~~~~~~l~~~~~~~~~~~~A~~~  351 (450)
T 2y4t_A          325 --EPDNVNALKDRAEAYLIEEMYDEAIQD  351 (450)
T ss_dssp             --CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             --CcccHHHHHHHHHHHHHhcCHHHHHHH
Confidence              134678899999999999999998764

>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=98.91  E-value=2.6e-08  Score=75.06  Aligned_cols=138  Identities=9%  Similarity=-0.020  Sum_probs=108.1

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      ++.++..+...+.+.|++++|..+|+.+.+. .+.+...+..+..+|.+.|                    ..|..+...
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  103 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHL  103 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHH
Confidence            3456788888899999999999999999875 2346888899989998888                    678889999


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccH----HHHHHHHH------------hhcCCCchHHHHHHHHhcccccccCCCcCC
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDG----VTFVAILT------------PCSHSGLVYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~------------~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                      |.+.|++++|.+.|+++.+..  |+.    ..+..+..            .+.+.|++++|...|+.+...         
T Consensus       104 ~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---------  172 (450)
T 2y4t_A          104 LLKQGKLDEAEDDFKKVLKSN--PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEV---------  172 (450)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------
T ss_pred             HHHcCCHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------
Confidence            999999999999999998743  433    45555533            378899999999999998543         


Q ss_pred             CCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          128 PYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       128 ~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                       ...+..+|..+...|...|++++|.+
T Consensus       173 -~~~~~~~~~~l~~~~~~~g~~~~A~~  198 (450)
T 2y4t_A          173 -CVWDAELRELRAECFIKEGEPRKAIS  198 (450)
T ss_dssp             -CTTCHHHHHHHHHHHHHTTCGGGGHH
T ss_pred             -CCCChHHHHHHHHHHHHCCCHHHHHH
Confidence             13356667777777777777777654

>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=98.88  E-value=7.8e-08  Score=67.03  Aligned_cols=136  Identities=8%  Similarity=-0.073  Sum_probs=69.8

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      .|..+-..+...|++++|...++.+.+.. +.+...+..+...|.+.|                    ..|..+...|..
T Consensus        39 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~  117 (252)
T 2ho1_A           39 AYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYE  117 (252)
T ss_dssp             HHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHH
Confidence            34444455555566666666666655432 223445555555555544                    345555555666


Q ss_pred             CCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           67 NEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      .|++++|.+.|++..+.+..| +...+..+...+.+.|++++|...++......          ..+...|..+...|..
T Consensus       118 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~----------~~~~~~~~~la~~~~~  187 (252)
T 2ho1_A          118 QKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN----------RNQPSVALEMADLLYK  187 (252)
T ss_dssp             TTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------SCCHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC----------cccHHHHHHHHHHHHH
Confidence            666666666666655532333 33345555555556666666666666553221          1234444444444555


Q ss_pred             cCCHhHHh
Q 041561          146 HSNVRLAK  153 (156)
Q Consensus       146 ~g~~~~a~  153 (156)
                      .|++++|.
T Consensus       188 ~g~~~~A~  195 (252)
T 2ho1_A          188 EREYVPAR  195 (252)
T ss_dssp             TTCHHHHH
T ss_pred             cCCHHHHH
Confidence            55554443

>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=98.82  E-value=3.5e-07  Score=63.66  Aligned_cols=140  Identities=4%  Similarity=-0.078  Sum_probs=112.6

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----------------------chHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----------------------VTWNEMI   61 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----------------------~~~~~li   61 (156)
                      +..++..+-..+.+.|+.++|...++...+.. +.+...+..+...|.+.|                      ..|..+.
T Consensus        70 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la  148 (252)
T 2ho1_A           70 SADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLG  148 (252)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHH
Confidence            44567777788888899999999999887653 235667777777777766                      4567788


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVS  141 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~  141 (156)
                      ..+...|++++|.+.|++..+.. ..+...+..+...+.+.|+.++|...++.....          ...+...|..+..
T Consensus       149 ~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~----------~~~~~~~~~~~~~  217 (252)
T 2ho1_A          149 LVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQYYDLFAQG----------GGQNARSLLLGIR  217 (252)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT----------SCCCHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CcCcHHHHHHHHH
Confidence            88999999999999999988754 234678888999999999999999999998443          2456788899999


Q ss_pred             HHhhcCCHhHHhhh
Q 041561          142 SCQVHSNVRLAKKA  155 (156)
Q Consensus       142 ~~~~~g~~~~a~~~  155 (156)
                      .+...|+.++|.+.
T Consensus       218 ~~~~~g~~~~A~~~  231 (252)
T 2ho1_A          218 LAKVFEDRDTAASY  231 (252)
T ss_dssp             HHHHTTCHHHHHHH
T ss_pred             HHHHccCHHHHHHH
Confidence            99999999999764

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

Probab=98.81  E-value=7.3e-08  Score=70.90  Aligned_cols=82  Identities=15%  Similarity=0.124  Sum_probs=44.7

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCC-ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVK-HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVS  141 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~  141 (156)
                      .+.+.|++++|.+.|+++.+.... ++..++..+...+.+.|++++|...|+.....          .+.+..+|+.+-.
T Consensus       186 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----------~p~~~~~~~~l~~  255 (365)
T 4eqf_A          186 SPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTV----------RPEDYSLWNRLGA  255 (365)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHH
T ss_pred             HHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----------CCCCHHHHHHHHH
Confidence            444444444444444444432211 14556666666666777777777777666332          1234566666666


Q ss_pred             HHhhcCCHhHHhh
Q 041561          142 SCQVHSNVRLAKK  154 (156)
Q Consensus       142 ~~~~~g~~~~a~~  154 (156)
                      .|...|++++|.+
T Consensus       256 ~~~~~g~~~~A~~  268 (365)
T 4eqf_A          256 TLANGDRSEEAVE  268 (365)
T ss_dssp             HHHHTTCHHHHHH
T ss_pred             HHHHcCCHHHHHH
Confidence            7777777666654

>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=98.80  E-value=1.5e-08  Score=77.47  Aligned_cols=125  Identities=9%  Similarity=-0.017  Sum_probs=78.1

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc------------chHHHHHHHHHcCCCH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------------VTWNEMIHGYAENEYV   70 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~------------~~~~~li~~~~~~g~~   70 (156)
                      |++.+.+.++.+|.+.|++++++++++       .|+..+|+.+-+.|...|            ..|..+..++.+.|++
T Consensus        92 ~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a~n~~~LA~~L~~Lg~y  164 (449)
T 1b89_A           92 RESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEY  164 (449)
T ss_dssp             -----------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHTTCHHHHHHHHHTTTCH
T ss_pred             ccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHhhhHHHHHHHHHHhccH
Confidence            456778899999999999999888885       378889999999999888            7899999999999999


Q ss_pred             HHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHh
Q 041561           71 EQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVR  150 (156)
Q Consensus        71 ~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~  150 (156)
                      ++|.+.++.+      .+..+|..++.+|...|+++.|......+.            ..||.  ...++..|.+.|+++
T Consensus       165 q~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~------------~~ad~--l~~lv~~Yek~G~~e  224 (449)
T 1b89_A          165 QAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV------------VHADE--LEELINYYQDRGYFE  224 (449)
T ss_dssp             HHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT------------TCHHH--HHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH------------hCHhh--HHHHHHHHHHCCCHH
Confidence            9999999988      378999999999999999999966655542            23444  457999999999999


Q ss_pred             HHhh
Q 041561          151 LAKK  154 (156)
Q Consensus       151 ~a~~  154 (156)
                      +|..
T Consensus       225 Eai~  228 (449)
T 1b89_A          225 ELIT  228 (449)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9954

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

Probab=98.78  E-value=3.2e-07  Score=63.24  Aligned_cols=140  Identities=8%  Similarity=0.027  Sum_probs=104.5

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      +...+..+-..+.+.|+.++|...++...+.. +.+...+..+...|.+.|                    ..|..+...
T Consensus        56 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~  134 (243)
T 2q7f_A           56 DAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTV  134 (243)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            34566677777788888888888888887653 235667777777777666                    557777788


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      +...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|...++.....          ...+..+|..+-..|
T Consensus       135 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~la~~~  203 (243)
T 2q7f_A          135 LVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQ----------DPGHADAFYNAGVTY  203 (243)
T ss_dssp             HHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH----------CTTCHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CcccHHHHHHHHHHH
Confidence            888888888888888877643 234567777788888888888888888887443          234577888888889


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ...|++++|.+.
T Consensus       204 ~~~~~~~~A~~~  215 (243)
T 2q7f_A          204 AYKENREKALEM  215 (243)
T ss_dssp             HHTTCTTHHHHH
T ss_pred             HHccCHHHHHHH
Confidence            999998888753

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

Probab=98.71  E-value=3.6e-07  Score=63.11  Aligned_cols=136  Identities=12%  Similarity=-0.055  Sum_probs=88.0

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhc-----------c--------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNC-----------G--------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-----------~--------------------   54 (156)
                      ..+..+-..+.+.|+.++|...++...+.. +.+...+..+-..|.+.           |                    
T Consensus        40 ~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~  118 (217)
T 2pl2_A           40 EALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYA  118 (217)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccH
Confidence            445555566667777777777777776543 22445566666666655           5                    


Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+...|++++|.+.|++..+..  .+...+..+-..+...|+.++|...|+.....          -+.+..
T Consensus       119 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~----------~P~~~~  186 (217)
T 2pl2_A          119 PLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQ----------APKDLD  186 (217)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------STTCHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCChH
Confidence            456667777778888888888888877655  56777777777888888888888888877433          133567


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                      .+..+-..+...|++++|.+
T Consensus       187 ~~~~la~~~~~~g~~~~A~~  206 (217)
T 2pl2_A          187 LRVRYASALLLKGKAEEAAR  206 (217)
T ss_dssp             HHHHHHHHHTC---------
T ss_pred             HHHHHHHHHHHccCHHHHHH
Confidence            77888888888888888765

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

Probab=98.68  E-value=9.3e-07  Score=61.28  Aligned_cols=86  Identities=8%  Similarity=-0.027  Sum_probs=44.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHH
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWG  137 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~  137 (156)
                      ..+-..+...|++++|.+.|++..+.. ..+..++..+-..+.+.|++++|...++.....          .+.+...|.
T Consensus       143 ~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~----------~~~~~~~~~  211 (258)
T 3uq3_A          143 RLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEK----------DPNFVRAYI  211 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh----------CHHHHHHHH
Confidence            344444555555555555555554432 123444555555555555555555555555222          122355555


Q ss_pred             HHHHHHhhcCCHhHHhh
Q 041561          138 DLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       138 ~li~~~~~~g~~~~a~~  154 (156)
                      .+-..|...|++++|.+
T Consensus       212 ~l~~~~~~~g~~~~A~~  228 (258)
T 3uq3_A          212 RKATAQIAVKEYASALE  228 (258)
T ss_dssp             HHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHH
Confidence            56666666666666554

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

Probab=98.67  E-value=1.2e-06  Score=59.51  Aligned_cols=139  Identities=8%  Similarity=-0.085  Sum_probs=108.4

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhc-c----------------------chHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNC-G----------------------VTWNEMI   61 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-~----------------------~~~~~li   61 (156)
                      ...+..+...+...|+.++|...++...+.. +.+...+..+...|... |                      ..|..+.
T Consensus        42 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~  120 (225)
T 2vq2_A           42 ELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKG  120 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHH
Confidence            4566667777778888888888888876653 23566677777777777 6                      4577788


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC-CChhhHHHHH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK-DDLVVWGDLV  140 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~-pd~~~~~~li  140 (156)
                      ..+...|++++|.+.|++..+.. ..+...+..+...+.+.|+.++|...++.....          .. .+...|..+.
T Consensus       121 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~~~~  189 (225)
T 2vq2_A          121 ICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKYQSR----------VEVLQADDLLLGW  189 (225)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------HCSCCHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCCHHHHHHHH
Confidence            88999999999999999988753 224677888889999999999999999998443          23 5777888888


Q ss_pred             HHHhhcCCHhHHhhh
Q 041561          141 SSCQVHSNVRLAKKA  155 (156)
Q Consensus       141 ~~~~~~g~~~~a~~~  155 (156)
                      ..+...|+.++|.+.
T Consensus       190 ~~~~~~~~~~~a~~~  204 (225)
T 2vq2_A          190 KIAKALGNAQAAYEY  204 (225)
T ss_dssp             HHHHHTTCHHHHHHH
T ss_pred             HHHHhcCcHHHHHHH
Confidence            999999999988753

>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=98.67  E-value=8.3e-07  Score=58.30  Aligned_cols=136  Identities=12%  Similarity=0.006  Sum_probs=96.2

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcC
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAEN   67 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~   67 (156)
                      |..+-..+...|+.++|...++.+.+.. +.+...+..+...|.+.|                    ..|..+...+...
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~   89 (186)
T 3as5_A           11 YRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQV   89 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Confidence            3344444555556666666555554321 123444555555554444                    5677778888899


Q ss_pred             CCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcC
Q 041561           68 EYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHS  147 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g  147 (156)
                      |++++|.+.|++..+.. ..+...+..+...+.+.|++++|...++.....          ...+...|..+...|...|
T Consensus        90 ~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~la~~~~~~~  158 (186)
T 3as5_A           90 QKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGL----------RPNEGKVHRAIAFSYEQMG  158 (186)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhc----------CccchHHHHHHHHHHHHcC
Confidence            99999999999987753 335677888888899999999999999988544          2346788999999999999


Q ss_pred             CHhHHhhh
Q 041561          148 NVRLAKKA  155 (156)
Q Consensus       148 ~~~~a~~~  155 (156)
                      ++++|.+.
T Consensus       159 ~~~~A~~~  166 (186)
T 3as5_A          159 RHEEALPH  166 (186)
T ss_dssp             CHHHHHHH
T ss_pred             CHHHHHHH
Confidence            99998763

>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=98.66  E-value=2.2e-06  Score=62.74  Aligned_cols=139  Identities=10%  Similarity=0.001  Sum_probs=91.9

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      ...+..+-..+.+.|++++|...++.+.+.. +.+...+..+-..|.+.|                    ..|..+...|
T Consensus        64 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~  142 (368)
T 1fch_A           64 HPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSF  142 (368)
T ss_dssp             CSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            4556666667777777777777777776643 235566666666666666                    4566666667


Q ss_pred             HcCCCHHHHHHHHHHHHHCCC-----------------------------------------------Cc---cHHHHHH
Q 041561           65 AENEYVEQAISLYKDIIASGV-----------------------------------------------KH---DGVTFVA   94 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~-----------------------------------------------~p---~~~t~~~   94 (156)
                      ...|++++|.+.|+++.+...                                               .|   +..++..
T Consensus       143 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~  222 (368)
T 1fch_A          143 TNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCG  222 (368)
T ss_dssp             HHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHH
Confidence            777777777766666554221                                               12   4667777


Q ss_pred             HHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           95 ILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        95 ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +...+.+.|++++|...++.....          ...+..+|..+-..|...|++++|.+
T Consensus       223 l~~~~~~~g~~~~A~~~~~~al~~----------~~~~~~~~~~l~~~~~~~g~~~~A~~  272 (368)
T 1fch_A          223 LGVLFNLSGEYDKAVDCFTAALSV----------RPNDYLLWNKLGATLANGNQSEEAVA  272 (368)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh----------CcCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            778888888888888888877433          12345677777777777777777764

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

Probab=98.66  E-value=1.1e-06  Score=60.97  Aligned_cols=136  Identities=9%  Similarity=-0.031  Sum_probs=102.9

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc---------------------------chHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------------------------VTWNE   59 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---------------------------~~~~~   59 (156)
                      +|..+-..+.+.|++++|...|+...+..  .+...+..+-..|.+.|                           ..|..
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            45555666667777777777777776665  66677777777777666                           34566


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCC------------------------CCc-cHHHHHHHHHhhcCCCchHHHHHHHHh
Q 041561           60 MIHGYAENEYVEQAISLYKDIIASG------------------------VKH-DGVTFVAILTPCSHSGLVYAEVEIFNS  114 (156)
Q Consensus        60 li~~~~~~g~~~~a~~~~~~m~~~g------------------------~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~  114 (156)
                      +-..|...|++++|.+.|++..+..                        ..| +...+..+-..+.+.|++++|...++.
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  164 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTE  164 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            7778888888888888888877621                        233 344677788888999999999999999


Q ss_pred             cccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          115 MEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       115 m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ....          ...+..+|..+-..|...|++++|.+
T Consensus       165 a~~~----------~~~~~~~~~~l~~~~~~~~~~~~A~~  194 (258)
T 3uq3_A          165 MIKR----------APEDARGYSNRAAALAKLMSFPEAIA  194 (258)
T ss_dssp             HHHH----------CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhc----------CcccHHHHHHHHHHHHHhCCHHHHHH
Confidence            8544          23467889999999999999999975

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

Probab=98.66  E-value=8.4e-07  Score=67.63  Aligned_cols=138  Identities=5%  Similarity=-0.108  Sum_probs=115.8

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      ..++..+-..+.+.|++++|...++.+.+...  +...+..+...|.+.|                    ..|..+...|
T Consensus       237 ~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  314 (514)
T 2gw1_A          237 AISLEHTGIFKFLKNDPLGAHEDIKKAIELFP--RVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMN  314 (514)
T ss_dssp             HHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCc--cHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHH
Confidence            34667777888899999999999999987653  3888888888888887                    5788899999


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHh
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQ  144 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~  144 (156)
                      ...|++++|.+.|++..+.... +..++..+...+.+.|++++|...++.....          ...+..+|..+-..|.
T Consensus       315 ~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~la~~~~  383 (514)
T 2gw1_A          315 FILQNYDQAGKDFDKAKELDPE-NIFPYIQLACLAYRENKFDDCETLFSEAKRK----------FPEAPEVPNFFAEILT  383 (514)
T ss_dssp             HHTTCTTHHHHHHHHHHHTCSS-CSHHHHHHHHHTTTTTCHHHHHHHHHHHHHH----------STTCSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHhChh-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH----------cccCHHHHHHHHHHHH
Confidence            9999999999999999875432 5668888999999999999999999998543          2346788999999999


Q ss_pred             hcCCHhHHhhh
Q 041561          145 VHSNVRLAKKA  155 (156)
Q Consensus       145 ~~g~~~~a~~~  155 (156)
                      ..|++++|.+.
T Consensus       384 ~~~~~~~A~~~  394 (514)
T 2gw1_A          384 DKNDFDKALKQ  394 (514)
T ss_dssp             HTTCHHHHHHH
T ss_pred             HCCCHHHHHHH
Confidence            99999999763

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

Probab=98.66  E-value=5.3e-07  Score=65.26  Aligned_cols=123  Identities=11%  Similarity=0.010  Sum_probs=89.6

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc------------------chHHHH----HHHHHcCCCH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------------------VTWNEM----IHGYAENEYV   70 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~------------------~~~~~l----i~~~~~~g~~   70 (156)
                      ..+.+.|+.++|.+.++.      +.+...+..+...|.+.|                  .+...+    +..+...|++
T Consensus       109 ~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~  182 (291)
T 3mkr_A          109 SIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKL  182 (291)
T ss_dssp             HHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTHH
T ss_pred             HHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhCchHH
Confidence            555666777777666665      345666666666666665                  112222    2333456899


Q ss_pred             HHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHh
Q 041561           71 EQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVR  150 (156)
Q Consensus        71 ~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~  150 (156)
                      ++|.++|+++.+. ...+...++.+-.++.+.|++++|...|++....          -+-+..+|..+...+...|+.+
T Consensus       183 ~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~----------~p~~~~~l~~l~~~~~~~g~~~  251 (291)
T 3mkr_A          183 QDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDK----------DSGHPETLINLVVLSQHLGKPP  251 (291)
T ss_dssp             HHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHHHHHcCCCH
Confidence            9999999999886 3457778999999999999999999999997443          1337788999999999999987


Q ss_pred             HH
Q 041561          151 LA  152 (156)
Q Consensus       151 ~a  152 (156)
                      ++
T Consensus       252 ea  253 (291)
T 3mkr_A          252 EV  253 (291)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

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

Probab=98.66  E-value=2.5e-07  Score=68.07  Aligned_cols=147  Identities=13%  Similarity=0.049  Sum_probs=105.4

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCC-CchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYG-NDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      +..+-..+.+.|++++|...++.+.+..-. ++..++..+-..|.+.|                    .+|+.+...|..
T Consensus       180 ~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  259 (365)
T 4eqf_A          180 TRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLAN  259 (365)
T ss_dssp             ---------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            344567788889999999999998776432 26778888888888777                    678999999999


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC--cCCCCCCChhhHHHHHHHHh
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK--CLMPYKDDLVVWGDLVSSCQ  144 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~--c~~~~~pd~~~~~~li~~~~  144 (156)
                      .|++++|.+.|++..+.. ..+..++..+-..+.+.|++++|...|+.......-..+  -......+..+|..+-.++.
T Consensus       260 ~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  338 (365)
T 4eqf_A          260 GDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALS  338 (365)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHH
Confidence            999999999999988753 224778888999999999999999999988432110000  00000113688999999999


Q ss_pred             hcCCHhHHhhh
Q 041561          145 VHSNVRLAKKA  155 (156)
Q Consensus       145 ~~g~~~~a~~~  155 (156)
                      ..|+.+.+.++
T Consensus       339 ~~g~~~~a~~~  349 (365)
T 4eqf_A          339 LMDQPELFQAA  349 (365)
T ss_dssp             HHTCHHHHHHH
T ss_pred             HcCcHHHHHHH
Confidence            99999988764

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

Probab=98.64  E-value=2.9e-07  Score=63.52  Aligned_cols=140  Identities=9%  Similarity=0.046  Sum_probs=96.2

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      +..+|..+-..+.+.|+.++|...|+...+.. +.+...+..+...|.+.|                    ..|..+...
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~  100 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNV  100 (243)
T ss_dssp             --------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            34566777778889999999999999998743 345777777878887777                    567788888


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      |...|++++|.+.|++..+.. ..+...+..+...+.+.|+.++|...++.....          ...+...|..+...+
T Consensus       101 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~l~~~~  169 (243)
T 2q7f_A          101 YVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL----------NENDTEARFQFGMCL  169 (243)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh----------CCccHHHHHHHHHHH
Confidence            999999999999999987754 235667888888888999999999999988443          234678888899999


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ...|++++|.+.
T Consensus       170 ~~~~~~~~A~~~  181 (243)
T 2q7f_A          170 ANEGMLDEALSQ  181 (243)
T ss_dssp             HHHTCCHHHHHH
T ss_pred             HHcCCHHHHHHH
Confidence            999999998763

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

Probab=98.63  E-value=2.4e-06  Score=56.81  Aligned_cols=139  Identities=9%  Similarity=-0.025  Sum_probs=112.2

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      ++..|..+=..+.+.|++++|...|+...+.. +-+...+..+-..|.+.|                    ..+..+-..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~   82 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSA   82 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHH
Confidence            56678888888899999999999999987753 236677888888888877                    556667778


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      +...++++++.+.+.+..+.. .-+...+..+-..+.+.|++++|.+.|+...+.          -+.+..+|..+=..|
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~----------~p~~~~~~~~lg~~~  151 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISI----------KPGFIRAYQSIGLAY  151 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHh----------cchhhhHHHHHHHHH
Confidence            888999999999999887643 224567777888888999999999999988443          134678899999999


Q ss_pred             hhcCCHhHHhh
Q 041561          144 QVHSNVRLAKK  154 (156)
Q Consensus       144 ~~~g~~~~a~~  154 (156)
                      ...|++++|.+
T Consensus       152 ~~~g~~~~A~~  162 (184)
T 3vtx_A          152 EGKGLRDEAVK  162 (184)
T ss_dssp             HHTTCHHHHHH
T ss_pred             HHCCCHHHHHH
Confidence            99999999976

>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=98.63  E-value=9.3e-07  Score=63.48  Aligned_cols=138  Identities=9%  Similarity=-0.144  Sum_probs=72.5

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYA   65 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~   65 (156)
                      ..|..+-..+...|+.++|...++...+..- .+...+..+-..|.+.|                    ..|..+...+.
T Consensus       126 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~  204 (330)
T 3hym_B          126 PAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAF  204 (330)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            3444455555555555555555555544321 12333333444444444                    44555566666


Q ss_pred             cCCCHHHHHHHHHHHHHCC--------CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHH
Q 041561           66 ENEYVEQAISLYKDIIASG--------VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWG  137 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g--------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~  137 (156)
                      ..|++++|.+.|++..+..        ...+..++..+-..+.+.|++++|...++.....          ...+...|.
T Consensus       205 ~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~----------~~~~~~~~~  274 (330)
T 3hym_B          205 QNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVL----------IPQNASTYS  274 (330)
T ss_dssp             HTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------STTCSHHHH
T ss_pred             HcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhh----------CccchHHHH
Confidence            6666666666666654321        1222345555666666666666666666655322          123455666


Q ss_pred             HHHHHHhhcCCHhHHhh
Q 041561          138 DLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       138 ~li~~~~~~g~~~~a~~  154 (156)
                      .+-..|...|++++|.+
T Consensus       275 ~la~~~~~~g~~~~A~~  291 (330)
T 3hym_B          275 AIGYIHSLMGNFENAVD  291 (330)
T ss_dssp             HHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHhccHHHHHH
Confidence            66666666777666654

>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=98.60  E-value=8.6e-07  Score=63.59  Aligned_cols=128  Identities=12%  Similarity=0.057  Sum_probs=104.9

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQAI   74 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a~   74 (156)
                      +...|+.++|...++.+.+.. +.+...+..+...|.+.|                    ..|..+...+...|++++|.
T Consensus       148 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  226 (327)
T 3cv0_A          148 FAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEAL  226 (327)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHH
Confidence            667788888888888887654 236677777877887777                    56888999999999999999


Q ss_pred             HHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-------------ChhhHHHHHH
Q 041561           75 SLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-------------DLVVWGDLVS  141 (156)
Q Consensus        75 ~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-------------d~~~~~~li~  141 (156)
                      +.|++..+.. ..+..++..+...+.+.|++++|.+.++.....           .|             +..+|..+..
T Consensus       227 ~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~-----------~~~~~~~~~~~~~~~~~~~~~~l~~  294 (327)
T 3cv0_A          227 DAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYM-----------QVGGTTPTGEASREATRSMWDFFRM  294 (327)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------HTTSCC-----CCTHHHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-----------CCccccccccchhhcCHHHHHHHHH
Confidence            9999987753 235678888999999999999999999988443           23             4788999999


Q ss_pred             HHhhcCCHhHHhhh
Q 041561          142 SCQVHSNVRLAKKA  155 (156)
Q Consensus       142 ~~~~~g~~~~a~~~  155 (156)
                      ++...|+.++|.++
T Consensus       295 ~~~~~g~~~~A~~~  308 (327)
T 3cv0_A          295 LLNVMNRPDLVELT  308 (327)
T ss_dssp             HHHHTTCHHHHHHH
T ss_pred             HHHhcCCHHHHHHH
Confidence            99999999999875

>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=98.59  E-value=1.3e-06  Score=63.86  Aligned_cols=116  Identities=15%  Similarity=0.081  Sum_probs=79.1

Q ss_pred             chHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHh
Q 041561           39 DIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTP   98 (156)
Q Consensus        39 ~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~   98 (156)
                      +..++..+-..|.+.|                    ..|..+...+...|++++|.+.|++..+.. ..+..++..+-..
T Consensus       216 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~  294 (368)
T 1fch_A          216 DPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGIS  294 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHH
Confidence            3566666666666666                    567778888888888888888888877643 2345677778888


Q ss_pred             hcCCCchHHHHHHHHhcccccccCCC-cCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           99 CSHSGLVYAEVEIFNSMEHDHEVKPK-CLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        99 ~~~~~~~~~a~~~~~~m~~~~~~~~~-c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +.+.|++++|...|+.......-..+ -.........+|..+..+|...|+.++|.++
T Consensus       295 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  352 (368)
T 1fch_A          295 CINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAA  352 (368)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHh
Confidence            88888888888888877432100000 0000001268899999999999999999864

>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=98.58  E-value=2.3e-06  Score=61.41  Aligned_cols=149  Identities=8%  Similarity=-0.060  Sum_probs=104.3

Q ss_pred             CcccHHHHHHHhcCCC-chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLS-SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIH   62 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~   62 (156)
                      +...|..+-..+...| +.++|...++...+.. +.+...|..+-..|.+.|                    ..+..+..
T Consensus        89 ~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~  167 (330)
T 3hym_B           89 NPVSWFAVGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGL  167 (330)
T ss_dssp             STHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHH
Confidence            3455666666777777 7778888887776543 234566677777776666                    45666778


Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      .|...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|...++.......-..+ ......+..+|..+-..
T Consensus       168 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~-~~~~~~~~~~~~~la~~  245 (330)
T 3hym_B          168 EYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGN-EVTVDKWEPLLNNLGHV  245 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSC-SCTTTTCCHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccc-cccccHHHHHHHHHHHH
Confidence            8888889999999888887643 234667888888888999999999888877432100000 00013346789999999


Q ss_pred             HhhcCCHhHHhhh
Q 041561          143 CQVHSNVRLAKKA  155 (156)
Q Consensus       143 ~~~~g~~~~a~~~  155 (156)
                      |...|++++|.+.
T Consensus       246 ~~~~g~~~~A~~~  258 (330)
T 3hym_B          246 CRKLKKYAEALDY  258 (330)
T ss_dssp             HHHTTCHHHHHHH
T ss_pred             HHHhcCHHHHHHH
Confidence            9999999999763

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

Probab=98.57  E-value=1.8e-06  Score=59.57  Aligned_cols=141  Identities=12%  Similarity=-0.035  Sum_probs=107.1

Q ss_pred             CCCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHH
Q 041561            1 VYPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEM   60 (156)
Q Consensus         1 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~l   60 (156)
                      +++++..+..+-..+.+.|+.++|...|+...+.. +.+...+..+-..|.+.|                    ..|..+
T Consensus         1 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~l   79 (217)
T 2pl2_A            1 MQTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVL   79 (217)
T ss_dssp             ---CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHH
Confidence            46778888888889999999999999999987753 235667777777777766                    466777


Q ss_pred             HHHHHcC-----------CCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           61 IHGYAEN-----------EYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        61 i~~~~~~-----------g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      -..+...           |++++|.+.|++..+... -+...+..+-..+.+.|+.++|...|++..+.          -
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~----------~  148 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNP-RYAPLHLQRGLVYALLGERDKAEASLKQALAL----------E  148 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------C
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcCChHHHHHHHHHHHhc----------c
Confidence            7777777           888888888888876432 13556777777888889999999888887443          2


Q ss_pred             CCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          130 KDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       130 ~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                       .+...|..+-..|...|++++|.+
T Consensus       149 -~~~~~~~~la~~~~~~g~~~~A~~  172 (217)
T 2pl2_A          149 -DTPEIRSALAELYLSMGRLDEALA  172 (217)
T ss_dssp             -CCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             -cchHHHHHHHHHHHHcCCHHHHHH
Confidence             567788888888999999988875

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

Probab=98.48  E-value=3.2e-06  Score=64.36  Aligned_cols=141  Identities=8%  Similarity=-0.094  Sum_probs=108.7

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      +..+|..+...+.+.|+.++|...++...+... .+...+..+...|.+.|                    ..|..+...
T Consensus       303 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~  381 (514)
T 2gw1_A          303 NSSVYYHRGQMNFILQNYDQAGKDFDKAKELDP-ENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEI  381 (514)
T ss_dssp             CTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCS-SCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCh-hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHH
Confidence            445677777778888888888888888776532 35567777777777776                    567888889


Q ss_pred             HHcCCCHHHHHHHHHHHHHCC-CCcc----HHHHHHHHHhhcC---CCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           64 YAENEYVEQAISLYKDIIASG-VKHD----GVTFVAILTPCSH---SGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~ll~~~~~---~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      |.+.|++++|.+.|+++.+.. -.|+    ..++..+...+.+   .|++++|...++.....          ...+..+
T Consensus       382 ~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~----------~~~~~~~  451 (514)
T 2gw1_A          382 LTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKL----------DPRSEQA  451 (514)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHH----------CTTCHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHh----------CcccHHH
Confidence            999999999999999987632 1222    3478888888888   99999999999988443          2346788


Q ss_pred             HHHHHHHHhhcCCHhHHhhh
Q 041561          136 WGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~~  155 (156)
                      |..+-..|...|++++|.+.
T Consensus       452 ~~~la~~~~~~g~~~~A~~~  471 (514)
T 2gw1_A          452 KIGLAQMKLQQEDIDEAITL  471 (514)
T ss_dssp             HHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHH
Confidence            89999999999999999763

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

Probab=98.48  E-value=5.9e-06  Score=59.80  Aligned_cols=142  Identities=8%  Similarity=-0.053  Sum_probs=106.0

Q ss_pred             CCc-ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc-hH-HHhHHHHHhhhcc--------------------chHHH
Q 041561            3 PTQ-FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND-IF-VGSAPINIYCNCG--------------------VTWNE   59 (156)
Q Consensus         3 p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-~~-~~~~li~~~~~~~--------------------~~~~~   59 (156)
                      |+. ..|..+...+.+.|++++|..+|+...+.  .|+ .. .|..+...+.+.|                    ..|..
T Consensus        96 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~  173 (308)
T 2ond_A           96 KKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVT  173 (308)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHH
T ss_pred             cccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            443 46888888888999999999999999873  454 33 7888888877766                    12221


Q ss_pred             HHHH-HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC--ChhhH
Q 041561           60 MIHG-YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD--DLVVW  136 (156)
Q Consensus        60 li~~-~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p--d~~~~  136 (156)
                      .... +...|++++|.++|++..+... -+...|..+++.+.+.|+.++|+.+|+.......        +.|  ....|
T Consensus       174 ~a~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~--------l~p~~~~~l~  244 (308)
T 2ond_A          174 AALMEYYCSKDKSVAFKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS--------LPPEKSGEIW  244 (308)
T ss_dssp             HHHHHHHTSCCHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSS--------SCGGGCHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccC--------CCHHHHHHHH
Confidence            1111 1236999999999999876421 2567888899999999999999999999854311        244  46789


Q ss_pred             HHHHHHHhhcCCHhHHhhh
Q 041561          137 GDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       137 ~~li~~~~~~g~~~~a~~~  155 (156)
                      ..++..+...|+.++|.++
T Consensus       245 ~~~~~~~~~~g~~~~a~~~  263 (308)
T 2ond_A          245 ARFLAFESNIGDLASILKV  263 (308)
T ss_dssp             HHHHHHHHHHSCHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHH
Confidence            9999999999999998764

>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=98.47  E-value=3.8e-06  Score=60.20  Aligned_cols=138  Identities=7%  Similarity=-0.117  Sum_probs=97.8

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      +...+...-..+.+.|++++|..+++.+.+.. +.+...+..+...|.+.|                    ..|..+...
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   98 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVS   98 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHH
Confidence            34556677778888999999999999987753 236677777777777777                    567788888


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHH-HHHHH--------------HH-hhcCCCchHHHHHHHHhcccccccCCCcCC
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGV-TFVAI--------------LT-PCSHSGLVYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~l--------------l~-~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                      |...|++++|.+.|++..+..  |+.. .+..+              -. .+...|++++|...++.....         
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---------  167 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQ--PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEM---------  167 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTS--TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHH---------
T ss_pred             HHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhh---------
Confidence            999999999999999987643  2222 22222              12 366788888888888887443         


Q ss_pred             CCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          128 PYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       128 ~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                       ...+..+|..+...|...|++++|.+
T Consensus       168 -~~~~~~~~~~la~~~~~~~~~~~A~~  193 (327)
T 3cv0_A          168 -NPNDAQLHASLGVLYNLSNNYDSAAA  193 (327)
T ss_dssp             -STTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             -CCCCHHHHHHHHHHHHHhccHHHHHH
Confidence             13356777777777777777777765

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

Probab=98.44  E-value=2.8e-06  Score=60.46  Aligned_cols=148  Identities=11%  Similarity=0.048  Sum_probs=107.8

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHh-------CCCCchHHHhHHHHHhhhcc-----------------------
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKD-------GYGNDIFVGSAPINIYCNCG-----------------------   54 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-------g~~~~~~~~~~li~~~~~~~-----------------------   54 (156)
                      ..++..+-..+...|++++|...++...+.       ........+..+-..|...|                       
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            355677778888889999999999888663       23334566677777777666                       


Q ss_pred             -----chHHHHHHHHHcCCCHHHHHHHHHHHHHC------CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccC
Q 041561           55 -----VTWNEMIHGYAENEYVEQAISLYKDIIAS------GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVK  122 (156)
Q Consensus        55 -----~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~  122 (156)
                           ..|..+...|...|++++|.+.|++..+.      +-.| ....+..+-..+.+.|++++|.+.++.......-.
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                 45777888999999999999999998753      3233 34567788888999999999999998884321000


Q ss_pred             CCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          123 PKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       123 ~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                         ..+..| ...+|..+-..|...|++++|.+.
T Consensus       187 ---~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  217 (311)
T 3nf1_A          187 ---LGPDDPNVAKTKNNLASCYLKQGKFKQAETL  217 (311)
T ss_dssp             ---SCTTCHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             ---hCCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence               000122 346788899999999999999764

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

Probab=98.41  E-value=4.9e-06  Score=58.29  Aligned_cols=108  Identities=7%  Similarity=-0.200  Sum_probs=73.4

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      ..+|..+-..+...|+.++|...|+...+.. +.+...|..+-..|.+.|                    ..|..+...|
T Consensus        43 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~  121 (275)
T 1xnf_A           43 AQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIAL  121 (275)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHH
Confidence            4566777777888888888888888887653 235667777777777766                    5677777788


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .+.|++++|.+.|++..+.  .|+.......+..+...|+.++|...+...
T Consensus       122 ~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  170 (275)
T 1xnf_A          122 YYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQH  170 (275)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            8888888888888887763  333333333344445556777777766544

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

Probab=98.40  E-value=8.5e-06  Score=58.92  Aligned_cols=139  Identities=8%  Similarity=-0.041  Sum_probs=100.1

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      +..+..+-..+.+.|+.++|...|+.+.+.. +.+...+..+-..|.+.|                    ..|..+-..+
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~   81 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLL   81 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHH
Confidence            3456666777788899999999999887753 235667777777777666                    6788888999


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCC--ccHHHHHHH------------HHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           65 AENEYVEQAISLYKDIIASGVK--HDGVTFVAI------------LTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~--p~~~t~~~l------------l~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      ...|++++|.+.|++..+....  .+...+..+            ...+...|++++|...++......          +
T Consensus        82 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~----------~  151 (359)
T 3ieg_A           82 LKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC----------V  151 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----------T
T ss_pred             HHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC----------C
Confidence            9999999999999999874320  133344333            467788999999999999885431          3


Q ss_pred             CChhhHHHHHHHHhhcCCHhHHhh
Q 041561          131 DDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       131 pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      .+...|..+-..+...|++++|.+
T Consensus       152 ~~~~~~~~~~~~~~~~~~~~~A~~  175 (359)
T 3ieg_A          152 WDAELRELRAECFIKEGEPRKAIS  175 (359)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CchHHHHHHHHHHHHCCCHHHHHH
Confidence            355666666667777777766654

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

Probab=98.38  E-value=1.9e-05  Score=57.11  Aligned_cols=141  Identities=11%  Similarity=-0.026  Sum_probs=101.7

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHH-----
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWN-----   58 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~-----   58 (156)
                      +...+..+-..+.+.|+.++|...++...+.. +.+...+..+-..|.+.|                    ..|.     
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~  231 (359)
T 3ieg_A          153 DAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQV  231 (359)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCccchHHHHHHHHH
Confidence            44566677777788888888888888887653 346677777777777766                    1121     


Q ss_pred             -------HHHHHHHcCCCHHHHHHHHHHHHHCCCC-ccH--HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCC
Q 041561           59 -------EMIHGYAENEYVEQAISLYKDIIASGVK-HDG--VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMP  128 (156)
Q Consensus        59 -------~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~  128 (156)
                             .+...+.+.|++++|.+.|++..+.... |..  ..+..+-..+.+.|++++|...++.....          
T Consensus       232 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------  301 (359)
T 3ieg_A          232 KKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQM----------  301 (359)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh----------
Confidence                   2255688899999999999998774322 111  22445667888899999999999988443          


Q ss_pred             CCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          129 YKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       129 ~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+.+..+|..+-..|...|++++|.+.
T Consensus       302 ~~~~~~~~~~~~~~~~~~g~~~~A~~~  328 (359)
T 3ieg_A          302 EPDNVNALKDRAEAYLIEEMYDEAIQD  328 (359)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            233778899999999999999998763

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=98.36  E-value=1.3e-05  Score=61.51  Aligned_cols=136  Identities=8%  Similarity=-0.080  Sum_probs=108.8

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      ++..+-..+...|++++|...++...+..  |+...+..+-..|.+.|                    ..|..+...+..
T Consensus       245 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  322 (537)
T 3fp2_A          245 ALCYTGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFI  322 (537)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHh
Confidence            35555566777888899999999887753  55777777777777776                    678888999999


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH  146 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~  146 (156)
                      .|++++|.+.|++..+... .+...+..+...+.+.|++++|...++.....          ...+...|..+-..+...
T Consensus       323 ~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~----------~~~~~~~~~~l~~~~~~~  391 (537)
T 3fp2_A          323 LQDYKNAKEDFQKAQSLNP-ENVYPYIQLACLLYKQGKFTESEAFFNETKLK----------FPTLPEVPTFFAEILTDR  391 (537)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCTHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCChHHHHHHHHHHHHh
Confidence            9999999999999987532 23567888889999999999999999998544          234567899999999999


Q ss_pred             CCHhHHhhh
Q 041561          147 SNVRLAKKA  155 (156)
Q Consensus       147 g~~~~a~~~  155 (156)
                      |++++|.+.
T Consensus       392 g~~~~A~~~  400 (537)
T 3fp2_A          392 GDFDTAIKQ  400 (537)
T ss_dssp             TCHHHHHHH
T ss_pred             CCHHHHHHH
Confidence            999999763

>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=98.35  E-value=4e-06  Score=54.94  Aligned_cols=90  Identities=9%  Similarity=-0.040  Sum_probs=75.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+.++.....          ...+..
T Consensus        43 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~  111 (186)
T 3as5_A           43 DVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEA----------NPINFN  111 (186)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc----------CcHhHH
Confidence            678888999999999999999999988753 335677888888899999999999999988544          245778


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|..+-..+...|++++|.+.
T Consensus       112 ~~~~~a~~~~~~~~~~~A~~~  132 (186)
T 3as5_A          112 VRFRLGVALDNLGRFDEAIDS  132 (186)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHH
Confidence            899999999999999999764

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

Probab=98.33  E-value=8.5e-06  Score=57.03  Aligned_cols=128  Identities=7%  Similarity=-0.070  Sum_probs=83.0

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCC---CchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYG---NDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVE   71 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~---~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~   71 (156)
                      ....|+.++|...++.+.+.+..   .+...+..+-..|.+.|                    ..|..+-..|...|+++
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~   94 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFD   94 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHH
Confidence            34668999999999999876421   24556666666666665                    55666777777777777


Q ss_pred             HHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhH
Q 041561           72 QAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRL  151 (156)
Q Consensus        72 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~  151 (156)
                      +|.+.|++..+.. ..+...+..+-..+.+.|++++|...++.....           .|+...+..++..+...|++++
T Consensus        95 ~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~-----------~~~~~~~~~~~~~~~~~~~~~~  162 (275)
T 1xnf_A           95 AAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD-----------DPNDPFRSLWLYLAEQKLDEKQ  162 (275)
T ss_dssp             HHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTCHHHHHHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh-----------CCCChHHHHHHHHHHHhcCHHH
Confidence            7777777776632 123556666777777777777777777777332           3444444444444455566666


Q ss_pred             Hhh
Q 041561          152 AKK  154 (156)
Q Consensus       152 a~~  154 (156)
                      |.+
T Consensus       163 A~~  165 (275)
T 1xnf_A          163 AKE  165 (275)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

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

Probab=98.33  E-value=9e-06  Score=59.51  Aligned_cols=127  Identities=9%  Similarity=0.027  Sum_probs=91.6

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      ++..++..+-.++...|+.++|.+.+......|-.++..             ..+-.++..+.+.|+++.|.+.+++|.+
T Consensus        98 ~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~l-------------ea~~l~vqi~L~~~r~d~A~k~l~~~~~  164 (310)
T 3mv2_B           98 NSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTT-------------ELLLLAIEVALLNNNVSTASTIFDNYTN  164 (310)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcH-------------HHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            344455566667777888888888888765544311121             5667788899999999999999999987


Q ss_pred             CCCCc-----cHHHHHHHHHhhc----CCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561           83 SGVKH-----DGVTFVAILTPCS----HSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus        83 ~g~~p-----~~~t~~~ll~~~~----~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                      .  .|     +..+...+..+..    ..++.++|..+|+++..+           .|+..+-..+++++.+.|++++|+
T Consensus       165 ~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~-----------~p~~~~~~lLln~~~~~g~~~eAe  231 (310)
T 3mv2_B          165 A--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT-----------FPTWKTQLGLLNLHLQQRNIAEAQ  231 (310)
T ss_dssp             H--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT-----------SCSHHHHHHHHHHHHHHTCHHHHH
T ss_pred             c--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh-----------CCCcccHHHHHHHHHHcCCHHHHH
Confidence            4  56     3566666665522    344999999999999543           466455555666999999999998


Q ss_pred             hh
Q 041561          154 KA  155 (156)
Q Consensus       154 ~~  155 (156)
                      ++
T Consensus       232 ~~  233 (310)
T 3mv2_B          232 GI  233 (310)
T ss_dssp             HH
T ss_pred             HH
Confidence            74

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

Probab=98.33  E-value=2.3e-05  Score=47.84  Aligned_cols=97  Identities=9%  Similarity=0.137  Sum_probs=79.7

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      ..+|..+-..+.+.|+.+.|...++.+.+.. +.+.              ..|..+...+.+.|++++|.+.|+++.+..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~--------------~~~~~la~~~~~~~~~~~A~~~~~~~~~~~   73 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNA--------------EAWYNLGNAYYKQGDYDEAIEYYQKALELD   73 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcH--------------HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            3567778888999999999999999997753 1233              566777888899999999999999998753


Q ss_pred             CCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           85 VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        85 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                       ..+..++..+...+.+.|++++|...++....
T Consensus        74 -~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           74 -PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence             33567888889999999999999999998844

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

Probab=98.30  E-value=8.7e-06  Score=57.85  Aligned_cols=150  Identities=9%  Similarity=0.006  Sum_probs=104.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHh------CC-CCchHHHhHHHHHhhhcc------------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKD------GY-GNDIFVGSAPINIYCNCG------------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~-~~~~~~~~~li~~~~~~~------------------------   54 (156)
                      .++..+-..+...|+.++|...++...+.      +- ......+..+-..|...|                        
T Consensus        70 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~  149 (311)
T 3nf1_A           70 TMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDH  149 (311)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCC
Confidence            34556666777788888888888877653      22 224556666666666666                        


Q ss_pred             ----chHHHHHHHHHcCCCHHHHHHHHHHHHHC------CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhccccc---c
Q 041561           55 ----VTWNEMIHGYAENEYVEQAISLYKDIIAS------GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDH---E  120 (156)
Q Consensus        55 ----~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~  120 (156)
                          ..+..+-..|...|++++|.+.|++..+.      +..|+ ..++..+-..+.+.|++++|...++......   +
T Consensus       150 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  229 (311)
T 3nf1_A          150 PDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHERE  229 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhc
Confidence                45777888899999999999999998763      22343 3467888899999999999999998875321   0


Q ss_pred             ---cCCC---------------------------------cCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          121 ---VKPK---------------------------------CLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       121 ---~~~~---------------------------------c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                         ..+.                                 +......+..+|..+-..|...|++++|.+.
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  300 (311)
T 3nf1_A          230 FGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETL  300 (311)
T ss_dssp             HC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             CCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHH
Confidence               0000                                 0000123457788999999999999999864

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

Probab=98.29  E-value=2.6e-05  Score=54.53  Aligned_cols=107  Identities=8%  Similarity=0.012  Sum_probs=56.6

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-----------------------chHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-----------------------VTWNEMIHG   63 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-----------------------~~~~~li~~   63 (156)
                      .+...-..+.+.|++++|...++...+... .+...+..+-..|.+.|                       ..|..+-..
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~   83 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKI   83 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHH
Confidence            444555666778888888888888766421 23323333333333333                       124555555


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      |...|++++|.+.|++..+... .+..++..+-..+.+.|++++|...++..
T Consensus        84 ~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  134 (272)
T 3u4t_A           84 LMKKGQDSLAIQQYQAAVDRDT-TRLDMYGQIGSYFYNKGNFPLAIQYMEKQ  134 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHGGG
T ss_pred             HHHcccHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            5555555555555555544221 12234555555555555555555555555

>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=98.27  E-value=4.6e-05  Score=52.28  Aligned_cols=126  Identities=7%  Similarity=-0.045  Sum_probs=98.2

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      |+..+...=..+.+.|+.++|...|+...+..-.++.              ..|..+-.++...|++++|.+.|++..+.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~--------------~~~~~~~~~~~~~~~~~~A~~~~~~al~~   71 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDS--------------VTAYNCGVCADNIKKYKEAADYFDIAIKK   71 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCc--------------HHHHHHHHHHHHhhcHHHHHHHHHHHHHh
Confidence            4556667777788999999999999999886543555              34444777888999999999999998875


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-Ch-------hhHHHHHHHHhhcCCHhHHhhh
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DL-------VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~-------~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ... +...+..+-..+.+.|+.++|...++.....           .| +.       ..|..+=..+...|++++|.+.
T Consensus        72 ~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-----------~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~  139 (228)
T 4i17_A           72 NYN-LANAYIGKSAAYRDMKNNQEYIATLTEGIKA-----------VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEEN  139 (228)
T ss_dssp             TCS-HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             Ccc-hHHHHHHHHHHHHHcccHHHHHHHHHHHHHH-----------CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHH
Confidence            422 5567888889999999999999999988443           33 34       4567777788889999998763

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

Probab=98.27  E-value=2.9e-05  Score=56.12  Aligned_cols=128  Identities=8%  Similarity=-0.074  Sum_probs=91.6

Q ss_pred             CCCch-------HHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------c-hHHHHHHHHHcCC
Q 041561           17 KLSSL-------FLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------V-TWNEMIHGYAENE   68 (156)
Q Consensus        17 ~~~~~-------~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~-~~~~li~~~~~~g   68 (156)
                      +.|+.       ++|..+|+...+.--+-+...|..+...+.+.|                    . .|..+...+.+.|
T Consensus        69 ~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~  148 (308)
T 2ond_A           69 EKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAE  148 (308)
T ss_dssp             HTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHH
T ss_pred             hccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhc
Confidence            35776       899999999887312235567888888877766                    2 6888888888888


Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhc-CCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcC
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCS-HSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHS  147 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~-~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g  147 (156)
                      ++++|.++|++..+... ++...|........ ..|+.++|..+|+...+..          .-+...|..++..+.+.|
T Consensus       149 ~~~~A~~~~~~a~~~~p-~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~----------p~~~~~~~~~~~~~~~~g  217 (308)
T 2ond_A          149 GIKSGRMIFKKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY----------GDIPEYVLAYIDYLSHLN  217 (308)
T ss_dssp             CHHHHHHHHHHHHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH----------TTCHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----------CCcHHHHHHHHHHHHHCC
Confidence            89999999988876532 22333433332222 3688999999998875442          236788999999999999


Q ss_pred             CHhHHhhh
Q 041561          148 NVRLAKKA  155 (156)
Q Consensus       148 ~~~~a~~~  155 (156)
                      ++++|+.+
T Consensus       218 ~~~~A~~~  225 (308)
T 2ond_A          218 EDNNTRVL  225 (308)
T ss_dssp             CHHHHHHH
T ss_pred             CHHHHHHH
Confidence            99998764

>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=98.22  E-value=2.9e-05  Score=63.08  Aligned_cols=136  Identities=10%  Similarity=0.014  Sum_probs=109.6

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      +.+|+.+=..+.+.|+.++|.+.|++..+.. +-+...|+.|=..|.+.|                    ..|+.+-.+|
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l   87 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTL   87 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            4567788888889999999999999987752 224677777877777777                    6788888899


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHH
Q 041561           65 AENEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSS  142 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~  142 (156)
                      .+.|++++|.+.|++..+-  .| +...|+.+-..+.+.|++++|.+.|++..+.           .| +...|..+...
T Consensus        88 ~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l-----------~P~~~~a~~~L~~~  154 (723)
T 4gyw_A           88 KEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKL-----------KPDFPDAYCNLAHC  154 (723)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CSCCHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----------CCCChHHHhhhhhH
Confidence            9999999999999988764  33 4567888888899999999999999987432           34 56788889999


Q ss_pred             HhhcCCHhHHhh
Q 041561          143 CQVHSNVRLAKK  154 (156)
Q Consensus       143 ~~~~g~~~~a~~  154 (156)
                      |...|++++|.+
T Consensus       155 l~~~g~~~~A~~  166 (723)
T 4gyw_A          155 LQIVCDWTDYDE  166 (723)
T ss_dssp             HHHTTCCTTHHH
T ss_pred             HHhcccHHHHHH
Confidence            999999988865

>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=98.19  E-value=1.3e-05  Score=49.51  Aligned_cols=89  Identities=11%  Similarity=0.165  Sum_probs=74.2

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .|..+...+...|++++|.++|+++.+... .+...+..+...+.+.|++++|..+++.....          ...+...
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~   71 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL----------DPRSAEA   71 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------CTTCHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCC-cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHH----------CCCchHH
Confidence            467788899999999999999999987542 35667888888899999999999999998543          2346788


Q ss_pred             HHHHHHHHhhcCCHhHHhhh
Q 041561          136 WGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~~  155 (156)
                      |..+...+...|++++|.+.
T Consensus        72 ~~~l~~~~~~~~~~~~A~~~   91 (136)
T 2fo7_A           72 WYNLGNAYYKQGDYDEAIEY   91 (136)
T ss_dssp             HHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHH
Confidence            99999999999999999764

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

Probab=98.18  E-value=2.4e-05  Score=47.72  Aligned_cols=90  Identities=11%  Similarity=0.185  Sum_probs=75.1

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+...+...|++++|.+.|+++.+.. ..+..++..+...+.+.|+.++|...++.....          ...+..
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~   78 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL----------DPNNAE   78 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh----------CCccHH
Confidence            456777888999999999999999998753 235678888889999999999999999998543          244778


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +|..+-..|...|++++|.+.
T Consensus        79 ~~~~la~~~~~~~~~~~A~~~   99 (125)
T 1na0_A           79 AWYNLGNAYYKQGDYDEAIEY   99 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHH
Confidence            899999999999999999764

>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=98.16  E-value=1.8e-05  Score=55.20  Aligned_cols=135  Identities=10%  Similarity=0.015  Sum_probs=99.5

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHh------CCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKD------GYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYK   78 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~------g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~   78 (156)
                      ..++..+-..+...|++++|...++...+.      +-.|+..             ..|..+-..|...|++++|.+.|+
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~-------------~~~~~l~~~~~~~g~~~~A~~~~~  109 (283)
T 3edt_B           43 ATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVA-------------ATLNNLAVLYGKRGKYKEAEPLCK  109 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHH-------------HHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHH-------------HHHHHHHHHHHHhccHHHHHHHHH
Confidence            346777788888999999999999988654      2222221             567888899999999999999999


Q ss_pred             HHHHC------CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHh
Q 041561           79 DIIAS------GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVR  150 (156)
Q Consensus        79 ~m~~~------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~  150 (156)
                      +....      .-.| ...++..+-..+...|++++|...++.......-.   ..+-.| ...++..+-..|...|+++
T Consensus       110 ~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~---~~~~~~~~~~~~~~la~~~~~~g~~~  186 (283)
T 3edt_B          110 RALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATR---LGPDDPNVAKTKNNLASCYLKQGKYQ  186 (283)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHH---SCTTCHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHcCCHH
Confidence            98653      1123 35578888899999999999999999884331000   000123 3567888999999999999


Q ss_pred             HHhhh
Q 041561          151 LAKKA  155 (156)
Q Consensus       151 ~a~~~  155 (156)
                      +|.+.
T Consensus       187 ~A~~~  191 (283)
T 3edt_B          187 DAETL  191 (283)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99864

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

Probab=98.14  E-value=5.5e-05  Score=46.48  Aligned_cols=119  Identities=8%  Similarity=-0.037  Sum_probs=92.5

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      ...+..+-..+...|+++.|...++...+.. +.+.              ..|..+...+...|++++|.+.|++..+..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~--------------~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~   76 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANA--------------VYFCNRAAAYSKLGNYAGAVQDCERAICID   76 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCH--------------HHHHHHHHHHHHhhchHHHHHHHHHHHhcC
Confidence            3456677778889999999999999987653 1233              556777888889999999999999988753


Q ss_pred             CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           85 VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        85 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                       ..+...+..+-..+.+.|+.++|...++.....          .+.+...+..+-..+...|+.
T Consensus        77 -~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~----------~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           77 -PAYSKAYGRMGLALSSLNKHVEAVAYYKKALEL----------DPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------STTCHHHHHHHHHHHHHHTTC
T ss_pred             -ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc----------CccchHHHHHHHHHHHHHhcC
Confidence             224667888888999999999999999988443          133677888888888887765

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

Probab=98.14  E-value=1.4e-05  Score=61.46  Aligned_cols=136  Identities=9%  Similarity=-0.072  Sum_probs=73.7

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhc---------c--------------------ch
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNC---------G--------------------VT   56 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~---------~--------------------~~   56 (156)
                      ..|..+-..+.+.|++++|...|+...+..  |+...+..+-..|.+.         |                    ..
T Consensus       138 ~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  215 (474)
T 4abn_A          138 EAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRS  215 (474)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHH
Confidence            445555555566666666666666655432  4445555555555554         3                    44


Q ss_pred             HHHHHHHHHcC--------CCHHHHHHHHHHHHHCCCC--ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcC
Q 041561           57 WNEMIHGYAEN--------EYVEQAISLYKDIIASGVK--HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCL  126 (156)
Q Consensus        57 ~~~li~~~~~~--------g~~~~a~~~~~~m~~~g~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~  126 (156)
                      |..+-.+|...        |++++|.+.|++..+....  -+...|..+-..+.+.|++++|.+.|+...+.        
T Consensus       216 ~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--------  287 (474)
T 4abn_A          216 WYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL--------  287 (474)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------
T ss_pred             HHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------
Confidence            55555555555        5566666666665543210  24455555556666666666666666655322        


Q ss_pred             CCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561          127 MPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus       127 ~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                        -.-+...|..+-..+...|++++|.
T Consensus       288 --~p~~~~a~~~l~~~~~~lg~~~eAi  312 (474)
T 4abn_A          288 --DPAWPEPQQREQQLLEFLSRLTSLL  312 (474)
T ss_dssp             --CTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --CCCCHHHHHHHHHHHHHHHHHHHHH
Confidence              1123445555556666666666554

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

Probab=98.12  E-value=0.0001  Score=57.09  Aligned_cols=140  Identities=8%  Similarity=-0.007  Sum_probs=104.1

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc--hHHHhHHHHHhhhcc------c-----------h---HHH-HH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND--IFVGSAPINIYCNCG------V-----------T---WNE-MI   61 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~li~~~~~~~------~-----------~---~~~-li   61 (156)
                      ...|..+...+.+.|+.+.|..+|+...+.  .|+  ...|..+...+.+.|      .           .   |-. ..
T Consensus       321 ~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~  398 (530)
T 2ooe_A          321 MLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAAL  398 (530)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHH
Confidence            556777788888899999999999999874  454  247888887777665      1           1   111 11


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC--hhhHHHH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD--LVVWGDL  139 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd--~~~~~~l  139 (156)
                      -.+...|++++|.++|+...+.. .-+...|..+++.+.+.|+.++|+.+|+.......        ..|+  ...|...
T Consensus       399 ~~~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~--------~~~~~~~~lw~~~  469 (530)
T 2ooe_A          399 MEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS--------LPPEKSGEIWARF  469 (530)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCC--------SCGGGCHHHHHHH
T ss_pred             HHHHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccC--------CCHHHHHHHHHHH
Confidence            12336899999999999887642 12467889999999999999999999999854321        2332  4589999


Q ss_pred             HHHHhhcCCHhHHhhh
Q 041561          140 VSSCQVHSNVRLAKKA  155 (156)
Q Consensus       140 i~~~~~~g~~~~a~~~  155 (156)
                      +.-....|+.+.+.++
T Consensus       470 ~~~e~~~G~~~~~~~~  485 (530)
T 2ooe_A          470 LAFESNIGDLASILKV  485 (530)
T ss_dssp             HHHHHHSSCHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHH
Confidence            9999999999988764

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=98.12  E-value=8.8e-05  Score=56.82  Aligned_cols=150  Identities=7%  Similarity=-0.089  Sum_probs=81.8

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIH   62 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~   62 (156)
                      |+..+|..+-..+.+.|+++.|...++...+.. +.+..++..+-..|.+.|                    ..|..+..
T Consensus       274 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~  352 (537)
T 3fp2_A          274 PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLAC  352 (537)
T ss_dssp             CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            444555566666666666666666666665542 224455555655665555                    34555555


Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCC-------------------
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKP-------------------  123 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-------------------  123 (156)
                      .|...|++++|.+.|++..+.. ..+...+..+-..+.+.|++++|...++.......-.+                   
T Consensus       353 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~  431 (537)
T 3fp2_A          353 LLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQ  431 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHH
Confidence            5555555555555555554432 11223444444444555555555544444321100000                   


Q ss_pred             ----------C--------c----CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          124 ----------K--------C----LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       124 ----------~--------c----~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                                .        +    .. .+.+...|..+-..|...|++++|.+.
T Consensus       432 ~~~~~~~~~~~~~~~A~~~~~~a~~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~  484 (537)
T 3fp2_A          432 SSQDPTQLDEEKFNAAIKLLTKACEL-DPRSEQAKIGLAQLKLQMEKIDEAIEL  484 (537)
T ss_dssp             HTC----CCHHHHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hhccchhhhHhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhccHHHHHHH
Confidence                      0        0    00 134678899999999999999999763

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

Probab=98.07  E-value=7.4e-05  Score=46.22  Aligned_cols=118  Identities=6%  Similarity=-0.060  Sum_probs=89.0

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +...|..+-..+.+.|++++|...++...+.. +.+.              ..|..+-..|...|++++|.+.|++..+.
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~--------------~~~~~la~~~~~~~~~~~A~~~~~~a~~~   79 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDA--------------KLYSNRAACYTKLLEFQLALKDCEECIQL   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCH--------------HHHHHHHHHHTTTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcH--------------HHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            34567777788889999999999999987642 1233              56677788889999999999999998875


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcC
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHS  147 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g  147 (156)
                      . ..+...+..+-..+.+.|++++|.+.|+.....          ...+...+..+-..+...|
T Consensus        80 ~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           80 E-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDL----------DSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CGGGTHHHHHHHHHHHHHT
T ss_pred             C-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHh----------CCCchHHHHHHHHHHHHhc
Confidence            3 235667888888999999999999999988433          1224456666666666554

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

Probab=98.06  E-value=0.00024  Score=49.57  Aligned_cols=139  Identities=9%  Similarity=-0.036  Sum_probs=102.8

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc--hHHHhHHHHHhhhcc--------------------chHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND--IFVGSAPINIYCNCG--------------------VTWNEMIH   62 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~--~~~~~~li~~~~~~~--------------------~~~~~li~   62 (156)
                      ...+..+-..+.+.|+.++|...++...+.+-.|+  ...|..+-..|.+.|                    ..|..+-.
T Consensus        37 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~  116 (272)
T 3u4t_A           37 PYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGS  116 (272)
T ss_dssp             STTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHH
Confidence            44788888899999999999999999988442222  223677777777777                    67889999


Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      .|...|++++|.+.|++..+.. ..+...+..+-..+-..+++++|...|+...+.          .+.+...|..+-..
T Consensus       117 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~----------~p~~~~~~~~~~~~  185 (272)
T 3u4t_A          117 YFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKADSSFVKVLEL----------KPNIYIGYLWRARA  185 (272)
T ss_dssp             HHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------STTCHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----------CccchHHHHHHHHH
Confidence            9999999999999999987652 223445555552344456999999999998543          12346777778888


Q ss_pred             HhhcCC---HhHHhh
Q 041561          143 CQVHSN---VRLAKK  154 (156)
Q Consensus       143 ~~~~g~---~~~a~~  154 (156)
                      +...|+   .++|.+
T Consensus       186 ~~~~~~~~~~~~A~~  200 (272)
T 3u4t_A          186 NAAQDPDTKQGLAKP  200 (272)
T ss_dssp             HHHHSTTCSSCTTHH
T ss_pred             HHHcCcchhhHHHHH
Confidence            888887   666654

>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=98.06  E-value=0.0001  Score=49.81  Aligned_cols=128  Identities=8%  Similarity=-0.077  Sum_probs=93.1

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      ..+-..+.+.|++++|...++..    +.|+.              ..|..+-..|.+.|++++|.+.|++..+.. ..+
T Consensus        10 ~~~g~~~~~~~~~~~A~~~~~~a----~~~~~--------------~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~   70 (213)
T 1hh8_A           10 WNEGVLAADKKDWKGALDAFSAV----QDPHS--------------RICFNIGCMYTILKNMTEAEKAFTRSINRD-KHL   70 (213)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTS----SSCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH----cCCCh--------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccc
Confidence            34445667889999999999876    35555              567777888899999999999999987753 235


Q ss_pred             HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC--c---CCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           89 GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK--C---LMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        89 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~--c---~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ...+..+-..+.+.|++++|...|+.......-.+.  .   .....| +...|..+-..|...|++++|.+.
T Consensus        71 ~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  143 (213)
T 1hh8_A           71 AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQ  143 (213)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHH
Confidence            667888889999999999999999988443110000  0   000111 236788888999999999999753

>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=98.04  E-value=7.9e-05  Score=51.92  Aligned_cols=137  Identities=8%  Similarity=0.002  Sum_probs=99.0

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhC------CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDG------YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKD   79 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g------~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~   79 (156)
                      .++..+-..+...|+.++|...+....+..      -.|+..             ..|..+-..|...|++++|.+.|++
T Consensus        86 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~-------------~~~~~la~~~~~~g~~~~A~~~~~~  152 (283)
T 3edt_B           86 ATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVA-------------KQLNNLALLCQNQGKAEEVEYYYRR  152 (283)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHH-------------HHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHH-------------HHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            467778888999999999999999886541      112221             5677888899999999999999999


Q ss_pred             HHHC------CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhccccc---cc---CCC-c--------------------
Q 041561           80 IIAS------GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDH---EV---KPK-C--------------------  125 (156)
Q Consensus        80 m~~~------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~---~~~-c--------------------  125 (156)
                      ..+.      +-.| ...++..+-..+.+.|++++|...++......   +.   .+. .                    
T Consensus       153 al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (283)
T 3edt_B          153 ALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSA  232 (283)
T ss_dssp             HHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC--
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHH
Confidence            8764      2233 34578888899999999999999998874321   00   000 0                    


Q ss_pred             ------------CCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          126 ------------LMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       126 ------------~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                                  .........+|..+-..|...|++++|.+.
T Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  274 (283)
T 3edt_B          233 PYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTL  274 (283)
T ss_dssp             ----------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence                        001122346788889999999999999764

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

Probab=98.04  E-value=6.5e-05  Score=58.24  Aligned_cols=127  Identities=9%  Similarity=-0.014  Sum_probs=84.6

Q ss_pred             CCchH-------HHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc---------------------chHHHHHHHHHcCCC
Q 041561           18 LSSLF-------LGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------------------VTWNEMIHGYAENEY   69 (156)
Q Consensus        18 ~~~~~-------~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---------------------~~~~~li~~~~~~g~   69 (156)
                      .|+++       +|..+++...+.-.+.+...|..+...+.+.|                     ..|......+.+.|+
T Consensus       292 ~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~  371 (530)
T 2ooe_A          292 KGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEG  371 (530)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcC
Confidence            68877       88999988875323346777777777777666                     246666666777778


Q ss_pred             HHHHHHHHHHHHHCCCC-ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCC
Q 041561           70 VEQAISLYKDIIASGVK-HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSN  148 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~  148 (156)
                      +++|.++|++-.+.... +......+.+. +...|+.++|+.+|+...+.          ..-+...|..++..+.+.|+
T Consensus       372 ~~~A~~~~~~Al~~~~~~~~~~~~~a~~~-~~~~~~~~~A~~~~e~al~~----------~p~~~~~~~~~~~~~~~~g~  440 (530)
T 2ooe_A          372 IKSGRMIFKKAREDARTRHHVYVTAALME-YYCSKDKSVAFKIFELGLKK----------YGDIPEYVLAYIDYLSHLNE  440 (530)
T ss_dssp             HHHHHHHHHHHHTCTTCCTHHHHHHHHHH-HHHTCCHHHHHHHHHHHHHH----------HTTCHHHHHHHHHHHTTTTC
T ss_pred             HHHHHHHHHHHHhccCCchHHHHHHHHHH-HHHcCChhHHHHHHHHHHHH----------CCCCHHHHHHHHHHHHhCCC
Confidence            88888888877654211 11112222222 12477888888888877443          12357888889988889999


Q ss_pred             HhHHhhh
Q 041561          149 VRLAKKA  155 (156)
Q Consensus       149 ~~~a~~~  155 (156)
                      .++|+.+
T Consensus       441 ~~~Ar~~  447 (530)
T 2ooe_A          441 DNNTRVL  447 (530)
T ss_dssp             HHHHHHH
T ss_pred             HhhHHHH
Confidence            9888764

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.03  E-value=0.00013  Score=46.99  Aligned_cols=123  Identities=9%  Similarity=-0.020  Sum_probs=91.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .+..+-..+...|+++.|...++...+... .+.              ..|..+-..+...|++++|.+.|++..+.. .
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~~-~~~--------------~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~   78 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELNP-SNA--------------IYYGNRSLAYLRTECYGYALGDATRAIELD-K   78 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCh--------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-c
Confidence            455566677889999999999999877531 233              566777788889999999999999987753 2


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhH--HHHHHHHhhcCCHhHHhhh
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVW--GDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~--~~li~~~~~~g~~~~a~~~  155 (156)
                      .+...+..+-..+.+.|+.++|...++......          ..+...+  -.+...+...|++++|.+.
T Consensus        79 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~----------p~~~~~~~~~~~~~~~~~~~~~~~A~~~  139 (166)
T 1a17_A           79 KYIKGYYRRAASNMALGKFRAALRDYETVVKVK----------PHDKDAKMKYQECNKIVKQKAFERAIAG  139 (166)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS----------TTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC----------CCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            356678888888899999999999999884431          2244455  3444447788999888753

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

Probab=97.97  E-value=9e-05  Score=57.02  Aligned_cols=125  Identities=13%  Similarity=0.034  Sum_probs=101.7

Q ss_pred             CcccHHHHHHHhcCCCch-HHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSL-FLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~-~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      +...+..+=..+...|+. ++|...|+...+..  |+..             ..|..+-..|...|++++|.+.|++..+
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~--p~~~-------------~a~~~lg~~~~~~g~~~~A~~~~~~al~  165 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE--PELV-------------EAWNQLGEVYWKKGDVTSAHTCFSGALT  165 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC--TTCH-------------HHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC--CCCH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            345666777788899999 99999999987753  4321             5677888889999999999999999887


Q ss_pred             CCCCccHHHHHHHHHhhcCC---------CchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc-------
Q 041561           83 SGVKHDGVTFVAILTPCSHS---------GLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH-------  146 (156)
Q Consensus        83 ~g~~p~~~t~~~ll~~~~~~---------~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~-------  146 (156)
                      .  .|+...+..+-..+.+.         |++++|.+.+++..+.          ..-+...|..+-.+|...       
T Consensus       166 ~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~----------~p~~~~~~~~lg~~~~~~~~~~~~~  233 (474)
T 4abn_A          166 H--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQM----------DVLDGRSWYILGNAYLSLYFNTGQN  233 (474)
T ss_dssp             T--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             h--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHh----------CCCCHHHHHHHHHHHHHHHHhhccc
Confidence            5  47778888899999999         9999999999998443          234678899999999988       


Q ss_pred             -CCHhHHhhh
Q 041561          147 -SNVRLAKKA  155 (156)
Q Consensus       147 -g~~~~a~~~  155 (156)
                       |++++|.+.
T Consensus       234 ~g~~~~A~~~  243 (474)
T 4abn_A          234 PKISQQALSA  243 (474)
T ss_dssp             HHHHHHHHHH
T ss_pred             cchHHHHHHH
Confidence             889998753

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

Probab=97.92  E-value=0.00063  Score=40.43  Aligned_cols=100  Identities=8%  Similarity=-0.053  Sum_probs=80.2

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +...+..+-..+.+.|+.++|...++...+... .+.              ..|..+-..+...|++++|.+.|++..+.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~--------------~~~~~~a~~~~~~~~~~~A~~~~~~a~~~   69 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDP-EES--------------KYWLMKGKALYNLERYEEAVDCYNYVINV   69 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCC-CCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCc-CCH--------------HHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            346677788888999999999999999877532 233              45667778889999999999999998875


Q ss_pred             CCC-ccHHHHHHHHHhhcCC-CchHHHHHHHHhcccc
Q 041561           84 GVK-HDGVTFVAILTPCSHS-GLVYAEVEIFNSMEHD  118 (156)
Q Consensus        84 g~~-p~~~t~~~ll~~~~~~-~~~~~a~~~~~~m~~~  118 (156)
                      ... .+...+..+-..+.+. |+.++|.+.+......
T Consensus        70 ~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           70 IEDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             SCCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             CcccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhc
Confidence            321 1467888888999999 9999999999998544

>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=97.88  E-value=0.0011  Score=46.52  Aligned_cols=56  Identities=7%  Similarity=0.081  Sum_probs=24.7

Q ss_pred             HHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcC----CCchHHHHHHHHhc
Q 041561           57 WNEMIHGYAE----NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSH----SGLVYAEVEIFNSM  115 (156)
Q Consensus        57 ~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m  115 (156)
                      +..+-..|..    .+++++|.+.|++..+.+   +...+..+-..+.+    .++.++|...|+..
T Consensus       113 ~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a  176 (273)
T 1ouv_A          113 CASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKA  176 (273)
T ss_dssp             HHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            3344444444    455555555555544433   22233333333333    44555555555444

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

Probab=97.85  E-value=0.00039  Score=49.82  Aligned_cols=140  Identities=9%  Similarity=-0.062  Sum_probs=98.3

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHh----CCCCc-hHHHhHHHHHhhhcc--------------------------c
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKD----GYGND-IFVGSAPINIYCNCG--------------------------V   55 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~-~~~~~~li~~~~~~~--------------------------~   55 (156)
                      .|......+...|++++|...|....+.    |-.++ ..+|+.+-..|.+.|                          .
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  118 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            3555556667788888888888876542    32222 456777777776665                          3


Q ss_pred             hHHHHHHHHHcC-CCHHHHHHHHHHHHHC----CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           56 TWNEMIHGYAEN-EYVEQAISLYKDIIAS----GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        56 ~~~~li~~~~~~-g~~~~a~~~~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      +|+.+-..|... |++++|.+.|++-.+-    +-.+. ..++..+-..+.+.|++++|...|+.......        -
T Consensus       119 ~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~--------~  190 (292)
T 1qqe_A          119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSM--------G  190 (292)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTS--------S
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHh--------c
Confidence            677788888886 9999999999987652    21111 34688888999999999999999998843311        1


Q ss_pred             CCCh-----hhHHHHHHHHhhcCCHhHHhh
Q 041561          130 KDDL-----VVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       130 ~pd~-----~~~~~li~~~~~~g~~~~a~~  154 (156)
                      .++.     ..|..+-.++...|++++|.+
T Consensus       191 ~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~  220 (292)
T 1qqe_A          191 NRLSQWSLKDYFLKKGLCQLAATDAVAAAR  220 (292)
T ss_dssp             CTTTGGGHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            1221     156777888999999999875

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

Probab=97.85  E-value=0.0003  Score=43.34  Aligned_cols=90  Identities=7%  Similarity=-0.058  Sum_probs=74.7

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+...|++++|.+.|++..+.. ..+...+..+-..+.+.|++++|...++.....          ...+..
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~----------~~~~~~   85 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQL----------EPTFIK   85 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHh----------CCCchH
Confidence            567778888999999999999999988643 225678888888999999999999999988543          234678


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|..+-..|...|++++|.+.
T Consensus        86 ~~~~la~~~~~~~~~~~A~~~  106 (133)
T 2lni_A           86 GYTRKAAALEAMKDYTKAMDV  106 (133)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHH
Confidence            899999999999999999763

>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=97.84  E-value=0.0014  Score=45.96  Aligned_cols=132  Identities=9%  Similarity=-0.057  Sum_probs=90.5

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhh----cc------------------chHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCN----CG------------------VTWNEMIH   62 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~------------------~~~~~li~   62 (156)
                      +.++..+=..+.+.|+.++|...|+...+.   .+...+..+-..|.+    .+                  ..+..+-.
T Consensus         6 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~   82 (273)
T 1ouv_A            6 PKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGN   82 (273)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            345555666677788889999888888773   344555556555555    33                  45666777


Q ss_pred             HHHc----CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcC----CCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           63 GYAE----NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSH----SGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        63 ~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      .|..    .+++++|.+.|++..+.+   +...+..+-..+.+    .++.++|...|+...+.            -+..
T Consensus        83 ~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~------------~~~~  147 (273)
T 1ouv_A           83 LYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL------------NDGD  147 (273)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT------------TCHH
T ss_pred             HHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhc------------CcHH
Confidence            7777    888999999888887765   56667777777777    88889998888877322            1344


Q ss_pred             hHHHHHHHHhh----cCCHhHHhh
Q 041561          135 VWGDLVSSCQV----HSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~----~g~~~~a~~  154 (156)
                      .+..+-..|..    .+++++|.+
T Consensus       148 a~~~lg~~~~~~~~~~~~~~~A~~  171 (273)
T 1ouv_A          148 GCTILGSLYDAGRGTPKDLKKALA  171 (273)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHH
Confidence            55555556665    677776654

>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=97.83  E-value=0.00029  Score=55.06  Aligned_cols=124  Identities=6%  Similarity=-0.045  Sum_probs=94.4

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      ...|..+-..+.+.|+.++|...+++..+.  .|+..             ..|..+-..|...|++++|.+.|++..+..
T Consensus        23 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~-------------~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   87 (568)
T 2vsy_A           23 FVAWLMLADAELGMGDTTAGEMAVQRGLAL--HPGHP-------------EAVARLGRVRWTQQRHAEAAVLLQQASDAA   87 (568)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--STTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCH-------------HHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            455666677777888888888888888764  23321             566777788889999999999999987643


Q ss_pred             CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc---CCHhHHhh
Q 041561           85 VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH---SNVRLAKK  154 (156)
Q Consensus        85 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~---g~~~~a~~  154 (156)
                       .-+...+..+-..+.+.|+.++|.+.++...+.          ...+...+..+-..+...   |+.++|.+
T Consensus        88 -p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~----------~p~~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A           88 -PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL----------LPEEPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             -CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHHHHHhhccccHHHHHH
Confidence             224567888888888999999999999988443          123567888888889888   89888875

>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=97.82  E-value=9.8e-05  Score=45.37  Aligned_cols=114  Identities=9%  Similarity=0.039  Sum_probs=85.6

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ..|..+-..+.+.|+++.|...++...+.. +.+.              ..|..+-..|...|++++|.+.|++......
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~--------------~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~   69 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNM--------------TYITNQAAVYFEKGDYNKCRELCEKAIEVGR   69 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccH--------------HHHHHHHHHHHHhccHHHHHHHHHHHHhhcc
Confidence            456677778889999999999999987753 2233              5566777888899999999999999876421


Q ss_pred             --Ccc----HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           86 --KHD----GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        86 --~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                        .++    ..++..+-..+.+.|++++|.+.|+.....           .|+...+..+-.....
T Consensus        70 ~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-----------~~~~~~~~~l~~~~~~  124 (131)
T 1elr_A           70 ENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE-----------HRTPDVLKKCQQAEKI  124 (131)
T ss_dssp             HSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CCCHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-----------CCCHHHHHHHHHHHHH
Confidence              222    667888888899999999999999988432           4666666655554433

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

Probab=97.82  E-value=0.00044  Score=45.11  Aligned_cols=89  Identities=7%  Similarity=-0.093  Sum_probs=72.2

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+.+.|++++|.+.|+...... .-+...|..+-.++.+.|++++|...|+.....          -+-+..
T Consensus        37 ~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l----------~P~~~~  105 (151)
T 3gyz_A           37 DDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL----------GKNDYT  105 (151)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------SSSCCH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh----------CCCCcH
Confidence            456667778889999999999999998753 225667888888888999999999999988443          123567


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                      .|..+=.+|...|++++|.+
T Consensus       106 ~~~~lg~~~~~lg~~~eA~~  125 (151)
T 3gyz_A          106 PVFHTGQCQLRLKAPLKAKE  125 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHH
Confidence            88888899999999999976

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

Probab=97.80  E-value=0.00021  Score=42.59  Aligned_cols=90  Identities=11%  Similarity=0.035  Sum_probs=72.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC--C
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD--D  132 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p--d  132 (156)
                      ..|..+-..+...|++++|.+.|++..+... .+...+..+-..+.+.|++++|...++...+.          ...  +
T Consensus         7 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~----------~~~~~~   75 (112)
T 2kck_A            7 EEYYLEGVLQYDAGNYTESIDLFEKAIQLDP-EESKYWLMKGKALYNLERYEEAVDCYNYVINV----------IEDEYN   75 (112)
T ss_dssp             TGGGGHHHHHHSSCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT----------SCCTTC
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh----------Ccccch
Confidence            3456677788899999999999999887532 35667888888889999999999999988443          123  5


Q ss_pred             hhhHHHHHHHHhhc-CCHhHHhhh
Q 041561          133 LVVWGDLVSSCQVH-SNVRLAKKA  155 (156)
Q Consensus       133 ~~~~~~li~~~~~~-g~~~~a~~~  155 (156)
                      ...|..+-..+... |++++|.+.
T Consensus        76 ~~~~~~l~~~~~~~~~~~~~A~~~   99 (112)
T 2kck_A           76 KDVWAAKADALRYIEGKEVEAEIA   99 (112)
T ss_dssp             HHHHHHHHHHHTTCSSCSHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHH
Confidence            78899999999999 999999763

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

Probab=97.79  E-value=0.00069  Score=44.60  Aligned_cols=111  Identities=11%  Similarity=-0.045  Sum_probs=86.0

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      ++.+|..+-..+.+.|+.++|...+........ .+...+..+-..+.+.+                    ..+..+-..
T Consensus        38 ~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~  116 (184)
T 3vtx_A           38 NVETLLKLGKTYMDIGLPNDAIESLKKFVVLDT-TSAEAYYILGSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLV  116 (184)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHH
Confidence            345677777888899999999999999876543 23444444444444444                    567888899


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      |.+.|++++|.+.|++..+.. .-+..+|..+-..+.+.|+.++|.+.|++..
T Consensus       117 ~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  168 (184)
T 3vtx_A          117 YDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKKAL  168 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999999999999999988753 2346678888899999999999999999873

>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=97.78  E-value=0.00027  Score=51.89  Aligned_cols=132  Identities=8%  Similarity=-0.148  Sum_probs=98.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc---h---HHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND---I---FVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKD   79 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~---~---~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~   79 (156)
                      ..|..+=..+.+.|++++|...|+...+..-...   .   .....+.      ...|..+-.+|.+.|++++|.+.|++
T Consensus       148 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~------~~~~~nla~~~~~~g~~~~A~~~~~~  221 (336)
T 1p5q_A          148 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALR------LASHLNLAMCHLKLQAFSAAIESCNK  221 (336)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHH------HHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHH------HHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            3455666677889999999999999877532111   0   0000000      05678888899999999999999999


Q ss_pred             HHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           80 IIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        80 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ..+.. ..+...+..+-.++.+.|++++|...|+...+.          -..+...+..+-..+...|+.++|.+
T Consensus       222 al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l----------~P~~~~a~~~l~~~~~~~~~~~~a~~  285 (336)
T 1p5q_A          222 ALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL----------YPNNKAAKTQLAVCQQRIRRQLAREK  285 (336)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            88753 235678888889999999999999999988443          13366788888899999999988854

>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=97.74  E-value=0.00057  Score=42.61  Aligned_cols=98  Identities=6%  Similarity=-0.107  Sum_probs=79.3

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +...|..+-..+.+.|+++.|...|....+..  |+..             ..|..+-..+...|++++|.+.|++..+.
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--~~~~-------------~~~~~l~~~~~~~~~~~~A~~~~~~al~~   72 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVA-------------VYYTNRALCYLKMQQPEQALADCRRALEL   72 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC--cCcH-------------HHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            45677777888899999999999999987753  3321             56777788889999999999999998875


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      .. .+...+..+-..+.+.|++++|...|.....
T Consensus        73 ~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           73 DG-QSVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             CT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             Cc-hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            42 2566788888889999999999999998743

>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=97.73  E-value=0.00041  Score=41.61  Aligned_cols=88  Identities=13%  Similarity=0.020  Sum_probs=63.5

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .|..+...+...|++++|.+.|++..... ..+...+..+-..+.+.|++++|...++.....          ...+...
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~   74 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL----------KPDWGKG   74 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------CTTCHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHh----------CcccHHH
Confidence            45566677778888888888888877643 224556677777777888888888888877433          1235677


Q ss_pred             HHHHHHHHhhcCCHhHHhh
Q 041561          136 WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~  154 (156)
                      |..+-..+...|++++|.+
T Consensus        75 ~~~~a~~~~~~~~~~~A~~   93 (118)
T 1elw_A           75 YSRKAAALEFLNRFEEAKR   93 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHH
Confidence            7778888888888888765

>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=97.73  E-value=0.00095  Score=39.94  Aligned_cols=97  Identities=7%  Similarity=-0.047  Sum_probs=77.4

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      ++..+..+-..+...|+++.|...++...+.. +.+.              ..|..+-..+...|++++|.+.+++..+.
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~--------------~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   67 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNH--------------VLYSNRSAAYAKKGDYQKAYEDGCKTVDL   67 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcH--------------HHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            34566777788889999999999999987753 1233              45666777888899999999999998875


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .. .+...+..+-..+.+.|+.++|.+.++...
T Consensus        68 ~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~   99 (118)
T 1elw_A           68 KP-DWGKGYSRKAAALEFLNRFEEAKRTYEEGL   99 (118)
T ss_dssp             CT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             Cc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            32 246678888889999999999999999884

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

Probab=97.68  E-value=0.00064  Score=41.48  Aligned_cols=90  Identities=13%  Similarity=-0.004  Sum_probs=73.5

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+...|++++|.+.|++..... ..+...+..+...+.+.|++++|...++.....          ...+..
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~   81 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICI----------DPAYSK   81 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhc----------CccCHH
Confidence            456677788889999999999999987653 235677888888899999999999999988543          234578


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|..+-..|...|++++|.+.
T Consensus        82 ~~~~~~~~~~~~~~~~~A~~~  102 (131)
T 2vyi_A           82 AYGRMGLALSSLNKHVEAVAY  102 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHH
Confidence            888899999999999999763

>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=97.67  E-value=0.00031  Score=46.11  Aligned_cols=114  Identities=11%  Similarity=0.057  Sum_probs=66.3

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVA   94 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~   94 (156)
                      +...|+.++|...++...+.. +.+.              ..|..+-..|...|++++|.+.|++..+... .+...+..
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~-p~~~--------------~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~   83 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRAN-PQNS--------------EQWALLGEYYLWQNDYSNSLLAYRQALQLRG-ENAELYAA   83 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHC-CSCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC-SCHHHHHH
T ss_pred             hhhccCHHHHHHHHHHHHHhC-CCcH--------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHH
Confidence            456678888888888876643 2244              4455556666677777777777777665321 13444555


Q ss_pred             HHHh-hcCCCch--HHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           95 ILTP-CSHSGLV--YAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        95 ll~~-~~~~~~~--~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +-.. +.+.|+.  ++|...++.....          ...+...|..+-..|...|++++|.+
T Consensus        84 la~~l~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~~~~la~~~~~~g~~~~A~~  136 (177)
T 2e2e_A           84 LATVLYYQASQHMTAQTRAMIDKALAL----------DSNEITALMLLASDAFMQANYAQAIE  136 (177)
T ss_dssp             HHHHHHHHTTTCCCHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhcCCcchHHHHHHHHHHHHh----------CCCcHHHHHHHHHHHHHcccHHHHHH
Confidence            5555 4566666  7777777766332          12245566666677777777777654

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

Probab=97.67  E-value=0.00081  Score=48.14  Aligned_cols=137  Identities=7%  Similarity=-0.104  Sum_probs=91.9

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcC
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAEN   67 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~   67 (156)
                      +..+-..+.+.|+.++|...++...+.. +-+...+..+-..|.+.|                    .........+...
T Consensus       120 ~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~  198 (287)
T 3qou_A          120 XAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIELLXQ  198 (287)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHHHHHhh
Confidence            3444556678899999999999987643 224555666666666665                    1111122224455


Q ss_pred             CCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcC
Q 041561           68 EYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHS  147 (156)
Q Consensus        68 g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g  147 (156)
                      ++.++|.+.|++..... ..+...+..+-..+.+.|+.++|.+.+.......        +-..+...+..+...|...|
T Consensus       199 ~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~--------p~~~~~~a~~~l~~~~~~~g  269 (287)
T 3qou_A          199 AADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXD--------LTAADGQTRXTFQEILAALG  269 (287)
T ss_dssp             HTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------TTGGGGHHHHHHHHHHHHHC
T ss_pred             cccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcc--------cccccchHHHHHHHHHHHcC
Confidence            55666677676665543 2345677788888899999999999999985441        01123678999999999999


Q ss_pred             CHhHHhh
Q 041561          148 NVRLAKK  154 (156)
Q Consensus       148 ~~~~a~~  154 (156)
                      +.++|..
T Consensus       270 ~~~~a~~  276 (287)
T 3qou_A          270 TGDALAS  276 (287)
T ss_dssp             TTCHHHH
T ss_pred             CCCcHHH
Confidence            9888764

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

Probab=97.66  E-value=0.00067  Score=42.61  Aligned_cols=89  Identities=6%  Similarity=-0.152  Sum_probs=70.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc----HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD----GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      ..|..+-..+...|++++|.+.|++..+.  .|+    ...+..+-..+.+.|++++|...++.....          ..
T Consensus        29 ~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~----------~~   96 (148)
T 2dba_A           29 EQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK----------DG   96 (148)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------TS
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh----------Cc
Confidence            45667778888999999999999998764  455    567777888888999999999999887443          13


Q ss_pred             CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          131 DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       131 pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+...|..+-..|...|++++|.+.
T Consensus        97 ~~~~~~~~~a~~~~~~~~~~~A~~~  121 (148)
T 2dba_A           97 GDVKALYRRSQALEKLGRLDQAVLD  121 (148)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3677888888899999999998753

>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=97.63  E-value=0.00068  Score=43.73  Aligned_cols=89  Identities=7%  Similarity=-0.044  Sum_probs=64.5

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..+..+-..+.+.|++++|.+.|+...... ..+...|..+-.++.+.|++++|...|+.....          -+.+..
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l----------~p~~~~   90 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM----------DIXEPR   90 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------STTCTH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc----------CCCCch
Confidence            345556667778888888888888877643 225566677777778888888888888887432          123567


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                      .|..+-.+|...|++++|.+
T Consensus        91 ~~~~lg~~~~~~g~~~~A~~  110 (148)
T 2vgx_A           91 FPFHAAECLLQXGELAEAES  110 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHH
Confidence            77777888888888888875

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

Probab=97.63  E-value=0.0025  Score=45.55  Aligned_cols=138  Identities=9%  Similarity=-0.060  Sum_probs=93.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHh----CCCC-chHHHhHHHHHhhhc-c-------------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKD----GYGN-DIFVGSAPINIYCNC-G-------------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~-~-------------------------   54 (156)
                      .+|+.+-..+.+.|+.++|...++...+.    |-.+ -..+++.+-..|.+. |                         
T Consensus        78 ~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~  157 (292)
T 1qqe_A           78 NTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALS  157 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHH
Confidence            45667777778888888888888876542    2111 134666777777764 5                         


Q ss_pred             -chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH------HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCC
Q 041561           55 -VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG------VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        55 -~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~------~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                       .+|+.+-..|.+.|++++|.+.|++..+.......      .+|..+...+...|+.++|...|+....          
T Consensus       158 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~----------  227 (292)
T 1qqe_A          158 NKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS----------  227 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC----------
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh----------
Confidence             34777888999999999999999999875433222      1566777778899999999999998843          


Q ss_pred             CCCCC------hhhHHHHHHHHh--hcCCHhHHhh
Q 041561          128 PYKDD------LVVWGDLVSSCQ--VHSNVRLAKK  154 (156)
Q Consensus       128 ~~~pd------~~~~~~li~~~~--~~g~~~~a~~  154 (156)
                       +.|+      ...+..++.+|.  ..+++++|.+
T Consensus       228 -l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~  261 (292)
T 1qqe_A          228 -EDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCK  261 (292)
T ss_dssp             -C---------HHHHHHHHHHHHTTCTTTHHHHHH
T ss_pred             -hCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence             2232      123455666664  3455666653

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

Probab=97.63  E-value=0.002  Score=40.37  Aligned_cols=101  Identities=9%  Similarity=-0.139  Sum_probs=78.3

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +...+..+-..+.+.|+++.|...|+...+.  .|+....          ...|..+-..|...|++++|.+.|++..+.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~----------~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   94 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQ----------AVLHRNRAACHLKLEDYDKAETEASKAIEK   94 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHH----------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHH----------HHHHHHHHHHHHHHccHHHHHHHHHHHHhh
Confidence            3456677778888999999999999998874  3442100          056677788889999999999999998764


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      . ..+...+..+-..+.+.|+.++|...|+....
T Consensus        95 ~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A           95 D-GGDVKALYRRSQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             T-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             C-ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3 22466777888888999999999999998843

>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=97.61  E-value=0.0012  Score=57.08  Aligned_cols=140  Identities=11%  Similarity=0.074  Sum_probs=90.6

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------chHHHHHHHHHcCCC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------VTWNEMIHGYAENEY   69 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------~~~~~li~~~~~~g~   69 (156)
                      |...|.-+...|.+.|++++|.+.+...++..  +++...+-+..+|++.+              ..|..+=..|...|+
T Consensus      1133 D~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI~~~n~ad~~~iGd~le~eg~ 1210 (1630)
T 1xi4_A         1133 DPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKM 1210 (1630)
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHHhCCCHHHHHHHHHHHHhcCC
Confidence            45567778888999999999999998776654  44444445778888776              345556666667777


Q ss_pred             HHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC----------------cCCCCCCCh
Q 041561           70 VEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK----------------CLMPYKDDL  133 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~----------------c~~~~~pd~  133 (156)
                      +++|..+|...         ..|..+...+.+.|++++|.+.++.-... ..+..                |...+.-+.
T Consensus      1211 YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~n~-~aWkev~~acve~~Ef~LA~~cgl~Iiv~~ 1280 (1630)
T 1xi4_A         1211 YDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKANST-RTWKEVCFACVDGKEFRLAQMCGLHIVVHA 1280 (1630)
T ss_pred             HHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhCCH-HHHHHHHHHHhhhhHHHHHHHHHHhhhcCH
Confidence            77777777663         36777777777777777777776644111 00000                122233355


Q ss_pred             hhHHHHHHHHhhcCCHhHHhhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ..+..++.-|-+.|.+++|.++
T Consensus      1281 deLeeli~yYe~~G~feEAI~L 1302 (1630)
T 1xi4_A         1281 DELEELINYYQDRGYFEELITM 1302 (1630)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHH
Confidence            5666777778888888777653

>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=97.58  E-value=0.001  Score=41.40  Aligned_cols=90  Identities=8%  Similarity=-0.169  Sum_probs=73.5

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+...|++++|.+.|++..... ..+...+..+-..+.+.|++++|...++.....          .+.+..
T Consensus        10 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~----------~p~~~~   78 (137)
T 3q49_B           10 QELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL----------DGQSVK   78 (137)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----------CchhHH
Confidence            456677788899999999999999987753 224667888888889999999999999988443          133678


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|..+-..|...|++++|.+.
T Consensus        79 ~~~~l~~~~~~~~~~~~A~~~   99 (137)
T 3q49_B           79 AHFFLGQCQLEMESYDEAIAN   99 (137)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHH
Confidence            899999999999999999753

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

Probab=97.58  E-value=0.00092  Score=42.47  Aligned_cols=87  Identities=7%  Similarity=-0.054  Sum_probs=61.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhH
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVW  136 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~  136 (156)
                      +..+-..+.+.|++++|.+.|+....... .+...|..+-..+.+.|++++|...|+.....          -+.+...|
T Consensus        21 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~----------~p~~~~~~   89 (142)
T 2xcb_A           21 LYALGFNQYQAGKWDDAQKIFQALCMLDH-YDARYFLGLGACRQSLGLYEQALQSYSYGALM----------DINEPRFP   89 (142)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCTHHH
T ss_pred             HHHHHHHHHHHccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc----------CCCCcHHH
Confidence            34455667788888888888888776432 24556666777777888888888888877433          12355667


Q ss_pred             HHHHHHHhhcCCHhHHhh
Q 041561          137 GDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       137 ~~li~~~~~~g~~~~a~~  154 (156)
                      ..+-.+|...|++++|.+
T Consensus        90 ~~lg~~~~~~g~~~~A~~  107 (142)
T 2xcb_A           90 FHAAECHLQLGDLDGAES  107 (142)
T ss_dssp             HHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHH
Confidence            777788888888888865

>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=97.57  E-value=0.00064  Score=51.07  Aligned_cols=135  Identities=7%  Similarity=-0.056  Sum_probs=81.6

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc---------------------chHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------------------VTWNEMIHGY   64 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---------------------~~~~~li~~~   64 (156)
                      ..|..+-..+.+.|+.++|...++...+.. +-+...|+.+-..|.+.|                     ..|+.+-.++
T Consensus        98 ~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~  176 (382)
T 2h6f_A           98 DVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLV  176 (382)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            356666777788899999999999988753 124545554444444333                     4556666666


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHh
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQ  144 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~  144 (156)
                      ...|++++|...|++..+... -+...|..+-.++.+.|++++|...++.....          -.-+...|+.+-..+.
T Consensus       177 ~~~g~~~eAl~~~~kal~ldP-~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l----------~P~~~~a~~~lg~~l~  245 (382)
T 2h6f_A          177 EWLRDPSQELEFIADILNQDA-KNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE----------DVRNNSVWNQRYFVIS  245 (382)
T ss_dssp             HHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH----------CTTCHHHHHHHHHHHH
T ss_pred             HHccCHHHHHHHHHHHHHhCc-cCHHHHHHHHHHHHHcCChHHHHHHHHHHHHh----------CCCCHHHHHHHHHHHH
Confidence            666666666666666655321 13445555556666666666666666666332          1224566666666666


Q ss_pred             h-cCCHhHH
Q 041561          145 V-HSNVRLA  152 (156)
Q Consensus       145 ~-~g~~~~a  152 (156)
                      . .|..++|
T Consensus       246 ~l~~~~~eA  254 (382)
T 2h6f_A          246 NTTGYNDRA  254 (382)
T ss_dssp             HTTCSCSHH
T ss_pred             HhcCcchHH
Confidence            6 4444555

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

Probab=97.56  E-value=0.00098  Score=43.26  Aligned_cols=88  Identities=14%  Similarity=0.031  Sum_probs=53.7

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .|..+-..+.+.|++++|.+.|++..+... -+...|..+-..+.+.|++++|...|+.....          -..+...
T Consensus        13 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----------~p~~~~~   81 (164)
T 3sz7_A           13 KLKSEGNAAMARKEYSKAIDLYTQALSIAP-ANPIYLSNRAAAYSASGQHEKAAEDAELATVV----------DPKYSKA   81 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-cCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh----------CCCCHHH
Confidence            344555566667777777777776655321 14455666666666777777777777666332          1224566


Q ss_pred             HHHHHHHHhhcCCHhHHhh
Q 041561          136 WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~  154 (156)
                      |..+-.+|...|++++|.+
T Consensus        82 ~~~lg~~~~~~g~~~~A~~  100 (164)
T 3sz7_A           82 WSRLGLARFDMADYKGAKE  100 (164)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHH
Confidence            6666677777777776654

>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=97.56  E-value=0.0012  Score=40.75  Aligned_cols=88  Identities=8%  Similarity=-0.040  Sum_probs=66.7

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .|..+-..+.+.|++++|.+.|++..+.. ..+...|..+-.++.+.|++++|...++.....          -..+...
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~   74 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEK----------DPNFVRA   74 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----------CCCcHHH
Confidence            34555667788899999999998887643 224667778888888899999999998887433          1235677


Q ss_pred             HHHHHHHHhhcCCHhHHhh
Q 041561          136 WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~  154 (156)
                      |..+-.++...|++++|.+
T Consensus        75 ~~~lg~~~~~~~~~~~A~~   93 (126)
T 3upv_A           75 YIRKATAQIAVKEYASALE   93 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhCHHHHHH
Confidence            8888888899999988875

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

Probab=97.56  E-value=0.00055  Score=44.62  Aligned_cols=96  Identities=11%  Similarity=-0.079  Sum_probs=76.8

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ..+..+=..+.+.|++++|...|+...+..  |+..             ..|..+-.+|...|++++|.+.|++..+-..
T Consensus        37 ~~~~~lg~~~~~~g~~~eA~~~~~~al~~~--P~~~-------------~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P  101 (151)
T 3gyz_A           37 DDIYSYAYDFYNKGRIEEAEVFFRFLCIYD--FYNV-------------DYIMGLAAIYQIKEQFQQAADLYAVAFALGK  101 (151)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCH-------------HHHHHHHHHHHHHccHHHHHHHHHHHHhhCC
Confidence            345555667788999999999999998753  4322             6778888899999999999999999987432


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      . +...|..+-.++.+.|+.++|...|+....
T Consensus       102 ~-~~~~~~~lg~~~~~lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          102 N-DYTPVFHTGQCQLRLKAPLKAKECFELVIQ  132 (151)
T ss_dssp             S-CCHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             C-CcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2 355777888889999999999999998843

>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=97.55  E-value=0.00046  Score=42.24  Aligned_cols=92  Identities=9%  Similarity=-0.016  Sum_probs=72.4

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC---
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD---  132 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd---  132 (156)
                      .|..+-..+...|++++|.+.|++..+.. ..+...+..+-..+.+.|++++|...++.......       ...++   
T Consensus         6 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-------~~~~~~~~   77 (131)
T 1elr_A            6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR-------ENREDYRQ   77 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH-------HSTTCHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc-------ccchhHHH
Confidence            46677788899999999999999988754 33566788888888999999999999998844311       01122   


Q ss_pred             -hhhHHHHHHHHhhcCCHhHHhhh
Q 041561          133 -LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       133 -~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       ..+|..+-..|...|++++|.+.
T Consensus        78 ~~~~~~~la~~~~~~~~~~~A~~~  101 (131)
T 1elr_A           78 IAKAYARIGNSYFKEEKYKDAIHF  101 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHH
Confidence             77888899999999999999763

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

Probab=97.53  E-value=0.0013  Score=41.17  Aligned_cols=88  Identities=5%  Similarity=-0.049  Sum_probs=66.2

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .|...=..|.+.|++++|.+.|++..+.. ..+...|..+-.++.+.|++++|...++...+.          -..+...
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~----------~p~~~~a   83 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRL----------DSKFIKG   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHh----------hhhhhHH
Confidence            34444556778899999999998877643 235667777888888899999999988887432          1345778


Q ss_pred             HHHHHHHHhhcCCHhHHhh
Q 041561          136 WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~  154 (156)
                      |..+=.+|...|++++|.+
T Consensus        84 ~~~lg~~~~~~~~~~~A~~  102 (126)
T 4gco_A           84 YIRKAACLVAMREWSKAQR  102 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHH
Confidence            8888888999999998875

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

Probab=97.52  E-value=0.0013  Score=42.74  Aligned_cols=97  Identities=5%  Similarity=-0.089  Sum_probs=78.7

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      ...|..+-..+.+.|++++|...|+...+..  | +.              ..|..+-.+|.+.|++++|.+.|++..+.
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~--------------~~~~~l~~~~~~~g~~~~A~~~~~~al~~   74 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIA--PANP--------------IYLSNRAAAYSASGQHEKAAEDAELATVV   74 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CcCH--------------HHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3456667778889999999999999987753  3 33              56777888899999999999999998875


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      .. -+...|..+-..+.+.|++++|...|+.....
T Consensus        75 ~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           75 DP-KYSKAWSRLGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             CT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CC-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            42 24667888888999999999999999988443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.51  E-value=0.0016  Score=43.21  Aligned_cols=132  Identities=8%  Similarity=-0.093  Sum_probs=86.5

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHh----CCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKD----GYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      .++..+-..+...|++++|...+++..+.    |..|...             ..++.+-..|...|++++|.+.|++..
T Consensus        27 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~-------------~~~~~l~~~~~~~g~~~~A~~~~~~al   93 (203)
T 3gw4_A           27 GARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEH-------------RALHQVGMVERMAGNWDAARRCFLEER   93 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34555556666777777777777776542    1111110             566778888899999999999998875


Q ss_pred             HC----CCCc--cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC-CCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           82 AS----GVKH--DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY-KDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        82 ~~----g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~-~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +.    +-.|  ....+..+-..+...|++++|...+++......     ..+. ..-..++..+-..+...|++++|.+
T Consensus        94 ~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~-----~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  168 (203)
T 3gw4_A           94 ELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQ-----QADDQVAIACAFRGLGDLAQQEKNLLEAQQ  168 (203)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH-----HTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH-----hccchHHHHHHHHHHHHHHHHCcCHHHHHH
Confidence            42    3222  234567777888889999999999887643211     0000 1112346777788999999999875


Q ss_pred             h
Q 041561          155 A  155 (156)
Q Consensus       155 ~  155 (156)
                      .
T Consensus       169 ~  169 (203)
T 3gw4_A          169 H  169 (203)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=97.50  E-value=0.0025  Score=44.45  Aligned_cols=127  Identities=9%  Similarity=-0.118  Sum_probs=89.3

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ..+-..-..+.+.|++++|...|+.+.+..  |+....          ...+..+-.+|.+.|++++|.+.|+...+...
T Consensus        16 ~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~----------~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p   83 (261)
T 3qky_A           16 QEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWA----------ADAQFYLARAYYQNKEYLLAASEYERFIQIYQ   83 (261)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTH----------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcch----------HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCC
Confidence            344455566778999999999999997753  322000          04556677788899999999999999987532


Q ss_pred             -Ccc-HHHHHHHHHhhcC--------CCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhH-----------------H
Q 041561           86 -KHD-GVTFVAILTPCSH--------SGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVW-----------------G  137 (156)
Q Consensus        86 -~p~-~~t~~~ll~~~~~--------~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~-----------------~  137 (156)
                       .|+ ...+..+-.++.+        .|+.++|...|+.....           .| +...+                 -
T Consensus        84 ~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~-----------~p~~~~~~~a~~~~~~~~~~~~~~~~  152 (261)
T 3qky_A           84 IDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR-----------YPNHELVDDATQKIRELRAKLARKQY  152 (261)
T ss_dssp             TCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH-----------CTTCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH-----------CcCchhHHHHHHHHHHHHHHHHHHHH
Confidence             222 3455556666666        99999999999998554           23 23333                 3


Q ss_pred             HHHHHHhhcCCHhHHhhh
Q 041561          138 DLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       138 ~li~~~~~~g~~~~a~~~  155 (156)
                      .+-..|...|++++|.+.
T Consensus       153 ~la~~~~~~g~~~~A~~~  170 (261)
T 3qky_A          153 EAARLYERRELYEAAAVT  170 (261)
T ss_dssp             HHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHH
Confidence            446778899999998753

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.50  E-value=0.00059  Score=52.62  Aligned_cols=115  Identities=9%  Similarity=-0.048  Sum_probs=86.2

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFV   93 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~   93 (156)
                      .+.+.|+.++|.+.+++..+.  .|+..             ..|..+-.+|.+.|++++|.+.|++..+... -+..++.
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~--~p~~~-------------~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~   78 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIEL--NPSNA-------------IYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYY   78 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHH--CTTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHh--CCccH-------------HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHH
Confidence            456789999999999998775  34321             6778888899999999999999999987532 2466788


Q ss_pred             HHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHH--HhhcCCHhHHhhh
Q 041561           94 AILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSS--CQVHSNVRLAKKA  155 (156)
Q Consensus        94 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~--~~~~g~~~~a~~~  155 (156)
                      .+-.++.+.|++++|.+.+++..+.           .| +...+..+-.+  +.+.|++++|.+.
T Consensus        79 ~lg~~~~~~g~~~eA~~~~~~al~~-----------~p~~~~~~~~l~~~~~~~~~g~~~~A~~~  132 (477)
T 1wao_1           79 RRAASNMALGKFRAALRDYETVVKV-----------KPHDKDAKMKYQECNKIVKQKAFERAIAG  132 (477)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH-----------STTCTTHHHHHHHHHHHHHHHHHCCC---
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh-----------CCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            8888999999999999999988443           22 33444444444  8888888888754

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

Probab=97.49  E-value=0.00019  Score=44.14  Aligned_cols=107  Identities=8%  Similarity=0.007  Sum_probs=75.3

Q ss_pred             CCCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAI   95 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l   95 (156)
                      ..|+.++|...|+...+.+. .|+..             ..|..+-..|...|++++|.+.|++..+.... +...+..+
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~-------------~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l   67 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLA-------------ECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFY   67 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHH
Confidence            46788999999999887542 13221             56777888899999999999999999875432 35677778


Q ss_pred             HHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           96 LTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        96 l~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      -.++.+.|+.++|...++.......        -.|+...|...|..|..
T Consensus        68 ~~~~~~~g~~~~A~~~~~~al~~~p--------~~~~~~~~~~ai~~~~~  109 (117)
T 3k9i_A           68 AMVLYNLGRYEQGVELLLKIIAETS--------DDETIQSYKQAILFYAD  109 (117)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHC--------CCHHHHHTHHHHHHHTT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC--------CcHHHHHHHHHHHHHHH
Confidence            8888999999999999998854421        24455556666666554

>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=97.49  E-value=0.00054  Score=44.22  Aligned_cols=109  Identities=6%  Similarity=-0.170  Sum_probs=66.8

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAIL   96 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll   96 (156)
                      ..|+++.|...+......  .|+..             ..+-.+-..|.+.|++++|.+.|++..+... -+..+|..+-
T Consensus         9 ~~~~~e~ai~~~~~a~~~--~p~~~-------------~~~~~la~~y~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg   72 (150)
T 4ga2_A            9 SKADVERYIASVQGSTPS--PRQKS-------------IKGFYFAKLYYEAKEYDLAKKYICTYINVQE-RDPKAHRFLG   72 (150)
T ss_dssp             CHHHHHHHHHHHHHHSCS--HHHHH-------------TTHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             HcChHHHHHHHHHHhccc--CcccH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHH
Confidence            445666666666554331  23221             3444556667777777777777777765321 1445666666


Q ss_pred             HhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHH
Q 041561           97 TPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLA  152 (156)
Q Consensus        97 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a  152 (156)
                      ..+.+.|++++|...|+...+.           .| +...|..+-..|...|+.++|
T Consensus        73 ~~~~~~~~~~~A~~~~~~al~~-----------~p~~~~~~~~la~~~~~~~~~~~a  118 (150)
T 4ga2_A           73 LLYELEENTDKAVECYRRSVEL-----------NPTQKDLVLKIAELLCKNDVTDGR  118 (150)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-----------CTTCHHHHHHHHHHHHHHCSSSSH
T ss_pred             HHHHHcCchHHHHHHHHHHHHh-----------CCCCHHHHHHHHHHHHHcCChHHH
Confidence            7777777777777777776332           33 456677777777777776544

>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=97.46  E-value=0.0016  Score=41.92  Aligned_cols=115  Identities=6%  Similarity=-0.037  Sum_probs=85.5

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ..+-.+=..|.+.|+.++|...|+...+.  .|+..             ..|..+-..|.+.|++++|.+.|++..+.  
T Consensus        32 ~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~-------------~a~~~lg~~~~~~~~~~~A~~~~~~al~~--   94 (150)
T 4ga2_A           32 IKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDP-------------KAHRFLGLLYELEENTDKAVECYRRSVEL--   94 (150)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCH-------------HHHHHHHHHHHHcCchHHHHHHHHHHHHh--
Confidence            34555667788999999999999998775  34332             67788888899999999999999998874  


Q ss_pred             Cc-cHHHHHHHHHhhcCCCchHHHHHH-HHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCC
Q 041561           86 KH-DGVTFVAILTPCSHSGLVYAEVEI-FNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSN  148 (156)
Q Consensus        86 ~p-~~~t~~~ll~~~~~~~~~~~a~~~-~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~  148 (156)
                      .| +...+..+-..+.+.|+.+++... ++...+           +.| +..+|+..-..+...|+
T Consensus        95 ~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~-----------l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           95 NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAK-----------LFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHH-----------HSTTCHHHHHHHHHHHHTCCC
T ss_pred             CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHH-----------hCcCCHHHHHHHHHHHHHhCc
Confidence            34 456788888888999998876655 465522           234 56677776666666664

>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=97.45  E-value=0.0016  Score=41.59  Aligned_cols=90  Identities=11%  Similarity=0.007  Sum_probs=73.7

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+...|++++|.+.|++..+.. ..+..++..+-..+.+.|++++|...++.....          ...+..
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~----------~~~~~~   82 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL----------DKKYIK   82 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CcccHH
Confidence            456777788899999999999999987743 225667888888889999999999999988443          234678


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|..+-..+...|++++|.+.
T Consensus        83 ~~~~~a~~~~~~~~~~~A~~~  103 (166)
T 1a17_A           83 GYYRRAASNMALGKFRAALRD  103 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHH
Confidence            898999999999999999763

>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=0.0024  Score=39.95  Aligned_cols=93  Identities=5%  Similarity=-0.082  Sum_probs=73.7

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      .-.=..+.+.|++++|...|++..+.. +.+.              ..|..+-.+|.+.|++++|.+.|++..+-. ..+
T Consensus        17 ~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~--------------~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~   80 (126)
T 4gco_A           17 KNKGNEYFKKGDYPTAMRHYNEAVKRD-PENA--------------ILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKF   80 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCH--------------HHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhh
Confidence            333345778899999999999987753 1234              567778888999999999999999988743 224


Q ss_pred             HHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           89 GVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        89 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      ...|..+-.++.+.|++++|.+.|+...+
T Consensus        81 ~~a~~~lg~~~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           81 IKGYIRKAACLVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            56788888899999999999999998843

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.43  E-value=0.0047  Score=42.24  Aligned_cols=76  Identities=14%  Similarity=0.060  Sum_probs=55.0

Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHH-HH-----------------HHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCC
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGV-TF-----------------VAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMP  128 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~-t~-----------------~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~  128 (156)
                      .|+.++|.+.|++..+.-  |+.. .+                 ..+-..+.+.|++++|...|+.+.+.          
T Consensus       109 ~~~~~~A~~~~~~~l~~~--P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~----------  176 (225)
T 2yhc_A          109 PQQARAAFSDFSKLVRGY--PNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRD----------  176 (225)
T ss_dssp             CHHHHHHHHHHHHHHTTC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------
T ss_pred             cHHHHHHHHHHHHHHHHC--cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHH----------
Confidence            567889999999988642  3221 11                 12344567889999999999998554          


Q ss_pred             CCCC----hhhHHHHHHHHhhcCCHhHHhhh
Q 041561          129 YKDD----LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       129 ~~pd----~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       -|+    ...+..+-.+|.+.|+.++|.+.
T Consensus       177 -~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~  206 (225)
T 2yhc_A          177 -YPDTQATRDALPLMENAYRQMQMNAQAEKV  206 (225)
T ss_dssp             -STTSHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             -CcCCCccHHHHHHHHHHHHHcCCcHHHHHH
Confidence             233    25688899999999999999763

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.42  E-value=0.00098  Score=48.05  Aligned_cols=142  Identities=6%  Similarity=-0.120  Sum_probs=89.7

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhC----CCC-chHHHhHHHHHhhhcc--------------------------c
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDG----YGN-DIFVGSAPINIYCNCG--------------------------V   55 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g----~~~-~~~~~~~li~~~~~~~--------------------------~   55 (156)
                      .|......+...|++++|...|....+..    -.+ -...|+.+-..|.+.|                          .
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  117 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAM  117 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            34555566667778888877777664421    111 1235555555555544                          4


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIAS----GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      +++.+-..|.. |++++|.+.|++-.+-    |-.+ ...++..+-..+.+.|++++|...|++......     ..+..
T Consensus       118 ~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~-----~~~~~  191 (307)
T 2ifu_A          118 ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYK-----EMENY  191 (307)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HTTCH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-----HcCCh
Confidence            56667777777 9999999998886541    2111 135677788888899999999999988743211     00011


Q ss_pred             CC-hhhHHHHHHHHhhcCCHhHHhh
Q 041561          131 DD-LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       131 pd-~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ++ ..+|..+...+...|++++|.+
T Consensus       192 ~~~~~~~~~~g~~~~~~g~~~~A~~  216 (307)
T 2ifu_A          192 PTCYKKCIAQVLVQLHRADYVAAQK  216 (307)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            11 2366777777888899988875

>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=97.40  E-value=0.0016  Score=44.45  Aligned_cols=89  Identities=8%  Similarity=-0.061  Sum_probs=73.3

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-Chh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLV  134 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~  134 (156)
                      .|...-..+...|++++|.+.|++..+....++...+..+-..+.+.|++++|...++.....           .| +..
T Consensus         9 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~-----------~p~~~~   77 (228)
T 4i17_A            9 QLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK-----------NYNLAN   77 (228)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-----------TCSHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh-----------CcchHH
Confidence            445556678899999999999999988665467777777888888999999999999988433           34 567


Q ss_pred             hHHHHHHHHhhcCCHhHHhhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|..+-..|...|++++|.+.
T Consensus        78 ~~~~l~~~~~~~~~~~~A~~~   98 (228)
T 4i17_A           78 AYIGKSAAYRDMKNNQEYIAT   98 (228)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHH
Confidence            888899999999999999763

>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=97.40  E-value=0.0031  Score=44.97  Aligned_cols=131  Identities=11%  Similarity=-0.024  Sum_probs=90.6

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhC-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-Ccc
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDG-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV-KHD   88 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~   88 (156)
                      .+..+.+.|+.++|..+++...+.. ..|+.   ..++       ..+..+...+...+++++|.+.|++...-.. .++
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~---~~~~-------~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~  150 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEF---QQFL-------QWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGID  150 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHH---HHHH-------HHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSC
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHH---HHHH-------HHHHHHHHHHHcccCHHHHHHHHHHHHHHhccccc
Confidence            3667788899999999999987632 22222   1111       2344466667778899999999999887322 233


Q ss_pred             ----HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-hhhHHHHHHHHhhcCCHhHHhhh
Q 041561           89 ----GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        89 ----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                          ..+++.+-..+.+.|++++|...|+.......-.+    ...|. ..+|..+-..|...|++++|.+.
T Consensus       151 ~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~----~~~~~~~~~~~nlg~~y~~~~~y~~A~~~  218 (293)
T 3u3w_A          151 VYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALH----DNEEFDVKVRYNHAKALYLDSRYEESLYQ  218 (293)
T ss_dssp             TTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSS----CCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcc----cchhHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence                23688888999999999999999998853211000    01222 34788899999999999999763

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

Probab=97.39  E-value=0.0024  Score=39.22  Aligned_cols=84  Identities=8%  Similarity=-0.111  Sum_probs=52.8

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCCCcc--HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC----h
Q 041561           60 MIHGYAENEYVEQAISLYKDIIASGVKHD--GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD----L  133 (156)
Q Consensus        60 li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd----~  133 (156)
                      +-..+...|++++|.+.|+...+......  ...+..+-..+.+.|++++|...|+.....           .|+    .
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~-----------~p~~~~~~   76 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSR-----------YPTHDKAA   76 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTSTTHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHH-----------CCCCcccH
Confidence            34556677778888888777766422111  135555666667778888888777777433           222    4


Q ss_pred             hhHHHHHHHHhhcCCHhHHhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ..+..+-.++...|++++|.+
T Consensus        77 ~~~~~la~~~~~~g~~~~A~~   97 (129)
T 2xev_A           77 GGLLKLGLSQYGEGKNTEAQQ   97 (129)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHH
Confidence            456666677777777777764

>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=97.38  E-value=0.0036  Score=41.97  Aligned_cols=100  Identities=13%  Similarity=-0.014  Sum_probs=80.3

Q ss_pred             CCCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561            2 YPTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus         2 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      .|+...|..+-..+.+.|+.++|...++...+.. +.+.              ..|..+-..|...|++++|.+.|++..
T Consensus        34 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~--------------~~~~~lg~~~~~~~~~~~A~~~~~~al   98 (213)
T 1hh8_A           34 DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLA--------------VAYFQRGMLYYQTEKYDLAIKDLKEAL   98 (213)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccch--------------HHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            4667788888889999999999999999987753 1233              567778888999999999999999988


Q ss_pred             HCC--------------CCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           82 ASG--------------VKHD-GVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        82 ~~g--------------~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      +..              ..|+ ...+..+-..+.+.|+.++|...|+...
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  148 (213)
T 1hh8_A           99 IQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALAT  148 (213)
T ss_dssp             HTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            742              1222 2567778888899999999999999884

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.37  E-value=0.0004  Score=51.46  Aligned_cols=141  Identities=11%  Similarity=-0.016  Sum_probs=93.9

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHh----CC-CCchHHHhHHHHHhhhcc--------------------------c
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKD----GY-GNDIFVGSAPINIYCNCG--------------------------V   55 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~-~~~~~~~~~li~~~~~~~--------------------------~   55 (156)
                      .|..+-..+...|+.++|...+++..+.    +- ......+..+-..|...|                          .
T Consensus        88 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  167 (411)
T 4a1s_A           88 IYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGR  167 (411)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHH
Confidence            5666777777888888888888877543    11 223455666666666665                          3


Q ss_pred             hHHHHHHHHHcCCC-----------------HHHHHHHHHHHHH----CCCCc-cHHHHHHHHHhhcCCCchHHHHHHHH
Q 041561           56 TWNEMIHGYAENEY-----------------VEQAISLYKDIIA----SGVKH-DGVTFVAILTPCSHSGLVYAEVEIFN  113 (156)
Q Consensus        56 ~~~~li~~~~~~g~-----------------~~~a~~~~~~m~~----~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~  113 (156)
                      .+..+-..|...|+                 +++|.+.|++..+    .+-.| ...++..+-..+.+.|++++|...++
T Consensus       168 ~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  247 (411)
T 4a1s_A          168 ALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQ  247 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            66777777888888                 8888888877543    12222 22366677777888889988888888


Q ss_pred             hcccccccCCCcCCCCCCC----hhhHHHHHHHHhhcCCHhHHhhh
Q 041561          114 SMEHDHEVKPKCLMPYKDD----LVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       114 ~m~~~~~~~~~c~~~~~pd----~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +......        -.++    ..+|..+-..|...|++++|.+.
T Consensus       248 ~al~~~~--------~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  285 (411)
T 4a1s_A          248 ERLRIAR--------EFGDRAAERRANSNLGNSHIFLGQFEDAAEH  285 (411)
T ss_dssp             HHHHHHH--------HHTCHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHH--------hcCCcHHHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            7743211        0011    23777888888888998888753

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

Probab=97.37  E-value=0.0081  Score=36.73  Aligned_cols=98  Identities=9%  Similarity=0.016  Sum_probs=71.6

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD   88 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   88 (156)
                      ..+-..+.+.|++++|...|+...+..  |+.....          ..+..+-.++.+.|++++|.+.|++..+......
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~----------~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~   73 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELY--PNGVYTP----------NALYWLGESYYATRNFQLAEAQFRDLVSRYPTHD   73 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHH----------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTST
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccH----------HHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCc
Confidence            344556678899999999999987753  3221000          2445566778899999999999999887532211


Q ss_pred             --HHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           89 --GVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        89 --~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                        ...+..+-..+.+.|+.++|...|+.....
T Consensus        74 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           74 KAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence              455667778888999999999999998544

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.37  E-value=0.0006  Score=48.37  Aligned_cols=96  Identities=8%  Similarity=-0.069  Sum_probs=69.3

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS----GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      ..+..+...+...|++++|.+.|++....    +..+. ..++..+-..+.+.|++++|...++.......-     .+.
T Consensus       224 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~-----~~~  298 (338)
T 3ro2_A          224 RAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQE-----LKD  298 (338)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-----HTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHh-----cCC
Confidence            37788888999999999999999887642    21111 456777888888999999999998877432110     000


Q ss_pred             -CCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 -KDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 -~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       .....+|..+-..|...|++++|.+.
T Consensus       299 ~~~~~~~~~~la~~~~~~g~~~~A~~~  325 (338)
T 3ro2_A          299 RIGEGRACWSLGNAYTALGNHDQAMHF  325 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHcCChHHHHHH
Confidence             11245788888999999999999764

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.36  E-value=0.00096  Score=48.93  Aligned_cols=96  Identities=8%  Similarity=-0.067  Sum_probs=70.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS----GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      ..|..+-..|...|++++|.+.|++..+.    +..+. ..++..+-..+.+.|++++|...++.......-     .+.
T Consensus       228 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~-----~~~  302 (406)
T 3sf4_A          228 RAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQE-----LND  302 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-----TTC
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHh-----cCC
Confidence            37888889999999999999999887642    22222 457778888888999999999999877432110     000


Q ss_pred             CC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 KD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+ ...+|..+-..|...|++++|.+.
T Consensus       303 ~~~~~~~~~~la~~~~~~g~~~~A~~~  329 (406)
T 3sf4_A          303 RIGEGRACWSLGNAYTALGNHDQAMHF  329 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            11 156788888999999999999763

>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=97.34  E-value=0.00089  Score=44.09  Aligned_cols=109  Identities=15%  Similarity=0.042  Sum_probs=75.2

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHH-hhhc-c-------------------chHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINI-YCNC-G-------------------VTWNEMIHG   63 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~-~~~~-~-------------------~~~~~li~~   63 (156)
                      ...+..+-..+.+.|+.++|...++...+..  |+...+..+-.. +.+. +                   ..+..+-..
T Consensus        40 ~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~  117 (176)
T 2r5s_A           40 GDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQ  117 (176)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3556677777888899999999888875432  233322221111 1110 0                   567778888


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           64 YAENEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +...|++++|.+.|++..+....+ +...+..+...+...|+.++|...|+..
T Consensus       118 ~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A          118 YNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHH
Confidence            889999999999999988765443 3567888888888899999988888754

>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=97.34  E-value=0.0033  Score=42.03  Aligned_cols=133  Identities=8%  Similarity=-0.089  Sum_probs=89.8

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhhc--cchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCNC--GVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      +..+-..+.+.|++++|...|....+..- .|+...  ..+....+.  ...|..+-.+|.+.|++++|.+.|+...+..
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~  118 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDD--QILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID  118 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCC--HHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccch--hhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            44445566788999999999999876421 121000  000000000  0566778888899999999999999988753


Q ss_pred             CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561           85 VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus        85 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                       ..+...+..+-.++.+.|++++|...|+.....          ..-+...+..+-..+...++.+++.
T Consensus       119 -p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          119 -KNNVKALYKLGVANMYFGFLEEAKENLYKAASL----------NPNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------STTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             -cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH----------CCCcHHHHHHHHHHHHHHHHHHHHH
Confidence             235667888888899999999999999988433          1235677777777777777666654

>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=97.34  E-value=0.0012  Score=51.63  Aligned_cols=112  Identities=8%  Similarity=-0.112  Sum_probs=74.7

Q ss_pred             CCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHH
Q 041561           18 LSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILT   97 (156)
Q Consensus        18 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~   97 (156)
                      .|+.++|.+.+++..+.  .|+..             ..|..+-..|.+.|++++|.+.|++..+.. .-+...+..+-.
T Consensus         2 ~g~~~~A~~~~~~al~~--~p~~~-------------~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   65 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH--RPQDF-------------VAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGR   65 (568)
T ss_dssp             ---------------------CCH-------------HHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHh--CCCCH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            46788899988887653  24321             566777788889999999999999988743 224667888888


Q ss_pred             hhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           98 PCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        98 ~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+.+.|++++|.+.+++..+.          -..+...|..+-..|...|++++|.+.
T Consensus        66 ~~~~~g~~~~A~~~~~~al~~----------~p~~~~~~~~la~~~~~~g~~~~A~~~  113 (568)
T 2vsy_A           66 VRWTQQRHAEAAVLLQQASDA----------APEHPGIALWLGHALEDAGQAEAAAAA  113 (568)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhc----------CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999999999988543          134678899999999999999999763

>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=97.34  E-value=0.0022  Score=41.23  Aligned_cols=96  Identities=5%  Similarity=-0.148  Sum_probs=74.9

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ..+..+-..+.+.|++++|...|+...+... .+.              ..|..+-.+|...|++++|.+.|++......
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~--------------~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p   86 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVLDH-YDS--------------RFFLGLGACRQAMGQYDLAIHSYSYGAVMDI   86 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHcCc-ccH--------------HHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC
Confidence            3455566677889999999999999876531 244              5667777888999999999999999887432


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                       -+...+..+-.++...|+.++|...|+....
T Consensus        87 -~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           87 -XEPRFPFHAAECLLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             -TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -CCchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             2445677778888899999999999998843

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.33  E-value=0.00084  Score=49.66  Aligned_cols=95  Identities=12%  Similarity=-0.025  Sum_probs=69.3

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCC-ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC-
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIAS----GVK-HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY-  129 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~-  129 (156)
                      .|..+-..|...|++++|.+.|++....    +.. ....++..+-..+.+.|++++|...++.......-     .+. 
T Consensus       265 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~-----~~~~  339 (411)
T 4a1s_A          265 ANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQE-----LGDR  339 (411)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-----HTCH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH-----CCCh
Confidence            7888899999999999999999887642    111 12457777888888999999999999887432110     000 


Q ss_pred             CCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 KDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .....+|..+-..|...|++++|.+.
T Consensus       340 ~~~~~~~~~la~~~~~~g~~~~A~~~  365 (411)
T 4a1s_A          340 IGEARACWSLGNAHSAIGGHERALKY  365 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHH
Confidence            11245788888999999999999763

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.32  E-value=0.0071  Score=43.03  Aligned_cols=139  Identities=9%  Similarity=-0.115  Sum_probs=90.3

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCC-Cch----HHHhHHHHHhhhcc--------------------------chH
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYG-NDI----FVGSAPINIYCNCG--------------------------VTW   57 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~~----~~~~~li~~~~~~~--------------------------~~~   57 (156)
                      ...+..+...|+.++|...+....+..-. ++.    ..+..+-..|...|                          ..|
T Consensus        79 ~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  158 (293)
T 2qfc_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIE  158 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHH
Confidence            34455666778888888877766553221 111    11222222333332                          367


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHH----CCCCc--cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIA----SGVKH--DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      +.+-..|...|++++|.+.|++..+    .+-.+  ...++..+-..|.+.|++++|...++....-..     ..+..+
T Consensus       159 ~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~-----~~~~~~  233 (293)
T 2qfc_A          159 NAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISC-----RINSMA  233 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HTTBCS
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHH-----hcCcHH
Confidence            8888999999999999999998762    22222  225788888899999999999999987632210     000111


Q ss_pred             -ChhhHHHHHHHHhhcCCHhHH
Q 041561          132 -DLVVWGDLVSSCQVHSNVRLA  152 (156)
Q Consensus       132 -d~~~~~~li~~~~~~g~~~~a  152 (156)
                       -..+|..+=..|...|+.++|
T Consensus       234 ~~~~~~~~lg~~y~~~g~~~~A  255 (293)
T 2qfc_A          234 LIGQLYYQRGECLRKLEYEEAE  255 (293)
T ss_dssp             SHHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcHHH
Confidence             156788888899999999998

>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=0.0028  Score=40.17  Aligned_cols=95  Identities=9%  Similarity=-0.099  Sum_probs=73.7

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .+..+-..+.+.|++++|...|+...+... .+.              ..|..+-.+|.+.|++++|.+.|+....... 
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~--------------~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-   83 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLDH-YDA--------------RYFLGLGACRQSLGLYEQALQSYSYGALMDI-   83 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhCC-ccH--------------HHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-
Confidence            344455667788999999999999877531 233              5567777888999999999999999887542 


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      -+...+..+-.++...|++++|...|+....
T Consensus        84 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           84 NEPRFPFHAAECHLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2445667777888899999999999998843

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

Probab=97.29  E-value=0.0031  Score=42.74  Aligned_cols=100  Identities=10%  Similarity=0.035  Sum_probs=65.3

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchH-HHhHHHHHhhhcc----chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIF-VGSAPINIYCNCG----VTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~-~~~~li~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      ..+.+.|++++|...|+...+..  |+.. .|..  ....+..    ..++.+-..|.+.|++++|.+.|++..+... -
T Consensus        12 ~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~--~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~   86 (208)
T 3urz_A           12 SAAIEAGQNGQAVSYFRQTIALN--IDRTEMYYW--TNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAP-N   86 (208)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--HHHHHHHHH--HHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-T
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHH--hhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-C
Confidence            34568899999999999987743  4321 1111  0000000    2223366777888888888888888776431 2


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +...+..+-..+...|+.++|...|+....
T Consensus        87 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  116 (208)
T 3urz_A           87 NVDCLEACAEMQVCRGQEKDALRMYEKILQ  116 (208)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455677777778888888888888887743

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.28  E-value=0.0031  Score=48.29  Aligned_cols=128  Identities=5%  Similarity=-0.110  Sum_probs=93.7

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchH--------HHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIF--------VGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYK   78 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~--------~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~   78 (156)
                      .|...=..+.+.|+++.|...|+...+..  |+..        ..+.+.      -..|..+-.+|.+.|++++|.+.|+
T Consensus       270 ~~~~~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~------~~~~~nla~~~~~~g~~~~A~~~~~  341 (457)
T 1kt0_A          270 IVKEKGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFL------LAAFLNLAMCYLKLREYTKAVECCD  341 (457)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHH------HHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHH------HHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            34555566778999999999999987642  2210        000000      0567888889999999999999999


Q ss_pred             HHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhh
Q 041561           79 DIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        79 ~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +..+... -+...|..+-.++.+.|++++|...|+...+.           .| +...|..+-..+.+.|+.++|.+
T Consensus       342 ~al~~~p-~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l-----------~P~~~~a~~~l~~~~~~~~~~~~a~~  406 (457)
T 1kt0_A          342 KALGLDS-ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV-----------NPQNKAARLQISMCQKKAKEHNERDR  406 (457)
T ss_dssp             HHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-----------C----CHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcCC-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-----------CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9887532 25677888889999999999999999988432           33 55778888888888888887764

>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=97.28  E-value=0.0052  Score=37.74  Aligned_cols=96  Identities=10%  Similarity=-0.029  Sum_probs=76.2

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ..|...=..+.+.|++++|...|+...+.. +.+.              ..|..+-.+|.+.|++++|.+.|++..+...
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~--------------~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p   69 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDA--------------RGYSNRAAALAKLMSFPEAIADCNKAIEKDP   69 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCh--------------HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC
Confidence            345555667788999999999999987753 1233              5677788889999999999999999887532


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                       -+...|..+-.++.+.|+.++|...|+....
T Consensus        70 -~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           70 -NFVRAYIRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -CcHHHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence             2466788888889999999999999998743

>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=97.27  E-value=0.0032  Score=47.28  Aligned_cols=137  Identities=11%  Similarity=0.024  Sum_probs=102.4

Q ss_pred             cccHHHHHHHhcCCCc-hHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSS-LFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~   63 (156)
                      ...|+.+-..+.+.|+ .++|...++...+..- -+...|+.+=..|.+.|                    ..|..+-.+
T Consensus       131 ~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P-~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~  209 (382)
T 2h6f_A          131 YTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWV  209 (382)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHH
Confidence            4567777778888896 9999999999987532 35677777777777666                    678888999


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcC-CCchHHH-----HHHHHhcccccccCCCcCCCCCC-ChhhH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSH-SGLVYAE-----VEIFNSMEHDHEVKPKCLMPYKD-DLVVW  136 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~-~~~~~~a-----~~~~~~m~~~~~~~~~c~~~~~p-d~~~~  136 (156)
                      +.+.|++++|++.|+++.+.... +...|+.+-..+.+ .|..++|     ...++.....           .| +...|
T Consensus       210 ~~~~g~~~eAl~~~~~al~l~P~-~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l-----------~P~~~~a~  277 (382)
T 2h6f_A          210 IQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL-----------VPHNESAW  277 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH-----------STTCHHHH
T ss_pred             HHHcCChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHH-----------CCCCHHHH
Confidence            99999999999999999885432 56678888888887 6665777     3666666332           33 56778


Q ss_pred             HHHHHHHhhcC--CHhHHhh
Q 041561          137 GDLVSSCQVHS--NVRLAKK  154 (156)
Q Consensus       137 ~~li~~~~~~g--~~~~a~~  154 (156)
                      +.+-..+...|  +.++|.+
T Consensus       278 ~~l~~ll~~~g~~~~~~a~~  297 (382)
T 2h6f_A          278 NYLKGILQDRGLSKYPNLLN  297 (382)
T ss_dssp             HHHHHHHTTTCGGGCHHHHH
T ss_pred             HHHHHHHHccCccchHHHHH
Confidence            88888888877  4666654

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

Probab=97.27  E-value=0.00025  Score=43.62  Aligned_cols=80  Identities=10%  Similarity=0.045  Sum_probs=60.3

Q ss_pred             cCCCHHHHHHHHHHHHHCCC-Cc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           66 ENEYVEQAISLYKDIIASGV-KH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~-~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      ..|++++|.+.|++..+.+. .| +...+..+-..+.+.|++++|...|++..+.          .+-+...|..+-.++
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~~~~l~~~~   71 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQ----------FPNHQALRVFYAMVL   71 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCchHHHHHHHHHH
Confidence            45788999999999887541 13 3457778888899999999999999998544          133678888899999


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ...|++++|.+.
T Consensus        72 ~~~g~~~~A~~~   83 (117)
T 3k9i_A           72 YNLGRYEQGVEL   83 (117)
T ss_dssp             HHHTCHHHHHHH
T ss_pred             HHcCCHHHHHHH
Confidence            999999999863

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

Probab=97.25  E-value=0.0022  Score=39.79  Aligned_cols=87  Identities=10%  Similarity=-0.022  Sum_probs=68.3

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-Chhh
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVV  135 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~  135 (156)
                      +-.+-..+.+.|++++|.+.|++..+... -+...|..+-..+.+.|+.++|...|+.....           .| +...
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l-----------~P~~~~~   87 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARML-----------DPKDIAV   87 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTCHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----------CCCCHHH
Confidence            34455677889999999999999887432 25567777778888999999999999988433           33 6678


Q ss_pred             HHHHHHHHhhcCCHhHHhhh
Q 041561          136 WGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~~  155 (156)
                      |..+-..|...|++++|.+.
T Consensus        88 ~~~la~~~~~~g~~~~A~~~  107 (121)
T 1hxi_A           88 HAALAVSHTNEHNANAALAS  107 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHH
Confidence            88888999999999998753

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.25  E-value=0.004  Score=44.01  Aligned_cols=141  Identities=13%  Similarity=0.038  Sum_probs=95.6

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHHhCCCC-c--hHHHhHHHHHhhhcc--------------------------chHHHH
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVKDGYGN-D--IFVGSAPINIYCNCG--------------------------VTWNEM   60 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~--~~~~~~li~~~~~~~--------------------------~~~~~l   60 (156)
                      ..-..+.+.|++++|...++...+..... .  ...+..+-..|...|                          ..+..+
T Consensus        10 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l   89 (338)
T 3ro2_A           10 LEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNL   89 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHH
Confidence            33445667888999999999887753211 1  356666666676666                          467778


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHC----CCCc-cHHHHHHHHHhhcCCCc--------------------hHHHHHHHHhc
Q 041561           61 IHGYAENEYVEQAISLYKDIIAS----GVKH-DGVTFVAILTPCSHSGL--------------------VYAEVEIFNSM  115 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~--------------------~~~a~~~~~~m  115 (156)
                      -..|...|++++|.+.|++..+.    +-.+ ...++..+-..+...|+                    +++|...++..
T Consensus        90 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a  169 (338)
T 3ro2_A           90 GNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEEN  169 (338)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHH
Confidence            88899999999999999987542    2111 13377778888888999                    99999888775


Q ss_pred             ccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          116 EHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       116 ~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .....-     .+..| ...+|..+-..|...|++++|.+.
T Consensus       170 ~~~~~~-----~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  205 (338)
T 3ro2_A          170 LSLVTA-----LGDRAAQGRAFGNLGNTHYLLGNFRDAVIA  205 (338)
T ss_dssp             HHHHHH-----HTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHh-----cCCHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence            321100     00111 235677788888899999888753

>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=97.24  E-value=0.0053  Score=43.71  Aligned_cols=130  Identities=12%  Similarity=-0.018  Sum_probs=91.7

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHHhCCC-CchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH----C-
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVKDGYG-NDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA----S-   83 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~-   83 (156)
                      .+-..+...++.++|...++...+.... +|.  + ..+       ..|+.+-..|...|++++|.+.|++..+    . 
T Consensus       120 ~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~--~-~~~-------~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~  189 (293)
T 3u3w_A          120 YVAAYVLKKVDYEYCILELKKLLNQQLTGIDV--Y-QNL-------YIENAIANIYAENGYLKKGIDLFEQILKQLEALH  189 (293)
T ss_dssp             HHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCT--T-HHH-------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHcccCHHHHHHHHHHHHHHhcccccH--H-HHH-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcc
Confidence            4556667788999999999998874332 232  1 111       4678888999999999999999999874    1 


Q ss_pred             CCCccHH-HHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-hhhHHHHHHHHhhcCC-HhHHhh
Q 041561           84 GVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-LVVWGDLVSSCQVHSN-VRLAKK  154 (156)
Q Consensus        84 g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~~~~~~li~~~~~~g~-~~~a~~  154 (156)
                      +..+... ++..+-..|.+.|++++|...++....-..     ..+..+. ..+|..+=..|.+.|+ .++|.+
T Consensus       190 ~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~-----~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~  258 (293)
T 3u3w_A          190 DNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISC-----RINSMALIGQLYYQRGECLRKLEYEEAEIED  258 (293)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HTTBCTTHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH-----HcCcHHHHHHHHHHHHHHHHHhCCcHHHHHH
Confidence            3333333 788888999999999999999887632210     0001122 5678888888999994 588764

>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=97.22  E-value=0.004  Score=50.05  Aligned_cols=127  Identities=7%  Similarity=-0.053  Sum_probs=77.9

Q ss_pred             cCCCchHHHHHHHHHHHH------hCC-CCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCC
Q 041561           16 AKLSSLFLGRQILTRIVK------DGY-GNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENE   68 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~------~g~-~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g   68 (156)
                      ...|+.++|.+.++...+      ... +.+...+..+-..|.+.|                    ..|..+-.+|...|
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g  481 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTG  481 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHT
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHcC
Confidence            567777788777777761      012 234455555555555555                    45666666777777


Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCC
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSN  148 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~  148 (156)
                      ++++|.+.|++..+.... +...+..+-..+.+.|++++ .+.|++..+.          -.-+...|..+=.++...|+
T Consensus       482 ~~~~A~~~~~~al~l~P~-~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~----------~P~~~~a~~~lg~~~~~~g~  549 (681)
T 2pzi_A          482 DYDSATKHFTEVLDTFPG-ELAPKLALAATAELAGNTDE-HKFYQTVWST----------NDGVISAAFGLARARSAEGD  549 (681)
T ss_dssp             CHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHHTCCCT-TCHHHHHHHH----------CTTCHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHcCChHH-HHHHHHHHHh----------CCchHHHHHHHHHHHHHcCC
Confidence            788888777776653211 33455556666667777777 6666665322          12245666677777777777


Q ss_pred             HhHHhh
Q 041561          149 VRLAKK  154 (156)
Q Consensus       149 ~~~a~~  154 (156)
                      +++|.+
T Consensus       550 ~~~A~~  555 (681)
T 2pzi_A          550 RVGAVR  555 (681)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777754

>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=97.22  E-value=0.0053  Score=40.06  Aligned_cols=98  Identities=4%  Similarity=-0.014  Sum_probs=75.7

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHH-HHcCCCH--HHHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHG-YAENEYV--EQAISLYKDI   80 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~-~~~~g~~--~~a~~~~~~m   80 (156)
                      +...|..+-..+...|+.++|...++...+..- .+.              ..|..+-.. +...|++  ++|.+.|++.
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~--------------~~~~~la~~l~~~~~~~~~~~A~~~~~~a  107 (177)
T 2e2e_A           43 NSEQWALLGEYYLWQNDYSNSLLAYRQALQLRG-ENA--------------ELYAALATVLYYQASQHMTAQTRAMIDKA  107 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC-SCH--------------HHHHHHHHHHHHHTTTCCCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCH--------------HHHHHHHHHHHHhcCCcchHHHHHHHHHH
Confidence            446677788888899999999999999876531 233              345555566 6788998  9999999998


Q ss_pred             HHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           81 IASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        81 ~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      .+... -+...+..+-..+.+.|+.++|...++....
T Consensus       108 l~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          108 LALDS-NEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhCC-CcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            87532 2356777788888999999999999998844

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.19  E-value=0.0051  Score=45.34  Aligned_cols=137  Identities=8%  Similarity=-0.066  Sum_probs=95.1

Q ss_pred             HhcCCCchHHHHHHHHHHHHhC-CCC----chHHHhHHHHHhhhcc---------------------------chHHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDG-YGN----DIFVGSAPINIYCNCG---------------------------VTWNEMI   61 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g-~~~----~~~~~~~li~~~~~~~---------------------------~~~~~li   61 (156)
                      .+...|+.++|...++...+.- -.+    ...++..+-..|...|                           .+++.+-
T Consensus       112 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg  191 (383)
T 3ulq_A          112 YELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFA  191 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHH
Confidence            3457789999999999886531 112    2355666666666655                           3567777


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHC----CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC-CCChhh
Q 041561           62 HGYAENEYVEQAISLYKDIIAS----GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY-KDDLVV  135 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~-~pd~~~  135 (156)
                      ..|...|++++|.+.|++..+-    +-.+ ...++..+-..+.+.|++++|...++....-..     ..+. .....+
T Consensus       192 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~-----~~~~~~~~~~~  266 (383)
T 3ulq_A          192 TNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFE-----ESNILPSLPQA  266 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HTTCGGGHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH-----hhccchhHHHH
Confidence            8899999999999999887642    2111 123677788888899999999999887743110     0001 223567


Q ss_pred             HHHHHHHHhhcCCHhHHhhh
Q 041561          136 WGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~~  155 (156)
                      +..+-..|...|++++|.+.
T Consensus       267 ~~~l~~~~~~~g~~~~A~~~  286 (383)
T 3ulq_A          267 YFLITQIHYKLGKIDKAHEY  286 (383)
T ss_dssp             HHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHH
Confidence            88888999999999999763

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.18  E-value=0.0023  Score=40.34  Aligned_cols=134  Identities=9%  Similarity=-0.068  Sum_probs=91.9

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC--
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS--   83 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--   83 (156)
                      ++..+-..+...|++++|...++...+..- .++..   .+.       ..+..+-..+...|++++|.+.|++..+.  
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~---~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~   80 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKA---AER-------IAYSNLGNAYIFLGEFETASEYYKKTLLLAR   80 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH---HHH-------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCch---HHH-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            456666777788999999999998765321 11111   111       46677888889999999999999987642  


Q ss_pred             --CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC-CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           84 --GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK-DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        84 --g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~-pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                        +-.+. ...+..+-..+...|++++|.+.++.......     ..+.. ....++..+-..|...|++++|.+.
T Consensus        81 ~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-----~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  151 (164)
T 3ro3_A           81 QLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQ-----ELKDRIGEGRACWSLGNAYTALGNHDQAMHF  151 (164)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH-----HccchHhHHHHHHHHHHHHHHccCHHHHHHH
Confidence              21121 44667777888899999999999887743211     00011 1245677888899999999998763

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.17  E-value=0.0052  Score=45.78  Aligned_cols=134  Identities=6%  Similarity=-0.087  Sum_probs=94.1

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchH---HHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIF---VGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG   84 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~---~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   84 (156)
                      +..+-..+.+.|++++|...++...+.-  ++..   ........--.....|..+-.+|.+.|++++|.+.+++..+..
T Consensus       226 ~~~~g~~~~~~g~~~~Ai~~y~kAl~~~--~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          226 LKNIGNTFFKSQNWEMAIKKYTKVLRYV--EGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHh--hcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            4555567778899999999999876520  0000   0000000000000677888899999999999999999998743


Q ss_pred             CCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           85 VKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        85 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      . -+...+..+-.++.+.|++++|...|+...+.           .| +...+..+-..+...++.+++.+.
T Consensus       304 p-~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l-----------~P~~~~~~~~l~~~~~~~~~~~~a~k~  363 (370)
T 1ihg_A          304 P-SNTKALYRRAQGWQGLKEYDQALADLKKAQEI-----------APEDKAIQAELLKVKQKIKAQKDKEKA  363 (370)
T ss_dssp             T-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             c-hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-----------CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2 25667888888999999999999999988433           34 667788888888888888887653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.14  E-value=0.0052  Score=44.93  Aligned_cols=144  Identities=13%  Similarity=0.026  Sum_probs=97.6

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCC-Cc--hHHHhHHHHHhhhcc--------------------------chH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYG-ND--IFVGSAPINIYCNCG--------------------------VTW   57 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~-~~--~~~~~~li~~~~~~~--------------------------~~~   57 (156)
                      .+...=..+.+.|++++|...|+...+.+.. |.  ..++..+-..|...|                          ..|
T Consensus        11 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   90 (406)
T 3sf4_A           11 ELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKAS   90 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHH
Confidence            3444555667889999999999988776321 11  345666666777666                          456


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHC----CCCc-cHHHHHHHHHhhcCCCc--------------------hHHHHHHH
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIAS----GVKH-DGVTFVAILTPCSHSGL--------------------VYAEVEIF  112 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~--------------------~~~a~~~~  112 (156)
                      ..+-..|...|++++|.+.|++..+.    +-.+ ...++..+-..+...|+                    +++|...+
T Consensus        91 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~  170 (406)
T 3sf4_A           91 GNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFY  170 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHH
Confidence            77888899999999999999887642    1111 13477777888888999                    99998888


Q ss_pred             HhcccccccCCCcCCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          113 NSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       113 ~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ........-     .+..| ...+|..+-..|...|++++|.+.
T Consensus       171 ~~al~~~~~-----~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  209 (406)
T 3sf4_A          171 EENLSLVTA-----LGDRAAQGRAFGNLGNTHYLLGNFRDAVIA  209 (406)
T ss_dssp             HHHHHHHHH-----TTCHHHHHHHHHHHHHHHHHHTBHHHHHHH
T ss_pred             HHHHHHHHh-----ccCcHHHHHHHHHHHHHHHHccCHHHHHHH
Confidence            765322110     00111 235677788888888998888753

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

Probab=97.14  E-value=0.0023  Score=46.77  Aligned_cols=99  Identities=8%  Similarity=-0.035  Sum_probs=69.1

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCc-----hHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGND-----IFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKD   79 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~-----~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~   79 (156)
                      ...+...+..+.+.|+.+.|+++++.|.+.  .||     ..+...|..          +-+......++..+|+.+|++
T Consensus       136 lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~~l~~Lae----------a~v~l~~g~~~~q~A~~~f~E  203 (310)
T 3mv2_B          136 TELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDNEMILNLAE----------SYIKFATNKETATSNFYYYEE  203 (310)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHHHHHHHHHH----------HHHHHHHTCSTTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CccccccchHHHHHHHH----------HHHHHHhCCccHHHHHHHHHH
Confidence            456677889999999999999999999774  462     322222221          111222234589999999999


Q ss_pred             HHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           80 IIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        80 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +.+.  .|+..+-..++.++.+.|++++|...++.+.+
T Consensus       204 l~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          204 LSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             HHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             HHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            8764  35433444555578899999999999997744

>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=97.14  E-value=0.0059  Score=49.64  Aligned_cols=87  Identities=10%  Similarity=0.063  Sum_probs=73.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-C
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-D  132 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d  132 (156)
                      ..|+.+-.+|.+.|++++|.+.|++..+-  .|+ ...|..+-..+.+.|++++|.+.|++..+.           .| +
T Consensus        44 ~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l-----------~P~~  110 (723)
T 4gyw_A           44 AAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI-----------NPAF  110 (723)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----------CCCC
Confidence            78888999999999999999999998764  343 567888888999999999999999987432           34 5


Q ss_pred             hhhHHHHHHHHhhcCCHhHHhh
Q 041561          133 LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       133 ~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ...|+.+=..|...|++++|.+
T Consensus       111 ~~a~~~Lg~~~~~~g~~~eAi~  132 (723)
T 4gyw_A          111 ADAHSNLASIHKDSGNIPEAIA  132 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHH
Confidence            6789999999999999999975

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.13  E-value=0.01  Score=42.65  Aligned_cols=138  Identities=9%  Similarity=-0.025  Sum_probs=88.8

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHh----CCC-CchHHHhHHHHHhhhcc--------------------------c
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKD----GYG-NDIFVGSAPINIYCNCG--------------------------V   55 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~-~~~~~~~~li~~~~~~~--------------------------~   55 (156)
                      +|+.+-..+.+.|++++|...++...+.    |-. .-..+++.+-..|.+ |                          .
T Consensus        78 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~  156 (307)
T 2ifu_A           78 AFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAE  156 (307)
T ss_dssp             HHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHH
Confidence            4555666677778888888777765442    211 113455555555555 4                          4


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHH----CCCCccH-HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIA----SGVKHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      +++.+-..|.+.|++++|.+.|++..+    .+..++. .++..+...+...|++++|...|+... ..   |    ...
T Consensus       157 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~~---p----~~~  228 (307)
T 2ifu_A          157 LIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-SI---P----GFS  228 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TS---T----TST
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-CC---C----CCC
Confidence            677788899999999999999999865    2332222 256666677778899999999999874 21   0    011


Q ss_pred             --CChhhHHHHHHHHhhcCCHhHHhh
Q 041561          131 --DDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       131 --pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                        ........++.++ ..|+.+...+
T Consensus       229 ~~~e~~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          229 GSEDCAALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             TSHHHHHHHHHHHHH-HTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHH-HhcCHHHHHH
Confidence              1123455666666 5677776654

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

Probab=97.13  E-value=0.0024  Score=38.07  Aligned_cols=87  Identities=10%  Similarity=0.080  Sum_probs=65.4

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC--
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD--  132 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd--  132 (156)
                      ..|..+-..+...|++++|.+.|++..+.. ..+...+..+-.++.+.|++++|...++....           ..|+  
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-----------~~p~~~   72 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR-----------YTSTAE   72 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-----------SCSSTT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-----------hCCCcc
Confidence            346667778889999999999999988753 22566788888889999999999999998843           3454  


Q ss_pred             -----hhhHHHHHHHHhhcCCHhHHh
Q 041561          133 -----LVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus       133 -----~~~~~~li~~~~~~g~~~~a~  153 (156)
                           ...+..+-.++...|+.++|.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~a~   98 (111)
T 2l6j_A           73 HVAIRSKLQYRLELAQGAVGSVQIPV   98 (111)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHCCCCCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHhhhH
Confidence                 455666666666777666554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.10  E-value=0.014  Score=42.60  Aligned_cols=137  Identities=5%  Similarity=-0.118  Sum_probs=87.8

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchH----HHhHHHHHhhhcc--------------------------chHHHHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIF----VGSAPINIYCNCG--------------------------VTWNEMIHG   63 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~----~~~~li~~~~~~~--------------------------~~~~~li~~   63 (156)
                      .+...|++++|...+++..+..-..+..    .++.+-..|...|                          .+++.+-..
T Consensus        23 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  102 (373)
T 1hz4_A           23 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEI  102 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            3446788888888888766543112221    3333334444444                          234567778


Q ss_pred             HHcCCCHHHHHHHHHHHHHC----CCC--cc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhH
Q 041561           64 YAENEYVEQAISLYKDIIAS----GVK--HD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVW  136 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~----g~~--p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~  136 (156)
                      +...|++++|.+.+++..+.    +..  |. ...+..+-..+...|++++|...++.......     ..+......+|
T Consensus       103 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~-----~~~~~~~~~~~  177 (373)
T 1hz4_A          103 LFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLS-----SYQPQQQLQCL  177 (373)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT-----TSCGGGGHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhh-----ccCcHHHHHHH
Confidence            88999999999999987642    222  33 34566677788899999999999987643211     00011123567


Q ss_pred             HHHHHHHhhcCCHhHHhhh
Q 041561          137 GDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       137 ~~li~~~~~~g~~~~a~~~  155 (156)
                      ..+-..+...|++++|.+.
T Consensus       178 ~~la~~~~~~g~~~~A~~~  196 (373)
T 1hz4_A          178 AMLIQCSLARGDLDNARSQ  196 (373)
T ss_dssp             HHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHH
Confidence            7788889999999998753

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

Probab=97.08  E-value=0.0076  Score=41.92  Aligned_cols=138  Identities=10%  Similarity=-0.027  Sum_probs=90.5

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCC-CC-chHHHhHHHHHhhh--------cc--------------------c
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGY-GN-DIFVGSAPINIYCN--------CG--------------------V   55 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~-~~~~~~~li~~~~~--------~~--------------------~   55 (156)
                      ..+..+-..+.+.|+.++|...|+...+..- .| ....+..+-.+|.+        .|                    .
T Consensus        53 ~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~  132 (261)
T 3qky_A           53 DAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHEL  132 (261)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTT
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchh
Confidence            4556666777888999999999998877532 12 23445555555555        44                    1


Q ss_pred             hH-----------------HHHHHHHHcCCCHHHHHHHHHHHHHCCCCc--cHHHHHHHHHhhcCC----------CchH
Q 041561           56 TW-----------------NEMIHGYAENEYVEQAISLYKDIIASGVKH--DGVTFVAILTPCSHS----------GLVY  106 (156)
Q Consensus        56 ~~-----------------~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~ll~~~~~~----------~~~~  106 (156)
                      .+                 -.+-..|.+.|++++|.+.|++..+.....  ....+..+-.++.+.          |+++
T Consensus       133 ~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~  212 (261)
T 3qky_A          133 VDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYR  212 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHH
Confidence            22                 445677889999999999999998753221  234566666777655          8999


Q ss_pred             HHHHHHHhcccccccCCCcCCCCCCCh----hhHHHHHHHHhhcCCHhHHhh
Q 041561          107 AEVEIFNSMEHDHEVKPKCLMPYKDDL----VVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       107 ~a~~~~~~m~~~~~~~~~c~~~~~pd~----~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +|...++.....           .|+.    .....+-..+...++++++..
T Consensus       213 ~A~~~~~~~~~~-----------~p~~~~~~~a~~~l~~~~~~~~~~~~~~~  253 (261)
T 3qky_A          213 RAVELYERLLQI-----------FPDSPLLRTAEELYTRARQRLTELEGDAS  253 (261)
T ss_dssp             HHHHHHHHHHHH-----------CTTCTHHHHHHHHHHHHHHHHHHHHTCTT
T ss_pred             HHHHHHHHHHHH-----------CCCChHHHHHHHHHHHHHHHHHHhhhhhH
Confidence            999999998554           3443    344455555666666655443

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.08  E-value=0.0052  Score=45.32  Aligned_cols=96  Identities=11%  Similarity=-0.013  Sum_probs=64.4

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS----GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      .+++.+-..|...|++++|.+.|++..+-    +-.+ ...++..+-..+.+.|+.++|...++....-..     ....
T Consensus       183 ~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~-----~~~~  257 (378)
T 3q15_A          183 QSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSR-----EKVP  257 (378)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH-----HHCG
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH-----hhCC
Confidence            45667777888889999999888876541    2111 234566677778888999999888887743100     0001


Q ss_pred             CCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 KDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .....++..+-..|...|++++|.+.
T Consensus       258 ~~~~~~~~~la~~~~~~g~~~~A~~~  283 (378)
T 3q15_A          258 DLLPKVLFGLSWTLCKAGQTQKAFQF  283 (378)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            22356777778888888998888753

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.08  E-value=0.0082  Score=44.22  Aligned_cols=124  Identities=10%  Similarity=-0.090  Sum_probs=84.7

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHh----CCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKD----GYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      ++..+=..+...|+.++|...+++..+.    +-.|+..             .++..+-..|.+.|++++|.+.|++..+
T Consensus       226 ~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~-------------~~~~~l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          226 TLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLP-------------QAYFLITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHH-------------HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4455555666677777777777766542    2212211             5677888899999999999999988764


Q ss_pred             C----CCCccHHHHHHHHHhhcCCCc---hHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561           83 S----GVKHDGVTFVAILTPCSHSGL---VYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        83 ~----g~~p~~~t~~~ll~~~~~~~~---~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      -    +-......+..+-..+...|+   +++|..+++... .          .......+..+-..|...|++++|.+
T Consensus       293 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~-~----------~~~~~~~~~~la~~y~~~g~~~~A~~  360 (383)
T 3ulq_A          293 YSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKM-L----------YADLEDFAIDVAKYYHERKNFQKASA  360 (383)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTT-C----------HHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCc-C----------HHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            2    222223345667777778888   888888888772 2          12344567788899999999999975

>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=97.06  E-value=0.0033  Score=39.26  Aligned_cols=93  Identities=9%  Similarity=0.086  Sum_probs=69.7

Q ss_pred             HHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCc
Q 041561           10 TVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASG--VKH   87 (156)
Q Consensus        10 ~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p   87 (156)
                      -+=..+.+.|++++|...|+...+.  .|+..             ..|+.+-.+|.+.|++++|.+.|++..+-.  ..+
T Consensus        13 ~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~-------------~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~   77 (127)
T 4gcn_A           13 DLGNAAYKQKDFEKAHVHYDKAIEL--DPSNI-------------TFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRA   77 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--CCCCH-------------HHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccch
Confidence            3345667889999999999998774  34332             567788889999999999999999876521  111


Q ss_pred             c----HHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           88 D----GVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        88 ~----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +    ..+|..+=..+...|++++|.+.|+.-..
T Consensus        78 ~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           78 DYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            1    23566666778889999999999987633

>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=97.04  E-value=0.0077  Score=42.89  Aligned_cols=88  Identities=8%  Similarity=-0.171  Sum_probs=66.5

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~  135 (156)
                      .+..+-..+.+.|++++|.+.|++..+... -+...|..+-..+.+.|++++|...++.....          -.-+...
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~   74 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALEL----------DGQSVKA   74 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS----------CTTCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----------CCCCHHH
Confidence            345566777888999999999988876421 25667777788888899999999998887332          1235677


Q ss_pred             HHHHHHHHhhcCCHhHHhh
Q 041561          136 WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~  154 (156)
                      |..+-.+|...|++++|.+
T Consensus        75 ~~~lg~~~~~~g~~~~A~~   93 (281)
T 2c2l_A           75 HFFLGQCQLEMESYDEAIA   93 (281)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHH
Confidence            8888888999999998875

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.00  E-value=0.015  Score=43.71  Aligned_cols=146  Identities=8%  Similarity=-0.068  Sum_probs=92.0

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc------------------------------
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG------------------------------   54 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~------------------------------   54 (156)
                      ..++..+-..+.+.|+.+.|...++...+.. +-+..++..+-..|...+                              
T Consensus       247 ~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  325 (472)
T 4g1t_A          247 TDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKK  325 (472)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            3456667777888899999999999887653 223444544433332211                              


Q ss_pred             ---------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHH--HHHHHHH-hhcCCCchHHHHHHHHhcccccccC
Q 041561           55 ---------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGV--TFVAILT-PCSHSGLVYAEVEIFNSMEHDHEVK  122 (156)
Q Consensus        55 ---------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--t~~~ll~-~~~~~~~~~~a~~~~~~m~~~~~~~  122 (156)
                               ..|..+-..|...|++++|.+.|++..+....|...  .+..+-. ...+.|+.++|...|.+..+-   .
T Consensus       326 a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i---~  402 (472)
T 4g1t_A          326 ADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKI---N  402 (472)
T ss_dssp             HHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHS---C
T ss_pred             HhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---C
Confidence                     567888899999999999999999988765444332  1222221 234778999998887765221   1


Q ss_pred             CCc----------------CCC-CCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          123 PKC----------------LMP-YKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       123 ~~c----------------~~~-~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      |+.                ... -+.+..+|+.+=..|...|++++|.+
T Consensus       403 ~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~  451 (472)
T 4g1t_A          403 QKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADE  451 (472)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC----
T ss_pred             cccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            110                000 12356788888888999999988865

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=96.99  E-value=0.021  Score=41.66  Aligned_cols=141  Identities=6%  Similarity=-0.076  Sum_probs=87.4

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHh----CCC--C-chHHHhHHHHHhhhcc-------------------------ch
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKD----GYG--N-DIFVGSAPINIYCNCG-------------------------VT   56 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~--~-~~~~~~~li~~~~~~~-------------------------~~   56 (156)
                      ..+-..+...|++++|...++...+.    |-.  | ....+..+-..|...|                         ..
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  176 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  176 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHH
Confidence            34455566778888888888876542    221  2 2334444555555555                         24


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-cHHHHH-----HHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVKH-DGVTFV-----AILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~-----~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      |..+-..+...|++++|.+.+++.....-.+ +...+.     .....+...|+.++|...++.......      ....
T Consensus       177 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~------~~~~  250 (373)
T 1hz4_A          177 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEF------ANNH  250 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCC------TTCG
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCC------Ccch
Confidence            6667778889999999999999886421111 111121     233446689999999999998843210      0000


Q ss_pred             CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          131 DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       131 pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .....+..+-..+...|++++|.+.
T Consensus       251 ~~~~~~~~la~~~~~~g~~~~A~~~  275 (373)
T 1hz4_A          251 FLQGQWRNIARAQILLGEFEPAEIV  275 (373)
T ss_dssp             GGHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            1123566777889999999988753

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

Probab=96.97  E-value=0.011  Score=36.50  Aligned_cols=94  Identities=16%  Similarity=0.033  Sum_probs=74.0

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .+..+-..+.+.|++++|...++...+..  |+..             ..|..+-.++...|++++|.+.|++..+....
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~-------------~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~   83 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE--PERE-------------EAWRSLGLTQAENEKDGLAIIALNHARMLDPK   83 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCCH-------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            34445567778999999999999988753  4322             56677777888999999999999998874322


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                       +...+..+-..+.+.|+.++|...++...
T Consensus        84 -~~~~~~~la~~~~~~g~~~~A~~~~~~al  112 (121)
T 1hxi_A           84 -DIAVHAALAVSHTNEHNANAALASLRAWL  112 (121)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             45577788888999999999999999874

>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=96.96  E-value=0.012  Score=39.25  Aligned_cols=91  Identities=11%  Similarity=0.008  Sum_probs=71.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCcc--------------HHHHHHHHHhhcCCCchHHHHHHHHhccccc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASG-VKHD--------------GVTFVAILTPCSHSGLVYAEVEIFNSMEHDH  119 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~  119 (156)
                      ..|..+-..+...|++++|.+.|++..+.. -.|+              ...+..+-.++.+.|++++|...++..... 
T Consensus        39 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~-  117 (198)
T 2fbn_A           39 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI-  117 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh-
Confidence            456667778889999999999999987632 1221              267778888888999999999999988443 


Q ss_pred             ccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          120 EVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       120 ~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                               ...+...|..+-.+|...|++++|.+.
T Consensus       118 ---------~p~~~~~~~~lg~~~~~~~~~~~A~~~  144 (198)
T 2fbn_A          118 ---------DKNNVKALYKLGVANMYFGFLEEAKEN  144 (198)
T ss_dssp             ---------STTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             ---------CcccHHHHHHHHHHHHHcccHHHHHHH
Confidence                     234678888899999999999999753

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=96.96  E-value=0.026  Score=41.52  Aligned_cols=137  Identities=7%  Similarity=-0.054  Sum_probs=80.3

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHh----CCCC-chHHHhHHHHHhhhcc-------------------------ch
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKD----GYGN-DIFVGSAPINIYCNCG-------------------------VT   56 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~~-------------------------~~   56 (156)
                      +++.+=..+...|+.++|...++...+.    |-.+ ...+++.|=..|.+.|                         .+
T Consensus       184 ~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  263 (378)
T 3q15_A          184 SLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKV  263 (378)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHH
Confidence            4556667778889999999988887552    1111 1233444444444444                         34


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCccHHHHHHHHHhhcCCCc---hHHHHHHHHhcccccccCCCcCCCC
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIAS----GVKHDGVTFVAILTPCSHSGL---VYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~t~~~ll~~~~~~~~---~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      +..+-..|.+.|++++|.+.|++..+-    +-......+..+-..+...++   +++|...++.. ..          .
T Consensus       264 ~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~-~~----------~  332 (378)
T 3q15_A          264 LFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK-NL----------H  332 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT-TC----------H
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC-CC----------h
Confidence            555666677777777777777766542    112223344444455555666   66666666653 11          1


Q ss_pred             CCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          130 KDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       130 ~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ......+..+-..|...|++++|.+
T Consensus       333 ~~~~~~~~~la~~y~~~g~~~~A~~  357 (378)
T 3q15_A          333 AYIEACARSAAAVFESSCHFEQAAA  357 (378)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            2233456677788889999988865

>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=96.96  E-value=0.0077  Score=39.47  Aligned_cols=134  Identities=7%  Similarity=-0.018  Sum_probs=89.9

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc---------------c---hHHHHHHH--HHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG---------------V---TWNEMIHG--YAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~---------------~---~~~~li~~--~~~   66 (156)
                      .+...-..+.+.|++++|...++...+.. +.+...+..+-..|.+.|               .   .+..+...  +..
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~   86 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQ   86 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHHHHHHHHHHHHh
Confidence            34555667788999999999999875532 235566777777777666               0   11111111  111


Q ss_pred             CCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC---ChhhHHHHHHH
Q 041561           67 NEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD---DLVVWGDLVSS  142 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p---d~~~~~~li~~  142 (156)
                      .+...++.+.|++..+.  .| +...+..+-..+.+.|+.++|...|+...+.           .|   +...+..+...
T Consensus        87 ~~~~~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~-----------~p~~~~~~a~~~l~~~  153 (176)
T 2r5s_A           87 QAAESPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKV-----------NLGAQDGEVKKTFMDI  153 (176)
T ss_dssp             HHTSCHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-----------CTTTTTTHHHHHHHHH
T ss_pred             hcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHh-----------CcccChHHHHHHHHHH
Confidence            12223456667666653  34 4567777888888999999999999988433           34   35688999999


Q ss_pred             HhhcCCHhHHhh
Q 041561          143 CQVHSNVRLAKK  154 (156)
Q Consensus       143 ~~~~g~~~~a~~  154 (156)
                      +...|+.++|..
T Consensus       154 ~~~~g~~~~A~~  165 (176)
T 2r5s_A          154 LSALGQGNAIAS  165 (176)
T ss_dssp             HHHHCSSCHHHH
T ss_pred             HHHhCCCCcHHH
Confidence            999999998865

>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=96.93  E-value=0.0068  Score=48.73  Aligned_cols=130  Identities=6%  Similarity=-0.099  Sum_probs=97.3

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGY   64 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~   64 (156)
                      ...+..+-..+.+.|+.++|...++...+.. +-+...|..+=.+|.+.|                    ..|..+-.+|
T Consensus       433 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~  511 (681)
T 2pzi_A          433 VELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFPGELAPKLALAATA  511 (681)
T ss_dssp             SHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence            4556667778888999999999999987643 235567776666666666                    6788888899


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-hhhHHHHHHHH
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-LVVWGDLVSSC  143 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~~~~~~li~~~  143 (156)
                      .+.|++++ .+.|++..+... -+...|..+-.++.+.|+.++|.+.|++..+           +.|+ ...|..+-.++
T Consensus       512 ~~~g~~~~-~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-----------l~P~~~~a~~~~~~~~  578 (681)
T 2pzi_A          512 ELAGNTDE-HKFYQTVWSTND-GVISAAFGLARARSAEGDRVGAVRTLDEVPP-----------TSRHFTTARLTSAVTL  578 (681)
T ss_dssp             HHHTCCCT-TCHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHTSCT-----------TSTTHHHHHHHHHHHT
T ss_pred             HHcCChHH-HHHHHHHHHhCC-chHHHHHHHHHHHHHcCCHHHHHHHHHhhcc-----------cCcccHHHHHHHHHHH
Confidence            99999999 999999877432 2456788888999999999999999998843           3454 56677777777


Q ss_pred             hhcCC
Q 041561          144 QVHSN  148 (156)
Q Consensus       144 ~~~g~  148 (156)
                      ...|+
T Consensus       579 ~~~~~  583 (681)
T 2pzi_A          579 LSGRS  583 (681)
T ss_dssp             C----
T ss_pred             HccCC
Confidence            66554

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

Probab=96.91  E-value=0.0093  Score=46.30  Aligned_cols=123  Identities=6%  Similarity=-0.107  Sum_probs=87.5

Q ss_pred             hcCCCchHHHHHHHHHHHHh--C-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH---C---CC
Q 041561           15 CAKLSSLFLGRQILTRIVKD--G-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA---S---GV   85 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~--g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~---g~   85 (156)
                      +-..|++++|+.++++..+.  . +.|+-..  .+        .+++.|..+|...|++++|..++++..+   .   .-
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~--~a--------~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~  388 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLY--VL--------RLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHN  388 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHH--HH--------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHH--HH--------HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCC
Confidence            45789999999999887542  1 2232211  11        6789999999999999999999998753   1   24


Q ss_pred             CccHH-HHHHHHHhhcCCCchHHHHHHHHhcc----cccccCCCcCCCCCCChhh-HHHHHHHHhhcCCHhHHhh
Q 041561           86 KHDGV-TFVAILTPCSHSGLVYAEVEIFNSME----HDHEVKPKCLMPYKDDLVV-WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        86 ~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~----~~~~~~~~c~~~~~pd~~~-~~~li~~~~~~g~~~~a~~  154 (156)
                      +|+.. +++.|-..|...|++++|..++++-.    ..+|       +-.|++.. .+.+-+++...|.+++|+.
T Consensus       389 Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG-------~~Hp~~~~~~~~l~~~~~e~~~~~~ae~  456 (490)
T 3n71_A          389 NAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHG-------PSHPITKDLEAMRMQTEMELRMFRQNEF  456 (490)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-------TTSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhC-------CCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56554 78889999999999999999887653    2234       14566644 4455577777888887764

>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=96.89  E-value=0.0074  Score=44.19  Aligned_cols=90  Identities=13%  Similarity=-0.009  Sum_probs=74.5

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcc--------------HHHHHHHHHhhcCCCchHHHHHHHHhcccccc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHD--------------GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHE  120 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  120 (156)
                      ..|..+-..|.+.|++++|.+.|++..+......              ...|..+-..+.+.|++++|...++.....  
T Consensus       148 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--  225 (336)
T 1p5q_A          148 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL--  225 (336)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--
Confidence            5677788889999999999999999877432221              478888889999999999999999988443  


Q ss_pred             cCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          121 VKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       121 ~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                              -..+...|..+=.+|...|++++|.+
T Consensus       226 --------~p~~~~a~~~lg~~~~~~g~~~~A~~  251 (336)
T 1p5q_A          226 --------DSNNEKGLSRRGEAHLAVNDFELARA  251 (336)
T ss_dssp             --------CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             --------CCCcHHHHHHHHHHHHHCCCHHHHHH
Confidence                    23477889999999999999999975

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

Probab=96.84  E-value=0.0043  Score=44.30  Aligned_cols=109  Identities=12%  Similarity=-0.027  Sum_probs=80.6

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHH-hhhcc--------------------chHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINI-YCNCG--------------------VTWNEMIHG   63 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~-~~~~~--------------------~~~~~li~~   63 (156)
                      ...+..+-..+.+.|+.++|...++.....  .|+.......... +.+.+                    ..+..+-..
T Consensus       151 ~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~  228 (287)
T 3qou_A          151 GEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQ  228 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHH
Confidence            456777888889999999999999988654  2444332222221 21111                    677888899


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCC-ccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           64 YAENEYVEQAISLYKDIIASGVK-HDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +...|++++|.+.|.+..+.... .+...+..+...+...|+.+++...+++-
T Consensus       229 l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          229 LHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXYRRQ  281 (287)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            99999999999999999885433 23668889999999999999988877653

>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=96.83  E-value=0.012  Score=47.49  Aligned_cols=137  Identities=7%  Similarity=-0.092  Sum_probs=70.3

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCC---------CC------------chHHHhHHHHHhhhcc------------
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGY---------GN------------DIFVGSAPINIYCNCG------------   54 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~---------~~------------~~~~~~~li~~~~~~~------------   54 (156)
                      |-..+...-+.|+++.|+++|+.+.+...         .|            ...+|...++..-+.|            
T Consensus       381 wl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A  460 (679)
T 4e6h_A          381 AFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKC  460 (679)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            44455566677889999999998876420         13            1224544444433332            


Q ss_pred             ------chHHHHHH---HHHc-CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCC
Q 041561           55 ------VTWNEMIH---GYAE-NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPK  124 (156)
Q Consensus        55 ------~~~~~li~---~~~~-~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~  124 (156)
                            .++...+.   .-.+ .++++.|.++|+...+. ..-+...+...++.....|+.+.|+.+|+.....      
T Consensus       461 ~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~------  533 (679)
T 4e6h_A          461 RRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDK------  533 (679)
T ss_dssp             HHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTT------
T ss_pred             HHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHh------
Confidence                  01111111   1112 23356666666665543 1223334445555555556666666666655322      


Q ss_pred             cCCCCC---CChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          125 CLMPYK---DDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       125 c~~~~~---pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                          ..   -....|..++.--...|+.+.+.+|
T Consensus       534 ----~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v  563 (679)
T 4e6h_A          534 ----ISDSHLLKMIFQKVIFFESKVGSLNSVRTL  563 (679)
T ss_dssp             ----SSSTTHHHHHHHHHHHHHHHTCCSHHHHHH
T ss_pred             ----cCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence                11   1235566666666666666666554

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

Probab=96.80  E-value=0.0017  Score=38.78  Aligned_cols=96  Identities=9%  Similarity=-0.063  Sum_probs=66.4

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      ++...|..+-..+.+.|+.++|...|+...+..  |+..             ..|..+-.++.+.|++++|.+.|++..+
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--p~~~-------------~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ--PQNP-------------VGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--TTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCCH-------------HHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            345667777788899999999999999987753  3221             5667778889999999999999999886


Q ss_pred             CCCCcc-------HHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           83 SGVKHD-------GVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        83 ~g~~p~-------~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .  .|+       ...+..+-.++...|+.+.+...++.+
T Consensus        67 ~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  104 (111)
T 2l6j_A           67 Y--TSTAEHVAIRSKLQYRLELAQGAVGSVQIPVVEVDEL  104 (111)
T ss_dssp             S--CSSTTSHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSC
T ss_pred             h--CCCccHHHHHHHHHHHHHHHHHHHHhHhhhHhHHHHh
Confidence            4  344       233444444444555555554444443

>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=96.80  E-value=0.024  Score=49.41  Aligned_cols=137  Identities=16%  Similarity=0.129  Sum_probs=85.4

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----------------chHHHHHHHHHcCCCH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----------------VTWNEMIHGYAENEYV   70 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----------------~~~~~li~~~~~~g~~   70 (156)
                      .|..+...+.+.|+++.|.+.+...      .|..+|.-+-.+|...|                ..+..++.-|-+.|.+
T Consensus      1223 ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~f 1296 (1630)
T 1xi4_A         1223 NFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYF 1296 (1630)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCH
Confidence            4555555666666666665555544      33455554444443332                3566788889999999


Q ss_pred             HHHHHHHHHHHH-CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCH
Q 041561           71 EQAISLYKDIIA-SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNV  149 (156)
Q Consensus        71 ~~a~~~~~~m~~-~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~  149 (156)
                      ++|.++++.-.. ..-+...+|.-.++.+-.+.+++.+..++|..-..-..+     ....-+...|.-++..|.+.|++
T Consensus      1297 eEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~-----~r~~e~~~lW~elv~LY~~~~e~ 1371 (1630)
T 1xi4_A         1297 EELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKV-----LRAAEQAHLWAELVFLYDKYEEY 1371 (1630)
T ss_pred             HHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchH-----hHHHHHHHHHHHHHHHHHhcccH
Confidence            999999966543 233444445555666666777888777777644111000     00012678899999999999999


Q ss_pred             hHHhh
Q 041561          150 RLAKK  154 (156)
Q Consensus       150 ~~a~~  154 (156)
                      +.|..
T Consensus      1372 dnA~~ 1376 (1630)
T 1xi4_A         1372 DNAII 1376 (1630)
T ss_pred             HHHHH
Confidence            99973

>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=96.76  E-value=0.02  Score=40.73  Aligned_cols=96  Identities=6%  Similarity=-0.102  Sum_probs=75.0

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      +...+..+-..+.+.|+.++|...++...+.  .| +.              ..|..+-.+|.+.|++++|.+.|++..+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~--------------~~~~~la~~~~~~~~~~~A~~~~~~al~   66 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVA--------------VYYTNRALCYLKMQQPEQALADCRRALE   66 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccH--------------HHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            3456667777888999999999999998775  24 34              5667777888899999999999998876


Q ss_pred             CCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           83 SGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        83 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .. .-+...+..+-.++.+.|++++|...|....
T Consensus        67 ~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           67 LD-GQSVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (281)
T ss_dssp             SC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            43 2245677778888889999999999888763

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

Probab=96.72  E-value=0.019  Score=32.57  Aligned_cols=80  Identities=11%  Similarity=0.160  Sum_probs=58.8

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..+...|++++|.+.|++..+.. ..+...+..+-..+.+.|++++|...++.....          ...+..
T Consensus        10 ~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~----------~p~~~~   78 (91)
T 1na3_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL----------DPNNAE   78 (91)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc----------CCCCHH
Confidence            355667778889999999999999987653 224567788888899999999999999988443          122455


Q ss_pred             hHHHHHHHHhh
Q 041561          135 VWGDLVSSCQV  145 (156)
Q Consensus       135 ~~~~li~~~~~  145 (156)
                      .+..+-..+..
T Consensus        79 ~~~~l~~~~~~   89 (91)
T 1na3_A           79 AKQNLGNAKQK   89 (91)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            56555555544

>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=96.69  E-value=0.0094  Score=37.10  Aligned_cols=91  Identities=10%  Similarity=0.006  Sum_probs=66.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC---
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD---  132 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd---  132 (156)
                      .+..+=..+.+.|++++|.+.|++..+-. .-+...|..+-.++.+.|++++|.+.++...+-..       ...++   
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~-------~~~~~~~~   81 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGR-------ETRADYKL   81 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-------HTTCCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCc-------ccchhhHH
Confidence            45556667889999999999999987743 22456788888899999999999999988743210       01111   


Q ss_pred             -hhhHHHHHHHHhhcCCHhHHhh
Q 041561          133 -LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       133 -~~~~~~li~~~~~~g~~~~a~~  154 (156)
                       ..+|..+=..+...|++++|.+
T Consensus        82 ~a~~~~~lg~~~~~~~~~~~A~~  104 (127)
T 4gcn_A           82 IAKAMSRAGNAFQKQNDLSLAVQ  104 (127)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHH
Confidence             2356666677888999998875

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

Probab=96.68  E-value=0.0077  Score=40.73  Aligned_cols=82  Identities=10%  Similarity=0.041  Sum_probs=64.6

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccH-HHHHH----------------HHHhhcCCCchHHHHHHHHhcccccccCCC
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDG-VTFVA----------------ILTPCSHSGLVYAEVEIFNSMEHDHEVKPK  124 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~----------------ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~  124 (156)
                      ..+...|++++|.+.|++..+.  .|+. ..|..                +-..+.+.|++++|...|+...+.      
T Consensus        12 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~------   83 (208)
T 3urz_A           12 SAAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK------   83 (208)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH------
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH------
Confidence            3456889999999999998764  3433 34555                777888999999999999988543      


Q ss_pred             cCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          125 CLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       125 c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                          -+-+...|..+=..|...|++++|.+.
T Consensus        84 ----~p~~~~~~~~lg~~~~~~g~~~~A~~~  110 (208)
T 3urz_A           84 ----APNNVDCLEACAEMQVCRGQEKDALRM  110 (208)
T ss_dssp             ----CTTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             ----CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence                133678899999999999999999763

>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=96.56  E-value=0.017  Score=46.59  Aligned_cols=126  Identities=12%  Similarity=0.078  Sum_probs=93.8

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHh-C-CCCchHHHhHHHHHhhhcc-------------------chHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKD-G-YGNDIFVGSAPINIYCNCG-------------------VTWNEMIHGYA   65 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~-g-~~~~~~~~~~li~~~~~~~-------------------~~~~~li~~~~   65 (156)
                      .|...++...+.|+++.|+++|+...+. + ..+...+..+.|...+...                   ..|...+.-..
T Consensus       436 vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~  515 (679)
T 4e6h_A          436 VYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLI  515 (679)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHH
Confidence            5777788888889999999999999876 3 3455666666666554321                   45667777777


Q ss_pred             cCCCHHHHHHHHHHHHHCCCC--ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           66 ENEYVEQAISLYKDIIASGVK--HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      ..|+.+.|..+|+........  -....|...++.-.+.|+.+.+..+.+.+.+.           .|+......+++=|
T Consensus       516 ~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~-----------~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          516 YVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK-----------FPEVNKLEEFTNKY  584 (679)
T ss_dssp             HHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH-----------STTCCHHHHHHHHT
T ss_pred             hCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----------CCCCcHHHHHHHHh
Confidence            789999999999998775432  24568999999999999999999999999554           46655555555444

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

Probab=96.49  E-value=0.04  Score=40.29  Aligned_cols=104  Identities=10%  Similarity=-0.070  Sum_probs=76.7

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhH------HHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHH
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSA------PINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDII   81 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~------li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   81 (156)
                      +..+=..+.+.|++++|...|+...+.  .|+...+..      .+..+  ....|..+-.+|.+.|++++|.+.|++..
T Consensus       182 ~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l--~~~~~~nla~~~~~~g~~~~A~~~~~~al  257 (338)
T 2if4_A          182 RKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAV--KNPCHLNIAACLIKLKRYDEAIGHCNIVL  257 (338)
T ss_dssp             HHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHH--HTHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHH--HHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            445556778899999999999998764  244332110      00000  00377888899999999999999999987


Q ss_pred             HCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           82 ASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        82 ~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      +.. .-+...|..+-.++.+.|++++|...|+...
T Consensus       258 ~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al  291 (338)
T 2if4_A          258 TEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQ  291 (338)
T ss_dssp             HHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTT
T ss_pred             HhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            743 2356788888899999999999999999884

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.47  E-value=0.02  Score=43.75  Aligned_cols=89  Identities=8%  Similarity=-0.125  Sum_probs=66.4

Q ss_pred             CCCchHHHHHHHHHHHHh--C-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH-----C-CCCc
Q 041561           17 KLSSLFLGRQILTRIVKD--G-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA-----S-GVKH   87 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~--g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~-g~~p   87 (156)
                      ..|++++|+.++++..+.  . +.|+-.  ..+        .+++.|..+|...|++++|..++++..+     - .-+|
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp--~~a--------~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp  379 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNV--YML--------HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSL  379 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSH--HHH--------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhch--HHH--------HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCCh
Confidence            456778888888876441  1 222221  011        6789999999999999999999999763     1 2466


Q ss_pred             cHH-HHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           88 DGV-TFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        88 ~~~-t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +.. +++.|-..|...|++++|..++++-
T Consensus       380 ~~a~~l~nLa~~~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          380 NVASMWLKLGRLYMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCHHHHHHHHHHH
Confidence            665 6889999999999999999988765

>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=96.44  E-value=0.11  Score=35.11  Aligned_cols=90  Identities=8%  Similarity=-0.040  Sum_probs=52.5

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCC----CHHHHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENE----YVEQAISLYKDI   80 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g----~~~~a~~~~~~m   80 (156)
                      +.++..+=..+...++.++|...|+...+.|   ++..+..|              =..|.. +    ++++|.+.|++-
T Consensus        18 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~l--------------g~~y~~-~g~~~~~~~A~~~~~~A   79 (212)
T 3rjv_A           18 RRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALL--------------AQLKIR-NPQQADYPQARQLAEKA   79 (212)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHH--------------HHHTTS-STTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHH--------------HHHHHc-CCCCCCHHHHHHHHHHH
Confidence            3344455555666789999999999887765   34333333              223333 3    666666666666


Q ss_pred             HHCCCCccHHHHHHHHHhhcC----CCchHHHHHHHHhc
Q 041561           81 IASGVKHDGVTFVAILTPCSH----SGLVYAEVEIFNSM  115 (156)
Q Consensus        81 ~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m  115 (156)
                      .+.|   +...+..+-..+..    .++.++|...|+.-
T Consensus        80 ~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A  115 (212)
T 3rjv_A           80 VEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDA  115 (212)
T ss_dssp             HHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHH
T ss_pred             HHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHH
Confidence            5544   33344444444444    56666666666665

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

Probab=96.43  E-value=0.018  Score=37.01  Aligned_cols=59  Identities=7%  Similarity=0.026  Sum_probs=24.8

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .|..+-.+|.+.|++++|.+.++...+.. ..+...|..+-.++...|++++|...|...
T Consensus        65 ~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~a  123 (162)
T 3rkv_A           65 LYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLL  123 (162)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHH
Confidence            34444444444444444444444444321 112333344444444444444444444443

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

Probab=96.39  E-value=0.022  Score=36.52  Aligned_cols=81  Identities=7%  Similarity=-0.070  Sum_probs=59.7

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHh--------C---------CCCchHHHhHHHHHhhhcc----------------
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKD--------G---------YGNDIFVGSAPINIYCNCG----------------   54 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~--------g---------~~~~~~~~~~li~~~~~~~----------------   54 (156)
                      +...=..+.+.|+++.|...|....+.        .         -+.+...|..+-.+|.+.|                
T Consensus        14 ~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~   93 (162)
T 3rkv_A           14 LRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE   93 (162)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            334445667889999999999987664        0         1123456777777777776                


Q ss_pred             ----chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHH
Q 041561           55 ----VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGV   90 (156)
Q Consensus        55 ----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   90 (156)
                          ..|..+-.+|...|++++|.+.|+...+-  .|+..
T Consensus        94 p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~  131 (162)
T 3rkv_A           94 ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAA  131 (162)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGH
T ss_pred             CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCH
Confidence                56788889999999999999999998763  45544

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.36  E-value=0.07  Score=41.28  Aligned_cols=135  Identities=11%  Similarity=0.079  Sum_probs=79.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHH-------------hh--h-----------ccchHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINI-------------YC--N-----------CGVTWNEM   60 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~-------------~~--~-----------~~~~~~~l   60 (156)
                      .|-.-+..+.+.|+++.|..+++...+.  +.+...|......             +.  .           ....|-..
T Consensus       215 lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y  292 (493)
T 2uy1_A          215 VYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINH  292 (493)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHH
Confidence            3444555667789999999999999887  4444444332221             10  0           00345555


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHH
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLV  140 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li  140 (156)
                      +.-.-+.+.++.|.++|+.....+..++.....+.+.... .++.+.|+.+|+...+..+          -+...|...+
T Consensus       293 ~~~~~r~~~~~~AR~i~~~A~~~~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~~----------~~~~~~~~yi  361 (493)
T 2uy1_A          293 LNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKHP----------DSTLLKEEFF  361 (493)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHCT----------TCHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHCC----------CCHHHHHHHH
Confidence            5555567789999999998822222222222223333322 2368999999998755432          1233455666


Q ss_pred             HHHhhcCCHhHHhh
Q 041561          141 SSCQVHSNVRLAKK  154 (156)
Q Consensus       141 ~~~~~~g~~~~a~~  154 (156)
                      .-....|+.++|+.
T Consensus       362 d~e~~~~~~~~aR~  375 (493)
T 2uy1_A          362 LFLLRIGDEENARA  375 (493)
T ss_dssp             HHHHHHTCHHHHHH
T ss_pred             HHHHHcCCHHHHHH
Confidence            66666777777664

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=96.24  E-value=0.038  Score=36.31  Aligned_cols=101  Identities=7%  Similarity=-0.110  Sum_probs=69.9

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhC-CCC-chHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH-
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDG-YGN-DIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA-   82 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g-~~~-~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-   82 (156)
                      .++..+-..+...|++++|...+++..+.- -.+ +...   ..       ..+..+-..+...|++++|.+.|++... 
T Consensus        67 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~---~~-------~~~~~lg~~~~~~g~~~~A~~~~~~al~~  136 (203)
T 3gw4_A           67 RALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLA---AS-------ANAYEVATVALHFGDLAGARQEYEKSLVY  136 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHH---HH-------HHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHH---HH-------HHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            345666677788999999999999875531 112 2100   00       4567777888899999999999998763 


Q ss_pred             ---CCCC-ccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           83 ---SGVK-HDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        83 ---~g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                         .+.. .-..++..+-..+.+.|++++|.+.+++..
T Consensus       137 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  174 (203)
T 3gw4_A          137 AQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRAR  174 (203)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence               2211 113345677788889999999999888764

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

Probab=96.23  E-value=0.027  Score=42.94  Aligned_cols=94  Identities=6%  Similarity=-0.038  Sum_probs=69.6

Q ss_pred             HHHhcCCCchHHHHHHHHHHHHh--C-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH------
Q 041561           12 LSSCAKLSSLFLGRQILTRIVKD--G-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA------   82 (156)
Q Consensus        12 l~~~~~~~~~~~a~~~~~~m~~~--g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~------   82 (156)
                      +..+.+.|+.++|+.+++...+.  . +.|+-..  .+        .+++.|..+|...|++++|++++++...      
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~--~~--------~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~l  363 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIY--QL--------KVLDCAMDACINLGLLEEALFYGTRTMEPYRIFF  363 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHH--HH--------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchH--HH--------HHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHc
Confidence            44455678888888888877642  2 2222211  11        6789999999999999999999998763      


Q ss_pred             CCCCccHH-HHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           83 SGVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        83 ~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      -..+|+.- +++.|-..|...|++++|..++++-
T Consensus       364 g~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~A  397 (429)
T 3qwp_A          364 PGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLA  397 (429)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            13456654 6888999999999999999887765

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.19  E-value=0.0077  Score=37.76  Aligned_cols=96  Identities=7%  Similarity=-0.011  Sum_probs=67.9

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCC-ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS----GVK-HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      ..+..+-..|...|++++|.+.|++..+.    +-. .-..++..+-..+...|++++|...++.......-     .+.
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~-----~~~   84 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQ-----LKD   84 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-----TTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH-----hCC
Confidence            45677778888999999999999987642    111 11246777888888999999999999887432110     000


Q ss_pred             CC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 KD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+ ....+..+-..+...|++++|.+.
T Consensus        85 ~~~~~~~~~~l~~~~~~~~~~~~A~~~  111 (164)
T 3ro3_A           85 RAVEAQSCYSLGNTYTLLQDYEKAIDY  111 (164)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            11 145677788899999999999763

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

Probab=96.18  E-value=0.023  Score=41.54  Aligned_cols=88  Identities=11%  Similarity=-0.037  Sum_probs=71.2

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHH------------------HHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGV------------------TFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------------------t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      ..|..+-..+.+.|++++|.+.|++....  .|+..                  .|..+-.++.+.|++++|...++...
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al  257 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVL  257 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45666777888999999999999997653  34443                  77788888899999999999999884


Q ss_pred             cccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          117 HDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       117 ~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      ..          -..+...|..+=.+|...|++++|.+
T Consensus       258 ~~----------~p~~~~a~~~lg~a~~~~g~~~~A~~  285 (338)
T 2if4_A          258 TE----------EEKNPKALFRRGKAKAELGQMDSARD  285 (338)
T ss_dssp             HH----------CTTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             Hh----------CCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            43          13367889999999999999999976

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.18  E-value=0.036  Score=39.91  Aligned_cols=105  Identities=10%  Similarity=-0.030  Sum_probs=68.1

Q ss_pred             HHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----------------------chHHHHHHHHHcCCC
Q 041561           12 LSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----------------------VTWNEMIHGYAENEY   69 (156)
Q Consensus        12 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----------------------~~~~~li~~~~~~g~   69 (156)
                      ...+...|++++|.++|+.+...+  |+....-.+-..|.+.+                      ..+-.+=.++.+.|+
T Consensus       109 A~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~  186 (282)
T 4f3v_A          109 AACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLAL  186 (282)
T ss_dssp             HHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCC
Confidence            345566788888888888776543  43322222222333333                      134445567889999


Q ss_pred             HHHHHHHHHHHHHCCCCccH--HHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           70 VEQAISLYKDIIASGVKHDG--VTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        70 ~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      +++|++.|++-......|..  ......-.++.+.|+.++|..+|+++...
T Consensus       187 ~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          187 FTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            99999999998754332642  24445556667899999999999999543

>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=96.15  E-value=0.036  Score=42.31  Aligned_cols=90  Identities=12%  Similarity=-0.096  Sum_probs=73.0

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-cc-------------HHHHHHHHHhhcCCCchHHHHHHHHhcccccc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVK-HD-------------GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHE  120 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~-------------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  120 (156)
                      ..|..+-..|.+.|++++|...|++..+.... ++             ...|..+-.++.+.|++++|...++.....  
T Consensus       269 ~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--  346 (457)
T 1kt0_A          269 AIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL--  346 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--
Confidence            46777788899999999999999998763211 11             477888888999999999999999988443  


Q ss_pred             cCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          121 VKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       121 ~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                              -..+...|..+=.+|...|++++|.+
T Consensus       347 --------~p~~~~a~~~~g~a~~~~g~~~~A~~  372 (457)
T 1kt0_A          347 --------DSANEKGLYRRGEAQLLMNEFESAKG  372 (457)
T ss_dssp             --------STTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             --------CCccHHHHHHHHHHHHHccCHHHHHH
Confidence                    23467889999999999999999975

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

Probab=96.12  E-value=0.019  Score=34.02  Aligned_cols=86  Identities=6%  Similarity=0.044  Sum_probs=63.1

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..|...|++++|.+.|++..+.... +...|..+-.++.+.|++++|.+.++.......        -.++..
T Consensus         8 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~--------~~~~~~   78 (100)
T 3ma5_A            8 FTRYALAQEHLKHDNASRALALFEELVETDPD-YVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAR--------EEGTQK   78 (100)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH--------HHSCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhh--------cCCchh
Confidence            45667778889999999999999998875422 345788888899999999999999998743211        235666


Q ss_pred             hHHHHHHHHhhcCCH
Q 041561          135 VWGDLVSSCQVHSNV  149 (156)
Q Consensus       135 ~~~~li~~~~~~g~~  149 (156)
                      ...-+-..+...+..
T Consensus        79 ~~~~l~~~l~~~~~~   93 (100)
T 3ma5_A           79 DLSELQDAKLKAEGL   93 (100)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcccc
Confidence            666666666555443

>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=96.04  E-value=0.033  Score=41.45  Aligned_cols=90  Identities=9%  Similarity=-0.082  Sum_probs=71.3

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHC--------------CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhccccc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIAS--------------GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDH  119 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~--------------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~  119 (156)
                      ..|..+-..+.+.|++++|.+.|++..+.              ...| +...|..+-.++.+.|++++|...++...+. 
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~-  302 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI-  302 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-
Confidence            45677788889999999999999988751              0222 3457778888888999999999999988432 


Q ss_pred             ccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          120 EVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       120 ~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                               -..+...|..+=.+|...|++++|.+
T Consensus       303 ---------~p~~~~a~~~lg~~~~~~g~~~eA~~  328 (370)
T 1ihg_A          303 ---------DPSNTKALYRRAQGWQGLKEYDQALA  328 (370)
T ss_dssp             ---------CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ---------CchhHHHHHHHHHHHHHccCHHHHHH
Confidence                     12367888888899999999999975

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=95.98  E-value=0.039  Score=33.46  Aligned_cols=64  Identities=8%  Similarity=0.076  Sum_probs=52.1

Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      |.-+..+-++.+....+.|+.....+.++||-|..|+..|.++|+..+.+.          .+...+|..+++-
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~----------~~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA----------GPHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT----------TTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh----------cCchhhHHHHHHH
Confidence            445666667777777899999999999999999999999999999997663          3445678887764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.94  E-value=0.068  Score=39.61  Aligned_cols=142  Identities=5%  Similarity=-0.139  Sum_probs=95.1

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHH-hCCCCchH---HHhHHHHHhhhc-c--------------------------ch
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVK-DGYGNDIF---VGSAPINIYCNC-G--------------------------VT   56 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~-~g~~~~~~---~~~~li~~~~~~-~--------------------------~~   56 (156)
                      +..+...|.+.|++++|...+..+.+ .+-.++..   ....++..+... |                          ..
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  137 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSL  137 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHH
Confidence            56778889999999999999988754 22222221   112222222221 1                          46


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIAS----GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      +..+...|...|++++|.+++++....    +-.|. ..++..+.+.|...|++++|..+++.......     ..+..|
T Consensus       138 ~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~-----~~~~~~  212 (434)
T 4b4t_Q          138 SIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAAN-----SIYCPT  212 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HSCCCH
T ss_pred             HHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhh-----cCCCch
Confidence            778899999999999999999987642    22333 34788888999999999999999887633211     011111


Q ss_pred             C--hhhHHHHHHHHhhcCCHhHHhh
Q 041561          132 D--LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       132 d--~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      .  ...|..+...+...|++++|.+
T Consensus       213 ~~~~~~~~~~g~~~~~~~~y~~A~~  237 (434)
T 4b4t_Q          213 QTVAELDLMSGILHCEDKDYKTAFS  237 (434)
T ss_dssp             HHHHHHHHHHHHHTTSSSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            1  3567777788888899888764

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=95.94  E-value=0.38  Score=36.61  Aligned_cols=16  Identities=13%  Similarity=0.011  Sum_probs=7.2

Q ss_pred             CCCHHHHHHHHHHHHH
Q 041561           67 NEYVEQAISLYKDIIA   82 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~   82 (156)
                      .++.++|.+.|++..+
T Consensus       164 ~~d~~~A~~~~~~a~~  179 (490)
T 2xm6_A          164 TRDYVMAREWYSKAAE  179 (490)
T ss_dssp             CCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            3344444444444443

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

Probab=95.87  E-value=0.028  Score=33.77  Aligned_cols=85  Identities=13%  Similarity=0.046  Sum_probs=60.3

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChh
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLV  134 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~  134 (156)
                      ..|..+-..|...|++++|.+.|++..+... .+...|..+-..+.+.|+.++|...|+.......        -.++..
T Consensus        20 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~--------~~~~~~   90 (115)
T 2kat_A           20 LLRFTLGKTYAEHEQFDAALPHLRAALDFDP-TYSVAWKWLGKTLQGQGDRAGARQAWESGLAAAQ--------SRGDQQ   90 (115)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH--------HHTCHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcc--------ccccHH
Confidence            5678888889999999999999999877532 2355777788888899999999999988743211        123555


Q ss_pred             hHHHHHHHHhhcCC
Q 041561          135 VWGDLVSSCQVHSN  148 (156)
Q Consensus       135 ~~~~li~~~~~~g~  148 (156)
                      ....+...+...++
T Consensus        91 ~~~~l~~~l~~l~~  104 (115)
T 2kat_A           91 VVKELQVFLRRLAR  104 (115)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc
Confidence            55555555544443

>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=95.82  E-value=0.035  Score=42.72  Aligned_cols=82  Identities=12%  Similarity=0.018  Sum_probs=66.7

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      .+.+.|++++|.+.|++..+.. .-+..+|..+-.++.+.|++++|...+++..+.          -..+...|..+=.+
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l----------~p~~~~~~~~lg~~   83 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL----------DKKYIKGYYRRAAS   83 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS----------CTTCHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHH
Confidence            4567899999999999987742 224678888889999999999999999988433          13367889999999


Q ss_pred             HhhcCCHhHHhhh
Q 041561          143 CQVHSNVRLAKKA  155 (156)
Q Consensus       143 ~~~~g~~~~a~~~  155 (156)
                      |...|++++|.+.
T Consensus        84 ~~~~g~~~eA~~~   96 (477)
T 1wao_1           84 NMALGKFRAALRD   96 (477)
T ss_dssp             HHHHTCHHHHHHH
T ss_pred             HHHcCCHHHHHHH
Confidence            9999999999763

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=95.67  E-value=0.21  Score=35.30  Aligned_cols=105  Identities=12%  Similarity=0.059  Sum_probs=69.8

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhCC---CCc--hHHHhHHHHHhhhcc---------------------------chHH
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDGY---GND--IFVGSAPINIYCNCG---------------------------VTWN   58 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g~---~~~--~~~~~~li~~~~~~~---------------------------~~~~   58 (156)
                      +-..+...|+.++|...+....+.-.   .+.  ..+++.+-..|...|                           .+|+
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            33445566777777777776654221   111  335555555565555                           3677


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHC----CCCc-cHHHHHHHHHhhcCCCchHHH-HHHHHhc
Q 041561           59 EMIHGYAENEYVEQAISLYKDIIAS----GVKH-DGVTFVAILTPCSHSGLVYAE-VEIFNSM  115 (156)
Q Consensus        59 ~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a-~~~~~~m  115 (156)
                      .+-..|...|++++|.+.|++..+-    +..+ -..+|..+-..+.+.|+.++| ...++.-
T Consensus       201 nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          201 NHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            7888999999999999999987542    2111 156778888888899999999 6655543

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.59  E-value=0.23  Score=36.67  Aligned_cols=138  Identities=9%  Similarity=-0.035  Sum_probs=84.6

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCC-Cch---------------HHHhHHHHHhhhcc----------------------
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYG-NDI---------------FVGSAPINIYCNCG----------------------   54 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~-~~~---------------~~~~~li~~~~~~~----------------------   54 (156)
                      +.+.+.|++++|.+.|..+.+..-. .+.               .....|...|.+.|                      
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            3456789999999999998764321 111               12445566666665                      


Q ss_pred             ----chHHHHHHHHHcCCCHHHHHHHHHHHHH----CCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCc
Q 041561           55 ----VTWNEMIHGYAENEYVEQAISLYKDIIA----SGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKC  125 (156)
Q Consensus        55 ----~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c  125 (156)
                          ...+.+=..+...|+.+++.+++.+...    .+..+. ..++..+...+...|++++|..+++.......     
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~-----  166 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFK-----  166 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHH-----
Confidence                1111122222345667777777776543    233333 34666777788888888888888877643321     


Q ss_pred             CCCCCC-ChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          126 LMPYKD-DLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       126 ~~~~~p-d~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      ...-+| ...+|..+...|...|++++|..+
T Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~  197 (434)
T 4b4t_Q          167 KLDDKPSLVDVHLLESKVYHKLRNLAKSKAS  197 (434)
T ss_dssp             TSSCSTHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcccchhHHHHHHHHHHHHHHhCcHHHHHHH
Confidence            001122 245788889999999999998753

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=95.42  E-value=0.13  Score=38.58  Aligned_cols=99  Identities=6%  Similarity=-0.148  Sum_probs=65.3

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHh-----CC--CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHH
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKD-----GY--GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLY   77 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~-----g~--~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~   77 (156)
                      ...||.+=..+-..|+.++|.+.|++..+.     +.  .|+..             .+|+.+-.+|...|++++|...|
T Consensus        51 a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~-------------~~~~nla~~y~~~g~~~~A~~~~  117 (472)
T 4g1t_A           51 ATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSL-------------VTWGNYAWVYYHMGRLSDVQIYV  117 (472)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTH-------------HHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHH-------------HHHHHHHHHHHHcCChHHHHHHH
Confidence            456788878888899999999999876441     11  22221             57788888888999999998888


Q ss_pred             HHHHHC-----C-CCcc-HHHHHHHHHhhc--CCCchHHHHHHHHhcc
Q 041561           78 KDIIAS-----G-VKHD-GVTFVAILTPCS--HSGLVYAEVEIFNSME  116 (156)
Q Consensus        78 ~~m~~~-----g-~~p~-~~t~~~ll~~~~--~~~~~~~a~~~~~~m~  116 (156)
                      ++..+-     + ..++ ..++...-.++.  ..++.++|...|+...
T Consensus       118 ~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal  165 (472)
T 4g1t_A          118 DKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKAL  165 (472)
T ss_dssp             HHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHH
Confidence            876531     1 1121 233433333333  3457889999988773

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

Probab=95.40  E-value=0.043  Score=32.94  Aligned_cols=28  Identities=14%  Similarity=0.134  Sum_probs=17.5

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      ..|..+-.+|...|++++|.+.|++..+
T Consensus        54 ~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           54 VAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4555566666666666666666666543

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

Probab=95.39  E-value=0.072  Score=41.32  Aligned_cols=100  Identities=7%  Similarity=-0.075  Sum_probs=76.1

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHH-----hCC-CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVK-----DGY-GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKD   79 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~-----~g~-~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~   79 (156)
                      .+++.+...|...|++++|+.++++..+     .|- .|++-             .+++.|-..|...|++++|..++++
T Consensus       352 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a-------------~~l~nLa~~~~~~G~~~eA~~~~~~  418 (490)
T 3n71_A          352 RLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLG-------------MAVMRAGLTNWHAGHIEVGHGMICK  418 (490)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHH-------------HHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHH-------------HHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            5788899999999999999999998754     221 23332             6789999999999999999999988


Q ss_pred             HHH-----CC-CCccHHH-HHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           80 IIA-----SG-VKHDGVT-FVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        80 m~~-----~g-~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      -.+     -| -+|++.. .+.+-.++...+.+++|..++..+++.
T Consensus       419 Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          419 AYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            653     23 3565553 444446666788999999999998553

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=95.22  E-value=0.72  Score=35.01  Aligned_cols=119  Identities=9%  Similarity=-0.002  Sum_probs=73.6

Q ss_pred             CCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhh----cc------------------chHHHHHHHHHc----CCCHH
Q 041561           18 LSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCN----CG------------------VTWNEMIHGYAE----NEYVE   71 (156)
Q Consensus        18 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~~------------------~~~~~li~~~~~----~g~~~   71 (156)
                      .++.+.|...|....+.|   ++..+..|=..|..    .+                  ..+..|=..|..    .++++
T Consensus        56 ~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~  132 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKA  132 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             CcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHH
Confidence            677888888888776654   34445555455544    22                  344555556666    67888


Q ss_pred             HHHHHHHHHHHCCCCccHHHHHHHHHhhcC----CCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh--
Q 041561           72 QAISLYKDIIASGVKHDGVTFVAILTPCSH----SGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV--  145 (156)
Q Consensus        72 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~--  145 (156)
                      +|.+.|++..+.|   +...+..+-..|..    .++.++|.+.|+...+.            .+...+..+-..|..  
T Consensus       133 ~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~------------~~~~a~~~Lg~~y~~g~  197 (490)
T 2xm6_A          133 ESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQ------------GNVWSCNQLGYMYSRGL  197 (490)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT------------TCHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC------------CCHHHHHHHHHHHhcCC
Confidence            8888888887766   34444444444544    67888888888876321            244555555555555  


Q ss_pred             --cCCHhHHhh
Q 041561          146 --HSNVRLAKK  154 (156)
Q Consensus       146 --~g~~~~a~~  154 (156)
                        .++.++|.+
T Consensus       198 g~~~~~~~A~~  208 (490)
T 2xm6_A          198 GVERNDAISAQ  208 (490)
T ss_dssp             SSCCCHHHHHH
T ss_pred             CCCcCHHHHHH
Confidence              566666654

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

Probab=95.21  E-value=0.16  Score=28.50  Aligned_cols=64  Identities=9%  Similarity=0.119  Sum_probs=50.3

Q ss_pred             cccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            5 QFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         5 ~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      ...+..+-..+.+.|++++|...++...+..  |+..             ..|..+-..+.+.|++++|.+.|++..+.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~-------------~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNA-------------EAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC--CCCH-------------HHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            3456666777889999999999999987753  3221             45667778889999999999999998764

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=95.17  E-value=0.21  Score=38.57  Aligned_cols=119  Identities=12%  Similarity=0.118  Sum_probs=80.0

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      .|...+....+.++++.|+.+|+.. +.   |.. ++...+         ..+.+.-.. .++++.|.++|+...+.-..
T Consensus       288 lw~~y~~~~~r~~~~~~AR~i~~~A-~~---~~~-~~~v~i---------~~A~lE~~~-~~d~~~ar~ife~al~~~~~  352 (493)
T 2uy1_A          288 LRINHLNYVLKKRGLELFRKLFIEL-GN---EGV-GPHVFI---------YCAFIEYYA-TGSRATPYNIFSSGLLKHPD  352 (493)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHH-TT---SCC-CHHHHH---------HHHHHHHHH-HCCSHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHh-hC---CCC-ChHHHH---------HHHHHHHHH-CCChHHHHHHHHHHHHHCCC
Confidence            3555555555677899999999988 32   211 121111         122233222 33699999999998775311


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       +...+...++-..+.|+.+.|+.+|+...              .....|...+.--...|+.+.++++
T Consensus       353 -~~~~~~~yid~e~~~~~~~~aR~l~er~~--------------k~~~lw~~~~~fE~~~G~~~~~r~v  406 (493)
T 2uy1_A          353 -STLLKEEFFLFLLRIGDEENARALFKRLE--------------KTSRMWDSMIEYEFMVGSMELFREL  406 (493)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHSC--------------CBHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHcCCHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHCCCHHHHHHH
Confidence             23345667887788999999999999882              2578899999888888998888764

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=95.17  E-value=0.098  Score=33.47  Aligned_cols=87  Identities=8%  Similarity=0.104  Sum_probs=57.7

Q ss_pred             HHHHhhhcc----chHHHHHHHHHcCCC--HHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhccccc
Q 041561           46 PINIYCNCG----VTWNEMIHGYAENEY--VEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDH  119 (156)
Q Consensus        46 li~~~~~~~----~~~~~li~~~~~~g~--~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~  119 (156)
                      -++.|+...    .-|++=-..|...-+  .-+..+-++.+....+.|+.....+.+++|-|.+|+..|.++|+..+.+ 
T Consensus        39 ~~R~~s~h~~Et~EeFdaRy~~~F~~~~iD~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-  117 (152)
T 2y69_E           39 SLRCYSHGSHETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-  117 (152)
T ss_dssp             ----------CCHHHHHHHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHhhcCCCCCcHHHHHHHHHHHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-
Confidence            345554433    334443444444443  4455566666666789999999999999999999999999999999776 


Q ss_pred             ccCCCcCCCCCCChhhHHHHHHH
Q 041561          120 EVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus       120 ~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                               +.+...+|..+++-
T Consensus       118 ---------~~~~~~iY~y~lqE  131 (152)
T 2y69_E          118 ---------AGPHKEIYPYVIQE  131 (152)
T ss_dssp             ---------TTTCTTHHHHHHHH
T ss_pred             ---------cCCchhhHHHHHHH
Confidence                     34556678887764

>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=95.13  E-value=0.08  Score=40.31  Aligned_cols=88  Identities=14%  Similarity=-0.002  Sum_probs=67.1

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHC---CC---CccH-HHHHHHHHhhcCCCchHHHHHHHHhccc----ccccCCCcCCCC
Q 041561           61 IHGYAENEYVEQAISLYKDIIAS---GV---KHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEH----DHEVKPKCLMPY  129 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~---g~---~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~~c~~~~  129 (156)
                      +..+.+.|++++|.+++++..+.   -+   +|+. .+++.+...|...|++++|..++++...    .+|       +.
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg-------~~  366 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFP-------GS  366 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSC-------SS
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcC-------CC
Confidence            55566788999999999988752   12   3333 4788899999999999999998886632    233       24


Q ss_pred             CCCh-hhHHHHHHHHhhcCCHhHHhhh
Q 041561          130 KDDL-VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       130 ~pd~-~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .|++ .+++.|=..|...|++++|+..
T Consensus       367 Hp~~a~~l~nLa~~~~~~g~~~eA~~~  393 (429)
T 3qwp_A          367 HPVRGVQVMKVGKLQLHQGMFPQAMKN  393 (429)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence            5655 6689999999999999999863

>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=0.073  Score=31.32  Aligned_cols=58  Identities=12%  Similarity=0.014  Sum_probs=47.0

Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +...+..+-..+.+.|++++|...|+...+.          -..+...|..+=.+|...|++++|.+.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~----------~p~~~~a~~~lg~~~~~~g~~~~A~~~   63 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVET----------DPDYVGTYYHLGKLYERLDRTDDAIDT   63 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------STTCTHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4556777788888999999999999998543          123567899999999999999999763

>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=94.75  E-value=0.23  Score=32.54  Aligned_cols=94  Identities=6%  Similarity=-0.096  Sum_probs=66.1

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-c-----c-----HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCc
Q 041561           57 WNEMIHGYAENEYVEQAISLYKDIIASGVK-H-----D-----GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKC  125 (156)
Q Consensus        57 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p-----~-----~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c  125 (156)
                      +...=..+.+.|++++|.+.|++-.+-... |     +     ...|...-.++.+.|++++|...++.-..-+.-    
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~----   89 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR----   89 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH----
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhc----
Confidence            344455667889999999999998763211 1     2     237888888999999999999988877321000    


Q ss_pred             CCCCCCC-hhhH----HHHHHHHhhcCCHhHHhh
Q 041561          126 LMPYKDD-LVVW----GDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       126 ~~~~~pd-~~~~----~~li~~~~~~g~~~~a~~  154 (156)
                      ...+.|| ...|    ...=.++...|++++|.+
T Consensus        90 ~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~  123 (159)
T 2hr2_A           90 RGELNQDEGKLWISAVYSRALALDGLGRGAEAMP  123 (159)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHH
Confidence            0012564 4567    777889999999999975

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=94.68  E-value=0.15  Score=34.50  Aligned_cols=60  Identities=5%  Similarity=-0.108  Sum_probs=47.2

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCC-cc-HHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           59 EMIHGYAENEYVEQAISLYKDIIASGVK-HD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        59 ~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      .+-..+.+.|++++|.+.|+++.+.... |. ...+..+-.++.+.|++++|...|+...+.
T Consensus         9 ~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   70 (225)
T 2yhc_A            9 ATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   70 (225)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            3455678889999999999999875322 22 346777788899999999999999998554

>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=94.53  E-value=0.32  Score=31.87  Aligned_cols=99  Identities=6%  Similarity=-0.102  Sum_probs=69.6

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCC-CchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC-----CCC
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYG-NDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS-----GVK   86 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~   86 (156)
                      ..+.+.|++++|...|+...+..-. |+....+.  .  ...-..|+.+-.++.+.|++++|+..|+.-.+-     .+.
T Consensus        19 ~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~--~--~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~   94 (159)
T 2hr2_A           19 QRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDH--A--GFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN   94 (159)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCH--H--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTT
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhh--c--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCC
Confidence            4456789999999999998764321 11100000  0  000037888889999999999999999998763     226


Q ss_pred             ccH-HHH----HHHHHhhcCCCchHHHHHHHHhc
Q 041561           87 HDG-VTF----VAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        87 p~~-~t~----~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      |+. ..|    ...=.++...|++++|...|+.-
T Consensus        95 pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kA  128 (159)
T 2hr2_A           95 QDEGKLWISAVYSRALALDGLGRGAEAMPEFKKV  128 (159)
T ss_dssp             STHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHH
Confidence            654 366    77778888999999999999877

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

Probab=94.39  E-value=0.69  Score=34.59  Aligned_cols=121  Identities=8%  Similarity=0.031  Sum_probs=82.0

Q ss_pred             CCcccHHHHHHHhcCC-----CchHHHHHHHHHHHHhCCCCch-HHHhHHHHHhh----hcc------------------
Q 041561            3 PTQFPFTTVLSSCAKL-----SSLFLGRQILTRIVKDGYGNDI-FVGSAPINIYC----NCG------------------   54 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~-----~~~~~a~~~~~~m~~~g~~~~~-~~~~~li~~~~----~~~------------------   54 (156)
                      .+...|...+++....     .+..+|..+|++..+.  .|+- ..|..+--+|.    ...                  
T Consensus       192 ~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a  269 (372)
T 3ly7_A          192 HRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVT  269 (372)
T ss_dssp             SSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHh
Confidence            4567888888776532     3457788888888764  3432 33332222221    100                  


Q ss_pred             --------chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcC
Q 041561           55 --------VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCL  126 (156)
Q Consensus        55 --------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~  126 (156)
                              ..|..+--.+...|++++|.+.+++...-+  |+...|..+=..+.-.|+.++|.+.+.+-. +        
T Consensus       270 ~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Al-r--------  338 (372)
T 3ly7_A          270 LPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAF-N--------  338 (372)
T ss_dssp             CGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H--------
T ss_pred             cccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-h--------
Confidence                    455556556666799999999999998864  787777677777788999999999998773 3        


Q ss_pred             CCCCCChhhHHH
Q 041561          127 MPYKDDLVVWGD  138 (156)
Q Consensus       127 ~~~~pd~~~~~~  138 (156)
                        +.|...||..
T Consensus       339 --L~P~~~t~~~  348 (372)
T 3ly7_A          339 --LRPGANTLYW  348 (372)
T ss_dssp             --HSCSHHHHHH
T ss_pred             --cCCCcChHHH
Confidence              4677766653

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

Probab=93.87  E-value=0.39  Score=27.51  Aligned_cols=79  Identities=11%  Similarity=0.047  Sum_probs=54.7

Q ss_pred             HHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccc-hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHH
Q 041561           13 SSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGV-TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVT   91 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t   91 (156)
                      ..+.+.|+.++|...++...+..  |+..             . .|..+-.+|...|++++|.+.|++..+..... ...
T Consensus         8 ~~~~~~~~~~~A~~~~~~al~~~--p~~~-------------~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~-~~~   71 (99)
T 2kc7_A            8 KELINQGDIENALQALEEFLQTE--PVGK-------------DEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDS-PAL   71 (99)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC--SSTH-------------HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTS-THH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC--CCcH-------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCc-HHH
Confidence            45567899999999999987753  4321             4 56667778889999999999999988743221 112


Q ss_pred             HHHHHHhhcCCCchHHHHHHHHhc
Q 041561           92 FVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        92 ~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +..        +.+.++...+++.
T Consensus        72 ~~~--------~~~~~a~~~~~~~   87 (99)
T 2kc7_A           72 QAR--------KMVMDILNFYNKD   87 (99)
T ss_dssp             HHH--------HHHHHHHHHHCCT
T ss_pred             HHH--------HHHHHHHHHHHHH
Confidence            211        6666777777665

>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=93.80  E-value=0.95  Score=30.30  Aligned_cols=118  Identities=12%  Similarity=-0.058  Sum_probs=74.0

Q ss_pred             HHHHHHHhcCCC----chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHc----CCCHHHHHHHHHH
Q 041561            8 FTTVLSSCAKLS----SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAE----NEYVEQAISLYKD   79 (156)
Q Consensus         8 ~~~ll~~~~~~~----~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~   79 (156)
                      +..+=..+.+ +    +.++|...|+...+.|   ++              ..+..|=..|..    .+++++|.+.|++
T Consensus        53 ~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~--------------~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~  114 (212)
T 3rjv_A           53 LALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SK--------------SGEIVLARVLVNRQAGATDVAHAITLLQD  114 (212)
T ss_dssp             HHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CH--------------HHHHHHHHHHTCGGGSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CH--------------HHHHHHHHHHHcCCCCccCHHHHHHHHHH
Confidence            3334444445 5    7888888888886654   23              333444444544    7899999999999


Q ss_pred             HHHCCCC-ccHHHHHHHHHhhcC----CCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhc-C-----C
Q 041561           80 IIASGVK-HDGVTFVAILTPCSH----SGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVH-S-----N  148 (156)
Q Consensus        80 m~~~g~~-p~~~t~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~-g-----~  148 (156)
                      -.+.|.. .+...+..|=..|.+    .++.++|...|+.-...           .++...+..|=..|... |     +
T Consensus       115 A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~-----------~~~~~a~~~Lg~~y~~g~gg~~~~d  183 (212)
T 3rjv_A          115 AARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL-----------SRTGYAEYWAGMMFQQGEKGFIEPN  183 (212)
T ss_dssp             HTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT-----------SCTTHHHHHHHHHHHHCBTTTBCCC
T ss_pred             HHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc-----------CCCHHHHHHHHHHHHcCCCCCCCCC
Confidence            8876643 124555555555555    78999999999988432           12344455555555433 2     6


Q ss_pred             HhHHhh
Q 041561          149 VRLAKK  154 (156)
Q Consensus       149 ~~~a~~  154 (156)
                      .++|.+
T Consensus       184 ~~~A~~  189 (212)
T 3rjv_A          184 KQKALH  189 (212)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777764

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=93.62  E-value=0.63  Score=29.07  Aligned_cols=76  Identities=4%  Similarity=-0.145  Sum_probs=41.5

Q ss_pred             CCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHH
Q 041561           18 LSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILT   97 (156)
Q Consensus        18 ~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~   97 (156)
                      .++.++|...|....+.|- |+..                  |=..|...+.+++|.+.|++-.+.|   +......+=.
T Consensus         8 ~~d~~~A~~~~~~aa~~g~-~~a~------------------lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~   65 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELNE-MFGC------------------LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGD   65 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTTC-TTHH------------------HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHcCCC-Hhhh------------------HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHH
Confidence            3567888888888877762 2221                  1222233344555666666665554   2333333333


Q ss_pred             hhcC----CCchHHHHHHHHhc
Q 041561           98 PCSH----SGLVYAEVEIFNSM  115 (156)
Q Consensus        98 ~~~~----~~~~~~a~~~~~~m  115 (156)
                      .|.+    .++.++|...|+.-
T Consensus        66 ~y~~G~g~~~d~~~A~~~~~~A   87 (138)
T 1klx_A           66 FYENGKYVKKDLRKAAQYYSKA   87 (138)
T ss_dssp             HHHHCSSSCCCHHHHHHHHHHH
T ss_pred             HHHcCCCCCccHHHHHHHHHHH
Confidence            3333    56666666666655

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

Probab=93.46  E-value=0.52  Score=26.94  Aligned_cols=57  Identities=9%  Similarity=0.074  Sum_probs=45.3

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHH-HHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      -..+.+.|++++|.+.|++..+.... +.. .+..+-..+.+.|++++|...|+.....
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTEPV-GKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCSS-THHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            44567889999999999998875322 345 7777778888999999999999988443

>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=93.29  E-value=0.29  Score=37.34  Aligned_cols=63  Identities=14%  Similarity=0.141  Sum_probs=52.2

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHH-----hC-CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVK-----DG-YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKD   79 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~-----~g-~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~   79 (156)
                      .+++.+..+|...|++++|+.++++..+     .| -.|++-             .+++.|-..|...|++++|..+|++
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a-------------~~l~nLa~~~~~qg~~~eA~~~~~~  407 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVA-------------SMWLKLGRLYMGLENKAAGEKALKK  407 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHH-------------HHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHH-------------HHHHHHHHHHHhccCHHHHHHHHHH
Confidence            6788999999999999999999998754     23 134442             6789999999999999999999988


Q ss_pred             HH
Q 041561           80 II   81 (156)
Q Consensus        80 m~   81 (156)
                      -.
T Consensus       408 Al  409 (433)
T 3qww_A          408 AI  409 (433)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=93.08  E-value=0.24  Score=35.62  Aligned_cols=81  Identities=7%  Similarity=-0.090  Sum_probs=49.1

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCCh----hh
Q 041561           60 MIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDL----VV  135 (156)
Q Consensus        60 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~----~~  135 (156)
                      ....+...|++++|.++|+.+...+  |+....-.+-..+.+.+++++|...|+... .           .||.    ..
T Consensus       108 yA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~-~-----------~~d~~~~~~a  173 (282)
T 4f3v_A          108 FAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAG-K-----------WPDKFLAGAA  173 (282)
T ss_dssp             HHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGG-G-----------CSCHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhh-c-----------cCCcccHHHH
Confidence            5567788999999999998887644  443332223334557777777777776441 1           1111    23


Q ss_pred             HHHHHHHHhhcCCHhHHhh
Q 041561          136 WGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       136 ~~~li~~~~~~g~~~~a~~  154 (156)
                      +..+=.++...|++++|.+
T Consensus       174 ~~~LG~al~~LG~~~eAl~  192 (282)
T 4f3v_A          174 GVAHGVAAANLALFTEAER  192 (282)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHH
Confidence            4444456666666666653

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.39  E-value=1.4  Score=28.43  Aligned_cols=102  Identities=11%  Similarity=0.038  Sum_probs=74.8

Q ss_pred             CCCchHHHHHHHHHHHHhC-C-CCchHHHhHH------------------------------HHHhhhcc---chHHHHH
Q 041561           17 KLSSLFLGRQILTRIVKDG-Y-GNDIFVGSAP------------------------------INIYCNCG---VTWNEMI   61 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g-~-~~~~~~~~~l------------------------------i~~~~~~~---~~~~~li   61 (156)
                      -.|.+++..++..+..++. . .-|++.+|.+                              +.+|++.+   ..++..+
T Consensus        19 ldG~v~qGveii~k~~~ssni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C~~~~n~~se~vd~AL   98 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNTLNEHVNKAL   98 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTCCCHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHcCCCCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHHHHHhcchHHHHHHHH
Confidence            4577888888888876543 2 3466666643                              33333333   6678888


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccc
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHE  120 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  120 (156)
                      +.....|.-|+..++..++.. ...|+....-.+-.||.+.|+..++.+++.+- -+.|
T Consensus        99 d~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~A-C~kG  155 (172)
T 1wy6_A           99 DILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEA-CKKG  155 (172)
T ss_dssp             HHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHTT
T ss_pred             HHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHH-HHhh
Confidence            899999999999999988644 34677888888999999999999999999877 3444

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=92.29  E-value=0.22  Score=40.01  Aligned_cols=26  Identities=12%  Similarity=0.267  Sum_probs=13.6

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHH
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDI   80 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m   80 (156)
                      ..|..+-..+.+.++++.|.+.|.++
T Consensus       682 ~~W~~la~~al~~~~~~~A~~~y~~~  707 (814)
T 3mkq_A          682 MKWRALGDASLQRFNFKLAIEAFTNA  707 (814)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCHHHHHHHHHHc
Confidence            44555555555555555555555543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=91.68  E-value=1.8  Score=28.07  Aligned_cols=81  Identities=10%  Similarity=0.062  Sum_probs=55.0

Q ss_pred             CchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCC---CHHHHHHHHHHHHHCCCCc---cHHHH
Q 041561           19 SSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENE---YVEQAISLYKDIIASGVKH---DGVTF   92 (156)
Q Consensus        19 ~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p---~~~t~   92 (156)
                      ..+..+++-|.+..+.|. ++.              .+.-.+-.++++++   +++++..+|++..+.. .|   -...|
T Consensus        12 ~~l~~~~~~y~~e~~~~~-~~~--------------~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY   75 (152)
T 1pc2_A           12 EDLLKFEKKFQSEKAAGS-VSK--------------STQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVF   75 (152)
T ss_dssp             HHHHHHHHHHHHHHHTTC-CCH--------------HHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCC-CcH--------------HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHH
Confidence            345667777776666554 444              33334455677777   6779999999998865 23   22334


Q ss_pred             HHHHHhhcCCCchHHHHHHHHhcc
Q 041561           93 VAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        93 ~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      +.-+ ++.+.|++++|++.++...
T Consensus        76 ~LAv-~~~kl~~Y~~A~~y~~~lL   98 (152)
T 1pc2_A           76 YLAV-GNYRLKEYEKALKYVRGLL   98 (152)
T ss_dssp             HHHH-HHHHTSCHHHHHHHHHHHH
T ss_pred             HHHH-HHHHccCHHHHHHHHHHHH
Confidence            4443 4589999999999999994

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=90.39  E-value=5.9  Score=31.72  Aligned_cols=88  Identities=16%  Similarity=0.138  Sum_probs=47.0

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHH-------------HHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYK-------------DII   81 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~-------------~m~   81 (156)
                      ....|+++.|.++...+      .+...|..|-+.+.+.+ -+.....+|.+.|+++.+..++.             ...
T Consensus       662 ~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~~-~~~~A~~~y~~~~d~~~l~~l~~~~~~~~~~~~~~~~a~  734 (814)
T 3mkq_A          662 ALKVGQLTLARDLLTDE------SAEMKWRALGDASLQRF-NFKLAIEAFTNAHDLESLFLLHSSFNNKEGLVTLAKDAE  734 (814)
T ss_dssp             HHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHTT-CHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHcC-CHHHHHHHHHHccChhhhHHHHHHcCCHHHHHHHHHHHH
Confidence            34567777777665433      45567777766666655 23444444555555544444433             333


Q ss_pred             HCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           82 ASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        82 ~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ..|      -++....++.+.|++++|.+++..+
T Consensus       735 ~~~------~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          735 TTG------KFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             HTT------CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HcC------chHHHHHHHHHcCCHHHHHHHHHHc
Confidence            322      1233344444566777776666665

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=90.14  E-value=4.8  Score=30.34  Aligned_cols=17  Identities=12%  Similarity=0.219  Sum_probs=12.3

Q ss_pred             chHHHHHHHHHHHHhCC
Q 041561           20 SLFLGRQILTRIVKDGY   36 (156)
Q Consensus        20 ~~~~a~~~~~~m~~~g~   36 (156)
                      +.++|...|+...+.|.
T Consensus        89 ~~~~A~~~~~~Aa~~g~  105 (452)
T 3e4b_A           89 EHHEAESLLKKAFANGE  105 (452)
T ss_dssp             HHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHCCC
Confidence            67788888887776553

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=89.95  E-value=2.3  Score=27.73  Aligned_cols=101  Identities=12%  Similarity=0.012  Sum_probs=62.6

Q ss_pred             ccHHHHHHHhcCCCch------HHHHHHHHHHHHhCCCCch-HHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSL------FLGRQILTRIVKDGYGNDI-FVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYK   78 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~------~~a~~~~~~m~~~g~~~~~-~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~   78 (156)
                      .+|=..+...-+.|++      +....+|+..... ++|+. ..|..-|..+    +-|..+ .   ..+++++|.++|+
T Consensus        14 d~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LW----IrYA~~-~---ei~D~d~aR~vy~   84 (161)
T 4h7y_A           14 EDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQ----VRFAEL-K---AIQEPDDARDYFQ   84 (161)
T ss_dssp             HHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHH----HHHHHH-H---HHHCGGGCHHHHH
T ss_pred             HHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHH----HHHHHH-H---HhcCHHHHHHHHH
Confidence            3444445555555777      7777777766553 55542 1122222222    222322 2   2389999999999


Q ss_pred             HHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           79 DIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        79 ~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .++..+-+. ...|...-+--.+.|+++.|++++..-.
T Consensus        85 ~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~Ai  121 (161)
T 4h7y_A           85 MARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAV  121 (161)
T ss_dssp             HHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHh
Confidence            997654444 6666666666678999999999999763

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=89.12  E-value=2.6  Score=27.29  Aligned_cols=75  Identities=9%  Similarity=-0.120  Sum_probs=51.1

Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCC---chHHHHHHHHhcccccccCCCcCCCCCC---ChhhHHHHHHH
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG---LVYAEVEIFNSMEHDHEVKPKCLMPYKD---DLVVWGDLVSS  142 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~~~~~~~c~~~~~p---d~~~~~~li~~  142 (156)
                      ++..+.+-|.+-...|. ++..+-..+--++++++   +++++..+++...++          -.|   -...|+.= -+
T Consensus        13 ~l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~----------~~p~~~rd~lY~LA-v~   80 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPK----------GSKEEQRDYVFYLA-VG   80 (152)
T ss_dssp             HHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHH----------SCHHHHHHHHHHHH-HH
T ss_pred             HHHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc----------CCccchHHHHHHHH-HH
Confidence            35566777777766665 56666666666777877   777999999998554          124   12334433 45


Q ss_pred             HhhcCCHhHHhhh
Q 041561          143 CQVHSNVRLAKKA  155 (156)
Q Consensus       143 ~~~~g~~~~a~~~  155 (156)
                      |.+.|++++|++.
T Consensus        81 ~~kl~~Y~~A~~y   93 (152)
T 1pc2_A           81 NYRLKEYEKALKY   93 (152)
T ss_dssp             HHHTSCHHHHHHH
T ss_pred             HHHccCHHHHHHH
Confidence            5999999999874

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=88.72  E-value=1.7  Score=32.43  Aligned_cols=105  Identities=9%  Similarity=0.051  Sum_probs=69.7

Q ss_pred             CCchHHHHHHHHHHHH--hC-CCCchH--HHhHHHHHhhhcc--chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHH
Q 041561           18 LSSLFLGRQILTRIVK--DG-YGNDIF--VGSAPINIYCNCG--VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGV   90 (156)
Q Consensus        18 ~~~~~~a~~~~~~m~~--~g-~~~~~~--~~~~li~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   90 (156)
                      .|+.+.+...+.....  .| +-++..  .|..-.....+.-  .....++..+...|+++++......+.... .-++.
T Consensus       128 ~~~~~~a~~~l~~Al~L~rG~~L~~~~~~~w~~~~r~~l~~~~~~a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~  206 (388)
T 2ff4_A          128 AGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEH-PYREP  206 (388)
T ss_dssp             TTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHH
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHH
Confidence            4666677777766654  24 333331  1211111111111  455667888889999999999888887543 34788


Q ss_pred             HHHHHHHhhcCCCchHHHHHHHHhccc----ccccCC
Q 041561           91 TFVAILTPCSHSGLVYAEVEIFNSMEH----DHEVKP  123 (156)
Q Consensus        91 t~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~  123 (156)
                      .+..++.++.+.|+..+|.+.|+....    +.|+.|
T Consensus       207 ~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P  243 (388)
T 2ff4_A          207 LWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDP  243 (388)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            999999999999999999999988743    467433

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=88.68  E-value=6.3  Score=29.69  Aligned_cols=28  Identities=11%  Similarity=0.247  Sum_probs=13.1

Q ss_pred             HHHHHHHHHcCC---CHHHHHHHHHHHHHCC
Q 041561           57 WNEMIHGYAENE---YVEQAISLYKDIIASG   84 (156)
Q Consensus        57 ~~~li~~~~~~g---~~~~a~~~~~~m~~~g   84 (156)
                      +..|-..|...|   +.++|.+.|+.-.+.|
T Consensus       179 ~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g  209 (452)
T 3e4b_A          179 YVELATVYQKKQQPEQQAELLKQMEAGVSRG  209 (452)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCcccHHHHHHHHHHHHHCC
Confidence            333444444444   4555555555544444

>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=88.65  E-value=2.3  Score=31.81  Aligned_cols=73  Identities=8%  Similarity=-0.032  Sum_probs=51.8

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      ++.+|..+--.+...|++++|...++.....+  |+.              ..|..+=..+...|++++|.+.|++-.. 
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~--------------~a~~llG~~~~~~G~~~eA~e~~~~Alr-  338 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSW--------------LNYVLLGKVYEMKGMNREAADAYLTAFN-  338 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHH-
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCH--------------HHHHHHHHHHHHCCCHHHHHHHHHHHHh-
Confidence            34455555445555699999999999988875  665              4444455667789999999999988766 


Q ss_pred             CCCccHHHHHH
Q 041561           84 GVKHDGVTFVA   94 (156)
Q Consensus        84 g~~p~~~t~~~   94 (156)
                       +.|...||..
T Consensus       339 -L~P~~~t~~~  348 (372)
T 3ly7_A          339 -LRPGANTLYW  348 (372)
T ss_dssp             -HSCSHHHHHH
T ss_pred             -cCCCcChHHH
Confidence             3555556544

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=88.39  E-value=2.7  Score=31.36  Aligned_cols=68  Identities=10%  Similarity=0.098  Sum_probs=46.2

Q ss_pred             HHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCC
Q 041561           12 LSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA-----SGVK   86 (156)
Q Consensus        12 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~   86 (156)
                      +..+...|+.+++......+.... +-+-              ..|-.+|.++.+.|+..+|.+.|+...+     -|+.
T Consensus       178 ~~~~l~~g~~~~a~~~l~~~~~~~-P~~E--------------~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~  242 (388)
T 2ff4_A          178 AEAEIACGRASAVIAELEALTFEH-PYRE--------------PLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGID  242 (388)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCH--------------HHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCH--------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            344445555555555555543321 1122              5788899999999999999999999764     3999


Q ss_pred             ccHHHHHH
Q 041561           87 HDGVTFVA   94 (156)
Q Consensus        87 p~~~t~~~   94 (156)
                      |...+=..
T Consensus       243 P~~~l~~l  250 (388)
T 2ff4_A          243 PGPTLRAL  250 (388)
T ss_dssp             CCHHHHHH
T ss_pred             CCHHHHHH
Confidence            98886443

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=87.92  E-value=2.6  Score=24.45  Aligned_cols=67  Identities=9%  Similarity=-0.075  Sum_probs=45.0

Q ss_pred             CCcccHHHHHHHhcCCC---chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLS---SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKD   79 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~   79 (156)
                      +|+..+..+-.++...+   ..++|..++++..+.  .|+..             .....+=..+.+.|++++|.+.|+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~-------------rA~~~lg~~~~~~g~y~~Ai~~w~~   68 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNE-------------AALSLIANDHFISFRFQEAIDTWVL   68 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCH-------------HHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34445555555554333   368999999988774  34433             3344455677889999999999999


Q ss_pred             HHHCC
Q 041561           80 IIASG   84 (156)
Q Consensus        80 m~~~g   84 (156)
                      +.+..
T Consensus        69 ~l~~~   73 (93)
T 3bee_A           69 LLDSN   73 (93)
T ss_dssp             HHTCC
T ss_pred             HHhhC
Confidence            98753

>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=87.66  E-value=3.2  Score=25.11  Aligned_cols=71  Identities=6%  Similarity=0.017  Sum_probs=54.9

Q ss_pred             HHhcCCC-chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHH
Q 041561           13 SSCAKLS-SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVT   91 (156)
Q Consensus        13 ~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t   91 (156)
                      ..+-+.. |.-++.+-++.+....+.|++              ....+.+++|.+-+++.-|.++|+-.+.+ ..+...+
T Consensus        17 ~~F~~~~iD~~e~rrglN~l~~~DlVP~P--------------~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~i   81 (109)
T 1v54_E           17 TYFNKPDIDAWELRKGMNTLVGYDLVPEP--------------KIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEI   81 (109)
T ss_dssp             HHHTCTTCCHHHHHHHHHHHTTSSBCCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTH
T ss_pred             HHcCCcCccHHHHHHHHHHHhccccCCCc--------------HHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhh
Confidence            3444555 677788888999888899999              67778889999999999999999998764 2223556


Q ss_pred             HHHHHHh
Q 041561           92 FVAILTP   98 (156)
Q Consensus        92 ~~~ll~~   98 (156)
                      |..+++-
T Consensus        82 Y~~~lqE   88 (109)
T 1v54_E           82 YPYVIQE   88 (109)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7777654

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=87.45  E-value=8.9  Score=31.47  Aligned_cols=106  Identities=16%  Similarity=0.089  Sum_probs=72.7

Q ss_pred             HHHHHHhcCCCc-hHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc-----------chH-------------------
Q 041561            9 TTVLSSCAKLSS-LFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG-----------VTW-------------------   57 (156)
Q Consensus         9 ~~ll~~~~~~~~-~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~-----------~~~-------------------   57 (156)
                      .++++.+...++ .+.|..+|+.+.+....-+.....++|....+.+           .+-                   
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~  331 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSAR  331 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccccc
Confidence            445666666666 5779999999887654334444444444433332           000                   


Q ss_pred             -----HHHHHH----HHcCCCHHHHHHHHHHHHHCCCCccHH-HHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           58 -----NEMIHG----YAENEYVEQAISLYKDIIASGVKHDGV-TFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        58 -----~~li~~----~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                           ..|+..    +-..|+++.|+++-++-+.  ..|+.+ ||..|...|.+.|+++.|.-.++.+.
T Consensus       332 ~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~--~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          332 LMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE--LALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             ccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh--cCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                 113322    3347899999999988765  567766 89999999999999999999999885

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=87.32  E-value=0.086  Score=41.25  Aligned_cols=127  Identities=11%  Similarity=0.117  Sum_probs=81.4

Q ss_pred             CcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561            4 TQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus         4 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      |+..|.-+|.++.+.|..++....+...++..-.|                ..=+.|+-+|++.+++.+..++.      
T Consensus        82 Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~----------------~IDteLi~ayAk~~rL~elEefl------  139 (624)
T 3lvg_A           82 DPSSYMEVVQAANTSGNWEELVKYLQMARKKARES----------------YVETELIFALAKTNRLAELEEFI------  139 (624)
T ss_dssp             CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCST----------------TTTHHHHHHHHTSCSSSTTTSTT------
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccc----------------ccHHHHHHHHHhhCcHHHHHHHH------
Confidence            44455566666666666665555555444432222                33367777888888776654443      


Q ss_pred             CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCc------------CCCCCCChhhHHHHHHHHhhcCCHhH
Q 041561           84 GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKC------------LMPYKDDLVVWGDLVSSCQVHSNVRL  151 (156)
Q Consensus        84 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c------------~~~~~pd~~~~~~li~~~~~~g~~~~  151 (156)
                       -.||..-...+=+=|-..|.++.|+-+|..+ ..+.-..+|            ...-..++.||.-+-.+|...++++.
T Consensus       140 -~~~N~A~iq~VGDrcf~e~lYeAAKilys~i-sN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrL  217 (624)
T 3lvg_A          140 -NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRL  217 (624)
T ss_dssp             -SCCSSSCTHHHHHHHHHSCCSTTSSTTGGGS-CCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTT
T ss_pred             -cCCCcccHHHHHHHHHHccCHHHHHHHHHhC-ccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHH
Confidence             2466666666667777777787777777777 444444443            22224588999999999999999987


Q ss_pred             Hhh
Q 041561          152 AKK  154 (156)
Q Consensus       152 a~~  154 (156)
                      |.-
T Consensus       218 Aqi  220 (624)
T 3lvg_A          218 AQM  220 (624)
T ss_dssp             TTH
T ss_pred             HHH
Confidence            753

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=85.60  E-value=3.8  Score=23.97  Aligned_cols=58  Identities=3%  Similarity=-0.107  Sum_probs=46.6

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHC------CCCccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           59 EMIHGYAENEYVEQAISLYKDIIAS------GVKHDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        59 ~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .|=..+.+.|+++.|...|+...+.      .-.+....+..+-.++.+.|+++.|...++...
T Consensus        10 ~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al   73 (104)
T 2v5f_A           10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLL   73 (104)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            4556677899999999999887642      123456778889999999999999999999884

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=85.48  E-value=8.3  Score=27.76  Aligned_cols=93  Identities=9%  Similarity=0.045  Sum_probs=62.2

Q ss_pred             chHHHHHHHHHcCCC------HHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCc-hHHHHHHHHhcccccccCCCcCC
Q 041561           55 VTWNEMIHGYAENEY------VEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGL-VYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        55 ~~~~~li~~~~~~g~------~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~-~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                      ..|+.--....+.+.      ++++++.++++.... .-|...|+-.-..+.+.|+ .+.+..+...+......      
T Consensus       181 sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~------  253 (306)
T 3dra_A          181 SAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKD------  253 (306)
T ss_dssp             HHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGT------
T ss_pred             HHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCC------
Confidence            566655555566665      788888888887754 3366677766666666665 44466677766332100      


Q ss_pred             CCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          128 PYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       128 ~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                       -..+...+..+...|...|+.++|.++
T Consensus       254 -~~~s~~al~~la~~~~~~~~~~~A~~~  280 (306)
T 3dra_A          254 -QVTSSFALETLAKIYTQQKKYNESRTV  280 (306)
T ss_dssp             -EESCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             -CCCCHHHHHHHHHHHHccCCHHHHHHH
Confidence             134778888888999999999998764

>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=85.20  E-value=5.5  Score=25.47  Aligned_cols=64  Identities=5%  Similarity=0.019  Sum_probs=46.7

Q ss_pred             chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHh
Q 041561           20 SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTP   98 (156)
Q Consensus        20 ~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~   98 (156)
                      |.-+..+-++.+....+.|++              ....+.+++|.+-+|+.-|.++|+-.+.+ ..+...+|..+++-
T Consensus        68 D~wElrrglN~l~~~DlVPeP--------------~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~lqE  131 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEP--------------KIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE  131 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCc--------------HHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHHHH
Confidence            444555666666666677777              67788899999999999999999998764 23335577777654

>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=85.02  E-value=1.3  Score=28.86  Aligned_cols=100  Identities=11%  Similarity=-0.023  Sum_probs=64.7

Q ss_pred             CCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCC----------CHHHHHHHHHHHHHCCCC
Q 041561           17 KLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENE----------YVEQAISLYKDIIASGVK   86 (156)
Q Consensus        17 ~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g----------~~~~a~~~~~~m~~~g~~   86 (156)
                      +.+.+++|.+.++...+.. +.+...|              +.+=.++...+          .+++|...|++-.+-  .
T Consensus        14 r~~~feeA~~~~~~Ai~l~-P~~aea~--------------~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--d   76 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSN-PLDADNL--------------TRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--D   76 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-TTCHHHH--------------HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--C
T ss_pred             HHhHHHHHHHHHHHHHHHC-CCCHHHH--------------HHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--C
Confidence            4456778888888776643 1244333              32223333333          367999999998774  3


Q ss_pred             c-cHHHHHHHHHhhcCC-----------CchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHh
Q 041561           87 H-DGVTFVAILTPCSHS-----------GLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQ  144 (156)
Q Consensus        87 p-~~~t~~~ll~~~~~~-----------~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~  144 (156)
                      | +...|..+=.+|...           |++++|.+.|++-. +          +.|+...|..-+...-
T Consensus        77 P~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl-~----------l~P~~~~y~~al~~~~  135 (158)
T 1zu2_A           77 PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAV-D----------EQPDNTHYLKSLEMTA  135 (158)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-H----------HCTTCHHHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHH-H----------hCCCCHHHHHHHHHHH
Confidence            4 345677777888765           48999999999883 3          5788777766665443

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=83.59  E-value=6.1  Score=24.68  Aligned_cols=13  Identities=15%  Similarity=-0.133  Sum_probs=6.5

Q ss_pred             HHhhcCCHhHHhh
Q 041561          142 SCQVHSNVRLAKK  154 (156)
Q Consensus       142 ~~~~~g~~~~a~~  154 (156)
                      ++.+.|++++|++
T Consensus        83 g~yklg~Y~~A~~   95 (126)
T 1nzn_A           83 GNYRLKEYEKALK   95 (126)
T ss_dssp             HHHHTTCHHHHHH
T ss_pred             HHHHhhhHHHHHH
Confidence            4445555555544

>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=81.40  E-value=9  Score=27.74  Aligned_cols=78  Identities=13%  Similarity=0.044  Sum_probs=57.8

Q ss_pred             chHHHHHHHHHc-----CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCC-CchHHHHHHHHhcccccccCCCcCCC
Q 041561           55 VTWNEMIHGYAE-----NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHS-GLVYAEVEIFNSMEHDHEVKPKCLMP  128 (156)
Q Consensus        55 ~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~~m~~~~~~~~~c~~~  128 (156)
                      ..|..+-..|.+     .|+.++|.+.|++-.+-...-+..++...-+.+++. ++.+++.+.+++-..-         +
T Consensus       200 sA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a---------~  270 (301)
T 3u64_A          200 AVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAI---------D  270 (301)
T ss_dssp             HHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHC---------C
T ss_pred             HHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcC---------C
Confidence            567777788888     599999999999988743322366677778888885 9999999999988432         1


Q ss_pred             CC--CChhhHHHHHH
Q 041561          129 YK--DDLVVWGDLVS  141 (156)
Q Consensus       129 ~~--pd~~~~~~li~  141 (156)
                      .+  |+....|..-+
T Consensus       271 p~~~P~~~lan~~~q  285 (301)
T 3u64_A          271 PESVPHNKLLVILSQ  285 (301)
T ss_dssp             GGGCSSCHHHHHHHH
T ss_pred             CCCCCChhHHHHHHH
Confidence            23  77777776543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=80.46  E-value=10  Score=25.21  Aligned_cols=45  Identities=16%  Similarity=0.248  Sum_probs=34.5

Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .+.|+++.|.++-+++      -+...|..+=+...+.|+++.|.+.|...
T Consensus        16 L~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~   60 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQ   60 (177)
T ss_dssp             HHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHh
Confidence            4678888888887765      25677888888888888888888877776

---

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	156
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.41
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.28
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.27
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.27
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.0
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.91
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.56
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.45
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.42
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.41
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.4
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.38
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.34
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.31
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.26
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.18
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.07
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.0
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.85
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.84
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	96.79
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.69
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.57
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.54
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.51
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.49
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.32
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.23
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.21
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.19
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.17
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.09
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	95.94
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	95.68
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	95.47
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.16
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.1
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	94.97
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	93.97
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	93.28
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	93.2
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	92.98
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	92.88
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	92.78
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	92.66
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	92.42
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	91.45
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	91.07
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	90.97
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	88.91
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	81.88
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	80.03

>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=98.41  E-value=7.8e-06  Score=57.72  Aligned_cols=135  Identities=11%  Similarity=0.070  Sum_probs=74.1

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHc
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAE   66 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~   66 (156)
                      +|..+-..+...|++++|...++...+... .+...+..+-..|.+.|                    ..|..+-..+..
T Consensus       205 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  283 (388)
T d1w3ba_         205 AYINLGNVLKEARIFDRAVAAYLRALSLSP-NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKE  283 (388)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhhhccccHHHHHHHHHHhHHHhh-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            344444555555666666665555544322 22333344444444444                    345555556666


Q ss_pred             CCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHHHHHhh
Q 041561           67 NEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLVSSCQV  145 (156)
Q Consensus        67 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li~~~~~  145 (156)
                      .|+.++|.+.|+...... ..+...+..+...+.+.|++++|...|++..+           ..| +..+|..+-..|..
T Consensus       284 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-----------~~p~~~~~~~~la~~~~~  351 (388)
T d1w3ba_         284 KGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALE-----------VFPEFAAAHSNLASVLQQ  351 (388)
T ss_dssp             HSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTT-----------SCTTCHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHH-----------hCCCCHHHHHHHHHHHHH
Confidence            666666666666554432 33445555566666666666666666666522           223 34556666677777


Q ss_pred             cCCHhHHhh
Q 041561          146 HSNVRLAKK  154 (156)
Q Consensus       146 ~g~~~~a~~  154 (156)
                      .|++++|.+
T Consensus       352 ~g~~~~A~~  360 (388)
T d1w3ba_         352 QGKLQEALM  360 (388)
T ss_dssp             TTCCHHHHH
T ss_pred             cCCHHHHHH
Confidence            777777654

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.28  E-value=2.3e-05  Score=54.76  Aligned_cols=87  Identities=9%  Similarity=0.002  Sum_probs=61.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-Chh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLV  134 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~  134 (156)
                      .|..+-..+...|++++|.+.|++....... +..+|..+-..+.+.|++++|.+.|+...+.           .| +..
T Consensus       174 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----------~p~~~~  241 (323)
T d1fcha_         174 VQCGLGVLFNLSGEYDKAVDCFTAALSVRPN-DYLLWNKLGATLANGNQSEEAVAAYRRALEL-----------QPGYIR  241 (323)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTCHH
T ss_pred             cchhhHHHHHHHHHHhhhhcccccccccccc-cccchhhhhhcccccccchhHHHHHHHHHHH-----------hhccHH
Confidence            3455566777788888888888877654321 3456667777777888888888888876332           23 466


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                      .|..+-.+|...|++++|.+
T Consensus       242 a~~~lg~~~~~~g~~~~A~~  261 (323)
T d1fcha_         242 SRYNLGISCINLGAHREAVE  261 (323)
T ss_dssp             HHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHH
Confidence            77778888888888888865

>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=98.27  E-value=8.3e-06  Score=57.42  Aligned_cols=140  Identities=8%  Similarity=-0.030  Sum_probs=101.2

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHH-HHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIH-GYA   65 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~-~~~   65 (156)
                      .|.......-+.|+.+.|+.+|+.+.+........+|...+....+.+                    ..|-.... -+.
T Consensus       101 l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~~  180 (308)
T d2onda1         101 LYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYY  180 (308)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            455566677788999999999999876543333456777777776655                    22222222 234


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC--hhhHHHHHHHH
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD--LVVWGDLVSSC  143 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd--~~~~~~li~~~  143 (156)
                      ..|+.+.|.++|+.+.+. ..-+...|...++.+.+.|+.+.|+.+|++-....+        ..|+  ...|...+.--
T Consensus       181 ~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~--------~~~~~~~~iw~~~~~fE  251 (308)
T d2onda1         181 CSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS--------LPPEKSGEIWARFLAFE  251 (308)
T ss_dssp             TSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSS--------SCGGGCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC--------CChHHHHHHHHHHHHHH
Confidence            468899999999999875 233466888899999999999999999998754432        3343  46899999999


Q ss_pred             hhcCCHhHHhhh
Q 041561          144 QVHSNVRLAKKA  155 (156)
Q Consensus       144 ~~~g~~~~a~~~  155 (156)
                      ..+|+.+.++++
T Consensus       252 ~~~G~~~~~~~~  263 (308)
T d2onda1         252 SNIGDLASILKV  263 (308)
T ss_dssp             HHHSCHHHHHHH
T ss_pred             HHcCCHHHHHHH
Confidence            999999988765

>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=98.27  E-value=3.2e-05  Score=54.40  Aligned_cols=138  Identities=13%  Similarity=0.110  Sum_probs=108.5

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYA   65 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~   65 (156)
                      ..+..+-..+...|+.+.|...++...+.. +-+...+..+-..|...|                    ..+..+-..+.
T Consensus       170 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  248 (388)
T d1w3ba_         170 VAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYY  248 (388)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHH
Confidence            455566677788999999999999887643 234566777777777666                    55677888899


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhh
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQV  145 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~  145 (156)
                      +.|++++|.+.|++..+... -+..++..+-..+.+.|+.++|.+.++.....          .+.+...+..+...+..
T Consensus       249 ~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~l~~~~~~  317 (388)
T d1w3ba_         249 EQGLIDLAIDTYRRAIELQP-HFPDAYCNLANALKEKGSVAEAEDCYNTALRL----------CPTHADSLNNLANIKRE  317 (388)
T ss_dssp             HTTCHHHHHHHHHHHHHTCS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHT
T ss_pred             HCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc----------CCccchhhhHHHHHHHH
Confidence            99999999999999876432 23567888888999999999999999987444          35677889999999999


Q ss_pred             cCCHhHHhhh
Q 041561          146 HSNVRLAKKA  155 (156)
Q Consensus       146 ~g~~~~a~~~  155 (156)
                      .|++++|.+.
T Consensus       318 ~~~~~~A~~~  327 (388)
T d1w3ba_         318 QGNIEEAVRL  327 (388)
T ss_dssp             TTCHHHHHHH
T ss_pred             CCCHHHHHHH
Confidence            9999999763

>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=98.00  E-value=5.5e-05  Score=53.04  Aligned_cols=113  Identities=13%  Similarity=0.198  Sum_probs=88.0

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHhCC-CCchHHHhHHHHHhhhcc-------------------chHHHHHHHHH
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKDGY-GNDIFVGSAPINIYCNCG-------------------VTWNEMIHGYA   65 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~~-------------------~~~~~li~~~~   65 (156)
                      ..|...+..+.+.|+.+.|+++|+...+.+. .+......+.+..+....                   ..|...++-..
T Consensus       135 ~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~  214 (308)
T d2onda1         135 LVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLS  214 (308)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence            3678888899999999999999999887653 344444444444333222                   67888899999


Q ss_pred             cCCCHHHHHHHHHHHHHC-CCCcc--HHHHHHHHHhhcCCCchHHHHHHHHhcccc
Q 041561           66 ENEYVEQAISLYKDIIAS-GVKHD--GVTFVAILTPCSHSGLVYAEVEIFNSMEHD  118 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~-g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~  118 (156)
                      +.|++++|..+|++-... +..|+  ...|...+.--.+.|+++.+..+++++.+.
T Consensus       215 ~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         215 HLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             TTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999998765 45554  457899999888999999999999999555

>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=97.91  E-value=0.00033  Score=48.58  Aligned_cols=130  Identities=12%  Similarity=0.051  Sum_probs=80.3

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHHcCCCHHHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYAENEYVEQAI   74 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~~~g~~~~a~   74 (156)
                      +.+.|++++|...|+...+.. +-+...|..+-..|.+.|                    ..|..+...|...|++++|.
T Consensus        29 ~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~  107 (323)
T d1fcha_          29 RLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQAC  107 (323)
T ss_dssp             HHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccccccc
Confidence            446666777777777665532 123455555555555555                    34555555666666666666


Q ss_pred             HHHHHHHHC--------------------------------------------------CCCccHHHHHHHHHhhcCCCc
Q 041561           75 SLYKDIIAS--------------------------------------------------GVKHDGVTFVAILTPCSHSGL  104 (156)
Q Consensus        75 ~~~~~m~~~--------------------------------------------------g~~p~~~t~~~ll~~~~~~~~  104 (156)
                      +.+++....                                                  .-.++...+..+-..+.+.|+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~  187 (323)
T d1fcha_         108 EILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGE  187 (323)
T ss_dssp             HHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTC
T ss_pred             cchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHH
Confidence            665554321                                                  112344556666677778888


Q ss_pred             hHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561          105 VYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       105 ~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +++|...++.....          .+-+...|..+-..|...|++++|.+.
T Consensus       188 ~~~A~~~~~~al~~----------~p~~~~~~~~lg~~~~~~g~~~~A~~~  228 (323)
T d1fcha_         188 YDKAVDCFTAALSV----------RPNDYLLWNKLGATLANGNQSEEAVAA  228 (323)
T ss_dssp             HHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             Hhhhhccccccccc----------ccccccchhhhhhcccccccchhHHHH
Confidence            88888888877433          123567788888888888888888753

>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=97.56  E-value=0.00029  Score=44.40  Aligned_cols=60  Identities=12%  Similarity=0.059  Sum_probs=28.4

Q ss_pred             chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           55 VTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        55 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ..|..+-.+|...|++++|.+.|+...+-. .-+..+|..+..++...|++++|...+++.
T Consensus        45 ~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~eA~~~~~~a  104 (159)
T d1a17a_          45 IYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETV  104 (159)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444445555555555555555555544321 112234444444555555555555555544

>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=97.45  E-value=0.00089  Score=42.04  Aligned_cols=79  Identities=13%  Similarity=0.008  Sum_probs=41.1

Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      |.+.|++++|...|++..+-. .-+...|..+-..+.+.|++++|.+.|+...+.          -+-+...|..+-.+|
T Consensus        20 ~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~----------~p~~~~a~~~~g~~~   88 (159)
T d1a17a_          20 YFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL----------DKKYIKGYYRRAASN   88 (159)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHH----------cccchHHHHHHHHHH
Confidence            345566666666666555432 113344445555555566666666666555322          122345555555666


Q ss_pred             hhcCCHhHHh
Q 041561          144 QVHSNVRLAK  153 (156)
Q Consensus       144 ~~~g~~~~a~  153 (156)
                      ...|++++|.
T Consensus        89 ~~~g~~~eA~   98 (159)
T d1a17a_          89 MALGKFRAAL   98 (159)
T ss_dssp             HHTTCHHHHH
T ss_pred             HHcCCHHHHH
Confidence            6666665554

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.42  E-value=0.0007  Score=43.86  Aligned_cols=114  Identities=8%  Similarity=0.019  Sum_probs=81.8

Q ss_pred             HHhcCCCchHHHHHHHHHHHHh--C-CCCchHH--HhHHHHHhhhcc--chHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 041561           13 SSCAKLSSLFLGRQILTRIVKD--G-YGNDIFV--GSAPINIYCNCG--VTWNEMIHGYAENEYVEQAISLYKDIIASGV   85 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~--g-~~~~~~~--~~~li~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   85 (156)
                      ......|++++|.+.|......  | +.++...  |-.-.....+..  ..+..+...+.+.|++++|.+.++...+.. 
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~al~~~-   97 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEH-   97 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhC-
Confidence            3567889999999999998763  3 2222211  111000000000  678889999999999999999999998754 


Q ss_pred             CccHHHHHHHHHhhcCCCchHHHHHHHHhccc----ccccCCCcCCCCCCChhh
Q 041561           86 KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEH----DHEVKPKCLMPYKDDLVV  135 (156)
Q Consensus        86 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~~~c~~~~~pd~~~  135 (156)
                      .-+...|..++.++.+.|+..+|.+.|++...    +.|        +.|+..+
T Consensus        98 P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG--------~~P~~~l  143 (179)
T d2ff4a2          98 PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLG--------IDPGPTL  143 (179)
T ss_dssp             TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHS--------CCCCHHH
T ss_pred             CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhC--------CCcCHHH
Confidence            34778999999999999999999999998733    456        5777654

>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=97.41  E-value=0.001  Score=42.77  Aligned_cols=96  Identities=7%  Similarity=-0.054  Sum_probs=76.8

Q ss_pred             CCcccHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 041561            3 PTQFPFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA   82 (156)
Q Consensus         3 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   82 (156)
                      |+...+.-.=..+.+.|++++|...|....+..  |+..             ..|+.+-.+|.+.|++++|.+.|+...+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~--p~~~-------------~~~~~lg~~y~~~~~~~~Ai~~~~~al~   66 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVA-------------VYYTNRALCYLKMQQPEQALADCRRALE   66 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCH-------------HHHHhHHHHHhhhhhhhhhhHHHHHHHH
Confidence            555555555567788999999999999987753  4332             6677888899999999999999999875


Q ss_pred             CCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           83 SGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        83 ~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                        +.|+ ..+|..+-.++.+.|++++|...|...
T Consensus        67 --l~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~a   98 (201)
T d2c2la1          67 --LDGQSVKAHFFLGQCQLEMESYDEAIANLQRA   98 (201)
T ss_dssp             --SCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             --hCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence              4454 557888889999999999999999876

>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=97.40  E-value=0.00063  Score=40.71  Aligned_cols=80  Identities=13%  Similarity=0.030  Sum_probs=49.2

Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHH
Q 041561           64 YAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSC  143 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~  143 (156)
                      +...|++++|...|++..+.. .-+...|..+-.++.+.|+.++|...+....+.          -+.+...|..+-.++
T Consensus        13 ~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~~~~~g~~~   81 (117)
T d1elwa_          13 ALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL----------KPDWGKGYSRKAAAL   81 (117)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHh----------ccchhhHHHHHHHHH
Confidence            456677777777777766532 223445666666666677777777777666332          134566666666777


Q ss_pred             hhcCCHhHHhh
Q 041561          144 QVHSNVRLAKK  154 (156)
Q Consensus       144 ~~~g~~~~a~~  154 (156)
                      ...|++++|.+
T Consensus        82 ~~~~~~~~A~~   92 (117)
T d1elwa_          82 EFLNRFEEAKR   92 (117)
T ss_dssp             HHTTCHHHHHH
T ss_pred             HHccCHHHHHH
Confidence            77777776654

>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=97.38  E-value=0.0008  Score=43.36  Aligned_cols=81  Identities=7%  Similarity=-0.133  Sum_probs=67.6

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHHHH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGDLV  140 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~li  140 (156)
                      ..|.+.|++++|.+.|.+..+.. .-+...|..+-.+|.+.|++++|...|+... +          +.| +...|..+=
T Consensus        12 n~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al-~----------l~p~~~~a~~~lg   79 (201)
T d2c2la1          12 NRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRAL-E----------LDGQSVKAHFFLG   79 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHT-T----------SCTTCHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHH-H----------hCCCcHHHHHHHH
Confidence            56789999999999999987653 2356678888889999999999999999883 3          345 577899999


Q ss_pred             HHHhhcCCHhHHhh
Q 041561          141 SSCQVHSNVRLAKK  154 (156)
Q Consensus       141 ~~~~~~g~~~~a~~  154 (156)
                      .+|...|++++|..
T Consensus        80 ~~~~~l~~~~~A~~   93 (201)
T d2c2la1          80 QCQLEMESYDEAIA   93 (201)
T ss_dssp             HHHHHTTCHHHHHH
T ss_pred             HHHHHCCCHHHHHH
Confidence            99999999999975

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.34  E-value=0.00047  Score=41.00  Aligned_cols=84  Identities=10%  Similarity=-0.008  Sum_probs=68.6

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHH
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLV  140 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li  140 (156)
                      -..+.+.|++++|...|++..+.... +...|..+-..+.+.|++++|...|+...+-          -+.+...|..+-
T Consensus        23 g~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~----------~p~~~~a~~~la   91 (112)
T d1hxia_          23 GLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARML----------DPKDIAVHAALA   91 (112)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHhhhcccccc-cchhhhhhhhhhhhhhhHHHhhccccccccc----------ccccccchHHHH
Confidence            34567899999999999998875422 5678888888899999999999999987433          133678899999


Q ss_pred             HHHhhcCCHhHHhhh
Q 041561          141 SSCQVHSNVRLAKKA  155 (156)
Q Consensus       141 ~~~~~~g~~~~a~~~  155 (156)
                      ..|...|+.++|.+.
T Consensus        92 ~~y~~~g~~~~A~~~  106 (112)
T d1hxia_          92 VSHTNEHNANAALAS  106 (112)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHH
Confidence            999999999999863

>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=97.31  E-value=0.0022  Score=38.16  Aligned_cols=87  Identities=8%  Similarity=-0.028  Sum_probs=72.6

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFV   93 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~   93 (156)
                      .+.+.|++++|...|....+.  .|+..             ..|..+-.+|.+.|++++|.+.|....+.. ..+...|.
T Consensus        12 ~~~~~g~~~eAi~~~~~al~~--~p~~~-------------~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~   75 (117)
T d1elwa_          12 KALSVGNIDDALQCYSEAIKL--DPHNH-------------VLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYS   75 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCH-------------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhc--CCcch-------------hhhhcccccccccccccccchhhhhHHHhc-cchhhHHH
Confidence            456789999999999999775  24332             667778888999999999999999998764 34667888


Q ss_pred             HHHHhhcCCCchHHHHHHHHhcc
Q 041561           94 AILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        94 ~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .+-.++...|++++|...|+...
T Consensus        76 ~~g~~~~~~~~~~~A~~~~~~a~   98 (117)
T d1elwa_          76 RKAAALEFLNRFEEAKRTYEEGL   98 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHH
Confidence            88899999999999999999884

>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=97.26  E-value=0.0028  Score=42.20  Aligned_cols=94  Identities=7%  Similarity=-0.049  Sum_probs=68.5

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      |..+=..+.+.|+.++|...|+...+.  .|+..             .+|+.+-.+|.+.|++++|.+.|++..+.... 
T Consensus        40 ~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~-------------~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-  103 (259)
T d1xnfa_          40 LYERGVLYDSLGLRALARNDFSQALAI--RPDMP-------------EVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT-  103 (259)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCH-------------HHHhhhchHHHHHHHHHHhhhhhhHHHHHHhh-
Confidence            333345667788999999999888764  34432             66777788888899999999999888774321 


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +..++..+-..+.+.|+.++|...|+...+
T Consensus       104 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_         104 YNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             CTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            344666777778888899999888887743

>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=97.18  E-value=0.0014  Score=39.63  Aligned_cols=94  Identities=12%  Similarity=0.103  Sum_probs=70.4

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCC---HHHHHHHHHHHHHCCC
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEY---VEQAISLYKDIIASGV   85 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~   85 (156)
                      ..+++.+...++++.|++.|+...+.+- .++              .++..+-.++.+.++   .++|.++|++......
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p-~~~--------------~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~   67 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGS-VSK--------------STQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGS   67 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCH--------------HHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCC-CCH--------------HHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccC
Confidence            4577788889999999999999887542 233              344455556666554   5579999999887665


Q ss_pred             CccH-HHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           86 KHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        86 ~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      .|+. .++..+-.+|.+.|++++|...|+...+
T Consensus        68 ~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          68 KEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            5553 3666777888899999999999999843

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.07  E-value=0.0019  Score=38.13  Aligned_cols=88  Identities=16%  Similarity=0.068  Sum_probs=71.3

Q ss_pred             HHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHH
Q 041561           12 LSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVT   91 (156)
Q Consensus        12 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t   91 (156)
                      =..+-+.|++++|...|+...+..  |+..             ..|..+-.++.+.|++++|...|+...+-. .-+...
T Consensus        23 g~~~~~~g~~~~A~~~~~~al~~~--p~~~-------------~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a   86 (112)
T d1hxia_          23 GLSMLKLANLAEAALAFEAVCQKE--PERE-------------EAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAV   86 (112)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS--TTCH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHHHHhhhHHHHHHHhhhcccc--cccc-------------hhhhhhhhhhhhhhhHHHhhcccccccccc-cccccc
Confidence            345667899999999999987753  4332             677778888999999999999999987743 224668


Q ss_pred             HHHHHHhhcCCCchHHHHHHHHhc
Q 041561           92 FVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        92 ~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +..+-..+...|+.++|.+.+++.
T Consensus        87 ~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          87 HAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHCCCHHHHHHHHHHH
Confidence            888889999999999999999865

>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=97.00  E-value=0.0034  Score=43.86  Aligned_cols=129  Identities=7%  Similarity=-0.036  Sum_probs=80.5

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCC-chHHHhHHHHHhhhcc---------------------chHHHHHHHH
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGN-DIFVGSAPINIYCNCG---------------------VTWNEMIHGY   64 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~~---------------------~~~~~li~~~   64 (156)
                      .|+.+=..+.+.+..++|.++++...+.  .| +...|+..-.++.+.+                     .+|+.+-..+
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~  122 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLV  122 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHH
Confidence            3444545566778899999999999885  34 4445555444444332                     5666667777


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHh
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQ  144 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~  144 (156)
                      .+.|++++|++.|+.+.+.. .-+...|..+-..+.+.|++++|.+.++...+.          -.-+...|+-+-..+.
T Consensus       123 ~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~----------~p~n~~a~~~r~~~l~  191 (315)
T d2h6fa1         123 EWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE----------DVRNNSVWNQRYFVIS  191 (315)
T ss_dssp             HHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH----------CTTCHHHHHHHHHHHH
T ss_pred             HhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHH----------CCccHHHHHHHHHHHH
Confidence            77777777777777776532 224556666667777777777777777777332          1224555665544444


Q ss_pred             hcCC
Q 041561          145 VHSN  148 (156)
Q Consensus       145 ~~g~  148 (156)
                      +.+.
T Consensus       192 ~~~~  195 (315)
T d2h6fa1         192 NTTG  195 (315)
T ss_dssp             HTTC
T ss_pred             Hccc
Confidence            4443

>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=96.85  E-value=0.0053  Score=40.75  Aligned_cols=87  Identities=14%  Similarity=-0.059  Sum_probs=70.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC-Chh
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLV  134 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~  134 (156)
                      .|..+=..|.+.|++++|.+.|++..+-. .-+..+|+.+-.++.+.|++++|...|+...+.           .| +..
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~-----------~p~~~~  106 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL-----------DPTYNY  106 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------CTTCTH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH-----------Hhhhhh
Confidence            44555677889999999999999988742 124567888889999999999999999998543           33 466


Q ss_pred             hHHHHHHHHhhcCCHhHHhh
Q 041561          135 VWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       135 ~~~~li~~~~~~g~~~~a~~  154 (156)
                      +|..+-..|...|++++|.+
T Consensus       107 a~~~lg~~~~~~g~~~~A~~  126 (259)
T d1xnfa_         107 AHLNRGIALYYGGRDKLAQD  126 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHhhHHHHHH
Confidence            78888899999999999875

>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=96.84  E-value=0.011  Score=38.12  Aligned_cols=121  Identities=7%  Similarity=-0.066  Sum_probs=82.1

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVA   94 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~   94 (156)
                      +...|+++.|.+.|+.+    ..|++              ..|..+=.+|...|++++|.+.|++-.+-.. -+...|..
T Consensus        15 ~~~~~d~~~Al~~~~~i----~~~~~--------------~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp-~~~~a~~~   75 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAV----QDPHS--------------RICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQ   75 (192)
T ss_dssp             HHHTTCHHHHHHHHHTS----SSCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHH
T ss_pred             HHHCCCHHHHHHHHHhc----CCCCH--------------HHHHHHHHHHHHcCCchhHHHHHHHHHHHhh-hhhhhHHH
Confidence            35678999999988764    24565              4566678889999999999999999887542 34557777


Q ss_pred             HHHhhcCCCchHHHHHHHHhccccc---ccCCC--cCCCCCCC-hhhHHHHHHHHhhcCCHhHHhh
Q 041561           95 ILTPCSHSGLVYAEVEIFNSMEHDH---EVKPK--CLMPYKDD-LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus        95 ll~~~~~~~~~~~a~~~~~~m~~~~---~~~~~--c~~~~~pd-~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      +-.++.+.|+.++|..-|+.-....   .....  -....+++ ..++..+=.++.+.|++++|.+
T Consensus        76 ~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~  141 (192)
T d1hh8a_          76 RGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEE  141 (192)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHH
Confidence            8888889999999998887652210   00000  00001111 2344455567889999999875

>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=96.79  E-value=0.0041  Score=37.47  Aligned_cols=88  Identities=9%  Similarity=-0.059  Sum_probs=63.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCC---chHHHHHHHHhcccccccCCCcCCCCCCC-h
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG---LVYAEVEIFNSMEHDHEVKPKCLMPYKDD-L  133 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~  133 (156)
                      ..+++.+...+++++|.+.|+.....+ ..+..++..+-.++.+++   +.++|..+++......         -.|+ .
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~---------~~~~~~   72 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG---------SKEEQR   72 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS---------CHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcc---------CCchHH
Confidence            467888889999999999999988754 235556666777777654   5567999999873321         1222 2


Q ss_pred             hhHHHHHHHHhhcCCHhHHhhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+|..+=.+|.+.|++++|++.
T Consensus        73 ~~~~~Lg~~y~~~g~~~~A~~~   94 (122)
T d1nzna_          73 DYVFYLAVGNYRLKEYEKALKY   94 (122)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHH
Confidence            3566677899999999999864

>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=96.69  E-value=0.013  Score=36.93  Aligned_cols=97  Identities=8%  Similarity=-0.122  Sum_probs=71.8

Q ss_pred             HhcCCCchHHHHHHHHHHHHhC-CCCc--h---HHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561           14 SCAKLSSLFLGRQILTRIVKDG-YGND--I---FVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g-~~~~--~---~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      .+.+.|++++|...|....+.- -.+.  .   .....+..      .+|+.+-.+|.+.|++++|.+.++...+... -
T Consensus        22 ~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~------~~~~nla~~y~k~~~~~~A~~~~~~al~~~p-~   94 (170)
T d1p5qa1          22 VYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRL------ASHLNLAMCHLKLQAFSAAIESCNKALELDS-N   94 (170)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHH------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-T
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHH------HHHHHHHHHHHhhhhcccccchhhhhhhccc-c
Confidence            4567899999999999886531 1111  0   11111111      5677888999999999999999999887532 2


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      +...+..+-.++.+.|++++|...|+...+
T Consensus        95 ~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          95 NEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            667788888999999999999999999843

>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=96.57  E-value=0.0049  Score=39.92  Aligned_cols=78  Identities=12%  Similarity=-0.051  Sum_probs=64.6

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           63 GYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        63 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      .+...|++++|.+.|.+.    ..|+..+|..+=..+...|++++|.+.|+.-.+.          -+.+...|..+=.+
T Consensus        14 ~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~l----------dp~~~~a~~~~g~~   79 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINR----------DKHLAVAYFQRGML   79 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHH----------hhhhhhhHHHHHHH
Confidence            346789999999999864    3567788888888999999999999999988433          13467888888899


Q ss_pred             HhhcCCHhHHhh
Q 041561          143 CQVHSNVRLAKK  154 (156)
Q Consensus       143 ~~~~g~~~~a~~  154 (156)
                      |...|++++|.+
T Consensus        80 ~~~~g~~~~A~~   91 (192)
T d1hh8a_          80 YYQTEKYDLAIK   91 (192)
T ss_dssp             HHHTTCHHHHHH
T ss_pred             HHhhccHHHHHH
Confidence            999999999974

>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=96.54  E-value=0.05  Score=36.94  Aligned_cols=144  Identities=9%  Similarity=-0.053  Sum_probs=90.1

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHh----CCCC-chHHHhHHHHHhhhcc--------------------------ch
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKD----GYGN-DIFVGSAPINIYCNCG--------------------------VT   56 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~~--------------------------~~   56 (156)
                      |.-.-..|-..+++++|...|....+.    +-.+ -..+|+.+-.+|.+.|                          ..
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  119 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANF  119 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHH
Confidence            444555666777888888888876542    1111 2356666666666666                          34


Q ss_pred             HHHHHHHHH-cCCCHHHHHHHHHHHHH----CCCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCC
Q 041561           57 WNEMIHGYA-ENEYVEQAISLYKDIIA----SGVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYK  130 (156)
Q Consensus        57 ~~~li~~~~-~~g~~~~a~~~~~~m~~----~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~  130 (156)
                      +..+...|- ..|++++|.+.|++..+    .+-.+. ..++..+...+.+.|++++|...|++........+    ...
T Consensus       120 ~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~----~~~  195 (290)
T d1qqea_         120 KFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNR----LSQ  195 (290)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCT----TTG
T ss_pred             HHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccch----hhh
Confidence            555666664 46999999999988643    232222 34577788899999999999999998743321000    011


Q ss_pred             CCh-hhHHHHHHHHhhcCCHhHHhhh
Q 041561          131 DDL-VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       131 pd~-~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      +.. ..|...+..+...|+++.|.+.
T Consensus       196 ~~~~~~~~~~~~~~l~~~d~~~A~~~  221 (290)
T d1qqea_         196 WSLKDYFLKKGLCQLAATDAVAAART  221 (290)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhccHHHHHHH
Confidence            111 2244555677788999888653

>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=96.51  E-value=0.0063  Score=39.13  Aligned_cols=70  Identities=11%  Similarity=0.104  Sum_probs=57.2

Q ss_pred             cHHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHH----
Q 041561            7 PFTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIA----   82 (156)
Q Consensus         7 t~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----   82 (156)
                      .+..+...+.+.|+.++|...++.+.+.  .|...             ..|..+|.+|.+.|+.++|++.|++...    
T Consensus        69 a~~~la~~~~~~g~~~~Al~~~~~al~~--~P~~e-------------~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~  133 (179)
T d2ff4a2          69 AHTAKAEAEIACGRASAVIAELEALTFE--HPYRE-------------PLWTQLITAYYLSDRQSDALGAYRRVKTTLAD  133 (179)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCH-------------HHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCchHHHHHHHHHHHh--CCccH-------------HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence            4566777888899999999999998774  34332             6789999999999999999999999853    


Q ss_pred             -CCCCccHHH
Q 041561           83 -SGVKHDGVT   91 (156)
Q Consensus        83 -~g~~p~~~t   91 (156)
                       -|+.|...+
T Consensus       134 eLG~~P~~~l  143 (179)
T d2ff4a2         134 DLGIDPGPTL  143 (179)
T ss_dssp             HHSCCCCHHH
T ss_pred             HhCCCcCHHH
Confidence             499998765

>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=96.49  E-value=0.021  Score=35.34  Aligned_cols=99  Identities=11%  Similarity=-0.026  Sum_probs=72.6

Q ss_pred             HhcCCCchHHHHHHHHHHHHhC----CCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDG----YGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDG   89 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g----~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   89 (156)
                      .+.+.|+++.|...|....+.-    -.++............   .+|+.+-.+|.+.|++++|++.++...+.. ..+.
T Consensus        26 ~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~---~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~  101 (153)
T d2fbna1          26 EFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEI---SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNV  101 (153)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHH---HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCH
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHH---HHHhhHHHHHHHhcccchhhhhhhcccccc-chhh
Confidence            4557899999999999877531    1112211111110000   567888999999999999999999987743 3366


Q ss_pred             HHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           90 VTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        90 ~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .+|..+-.++...|++++|...|+...
T Consensus       102 ka~~~~g~~~~~lg~~~~A~~~~~~al  128 (153)
T d2fbna1         102 KALYKLGVANMYFGFLEEAKENLYKAA  128 (153)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hhhHHhHHHHHHcCCHHHHHHHHHHHH
Confidence            799999999999999999999999883

>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=96.32  E-value=0.0028  Score=38.30  Aligned_cols=84  Identities=7%  Similarity=-0.038  Sum_probs=62.3

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-----hhhH
Q 041561           62 HGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-----LVVW  136 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-----~~~~  136 (156)
                      ..|.+.|++++|.+.|.+..+... .+...+..+-.+|.+.|++++|.+.++...+-..        -.++     ..+|
T Consensus        12 ~~~~~~~~y~~Ai~~y~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~--------~~~~~~~~~a~~~   82 (128)
T d1elra_          12 NDAYKKKDFDTALKHYDKAKELDP-TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR--------ENREDYRQIAKAY   82 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH--------HSTTCHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCc--------ccHHHHHHHHHHH
Confidence            457789999999999999887542 3577888889999999999999999998743210        0111     2456


Q ss_pred             HHHHHHHhhcCCHhHHhh
Q 041561          137 GDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       137 ~~li~~~~~~g~~~~a~~  154 (156)
                      ..+=..+...+++++|.+
T Consensus        83 ~~lg~~~~~~~~~~~A~~  100 (128)
T d1elra_          83 ARIGNSYFKEEKYKDAIH  100 (128)
T ss_dssp             HHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHH
Confidence            666677777888888765

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=96.23  E-value=0.037  Score=37.40  Aligned_cols=142  Identities=6%  Similarity=-0.135  Sum_probs=93.0

Q ss_pred             HHHHHHhcCCCchHHHHHHHHHHHHhCC----CCchHHHhHHHHHhhhcc---------------------------chH
Q 041561            9 TTVLSSCAKLSSLFLGRQILTRIVKDGY----GNDIFVGSAPINIYCNCG---------------------------VTW   57 (156)
Q Consensus         9 ~~ll~~~~~~~~~~~a~~~~~~m~~~g~----~~~~~~~~~li~~~~~~~---------------------------~~~   57 (156)
                      ..+-..+...|+++.+...+.......-    ......+..+...+...+                           ..+
T Consensus       137 ~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~  216 (366)
T d1hz4a_         137 RIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNAN  216 (366)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHH
T ss_pred             HHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHH
Confidence            3344566788999999999988866432    112222222223333333                           346


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCC---CccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-h
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGV---KHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-L  133 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~---~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~  133 (156)
                      ..+...+...|++++|.+.++.......   ......+..+-..+...|+.++|...++.......     ..+..|+ .
T Consensus       217 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~-----~~~~~~~~~  291 (366)
T d1hz4a_         217 KVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENAR-----SLRLMSDLN  291 (366)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----HTTCHHHHH
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHh-----hcccChHHH
Confidence            6677788899999999999988655322   22234556677888899999999999987742211     0113343 3


Q ss_pred             hhHHHHHHHHhhcCCHhHHhhh
Q 041561          134 VVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus       134 ~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+|..+=..|...|++++|.+.
T Consensus       292 ~~~~~la~~~~~~g~~~~A~~~  313 (366)
T d1hz4a_         292 RNLLLLNQLYWQAGRKSDAQRV  313 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHH
Confidence            5677777899999999999863

>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=96.21  E-value=0.027  Score=34.76  Aligned_cols=83  Identities=12%  Similarity=0.037  Sum_probs=64.4

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHC----CCCcc-----------HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcC
Q 041561           62 HGYAENEYVEQAISLYKDIIAS----GVKHD-----------GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCL  126 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~----g~~p~-----------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~  126 (156)
                      ..+.+.|++++|...|.+....    ...++           ..+|+.+-.++.+.|++++|.+.++.....        
T Consensus        25 ~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~--------   96 (153)
T d2fbna1          25 NEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI--------   96 (153)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccc--------
Confidence            4566889999999999887642    11112           235667778888999999999999988433        


Q ss_pred             CCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          127 MPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       127 ~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                        -+.+..+|-.+-.++...|++++|..
T Consensus        97 --~p~~~ka~~~~g~~~~~lg~~~~A~~  122 (153)
T d2fbna1          97 --DKNNVKALYKLGVANMYFGFLEEAKE  122 (153)
T ss_dssp             --STTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             --cchhhhhhHHhHHHHHHcCCHHHHHH
Confidence              23478999999999999999999975

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.19  E-value=0.061  Score=33.46  Aligned_cols=128  Identities=5%  Similarity=-0.096  Sum_probs=82.4

Q ss_pred             HHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc----chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 041561           12 LSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG----VTWNEMIHGYAENEYVEQAISLYKDIIASGVKH   87 (156)
Q Consensus        12 l~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   87 (156)
                      -..+.+.|+++.|...|.+..+.-  +........... ....    ..|+.+-.+|.+.|++++|+..|.+..+-. .-
T Consensus        34 ~~~~~~~~~y~~Ai~~y~~al~~~--~~~~~~~~~~~~-~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~  109 (169)
T d1ihga1          34 GNTFFKSQNWEMAIKKYTKVLRYV--EGSRAAAEDADG-AKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PS  109 (169)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH--HHHHHHSCHHHH-GGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhh--hhhhhhhhhHHH-HHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hh
Confidence            344567788888888887765420  000000000000 0000    567778889999999999999999988754 23


Q ss_pred             cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHh
Q 041561           88 DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAK  153 (156)
Q Consensus        88 ~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~  153 (156)
                      +...|..+-.++.+.|++++|.+.|....+-          -+.|...+..+-....+.....+++
T Consensus       110 ~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l----------~p~n~~~~~~l~~~~~~l~~~~~~~  165 (169)
T d1ihga1         110 NTKALYRRAQGWQGLKEYDQALADLKKAQEI----------APEDKAIQAELLKVKQKIKAQKDKE  165 (169)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------CTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHhHHHHHHHccCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            5667888889999999999999999988432          1235566666666555544444443

>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=96.17  E-value=0.014  Score=36.81  Aligned_cols=83  Identities=13%  Similarity=0.058  Sum_probs=63.4

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHC-----CCCcc---------HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCC
Q 041561           62 HGYAENEYVEQAISLYKDIIAS-----GVKHD---------GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        62 ~~~~~~g~~~~a~~~~~~m~~~-----g~~p~---------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                      ..+.+.|++++|.+.|.+....     +....         ..+|+.+-.+|.+.|++++|...++.....         
T Consensus        21 ~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~---------   91 (170)
T d1p5qa1          21 TVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL---------   91 (170)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhc---------
Confidence            4567889999999999887642     11111         245666777788999999999999988433         


Q ss_pred             CCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          128 PYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       128 ~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                       -+.+...|..+-.+|...|++++|.+
T Consensus        92 -~p~~~~a~~~~g~~~~~~g~~~~A~~  117 (170)
T d1p5qa1          92 -DSNNEKGLSRRGEAHLAVNDFELARA  117 (170)
T ss_dssp             -CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             -cccchhhhHHHHHHHHHhhhHHHHHH
Confidence             13378889999999999999999975

>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=96.09  E-value=0.11  Score=35.25  Aligned_cols=140  Identities=9%  Similarity=-0.046  Sum_probs=84.1

Q ss_pred             ccHHHHHHHhcCCCchHHHHHHHHHHHHh----CC-CCchHHHhHHHHHhhh-cc-------------------------
Q 041561            6 FPFTTVLSSCAKLSSLFLGRQILTRIVKD----GY-GNDIFVGSAPINIYCN-CG-------------------------   54 (156)
Q Consensus         6 ~t~~~ll~~~~~~~~~~~a~~~~~~m~~~----g~-~~~~~~~~~li~~~~~-~~-------------------------   54 (156)
                      .+|.-+-..|.+.|++++|...++...+.    |- .....++..+...|-. .|                         
T Consensus        78 ~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~  157 (290)
T d1qqea_          78 NTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALS  157 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhh
Confidence            35666667777888888888888765432    21 1123334444444432 23                         


Q ss_pred             -chHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-----ccHH-HHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCC
Q 041561           55 -VTWNEMIHGYAENEYVEQAISLYKDIIASGVK-----HDGV-TFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLM  127 (156)
Q Consensus        55 -~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-----p~~~-t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~  127 (156)
                       .+|..+...|...|++++|.+.|++.......     .... .+....-.+...++.+.|...++...+...       
T Consensus       158 ~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~-------  230 (290)
T d1qqea_         158 NKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDP-------  230 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------
T ss_pred             hhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-------
Confidence             55788899999999999999999998764211     1111 122333345578999999999999843310       


Q ss_pred             CCCCC---hhhHHHHHHHHhhc--CCHhHHh
Q 041561          128 PYKDD---LVVWGDLVSSCQVH--SNVRLAK  153 (156)
Q Consensus       128 ~~~pd---~~~~~~li~~~~~~--g~~~~a~  153 (156)
                       --++   ......++.++-..  +.+++|.
T Consensus       231 -~~~~sre~~~l~~l~~a~~~~d~e~~~eai  260 (290)
T d1qqea_         231 -NFADSRESNFLKSLIDAVNEGDSEQLSEHC  260 (290)
T ss_dssp             --------HHHHHHHHHHHHTTCTTTHHHHH
T ss_pred             -CccchHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence             0122   23556677776552  2345554

>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=95.94  E-value=0.015  Score=34.85  Aligned_cols=88  Identities=8%  Similarity=0.006  Sum_probs=67.8

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC---CCC--cc
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS---GVK--HD   88 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~--p~   88 (156)
                      .+.+.|++++|...|....+..  |+..             ..|..+-.+|.+.|++++|.+.+++..+-   ...  ++
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~--p~~~-------------~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~   77 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELD--PTNM-------------TYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQ   77 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC--TTCH-------------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC--cccH-------------HHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHH
Confidence            4667899999999999998753  4322             67788889999999999999999998752   111  11


Q ss_pred             -HHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           89 -GVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        89 -~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                       ..+|..+-+.+...+++++|...|..-.
T Consensus        78 ~a~~~~~lg~~~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          78 IAKAYARIGNSYFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence             2366677778888999999999998763

>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=95.68  E-value=0.041  Score=38.11  Aligned_cols=134  Identities=11%  Similarity=0.062  Sum_probs=89.7

Q ss_pred             cHHHHHHHhcCCC-chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc--------------------chHHHHHHHHH
Q 041561            7 PFTTVLSSCAKLS-SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG--------------------VTWNEMIHGYA   65 (156)
Q Consensus         7 t~~~ll~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~--------------------~~~~~li~~~~   65 (156)
                      .|+..-..+...| +.++|...++...+.. +-+..+|+.+-..+.+.|                    ..|+.+-..+.
T Consensus        79 a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~  157 (315)
T d2h6fa1          79 VWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQ  157 (315)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHH
Confidence            4454444555554 5889999888886653 235667777666666666                    78899999999


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhc------CCCchHHHHHHHHhcccccccCCCcCCCCCC-ChhhHHH
Q 041561           66 ENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCS------HSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD-DLVVWGD  138 (156)
Q Consensus        66 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~------~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p-d~~~~~~  138 (156)
                      +.|++++|.+.|+...+.... +...|+..-..+.      ..+.+++|.+.+.....           ..| |...|+-
T Consensus       158 ~~~~~~~Al~~~~~al~~~p~-n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~-----------~~P~~~~~~~~  225 (315)
T d2h6fa1         158 EFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIK-----------LVPHNESAWNY  225 (315)
T ss_dssp             HHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHH-----------HSTTCHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHCCc-cHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHH-----------hCCCchHHHHH
Confidence            999999999999999885422 3445554333322      33446788888887743           356 6777888


Q ss_pred             HHHHHhhcCCHhHHhh
Q 041561          139 LVSSCQVHSNVRLAKK  154 (156)
Q Consensus       139 li~~~~~~g~~~~a~~  154 (156)
                      +-..+...| .+++.+
T Consensus       226 l~~ll~~~~-~~~~~~  240 (315)
T d2h6fa1         226 LKGILQDRG-LSKYPN  240 (315)
T ss_dssp             HHHHHTTTC-GGGCHH
T ss_pred             HHHHHHhcC-hHHHHH
Confidence            877655444 455543

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.47  E-value=0.039  Score=31.77  Aligned_cols=64  Identities=8%  Similarity=0.076  Sum_probs=51.2

Q ss_pred             CHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHH
Q 041561           69 YVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSS  142 (156)
Q Consensus        69 ~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~  142 (156)
                      |.-+..+-+..+..-.+.|+.....+.++||-|..|+..|.++|+..+.+.          .++...|.-+++-
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~----------~~~k~~y~yilqe   84 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA----------GPHKEIYPYVIQE   84 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT----------TTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh----------cCcHHHHHHHHHH
Confidence            444566666666677899999999999999999999999999999997663          3456677777653

>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=95.16  E-value=0.042  Score=37.35  Aligned_cols=115  Identities=9%  Similarity=-0.053  Sum_probs=71.2

Q ss_pred             hcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHH-HHH
Q 041561           15 CAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGV-TFV   93 (156)
Q Consensus        15 ~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~   93 (156)
                      ..+.|++++|...+++.++.  .|+..             ..+..+...++..|++++|.+.|+...+.  .|+.. .+.
T Consensus         6 aL~~G~l~eAl~~l~~al~~--~P~d~-------------~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~~~~~   68 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKA--SPKDA-------------SLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYLPGAS   68 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHT--CTTCH-------------HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHH--CCCCH-------------HHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcHHHHH
Confidence            45679999999999999875  34332             67788889999999999999999998764  45433 333


Q ss_pred             HHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhHHHHHHHHhhcCCHhHHhhh
Q 041561           94 AILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKKA  155 (156)
Q Consensus        94 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~~  155 (156)
                      .+-..+...+..++   .+... ....+     ..-.++...+......+.+.|+.++|.+.
T Consensus        69 ~l~~ll~a~~~~~~---a~~~~-~~~~~-----~~~p~~~~~~l~~a~~~~~~gd~~~A~~~  121 (264)
T d1zbpa1          69 QLRHLVKAAQARKD---FAQGA-ATAKV-----LGENEELTKSLVSFNLSMVSQDYEQVSEL  121 (264)
T ss_dssp             HHHHHHHHHHHHHH---HTTSC-CCEEC-----CCSCHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHhccccHH---HHHHh-hhhhc-----ccCchHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            33333322222222   22222 11110     00122334445556778888999998764

>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=0.18  Score=31.22  Aligned_cols=97  Identities=8%  Similarity=-0.044  Sum_probs=70.7

Q ss_pred             HHhcCCCchHHHHHHHHHHHHh---CCCCchH---HHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 041561           13 SSCAKLSSLFLGRQILTRIVKD---GYGNDIF---VGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVK   86 (156)
Q Consensus        13 ~~~~~~~~~~~a~~~~~~m~~~---g~~~~~~---~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   86 (156)
                      ..+.+.|++..|...|......   -..++..   ....+..      ..|+.+-.+|.+.|++++|.+.++...+-. .
T Consensus        23 ~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~------~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p   95 (168)
T d1kt1a1          23 TVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLL------AAFLNLAMCYLKLREYTKAVECCDKALGLD-S   95 (168)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHH------HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHH------HHHHhHHHHHHHhhhcccchhhhhhhhhcc-c
Confidence            3456789999999999886542   1111111   1111111      456778888999999999999999988743 3


Q ss_pred             ccHHHHHHHHHhhcCCCchHHHHHHHHhcc
Q 041561           87 HDGVTFVAILTPCSHSGLVYAEVEIFNSME  116 (156)
Q Consensus        87 p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~  116 (156)
                      .+..+|...-.++...|++++|...|....
T Consensus        96 ~~~~a~~~~~~~~~~l~~~~~A~~~~~~al  125 (168)
T d1kt1a1          96 ANEKGLYRRGEAQLLMNEFESAKGDFEKVL  125 (168)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            456678888899999999999999999984

>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=94.97  E-value=0.089  Score=32.66  Aligned_cols=87  Identities=9%  Similarity=-0.075  Sum_probs=63.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHC--------------CCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccC
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIAS--------------GVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVK  122 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~--------------g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~  122 (156)
                      ...-..+...|++++|.+.|.+..+-              .+.| +...|..+-.++.+.|++++|...+....+.    
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~----  106 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI----  106 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT----
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhh----
Confidence            33445567888888888888775421              1223 2334566667788899999999999988433    


Q ss_pred             CCcCCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          123 PKCLMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       123 ~~c~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                            -+.+...|..+=.+|...|++++|.+
T Consensus       107 ------~p~~~~a~~~~g~~~~~l~~~~~A~~  132 (169)
T d1ihga1         107 ------DPSNTKALYRRAQGWQGLKEYDQALA  132 (169)
T ss_dssp             ------CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ------hhhhhhHHHhHHHHHHHccCHHHHHH
Confidence                  13477889999999999999999975

>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=93.97  E-value=0.084  Score=32.86  Aligned_cols=85  Identities=12%  Similarity=-0.078  Sum_probs=62.1

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHH---CCCCcc-----------HHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCc
Q 041561           60 MIHGYAENEYVEQAISLYKDIIA---SGVKHD-----------GVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKC  125 (156)
Q Consensus        60 li~~~~~~g~~~~a~~~~~~m~~---~g~~p~-----------~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c  125 (156)
                      .=..+.+.|++++|.+.|++-..   ....++           ...|+.+-.++.+.|++++|...++.....       
T Consensus        21 ~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l-------   93 (168)
T d1kt1a1          21 KGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL-------   93 (168)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhc-------
Confidence            33456788999999999977543   111111           123445556778899999999999988543       


Q ss_pred             CCCCCCChhhHHHHHHHHhhcCCHhHHhh
Q 041561          126 LMPYKDDLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       126 ~~~~~pd~~~~~~li~~~~~~g~~~~a~~  154 (156)
                         -+.+...|..+-.+|...|++++|.+
T Consensus        94 ---~p~~~~a~~~~~~~~~~l~~~~~A~~  119 (168)
T d1kt1a1          94 ---DSANEKGLYRRGEAQLLMNEFESAKG  119 (168)
T ss_dssp             ---CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ---ccchHHHHHHHHHHHHHcCCHHHHHH
Confidence               24578889999999999999999975

>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=93.28  E-value=0.22  Score=30.34  Aligned_cols=90  Identities=6%  Similarity=-0.110  Sum_probs=60.7

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHC-CCCc----------cHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCC
Q 041561           61 IHGYAENEYVEQAISLYKDIIAS-GVKH----------DGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPY  129 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~-g~~p----------~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~  129 (156)
                      -..+.+.|++++|.+.|++-.+- .-.|          ....|+.+-.++.+.|++++|..-++....-...    ....
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~----~~~~   91 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR----RGEL   91 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH----HCCT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc----cccc
Confidence            34456779999999999998751 1122          2457888889999999999999887776321000    0001


Q ss_pred             CCC-----hhhHHHHHHHHhhcCCHhHHhh
Q 041561          130 KDD-----LVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       130 ~pd-----~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      .++     ...|+.+=.+|...|++++|.+
T Consensus        92 ~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~  121 (156)
T d2hr2a1          92 NQDEGKLWISAVYSRALALDGLGRGAEAMP  121 (156)
T ss_dssp             TSTHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccccchhHHHHhhhHHHHHHHHHHHHHHH
Confidence            121     2246667789999999999875

>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=93.20  E-value=0.69  Score=30.66  Aligned_cols=135  Identities=6%  Similarity=-0.128  Sum_probs=71.6

Q ss_pred             HhcCCCchHHHHHHHHHHHHhCCCCc----hHHHhHHHHHhhhcc--------------------------chHHHHHHH
Q 041561           14 SCAKLSSLFLGRQILTRIVKDGYGND----IFVGSAPINIYCNCG--------------------------VTWNEMIHG   63 (156)
Q Consensus        14 ~~~~~~~~~~a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~~--------------------------~~~~~li~~   63 (156)
                      .+...|++++|.+++++..+.--..+    ...++.+-..|...|                          ..+..+...
T Consensus        21 ~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  100 (366)
T d1hz4a_          21 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEI  100 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHH
Confidence            34577888888888888765421111    123333334444444                          334455566


Q ss_pred             HHcCCCHHHHHHHHHHHHH----CCC--CccH-HHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCChhhH
Q 041561           64 YAENEYVEQAISLYKDIIA----SGV--KHDG-VTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDDLVVW  136 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~----~g~--~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd~~~~  136 (156)
                      +...|+++.+.+.+.+...    .+.  .+.. ..+..+-..+...|+++.+...+........     ..+.......+
T Consensus       101 ~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~~~  175 (366)
T d1hz4a_         101 LFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLS-----SYQPQQQLQCL  175 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT-----TSCGGGGHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhh-----hhhhhhHHHHH
Confidence            6677777777777766542    111  1111 2334444556677788877777766633211     00112233444


Q ss_pred             HHHHHHHhhcCCHhHHh
Q 041561          137 GDLVSSCQVHSNVRLAK  153 (156)
Q Consensus       137 ~~li~~~~~~g~~~~a~  153 (156)
                      ..+-..+...|+..++.
T Consensus       176 ~~~~~~~~~~~~~~~a~  192 (366)
T d1hz4a_         176 AMLIQCSLARGDLDNAR  192 (366)
T ss_dssp             HHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHhhhhHHHHH
Confidence            55555666666666554

>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=92.98  E-value=0.12  Score=35.06  Aligned_cols=76  Identities=12%  Similarity=-0.011  Sum_probs=55.5

Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCCC-hhhHHHHHHHH
Q 041561           65 AENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKDD-LVVWGDLVSSC  143 (156)
Q Consensus        65 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~pd-~~~~~~li~~~  143 (156)
                      .+.|++++|.+.+++-++.. .-|...+..+...++..|++++|...++...+.           .|+ ...+..+-..+
T Consensus         7 L~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l-----------~P~~~~~~~~l~~ll   74 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL-----------FPEYLPGASQLRHLV   74 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----------CGGGHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----------CCCcHHHHHHHHHHH
Confidence            46799999999999998864 336678999999999999999999999998433           453 44454444444


Q ss_pred             hhcCCHhHH
Q 041561          144 QVHSNVRLA  152 (156)
Q Consensus       144 ~~~g~~~~a  152 (156)
                      ...+..+++
T Consensus        75 ~a~~~~~~a   83 (264)
T d1zbpa1          75 KAAQARKDF   83 (264)
T ss_dssp             HHHHHHHHH
T ss_pred             HhccccHHH
Confidence            444444433

>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=92.88  E-value=0.97  Score=31.50  Aligned_cols=46  Identities=4%  Similarity=-0.091  Sum_probs=33.9

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhcc
Q 041561            8 FTTVLSSCAKLSSLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCG   54 (156)
Q Consensus         8 ~~~ll~~~~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~   54 (156)
                      ...++..|-..|..++...+++..... -.++...++-++..|++.+
T Consensus       102 l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_         102 LEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC
Confidence            345677777778888877777765422 2467778899999999988

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=92.78  E-value=0.55  Score=28.38  Aligned_cols=99  Identities=13%  Similarity=0.089  Sum_probs=72.3

Q ss_pred             cCCCchHHHHHHHHHHHHhC-C-CCchHHHhHHHHHhh------------------------------hcc---chHHHH
Q 041561           16 AKLSSLFLGRQILTRIVKDG-Y-GNDIFVGSAPINIYC------------------------------NCG---VTWNEM   60 (156)
Q Consensus        16 ~~~~~~~~a~~~~~~m~~~g-~-~~~~~~~~~li~~~~------------------------------~~~---~~~~~l   60 (156)
                      .-.|.+++..++..+..++. . .-|++.+|.+=.+=|                              +.+   ..++-.
T Consensus        13 ildG~ve~Gveii~k~~~ss~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~n~~se~vdlA   92 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNTLNEHVNKA   92 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTCCCHHHHHH
T ss_pred             HHhhhHHhHHHHHHHHcccCCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHhcchHHHHHHH
Confidence            34577888888888776543 2 346666664433222                              222   667888


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           61 IHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      ++.....|.-|+..++++++.+++ +|+....-.+-.||.+.|+..++-+++.+-
T Consensus        93 Ld~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~A  146 (161)
T d1wy6a1          93 LDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEA  146 (161)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            899999999999999999987754 677778888899999999999999998876

>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=92.66  E-value=0.85  Score=31.81  Aligned_cols=45  Identities=18%  Similarity=0.276  Sum_probs=26.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCC
Q 041561           58 NEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSG  103 (156)
Q Consensus        58 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~  103 (156)
                      ..++..|-..|.+++...+++..... -.++...|+-++..+++.+
T Consensus       103 ~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_         103 EELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC
Confidence            45666666666666666666654321 2344555666666666654

>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=92.42  E-value=1  Score=30.52  Aligned_cols=89  Identities=7%  Similarity=-0.018  Sum_probs=61.4

Q ss_pred             chHHHHHHHHHcCCC--HHHHHHHHHHHHHCCCCccHHHHHH-HHHhhcCCCchHHHHHHHHhcccccccCCCcCCCCCC
Q 041561           55 VTWNEMIHGYAENEY--VEQAISLYKDIIASGVKHDGVTFVA-ILTPCSHSGLVYAEVEIFNSMEHDHEVKPKCLMPYKD  131 (156)
Q Consensus        55 ~~~~~li~~~~~~g~--~~~a~~~~~~m~~~g~~p~~~t~~~-ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~c~~~~~p  131 (156)
                      ..|..+-.++...++  .+++...+....+... ++...+.. .-..+...+..++|...++......          .-
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~----------p~  176 (334)
T d1dcea1         108 GTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN----------FS  176 (334)
T ss_dssp             HHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT----------CC
T ss_pred             HHHHHhhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC----------CC
Confidence            456666666666654  7899999999877532 23344433 3356667889999999998884431          23


Q ss_pred             ChhhHHHHHHHHhhcCCHhHHhh
Q 041561          132 DLVVWGDLVSSCQVHSNVRLAKK  154 (156)
Q Consensus       132 d~~~~~~li~~~~~~g~~~~a~~  154 (156)
                      |...|+.+-..+...|++++|..
T Consensus       177 ~~~a~~~l~~~~~~~~~~~~A~~  199 (334)
T d1dcea1         177 NYSSWHYRSCLLPQLHPQPDSGP  199 (334)
T ss_dssp             CHHHHHHHHHHHHHHSCCCCSSS
T ss_pred             CHHHHHHHHHHHHHhcCHHHHHH
Confidence            67778888888888888887643

>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=91.45  E-value=0.091  Score=36.12  Aligned_cols=50  Identities=4%  Similarity=-0.000  Sum_probs=27.5

Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCc-cHHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           64 YAENEYVEQAISLYKDIIASGVKH-DGVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        64 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      +...++.+++.+.|.+..+  ..| +..++..+-..+.+.|+.++|.+.++..
T Consensus       252 ~~~~~~~~~a~~~~~~~~~--~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~a  302 (334)
T d1dcea1         252 STVLQSELESCKELQELEP--ENKWCLLTIILLMRALDPLLYEKETLQYFSTL  302 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHh--hCchHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3334444455554444332  223 2335555666667777777777777766

>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=91.07  E-value=0.35  Score=26.83  Aligned_cols=57  Identities=4%  Similarity=-0.156  Sum_probs=44.2

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHC-----CCCcc-HHHHHHHHHhhcCCCchHHHHHHHHhccc
Q 041561           61 IHGYAENEYVEQAISLYKDIIAS-----GVKHD-GVTFVAILTPCSHSGLVYAEVEIFNSMEH  117 (156)
Q Consensus        61 i~~~~~~g~~~~a~~~~~~m~~~-----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~m~~  117 (156)
                      =..+.+.|++++|.+.|++-.+.     ...++ ..+++.+-.++.+.|++++|...+++..+
T Consensus        12 G~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_          12 GKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            34567899999999999887542     12222 45788889999999999999999999843

>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=90.97  E-value=0.35  Score=26.86  Aligned_cols=60  Identities=7%  Similarity=0.026  Sum_probs=45.4

Q ss_pred             HHHHhcCCCchHHHHHHHHHHHHhCC-----CCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 041561           11 VLSSCAKLSSLFLGRQILTRIVKDGY-----GNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIAS   83 (156)
Q Consensus        11 ll~~~~~~~~~~~a~~~~~~m~~~g~-----~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   83 (156)
                      +=..+-+.|+.+.|...|++..+..-     .++..             ..++.+-.+|.+.|++++|.+.|++..+-
T Consensus        11 lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~-------------~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_          11 LGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKV-------------SVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHH-------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHH-------------HHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            34456788999999999998765321     11111             56778889999999999999999998874

>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=88.91  E-value=1.4  Score=26.37  Aligned_cols=104  Identities=6%  Similarity=-0.111  Sum_probs=69.3

Q ss_pred             ccHHHHHH--HhcCCCchHHHHHHHHHHHHhC-CCCchHHH--hHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHH
Q 041561            6 FPFTTVLS--SCAKLSSLFLGRQILTRIVKDG-YGNDIFVG--SAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDI   80 (156)
Q Consensus         6 ~t~~~ll~--~~~~~~~~~~a~~~~~~m~~~g-~~~~~~~~--~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m   80 (156)
                      .+|..+-.  ...+.|++++|.+.|++..+.. -.|+....  ....      ...|+.+-.+|...|++++|.+-+++.
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~------a~~~~nlg~~~~~lg~~~~A~~~~~~a   81 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFD------AFCHAGLAEALAGLRSFDEALHSADKA   81 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHH------HHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhH------HHHHHHHHHHHHHcCccchhhHhhhhh
Confidence            34555533  4456699999999999987632 12322110  0000      056788899999999999999998887


Q ss_pred             HHC-----CCCcc-----HHHHHHHHHhhcCCCchHHHHHHHHhc
Q 041561           81 IAS-----GVKHD-----GVTFVAILTPCSHSGLVYAEVEIFNSM  115 (156)
Q Consensus        81 ~~~-----g~~p~-----~~t~~~ll~~~~~~~~~~~a~~~~~~m  115 (156)
                      .+-     ...++     ...++.+-.++...|+.++|...|++.
T Consensus        82 l~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~A  126 (156)
T d2hr2a1          82 LHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKV  126 (156)
T ss_dssp             HHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            631     22222     224566678888999999999998875

>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=81.88  E-value=3  Score=23.63  Aligned_cols=71  Identities=6%  Similarity=0.017  Sum_probs=53.9

Q ss_pred             HHhcCCC-chHHHHHHHHHHHHhCCCCchHHHhHHHHHhhhccchHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHH
Q 041561           13 SSCAKLS-SLFLGRQILTRIVKDGYGNDIFVGSAPINIYCNCGVTWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVT   91 (156)
Q Consensus        13 ~~~~~~~-~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t   91 (156)
                      ..+.+.. |.-++.+-++.+....+.|++              ..-.+.+++|.+-+++.-|.++|+-.+.+ ..++...
T Consensus        13 ~~F~~~~iD~we~rrgmN~l~~~DlVPeP--------------~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~   77 (105)
T d1v54e_          13 TYFNKPDIDAWELRKGMNTLVGYDLVPEP--------------KIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEI   77 (105)
T ss_dssp             HHHTCTTCCHHHHHHHHHHHTTSSBCCCH--------------HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTH
T ss_pred             HHhcCcCccHHHHHHHHHHHhccccCCCc--------------HHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHH
Confidence            3444444 677788888888888889999              66677889999999999999999988754 2334557


Q ss_pred             HHHHHHh
Q 041561           92 FVAILTP   98 (156)
Q Consensus        92 ~~~ll~~   98 (156)
                      |..+++-
T Consensus        78 y~yilqe   84 (105)
T d1v54e_          78 YPYVIQE   84 (105)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776654

>d2nsza1 a.118.1.14 (A:322-450) Programmed cell death 4, PDCD4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Programmed cell death 4, PDCD4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.03  E-value=2  Score=25.40  Aligned_cols=62  Identities=11%  Similarity=0.180  Sum_probs=43.1

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCccHHHHHHHHHhhcCCCch--HHHHHHHHhcccc
Q 041561           56 TWNEMIHGYAENEYVEQAISLYKDIIASGVKHDGVTFVAILTPCSHSGLV--YAEVEIFNSMEHD  118 (156)
Q Consensus        56 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~--~~a~~~~~~m~~~  118 (156)
                      -...+|+-|..+|+.++|.+-++++.....+ ..+.+.++..++-+.+.-  +.+..++..+..+
T Consensus         9 k~~~ll~EY~~~~D~~Ea~~~l~eL~~p~~~-~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~~~   72 (129)
T d2nsza1           9 EIDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKS   72 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCchhh-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHC
Confidence            3578899999999999999999998644333 355666666666565543  3356688877433