Citrus Sinensis ID: 034447

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90----
Protein Sequence
MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITWI
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccEHHHHHHHHHHHccccHHHHHHHHHHHHHccccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHccEEcc
Coil and Loop (DISEMBL)
mqqhgktsiSSYSSYIKFLGKNGNSLKALEIYNsitdesdkVNVFICNLILSCLVRNGKFESSLKLFDKIkqsgltpdavtyntvyqsDHITWI
Flexible Loop (DISEMBL)
mqqhgktsisSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIkqsgltpdavtyntvyqsdhitwi
Low Complexity Region (SEG)
MQQHGKTsissyssyiKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITWI
Disordered region (IsUnstruct)
***********YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITW*
Disordered Region (DISOPRED)
***HGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITWI
Disordered Region (DISEMBL)
**********SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITWI
Disordered Region (DISPRO)
****GKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITWI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITWI
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	94	2.2.26 [Sep-21-2011]
Q0WVV0	664	Pentatricopeptide repeat-	yes	no	0.893	0.126	0.670	1e-26
Q9ZU27	650	Pentatricopeptide repeat-	no	no	0.904	0.130	0.302	1e-07
Q9S7Q2	862	Pentatricopeptide repeat-	no	no	0.776	0.084	0.337	2e-07
Q9SZ52	1112	Pentatricopeptide repeat-	no	no	0.829	0.070	0.317	2e-07
Q9FIT7	974	Pentatricopeptide repeat-	no	no	0.776	0.074	0.363	5e-07
Q9LMH5	883	Putative pentatricopeptid	no	no	0.936	0.099	0.280	7e-07
Q9SJN2	497	Pentatricopeptide repeat-	no	no	0.819	0.154	0.308	8e-07
Q9LYZ9	819	Pentatricopeptide repeat-	no	no	0.797	0.091	0.315	2e-06
Q9LIL5	523	Putative pentatricopeptid	no	no	0.872	0.156	0.304	2e-06
Q9SAH2	540	Pentatricopeptide repeat-	no	no	0.797	0.138	0.32	5e-06

>sp|Q0WVV0|PPR31_ARATH Pentatricopeptide repeat-containing protein At1g10910, chloroplastic OS=Arabidopsis thaliana GN=At1g10910 PE=2 SV=1

 Score =  118 bits (295), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 69/85 (81%), Gaps = 1/85 (1%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQQHGK S+S+YSS IKF+G   N  KALEIY SI DES K+NV+ICN ILSCLV+NGK 
Sbjct: 124 MQQHGKISVSTYSSCIKFVGAK-NVSKALEIYQSIPDESTKINVYICNSILSCLVKNGKL 182

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +S +KLFD++K+ GL PD VTYNT+
Sbjct: 183 DSCIKLFDQMKRDGLKPDVVTYNTL 207

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZU27|PPR76_ARATH Pentatricopeptide repeat-containing protein At1g51965, mitochondrial OS=Arabidopsis thaliana GN=At1g51965 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 1/86 (1%)

Query: 1   MQQHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGK 59
           MQ+ G    + +YS+ ++  GK      A  ++  +  +  + N+   N++L CL +NG+
Sbjct: 538 MQEKGLNPDVVTYSTLMECFGKTERVEMAYSLFEEMLVKGCQPNIVTYNILLDCLEKNGR 597

Query: 60  FESSLKLFDKIKQSGLTPDAVTYNTV 85
              ++ L+ K+KQ GLTPD++TY  +
Sbjct: 598 TAEAVDLYSKMKQQGLTPDSITYTVL 623

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S7Q2|PP124_ARATH Pentatricopeptide repeat-containing protein At1g74850, chloroplastic OS=Arabidopsis thaliana GN=PTAC2 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 45/74 (60%)

Query: 12  YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK 71
           Y+  I  LG+ G   K LE+++ +  +    +VF    +++   RNG++E+SL+L D++K
Sbjct: 144 YTIMISLLGREGLLDKCLEVFDEMPSQGVSRSVFSYTALINAYGRNGRYETSLELLDRMK 203

Query: 72  QSGLTPDAVTYNTV 85
              ++P  +TYNTV
Sbjct: 204 NEKISPSILTYNTV 217

Involved in plastid gene expression.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZ52|PP344_ARATH Pentatricopeptide repeat-containing protein At4g31850, chloroplastic OS=Arabidopsis thaliana GN=PGR3 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/82 (31%), Positives = 46/82 (56%)

Query: 6   KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLK 65
           K +  +Y  +I + GK+G+S+ ALE +  +  +    N+  CN  L  L + G+   + +
Sbjct: 430 KPTAYTYIVFIDYYGKSGDSVSALETFEKMKTKGIAPNIVACNASLYSLAKAGRDREAKQ 489

Query: 66  LFDKIKQSGLTPDAVTYNTVYQ 87
           +F  +K  GL PD+VTYN + +
Sbjct: 490 IFYGLKDIGLVPDSVTYNMMMK 511

Plays a role in the stabilization of the primary polycistronic transcript of the petL operon encoding subunits of the cytochrome b6-f complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIT7|PP442_ARATH Pentatricopeptide repeat-containing protein At5g61990, mitochondrial OS=Arabidopsis thaliana GN=At5g61990 PE=2 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 28/77 (36%), Positives = 43/77 (55%)

Query: 9   ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFD 68
           + SY   I    K GN  KA  I++ + +E    NV I N++L    R+G+ E + +L D
Sbjct: 627 VFSYGVLINGFSKLGNMQKASSIFDEMVEEGLTPNVIIYNMLLGGFCRSGEIEKAKELLD 686

Query: 69  KIKQSGLTPDAVTYNTV 85
           ++   GL P+AVTY T+
Sbjct: 687 EMSVKGLHPNAVTYCTI 703

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LMH5|PPR42_ARATH Putative pentatricopeptide repeat-containing protein At1g13800 OS=Arabidopsis thaliana GN=At1g13800 PE=3 SV=1

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 25/89 (28%), Positives = 49/89 (55%), Gaps = 1/89 (1%)

Query: 1   MQQHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGK 59
           M++HG    +  YS+ I+   KN N  KA++++N +  +  ++N  I + IL C  + G 
Sbjct: 317 MEKHGIDPDVYVYSAIIEGHRKNMNIPKAVDVFNKMLKKRKRINCVIVSSILQCYCQMGN 376

Query: 60  FESSLKLFDKIKQSGLTPDAVTYNTVYQS 88
           F  +  LF + +++ ++ D V YN  + +
Sbjct: 377 FSEAYDLFKEFRETNISLDRVCYNVAFDA 405

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJN2|PP187_ARATH Pentatricopeptide repeat-containing protein At2g36240 OS=Arabidopsis thaliana GN=At2g36240 PE=2 SV=1

 Score = 52.4 bits (124), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 48/81 (59%)

Query: 5   GKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSL 64
           GK ++  Y++ +    K+G+  KAL  Y  +  E  K +V   N++++   R+ KF+ +L
Sbjct: 189 GKPNVGVYNTVVNGYVKSGDMDKALRFYQRMGKERAKPDVCTFNILINGYCRSSKFDLAL 248

Query: 65  KLFDKIKQSGLTPDAVTYNTV 85
            LF ++K+ G  P+ V++NT+
Sbjct: 249 DLFREMKEKGCEPNVVSFNTL 269

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYZ9|PP362_ARATH Pentatricopeptide repeat-containing protein At5g02860 OS=Arabidopsis thaliana GN=At5g02860 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 46/76 (60%)

Query: 8   SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLF 67
           SI +Y+S I    ++G   +A+E+ N + ++  K +VF    +LS   R GK ES++ +F
Sbjct: 348 SIVTYNSLISAYARDGMLDEAMELKNQMAEKGTKPDVFTYTTLLSGFERAGKVESAMSIF 407

Query: 68  DKIKQSGLTPDAVTYN 83
           ++++ +G  P+  T+N
Sbjct: 408 EEMRNAGCKPNICTFN 423

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIL5|PP233_ARATH Putative pentatricopeptide repeat-containing protein At3g15200 OS=Arabidopsis thaliana GN=At3g15200 PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 45/82 (54%)

Query: 6   KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLK 65
           +  + SY + I  L K G   KA+E+Y ++ D     +V ICN ++  L    +   +L+
Sbjct: 279 RPDVVSYGTMINALTKKGKLGKAMELYRAMWDTRRNPDVKICNNVIDALCFKKRIPEALE 338

Query: 66  LFDKIKQSGLTPDAVTYNTVYQ 87
           +F +I + G  P+ VTYN++ +
Sbjct: 339 VFREISEKGPDPNVVTYNSLLK 360

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SAH2|PP137_ARATH Pentatricopeptide repeat-containing protein At1g80880, mitochondrial OS=Arabidopsis thaliana GN=At1g80880 PE=2 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 11  SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI 70
           SYS  I    K GN   +L +Y+ +        + + N ++  L R   F+ ++KL  K+
Sbjct: 296 SYSHMISCFSKVGNLFDSLRLYDEMKKRGLAPGIEVYNSLVYVLTREDCFDEAMKLMKKL 355

Query: 71  KQSGLTPDAVTYNTV 85
            + GL PD+VTYN++
Sbjct: 356 NEEGLKPDSVTYNSM 370

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	94
255576798	672	pentatricopeptide repeat-containing prot	0.904	0.126	0.705	9e-28
359486048	659	PREDICTED: pentatricopeptide repeat-cont	0.904	0.128	0.670	2e-26
1931651	652	membrane-associated salt-inducible prote	0.893	0.128	0.670	5e-25
145335386	664	pentatricopeptide repeat-containing prot	0.893	0.126	0.670	6e-25
297843920	665	hypothetical protein ARALYDRAFT_888388 [	0.893	0.126	0.658	1e-24
449446895	668	PREDICTED: pentatricopeptide repeat-cont	0.904	0.127	0.623	8e-24
224058965	562	predicted protein [Populus trichocarpa]	0.872	0.145	0.670	2e-19
357135236	644	PREDICTED: pentatricopeptide repeat-cont	0.904	0.131	0.470	1e-18
218188463	647	hypothetical protein OsI_02428 [Oryza sa	0.904	0.131	0.470	7e-18
297597021	690	Os01g0559500 [Oryza sativa Japonica Grou	0.904	0.123	0.458	1e-17

>gi|255576798|ref|XP_002529286.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223531275|gb|EEF33118.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  127 bits (319), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 60/85 (70%), Positives = 73/85 (85%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQQH K S+SSY+SY+KF+GK+ N  KALEIYNSI DES K NVFICN +LSCLVR+GKF
Sbjct: 138 MQQHSKISVSSYTSYMKFMGKSLNPAKALEIYNSIADESVKNNVFICNSVLSCLVRSGKF 197

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           + SLKLF K+KQ+GLTPD +TY+T+
Sbjct: 198 DISLKLFHKMKQNGLTPDTITYSTL 222

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486048|ref|XP_002270184.2| PREDICTED: pentatricopeptide repeat-containing protein At1g10910, chloroplastic [Vitis vinifera] gi|298204537|emb|CBI23812.3| unnamed protein product [Vitis vinifera]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 72/85 (84%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQ+H K + SSYS+YIKF+GK+ N +KALEIYNSI DES + NV +CN +LSCL+RNGKF
Sbjct: 127 MQKHEKITFSSYSTYIKFMGKSLNPIKALEIYNSIQDESVRNNVSVCNSVLSCLIRNGKF 186

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           E+SLKLF ++KQ GL PDAVTY+T+
Sbjct: 187 ENSLKLFHQMKQDGLRPDAVTYSTL 211

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|1931651|gb|AAB65486.1| membrane-associated salt-inducible protein isolog; 88078-84012 [Arabidopsis thaliana]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 69/85 (81%), Gaps = 1/85 (1%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQQHGK S+S+YSS IKF+G   N  KALEIY SI DES K+NV+ICN ILSCLV+NGK 
Sbjct: 124 MQQHGKISVSTYSSCIKFVGAK-NVSKALEIYQSIPDESTKINVYICNSILSCLVKNGKL 182

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +S +KLFD++K+ GL PD VTYNT+
Sbjct: 183 DSCIKLFDQMKRDGLKPDVVTYNTL 207

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145335386|ref|NP_172560.2| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|122242678|sp|Q0WVV0.1|PPR31_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At1g10910, chloroplastic; Flags: Precursor gi|110741600|dbj|BAE98748.1| membrane-associated salt-inducible protein isolog [Arabidopsis thaliana] gi|332190541|gb|AEE28662.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  118 bits (295), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 69/85 (81%), Gaps = 1/85 (1%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQQHGK S+S+YSS IKF+G   N  KALEIY SI DES K+NV+ICN ILSCLV+NGK 
Sbjct: 124 MQQHGKISVSTYSSCIKFVGAK-NVSKALEIYQSIPDESTKINVYICNSILSCLVKNGKL 182

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +S +KLFD++K+ GL PD VTYNT+
Sbjct: 183 DSCIKLFDQMKRDGLKPDVVTYNTL 207

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843920|ref|XP_002889841.1| hypothetical protein ARALYDRAFT_888388 [Arabidopsis lyrata subsp. lyrata] gi|297335683|gb|EFH66100.1| hypothetical protein ARALYDRAFT_888388 [Arabidopsis lyrata subsp. lyrata]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 56/85 (65%), Positives = 69/85 (81%), Gaps = 1/85 (1%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQQHGK S+S+YSS IKF+G   N  KALEIY SI DES K+NV+ICN ILSCLV+NGK 
Sbjct: 125 MQQHGKISVSTYSSCIKFVGAK-NVSKALEIYQSIPDESTKINVYICNSILSCLVKNGKL 183

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +S +KLFD++K+ GL PD +TYNT+
Sbjct: 184 DSCIKLFDQMKRGGLKPDVITYNTL 208

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446895|ref|XP_004141206.1| PREDICTED: pentatricopeptide repeat-containing protein At1g10910, chloroplastic-like [Cucumis sativus]

 Score =  114 bits (285), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 53/85 (62%), Positives = 71/85 (83%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQ+ GKT++SSYSSYIKF+G+  N LKALE+YN+I + S K ++FICN IL+CLVRNGKF
Sbjct: 129 MQETGKTNVSSYSSYIKFMGRGLNPLKALEVYNNIEEVSIKNSIFICNSILNCLVRNGKF 188

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           ++S+KLF ++K  GL PD VTY+T+
Sbjct: 189 DTSVKLFHQMKNDGLCPDTVTYSTM 213

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224058965|ref|XP_002299667.1| predicted protein [Populus trichocarpa] gi|222846925|gb|EEE84472.1| predicted protein [Populus trichocarpa]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 69/85 (81%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQ+H K S SSYSSYIKF+G + N  KALEIY+SI DES K NVFICN +L CLVRN KF
Sbjct: 30  MQRHNKISASSYSSYIKFMGTSLNPAKALEIYHSIPDESTKTNVFICNSLLRCLVRNTKF 89

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +SS+K F K+K +GLTPDA+TY+T+
Sbjct: 90  DSSMKFFHKMKNNGLTPDAITYSTL 114

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357135236|ref|XP_003569217.1| PREDICTED: pentatricopeptide repeat-containing protein At1g10910, chloroplastic-like [Brachypodium distachyon]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/85 (47%), Positives = 67/85 (78%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQ+H   +++SYSSY K+LG + N+ +AL++Y SI D+S +V+V +CN +L CLV+NG++
Sbjct: 105 MQEHEMLNVASYSSYFKYLGLSRNAARALQVYGSIQDQSIRVHVSVCNSVLGCLVKNGRY 164

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +S+ KL+D++ + GL+PD  TY+T+
Sbjct: 165 DSTFKLYDEMIRGGLSPDLFTYSTL 189

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218188463|gb|EEC70890.1| hypothetical protein OsI_02428 [Oryza sativa Indica Group]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 40/85 (47%), Positives = 64/85 (75%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQ+H   +I+SYSSY KFLG + N  +AL++Y +I +   +++V +CN +L CLV+NG+F
Sbjct: 111 MQEHDMLNIASYSSYFKFLGLSRNPARALQVYGAIRENPTRIHVSVCNSVLGCLVKNGRF 170

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +SS KL+D++ + GL+PD  TY+T+
Sbjct: 171 DSSFKLYDEMIREGLSPDLFTYSTL 195

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297597021|ref|NP_001043343.2| Os01g0559500 [Oryza sativa Japonica Group] gi|255673364|dbj|BAF05257.2| Os01g0559500 [Oryza sativa Japonica Group]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/85 (45%), Positives = 64/85 (75%)

Query: 1   MQQHGKTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
           MQ+H   +I+SYSSY K+LG + N  +AL++Y +I +   +++V +CN +L CLV+NG+F
Sbjct: 114 MQEHDMLNIASYSSYFKYLGLSRNPARALQVYGAIRENPTRIHVSVCNSVLGCLVKNGRF 173

Query: 61  ESSLKLFDKIKQSGLTPDAVTYNTV 85
           +SS KL+D++ + GL+PD  TY+T+
Sbjct: 174 DSSFKLYDEMIREGLSPDLFTYSTL 198

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	94
TAIR|locus:2197424	664	EMB3103 "EMBRYO DEFECTIVE 3103	0.893	0.126	0.6	1.9e-21
TAIR|locus:2027166	862	PTAC2 "plastid transcriptional	0.712	0.077	0.343	1.4e-06
TAIR|locus:504956171	650	ABO5 "ABA Overly-Sensitive 5"	0.702	0.101	0.318	4.3e-06
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.712	0.108	0.298	5.2e-06
TAIR|locus:2174008	974	AT5G61990 "AT5G61990" [Arabido	0.691	0.066	0.384	5.6e-06
TAIR|locus:2116772	1112	PGR3 "AT4G31850" [Arabidopsis	0.702	0.059	0.348	6.6e-06
TAIR|locus:2082727	851	AT3G54980 [Arabidopsis thalian	0.617	0.068	0.372	1.3e-05
TAIR|locus:2049465	497	AT2G36240 "AT2G36240" [Arabido	0.691	0.130	0.338	2.8e-05
TAIR|locus:2177028	816	AT5G12100 [Arabidopsis thalian	0.680	0.078	0.312	3.3e-05
TAIR|locus:2060226	624	AT2G32630 "AT2G32630" [Arabido	0.606	0.091	0.350	4.9e-05

TAIR|locus:2197424 EMB3103 "EMBRYO DEFECTIVE 3103" [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 51/85 (60%), Positives = 61/85 (71%)

Query:     1 MQQHGKTXXXXXXXXXKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF 60
             MQQHGK          KF+G   N  KALEIY SI DES K+NV+ICN ILSCLV+NGK 
Sbjct:   124 MQQHGKISVSTYSSCIKFVGAK-NVSKALEIYQSIPDESTKINVYICNSILSCLVKNGKL 182

Query:    61 ESSLKLFDKIKQSGLTPDAVTYNTV 85
             +S +KLFD++K+ GL PD VTYNT+
Sbjct:   183 DSCIKLFDQMKRDGLKPDVVTYNTL 207

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:2027166 PTAC2 "plastid transcriptionally active 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 1.4e-06, P = 1.4e-06
 Identities = 23/67 (34%), Positives = 42/67 (62%)

Query:    19 LGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPD 78
             LG+ G   K LE+++ +  +    +VF    +++   RNG++E+SL+L D++K   ++P 
Sbjct:   151 LGREGLLDKCLEVFDEMPSQGVSRSVFSYTALINAYGRNGRYETSLELLDRMKNEKISPS 210

Query:    79 AVTYNTV 85
              +TYNTV
Sbjct:   211 ILTYNTV 217

GO:0009507 "chloroplast" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0042793 "transcription from plastid promoter" evidence=RCA;IMP

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

TAIR|locus:504956171 ABO5 "ABA Overly-Sensitive 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 117 (46.2 bits), Expect = 4.3e-06, P = 4.3e-06
 Identities = 21/66 (31%), Positives = 38/66 (57%)

Query:    20 GKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDA 79
             GK      A  ++  +  +  + N+   N++L CL +NG+   ++ L+ K+KQ GLTPD+
Sbjct:   558 GKTERVEMAYSLFEEMLVKGCQPNIVTYNILLDCLEKNGRTAEAVDLYSKMKQQGLTPDS 617

Query:    80 VTYNTV 85
             +TY  +
Sbjct:   618 ITYTVL 623

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008380 "RNA splicing" evidence=IMP

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

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

 Score = 116 (45.9 bits), Expect = 5.2e-06, P = 5.2e-06
 Identities = 20/67 (29%), Positives = 44/67 (65%)

Query:    19 LGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPD 78
             L K+GNS  AL+++  + + + K +V   ++++  L ++G F+ +L LF++++  G+  D
Sbjct:   220 LCKSGNSALALDLFRKMEERNIKASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKAD 279

Query:    79 AVTYNTV 85
              VTY+++
Sbjct:   280 VVTYSSL 286

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2174008 AT5G61990 "AT5G61990" [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 5.6e-06, P = 5.6e-06
 Identities = 25/65 (38%), Positives = 39/65 (60%)

Query:    21 KNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAV 80
             K GN  KA  I++ + +E    NV I N++L    R+G+ E + +L D++   GL P+AV
Sbjct:   639 KLGNMQKASSIFDEMVEEGLTPNVIIYNMLLGGFCRSGEIEKAKELLDEMSVKGLHPNAV 698

Query:    81 TYNTV 85
             TY T+
Sbjct:   699 TYCTI 703

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2116772 PGR3 "AT4G31850" [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 6.6e-06, P = 6.6e-06
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query:    18 FLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP 77
             + GK+G+S+ ALE +  +  +    N+  CN  L  L + G+   + ++F  +K  GL P
Sbjct:   442 YYGKSGDSVSALETFEKMKTKGIAPNIVACNASLYSLAKAGRDREAKQIFYGLKDIGLVP 501

Query:    78 DAVTYN 83
             D+VTYN
Sbjct:   502 DSVTYN 507

GO:0008150 "biological_process" evidence=ND

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0000272 "polysaccharide catabolic process" evidence=RCA

GO:0005982 "starch metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

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

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

TAIR|locus:2082727 AT3G54980 [Arabidopsis thaliana (taxid:3702)]

 Score = 114 (45.2 bits), Expect = 1.3e-05, P = 1.3e-05
 Identities = 22/59 (37%), Positives = 39/59 (66%)

Query:    27 KALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV 85
             +AL++++  + E+   NVF+CN ILS L + GK + + +L  K++  G+ P+ V+YN V
Sbjct:   427 EALKLFDE-SFETGLANVFVCNTILSWLCKQGKTDEATELLSKMESRGIGPNVVSYNNV 484

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2049465 AT2G36240 "AT2G36240" [Arabidopsis thaliana (taxid:3702)]

 Score = 108 (43.1 bits), Expect = 2.8e-05, P = 2.8e-05
 Identities = 22/65 (33%), Positives = 40/65 (61%)

Query:    21 KNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAV 80
             K+G+  KAL  Y  +  E  K +V   N++++   R+ KF+ +L LF ++K+ G  P+ V
Sbjct:   205 KSGDMDKALRFYQRMGKERAKPDVCTFNILINGYCRSSKFDLALDLFREMKEKGCEPNVV 264

Query:    81 TYNTV 85
             ++NT+
Sbjct:   265 SFNTL 269

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2177028 AT5G12100 [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 3.3e-05, P = 3.2e-05
 Identities = 20/64 (31%), Positives = 36/64 (56%)

Query:    22 NGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVT 81
             N  +  AL +Y +  D   K+N + C+++L+ L + GK E + ++  +    GL P+ V 
Sbjct:   332 NEKAEAALGVYETAVDSGVKMNAYTCSILLNALCKEGKIEKAEEILGREMAKGLVPNEVI 391

Query:    82 YNTV 85
             YNT+
Sbjct:   392 YNTM 395

GO:0005739 "mitochondrion" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IDA

TAIR|locus:2060226 AT2G32630 "AT2G32630" [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 4.9e-05, P = 4.8e-05
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query:    29 LEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV 85
             LEI+  + D   K+ V+   +++  L R G+ E S KL  +    G+ P+A TYNT+
Sbjct:   209 LEIFRRMVDSGVKITVYSLTIVVEGLCRRGEVEKSKKLIKEFSVKGIKPEAYTYNTI 265

GO:0003674 "molecular_function" evidence=ND

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: GSVIVG00026521001 SubName- Full=Chromosome chr12 scaffold_38, whole genome shotgun sequence; (644 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	94
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-10
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	3e-06
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	5e-05
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	6e-04
pfam01535	31	pfam01535, PPR, PPR repeat	0.001

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

 Score = 51.3 bits (124), Expect = 1e-10
 Identities = 14/43 (32%), Positives = 27/43 (62%)

Query: 43 NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV 85
          +V   N ++    + GK E +LKLF+++K+ G+ P+  TY+ +
Sbjct: 2  DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSIL 44

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

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

 Score = 39.8 bits (94), Expect = 3e-06
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 45 FICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDA 79
             N ++  L + G+ E +L+LF ++K+ G+ PD 
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 39.9 bits (93), Expect = 5e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%)

Query: 6   KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLK 65
           K    SYSS +       N  KALE+Y  I     +  V   N +++ L    +   +L+
Sbjct: 681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALE 740

Query: 66  LFDKIKQSGLTPDAVTY 82
           +  ++K+ GL P+ +TY
Sbjct: 741 VLSEMKRLGLCPNTITY 757

Length = 1060

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

 Score = 34.1 bits (79), Expect = 6e-04
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 44 VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP 77
          +   N +L  L + G  + +L + +++K SGL P
Sbjct: 1  LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

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

 Score = 33.2 bits (77), Expect = 0.001
 Identities = 10/31 (32%), Positives = 19/31 (61%)

Query: 45 FICNLILSCLVRNGKFESSLKLFDKIKQSGL 75
             N ++S   + GK E +L+LF ++K+ G+
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	94
PLN03218	1060	maturation of RBCL 1; Provisional	99.88
PLN03218	1060	maturation of RBCL 1; Provisional	99.87
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.84
PF13041	50	PPR_2: PPR repeat family	99.84
PF13041	50	PPR_2: PPR repeat family	99.84
PLN03077	857	Protein ECB2; Provisional	99.82
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.82
PLN03077	857	Protein ECB2; Provisional	99.78
PF12854	34	PPR_1: PPR repeat	99.53
PF12854	34	PPR_1: PPR repeat	99.4
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.21
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.17
PF13812	34	PPR_3: Pentatricopeptide repeat domain	99.17
PF13812	34	PPR_3: Pentatricopeptide repeat domain	99.14
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	99.02
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	99.01
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.96
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.95
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.79
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.64
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.62
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	98.44
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.35
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.25
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.18
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.08
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.98
KOG3941	406	consensus Intermediate in Toll signal transduction	97.93
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.93
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.91
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.81
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.7
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.64
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	97.48
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.47
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	97.35
COG3629	280	DnrI DNA-binding transcriptional activator of the	97.28
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.17
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.87
PF13762	145	MNE1: Mitochondrial splicing apparatus component	96.85
PF13371	73	TPR_9: Tetratricopeptide repeat	96.74
PRK12370	553	invasion protein regulator; Provisional	96.7
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	96.64
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.63
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.58
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.54
PRK15359	144	type III secretion system chaperone protein SscB;	96.42
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.4
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.29
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	96.27
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	96.26
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.23
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	96.2
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.14
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	96.12
KOG2003	840	consensus TPR repeat-containing protein [General f	96.11
KOG3941	406	consensus Intermediate in Toll signal transduction	96.08
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	96.0
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	95.99
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.98
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	95.81
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.81
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.81
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	95.66
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	95.66
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	95.65
PRK15359	144	type III secretion system chaperone protein SscB;	95.55
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.48
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	95.42
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	95.36
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.36
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	95.34
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.24
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	95.24
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	95.23
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	95.2
PF12688	120	TPR_5: Tetratrico peptide repeat	95.15
PRK11189	296	lipoprotein NlpI; Provisional	94.86
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	94.71
PF13428	44	TPR_14: Tetratricopeptide repeat	94.61
PF03704	146	BTAD: Bacterial transcriptional activator domain;	94.6
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	94.6
PRK12370	553	invasion protein regulator; Provisional	94.53
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	94.47
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.47
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.33
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	94.3
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	94.29
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	94.2
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	94.11
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	94.07
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	94.03
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	94.03
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	93.99
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	93.93
PF13929	292	mRNA_stabil: mRNA stabilisation	93.88
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	93.83
KOG4570	418	consensus Uncharacterized conserved protein [Funct	93.77
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	93.68
PRK10370	198	formate-dependent nitrite reductase complex subuni	93.64
PRK14574	822	hmsH outer membrane protein; Provisional	93.62
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	93.57
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	93.51
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.46
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	93.45
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	93.34
PRK10370	198	formate-dependent nitrite reductase complex subuni	93.31
PRK10803	263	tol-pal system protein YbgF; Provisional	93.24
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	93.13
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	92.97
PF10579	80	Rapsyn_N: Rapsyn N-terminal myristoylation and lin	92.95
PRK14574	822	hmsH outer membrane protein; Provisional	92.85
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	92.8
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	92.76
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	92.74
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	92.7
PRK11189	296	lipoprotein NlpI; Provisional	92.66
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	92.49
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	92.37
PF13428	44	TPR_14: Tetratricopeptide repeat	92.35
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	92.31
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	92.28
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	92.28
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	92.16
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	92.07
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	92.02
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.98
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	91.91
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	91.91
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	91.88
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	91.72
PF13512	142	TPR_18: Tetratricopeptide repeat	91.71
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	91.68
KOG3785	557	consensus Uncharacterized conserved protein [Funct	91.65
COG4783	484	Putative Zn-dependent protease, contains TPR repea	91.39
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	91.38
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	91.35
KOG1125	579	consensus TPR repeat-containing protein [General f	91.13
KOG2796	366	consensus Uncharacterized conserved protein [Funct	91.05
KOG2076	895	consensus RNA polymerase III transcription factor	91.03
KOG1129	478	consensus TPR repeat-containing protein [General f	91.01
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	90.95
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	90.92
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	90.92
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	90.58
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	90.41
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	90.38
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	90.31
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	90.25
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	90.25
PRK10564	303	maltose regulon periplasmic protein; Provisional	90.01
KOG1915	677	consensus Cell cycle control protein (crooked neck	89.63
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	89.28
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	89.15
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	89.11
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	89.08
KOG1129	478	consensus TPR repeat-containing protein [General f	89.02
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	88.96
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	88.91
KOG4567	370	consensus GTPase-activating protein [General funct	88.37
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	88.29
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	88.28
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	88.05
KOG3616	1636	consensus Selective LIM binding factor [Transcript	87.93
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	87.84
KOG1915	677	consensus Cell cycle control protein (crooked neck	87.76
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	87.75
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	87.56
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	87.52
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	87.43
KOG0553	304	consensus TPR repeat-containing protein [General f	87.32
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	87.02
PRK15331	165	chaperone protein SicA; Provisional	86.84
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	86.59
PF13431	34	TPR_17: Tetratricopeptide repeat	86.42
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	86.36
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	86.3
PRK10564	303	maltose regulon periplasmic protein; Provisional	86.29
COG3629	280	DnrI DNA-binding transcriptional activator of the	85.56
KOG0553	304	consensus TPR repeat-containing protein [General f	85.54
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	85.14
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	85.13
PF12926	88	MOZART2: Mitotic-spindle organizing gamma-tubulin	85.1
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	85.09
PRK14720	906	transcript cleavage factor/unknown domain fusion p	84.98
PF14840	125	DNA_pol3_delt_C: Processivity clamp loader gamma c	84.41
COG4783	484	Putative Zn-dependent protease, contains TPR repea	84.35
COG4455	273	ImpE Protein of avirulence locus involved in tempe	84.33
PF13762	145	MNE1: Mitochondrial splicing apparatus component	84.31
KOG1128	777	consensus Uncharacterized conserved protein, conta	83.83
KOG2003	840	consensus TPR repeat-containing protein [General f	83.33
COG5108	1117	RPO41 Mitochondrial DNA-directed RNA polymerase [T	82.67
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	82.61
KOG4340	459	consensus Uncharacterized conserved protein [Funct	82.48
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	82.02
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	81.92
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	81.68
PF02847	113	MA3: MA3 domain; InterPro: IPR003891 This entry re	81.57
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	81.56
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	81.13
PRK10803	263	tol-pal system protein YbgF; Provisional	81.03
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	80.36
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	80.21
KOG4570	418	consensus Uncharacterized conserved protein [Funct	80.17
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	80.13

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.88  E-value=6.3e-22  Score=140.99  Aligned_cols=89  Identities=18%  Similarity=0.382  Sum_probs=66.2

Q ss_pred             cccC-CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHH
Q 034447            2 QQHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAV   80 (94)
Q Consensus         2 ~~~~-~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   80 (94)
                      .+.+ .||..+||++|.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|.+.|+.||.+
T Consensus       464 ~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~v  543 (1060)
T PLN03218        464 QEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRV  543 (1060)
T ss_pred             HHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHH
Confidence            3445 677777777777777777777777777777777777777777777777777777777777777777777777777


Q ss_pred             HHHHHHHHhh
Q 034447           81 TYNTVYQSDH   90 (94)
Q Consensus        81 ~~~~ll~~~~   90 (94)
                      +|++||++|+
T Consensus       544 TYnsLI~a~~  553 (1060)
T PLN03218        544 VFNALISACG  553 (1060)
T ss_pred             HHHHHHHHHH
Confidence            7777777744

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.87  E-value=2e-21  Score=138.44  Aligned_cols=88  Identities=26%  Similarity=0.440  Sum_probs=63.8

Q ss_pred             ccC-CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHH
Q 034447            3 QHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus         3 ~~~-~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      +.+ .||..+|+++|.+|++.|++++|.++|++|.+.|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..|
T Consensus       677 k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~T  756 (1060)
T PLN03218        677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTIT  756 (1060)
T ss_pred             HcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHH
Confidence            344 6777777777777777777777777777777777777777777777777777777777777777777777777777


Q ss_pred             HHHHHHHhh
Q 034447           82 YNTVYQSDH   90 (94)
Q Consensus        82 ~~~ll~~~~   90 (94)
                      |+++|++|+
T Consensus       757 y~sLL~a~~  765 (1060)
T PLN03218        757 YSILLVASE  765 (1060)
T ss_pred             HHHHHHHHH
Confidence            777777744

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

Probab=99.84  E-value=4.8e-21  Score=132.40  Aligned_cols=79  Identities=16%  Similarity=0.377  Sum_probs=40.8

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      .||..+||+|+++|++.|++++|.++|++|.+    ||..+||+||.+|++.|+.++|+++|++|.+.|+.||.+||+++
T Consensus       357 ~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~l  432 (697)
T PLN03081        357 PLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAV  432 (697)
T ss_pred             CCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            44444444444444444444444444444432    45555555555555555555555555555555555555555555


Q ss_pred             HHH
Q 034447           86 YQS   88 (94)
Q Consensus        86 l~~   88 (94)
                      |++
T Consensus       433 l~a  435 (697)
T PLN03081        433 LSA  435 (697)
T ss_pred             HHH
Confidence            555

>PF13041 PPR_2: PPR repeat family

Probab=99.84  E-value=1.7e-20  Score=90.46  Aligned_cols=49  Identities=37%  Similarity=0.642  Sum_probs=26.7

Q ss_pred             chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHhh
Q 034447           42 VNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDH   90 (94)
Q Consensus        42 p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~   90 (94)
                      ||+.+||++|++|++.|++++|.++|++|.+.|+.||..||+++|++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            4555555555555555555555555555555555555555555555544

>PF13041 PPR_2: PPR repeat family

Probab=99.84  E-value=1.4e-20  Score=90.75  Aligned_cols=50  Identities=18%  Similarity=0.389  Sum_probs=49.0

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHh
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVR   56 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   56 (94)
                      ||+.+||++|++|++.|++++|.++|++|++.|++||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            89999999999999999999999999999999999999999999999985

>PLN03077 Protein ECB2; Provisional

Probab=99.82  E-value=1.3e-19  Score=127.47  Aligned_cols=86  Identities=16%  Similarity=0.269  Sum_probs=77.7

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCccHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK-QSGLTPDAVTYNT   84 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~-~~g~~p~~~~~~~   84 (94)
                      .||..+||++|.+|++.|+.++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|. +.|+.|+..+|++
T Consensus       551 ~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~  630 (857)
T PLN03077        551 EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYAC  630 (857)
T ss_pred             CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHH
Confidence            678899999999999999999999999999999999999999999999999999999999999998 6799999999999


Q ss_pred             HHHHhhc
Q 034447           85 VYQSDHI   91 (94)
Q Consensus        85 ll~~~~~   91 (94)
                      +++++++
T Consensus       631 lv~~l~r  637 (857)
T PLN03077        631 VVDLLGR  637 (857)
T ss_pred             HHHHHHh
Confidence            9999443

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

Probab=99.82  E-value=8.6e-20  Score=126.20  Aligned_cols=86  Identities=20%  Similarity=0.317  Sum_probs=80.1

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCccHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ-SGLTPDAVTYNT   84 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~~~~~   84 (94)
                      +||..+||+||.+|++.|+.++|.++|++|.+.|+.||..||+++|.+|++.|.+++|.++|++|.+ .|+.|+..+|++
T Consensus       388 ~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~  467 (697)
T PLN03081        388 RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYAC  467 (697)
T ss_pred             CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHh
Confidence            6899999999999999999999999999999999999999999999999999999999999999976 599999999999


Q ss_pred             HHHHhhc
Q 034447           85 VYQSDHI   91 (94)
Q Consensus        85 ll~~~~~   91 (94)
                      +|++|++
T Consensus       468 li~~l~r  474 (697)
T PLN03081        468 MIELLGR  474 (697)
T ss_pred             HHHHHHh
Confidence            9999543

>PLN03077 Protein ECB2; Provisional

Probab=99.78  E-value=2.9e-18  Score=120.79  Aligned_cols=85  Identities=16%  Similarity=0.223  Sum_probs=55.3

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      .||.++||++|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|+.+.+.+++..|.+.|+.||..+|++|
T Consensus       250 ~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~L  329 (857)
T PLN03077        250 RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSL  329 (857)
T ss_pred             CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHH
Confidence            45666666666666666666666666666666666666666666666666666666666666666666666666666666


Q ss_pred             HHHhh
Q 034447           86 YQSDH   90 (94)
Q Consensus        86 l~~~~   90 (94)
                      |++|+
T Consensus       330 i~~y~  334 (857)
T PLN03077        330 IQMYL  334 (857)
T ss_pred             HHHHH
Confidence            66643

>PF12854 PPR_1: PPR repeat

Probab=99.53  E-value=1.7e-14  Score=64.05  Aligned_cols=34  Identities=21%  Similarity=0.489  Sum_probs=25.4

Q ss_pred             CCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           38 ESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        38 ~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +|+.||..|||+||++||+.|++++|+++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3677777777777777777777777777777763

>PF12854 PPR_1: PPR repeat

Probab=99.40  E-value=6.1e-13  Score=59.00  Aligned_cols=32  Identities=19%  Similarity=0.395  Sum_probs=30.6

Q ss_pred             CCccHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 034447            5 GKTSISSYSSYIKFLGKNGNSLKALEIYNSIT   36 (94)
Q Consensus         5 ~~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~   36 (94)
                      ..||..|||+||++||+.|++++|.++|++|+
T Consensus         3 ~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    3 CEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            48999999999999999999999999999985

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.21  E-value=3.9e-11  Score=52.86  Aligned_cols=33  Identities=30%  Similarity=0.683  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcc
Q 034447           46 ICNLILSCLVRNGKFESSLKLFDKIKQSGLTPD   78 (94)
Q Consensus        46 t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   78 (94)
                      +||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            577777777777777777777777777777765

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

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.17  E-value=5.9e-11  Score=52.27  Aligned_cols=35  Identities=26%  Similarity=0.420  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNV   44 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~   44 (94)
                      .+||++|.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999983

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=99.17  E-value=6.6e-11  Score=52.05  Aligned_cols=33  Identities=30%  Similarity=0.645  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc
Q 034447           45 FICNLILSCLVRNGKFESSLKLFDKIKQSGLTP   77 (94)
Q Consensus        45 ~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   77 (94)
                      .+|+++|++|++.|+++.|.++|++|.+.|+.|
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            355666666666666666666666665555554

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=99.14  E-value=1e-10  Score=51.42  Aligned_cols=33  Identities=18%  Similarity=0.459  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKV   42 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p   42 (94)
                      .|||++|.+|++.|+++.|.++|++|++.|++|
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            689999999999999999999999999999988

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

Probab=99.02  E-value=4.1e-10  Score=48.41  Aligned_cols=29  Identities=31%  Similarity=0.691  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           46 ICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        46 t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      |||++|++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            55666666666666666666666665554

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.

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

Probab=99.01  E-value=3.1e-08  Score=54.76  Aligned_cols=84  Identities=20%  Similarity=0.193  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-CchHHHHHHHHHHHHhcCC--------HHHHHHHHHHHHHcCCCccHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESD-KVNVFICNLILSCLVRNGK--------FESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~~~~~g~--------~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      |-...|..+...+++..--.+|+.+++.|+ .|++.+|+.++.+.+++..        .-+.+.+|++|...++.|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            334567777777999999999999999999 8999999999999987753        3356789999999999999999


Q ss_pred             HHHHHHHhhcccC
Q 034447           82 YNTVYQSDHITWI   94 (94)
Q Consensus        82 ~~~ll~~~~~~~~   94 (94)
                      |+++|..+.+|-|
T Consensus       107 Ynivl~~LlkgSi  119 (120)
T PF08579_consen  107 YNIVLGSLLKGSI  119 (120)
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999877753

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

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

Probab=98.96  E-value=1.1e-09  Score=47.00  Aligned_cols=31  Identities=26%  Similarity=0.376  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESD   40 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~   40 (94)
                      +|||++|++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4899999999999999999999999998875

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.

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.95  E-value=8e-09  Score=68.54  Aligned_cols=81  Identities=21%  Similarity=0.399  Sum_probs=62.6

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHH----HHHHHHHHHcCCCccHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESS----LKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a----~~~~~~m~~~g~~p~~~~   81 (94)
                      +.+..+||.+|.+-+    +....++..+|....++||..|||+++.+.++.|+++.|    .+++.+|++-|+.|...+
T Consensus       239 kv~~~aFN~lI~~~S----~~~~K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsS  314 (625)
T KOG4422|consen  239 KVYREAFNGLIGASS----YSVGKKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSS  314 (625)
T ss_pred             eeeHHhhhhhhhHHH----hhccHHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhh
Confidence            445555555555444    222256677888888999999999999999999988764    568889999999999999


Q ss_pred             HHHHHHHhh
Q 034447           82 YNTVYQSDH   90 (94)
Q Consensus        82 ~~~ll~~~~   90 (94)
                      |-.+|.-++
T Consensus       315 yh~iik~f~  323 (625)
T KOG4422|consen  315 YHLIIKNFK  323 (625)
T ss_pred             HHHHHHHhc
Confidence            999988744

>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=98.79  E-value=1.3e-07  Score=57.75  Aligned_cols=85  Identities=9%  Similarity=0.214  Sum_probs=74.5

Q ss_pred             CccHHHHHHHHHHHHhc-----CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhc----------------CCHHHHH
Q 034447            6 KTSISSYSSYIKFLGKN-----GNSLKALEIYNSITDESDKVNVFICNLILSCLVRN----------------GKFESSL   64 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~----------------g~~~~a~   64 (94)
                      ..|-.+|..+++.|.+.     |.++=-...++.|.+-|+.-|+.+|+.||+.+-+.                .+.+-|+
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i  123 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAI  123 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHH
Confidence            56788999999999865     78888888999999999999999999999998653                2346788


Q ss_pred             HHHHHHHHcCCCccHHHHHHHHHHhh
Q 034447           65 KLFDKIKQSGLTPDAVTYNTVYQSDH   90 (94)
Q Consensus        65 ~~~~~m~~~g~~p~~~~~~~ll~~~~   90 (94)
                      +++++|...|+.||..|+..|++.+-
T Consensus       124 ~lL~qME~~gV~Pd~Et~~~ll~iFG  149 (228)
T PF06239_consen  124 DLLEQMENNGVMPDKETEQMLLNIFG  149 (228)
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhc
Confidence            99999999999999999999999853

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

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.64  E-value=2.3e-07  Score=61.78  Aligned_cols=79  Identities=20%  Similarity=0.167  Sum_probs=71.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +..||.++|.+.|+.-..+.|.+++++-.....+.+..+||.+|.+-.-..+    .+++.+|......||..|||++++
T Consensus       206 T~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL~  281 (625)
T KOG4422|consen  206 TDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALLS  281 (625)
T ss_pred             CchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHHH
Confidence            5679999999999999999999999999999999999999999998665443    689999999999999999999999


Q ss_pred             Hhh
Q 034447           88 SDH   90 (94)
Q Consensus        88 ~~~   90 (94)
                      +.+
T Consensus       282 c~a  284 (625)
T KOG4422|consen  282 CAA  284 (625)
T ss_pred             HHH
Confidence            843

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

Probab=98.62  E-value=4.5e-07  Score=60.49  Aligned_cols=81  Identities=15%  Similarity=0.132  Sum_probs=72.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHh
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSD   89 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~   89 (94)
                      .|..++++.|.+.|..+.+..+++.=...|+-||-+|||.+|+.+.+.|++..|.++...|...+.-.+..|+..-+-+|
T Consensus       104 ~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~  183 (429)
T PF10037_consen  104 STHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSC  183 (429)
T ss_pred             ccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHH
Confidence            45569999999999999999999999999999999999999999999999999999999998887777888887766664


Q ss_pred             h
Q 034447           90 H   90 (94)
Q Consensus        90 ~   90 (94)
                      .
T Consensus       184 ~  184 (429)
T PF10037_consen  184 Y  184 (429)
T ss_pred             H
Confidence            3

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 [].

>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=98.44  E-value=1.4e-05  Score=45.22  Aligned_cols=81  Identities=16%  Similarity=0.092  Sum_probs=70.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHh---------------hCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSIT---------------DESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~---------------~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      |..++..+|.++++.|+++....+++..=               ...+.|+..+..+++.+|+..+++..|.++.+...+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            67899999999999999999999987651               234569999999999999999999999999999875


Q ss_pred             -cCCCccHHHHHHHHHH
Q 034447           73 -SGLTPDAVTYNTVYQS   88 (94)
Q Consensus        73 -~g~~p~~~~~~~ll~~   88 (94)
                       -+++.+..+|..|++=
T Consensus        81 ~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             HcCCCCCHHHHHHHHHH
Confidence             4788788999988875

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

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

Probab=98.35  E-value=3e-06  Score=60.48  Aligned_cols=81  Identities=9%  Similarity=0.049  Sum_probs=75.6

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      .|+..+|.++++.-..+|+.+.|..++.+|++.|++.+..-|..++-+   .++...++.+++-|...|+.|++.|+..-
T Consensus       201 ~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~ady  277 (1088)
T KOG4318|consen  201 APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADY  277 (1088)
T ss_pred             CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHH
Confidence            589999999999999999999999999999999999999999999887   89999999999999999999999999876


Q ss_pred             HHHh
Q 034447           86 YQSD   89 (94)
Q Consensus        86 l~~~   89 (94)
                      +-.+
T Consensus       278 vip~  281 (1088)
T KOG4318|consen  278 VIPQ  281 (1088)
T ss_pred             HHhh
Confidence            6554

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

Probab=98.25  E-value=3.5e-07  Score=64.98  Aligned_cols=78  Identities=18%  Similarity=0.148  Sum_probs=56.9

Q ss_pred             CcccC-CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccH
Q 034447            1 MQQHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDA   79 (94)
Q Consensus         1 M~~~~-~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   79 (94)
                      |+..| .||.+||..++.-||..|+.+.|- +|.-|+....+.+...|++++.+..++++.+.+.           .|..
T Consensus        16 ~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-----------ep~a   83 (1088)
T KOG4318|consen   16 HEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-----------EPLA   83 (1088)
T ss_pred             HHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-----------CCch
Confidence            35567 999999999999999999999998 9988887666656666666666666665555444           4555


Q ss_pred             HHHHHHHHHhh
Q 034447           80 VTYNTVYQSDH   90 (94)
Q Consensus        80 ~~~~~ll~~~~   90 (94)
                      -||..|+.+|+
T Consensus        84 Dtyt~Ll~ayr   94 (1088)
T KOG4318|consen   84 DTYTNLLKAYR   94 (1088)
T ss_pred             hHHHHHHHHHH
Confidence            66666666644

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.18  E-value=5.4e-05  Score=49.44  Aligned_cols=75  Identities=11%  Similarity=0.118  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      .+++.+..+|.+.|++++|...++++.+.  .|+...+..+...+.+.|++++|.++++++.+.  .|+..++..++..
T Consensus       250 ~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~  324 (389)
T PRK11788        250 EVLPKLMECYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDY  324 (389)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHH
Confidence            45677777777888888888877777654  355566677777788888888888888777654  4777777777665

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.08  E-value=0.00012  Score=47.81  Aligned_cols=77  Identities=12%  Similarity=0.115  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..+..+...+.+.|++++|.+.|+++...+-.....+++.+..+|.+.|++++|...++++.+..  |+...+..+...
T Consensus       215 ~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~la~~  291 (389)
T PRK11788        215 RASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEY--PGADLLLALAQL  291 (389)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchHHHHHHHH
Confidence            34455555666666666666666666543211123445566666666666666666666655542  443444444443

>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=97.98  E-value=4.4e-05  Score=46.90  Aligned_cols=71  Identities=10%  Similarity=0.207  Sum_probs=57.3

Q ss_pred             CcccC-CccHHHHHHHHHHHHhcC----------------CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCH-HH
Q 034447            1 MQQHG-KTSISSYSSYIKFLGKNG----------------NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF-ES   62 (94)
Q Consensus         1 M~~~~-~p~~~~~~~ll~~~~~~g----------------~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~-~~   62 (94)
                      |.+-| .-|..+|+.||+.+=+..                +-+-|.+++++|...|+-||..|+..+++.|++.+.+ .+
T Consensus        78 M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K  157 (228)
T PF06239_consen   78 MDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKK  157 (228)
T ss_pred             HHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHH
Confidence            55667 889999999999998742                3377899999999999999999999999999988854 34


Q ss_pred             HHHHHHHHH
Q 034447           63 SLKLFDKIK   71 (94)
Q Consensus        63 a~~~~~~m~   71 (94)
                      ..++.=-|.
T Consensus       158 ~~rmmYWmp  166 (228)
T PF06239_consen  158 YRRMMYWMP  166 (228)
T ss_pred             HHHHHHHHH
Confidence            555544443

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

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

Probab=97.93  E-value=0.00026  Score=45.49  Aligned_cols=85  Identities=8%  Similarity=0.142  Sum_probs=69.4

Q ss_pred             CccHHHHHHHHHHHHhc-----CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC----------------CHHHHH
Q 034447            6 KTSISSYSSYIKFLGKN-----GNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG----------------KFESSL   64 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g----------------~~~~a~   64 (94)
                      +-|-.+|-+.+..+...     +.++---..++.|.+.|+..|..+|+.||+.+-+..                ..+-++
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I  143 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAI  143 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHH
Confidence            44667777777777654     556766777899999999999999999999986553                234577


Q ss_pred             HHHHHHHHcCCCccHHHHHHHHHHhh
Q 034447           65 KLFDKIKQSGLTPDAVTYNTVYQSDH   90 (94)
Q Consensus        65 ~~~~~m~~~g~~p~~~~~~~ll~~~~   90 (94)
                      +++++|...|+.||..+-..||+++-
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~FG  169 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNAFG  169 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHHhc
Confidence            89999999999999999999999863

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

Probab=97.93  E-value=5.6e-05  Score=42.01  Aligned_cols=52  Identities=23%  Similarity=0.334  Sum_probs=45.9

Q ss_pred             CccHHHHHHHHHHHHhcC--------CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhc
Q 034447            6 KTSISSYSSYIKFLGKNG--------NSLKALEIYNSITDESDKVNVFICNLILSCLVRN   57 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g--------~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   57 (94)
                      .|++.+||.+|.+-++..        .+.+...+++.|...+++|+..||+.++.+..+.
T Consensus        58 lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen   58 LPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             CCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHh
Confidence            799999999999999863        3567788999999999999999999999987654

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 [, , ].

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

Probab=97.91  E-value=0.00035  Score=40.01  Aligned_cols=72  Identities=15%  Similarity=0.289  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCccHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ-----SGLTPDAVTYN   83 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~~   83 (94)
                      ....+...+...|++++|..+.+...... +.|...|..+|.+|...|+..+|.++|+++.+     -|+.|+..+-.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            44566677778999999999999988642 34899999999999999999999999988743     39999887643

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

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

Probab=97.81  E-value=0.00016  Score=48.61  Aligned_cols=87  Identities=10%  Similarity=0.124  Sum_probs=73.1

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC--CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDE--SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYN   83 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   83 (94)
                      ..+......+++.+...-+++++..++-+....  ....-..|..++|+.|.+.|..+.++.+++.=..-|+-||..+|+
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            557788888999999888999999998888754  332334455699999999999999999999999999999999999


Q ss_pred             HHHHH-hhcc
Q 034447           84 TVYQS-DHIT   92 (94)
Q Consensus        84 ~ll~~-~~~~   92 (94)
                      .|++. ...|
T Consensus       143 ~Lmd~fl~~~  152 (429)
T PF10037_consen  143 LLMDHFLKKG  152 (429)
T ss_pred             HHHHHHhhcc
Confidence            99998 4444

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 [].

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

Probab=97.70  E-value=0.00072  Score=33.36  Aligned_cols=57  Identities=14%  Similarity=0.258  Sum_probs=48.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      -..+.+.|++++|..+|++..+.. +-+...+..+-..+...|++++|...|++..+.
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            356788999999999999999765 338889999999999999999999999998654

>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=97.64  E-value=0.00063  Score=33.76  Aligned_cols=63  Identities=19%  Similarity=0.410  Sum_probs=49.2

Q ss_pred             HhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447           20 GKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus        20 ~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      .+.|++++|.++|++..... +-|...+-.+..+|.+.|++++|..++++.....  |+...|..+
T Consensus         2 l~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~--~~~~~~~~l   64 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQD--PDNPEYQQL   64 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG--TTHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCHHHHHHH
Confidence            46799999999999987642 2277788889999999999999999999988764  554444443

...

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

Probab=97.48  E-value=0.0041  Score=43.92  Aligned_cols=62  Identities=11%  Similarity=0.126  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .++..+...+.+.|++++|..+++.+.... +.+...+..+...+...|++++|.+.|+++.+
T Consensus       670 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  731 (899)
T TIGR02917       670 EAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALK  731 (899)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            333444444444444444444444443322 12333344444444444444444444444433

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.

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

Probab=97.47  E-value=0.0021  Score=32.82  Aligned_cols=63  Identities=22%  Similarity=0.374  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----C-CCch-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----S-DKVN-VFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~-~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ..+|+.+-..|.+.|++++|...|++..+.    | -.|+ ..+++.+-..|...|++++|++.+++-.
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            357888899999999999999999988643    2 1244 7788899999999999999999998754

...

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

Probab=97.35  E-value=0.0023  Score=45.20  Aligned_cols=85  Identities=13%  Similarity=-0.005  Sum_probs=66.7

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      ..+...++.+...+.+.|+ ++|...+++..... +-+..++..+...+...|++++|...++++.+.+.. +..++..+
T Consensus       801 p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l  877 (899)
T TIGR02917       801 PDNAVVLNNLAWLYLELKD-PRALEYAEKALKLA-PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHL  877 (899)
T ss_pred             CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHH
Confidence            3577888999999999999 88999998887542 225566777888889999999999999999887643 77888888


Q ss_pred             HHH-hhccc
Q 034447           86 YQS-DHITW   93 (94)
Q Consensus        86 l~~-~~~~~   93 (94)
                      ..+ +..|+
T Consensus       878 ~~~~~~~g~  886 (899)
T TIGR02917       878 ALALLATGR  886 (899)
T ss_pred             HHHHHHcCC
Confidence            877 44443

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.

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

Probab=97.28  E-value=0.014  Score=37.41  Aligned_cols=78  Identities=10%  Similarity=0.169  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCccHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ-----SGLTPDAVTYNT   84 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~~~   84 (94)
                      .++..+...+...|+.+.+.+.++++.... +.|...|..+|.+|.+.|+...|++.|+++.+     -|+.|...+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            467778889999999999999999998653 35999999999999999999999999999876     499999888776


Q ss_pred             HHHH
Q 034447           85 VYQS   88 (94)
Q Consensus        85 ll~~   88 (94)
                      ..+.
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            6655

>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=97.17  E-value=0.0073  Score=29.93  Aligned_cols=64  Identities=13%  Similarity=0.190  Sum_probs=54.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC-CHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG-KFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g-~~~~a~~~~~~m~~   72 (94)
                      ++..|..+=..+.+.|++++|...|++..+.. +-+...|..+-.+|.+.| ++++|++.+++-.+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            46678888889999999999999999888753 338888999999999999 79999999988654

...

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

Probab=96.87  E-value=0.0048  Score=32.01  Aligned_cols=47  Identities=23%  Similarity=0.459  Sum_probs=19.8

Q ss_pred             CCHHHHHHHHHHHhhCCC-CchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447           23 GNSLKALEIYNSITDESD-KVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus        23 g~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      |+++.|..+++++.+..- .++...+-.+..+|.+.|++++|+.++++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            444455555554443211 11222333344445555555555555544

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=96.85  E-value=0.034  Score=32.32  Aligned_cols=84  Identities=13%  Similarity=0.133  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-----CchHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHcCCCccHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESD-----KVNVFICNLILSCLVRNGK-FESSLKLFDKIKQSGLTPDAVTY   82 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-----~p~~~t~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~~~   82 (94)
                      ....|++|...+..+++.....+++.+.....     ..+-..|.+++++.+++.- --.+..+|+.|++.+.+++..-|
T Consensus        39 ~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy  118 (145)
T PF13762_consen   39 TIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDY  118 (145)
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            46678999999999999999999988853211     1455679999999987776 44677889999998999999999


Q ss_pred             HHHHHHhhcc
Q 034447           83 NTVYQSDHIT   92 (94)
Q Consensus        83 ~~ll~~~~~~   92 (94)
                      ..+|+++-+|
T Consensus       119 ~~li~~~l~g  128 (145)
T PF13762_consen  119 SCLIKAALRG  128 (145)
T ss_pred             HHHHHHHHcC
Confidence            9999998776

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.74  E-value=0.021  Score=28.55  Aligned_cols=58  Identities=14%  Similarity=0.195  Sum_probs=49.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      -..|.+.+++++|.++++.+...+ +.+...|...-..+.+.|++++|...|++..+.+
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            356889999999999999998752 2377778888888999999999999999988654

>PRK12370 invasion protein regulator; Provisional

Probab=96.70  E-value=0.085  Score=36.77  Aligned_cols=65  Identities=9%  Similarity=-0.008  Sum_probs=35.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..+...|++++|...|++..+.+ +-+...|..+-..+...|++++|+..+++..+.
T Consensus       337 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l  401 (553)
T PRK12370        337 NPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKL  401 (553)
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            34444444455555666666666666655432 113445555555566666666666666665443

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

Probab=96.64  E-value=0.043  Score=34.66  Aligned_cols=80  Identities=13%  Similarity=0.081  Sum_probs=47.9

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcc-HHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDE-SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPD-AVTYNT   84 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~   84 (94)
                      ++...+...+..+.+.++++++.+++++.... ..+.+...|..+...+.+.|+.++|++.+++..+..  |+ ......
T Consensus       108 ~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--P~~~~~~~~  185 (280)
T PF13429_consen  108 GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELD--PDDPDARNA  185 (280)
T ss_dssp             ----------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHH
T ss_pred             cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHH
Confidence            45566777888888889999999998887643 345677888888888889999999999998877653  43 444544


Q ss_pred             HHHH
Q 034447           85 VYQS   88 (94)
Q Consensus        85 ll~~   88 (94)
                      ++..
T Consensus       186 l~~~  189 (280)
T PF13429_consen  186 LAWL  189 (280)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5444

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

Probab=96.63  E-value=0.044  Score=30.56  Aligned_cols=65  Identities=11%  Similarity=0.114  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ......+...+.+.|++++|...|+.....+ +.+...|..+-..+...|++++|...+++..+.+
T Consensus        17 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~   81 (135)
T TIGR02552        17 LEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD   81 (135)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3445556666667777777777777776543 2366666677777777777777777777765543

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

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

Probab=96.58  E-value=0.0099  Score=30.81  Aligned_cols=60  Identities=22%  Similarity=0.331  Sum_probs=43.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      +...+-.+-.+|.+.|++++|..+++. ...+- .+....-.+-.++.+.|++++|++++++
T Consensus        24 ~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   24 NSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             HHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence            344455578899999999999999988 32221 1334444557889999999999999875

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

Probab=96.54  E-value=0.052  Score=30.25  Aligned_cols=75  Identities=15%  Similarity=0.090  Sum_probs=59.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      +...+..+-..+.+.|++++|...++...... +.+...+..+-..+...|++++|.+.|++..+..  |+...+..+
T Consensus        50 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~  124 (135)
T TIGR02552        50 NSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGEPESALKALDLAIEIC--GENPEYSEL  124 (135)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc--cccchHHHH
Confidence            56777788888889999999999999887653 3467777778889999999999999999887754  555544433

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

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=96.42  E-value=0.073  Score=30.59  Aligned_cols=64  Identities=11%  Similarity=-0.054  Sum_probs=29.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|..+-.++.+.|++++|...|+...... +.+...+..+-.++...|+.++|+..|++..+
T Consensus        57 ~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359         57 SWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33444444444444555555555555444321 12444444444445555555555555554433

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

Probab=96.40  E-value=0.11  Score=33.28  Aligned_cols=84  Identities=13%  Similarity=0.186  Sum_probs=61.1

Q ss_pred             cHHHHHHHHHHHHhc----CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHH
Q 034447            8 SISSYSSYIKFLGKN----GNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYN   83 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~----g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   83 (94)
                      +..|.+.|-.+|.+.    +...+|.-+|++|-+ ...|+.-+-|-...++...|++++|..+++....+.-. ++.+..
T Consensus       168 ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL~  245 (299)
T KOG3081|consen  168 EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETLA  245 (299)
T ss_pred             hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHHH
Confidence            345667676666653    568999999999975 36789999999999999999999999999998765432 233333


Q ss_pred             HHH-HHhhccc
Q 034447           84 TVY-QSDHITW   93 (94)
Q Consensus        84 ~ll-~~~~~~~   93 (94)
                      .+| .+.+.|+
T Consensus       246 Nliv~a~~~Gk  256 (299)
T KOG3081|consen  246 NLIVLALHLGK  256 (299)
T ss_pred             HHHHHHHHhCC
Confidence            333 3355553

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.29  E-value=0.099  Score=30.75  Aligned_cols=66  Identities=15%  Similarity=0.155  Sum_probs=53.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-..+.+.|++++|...|++.....-.+  ....+..+...+.+.|++++|...+++..+.
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  101 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL  101 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            34566777778888999999999999887643222  2467888889999999999999999998764

>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=96.27  E-value=0.088  Score=33.93  Aligned_cols=67  Identities=16%  Similarity=0.247  Sum_probs=42.6

Q ss_pred             CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH-hhcc
Q 034447           24 NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS-DHIT   92 (94)
Q Consensus        24 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~-~~~~   92 (94)
                      .+.+|.-+|+++.+. +.++..+.|.+..++...|++++|.+++++-...+- -+..+...++.. .+.|
T Consensus       182 ~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-~~~d~LaNliv~~~~~g  249 (290)
T PF04733_consen  182 KYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-NDPDTLANLIVCSLHLG  249 (290)
T ss_dssp             CCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhC
Confidence            577788888887553 557788888888888888888888888888654432 233444444444 4444

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=96.26  E-value=0.11  Score=30.86  Aligned_cols=62  Identities=10%  Similarity=-0.003  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+..+-..+.+.|++++|...+++..... +.+...+..+...+...|++++|.+.+++..+
T Consensus        32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~   93 (234)
T TIGR02521        32 KIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALT   93 (234)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            334444445555555555555555444321 12334444444555555555555555554443

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.

>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=96.23  E-value=0.052  Score=26.99  Aligned_cols=62  Identities=19%  Similarity=0.188  Sum_probs=46.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +..+...+.+.|++++|...+++..+.. +.+...+..+...+...+++++|.+.+++..+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~   64 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD   64 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            4556667778899999999998876542 2244667778888888899999999998877654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=96.20  E-value=0.12  Score=30.68  Aligned_cols=61  Identities=10%  Similarity=-0.011  Sum_probs=33.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +..+-..+.+.|++++|...+++..... +.+...+..+...+...|++++|...+++..+.
T Consensus       138 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  198 (234)
T TIGR02521       138 LENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQT  198 (234)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3344445555566666666665554321 123445555666666666666666666665544

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.

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

Probab=96.14  E-value=0.06  Score=30.51  Aligned_cols=53  Identities=11%  Similarity=0.085  Sum_probs=46.6

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHh-hCCCCchHHHHHHHHHHHHhcC
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSIT-DESDKVNVFICNLILSCLVRNG   58 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~-~~~~~p~~~t~~~li~~~~~~g   58 (94)
                      .|+..+..+++.+|+..+++..|.++.+... ..+++.+..+|..|+.=....-
T Consensus        49 ~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s  102 (126)
T PF12921_consen   49 YPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLS  102 (126)
T ss_pred             CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhc
Confidence            7999999999999999999999999999886 4588888999999998765443

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

>TIGR00540 hemY_coli hemY protein

Probab=96.12  E-value=0.083  Score=35.37  Aligned_cols=60  Identities=8%  Similarity=0.142  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      ...++=..+.+.|++++|.+.|+.-......||...+..+...+-+.|+.++|.+++++-
T Consensus       337 ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       337 INRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            334555566677777777777774333334577777777777777777777777777763

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.

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

Probab=96.11  E-value=0.16  Score=35.16  Aligned_cols=78  Identities=14%  Similarity=0.222  Sum_probs=59.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLV-RNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~-~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      |..|-..|-..|....-++++...|++-..  +.|+..-|..||..|. +.|++++|+++|++.-++ ++-|..+..-|+
T Consensus       625 nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflv  701 (840)
T KOG2003|consen  625 NIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLV  701 (840)
T ss_pred             chHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHH
Confidence            666777777888888888999998887653  5799999999998876 568999999999998654 444555555555


Q ss_pred             HH
Q 034447           87 QS   88 (94)
Q Consensus        87 ~~   88 (94)
                      +.
T Consensus       702 ri  703 (840)
T KOG2003|consen  702 RI  703 (840)
T ss_pred             HH
Confidence            54

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

Probab=96.08  E-value=0.033  Score=36.18  Aligned_cols=72  Identities=10%  Similarity=0.153  Sum_probs=55.5

Q ss_pred             CcccC-CccHHHHHHHHHHHHhcC----------------CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCH-HH
Q 034447            1 MQQHG-KTSISSYSSYIKFLGKNG----------------NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKF-ES   62 (94)
Q Consensus         1 M~~~~-~p~~~~~~~ll~~~~~~g----------------~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~-~~   62 (94)
                      |.+-| .-|..+|+.||..+-+-.                .-+=+..++++|...|+-||..+-..++++|++-+.+ .+
T Consensus        98 m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K  177 (406)
T KOG3941|consen   98 MKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKK  177 (406)
T ss_pred             HHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccHHH
Confidence            44556 779999999999887653                2244688999999999999999999999999998854 35


Q ss_pred             HHHHHHHHHH
Q 034447           63 SLKLFDKIKQ   72 (94)
Q Consensus        63 a~~~~~~m~~   72 (94)
                      ..++.--|.+
T Consensus       178 ~~Rm~yWmPk  187 (406)
T KOG3941|consen  178 VKRMLYWMPK  187 (406)
T ss_pred             HHHHHHhhhh
Confidence            5555555543

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

Probab=96.00  E-value=0.033  Score=35.16  Aligned_cols=64  Identities=14%  Similarity=0.190  Sum_probs=33.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      |...|..+-..+.+.|+.++|.+++++..+.  .| |....+.++..+...|+.+++..+++...+.
T Consensus       145 ~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~  209 (280)
T PF13429_consen  145 SARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKA  209 (280)
T ss_dssp             -HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHH
Confidence            4455555555556666666666666655442  24 3445555555555555555555555554433

>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=95.99  E-value=0.072  Score=26.45  Aligned_cols=65  Identities=20%  Similarity=0.190  Sum_probs=52.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..+...+++++|.+.++...... +.+..++..+...+...|++++|...+++..+.
T Consensus        33 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          33 NADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGKYEEALEAYEKALEL   97 (100)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHhHHHHHHHHHHHHcc
Confidence            33567778888888999999999999887653 234468888889999999999999999887653

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

Probab=95.98  E-value=0.25  Score=32.68  Aligned_cols=66  Identities=11%  Similarity=-0.027  Sum_probs=53.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+-.+|.+.|++++|...++...... +.+...|..+-.+|...|++++|+..|++..+..
T Consensus        35 ~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~eA~~~~~~al~l~  100 (356)
T PLN03088         35 NAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQTAKAALEKGASLA  100 (356)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            55677778888899999999999999887642 2367778888888999999999999999987643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=95.81  E-value=0.17  Score=33.85  Aligned_cols=61  Identities=10%  Similarity=0.153  Sum_probs=50.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP   77 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   77 (94)
                      -..+...|++++|...+++..+.. +-+......+...|.+.|++++|.+++.++.+.+..+
T Consensus       160 a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~  220 (398)
T PRK10747        160 VRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGD  220 (398)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCC
Confidence            457778899999999999887654 3377888888999999999999999999998876653

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=95.81  E-value=0.033  Score=24.28  Aligned_cols=26  Identities=12%  Similarity=0.299  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           46 ICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        46 t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +|+.|-+.|.+.|++++|+.+|++..
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            47788889999999999999998843

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.81  E-value=0.26  Score=33.76  Aligned_cols=65  Identities=9%  Similarity=-0.008  Sum_probs=55.8

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNV----FICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+...++.+=.+|.+.|++++|...|++-.+.  .|+.    .+|..+-.+|...|+.++|+..+++..+.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            36788999999999999999999999986654  3653    46899999999999999999999987764

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=95.66  E-value=0.35  Score=33.73  Aligned_cols=73  Identities=10%  Similarity=-0.057  Sum_probs=57.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCccHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ-SGLTPDAVTY   82 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~~~   82 (94)
                      +...|.++-......|++++|...+++....+  |+...|..+-..+...|+.++|...+++-.+ +...|+.+.+
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt~~~~  492 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENTLYWI  492 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCchHHHH
Confidence            44667766555566799999999999988765  7889999999999999999999999988654 3444544333

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=95.66  E-value=0.21  Score=33.46  Aligned_cols=57  Identities=16%  Similarity=0.155  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      .+.++=..+.+.+++++|.+.|+...+.  .|+..+|-.+...+.+.|+.++|.+.+++
T Consensus       330 l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~  386 (398)
T PRK10747        330 LWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRD  386 (398)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            3444555555556666666666555543  35555555666666666666666555554

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=95.65  E-value=0.48  Score=33.90  Aligned_cols=59  Identities=17%  Similarity=-0.034  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +..+-..+.+.|++++|...+++..... +.+...+..+...+...|++++|...++++.
T Consensus       113 ~~~la~~l~~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~  171 (656)
T PRK15174        113 VLLVASVLLKSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQA  171 (656)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            3334444444455555555554444320 1133444444444555555555555544443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=95.55  E-value=0.21  Score=28.64  Aligned_cols=62  Identities=3%  Similarity=-0.061  Sum_probs=52.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +..+-..+.+.|++++|...|+...... +.+...|..+-..+...|++++|+..|++..+..
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~   88 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD   88 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            4456677788999999999999987543 3488899999999999999999999999998743

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.48  E-value=0.17  Score=27.13  Aligned_cols=60  Identities=12%  Similarity=0.137  Sum_probs=28.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCC--CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESD--KVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      -.+...+.+.|++++|...|+......=  ......+..+...+.+.|+++.|.+.|++...
T Consensus         6 ~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~   67 (119)
T TIGR02795         6 YDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVK   67 (119)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            3444445555555555555555543210  00122333455555555555555555555543

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.

>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=95.42  E-value=0.6  Score=32.97  Aligned_cols=58  Identities=17%  Similarity=0.131  Sum_probs=22.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      |..+-..+...|++++|...|++..+.. +.+...+..+...+.+.|++++|+..|++.
T Consensus       402 ~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~a  459 (615)
T TIGR00990       402 YYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRC  459 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3333333444444444444444333221 112333333333344444444444444443

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

Probab=95.36  E-value=0.22  Score=33.44  Aligned_cols=62  Identities=15%  Similarity=-0.073  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+..|=..|.+.+.+.+|...|+.-.  ...|+..+|+-+-+++.+.|++++|.+++++-...
T Consensus       329 ~L~~tLG~L~~k~~~w~kA~~~leaAl--~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         329 LLLSTLGRLALKNKLWGKASEALEAAL--KLRPSASDYAELADALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHHH--hcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            455666677889999999999999444  45799999999999999999999999999886543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.36  E-value=0.19  Score=26.94  Aligned_cols=65  Identities=8%  Similarity=-0.067  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--CCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDES--DKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~--~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..+..+-..+.+.|+++.|...|+......  .+.....+..+...+.+.|+.++|.+.+++..+..
T Consensus        40 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        40 NAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHHC
Confidence            455668888999999999999999987532  11224567777888999999999999999998774

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=95.34  E-value=0.68  Score=33.16  Aligned_cols=63  Identities=8%  Similarity=0.044  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...+..+...+.+.|++++|...++.+....-.+ ...+..+ ..+...|++++|...++++.+.
T Consensus       144 ~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~  206 (656)
T PRK15174        144 SQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIATC-LSFLNKSRLPEDHDLARALLPF  206 (656)
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHHH-HHHHHcCCHHHHHHHHHHHHhc
Confidence            4455556666666666666666666554322111 1112112 2345556666666666655443

>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=95.24  E-value=0.22  Score=33.60  Aligned_cols=63  Identities=17%  Similarity=0.183  Sum_probs=49.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      |....+.-...+.+.++.+.|..+.++....  .| +..+|..|..+|.+.|+++.|+..++.+..
T Consensus       233 d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  233 DSELLNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            4445555556677888899999999888754  46 555999999999999999999988888753

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

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

Probab=95.24  E-value=0.22  Score=28.41  Aligned_cols=58  Identities=12%  Similarity=0.186  Sum_probs=39.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCchH--HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESDKVNV--FICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~--~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +-..+...|++++|...|+......-.|+.  ...-.+...+...|++++|+..++....
T Consensus        54 lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~  113 (145)
T PF09976_consen   54 LAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPD  113 (145)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccC
Confidence            445666778888888888888776533332  2344456677788888888888866433

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=95.23  E-value=0.84  Score=34.42  Aligned_cols=67  Identities=12%  Similarity=0.110  Sum_probs=41.9

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .|+...|..+-..+.+.|++++|...+++..... +-+...++.+-..+...|+.++|+..+++..+.
T Consensus       606 ~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l  672 (987)
T PRK09782        606 APSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREMLERAHKG  672 (987)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            3555666666666777777777777776665432 124555555556666777777777777666553

>TIGR00540 hemY_coli hemY protein

Probab=95.20  E-value=0.57  Score=31.45  Aligned_cols=62  Identities=13%  Similarity=0.177  Sum_probs=51.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP   77 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   77 (94)
                      ....+.+.|++++|...++.+.+.. +-+......+...+.+.|++++|.+.+++..+.+..+
T Consensus       159 ~a~l~l~~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~  220 (409)
T TIGR00540       159 RTRILLAQNELHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFD  220 (409)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCC
Confidence            4666777899999999999998764 2367788899999999999999999999999887643

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.

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.15  E-value=0.28  Score=27.59  Aligned_cols=56  Identities=14%  Similarity=0.157  Sum_probs=41.0

Q ss_pred             HHHhcCCHHHHHHHHHHHhhCCCCch--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           18 FLGKNGNSLKALEIYNSITDESDKVN--VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        18 ~~~~~g~~~~a~~~~~~m~~~~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ++-..|+.++|..+|++-...|....  ...+-.+-..+...|++++|..++++....
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~   67 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEE   67 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34456888888888888888777654  345555666777888888888888877654

>PRK11189 lipoprotein NlpI; Provisional

Probab=94.86  E-value=0.6  Score=29.99  Aligned_cols=63  Identities=17%  Similarity=0.139  Sum_probs=38.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|+.+=..+...|++++|...|+...+.  .| +..+|..+-..+...|++++|++.|++..+
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~  160 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQ  160 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4455666666666667777777666666542  23 345555555666666677777666666554

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

Probab=94.71  E-value=0.51  Score=30.19  Aligned_cols=76  Identities=11%  Similarity=0.248  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE-SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      .+|..++...-+.+..+.|..+|.+..+. .+..+++...+++. |...++.+.|.++|+...+. +..+...|..-|+
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E-~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~   78 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALME-YYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLD   78 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHH-HHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHH
Confidence            46777777777777777788887777643 23455555555554 22345666677777776654 2233333443333

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.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=94.61  E-value=0.15  Score=23.06  Aligned_cols=29  Identities=10%  Similarity=0.084  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           46 ICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        46 t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +|..+-..|.+.|++++|+++|++..+..
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~   31 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALD   31 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            56778888999999999999999988753

>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=94.60  E-value=0.12  Score=29.40  Aligned_cols=42  Identities=14%  Similarity=0.181  Sum_probs=30.5

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHh-----hCCCCchHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSIT-----DESDKVNVFICN   48 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~-----~~~~~p~~~t~~   48 (94)
                      -|...|..+|.+|.+.|+...|.++|+.+.     +.|+.|+..+-.
T Consensus        94 ~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   94 YDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            378899999999999999999999999885     468888776543

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

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

Probab=94.60  E-value=0.64  Score=30.08  Aligned_cols=63  Identities=14%  Similarity=0.176  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-CchH--HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESD-KVNV--FICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p~~--~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ...+..+-..+...|++++|...+++.....- .|+.  ..|..+...+...|++++|+.++++..
T Consensus       148 ~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         148 AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            34455556666677777777777666554211 1222  234456666777777777777777764

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

>PRK12370 invasion protein regulator; Provisional

Probab=94.53  E-value=1.1  Score=31.42  Aligned_cols=63  Identities=14%  Similarity=-0.001  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN-VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...+..+-..+...|++++|...+++..+..  |+ ...+..+...+...|++++|+..+++..+.
T Consensus       372 ~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~  435 (553)
T PRK12370        372 ADIKYYYGWNLFMAGQLEEALQTINECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQ  435 (553)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHh
Confidence            3445555555666666666666666655432  32 112222333344556666666666665443

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

Probab=94.47  E-value=0.27  Score=32.56  Aligned_cols=60  Identities=15%  Similarity=0.187  Sum_probs=38.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      -.=|.+.|.++.|+++|..+.+.+. .-...--.|+.-|-...+|++|+++-+++.+.+-.
T Consensus       114 ~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q  173 (389)
T COG2956         114 GRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQ  173 (389)
T ss_pred             HHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCc
Confidence            3445666777777777777765332 23345556677777777777777777777665433

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=94.47  E-value=0.14  Score=22.20  Aligned_cols=26  Identities=19%  Similarity=0.328  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHh
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSIT   36 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~   36 (94)
                      +|+.|=..|.+.|++++|.+++++..
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            47788899999999999999999854

>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=94.33  E-value=0.63  Score=27.87  Aligned_cols=63  Identities=16%  Similarity=0.237  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+..+-..|++.|+.++|.+.+.++.+....+  -+..+-.+|+.....+++..+...+.+...
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~  101 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES  101 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            567789999999999999999999998776555  455678889999999999999998877654

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.

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

Probab=94.30  E-value=0.83  Score=29.12  Aligned_cols=65  Identities=15%  Similarity=0.129  Sum_probs=51.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      |....+.......+.|++..|...|.+.... -++|-..|+.+=-+|-+.|+.++|..-|.+..+-
T Consensus        99 d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L  163 (257)
T COG5010          99 DRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLGRFDEARRAYRQALEL  163 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHh
Confidence            3444555777788889999999999888753 3579999999999999999999999988887653

>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=94.29  E-value=1.3  Score=31.33  Aligned_cols=61  Identities=18%  Similarity=0.073  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|..+-..+...|++++|...|++..+.. +-+...|..+-..+...|++++|+..|++..+
T Consensus       367 ~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~  427 (615)
T TIGR00990       367 SYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSID  427 (615)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34444444445555555555555443321 11344445555555555555555555555443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=94.20  E-value=0.74  Score=28.14  Aligned_cols=59  Identities=8%  Similarity=0.135  Sum_probs=47.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCC--CCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDES--DKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~--~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +-..|.+.|++++|...+++.....  -+.....+..+..++.+.|++++|...++.+...
T Consensus       172 ~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       172 VARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            3456778899999999999887542  2234678889999999999999999999988765

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).

>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=94.11  E-value=0.97  Score=29.20  Aligned_cols=78  Identities=9%  Similarity=0.129  Sum_probs=51.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHH---HHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFIC---NLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~---~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      +.......+..|.+.++++.|.+.++.|++..  .|....   .++++.+.....+.+|..+|+++.+. +.+++.+.+.
T Consensus       130 ~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng  206 (290)
T PF04733_consen  130 SLELLALAVQILLKMNRPDLAEKELKNMQQID--EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNG  206 (290)
T ss_dssp             CHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHH
T ss_pred             cccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHH
Confidence            45566678889999999999999999998653  343322   23333333345799999999998554 5567777665


Q ss_pred             HHHH
Q 034447           85 VYQS   88 (94)
Q Consensus        85 ll~~   88 (94)
                      +..+
T Consensus       207 ~A~~  210 (290)
T PF04733_consen  207 LAVC  210 (290)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

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.

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

Probab=94.07  E-value=0.4  Score=33.80  Aligned_cols=59  Identities=15%  Similarity=0.409  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      .+|..+|..--+..-+..|..+|.+..+.+..+ +++.++++|.-||. ++.+-|+++|+-
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeL  426 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFEL  426 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHH
Confidence            457777777777778899999999999888777 88999999987764 566777776665

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

Probab=94.03  E-value=0.7  Score=30.32  Aligned_cols=69  Identities=17%  Similarity=0.185  Sum_probs=48.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHh
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSD   89 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~   89 (94)
                      +.+..|.-+...|+...|.++-.+.+-    ||..-|...|++++..++|++..++... .++     +.-|..++++|
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv----~dkrfw~lki~aLa~~~~w~eL~~fa~s-kKs-----PIGyepFv~~~  247 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFKV----PDKRFWWLKIKALAENKDWDELEKFAKS-KKS-----PIGYEPFVEAC  247 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcCC----cHHHHHHHHHHHHHhcCCHHHHHHHHhC-CCC-----CCChHHHHHHH
Confidence            455567777778888888888777753    7888888888888888888887776543 222     24455555553

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

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

Probab=94.03  E-value=0.77  Score=30.54  Aligned_cols=58  Identities=14%  Similarity=0.252  Sum_probs=46.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      =+.....|+++.|.+.|+...+.+-..-..+-..|..+|.+.|+.++...++.++.+.
T Consensus       221 G~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         221 GRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             hHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            3456677899999999988887766666677888899999999999999888887664

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=93.99  E-value=1  Score=32.67  Aligned_cols=64  Identities=13%  Similarity=-0.026  Sum_probs=38.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +....+.+-.++.+.|++++|.++|++.... .+-+..++..+-.++-+.|+.++|...|++-.+
T Consensus       153 ~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~-~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        153 SAREILLEAKSWDEIGQSEQADACFERLSRQ-HPEFENGYVGWAQSLTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             CHHHHHHHHHHHHHhcchHHHHHHHHHHHhc-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3444555555666666667776666666652 222355666666666666666666666666543

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=93.93  E-value=0.24  Score=21.54  Aligned_cols=27  Identities=19%  Similarity=0.351  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           45 FICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        45 ~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      .+++.+-..|...|++++|..++++..
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            466777777777777777777777754

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=93.88  E-value=1.1  Score=29.09  Aligned_cols=85  Identities=12%  Similarity=0.097  Sum_probs=61.1

Q ss_pred             CCccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCchHHHHHHHHHHHHhcCCHHHHHHHHHH-----HHHcCCCcc
Q 034447            5 GKTSISSYSSYIKFLGKNGNSLKALEIYNSITDE-SDKVNVFICNLILSCLVRNGKFESSLKLFDK-----IKQSGLTPD   78 (94)
Q Consensus         5 ~~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~-----m~~~g~~p~   78 (94)
                      +.++..+-..+|..+++.+++..-.++|+..... +-.-|...|...|+...+.|+..-..++.++     +.+.++..+
T Consensus       198 ~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~  277 (292)
T PF13929_consen  198 KSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVT  277 (292)
T ss_pred             cCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCC
Confidence            3677777788888888888888888888877654 5556888888888888888888777766655     244556555


Q ss_pred             HHHHHHHHHHh
Q 034447           79 AVTYNTVYQSD   89 (94)
Q Consensus        79 ~~~~~~ll~~~   89 (94)
                      ...-..+-+.+
T Consensus       278 ~~L~~~L~~LF  288 (292)
T PF13929_consen  278 DELRSQLSELF  288 (292)
T ss_pred             HHHHHHHHHHH
Confidence            55555444433

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

Probab=93.83  E-value=1.1  Score=31.23  Aligned_cols=66  Identities=9%  Similarity=0.027  Sum_probs=57.3

Q ss_pred             Cc-cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            6 KT-SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         6 ~p-~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +| |...|.+|=..|.+.+++++|..+|+.-...|-. +...+..|-+.|-+.++.++|.+.|++-.+
T Consensus       428 kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  428 KPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             CCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            55 8899999999999999999999999988876542 668899999999999999999998877554

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.77  E-value=0.21  Score=33.01  Aligned_cols=50  Identities=8%  Similarity=0.163  Sum_probs=41.4

Q ss_pred             CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           24 NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        24 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +++++.-+...=...|+-||-++++.+|+.+.+.+++.+|.++.-.|...
T Consensus       115 ~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             ChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            45667766666667899999999999999999999999999987776554

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=93.68  E-value=0.27  Score=21.36  Aligned_cols=29  Identities=17%  Similarity=0.222  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD   37 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~   37 (94)
                      ..+++.+-..|...|++++|..++++...
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            46889999999999999999999998764

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

Probab=93.64  E-value=0.95  Score=27.48  Aligned_cols=46  Identities=13%  Similarity=0.169  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           26 LKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        26 ~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ++|.+++++..+.. +-+..++..+-..+.+.|++++|+..|+++.+
T Consensus       127 ~~A~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~  172 (198)
T PRK10370        127 PQTREMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQKVLD  172 (198)
T ss_pred             HHHHHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44444444443321 11344444444444555555555555555443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=93.62  E-value=1.3  Score=32.76  Aligned_cols=60  Identities=12%  Similarity=0.107  Sum_probs=47.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      -.|-++.+.|++.++.+-++.++..+.+....+--++.++|...+.+++|+.+|++....
T Consensus       297 Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~  356 (822)
T PRK14574        297 DRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYS  356 (822)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhc
Confidence            456667778888888888888888777655557777888888888888888888887553

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=93.57  E-value=0.83  Score=26.62  Aligned_cols=65  Identities=15%  Similarity=0.076  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...|..+...+...|++++|...|++.....-.+  ...+|..+-..+...|+.++|+..+++..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4556677777778899999999999887542222  2458888889999999999999999998764

>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=93.51  E-value=1.8  Score=30.44  Aligned_cols=67  Identities=18%  Similarity=0.235  Sum_probs=45.6

Q ss_pred             HHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           18 FLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        18 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      .+...|++++|.+.+++-.. .+.-...........+.+.|+.++|..+|..+.+.+  |+-..|-..+.
T Consensus        13 il~e~g~~~~AL~~L~~~~~-~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~   79 (517)
T PF12569_consen   13 ILEEAGDYEEALEHLEKNEK-QILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLE   79 (517)
T ss_pred             HHHHCCCHHHHHHHHHhhhh-hCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHH
Confidence            34677888888888876443 233445555666677788888888888888888776  55554444333

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 [], [].

>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=93.46  E-value=0.88  Score=26.52  Aligned_cols=68  Identities=18%  Similarity=0.216  Sum_probs=50.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      +.......|+...+.|.-++..++.+++.. +-+++....-.+..+|.+-|+..++.+++.+.-+.|+.
T Consensus        85 ~se~vD~ALd~lv~~~kkDqLdki~~~l~k-n~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   85 LSEYVDLALDILVKQGKKDQLDKIYNELKK-NEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             --HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHhh-ccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            345567888999999999999999999875 23467777778899999999999999999999999875

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

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=93.45  E-value=1.9  Score=32.91  Aligned_cols=64  Identities=8%  Similarity=0.048  Sum_probs=41.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      |...+..+...+.+.|++++|...++.....  .| +...+..+...+...|++++|.+++++..+.
T Consensus       636 ~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~--~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        636 NADARLGLIEVDIAQGDLAAARAQLAKLPAT--ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            4556666677777777777777777765532  23 3445555666667777777777777776653

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

Probab=93.34  E-value=0.94  Score=31.56  Aligned_cols=59  Identities=10%  Similarity=0.237  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDES-DKVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      ..|.+.|.+--+..-++.|..+|-+..+.| +.+++..++++|.-++ .|+...|.++|+-
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifel  457 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFEL  457 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHH
Confidence            467788888888888999999999999888 6789999999998766 4667778888775

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

Probab=93.31  E-value=1.1  Score=27.21  Aligned_cols=68  Identities=12%  Similarity=0.089  Sum_probs=54.4

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHH-HhcCC--HHHHHHHHHHHHHcCC
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCL-VRNGK--FESSLKLFDKIKQSGL   75 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~-~~~g~--~~~a~~~~~~m~~~g~   75 (94)
                      .|...|..+-..|...|++++|...|++..+.. +-|...+..+-.++ ...|+  .++|.+++++..+.+-
T Consensus        71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP  141 (198)
T PRK10370         71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDA  141 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC
Confidence            477788888899999999999999999887643 23777777777764 67776  5999999999887653

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=93.24  E-value=1.2  Score=28.43  Aligned_cols=63  Identities=10%  Similarity=0.138  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNV----FICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...|...+....+.|++++|...|+.+...-  |+.    ..+-.+-..|...|++++|...|+++.+.
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~  209 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN  209 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5668888877788899999999999987531  332    35556778889999999999999999754

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

Probab=93.13  E-value=0.22  Score=36.97  Aligned_cols=70  Identities=10%  Similarity=0.248  Sum_probs=48.2

Q ss_pred             HHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCccHHHHHHHHHH
Q 034447           18 FLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS-GLTPDAVTYNTVYQS   88 (94)
Q Consensus        18 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~ll~~   88 (94)
                      .++..|++..|..||.+..+... -+.-+|--+-.+|...|++..|+++|+.-.++ ....+...-..|-++
T Consensus       655 VLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara  725 (1018)
T KOG2002|consen  655 VLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARA  725 (1018)
T ss_pred             hhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHH
Confidence            45667888888888888876532 23456777788888888888888888875554 334455555555555

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=92.97  E-value=0.48  Score=22.15  Aligned_cols=32  Identities=19%  Similarity=0.387  Sum_probs=17.5

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           56 RNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        56 ~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +.|-..++...+++|.+.|+..+...|..+++
T Consensus        14 ~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen   14 RRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            44555555555666655555555555555443

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane

Probab=92.95  E-value=0.72  Score=24.13  Aligned_cols=55  Identities=11%  Similarity=0.254  Sum_probs=41.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHH-HHH
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLF-DKI   70 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~-~~m   70 (94)
                      -|..| ...+-++|..+|+.-.+.-..|  --.++..++.+|+..|++++++.+- .+|
T Consensus        13 GlkLY-~~~~~~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~~L~fA~~Q~   70 (80)
T PF10579_consen   13 GLKLY-HQNETQQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYREMLAFALQQL   70 (80)
T ss_pred             HHHHh-ccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45545 7788899999999887554333  3467889999999999999998863 444

Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane

>PRK14574 hmsH outer membrane protein; Provisional

Probab=92.85  E-value=0.97  Score=33.43  Aligned_cols=62  Identities=8%  Similarity=0.010  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCC-----CCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDES-----DKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-----~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .--++-++|...+.+++|..++.+.....     ..++......|.-+|...+++++|..+++++.+
T Consensus       329 ~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~  395 (822)
T PRK14574        329 ARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSE  395 (822)
T ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHh
Confidence            55678899999999999999999986532     234666678999999999999999999999987

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=92.80  E-value=0.49  Score=21.81  Aligned_cols=25  Identities=16%  Similarity=0.478  Sum_probs=15.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           50 ILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        50 li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +..+|...|+.+.|..++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            3456666666666666666665443

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=92.76  E-value=1.6  Score=33.39  Aligned_cols=65  Identities=11%  Similarity=0.105  Sum_probs=51.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..+.+.|++++|...|++..+.. +-+...+..+...+...|+.++|++.+++..+.
T Consensus       602 ~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~  666 (1157)
T PRK11447        602 STRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPAT  666 (1157)
T ss_pred             CchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence            34455667777888899999999999887642 236788888999999999999999999987653

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

Probab=92.74  E-value=1.8  Score=28.06  Aligned_cols=62  Identities=11%  Similarity=0.160  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ....+-..+...|++++|...+++..+.. +.+...+..+-..+...|++++|...+++..+.
T Consensus       116 ~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~  177 (355)
T cd05804         116 LLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDT  177 (355)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhc
Confidence            33445567788999999999999998753 345677888888999999999999999987664

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.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=92.70  E-value=0.93  Score=24.77  Aligned_cols=63  Identities=14%  Similarity=0.171  Sum_probs=50.4

Q ss_pred             CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCccHHHHHHHHHH
Q 034447           24 NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS-GLTPDAVTYNTVYQS   88 (94)
Q Consensus        24 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~ll~~   88 (94)
                      +..+..+-++.+....+-|+.....+.+++|-+..++.-|.++|+-.+.+ |-  +...|..+++-
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~--~~~~y~~~lqe   85 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGA--HKEIYPYILQE   85 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccC--chhhHHHHHHH
Confidence            66777888888888889999999999999999999999999999987633 32  34456666653

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=92.66  E-value=1.8  Score=27.86  Aligned_cols=63  Identities=13%  Similarity=0.050  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..|..+=..|.+.|+.++|...|++..+.. +-+...|+.+-..+...|++++|...|++..+.
T Consensus        65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l  127 (296)
T PRK11189         65 QLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLEL  127 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            446666667888999999999999887642 236789999999999999999999999998764

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=92.49  E-value=1.4  Score=26.41  Aligned_cols=60  Identities=5%  Similarity=-0.072  Sum_probs=43.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHh-hCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           14 SYIKFLGKNGNSLKALEIYNSIT-DESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~-~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+.......+.+......+-.+ .....|+..+|..++..+...|+.++|.+..+++..-
T Consensus       113 ~~l~~~~~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~l  173 (193)
T PF11846_consen  113 ALLLLARLPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARARRL  173 (193)
T ss_pred             HHHHhhcCCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            33333345555555555544443 2345799999999999999999999999999988653

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=92.37  E-value=3.9  Score=31.09  Aligned_cols=52  Identities=10%  Similarity=-0.019  Sum_probs=27.5

Q ss_pred             HhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           20 GKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        20 ~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+.|++++|...|++....  +|+...+..+...+.+.|+.++|...+++..+.
T Consensus       520 ~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l  571 (987)
T PRK09782        520 YQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQR  571 (987)
T ss_pred             HHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            4566666666666655432  233333444444555566666666666555543

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=92.35  E-value=0.54  Score=21.17  Aligned_cols=28  Identities=7%  Similarity=0.063  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDE   38 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~   38 (94)
                      ++..+-.+|.+.|++++|.++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5677888999999999999999999864

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=92.31  E-value=3.4  Score=30.26  Aligned_cols=59  Identities=14%  Similarity=0.064  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +..+...+.+.|++++|...+++..+. .+.+.. +..+...+...|+.++|+..+++..+
T Consensus        86 ~~~la~~l~~~g~~~eA~~~l~~~l~~-~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~  144 (765)
T PRK10049         86 QRGLILTLADAGQYDEALVKAKQLVSG-APDKAN-LLALAYVYKRAGRHWDELRAMTQALP  144 (765)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            344444555555555555555555433 111333 55555555555555555555555544

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

Probab=92.28  E-value=1.1  Score=24.69  Aligned_cols=71  Identities=17%  Similarity=0.223  Sum_probs=48.6

Q ss_pred             HHHHHH-hcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCccHHHHHHHHH
Q 034447           15 YIKFLG-KNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS-GLTPDAVTYNTVYQ   87 (94)
Q Consensus        15 ll~~~~-~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~ll~   87 (94)
                      ....+- ..-+..+..+-++.+....+-|+.....+.+++|-+..++..|.++|+-.+.+ |-.-+  .|.-+++
T Consensus        15 y~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~--~Y~~~lq   87 (108)
T PF02284_consen   15 YEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKE--IYPYILQ   87 (108)
T ss_dssp             HHHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TT--HHHHHHH
T ss_pred             HHHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHH--HHHHHHH
Confidence            333344 23456677888888888899999999999999999999999999999988754 32222  5666665

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 ....

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

Probab=92.28  E-value=2.3  Score=28.25  Aligned_cols=70  Identities=14%  Similarity=0.046  Sum_probs=51.8

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..+...|++++|...|++..+.. +-+...|..+..+|.+.|++++|+..+++..+..- .+...|..+-.+
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P-~~~~a~~~lg~~   79 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDP-SLAKAYLRKGTA   79 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCHHHHHHHHHH
Confidence            34556799999999999998642 23677888888999999999999999999877532 234445444333

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=92.16  E-value=0.65  Score=21.70  Aligned_cols=37  Identities=8%  Similarity=0.141  Sum_probs=31.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILS   52 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~   52 (94)
                      |...-+.|..+++..++++|.+.|+..+...|..+++
T Consensus         9 L~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~   45 (48)
T PF11848_consen    9 LLLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILR   45 (48)
T ss_pred             HHHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHH
Confidence            4445678899999999999999999998888887765

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

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

Probab=92.07  E-value=2.1  Score=27.36  Aligned_cols=79  Identities=18%  Similarity=0.085  Sum_probs=63.2

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      .+|...||.+=-+|-+.|+++.|..-|.+-.+.  .| +....|-+--.+.-.|+.++|..++..-...+-....+--|.
T Consensus       131 p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NL  208 (257)
T COG5010         131 PTDWEAWNLLGAALDQLGRFDEARRAYRQALEL--APNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNL  208 (257)
T ss_pred             CCChhhhhHHHHHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHH
Confidence            578899999999999999999999988777653  33 566777888888899999999999999887776555555554


Q ss_pred             HH
Q 034447           85 VY   86 (94)
Q Consensus        85 ll   86 (94)
                      .+
T Consensus       209 Al  210 (257)
T COG5010         209 AL  210 (257)
T ss_pred             HH
Confidence            43

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

Probab=92.02  E-value=2.4  Score=30.17  Aligned_cols=69  Identities=16%  Similarity=0.162  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-cHHHHHHHHHHhhccc
Q 034447           25 SLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP-DAVTYNTVYQSDHITW   93 (94)
Q Consensus        25 ~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~~   93 (94)
                      .+.....+++....-..--..+|...++.--+...++.|..+|.+.++.+..+ ..+.++++++-+|.++
T Consensus       347 ~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD  416 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKD  416 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCC
Confidence            45566667766654333344678888999999999999999999999999888 8999999999877653

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.98  E-value=1.6  Score=25.73  Aligned_cols=53  Identities=8%  Similarity=0.229  Sum_probs=41.1

Q ss_pred             hcCCHHHHHHHHHHHhh-CCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 034447           21 KNGNSLKALEIYNSITD-ESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGL   75 (94)
Q Consensus        21 ~~g~~~~a~~~~~~m~~-~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~   75 (94)
                      ...+++++..+++.|.- +.-.|...+|-..+.  ...|+|.+|.++|++..+.+.
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~--i~rg~w~eA~rvlr~l~~~~~   75 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFDGWLL--IARGNYDEAARILRELLSSAG   75 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhHHHHH--HHcCCHHHHHHHHHhhhccCC
Confidence            47889999999999873 223345666766665  789999999999999988764

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=91.91  E-value=3.8  Score=30.01  Aligned_cols=65  Identities=9%  Similarity=0.090  Sum_probs=50.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-.++.+.|++++|..+|++..... +.+...+..+...+...|++++|...+++..+.
T Consensus        48 ~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~  112 (765)
T PRK10049         48 PARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAGQYDEALVKAKQLVSG  112 (765)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            44567788888888999999999998876541 234566778888888999999999999988765

>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=91.91  E-value=0.8  Score=22.21  Aligned_cols=42  Identities=12%  Similarity=0.031  Sum_probs=31.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLIL   51 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li   51 (94)
                      |...+-.+..+|.+.|++++|..+++.....  .|+-..|..++
T Consensus        24 ~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen   24 NPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            6667778999999999999999999998865  36645555443

...

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

Probab=91.88  E-value=1.3  Score=24.48  Aligned_cols=46  Identities=15%  Similarity=0.097  Sum_probs=32.8

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILS   52 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~   52 (94)
                      .|+.....+.|++|-+..++..|.++|+..+... .+....|..++.
T Consensus        42 VP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lq   87 (108)
T PF02284_consen   42 VPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQ   87 (108)
T ss_dssp             ---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHH
Confidence            6889999999999999999999999999888431 122227777665

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 ....

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

Probab=91.72  E-value=3.2  Score=31.03  Aligned_cols=60  Identities=15%  Similarity=0.324  Sum_probs=40.1

Q ss_pred             HHHHHHHH--hcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           13 SSYIKFLG--KNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        13 ~~ll~~~~--~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...+.++.  +.|..++|..+++.....+-. |..|..++-.+|-..++.++|..+|++..+.
T Consensus        45 a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~  106 (932)
T KOG2053|consen   45 AKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK  106 (932)
T ss_pred             HHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh
Confidence            33444443  567777777777776654443 7777777777777777777777777776543

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=91.71  E-value=1.6  Score=25.36  Aligned_cols=80  Identities=13%  Similarity=0.175  Sum_probs=54.0

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCccHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDE-SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG-LTPDAVTYN   83 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~   83 (94)
                      |....|+.-..+ .+.|++++|.+.|+.+..+ ...| ....---++.+|.+.+++++|...+++..+-. -.|+ +-|.
T Consensus         9 ~~~~ly~~a~~~-l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~-vdYa   86 (142)
T PF13512_consen    9 SPQELYQEAQEA-LQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPN-VDYA   86 (142)
T ss_pred             CHHHHHHHHHHH-HHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCC-ccHH
Confidence            444455544443 4679999999999999864 1111 34555668899999999999999999988753 3333 3344


Q ss_pred             HHHHH
Q 034447           84 TVYQS   88 (94)
Q Consensus        84 ~ll~~   88 (94)
                      -...|
T Consensus        87 ~Y~~g   91 (142)
T PF13512_consen   87 YYMRG   91 (142)
T ss_pred             HHHHH
Confidence            44444

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=91.68  E-value=1.8  Score=25.66  Aligned_cols=56  Identities=9%  Similarity=0.026  Sum_probs=36.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..+...|++++|..+|+......  | +..-|-.|--++-..|++++|+..|.....-.
T Consensus        43 ~~ly~~G~l~~A~~~f~~L~~~D--p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~   99 (157)
T PRK15363         43 MQLMEVKEFAGAARLFQLLTIYD--AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK   99 (157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            34456788888888888776532  4 44444445555556678888888887766544

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.65  E-value=0.8  Score=31.01  Aligned_cols=56  Identities=20%  Similarity=0.278  Sum_probs=34.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      +-.+++..|++.+|+++|-....-.++-+..-...+.++|.+.++++-|.+++=.+
T Consensus       399 ~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  399 LAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             HHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhc
Confidence            45667777777777777755554444333444444556677777777777665444

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

Probab=91.39  E-value=3.6  Score=28.67  Aligned_cols=80  Identities=11%  Similarity=0.109  Sum_probs=57.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN-VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      |........+.+.+.++.++|.+-++.+...  .|+ ...+-.+-.++.+.|++.+|++++++-.... +-|+..|..|-
T Consensus       339 N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~-p~dp~~w~~LA  415 (484)
T COG4783         339 NPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLA  415 (484)
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHH
Confidence            4444556667788888889998888888764  465 5556666778888888888888888876543 34667777777


Q ss_pred             HHhh
Q 034447           87 QSDH   90 (94)
Q Consensus        87 ~~~~   90 (94)
                      ++|.
T Consensus       416 qay~  419 (484)
T COG4783         416 QAYA  419 (484)
T ss_pred             HHHH
Confidence            7754

>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=91.38  E-value=2.7  Score=28.55  Aligned_cols=56  Identities=13%  Similarity=0.261  Sum_probs=36.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..|+..+...++++.|..+|+++.+..  |+.  ...+++.+...++-.+|.+++++..+
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~  228 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALK  228 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            355666666788888888888887654  443  33456666666666666666666554

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

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

Probab=91.35  E-value=2.6  Score=27.00  Aligned_cols=50  Identities=14%  Similarity=0.143  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           23 GNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        23 g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ++.+.|..+|+...+. +..+...|..-++-+...++.+.|..+|++....
T Consensus        50 ~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~   99 (280)
T PF05843_consen   50 KDPKRARKIFERGLKK-FPSDPDFWLEYLDFLIKLNDINNARALFERAISS   99 (280)
T ss_dssp             S-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCT
T ss_pred             CCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHh
Confidence            4445566666655432 3345555556666666666666666666665443

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.

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.13  E-value=1.9  Score=30.51  Aligned_cols=66  Identities=14%  Similarity=0.176  Sum_probs=54.3

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ++|...++.|=-.|--.|+++.|.++|+....  ++| |...||-|=...+...+.++|+..|++-.+-
T Consensus       427 ~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~--v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL  493 (579)
T KOG1125|consen  427 KIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQ--VKPNDYLLWNRLGATLANGNRSEEAISAYNRALQL  493 (579)
T ss_pred             CCChhHHhhhHHHHhcchHHHHHHHHHHHHHh--cCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc
Confidence            45666666666667778999999999998775  356 8999999988899999999999999997653

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.05  E-value=3  Score=27.25  Aligned_cols=77  Identities=10%  Similarity=0.079  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      .-++++..+--.|++.-....+++..+..-+-+..--..+.+.--+.|+.+.|...|++..+..-..|..+++.++.
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~  255 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVL  255 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHH
Confidence            34566666666788888888888888765556777778888888899999999999998887655566666665553

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

Probab=91.03  E-value=2.7  Score=31.30  Aligned_cols=66  Identities=20%  Similarity=0.410  Sum_probs=56.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +.-.|.-+-.+|.+.|.+.+|.++|........--+...|--+-++|-..|..++|.+.|+.....
T Consensus       413 ~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~  478 (895)
T KOG2076|consen  413 DVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLIL  478 (895)
T ss_pred             hHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            445677888999999999999999999988766667889999999999999999999999887653

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

Probab=91.01  E-value=3.5  Score=27.81  Aligned_cols=31  Identities=10%  Similarity=-0.006  Sum_probs=18.6

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSIT   36 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~   36 (94)
                      .|-..||-.|-++|-+...+..|..+|.+-.
T Consensus       253 ~~~~dTfllLskvY~ridQP~~AL~~~~~gl  283 (478)
T KOG1129|consen  253 FPHPDTFLLLSKVYQRIDQPERALLVIGEGL  283 (478)
T ss_pred             CCchhHHHHHHHHHHHhccHHHHHHHHhhhh
Confidence            4555566666666666666666666555443

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=90.95  E-value=1.6  Score=23.92  Aligned_cols=45  Identities=16%  Similarity=0.107  Sum_probs=36.6

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-CCCCchHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITD-ESDKVNVFICNLILS   52 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~t~~~li~   52 (94)
                      .|+....++.|++|-+..++..|.++|+..+. .|.  +...|..++.
T Consensus        39 VP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~--~~~~y~~~lq   84 (103)
T cd00923          39 VPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGA--HKEIYPYILQ   84 (103)
T ss_pred             CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccC--chhhHHHHHH
Confidence            58888999999999999999999999998873 332  4556777665

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.

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=90.92  E-value=1.7  Score=24.05  Aligned_cols=64  Identities=17%  Similarity=0.126  Sum_probs=47.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      +-+..+...|++++|..+.+.+.    .||...|-++-.  .+.|..++...-+.+|..+|- |....|..
T Consensus        44 IRlsSLmNrG~Yq~Al~l~~~~~----~pdlepw~ALce--~rlGl~s~l~~rl~rla~sg~-p~lq~Faa  107 (115)
T TIGR02508        44 IRLSSLMNRGDYQSALQLGNKLC----YPDLEPWLALCE--WRLGLGSALESRLNRLAASGD-PRLQTFVA  107 (115)
T ss_pred             HHHHHHHccchHHHHHHhcCCCC----CchHHHHHHHHH--HhhccHHHHHHHHHHHHhCCC-HHHHHHHH
Confidence            44566778888888888887773    599999988766  677888888888888887774 55555543

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B

Probab=90.92  E-value=1.1  Score=22.05  Aligned_cols=48  Identities=13%  Similarity=0.253  Sum_probs=35.8

Q ss_pred             CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           24 NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        24 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+++..++++.++..  +.|..-.--+|.++.+.|++++|.+.++++.+.
T Consensus         5 ~~~~~~~~~~~lR~~--RHD~~NhLqvI~gllqlg~~~~a~eYi~~~~~~   52 (62)
T PF14689_consen    5 QLEELEELIDSLRAQ--RHDFLNHLQVIYGLLQLGKYEEAKEYIKELSKD   52 (62)
T ss_dssp             -HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            455666677766532  468888888999999999999999999888653

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=90.58  E-value=2.6  Score=25.70  Aligned_cols=67  Identities=7%  Similarity=0.039  Sum_probs=52.5

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDES-DKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .....+-.+...+.+.|++++|...|++..... -.| ...++..+-.++.+.|++++|+..+++..+.
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~   99 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL   99 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            355667777788899999999999999887532 111 1246777888999999999999999999764

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).

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

Probab=90.41  E-value=0.57  Score=32.57  Aligned_cols=51  Identities=20%  Similarity=0.277  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCccHHHHHHHHHHhhccc
Q 034447           43 NVFICNLILSCLVRNGKFESSLKLFDKIKQSG-LTPDAVTYNTVYQSDHITW   93 (94)
Q Consensus        43 ~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~ll~~~~~~~   93 (94)
                      =..+|++.|+..-+...++.|..+|-+.++.| +.++.+.++++++-++.|+
T Consensus       396 ~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d  447 (660)
T COG5107         396 LTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGD  447 (660)
T ss_pred             hhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCC
Confidence            35789999999999999999999999999999 5689999999999887764

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=90.38  E-value=2.3  Score=24.74  Aligned_cols=61  Identities=20%  Similarity=0.092  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHH-------hcCCHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLV-------RNGKFESSLKLFDKI   70 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~-------~~g~~~~a~~~~~~m   70 (94)
                      ..+|..+-..+...|++++|...++...... +....++..+...+.       ..|+++.|...+++-
T Consensus        72 ~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033         72 SYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            3478888889999999999999999887542 224556666666676       788888776666543

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

Probab=90.31  E-value=5.1  Score=28.61  Aligned_cols=77  Identities=14%  Similarity=0.107  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..+++.|=++|-+.+.+++|...+++-.... +-|..+|.++--.|...|+++.|++.|.+-.  .+.|+-.+-..+|..
T Consensus       455 ~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~  531 (611)
T KOG1173|consen  455 EPTLNNLGHAYRKLNKYEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKL  531 (611)
T ss_pred             hHHHHhHHHHHHHHhhHHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHH
Confidence            3457777788889999999999999876542 3488999999999999999999999998754  345777777766654

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=90.25  E-value=0.68  Score=18.45  Aligned_cols=20  Identities=15%  Similarity=0.326  Sum_probs=10.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHH
Q 034447           49 LILSCLVRNGKFESSLKLFD   68 (94)
Q Consensus        49 ~li~~~~~~g~~~~a~~~~~   68 (94)
                      .+-..+...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34444555555555555543

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=90.25  E-value=3.6  Score=28.91  Aligned_cols=63  Identities=13%  Similarity=0.176  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC-----CC-CchHHH-HHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE-----SD-KVNVFI-CNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~~-~p~~~t-~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+..-+-..|...|+++.|..+++.-.+.     |. .|.+.+ -+.+-..|...+++++|..+|+++..
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~  269 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALT  269 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            44455889999999999999999877643     21 233333 33466778899999999999999854

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=90.01  E-value=1.4  Score=28.85  Aligned_cols=47  Identities=21%  Similarity=0.287  Sum_probs=34.6

Q ss_pred             CchHHH-HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           41 KVNVFI-CNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        41 ~p~~~t-~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      .||..+ |+..|..-.+.||+++|++++++-.+.|+.--..+|-.-++
T Consensus       253 ~~dTe~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V~  300 (303)
T PRK10564        253 LNDTESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSVK  300 (303)
T ss_pred             CchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHhh
Confidence            354444 56888888888888888888888888888766666654443

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

Probab=89.63  E-value=5.2  Score=28.31  Aligned_cols=65  Identities=14%  Similarity=0.141  Sum_probs=46.8

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|+...|++.++.=.+-.+.+.|..+++...-.  .|++.+|--..+==-++|.+..+.++|+...+
T Consensus       171 ~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~VyerAie  235 (677)
T KOG1915|consen  171 EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVYERAIE  235 (677)
T ss_pred             CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            677777888887777777778888887777653  37777777666666677777777777766543

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=89.28  E-value=3.1  Score=24.70  Aligned_cols=56  Identities=11%  Similarity=0.239  Sum_probs=40.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHhh-CCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           17 KFLGKNGNSLKALEIYNSITD-ESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..-.+.++.+++..+++.+.- +.-.|...++-.++.  ...|+|.+|+++|+++....
T Consensus        18 ~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~--i~r~~w~dA~rlLr~l~~~~   74 (160)
T PF09613_consen   18 SVALRLGDPDDAEALLDALRVLRPEFPELDLFDGWLH--IVRGDWDDALRLLRELEERA   74 (160)
T ss_pred             HHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHHHH--HHhCCHHHHHHHHHHHhccC
Confidence            333456889999999998874 222345556666554  78899999999999987654

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=89.15  E-value=6.1  Score=27.84  Aligned_cols=58  Identities=14%  Similarity=0.156  Sum_probs=44.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhC------CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDE------SDKV-NVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      +.+-..|...+.+.+|..+|+++..-      ...| -..+++.|-..|.+.|++++|...+++-
T Consensus       245 ~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~A  309 (508)
T KOG1840|consen  245 NILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERA  309 (508)
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHH
Confidence            34667888899999999999998641      1123 4567777888899999999999877764

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=89.11  E-value=0.69  Score=18.89  Aligned_cols=24  Identities=13%  Similarity=0.616  Sum_probs=16.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           50 ILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        50 li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +-.++.+.|++++|.+.|+++.+.
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHH
Confidence            345566778888888888877654

>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=89.08  E-value=0.51  Score=27.25  Aligned_cols=31  Identities=19%  Similarity=0.458  Sum_probs=22.2

Q ss_pred             cCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHh
Q 034447           57 NGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSD   89 (94)
Q Consensus        57 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~   89 (94)
                      .|.-.+|..+|++|.++|-+||.  |+.|+..+
T Consensus       108 ygsk~DaY~VF~kML~~G~pPdd--W~~Ll~~a  138 (140)
T PF11663_consen  108 YGSKTDAYAVFRKMLERGNPPDD--WDALLKEA  138 (140)
T ss_pred             hccCCcHHHHHHHHHhCCCCCcc--HHHHHHHh
Confidence            34555677888888888888864  66777654

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 [].

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

Probab=89.02  E-value=5.3  Score=26.97  Aligned_cols=67  Identities=19%  Similarity=0.031  Sum_probs=54.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYN   83 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   83 (94)
                      +.+=+.|.+.|.+.+|.+-++.-.+.  .|-.-||-.|-+.|-+-..++.|+.++.+-.++  .|..+||-
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l  293 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYL  293 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhh
Confidence            45667888999999999999876654  477888999999999999999999999876543  46666663

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

Probab=88.96  E-value=4.9  Score=29.43  Aligned_cols=63  Identities=22%  Similarity=0.298  Sum_probs=54.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      -..+|..+-..+-..|++++|...++.+.+.  +| .+-.|.-+-.++...|+.+.|.+.|.+-.+
T Consensus       115 ~ae~ysn~aN~~kerg~~~~al~~y~~aiel--~p~fida~inla~al~~~~~~~~a~~~~~~alq  178 (966)
T KOG4626|consen  115 GAEAYSNLANILKERGQLQDALALYRAAIEL--KPKFIDAYINLAAALVTQGDLELAVQCFFEALQ  178 (966)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHHHHhc--CchhhHHHhhHHHHHHhcCCCcccHHHHHHHHh
Confidence            3578888999999999999999999999864  45 778899999999999999999998877655

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=88.91  E-value=5.5  Score=26.97  Aligned_cols=76  Identities=13%  Similarity=0.044  Sum_probs=52.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCC---chHHHHHHHHHHHHh---cCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDK---VNVFICNLILSCLVR---NGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~---p~~~t~~~li~~~~~---~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      .++.+|-...+++...++++.+......   -....---..-++-+   .|+.++|++++.........+++.+|..+=.
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            5666788999999999999999875211   111111122334455   8999999999999766666677788876654


Q ss_pred             Hh
Q 034447           88 SD   89 (94)
Q Consensus        88 ~~   89 (94)
                      .|
T Consensus       226 Iy  227 (374)
T PF13281_consen  226 IY  227 (374)
T ss_pred             HH
Confidence            44

>KOG4567 consensus GTPase-activating protein [General function prediction only]

Probab=88.37  E-value=2.5  Score=27.98  Aligned_cols=58  Identities=9%  Similarity=0.153  Sum_probs=45.8

Q ss_pred             HHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHhhc
Q 034447           29 LEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHI   91 (94)
Q Consensus        29 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~   91 (94)
                      .++|+.|++.++.|..++|--+.-.+.+.=...+++.+++.+..+...     |..|+..||+
T Consensus       263 ~EL~~~L~~~~i~PqfyaFRWitLLLsQEF~lpDvi~lWDsl~sD~~r-----fd~Ll~iCcs  320 (370)
T KOG4567|consen  263 EELWRHLEEKEIHPQFYAFRWITLLLSQEFPLPDVIRLWDSLLSDPQR-----FDFLLYICCS  320 (370)
T ss_pred             HHHHHHHHhcCCCccchhHHHHHHHHhccCCchhHHHHHHHHhcChhh-----hHHHHHHHHH
Confidence            568888888899999998888888888888999999999998765333     6666666553

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

Probab=88.29  E-value=3.2  Score=23.58  Aligned_cols=68  Identities=12%  Similarity=0.203  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC--CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESD--KVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP   77 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   77 (94)
                      ...|..++..+. .++...+...++.+....=  .......-.+-..+...|++++|...|+......-.|
T Consensus        12 ~~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~   81 (145)
T PF09976_consen   12 SALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDP   81 (145)
T ss_pred             HHHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCH
Confidence            356777777774 8889999999999886421  1122333345577889999999999999999877333

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=88.28  E-value=4.9  Score=25.66  Aligned_cols=84  Identities=11%  Similarity=0.141  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-----CchHHH-HHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCc--cH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESD-----KVNVFI-CNLILSCLVRNGKFESSLKLFDKIKQS--GLTP--DA   79 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-----~p~~~t-~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p--~~   79 (94)
                      ..+.-+...+.+.|++++|.++|++......     ++++.. |-..+-++...|++..|.+.+++....  ++..  ..
T Consensus       156 ~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~  235 (282)
T PF14938_consen  156 ECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREY  235 (282)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHH
Confidence            4566778889999999999999998865332     344443 233444777789999999999998754  3432  35


Q ss_pred             HHHHHHHHHhhccc
Q 034447           80 VTYNTVYQSDHITW   93 (94)
Q Consensus        80 ~~~~~ll~~~~~~~   93 (94)
                      ..-..||+++-.|+
T Consensus       236 ~~~~~l~~A~~~~D  249 (282)
T PF14938_consen  236 KFLEDLLEAYEEGD  249 (282)
T ss_dssp             HHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHhCC
Confidence            55666777776554

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=88.05  E-value=7.4  Score=27.48  Aligned_cols=67  Identities=15%  Similarity=0.255  Sum_probs=49.7

Q ss_pred             HhcCCHHHHHHHHHHHhh-CCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CccHHHHHHHH
Q 034447           20 GKNGNSLKALEIYNSITD-ESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGL-TPDAVTYNTVY   86 (94)
Q Consensus        20 ~~~g~~~~a~~~~~~m~~-~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~~~~~ll   86 (94)
                      -+.|+.++|.+.|++|.+ ....-+....-.||.++-..+.+.++..++.+=.+... ..-..+|+..+
T Consensus       270 rklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  270 RKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             HHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            367999999999999964 33333567888899999999999999999988643222 22345666655

The molecular function of this protein is uncertain.

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=87.93  E-value=1.3  Score=32.85  Aligned_cols=50  Identities=18%  Similarity=0.300  Sum_probs=34.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      |..+-+.|+..|+++.|.++|-+-         ..++-.|..|.+.|+|++|+++-++.
T Consensus       768 y~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw~da~kla~e~  817 (1636)
T KOG3616|consen  768 YGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWEDAFKLAEEC  817 (1636)
T ss_pred             chHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHHHHHHHHHHh
Confidence            455666777777777777777432         23566678888888888887765543

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

Probab=87.84  E-value=6.7  Score=26.72  Aligned_cols=74  Identities=16%  Similarity=0.254  Sum_probs=58.8

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAV   80 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   80 (94)
                      .++...+-..-......|+.+.|..-+++..+.+ +.+...-....++|.+.|++.....++..|.+.|.-.++.
T Consensus       150 ~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e  223 (400)
T COG3071         150 DDTLAVELTRARLLLNRRDYPAARENVDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEE  223 (400)
T ss_pred             CchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHH
Confidence            4555666677777778888888888887776543 2377888999999999999999999999999998765543

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

Probab=87.76  E-value=3.4  Score=29.15  Aligned_cols=58  Identities=12%  Similarity=0.168  Sum_probs=39.7

Q ss_pred             cCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHH
Q 034447           22 NGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYN   83 (94)
Q Consensus        22 ~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   83 (94)
                      .|+...|.++|+...+.  .|+...|++.|+-=.+-..++.|..++++..--  +|+..+|-
T Consensus       154 LgNi~gaRqiferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wi  211 (677)
T KOG1915|consen  154 LGNIAGARQIFERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWI  211 (677)
T ss_pred             hcccHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHH
Confidence            36666677777666543  578888888887777777788888888776543  36666653

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=87.75  E-value=4.4  Score=24.55  Aligned_cols=57  Identities=9%  Similarity=0.234  Sum_probs=41.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhC--CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           17 KFLGKNGNSLKALEIYNSITDE--SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+.+.|++.+|...|+++...  +-+.-....-.+..++.+.|+++.|...++++.+.
T Consensus        13 ~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen   13 LEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3456789999999999999853  11123344556788899999999999999998764

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=87.56  E-value=1.3  Score=18.33  Aligned_cols=28  Identities=11%  Similarity=0.223  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           45 FICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        45 ~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+|..+-..|...|++++|+..|++..+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            3566777778888888888888877654

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=87.52  E-value=0.67  Score=26.77  Aligned_cols=31  Identities=10%  Similarity=0.238  Sum_probs=24.5

Q ss_pred             cCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHH
Q 034447           22 NGNSLKALEIYNSITDESDKVNVFICNLILSCL   54 (94)
Q Consensus        22 ~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   54 (94)
                      .|.-.+|-.+|.+|..+|-+||  .|+.|+...
T Consensus       108 ygsk~DaY~VF~kML~~G~pPd--dW~~Ll~~a  138 (140)
T PF11663_consen  108 YGSKTDAYAVFRKMLERGNPPD--DWDALLKEA  138 (140)
T ss_pred             hccCCcHHHHHHHHHhCCCCCc--cHHHHHHHh
Confidence            3555788999999999999997  477777654

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 [].

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=87.43  E-value=3.9  Score=26.67  Aligned_cols=80  Identities=10%  Similarity=0.196  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHHh--cCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHh--cC----CHHHHHHHHHHHHHcCC---Cc
Q 034447            9 ISSYSSYIKFLGK--NGNSLKALEIYNSITDESDKVNVFICNLILSCLVR--NG----KFESSLKLFDKIKQSGL---TP   77 (94)
Q Consensus         9 ~~~~~~ll~~~~~--~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~--~g----~~~~a~~~~~~m~~~g~---~p   77 (94)
                      ..++.++|.....  ...+++...+++.|.+.|++-+.++|-+..--...  ..    ...++..+|+.|++...   .+
T Consensus        60 ~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~  139 (297)
T PF13170_consen   60 RFILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSP  139 (297)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCc
Confidence            3444444444443  12356677889999999999988888773332222  22    44567889999988642   35


Q ss_pred             cHHHHHHHHHH
Q 034447           78 DAVTYNTVYQS   88 (94)
Q Consensus        78 ~~~~~~~ll~~   88 (94)
                      +-+++.+++..
T Consensus       140 ~D~~~a~lLA~  150 (297)
T PF13170_consen  140 EDYPFAALLAM  150 (297)
T ss_pred             cchhHHHHHhc
Confidence            66677776654

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

Probab=87.32  E-value=6.3  Score=25.86  Aligned_cols=78  Identities=18%  Similarity=0.191  Sum_probs=60.5

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      -|.+-|..--.+|++.|.++.|++=-+.-..  +-| -..+|..|=.+|...|++++|++.|++-..  +.|+..+|..=
T Consensus       113 ~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~~~A~~aykKaLe--ldP~Ne~~K~n  188 (304)
T KOG0553|consen  113 TNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKYEEAIEAYKKALE--LDPDNESYKSN  188 (304)
T ss_pred             CcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcHHHHHHHHHhhhc--cCCCcHHHHHH
Confidence            3778888899999999999998775554443  234 567888888999999999999999887654  56887788766


Q ss_pred             HHH
Q 034447           86 YQS   88 (94)
Q Consensus        86 l~~   88 (94)
                      |+.
T Consensus       189 L~~  191 (304)
T KOG0553|consen  189 LKI  191 (304)
T ss_pred             HHH
Confidence            654

>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=87.02  E-value=2.6  Score=21.04  Aligned_cols=29  Identities=14%  Similarity=0.291  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           44 VFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        44 ~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+|+.+-..|...|++++|+..|++..+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~   33 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALD   33 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45788889999999999999999998764

...

>PRK15331 chaperone protein SicA; Provisional

Probab=86.84  E-value=4.6  Score=24.15  Aligned_cols=51  Identities=10%  Similarity=-0.039  Sum_probs=38.0

Q ss_pred             HhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           20 GKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        20 ~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      -..|++++|..+|.-+...+. -|..-|..|-.++-..+.+++|+..|....
T Consensus        48 y~~Gk~~eA~~~F~~L~~~d~-~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~   98 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCIYDF-YNPDYTMGLAAVCQLKKQFQKACDLYAVAF   98 (165)
T ss_pred             HHCCCHHHHHHHHHHHHHhCc-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457999999999998875432 244456777777777889999999887643

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=86.59  E-value=11  Score=27.73  Aligned_cols=65  Identities=8%  Similarity=-0.023  Sum_probs=48.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +......+...+.+.+.+++|....+.....  .| +....+.+-.++.+.|+.++|+.+|++....+
T Consensus       119 ~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~  184 (694)
T PRK15179        119 SSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILLEAKSWDEIGQSEQADACFERLSRQH  184 (694)
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhcC
Confidence            3445556677777888888888888877754  25 56666677777788899999999999988743

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=86.42  E-value=1.1  Score=19.17  Aligned_cols=22  Identities=18%  Similarity=0.353  Sum_probs=16.0

Q ss_pred             hHHHHHHHHHHHHhcCCHHHHH
Q 034447           43 NVFICNLILSCLVRNGKFESSL   64 (94)
Q Consensus        43 ~~~t~~~li~~~~~~g~~~~a~   64 (94)
                      |...|+-+-..|...|++++|+
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            6677777777777777777764

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

Probab=86.36  E-value=3.5  Score=27.17  Aligned_cols=58  Identities=14%  Similarity=0.056  Sum_probs=41.0

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      .||...|-..+.++++.++|++-..+-.. ++     ...-|-..+..|.+.|+..+|..+..+
T Consensus       205 v~dkrfw~lki~aLa~~~~w~eL~~fa~s-kK-----sPIGyepFv~~~~~~~~~~eA~~yI~k  262 (319)
T PF04840_consen  205 VPDKRFWWLKIKALAENKDWDELEKFAKS-KK-----SPIGYEPFVEACLKYGNKKEASKYIPK  262 (319)
T ss_pred             CcHHHHHHHHHHHHHhcCCHHHHHHHHhC-CC-----CCCChHHHHHHHHHCCCHHHHHHHHHh
Confidence            67888888999999999999887776543 21     225566666777777777777666655

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

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

Probab=86.30  E-value=6.3  Score=29.89  Aligned_cols=79  Identities=11%  Similarity=0.170  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE-SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      -+|-.+-+.|...|++..|+++|+...+. .-.-+...-+.|-+++-+.|.+.+|.+.+-.-......-..+-||..+-.
T Consensus       681 dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~a~v~  760 (1018)
T KOG2002|consen  681 DVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNLALVL  760 (1018)
T ss_pred             ceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHHHHHH
Confidence            45667788899999999999999976543 33347888899999999999999999988776665544455667776654

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=86.29  E-value=3.3  Score=27.13  Aligned_cols=44  Identities=18%  Similarity=0.086  Sum_probs=35.7

Q ss_pred             CccH-HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHH
Q 034447            6 KTSI-SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNL   49 (94)
Q Consensus         6 ~p~~-~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~   49 (94)
                      .||. .-||..|....+.|++++|..+++|-++.|++--..+|--
T Consensus       253 ~~dTe~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik  297 (303)
T PRK10564        253 LNDTESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFIS  297 (303)
T ss_pred             CchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHH
Confidence            3444 4568999999999999999999999999998765555543

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

Probab=85.56  E-value=6  Score=25.70  Aligned_cols=47  Identities=15%  Similarity=0.111  Sum_probs=41.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CCCCchHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITD-----ESDKVNVFICNLILSCL   54 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~t~~~li~~~   54 (94)
                      |...|..+|.+|.+.|+...|...++.+.+     .|+.|...+........
T Consensus       186 ~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~~~~  237 (280)
T COG3629         186 DEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYEEIL  237 (280)
T ss_pred             chHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHHHHh
Confidence            778899999999999999999999998864     79999999888887773

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

Probab=85.54  E-value=8.1  Score=25.39  Aligned_cols=71  Identities=14%  Similarity=0.116  Sum_probs=51.1

Q ss_pred             HHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH-hhcc
Q 034447           19 LGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS-DHIT   92 (94)
Q Consensus        19 ~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~-~~~~   92 (94)
                      ..+.+++++|+..|.+-...  .| |.+-|.--..+|.+.|.++.|++=.+.-..-+- --+.+|..|=.+ ++.|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l--~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp-~yskay~RLG~A~~~~g  163 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIEL--DPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDP-HYSKAYGRLGLAYLALG  163 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhc--CCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcCh-HHHHHHHHHHHHHHccC
Confidence            45678999999999988763  45 889999999999999999999887666544221 134555555555 4443

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

Probab=85.14  E-value=11  Score=26.56  Aligned_cols=70  Identities=16%  Similarity=0.227  Sum_probs=47.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CC-ccHHHHHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG-LT-PDAVTYNTVY   86 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~-p~~~~~~~ll   86 (94)
                      .++-+....+++..=.+.....|++-+...-+-...+.-...+++.|+.+|++..+.. .. -|..+|+.++
T Consensus       235 ~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~L  306 (559)
T KOG1155|consen  235 KAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVL  306 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHH
Confidence            3444555667777777777777886555555555555567789999999999998763 22 3666776655

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=85.13  E-value=7.3  Score=24.51  Aligned_cols=56  Identities=9%  Similarity=0.088  Sum_probs=41.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCchHHHH---HHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKVNVFIC---NLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~---~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+.+.|++++|.+.|++....--. +...-   -.+..++.+.+++++|...+++..+.
T Consensus        40 ~~~~~~g~y~~Ai~~f~~l~~~yP~-s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~   98 (243)
T PRK10866         40 QQKLQDGNWKQAITQLEALDNRYPF-GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   98 (243)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            3345679999999999999864211 22222   24567788999999999999998775

>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation

Probab=85.10  E-value=4.2  Score=21.69  Aligned_cols=66  Identities=11%  Similarity=0.124  Sum_probs=50.3

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .|+...|..-++......  .+=.++|+-.+..|+..|...|-++++-..-.=.++...++++.|...
T Consensus         7 ~~~~~~~k~~~~rk~~Ls--~eE~EL~ELa~~AGv~~dp~VFriildLL~~nVsP~AI~qmLK~m~s~   72 (88)
T PF12926_consen    7 SPTAQVYKYSLRRKKVLS--AEEVELYELAQLAGVPMDPEVFRIILDLLRLNVSPDAIFQMLKSMCSG   72 (88)
T ss_pred             CChHHHHHHHHHHHhccC--HHHHHHHHHHHHhCCCcChHHHHHHHHHHHcCCCHHHHHHHHHHHHcc
Confidence            455566665554333222  344489999999999999999999999888888999999999999653

This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=85.09  E-value=5.5  Score=23.04  Aligned_cols=63  Identities=13%  Similarity=0.157  Sum_probs=48.2

Q ss_pred             CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           24 NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        24 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +..+..+.++.+....+-|+.....+-+++|-+..++..|.++|+-.+.+ +.+....|-.+++
T Consensus        64 D~wEvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K-~g~~k~~Y~y~v~  126 (149)
T KOG4077|consen   64 DGWEVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDK-CGAQKQVYPYYVK  126 (149)
T ss_pred             hHHHHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHh-cccHHHHHHHHHH
Confidence            34566667777788889999999999999999999999999999988644 2233334555554

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

Probab=84.98  E-value=14  Score=28.11  Aligned_cols=58  Identities=10%  Similarity=0.118  Sum_probs=47.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      -.+-.+|-+.|+.+++..+|++..+.. +-|..+-|-+...|+.. +.++|.+++.+...
T Consensus       120 ~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~  177 (906)
T PRK14720        120 RTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIY  177 (906)
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHH
Confidence            344555666699999999999999876 45899999999999999 99999988777644

>PF14840 DNA_pol3_delt_C: Processivity clamp loader gamma complex DNA pol III C-term; PDB: 3GLG_F 1XXH_A 3GLF_F 1JQJ_C 3GLI_F

Probab=84.41  E-value=1.8  Score=24.54  Aligned_cols=27  Identities=19%  Similarity=0.381  Sum_probs=13.4

Q ss_pred             cCCHHHHHHHHHHHhhCCCCchHHHHH
Q 034447           22 NGNSLKALEIYNSITDESDKVNVFICN   48 (94)
Q Consensus        22 ~g~~~~a~~~~~~m~~~~~~p~~~t~~   48 (94)
                      .|+.+.+.++++.++..|+.|....|.
T Consensus        10 ~G~~~ra~riL~~L~~Eg~ep~~lLw~   36 (125)
T PF14840_consen   10 AGDAKRALRILQGLQAEGVEPPILLWA   36 (125)
T ss_dssp             TT-HHHHHHHHHHHHHTT--HHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCccHHHHHHH
Confidence            355555556666665555555555444

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

Probab=84.35  E-value=12  Score=26.26  Aligned_cols=63  Identities=16%  Similarity=0.067  Sum_probs=47.6

Q ss_pred             Ccc-HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447            6 KTS-ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus         6 ~p~-~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      .|+ ....-.+=.++.+.|.+.+|..+++.-... .+-|...|..|-.+|...|+..++..-..+
T Consensus       370 ~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~AE  433 (484)
T COG4783         370 DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARAE  433 (484)
T ss_pred             CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHHH
Confidence            354 444556678889999999999999888754 355899999999999888877766654433

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=84.33  E-value=8.4  Score=24.54  Aligned_cols=77  Identities=13%  Similarity=0.125  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH--cCCCccHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ--SGLTPDAVTYNTVYQS   88 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~p~~~~~~~ll~~   88 (94)
                      |.+..+..+.+.+.++++....++-.+.. +-|..+-.-++.-+|-.|+|++|..=++-..+  -...+....|..+|.+
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            44566777888888999988777665432 23777777889999999999999865444322  2344667778888776

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=84.31  E-value=5.2  Score=23.40  Aligned_cols=52  Identities=15%  Similarity=0.206  Sum_probs=43.3

Q ss_pred             CccHHHHHHHHHHHHhcCC-HHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhc
Q 034447            6 KTSISSYSSYIKFLGKNGN-SLKALEIYNSITDESDKVNVFICNLILSCLVRN   57 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~-~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   57 (94)
                      ..+..+|.+++.+.++... --.+..+|+-|++.+.+++..-|..+|.++.+-
T Consensus        76 ~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g  128 (145)
T PF13762_consen   76 WLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRG  128 (145)
T ss_pred             hcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC
Confidence            3466789999999987776 455677999999988999999999999987665

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

Probab=83.83  E-value=3.2  Score=30.39  Aligned_cols=66  Identities=11%  Similarity=0.138  Sum_probs=52.6

Q ss_pred             Cc-cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            6 KT-SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         6 ~p-~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .| +...||.+-.+|.+.+.-.+|...+.+-.+.+ .-+-..|-.-+-...+-|.+++|++.+.++..
T Consensus       549 ~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  549 EPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             CCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence            45 66889999999999999999999999888766 34445555556667888999999999988754

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

Probab=83.33  E-value=14  Score=26.23  Aligned_cols=81  Identities=11%  Similarity=0.128  Sum_probs=62.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      |.....-|-+.|-+.|+-.+|.+++-+--+ =++-|+.|...|-.-|....-++++++.|++-.  -++|+..-|..+|.
T Consensus       591 dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ayyidtqf~ekai~y~ekaa--liqp~~~kwqlmia  667 (840)
T KOG2003|consen  591 DPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--LIQPNQSKWQLMIA  667 (840)
T ss_pred             CHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--hcCccHHHHHHHHH
Confidence            666777778888888888888887655442 244588888888888888888999999998753  46799999999998


Q ss_pred             Hhhc
Q 034447           88 SDHI   91 (94)
Q Consensus        88 ~~~~   91 (94)
                      .|.+
T Consensus       668 sc~r  671 (840)
T KOG2003|consen  668 SCFR  671 (840)
T ss_pred             HHHH
Confidence            8643

>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]

Probab=82.67  E-value=18  Score=27.00  Aligned_cols=75  Identities=27%  Similarity=0.409  Sum_probs=54.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhC--CCCchHHHHHHHHHHHHhcCCHHH--HHH-HHHHHHHcCCCccHHHHHHHHHH
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDE--SDKVNVFICNLILSCLVRNGKFES--SLK-LFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~--~~~p~~~t~~~li~~~~~~g~~~~--a~~-~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      +|+.+|..+|++..+.++++.+...  |-+.=...||-.|+.+.+.|.++-  ... .-+.+.+.-+.-|..||..++++
T Consensus        33 sl~eacv~n~~~~rs~~ll~s~~~~~~~~k~~l~~~nlyi~~~~q~~sf~l~~~~~~~~~~lq~a~ln~d~~t~all~~~  112 (1117)
T COG5108          33 SLFEACVYNGDFLRSKQLLKSFIDHNKGDKILLPMINLYIREIIQRGSFELTDVLSNAKELLQQARLNGDSLTYALLCQA  112 (1117)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHhcCCcCCeeehhHHHHHHHHHHhcCCccHHHHHHHHHHHHHHhhcCCcchHHHHHHHh
Confidence            7999999999999999999998753  444556778888999999997642  111 12223333456688999988876

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=82.61  E-value=7.9  Score=22.96  Aligned_cols=61  Identities=7%  Similarity=-0.050  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      |-.|=..+-..|++++|...|........ -|...+-.+-.++...|+.+.|.+.|+.-...
T Consensus        72 ~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363         72 WFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            33444445567999999999999887663 47788888899999999999999999986653

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.48  E-value=5.9  Score=26.45  Aligned_cols=65  Identities=18%  Similarity=0.245  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh-CCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD-ESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGL   75 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~   75 (94)
                      +.+-+..=....+.|+.+.|.+-|++-.+ .|+.| ...||..+. ..+.|+...|++...++.+.|+
T Consensus       144 Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqp-llAYniALa-Hy~~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  144 ADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQP-LLAYNLALA-HYSSRQYASALKHISEIIERGI  209 (459)
T ss_pred             cchhccchheeeccccHHHHHHHHHHHHhhcCCCc-hhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhh
Confidence            33344444445678999999998887654 45544 567887654 4567888899988888777665

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

Probab=82.02  E-value=20  Score=27.19  Aligned_cols=82  Identities=11%  Similarity=0.058  Sum_probs=62.3

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      -|..|...+-..|-+.+..+++..+|+....  .-|+..--..+.-+|.+.+++.+-.++-=+|.+ .++-+.+.|.+++
T Consensus        75 ~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~--~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~  151 (932)
T KOG2053|consen   75 TDDLTLQFLQNVYRDLGKLDEAVHLYERANQ--KYPSEELLYHLFMAYVREKSYKKQQKAALQLYK-NFPKRAYYFWSVI  151 (932)
T ss_pred             CchHHHHHHHHHHHHHhhhhHHHHHHHHHHh--hCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCcccchHHHHH
Confidence            3788999999999999999999999998764  347877778888888888877665555444443 3445678888888


Q ss_pred             HHhhc
Q 034447           87 QSDHI   91 (94)
Q Consensus        87 ~~~~~   91 (94)
                      +....
T Consensus       152 Slilq  156 (932)
T KOG2053|consen  152 SLILQ  156 (932)
T ss_pred             HHHHH
Confidence            76443

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=81.92  E-value=2.7  Score=17.13  Aligned_cols=27  Identities=15%  Similarity=0.327  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           46 ICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        46 t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|..+-..+...|++++|++.|++..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            345556677778888888888877654

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=81.68  E-value=5  Score=24.04  Aligned_cols=33  Identities=15%  Similarity=0.138  Sum_probs=30.4

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDE   38 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~   38 (94)
                      .|+...|..++.++...|+.++|.+...++...
T Consensus       141 ~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~l  173 (193)
T PF11846_consen  141 RPDPNVYQRYALALALLGDPEEARQWLARARRL  173 (193)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            699999999999999999999999999988753

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]

Probab=81.57  E-value=6.5  Score=21.27  Aligned_cols=63  Identities=19%  Similarity=0.171  Sum_probs=36.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCCc
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG--KFESSLKLFDKIKQSGLTP   77 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p   77 (94)
                      ..+|.-|...|+.++|...++++....  ........++..+...+  .-+-+..++.++.+.+..+
T Consensus         6 ~~~l~ey~~~~d~~ea~~~l~el~~~~--~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~   70 (113)
T PF02847_consen    6 FSILMEYFSSGDVDEAVECLKELKLPS--QHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLIS   70 (113)
T ss_dssp             HHHHHHHHHHT-HHHHHHHHHHTT-GG--GHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHhCCCc--cHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCC
Confidence            456677778899999999999875431  22233334444444442  2334556667777666543

It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=81.56  E-value=11  Score=24.02  Aligned_cols=64  Identities=14%  Similarity=0.297  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHhc-CCHHHHHHHHHHHhh----CCCC-chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           11 SYSSYIKFLGKN-GNSLKALEIYNSITD----ESDK-VNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        11 ~~~~ll~~~~~~-g~~~~a~~~~~~m~~----~~~~-p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .+.-+-..|-+. |++++|.+.|++-.+    .+-+ --...+.-+...+.+.|++++|+++|++....-
T Consensus       116 ~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~  185 (282)
T PF14938_consen  116 CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKC  185 (282)
T ss_dssp             HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh
Confidence            333444444444 566666666665432    2211 124455667777899999999999999987653

>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=81.13  E-value=0.81  Score=25.87  Aligned_cols=59  Identities=15%  Similarity=0.191  Sum_probs=40.1

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      .-+....|.++..|++.+..++..++++...       .+-...+++-|.+.|.++++.-++.++.
T Consensus        39 ~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~-------~yd~~~~~~~c~~~~l~~~a~~Ly~~~~   97 (143)
T PF00637_consen   39 ENNPDLHTLLLELYIKYDPYEKLLEFLKTSN-------NYDLDKALRLCEKHGLYEEAVYLYSKLG   97 (143)
T ss_dssp             C-SHHHHHHHHHHHHCTTTCCHHHHTTTSSS-------SS-CTHHHHHHHTTTSHHHHHHHHHCCT
T ss_pred             ccCHHHHHHHHHHHHhcCCchHHHHHccccc-------ccCHHHHHHHHHhcchHHHHHHHHHHcc
Confidence            3467788899999999987788877776221       1334556666777777777777776653

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=81.03  E-value=12  Score=23.96  Aligned_cols=63  Identities=6%  Similarity=0.015  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhC-CC-CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDE-SD-KVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+-.+-..|...|++++|...|+.+.+. .- +.....+--+...+...|+.++|..+|++..+.
T Consensus       182 A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        182 ANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4456667788899999999999999743 11 111223333455677899999999999998775

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

Probab=80.36  E-value=26  Score=27.52  Aligned_cols=74  Identities=16%  Similarity=0.102  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHh
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSD   89 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~   89 (94)
                      ..|..+-.+--+.|...+|.+-|-+-      -|...|.-.|+...+.|.+++-.+.+.-.+++..+|...  +.||-+|
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~Ay 1176 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAY 1176 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHH
Confidence            45667777777777777777666332      367788888899999999998888887666666666544  3466665


Q ss_pred             hc
Q 034447           90 HI   91 (94)
Q Consensus        90 ~~   91 (94)
                      ++
T Consensus      1177 Ak 1178 (1666)
T KOG0985|consen 1177 AK 1178 (1666)
T ss_pred             HH
Confidence            54

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

Probab=80.21  E-value=13  Score=29.73  Aligned_cols=58  Identities=12%  Similarity=0.102  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDK   69 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~   69 (94)
                      .|..|+.-|.+.+..++|-++++.|.+. +.-....|.-.+..+.+..+.++|..++++
T Consensus      1532 V~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~r 1589 (1710)
T KOG1070|consen 1532 VHLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKR 1589 (1710)
T ss_pred             HHHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHH
Confidence            3444455555555555555555555432 112334444444444444444444444433

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.17  E-value=3  Score=27.87  Aligned_cols=32  Identities=9%  Similarity=0.024  Sum_probs=28.0

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITD   37 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~   37 (94)
                      =||..+++.+|+.+.+.++..+|..+.-.|..
T Consensus       132 F~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  132 FPDQFTFCLLMDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             ccchhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            58999999999999999999999887766643

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

Probab=80.13  E-value=16  Score=29.32  Aligned_cols=62  Identities=8%  Similarity=0.132  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..|.++++.-...|.-+...++|++..+..  -....|..|..-|.+.+..++|.+++++|.++
T Consensus      1498 NiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK 1559 (1710)
T KOG1070|consen 1498 NIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTVHLKLLGIYEKSEKNDEADELLRLMLKK 1559 (1710)
T ss_pred             HHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHHHHHHHHHHHHhhcchhHHHHHHHHHHH
Confidence            345556665555565566666666655431  24567778888888888889999999998765

---

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	94
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-10
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	2e-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 = 54.1 bits (128), Expect = 3e-10
 Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 3/85 (3%)

Query: 6   KTSISSYSSYIKFLGKNGN---SLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFES 62
                   ++ K          +   L +++    +   + + + N ++    R G F+ 
Sbjct: 124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKE 183

Query: 63  SLKLFDKIKQSGLTPDAVTYNTVYQ 87
            + +   +K +GLTPD ++Y    Q
Sbjct: 184 LVYVLFMVKDAGLTPDLLSYAAALQ 208

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 39.5 bits (91), Expect = 2e-05
 Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 12/31 (38%)

Query: 59 KFESSLKLFDKIKQSGLTPD---AVTYN-TV 85
          K ++SLKL+          D   A+    T+
Sbjct: 24 KLQASLKLY--------ADDSAPALAIKATM 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	94
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.94
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.91
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.9
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.89
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	98.85
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	98.8
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.04
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	98.02
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.95
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	97.93
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	97.9
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.86
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	97.85
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	97.82
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	97.75
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.75
2gw1_A	514	Mitochondrial precursor proteins import receptor;	97.75
2gw1_A	514	Mitochondrial precursor proteins import receptor;	97.66
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.66
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	97.65
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	97.64
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	97.61
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	97.6
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.59
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	97.58
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.57
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	97.57
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	97.56
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	97.51
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	97.49
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	97.48
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	97.47
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.45
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	97.45
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.39
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.36
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	97.35
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	97.35
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.33
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	97.33
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	97.33
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	97.33
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.31
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	97.31
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	97.29
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.27
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.25
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.24
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	97.22
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.21
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	97.2
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.19
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	97.17
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.16
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	97.16
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.16
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.14
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.14
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.11
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.11
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.11
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.1
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.1
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.1
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	97.09
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.08
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.06
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.06
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.05
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.04
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	97.04
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	97.03
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.0
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	97.0
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.99
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	96.97
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.96
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	96.94
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	96.93
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	96.93
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	96.9
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	96.89
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.89
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.88
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.86
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	96.81
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.8
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	96.75
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	96.75
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	96.74
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.73
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	96.72
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	96.71
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	96.67
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	96.67
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	96.64
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.62
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.62
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.62
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	96.6
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	96.56
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	96.51
3u4t_A	272	TPR repeat-containing protein; structural genomics	96.5
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.45
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.45
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.43
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	96.42
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	96.4
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	96.36
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	96.32
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	96.29
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	96.28
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	96.26
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	96.25
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	96.25
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.23
3u4t_A	272	TPR repeat-containing protein; structural genomics	96.22
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	96.21
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.19
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	96.18
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	96.18
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.17
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	96.15
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	96.14
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	96.08
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.07
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.03
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	96.0
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	96.0
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	96.0
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	95.98
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	95.97
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	95.97
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	95.95
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	95.89
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	95.84
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	95.83
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	95.76
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	95.74
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	95.74
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	95.73
4g1t_A	472	Interferon-induced protein with tetratricopeptide	95.64
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	95.64
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	95.63
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	95.62
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	95.6
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	95.56
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	95.52
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	95.47
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	95.45
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	95.44
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	95.38
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	95.37
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	95.34
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	95.27
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	95.25
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	95.24
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	95.19
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	95.18
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	95.07
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	95.03
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	94.84
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	94.83
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	94.76
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	94.6
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	94.59
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	94.56
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	94.52
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.49
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	94.47
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	94.44
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	94.43
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	94.41
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.32
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.3
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	93.93
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	93.89
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.65
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	93.6
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	93.4
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	93.29
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	92.94
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	92.92
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	92.89
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	92.89
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	92.87
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	92.85
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	92.75
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	92.63
1pc2_A	152	Mitochondria fission protein; unknown function; NM	92.48
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	92.33
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	92.19
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	91.93
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	91.36
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	91.32
2p58_C	116	Putative type III secretion protein YSCG; type III	91.11
4g1t_A	472	Interferon-induced protein with tetratricopeptide	90.38
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	90.32
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	88.99
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	88.76
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	88.67
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	88.33
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	88.3
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	88.07
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	87.59
2ion_A	152	PDCD4, programmed cell death 4, PDCD4; alpha-helic	87.43
2kat_A	115	Uncharacterized protein; NESG, structure, structur	87.42
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	86.85
1klx_A	138	Cysteine rich protein B; structural genomics, heli	86.85
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	86.22
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	85.16
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	84.79
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	83.79
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	83.71
3eiq_C	358	Programmed cell death protein 4; PDCD4, anti-oncog	82.1
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	81.4

>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=99.94  E-value=4.6e-26  Score=151.61  Aligned_cols=91  Identities=8%  Similarity=0.096  Sum_probs=85.6

Q ss_pred             CcccC-CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccH
Q 034447            1 MQQHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDA   79 (94)
Q Consensus         1 M~~~~-~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   79 (94)
                      |.+.| .||..|||++|.+|++.|++++|.++|++|.+.|+.||..|||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus        96 M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~  175 (501)
T 4g26_A           96 MIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEE  175 (501)
T ss_dssp             HHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCH
Confidence            45566 89999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhc
Q 034447           80 VTYNTVYQSDHI   91 (94)
Q Consensus        80 ~~~~~ll~~~~~   91 (94)
                      .||++||++|++
T Consensus       176 ~ty~~Li~~~~~  187 (501)
T 4g26_A          176 PELAALLKVSMD  187 (501)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh
Confidence            999999999654

>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=99.91  E-value=6e-24  Score=141.45  Aligned_cols=91  Identities=12%  Similarity=0.140  Sum_probs=87.1

Q ss_pred             CcccC-CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccH
Q 034447            1 MQQHG-KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDA   79 (94)
Q Consensus         1 M~~~~-~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   79 (94)
                      |++.| .||..|||++|.+|++.|++++|.++|++|.+.|+.||..||++||++|++.|++++|.+++++|++.|+.|+.
T Consensus       131 M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~  210 (501)
T 4g26_A          131 MKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSK  210 (501)
T ss_dssp             HHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCH
T ss_pred             HHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCH
Confidence            55666 99999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhc
Q 034447           80 VTYNTVYQSDHI   91 (94)
Q Consensus        80 ~~~~~ll~~~~~   91 (94)
                      .||++++..|++
T Consensus       211 ~T~~~l~~~F~s  222 (501)
T 4g26_A          211 STFDMIEEWFKS  222 (501)
T ss_dssp             HHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhc
Confidence            999999998764

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.90  E-value=1.3e-24  Score=152.57  Aligned_cols=81  Identities=12%  Similarity=0.208  Sum_probs=40.2

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHcCCCccHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGK-FESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      .||++|||+||++||+.|++++|.++|++|.+.|+.||.+|||++|+++|+.|+ .++|.++|++|.+.|+.||.++|++
T Consensus       162 ~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~  241 (1134)
T 3spa_A          162 LLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAV  241 (1134)
T ss_dssp             TCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHS
T ss_pred             CCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhccc
Confidence            445555555555555555555555555555555555555555555555555444 2344455555555555555555554


Q ss_pred             HH
Q 034447           85 VY   86 (94)
Q Consensus        85 ll   86 (94)
                      ++
T Consensus       242 ll  243 (1134)
T 3spa_A          242 LL  243 (1134)
T ss_dssp             CC
T ss_pred             cc
Confidence            33

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.89  E-value=3.8e-23  Score=145.16  Aligned_cols=84  Identities=17%  Similarity=0.207  Sum_probs=79.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHh---hCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSIT---DESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~---~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      -..|||++|++||+.|++++|.++|++|.   ..|+.||++|||+||++||+.|++++|.++|++|.+.|+.||.+||++
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYnt  205 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA  205 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence            35799999999999999999999998876   458999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhc
Q 034447           85 VYQSDHI   91 (94)
Q Consensus        85 ll~~~~~   91 (94)
                      ||+++++
T Consensus       206 LI~glcK  212 (1134)
T 3spa_A          206 ALQCMGR  212 (1134)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9999654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=98.85  E-value=8.2e-08  Score=63.73  Aligned_cols=80  Identities=5%  Similarity=-0.064  Sum_probs=40.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCch--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKVN--VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      +..+|+.+...|.+.|++++|.++|+++.+.    +..|+  ..+|..+..+|.+.|++++|.+.|+++.+.+ +.+..+
T Consensus       474 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~  552 (597)
T 2xpi_A          474 DPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANV  552 (597)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHH
T ss_pred             ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHH
Confidence            3445555555555555555555555555433    34444  4555555555555555555555555554433 224445


Q ss_pred             HHHHHHH
Q 034447           82 YNTVYQS   88 (94)
Q Consensus        82 ~~~ll~~   88 (94)
                      |..+..+
T Consensus       553 ~~~l~~~  559 (597)
T 2xpi_A          553 HTAIALV  559 (597)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555444

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=98.80  E-value=5.6e-08  Score=64.53  Aligned_cols=82  Identities=13%  Similarity=0.032  Sum_probs=56.8

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCcc--HH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS----GLTPD--AV   80 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~   80 (94)
                      .+..+|+.+..+|.+.|++++|.++|+++.+.. +.+..+|+.+...|.+.|++++|.++|+++.+.    +..|+  ..
T Consensus       439 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~  517 (597)
T 2xpi_A          439 GTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAA  517 (597)
T ss_dssp             TCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHH
T ss_pred             cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHH
Confidence            356677777777777777777777777776532 235677777777777777777777777777654    55666  66


Q ss_pred             HHHHHHHHh
Q 034447           81 TYNTVYQSD   89 (94)
Q Consensus        81 ~~~~ll~~~   89 (94)
                      +|..+..+|
T Consensus       518 ~~~~l~~~~  526 (597)
T 2xpi_A          518 TWANLGHAY  526 (597)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777777763

>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=98.04  E-value=0.00023  Score=37.66  Aligned_cols=79  Identities=11%  Similarity=0.156  Sum_probs=56.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+...+.+.|++++|...+++..... +.+...+..+...+...|++++|.+.++++.+..- .+...+..+..
T Consensus        34 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~  111 (136)
T 2fo7_A           34 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGN  111 (136)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CChHHHHHHHH
Confidence            55667777778888888888888888876543 23566777788888888888888888888776532 24455555555


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       112 ~  112 (136)
T 2fo7_A          112 A  112 (136)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.02  E-value=0.00015  Score=45.79  Aligned_cols=60  Identities=18%  Similarity=0.246  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +|..+...+.+.|++++|...|+++.+. .+.+..+|+.+...+.+.|++++|...++++.
T Consensus       273 ~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  332 (388)
T 1w3b_A          273 AYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIEEAVRLYRKAL  332 (388)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhh-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444444444444444444444444332 12234444444444444444444444444443

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.95  E-value=0.00034  Score=36.62  Aligned_cols=78  Identities=12%  Similarity=0.168  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ...|..+...+.+.|++++|...+++..... +.+..++..+...+...|++++|...++++.+..- .+...+..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHH
Confidence            4556666667777777777777777665432 23456666677777777777777777777665431 234444444443

>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=97.93  E-value=0.00039  Score=36.70  Aligned_cols=76  Identities=11%  Similarity=0.155  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      .|..+...+.+.|++++|..+++++.... +.+...+..+...+...|++++|...+++..+.+- .+...+..+...
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~   78 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNA   78 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCC-CchHHHHHHHHH
Confidence            56778888999999999999999987653 23677888899999999999999999999887642 345556555554

>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=97.90  E-value=0.00046  Score=43.57  Aligned_cols=80  Identities=9%  Similarity=0.001  Sum_probs=65.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +..++..+...+.+.|++++|...|+++.+.. +.+..+|..+...+.+.|++++|+..|+++.+.. +.+..+|..+..
T Consensus       236 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  313 (388)
T 1w3b_A          236 HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLAN  313 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHH
Confidence            57788889999999999999999999988653 2256788999999999999999999999987753 346677777766


Q ss_pred             Hh
Q 034447           88 SD   89 (94)
Q Consensus        88 ~~   89 (94)
                      .+
T Consensus       314 ~~  315 (388)
T 1w3b_A          314 IK  315 (388)
T ss_dssp             HH
T ss_pred             HH
Confidence            63

>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=97.86  E-value=0.00095  Score=39.48  Aligned_cols=60  Identities=12%  Similarity=0.035  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      .+..+...|.+.|++++|...+++....+..| +...+..+...+...|++++|...+++.
T Consensus       107 ~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  167 (252)
T 2ho1_A          107 VLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKS  167 (252)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            33333444444444444444444443321122 3333334444444444444444444443

>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=97.85  E-value=0.00044  Score=44.24  Aligned_cols=79  Identities=16%  Similarity=0.067  Sum_probs=52.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+...+.+.|++++|..+|+++.+. .+.+..+|..+..++...|++++|+..|+++.+.+- .+...+..+..
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~  102 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKM-DFTAARLQRGH  102 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CcHHHHHHHHH
Confidence            5566777777777777777777777777653 223567777777777777777777777777766532 23455555554


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       103 ~  103 (450)
T 2y4t_A          103 L  103 (450)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=97.82  E-value=0.00037  Score=43.21  Aligned_cols=31  Identities=10%  Similarity=0.223  Sum_probs=15.0

Q ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           43 NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        43 ~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+...+.+.|++++|.+.|+++.+.
T Consensus       129 ~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~  159 (291)
T 3mkr_A          129 SLECMAMTVQILLKLDRLDLARKELKKMQDQ  159 (291)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence            3444444444445555555555555554443

>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=97.75  E-value=5.7e-05  Score=50.10  Aligned_cols=70  Identities=14%  Similarity=0.040  Sum_probs=39.4

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      .|+..+|+.+-..|...|.+++|...|..+         ..|..+..++.+.|++++|.+.+++.      .+..+|..+
T Consensus       119 ~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v  183 (449)
T 1b89_A          119 GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEV  183 (449)
T ss_dssp             CC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHH
Confidence            466667777777777777777777777755         36777778888888888888877777      256777777


Q ss_pred             HHHhh
Q 034447           86 YQSDH   90 (94)
Q Consensus        86 l~~~~   90 (94)
                      +.+|.
T Consensus       184 ~~aCv  188 (449)
T 1b89_A          184 CFACV  188 (449)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77754

>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=97.75  E-value=0.0012  Score=39.00  Aligned_cols=80  Identities=14%  Similarity=0.100  Sum_probs=49.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-cHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP-DAVTYNTVY   86 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~ll   86 (94)
                      +...+..+-..+.+.|++++|...+++..... +.+...|..+...|...|++++|.+.+++..+.+..| +...+..+.
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            45566666677777777777777777665432 2255666777777777777777777777776633334 333444443


Q ss_pred             HH
Q 034447           87 QS   88 (94)
Q Consensus        87 ~~   88 (94)
                      ..
T Consensus       149 ~~  150 (252)
T 2ho1_A          149 LV  150 (252)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=97.75  E-value=0.00069  Score=43.88  Aligned_cols=67  Identities=15%  Similarity=0.051  Sum_probs=39.7

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ||...|..+..+|.+.|++++|...+++..+.. +-+..+|..+..++.+.|++++|...|+++.+.+
T Consensus        37 p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  103 (514)
T 2gw1_A           37 EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFDLSVLSLNG  103 (514)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS
T ss_pred             ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            555666666666666666666666666655432 2244566666666666666666666666655543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=97.66  E-value=0.00076  Score=43.66  Aligned_cols=78  Identities=10%  Similarity=0.047  Sum_probs=65.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+...-..+.+.|++++|...|+++....  ||...|..+..++.+.|++++|+..+++..+.+ +.+...|..+..
T Consensus         5 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~   81 (514)
T 2gw1_A            5 YALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRAS   81 (514)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHH
Confidence            34556677788899999999999999998765  899999999999999999999999999998764 235566766666


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      +
T Consensus        82 ~   82 (514)
T 2gw1_A           82 A   82 (514)
T ss_dssp             H
T ss_pred             H
Confidence            6

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.66  E-value=0.0012  Score=34.37  Aligned_cols=66  Identities=12%  Similarity=0.188  Sum_probs=57.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...+..+...+.+.|++++|...+++..... +.+..++..+...+...|++++|...+++..+..
T Consensus        42 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  107 (125)
T 1na0_A           42 NAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD  107 (125)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            56788889999999999999999999987653 3467888999999999999999999999987654

>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=97.65  E-value=0.0018  Score=36.04  Aligned_cols=62  Identities=15%  Similarity=0.128  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ...+..+...+.+.|++++|...+++..+.. +.+...+..+...+...|++++|.+.+++..
T Consensus        42 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~  103 (186)
T 3as5_A           42 VDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQVQKYDLAVPLLIKVA  103 (186)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            3444444444444455555554444443321 1233444444444444444444444444443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=97.64  E-value=0.0018  Score=40.43  Aligned_cols=79  Identities=9%  Similarity=0.047  Sum_probs=64.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+-..|.+.|++++|...|++..+.. +.+..+|+.+...|.+.|++++|+..|++..+.. +.+..+|..+-.
T Consensus       212 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  289 (365)
T 4eqf_A          212 DPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGI  289 (365)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHH
Confidence            67889999999999999999999999887642 2368899999999999999999999999987753 224666666666


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       290 ~  290 (365)
T 4eqf_A          290 S  290 (365)
T ss_dssp             H
T ss_pred             H
Confidence            5

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=97.61  E-value=0.002  Score=39.83  Aligned_cols=49  Identities=14%  Similarity=0.298  Sum_probs=23.9

Q ss_pred             CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           23 GNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        23 g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      |++++|..+|+++.+. .+.+...|+.+..++.+.|++++|...|++..+
T Consensus       180 ~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~  228 (291)
T 3mkr_A          180 EKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALD  228 (291)
T ss_dssp             THHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4444444444444433 223444555555555555555555555555443

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=97.60  E-value=0.0027  Score=36.54  Aligned_cols=26  Identities=12%  Similarity=0.137  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           45 FICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        45 ~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      ..+..+...+...|++++|+..+++.
T Consensus       114 ~~~~~l~~~~~~~~~~~~A~~~~~~~  139 (225)
T 2vq2_A          114 IANLNKGICSAKQGQFGLAEAYLKRS  139 (225)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            33333344444444444444444443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.59  E-value=0.0014  Score=34.05  Aligned_cols=64  Identities=9%  Similarity=0.053  Sum_probs=54.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+..+-..|.+.|++++|...|++..+.. +-+...|..+-.+|...|++++|++.|++..+
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            56778888889999999999999999987653 22567889999999999999999999998764

>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=97.58  E-value=0.0021  Score=39.12  Aligned_cols=62  Identities=13%  Similarity=0.112  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ...+..+-..+.+.|++++|...+++..+.. +.+...|..+...+...|++++|.+.+++..
T Consensus       206 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~  267 (327)
T 3cv0_A          206 AQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAI  267 (327)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            3444444455555555555555555444321 1234445555555555555555555555543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.57  E-value=0.0019  Score=34.25  Aligned_cols=81  Identities=14%  Similarity=0.069  Sum_probs=63.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCccHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS-GLTPDAVTYNTVY   86 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~ll   86 (94)
                      +...+..+-..|.+.|++++|...|++..+.. +-+...+..+-.++.+.|++++|+..+++..+. .-.|+...|...|
T Consensus        26 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~ai  104 (117)
T 3k9i_A           26 LAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGVELLLKIIAETSDDETIQSYKQAI  104 (117)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHTHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            45678888889999999999999999987653 225778888999999999999999999987654 4445555665555


Q ss_pred             HHh
Q 034447           87 QSD   89 (94)
Q Consensus        87 ~~~   89 (94)
                      ..+
T Consensus       105 ~~~  107 (117)
T 3k9i_A          105 LFY  107 (117)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=97.57  E-value=0.003  Score=36.34  Aligned_cols=63  Identities=16%  Similarity=-0.007  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhc-CCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRN-GKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~-g~~~~a~~~~~~m~~   72 (94)
                      ...+..+...+...|++++|...+++..... +.+..++..+...+... |++++|...+++..+
T Consensus        42 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~  105 (225)
T 2vq2_A           42 ELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKALA  105 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHc
Confidence            4455555555555666666666555554321 12444555555555555 666666666655554

>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=97.56  E-value=0.003  Score=39.27  Aligned_cols=79  Identities=9%  Similarity=0.051  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +..++..+-..|.+.|++++|...+++..... +.+..+|..+...+...|++++|+..|++..+.. +.+...+..+-.
T Consensus       216 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~  293 (368)
T 1fch_A          216 DPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGI  293 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            57888999999999999999999999887642 2357889999999999999999999999987653 234566666655


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       294 ~  294 (368)
T 1fch_A          294 S  294 (368)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=97.51  E-value=0.0031  Score=40.29  Aligned_cols=67  Identities=16%  Similarity=0.087  Sum_probs=59.4

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .+...|..+...|.+.|++++|...|+++.+.+ +.+..+|..+...|.+.|++++|...|+++.+..
T Consensus        58 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  124 (450)
T 2y4t_A           58 DNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN  124 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC
T ss_pred             ccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            468889999999999999999999999998753 2368899999999999999999999999998754

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=97.49  E-value=0.0035  Score=36.89  Aligned_cols=78  Identities=10%  Similarity=-0.053  Sum_probs=64.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+=..+.+.|++++|...|++..+..  .+...+..+-..+...|++++|+..|++..+..- -+...+..+-.
T Consensus       117 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P-~~~~~~~~la~  193 (217)
T 2pl2_A          117 YAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQAP-KDLDLRVRYAS  193 (217)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHH
Confidence            56778888889999999999999999998877  7888899999999999999999999999877531 24555555554


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       194 ~  194 (217)
T 2pl2_A          194 A  194 (217)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=97.48  E-value=0.0034  Score=34.90  Aligned_cols=79  Identities=9%  Similarity=0.030  Sum_probs=55.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+...+.+.|++++|...+++..... +.+...+..+...+...|++++|...+++..+.. +.+...+..+..
T Consensus        75 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~  152 (186)
T 3as5_A           75 NVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAF  152 (186)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHH
Confidence            55667777777888888888888888776542 2356777777788888888888888888876653 224455555555


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       153 ~  153 (186)
T 3as5_A          153 S  153 (186)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=97.47  E-value=0.0054  Score=37.25  Aligned_cols=79  Identities=9%  Similarity=-0.015  Sum_probs=64.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+-..+.+.|++++|...+++..... +.+..+|..+...+...|++++|...+++..+..- .+...|..+..
T Consensus       171 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~  248 (327)
T 3cv0_A          171 DAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDINP-GYVRVMYNMAV  248 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHH
Confidence            67788889999999999999999999987643 23678899999999999999999999999877542 24566666655


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       249 ~  249 (327)
T 3cv0_A          249 S  249 (327)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.45  E-value=0.0025  Score=32.83  Aligned_cols=67  Identities=12%  Similarity=0.117  Sum_probs=56.7

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ++...+..+-..+.+.|++++|...|++..+.. +.+...|..+-.++.+.|++++|+..+++..+..
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   68 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT   68 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            456778888889999999999999999887642 2367888899999999999999999999987653

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=97.45  E-value=0.0016  Score=38.28  Aligned_cols=64  Identities=13%  Similarity=0.086  Sum_probs=57.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ....|..+-..+.+.|++++|...|++..+..  .+...|..+...+...|++++|...+++..+.
T Consensus         4 ~a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~   67 (258)
T 3uq3_A            4 MADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQ   67 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHh
Confidence            45678888899999999999999999998877  78889999999999999999999999998653

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.39  E-value=0.0035  Score=32.93  Aligned_cols=64  Identities=9%  Similarity=-0.043  Sum_probs=55.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+..+-..|.+.|++++|...|++..... +.+...|..+-..|...|++++|...|++..+
T Consensus        18 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           18 NMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            67788888899999999999999999887643 23577888899999999999999999998765

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.36  E-value=0.0035  Score=32.87  Aligned_cols=64  Identities=13%  Similarity=0.064  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...|..+-..+.+.|++++|...|++..... +.+...+..+...+...|++++|...+++..+.
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~   67 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEV   67 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhh
Confidence            4567788888999999999999999887653 346788889999999999999999999998664

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=97.35  E-value=0.0044  Score=35.01  Aligned_cols=65  Identities=17%  Similarity=0.117  Sum_probs=48.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..|.+.|++++|...|++..+.. +-+..+|..+-..|.+.|++++|++.|++..+.
T Consensus       106 ~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          106 YADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence            45566777777788888888888888776542 236677778888888888888888888887653

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=97.35  E-value=0.0068  Score=35.35  Aligned_cols=23  Identities=22%  Similarity=0.478  Sum_probs=8.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNS   34 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~   34 (94)
                      +..+...+.+.|++++|...+++
T Consensus        60 ~~~la~~~~~~~~~~~A~~~~~~   82 (243)
T 2q7f_A           60 YINFANLLSSVNELERALAFYDK   82 (243)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            33333333333444444333333

>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=97.33  E-value=0.0041  Score=32.59  Aligned_cols=77  Identities=8%  Similarity=0.121  Sum_probs=60.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC--Cch----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESD--KVN----VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~p~----~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      +...+..+-..+.+.|++++|...+++.....-  .++    ..+|..+...+...|++++|.+.|++..+..  |+...
T Consensus        37 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~  114 (131)
T 1elr_A           37 NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDV  114 (131)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHH
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHH
Confidence            567788888899999999999999998875421  111    7788889999999999999999999988754  45554


Q ss_pred             HHHHH
Q 034447           82 YNTVY   86 (94)
Q Consensus        82 ~~~ll   86 (94)
                      ...+-
T Consensus       115 ~~~l~  119 (131)
T 1elr_A          115 LKKCQ  119 (131)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

>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=97.33  E-value=0.0044  Score=38.50  Aligned_cols=81  Identities=10%  Similarity=0.025  Sum_probs=64.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC---Cc-------
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGL---TP-------   77 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~---~p-------   77 (94)
                      +...|..+-..+.+.|++++|...|++..+.. +.+...+..+...|.+.|++++|...|++..+..-   .|       
T Consensus       250 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  328 (368)
T 1fch_A          250 DYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAM  328 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCC
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccch
Confidence            56789999999999999999999999987642 24678999999999999999999999999865321   11       


Q ss_pred             cHHHHHHHHHHh
Q 034447           78 DAVTYNTVYQSD   89 (94)
Q Consensus        78 ~~~~~~~ll~~~   89 (94)
                      ....|..+..++
T Consensus       329 ~~~~~~~l~~~~  340 (368)
T 1fch_A          329 SENIWSTLRLAL  340 (368)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHH
Confidence            156777776663

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=97.33  E-value=0.0073  Score=35.39  Aligned_cols=79  Identities=9%  Similarity=-0.046  Sum_probs=51.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+-..+.+.|++++|...+++..... +.+...|..+...+...|++++|...+++..+..- .+...|..+-.
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~l~~  215 (258)
T 3uq3_A          138 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKAT  215 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCH-HHHHHHHHHHH
Confidence            34556667777777788888888777776532 23566777777777777888888887777765431 23444544444


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       216 ~  216 (258)
T 3uq3_A          216 A  216 (258)
T ss_dssp             H
T ss_pred             H
Confidence            4

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=97.33  E-value=0.0034  Score=39.16  Aligned_cols=60  Identities=5%  Similarity=-0.102  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +..+-..+.+.|++++|...|++..... +.+..+|..+...|...|++++|+..|++..+
T Consensus        68 ~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  127 (365)
T 4eqf_A           68 AFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLE  127 (365)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            4444444445555555555555444321 12344444455555555555555555554443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.31  E-value=0.0039  Score=31.81  Aligned_cols=79  Identities=6%  Similarity=0.030  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-ccHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT-PDAVTYNTVYQ   87 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~~~~~ll~   87 (94)
                      ...+..+-..+.+.|++++|...|++..+.. +.+...|..+-..+...|++++|...+++..+..-. .+...+..+-.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~   84 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKAD   84 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHH
Confidence            4455666677778888888888888776542 235667777888888888888888888887765311 13455555544


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus        85 ~   85 (112)
T 2kck_A           85 A   85 (112)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=97.31  E-value=3.6e-05  Score=51.03  Aligned_cols=54  Identities=13%  Similarity=0.068  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      .+.+.++.+|.+.|+++++.++++       .|+..+|+.+-..|...|++++|...|.++
T Consensus        95 ~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a  148 (449)
T 1b89_A           95 YVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV  148 (449)
T ss_dssp             --------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT
T ss_pred             hhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence            344444444444444444444442       144445555555555555555555555544

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=97.29  E-value=0.008  Score=35.03  Aligned_cols=79  Identities=9%  Similarity=0.004  Sum_probs=62.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+...+.+.|++++|...+++..+.. +.+...+..+...+...|++++|...+++..+..- .+...+..+..
T Consensus        90 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~  167 (243)
T 2q7f_A           90 AATAYYGAGNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNE-NDTEARFQFGM  167 (243)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-ccHHHHHHHHH
Confidence            56778888899999999999999999887643 24677888889999999999999999999876532 24555655555


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       168 ~  168 (243)
T 2q7f_A          168 C  168 (243)
T ss_dssp             H
T ss_pred             H
Confidence            5

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.27  E-value=0.0059  Score=34.07  Aligned_cols=65  Identities=11%  Similarity=0.014  Sum_probs=38.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-..+.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|+..|++..+.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~   74 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVV   74 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            44555555666666666666666666555432 125555666666666666666666666665543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.25  E-value=0.0054  Score=32.07  Aligned_cols=63  Identities=11%  Similarity=-0.006  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...+..+-..+...|++++|...+++..... +.+...+..+...+...|++++|...+++..+
T Consensus        46 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  108 (131)
T 2vyi_A           46 AVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSSLNKHVEAVAYYKKALE  108 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHh
Confidence            3444444445555555555555555444321 12344445555555555555555555555443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.24  E-value=0.0049  Score=31.44  Aligned_cols=66  Identities=15%  Similarity=-0.044  Sum_probs=56.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRN-GKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~-g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+-..+.+.|++++|...+++..+.. +.  +...+..+...+... |++++|.+.+++..+..
T Consensus        39 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           39 ESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhcc
Confidence            56678888889999999999999999988653 22  578899999999999 99999999999987754

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=97.22  E-value=0.0071  Score=36.47  Aligned_cols=66  Identities=8%  Similarity=0.146  Sum_probs=56.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-------CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE-------SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-------~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..+...|++++|..++++..+.       .-+.....+..+...|...|++++|...+++..+.
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   98 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAI   98 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            5678889999999999999999999998763       33456788999999999999999999999987653

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.21  E-value=0.006  Score=33.35  Aligned_cols=63  Identities=11%  Similarity=0.014  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+..+-..+.+.|++++|...|++..... +.+...|..+-.++...|++++|+..|++..+.
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   81 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALM   81 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            344444555666677777777776665432 125556666666666677777777777666553

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=97.20  E-value=0.0089  Score=33.70  Aligned_cols=66  Identities=12%  Similarity=0.057  Sum_probs=53.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+=..|.+.|++++|...|++..+.. +-+...|..+...|.+.|++++|...+++.....
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~   69 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD   69 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            46678888888999999999999999887542 2267788888889999999999999988876654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.19  E-value=0.0092  Score=33.61  Aligned_cols=65  Identities=12%  Similarity=0.012  Sum_probs=46.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+=..+.+.|++++|...|++..... +-+...|..+-.+|...|++++|+..|++..+.
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l   99 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL   99 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh
Confidence            34455666667777888888888888776542 226677777777888888888888888877654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=97.17  E-value=0.0056  Score=36.39  Aligned_cols=63  Identities=13%  Similarity=0.081  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...|..+-..+.+.|++++|...|++..... +.+..+|..+...|...|++++|...|++..+
T Consensus        43 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~  105 (275)
T 1xnf_A           43 AQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLE  105 (275)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            4445555555555555555555555554321 12344555555555555555555555555544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.16  E-value=0.0071  Score=31.86  Aligned_cols=64  Identities=13%  Similarity=0.078  Sum_probs=35.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|..+-..+.+.|++++|...|++..+.. +.+...+..+...+...|++++|+..+++..+
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~   78 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQ   78 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            44555555555566666666666666554321 12445555555555556666666666655544

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=97.16  E-value=0.013  Score=34.80  Aligned_cols=66  Identities=14%  Similarity=0.042  Sum_probs=57.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+-..|.+.|++++|...|++..+.. +.+...|..+...|.+.|++++|...+++..+..
T Consensus        76 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  141 (275)
T 1xnf_A           76 MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD  141 (275)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            57888999999999999999999999988642 2367889999999999999999999999998753

>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=97.16  E-value=0.0064  Score=31.22  Aligned_cols=63  Identities=17%  Similarity=0.016  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...+..+-..+.+.|++++|...+++..... +.+...+..+...+...|++++|.+.+++..+
T Consensus        38 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           38 HVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            3444444445555555555555555444321 11344445555555555555555555555443

>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=97.14  E-value=0.0082  Score=32.08  Aligned_cols=66  Identities=11%  Similarity=-0.003  Sum_probs=42.9

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+...|..+-..+.+.|++++|...|++..... +.+...|..+-..+...|++++|...+++..+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~   72 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL   72 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            355666666667777777777777777665432 124566666666777777777777777766554

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.14  E-value=0.01  Score=33.11  Aligned_cols=65  Identities=11%  Similarity=-0.045  Sum_probs=56.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-..|.+.|++++|...|++..+.. +-+...|..+-..|...|++++|+..|++..+.
T Consensus        44 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           44 NPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            67788889999999999999999999987653 236888999999999999999999999998764

>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=97.11  E-value=0.012  Score=33.78  Aligned_cols=67  Identities=7%  Similarity=-0.083  Sum_probs=53.9

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .|+...|..+-..|.+.|++++|...|++..... +.+...|..+-..|...|++++|+..|++..+.
T Consensus        34 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  100 (213)
T 1hh8_A           34 DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQ  100 (213)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccHHHHHHHHHHHHHh
Confidence            4577788888888888999999999888877543 336778888888888999999999998887763

>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=97.11  E-value=0.0085  Score=31.79  Aligned_cols=64  Identities=16%  Similarity=0.093  Sum_probs=33.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|..+-.++.+.|++++|...+++..+.. +-+...|..+-.++...|++++|...|++..+
T Consensus        37 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           37 DARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence            34455555555555566666655555554321 11344555555555555666666655555443

>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=97.11  E-value=0.0084  Score=33.30  Aligned_cols=63  Identities=8%  Similarity=0.063  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...+..+-..+.+.|++++|...|++..... +.+...|..+-.+|...|++++|+..|++..+
T Consensus        21 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   83 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAV   83 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            3344445555566666666666666554321 12455555555566666666666666666544

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.10  E-value=0.0074  Score=34.00  Aligned_cols=66  Identities=11%  Similarity=0.033  Sum_probs=56.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+=.+|.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|...|++..+..
T Consensus        69 ~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A           69 NVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            67788888899999999999999999987642 2257788889999999999999999999988754

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.10  E-value=0.0085  Score=31.55  Aligned_cols=66  Identities=11%  Similarity=-0.009  Sum_probs=56.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...+..+-..+.+.|++++|...+++..+.. +.+...+..+...+.+.|++++|.+.|++..+..
T Consensus        49 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  114 (133)
T 2lni_A           49 DAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLD  114 (133)
T ss_dssp             CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            66788888889999999999999999887642 2367888899999999999999999999987653

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.10  E-value=0.0093  Score=32.05  Aligned_cols=65  Identities=14%  Similarity=0.104  Sum_probs=44.5

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN----VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+...+..+-..+.+.|++++|...|++..+.  .|+    ...|..+...|...|++++|+..+++..+.
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   94 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK   94 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh
Confidence            35666667777777777777777777776653  243    566666777777777777777777776554

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=97.09  E-value=0.01  Score=34.81  Aligned_cols=77  Identities=6%  Similarity=-0.079  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHHHhc-----------CCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 034447            8 SISSYSSYIKFLGKN-----------GNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGL   75 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~-----------g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~   75 (94)
                      +...+..+-..+.+.           |++++|...+++..+.  .| +...|..+-..+...|++++|+..|++..+.. 
T Consensus        72 ~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-  148 (217)
T 2pl2_A           72 YLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE-  148 (217)
T ss_dssp             CHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             cHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc-
Confidence            566778888888888           9999999999988764  35 57788888899999999999999999998877 


Q ss_pred             CccHHHHHHHHHH
Q 034447           76 TPDAVTYNTVYQS   88 (94)
Q Consensus        76 ~p~~~~~~~ll~~   88 (94)
                       .+...+..+-..
T Consensus       149 -~~~~~~~~la~~  160 (217)
T 2pl2_A          149 -DTPEIRSALAEL  160 (217)
T ss_dssp             -CCHHHHHHHHHH
T ss_pred             -cchHHHHHHHHH
Confidence             566666666555

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.08  E-value=0.0084  Score=31.28  Aligned_cols=81  Identities=9%  Similarity=0.014  Sum_probs=63.4

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      ..+...+..+-..+...|++++|...|++..... +.+...|..+...+...|++++|...+++..+..- .+...+..+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~   86 (131)
T 2vyi_A            9 SAEAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDP-AYSKAYGRM   86 (131)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCc-cCHHHHHHH
Confidence            3466788888899999999999999999887642 23678889999999999999999999999877532 234555544


Q ss_pred             HHH
Q 034447           86 YQS   88 (94)
Q Consensus        86 l~~   88 (94)
                      -..
T Consensus        87 ~~~   89 (131)
T 2vyi_A           87 GLA   89 (131)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

>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=97.06  E-value=0.011  Score=32.35  Aligned_cols=65  Identities=12%  Similarity=0.002  Sum_probs=45.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..+.+.|++++|...+++..... +.+...|..+...+...|++++|...|++..+.
T Consensus        46 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~  110 (166)
T 1a17_A           46 NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKV  110 (166)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            45566666777777777777777777766532 235666777777777777888888777776654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.06  E-value=0.011  Score=32.00  Aligned_cols=62  Identities=15%  Similarity=0.082  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ...|..+-.+|.+.|++++|...|++..+.. +.+...|..+-.++...|++++|++.|++..
T Consensus        47 ~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al  108 (126)
T 4gco_A           47 AILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVAMREWSKAQRAYEDAL  108 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3444444444444444444444444443321 1133444444444444444444444444443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.05  E-value=0.0097  Score=31.43  Aligned_cols=61  Identities=7%  Similarity=-0.120  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVN----VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+..+-..+.+.|++++|...|++.....  |+    ...+..+-.++...|++++|...|++..+.
T Consensus        41 ~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           41 ALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            55566677778888888888888776542  32    556677777888888888888888887765

>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=97.04  E-value=0.015  Score=33.43  Aligned_cols=75  Identities=15%  Similarity=0.036  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ...+..+-..+.+.|++++|...|++..    .|+...|..+-..|...|++++|+..|++..+.. +.+...|..+-..
T Consensus         6 ~~~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~   80 (213)
T 1hh8_A            6 AISLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGML   80 (213)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHH
Confidence            3445566677889999999999998774    5788999999999999999999999999987654 2245555555444

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=97.04  E-value=0.0099  Score=35.82  Aligned_cols=65  Identities=17%  Similarity=0.248  Sum_probs=54.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE------SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ....+..+-..+.+.|++++|...+++....      +-.| ...++..+...|...|++++|...+++..+
T Consensus       152 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          152 VAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4566788888999999999999999988764      2234 566888999999999999999999999875

>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=97.03  E-value=0.015  Score=35.33  Aligned_cols=65  Identities=9%  Similarity=-0.088  Sum_probs=35.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--------CCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDES--------DKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~--------~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+..+...+.+.|++++|...+++..+..        .+.+..+|..+...+...|++++|...+++..+
T Consensus       192 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  264 (330)
T 3hym_B          192 DPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALV  264 (330)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            34555555555666666666666655554321        022344555555566666666666666655544

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.00  E-value=0.012  Score=31.63  Aligned_cols=65  Identities=9%  Similarity=-0.084  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ...|..+-..|.+.|++++|...+++..... +.+...|..+-.++...|++++|...|++..+..
T Consensus        65 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~  129 (148)
T 2dba_A           65 AVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRRSQALEKLGRLDQAVLDLQRCVSLE  129 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            6778888889999999999999999887642 2367788888999999999999999999987653

>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=97.00  E-value=0.016  Score=35.17  Aligned_cols=62  Identities=15%  Similarity=0.103  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+..+-..|.+.|++++|...+++..... +.+...+..+...+...|++++|...+++..+
T Consensus       160 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  221 (330)
T 3hym_B          160 LPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALE  221 (330)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            344455566666666666666666665432 23556666667777777777777777766654

>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=96.99  E-value=0.012  Score=31.41  Aligned_cols=64  Identities=9%  Similarity=0.056  Sum_probs=55.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|..+-..+.+.|++++|...+++..+.. +-+...|..+-..+...|++++|+..|++..+
T Consensus        42 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           42 VAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            56788888899999999999999999887643 23678899999999999999999999998765

>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=96.97  E-value=0.013  Score=34.68  Aligned_cols=66  Identities=11%  Similarity=0.061  Sum_probs=55.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CC-CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE------SD-KVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~------~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ....+..+-..|...|++++|...+++....      +- +....++..+-..|...|++++|...+++..+.
T Consensus        42 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  114 (283)
T 3edt_B           42 VATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEI  114 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            4677888999999999999999999988754      22 336778999999999999999999999987654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.96  E-value=0.0089  Score=29.54  Aligned_cols=78  Identities=13%  Similarity=0.155  Sum_probs=60.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+-..+.+.|++++|...|++..+.. +.+...+..+-..+.+.|++++|...+++..+..- .+...+..+-.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCHHHHHHHHH
Confidence            45677788888999999999999999887643 23677888899999999999999999999876531 23444444433

>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=96.94  E-value=0.016  Score=32.12  Aligned_cols=65  Identities=9%  Similarity=-0.036  Sum_probs=55.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-.+|.+.|++++|...|++..... +-+...|..+-.+|...|++++|...|++..+.
T Consensus        54 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           54 DSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            66778888888999999999999999987642 226678888899999999999999999997653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=96.93  E-value=0.024  Score=37.56  Aligned_cols=75  Identities=13%  Similarity=0.168  Sum_probs=62.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      |...|..++. +.+.|++++|..+|+.+.+. .+-+...|...+..+.+.|++++|.++|++..+..  |+...|...+
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~-~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p~~~lw~~~~   86 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQ-FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--LHIDLWKCYL   86 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTT-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--CCHHHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CChHHHHHHH
Confidence            6788998888 47899999999999999864 34478889999999999999999999999998764  6665555444

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=96.93  E-value=0.016  Score=35.68  Aligned_cols=62  Identities=15%  Similarity=0.118  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDES-DKV--NVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ..|..+...+.+.|++++|..+|+...... +.|  +...|..++....+.|+.++|..++++..
T Consensus       204 ~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~  268 (308)
T 2ond_A          204 EYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRF  268 (308)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334444444444444444444444444431 233  23344444444444444444444444443

>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=96.90  E-value=0.011  Score=34.94  Aligned_cols=66  Identities=15%  Similarity=0.251  Sum_probs=55.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE------SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ....+..+-..|...|++++|...+++....      +-.| ...++..+...|...|++++|...+++..+.
T Consensus       126 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          126 VAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4577888889999999999999999988764      2233 5778999999999999999999999988653

>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=96.89  E-value=0.018  Score=31.93  Aligned_cols=77  Identities=3%  Similarity=-0.115  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..+-.+=..|.+.|++++|...|++..+.. +-+..+|..+-..|.+.|++++|+..|++..+..- -+...|..+-..
T Consensus        32 ~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~  108 (150)
T 4ga2_A           32 IKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVECYRRSVELNP-TQKDLVLKIAEL  108 (150)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            344556677888899999999888877542 12677888888888888999999988888776431 134455544444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.89  E-value=0.016  Score=32.16  Aligned_cols=65  Identities=11%  Similarity=0.045  Sum_probs=55.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-.+|.+.|++++|...+++..... +-+...|..+-.+|...|++++|...|++..+.
T Consensus        62 ~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           62 NIPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            34678888889999999999999999887653 336888999999999999999999999998765

>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=96.88  E-value=0.013  Score=38.67  Aligned_cols=64  Identities=8%  Similarity=-0.140  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CC-CCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD-----ES-DKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-----~~-~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+++.+..+|...|++++|..++++...     .| -.| -..+++.|-..|...|++++|+.++++-.+
T Consensus       340 a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          340 LHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            47899999999999999999999988753     12 224 567799999999999999999999988643

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.86  E-value=0.0038  Score=33.01  Aligned_cols=67  Identities=9%  Similarity=-0.081  Sum_probs=46.9

Q ss_pred             hcCCHHHHHHHHHHHhhCC--CCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           21 KNGNSLKALEIYNSITDES--DKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        21 ~~g~~~~a~~~~~~m~~~~--~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..|++++|...|++..+.+  -+-+...|..+-..|...|++++|+..|++..+..-. +...+..+-.+
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~   70 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMV   70 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHH
Confidence            4688999999999988754  2346788899999999999999999999998776422 34444444443

>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=96.81  E-value=0.027  Score=32.84  Aligned_cols=64  Identities=2%  Similarity=-0.194  Sum_probs=31.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+..+-..+.+.|++++|...|++..+.. +-+...|..+-..|...|++++|+..+++..+
T Consensus        41 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  104 (228)
T 4i17_A           41 DSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKSAAYRDMKNNQEYIATLTEGIK  104 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            33344444445555555555555555544321 11444555555555555555555555555444

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=96.80  E-value=0.011  Score=31.75  Aligned_cols=63  Identities=8%  Similarity=-0.097  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .+-.+-..+.+.|++++|...|++..+.. +-+...|..+-.++...|++++|+..|++..+..
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~   81 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD   81 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            34455567778899999999998887542 2267778888888888999999999998877653

>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=96.75  E-value=0.03  Score=36.47  Aligned_cols=65  Identities=18%  Similarity=0.154  Sum_probs=41.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-..+.+.|++++|...+++..... +-+...|..+...+...|++++|...+++..+.
T Consensus       309 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  373 (537)
T 3fp2_A          309 YPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLK  373 (537)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            34556666666667777777777776665432 123456666666677777777777777766554

>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=96.75  E-value=0.019  Score=30.34  Aligned_cols=79  Identities=9%  Similarity=-0.046  Sum_probs=60.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...|..+=..+.+.|++++|...|++..+.. +.+...|..+-.++.+.|++++|+..+++..+..- .+...|..+-.
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~   80 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKAT   80 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHH
Confidence            34567777788899999999999999887642 23688999999999999999999999999877542 23444444433


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      +
T Consensus        81 ~   81 (126)
T 3upv_A           81 A   81 (126)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=96.74  E-value=0.04  Score=33.70  Aligned_cols=61  Identities=18%  Similarity=0.114  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+..+-..+.+.|++++|...|++..... +.+...|..+...+...|++++|...+++..+
T Consensus         5 ~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~   65 (359)
T 3ieg_A            5 KHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIA   65 (359)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            33444444444555555555554444321 11334444444444455555555555544443

>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=96.73  E-value=0.022  Score=30.67  Aligned_cols=63  Identities=14%  Similarity=0.086  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +..+..+=..+.+.|++++|...|++..+.. +-+...|+.+-.+|.+.|++++|+..+++..+
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~   70 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVE   70 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3456666678889999999999999887642 23688899999999999999999999998764

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=96.72  E-value=0.03  Score=34.25  Aligned_cols=65  Identities=15%  Similarity=0.028  Sum_probs=52.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+..+-..+.+.|++++|...+++..... +.+..+|..+...+...|++++|...+++..+.
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  217 (359)
T 3ieg_A          153 DAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  217 (359)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            56677788888888899999999888887642 346778888888888899999999988887764

>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=96.71  E-value=0.018  Score=29.43  Aligned_cols=80  Identities=11%  Similarity=0.016  Sum_probs=62.5

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      .+...+..+-..+...|++++|...|++..... +.+...+..+...+...|++++|...+++..+..- .+...+..+-
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a   79 (118)
T 1elw_A            2 EQVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKA   79 (118)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCc-ccHHHHHHHH
Confidence            345677888889999999999999999987642 23678888899999999999999999999877542 2455555554


Q ss_pred             HH
Q 034447           87 QS   88 (94)
Q Consensus        87 ~~   88 (94)
                      .+
T Consensus        80 ~~   81 (118)
T 1elw_A           80 AA   81 (118)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=96.67  E-value=0.026  Score=30.71  Aligned_cols=65  Identities=11%  Similarity=-0.018  Sum_probs=55.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-.+|.+.|++++|...|++..... +-+...|..+-.+|...|++++|...|++..+.
T Consensus        51 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           51 DARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66778888889999999999999999987653 236677888889999999999999999997654

>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=96.67  E-value=0.02  Score=37.32  Aligned_cols=63  Identities=13%  Similarity=0.156  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..|..+-..+.+.|++++|...|++..... +.+...|..+..+|.+.|++++|++.+++..+.
T Consensus        26 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   88 (537)
T 3fp2_A           26 VQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEI   88 (537)
T ss_dssp             HHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            344555555566666666666666655432 225556666666666666666666666665543

>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=96.64  E-value=0.018  Score=32.54  Aligned_cols=61  Identities=16%  Similarity=0.089  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-cHHHHHHHHHH
Q 034447           26 LKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP-DAVTYNTVYQS   88 (94)
Q Consensus        26 ~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~ll~~   88 (94)
                      .++...+++..+.  .| +...+..+-..+...|++++|...|++..+..-.+ +...+..+...
T Consensus        91 ~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~  153 (176)
T 2r5s_A           91 SPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDI  153 (176)
T ss_dssp             CHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHH
T ss_pred             chHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHH
Confidence            3456666666543  24 46777777778888888888888888876654221 23445545444

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.62  E-value=0.025  Score=37.90  Aligned_cols=64  Identities=11%  Similarity=-0.085  Sum_probs=52.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CC-CCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITD-----ES-DKV-NVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-----~~-~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      -..+++.|..+|...|++++|..++++...     .| -.| -..+++.|-..|...|++++|+.++++-.
T Consensus       350 ~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al  420 (490)
T 3n71_A          350 VLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAY  420 (490)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            357899999999999999999999887653     11 123 56789999999999999999999998864

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.62  E-value=0.02  Score=28.89  Aligned_cols=58  Identities=17%  Similarity=0.189  Sum_probs=47.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCchHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKVNVF-ICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      -..+.+.|++++|...|++..+.. +-+.. .|..+-.+|...|++++|...|++..+..
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            446778899999999999987642 22556 88888899999999999999999987654

>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=96.62  E-value=0.024  Score=37.29  Aligned_cols=63  Identities=10%  Similarity=-0.054  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----C-CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD-----E-SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-----~-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ..+++.+..+|...|++++|..++++...     . .-.| -..+++.|-..|...|++++|+.++++..
T Consensus       329 ~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          329 LKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            57899999999999999999999987753     1 2224 56779999999999999999999998864

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=96.60  E-value=0.029  Score=34.56  Aligned_cols=65  Identities=15%  Similarity=0.169  Sum_probs=51.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch-HH-HHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN-VF-ICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~-t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+...+.+.|++++|..+|++..+.  .|+ .. .|..+...+.+.|++++|..+|++..+.+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~  164 (308)
T 2ond_A           98 NMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA  164 (308)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            4567888888888889999999999888763  453 32 78888888888888888888888877643

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=96.56  E-value=0.034  Score=36.64  Aligned_cols=62  Identities=11%  Similarity=0.048  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhc---------CCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRN---------GKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~---------g~~~~a~~~~~~m~~   72 (94)
                      ...|..+-..|.+.|++++|...|++..+.  .|+...+..+-..+...         |++++|+..|++..+
T Consensus       137 ~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~  207 (474)
T 4abn_A          137 VEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQ  207 (474)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHH
Confidence            344444455555555555555555544433  24444444445555554         555555555555443

>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=96.51  E-value=0.047  Score=31.76  Aligned_cols=81  Identities=14%  Similarity=0.041  Sum_probs=62.4

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      .|...+...=..+.+.|++++|...|++..+..-+++...+..+-.++...|++++|+..+++..+..-. +...|..+-
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYN-LANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCS-HHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcc-hHHHHHHHH
Confidence            3567778888889999999999999999887653366777777899999999999999999998865421 344454444


Q ss_pred             HH
Q 034447           87 QS   88 (94)
Q Consensus        87 ~~   88 (94)
                      ..
T Consensus        84 ~~   85 (228)
T 4i17_A           84 AA   85 (228)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=96.50  E-value=0.039  Score=32.70  Aligned_cols=62  Identities=6%  Similarity=-0.025  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+..+-..|.+.|++++|...+++..+.+-.|  ....|..+-..+...|++++|+..|++..+
T Consensus        39 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~  102 (272)
T 3u4t_A           39 IYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVD  102 (272)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            45555556666666666666666655522111  122355555566666666666666665554

>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=96.45  E-value=0.048  Score=31.20  Aligned_cols=63  Identities=17%  Similarity=0.037  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..|..+-.+|.+.|++++|...++...... +.+...|..+-.+|...|++++|+..|++..+.
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  151 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL  151 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            677888888999999999999999887642 347788899999999999999999999998764

>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=96.45  E-value=0.037  Score=29.77  Aligned_cols=75  Identities=5%  Similarity=0.071  Sum_probs=56.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--CCch----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDES--DKVN----VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~--~~p~----~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      +...|+.+-.+|.+.|++++|...+++..+..  ..++    ..+|..+=..+...|++++|++.|++-.+..  ||...
T Consensus        41 ~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~~--~~~~~  118 (127)
T 4gcn_A           41 NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLSEF--RDPEL  118 (127)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCHHH
T ss_pred             CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cCHHH
Confidence            57788889999999999999999999876421  1111    2467777788899999999999999977643  55554


Q ss_pred             HHH
Q 034447           82 YNT   84 (94)
Q Consensus        82 ~~~   84 (94)
                      ...
T Consensus       119 ~~~  121 (127)
T 4gcn_A          119 VKK  121 (127)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=96.43  E-value=0.061  Score=32.90  Aligned_cols=63  Identities=10%  Similarity=0.056  Sum_probs=39.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +...|..+-..|.+.|++++|...+++..+.. +-+...+..+-.++...|++++|...|++..
T Consensus        37 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           37 VAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45556666666667777777777776665431 1255666666666777777777777666654

>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=96.42  E-value=0.039  Score=33.70  Aligned_cols=64  Identities=16%  Similarity=0.228  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh----C-CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD----E-SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~----~-~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...|+.+-..|.+.|++++|...|++..+    . +..+ ...+|..+-..|.+.|++++|+..+++..+
T Consensus       155 ~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~  224 (293)
T 3u3w_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIE  224 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            34689999999999999999999998873    1 2333 344888999999999999999999988653

>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=96.40  E-value=0.063  Score=34.79  Aligned_cols=69  Identities=10%  Similarity=0.147  Sum_probs=56.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCccHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ-----SGLTPDAVTY   82 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~   82 (94)
                      ..++.++.+.|+.+++.......... -+.+...|-.+|.++.+.|+..+|++.|++..+     -|+.|+..+-
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            35566777889999999888887643 234888999999999999999999999988754     3999988754

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=96.36  E-value=0.081  Score=33.56  Aligned_cols=68  Identities=15%  Similarity=0.109  Sum_probs=56.5

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESD-KVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .++..++..+-.++...|++++|.+++.+-...+- .-+...+..++..+.+.|+++.|.+.+++|.+.
T Consensus        97 ~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~  165 (310)
T 3mv2_B           97 QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA  165 (310)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            35556666788889999999999999998755442 237888889999999999999999999999775

>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=96.32  E-value=0.058  Score=33.92  Aligned_cols=78  Identities=14%  Similarity=-0.064  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.+|...|++++|+..|++..+..- -+...+..+-..
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~  273 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYP-NNKAAKTQLAVC  273 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-SCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHH
Confidence            5788889999999999999999999887653 23788999999999999999999999999876531 234444444433

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=96.29  E-value=0.071  Score=35.11  Aligned_cols=79  Identities=11%  Similarity=-0.021  Sum_probs=64.3

Q ss_pred             cHHHHHHHHHHHHhcCCH-HHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNS-LKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~-~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      +...+..+-..+...|++ ++|...|++..+.. +-+...|..+-..|.+.|++++|...|++..+..  |+...+..+-
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg  177 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLS  177 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHH
Confidence            677788888889999999 99999999887642 2258899999999999999999999999988764  6656665555


Q ss_pred             HHh
Q 034447           87 QSD   89 (94)
Q Consensus        87 ~~~   89 (94)
                      ..+
T Consensus       178 ~~~  180 (474)
T 4abn_A          178 MVL  180 (474)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>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=96.28  E-value=0.077  Score=31.72  Aligned_cols=16  Identities=19%  Similarity=0.416  Sum_probs=6.7

Q ss_pred             cCCHHHHHHHHHHHHH
Q 034447           57 NGKFESSLKLFDKIKQ   72 (94)
Q Consensus        57 ~g~~~~a~~~~~~m~~   72 (94)
                      .+++++|+..|++..+
T Consensus       127 ~~~~~~A~~~~~~a~~  142 (273)
T 1ouv_A          127 TRDFKKAVEYFTKACD  142 (273)
T ss_dssp             CCCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHh
Confidence            4444444444444333

>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=96.26  E-value=0.079  Score=31.68  Aligned_cols=61  Identities=15%  Similarity=0.098  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHh----cCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcC
Q 034447           11 SYSSYIKFLGK----NGNSLKALEIYNSITDESDKVNVFICNLILSCLVR----NGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        11 ~~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~~g   74 (94)
                      .+..+-..|.+    .+++++|...|++..+.+   +...+..+-..|..    .+++++|+..|++..+.+
T Consensus        40 a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~  108 (273)
T 1ouv_A           40 GCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK  108 (273)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC
Confidence            34444444555    555555555555555443   44445555555555    556666665555555443

>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=96.25  E-value=0.12  Score=36.30  Aligned_cols=63  Identities=16%  Similarity=0.210  Sum_probs=38.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|+.+=..|.+.|++++|...|++..+.  .| +..+|+.+-..|.+.|++++|+..|++..+
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~   71 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR   71 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3455666666666666666666666665542  23 455666666666666666666666666554

>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=96.25  E-value=0.059  Score=30.10  Aligned_cols=65  Identities=8%  Similarity=0.057  Sum_probs=35.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHH-HHhcCCH--HHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSC-LVRNGKF--ESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~-~~~~g~~--~~a~~~~~~m~~~   73 (94)
                      +...|..+-..|...|++++|...|++..... +.+...+..+... +...|++  ++|...+++..+.
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~  110 (177)
T 2e2e_A           43 NSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQTRAMIDKALAL  110 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHh
Confidence            34555555566666666666666666554321 1134445555555 4555665  6666666665543

>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=96.23  E-value=0.072  Score=34.15  Aligned_cols=65  Identities=9%  Similarity=-0.073  Sum_probs=56.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|+.+-.+|.+.|++++|...+++..+.. +-+...|..+-.+|...|++++|+..|++..+.
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            45778888889999999999999999988643 236788999999999999999999999998765

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=96.22  E-value=0.08  Score=31.32  Aligned_cols=63  Identities=21%  Similarity=0.342  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..|..+-..+.+.|++++|...|++..+.. +-+...|..+-..|...|++++|+..+++..+.
T Consensus        75 ~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  137 (272)
T 3u4t_A           75 ADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP  137 (272)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc
Confidence            346666666777777777777777665432 124456667777777777777777777766554

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=96.21  E-value=0.074  Score=30.87  Aligned_cols=72  Identities=19%  Similarity=0.132  Sum_probs=56.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      +-..|.+.|++++|...|++..+.. +-+...|..+-..+...|++++|+..|++..+..- -+...|..+-..
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~  131 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEA-DNLAANIFLGNY  131 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHH
Confidence            7778889999999999999887642 22788899999999999999999999999877531 234455444333

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=96.19  E-value=0.073  Score=30.55  Aligned_cols=78  Identities=14%  Similarity=-0.005  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-----CCCc-hHHHH----HHHHHHHHhcCCHHHHHHHHHHHHH-----c
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE-----SDKV-NVFIC----NLILSCLVRNGKFESSLKLFDKIKQ-----S   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~~~p-~~~t~----~~li~~~~~~g~~~~a~~~~~~m~~-----~   73 (94)
                      ...|+.+-.++.+.|++++|...+++-.+.     .+.| +...|    ...=.++...|++++|+..|++-.+     .
T Consensus        57 a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~  136 (159)
T 2hr2_A           57 AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERK  136 (159)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcH
Confidence            448899999999999999999999988763     2256 56677    7888889999999999999998743     4


Q ss_pred             CCCccHHHHHHHH
Q 034447           74 GLTPDAVTYNTVY   86 (94)
Q Consensus        74 g~~p~~~~~~~ll   86 (94)
                      |+.+........+
T Consensus       137 ~~~~~~~~~~~~~  149 (159)
T 2hr2_A          137 GETPGKERMMEVA  149 (159)
T ss_dssp             SCCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            6666555444333

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=96.18  E-value=0.08  Score=33.57  Aligned_cols=76  Identities=13%  Similarity=0.062  Sum_probs=54.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-----hHHHHHHHHHHH--Hh--cCCHHHHHHHHHHHHHcCCCcc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-----NVFICNLILSCL--VR--NGKFESSLKLFDKIKQSGLTPD   78 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-----~~~t~~~li~~~--~~--~g~~~~a~~~~~~m~~~g~~p~   78 (94)
                      +...+-.++..+.+.|+++.|.+.+++|.+.  .|     +-.+..-+..++  ..  .++.++|+.+|+++.+..  |+
T Consensus       135 ~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~--p~  210 (310)
T 3mv2_B          135 TTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--PT  210 (310)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--CS
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--CC
Confidence            6677888999999999999999999999864  46     355555566552  22  348999999999986553  55


Q ss_pred             HHHHHHHHH
Q 034447           79 AVTYNTVYQ   87 (94)
Q Consensus        79 ~~~~~~ll~   87 (94)
                      ..+-..+++
T Consensus       211 ~~~~~lLln  219 (310)
T 3mv2_B          211 WKTQLGLLN  219 (310)
T ss_dssp             HHHHHHHHH
T ss_pred             cccHHHHHH
Confidence            333333333

>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=96.18  E-value=0.11  Score=32.61  Aligned_cols=78  Identities=12%  Similarity=0.033  Sum_probs=61.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch----------------HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN----------------VFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----------------~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +...|..+=..|.+.|++++|...|++.....  |+                ...|..+-.+|.+.|++++|+..+++..
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al  223 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKAL  223 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45677788888999999999999999887643  33                5899999999999999999999999987


Q ss_pred             HcCCCccHHHHHHHHHH
Q 034447           72 QSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        72 ~~g~~p~~~~~~~ll~~   88 (94)
                      +..- .+...|..+-.+
T Consensus       224 ~~~p-~~~~a~~~lg~~  239 (336)
T 1p5q_A          224 ELDS-NNEKGLSRRGEA  239 (336)
T ss_dssp             HHCT-TCHHHHHHHHHH
T ss_pred             HhCC-CcHHHHHHHHHH
Confidence            7542 245555544444

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=96.17  E-value=0.074  Score=35.20  Aligned_cols=65  Identities=12%  Similarity=0.002  Sum_probs=56.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-.+|.+.|++++|...+++..+.. +-+...|..+-.+|.+.|++++|++.|++..+.
T Consensus        39 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~  103 (477)
T 1wao_1           39 NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKV  103 (477)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            57788889999999999999999999888752 236788899999999999999999999998764

>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=96.15  E-value=0.061  Score=29.29  Aligned_cols=78  Identities=10%  Similarity=-0.011  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ...+..+-..+.+.|++++|...|++..... +.+...+..+...+...|++++|+..+++..+..- .+...|..+-..
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~   90 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHH
Confidence            4567777788889999999999999887642 23678889999999999999999999999876532 244555444444

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=96.14  E-value=0.099  Score=32.93  Aligned_cols=63  Identities=10%  Similarity=-0.040  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CC-CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE----SD-KVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+++.+-..|.+.|++++|...+++..+.    +- +....++..+-..|.+.|++++|...+++..+
T Consensus       225 ~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46777788888889999999988877651    33 44677788888889999999999998887654

>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=96.08  E-value=0.2  Score=35.12  Aligned_cols=62  Identities=13%  Similarity=0.093  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...|+.+=.+|.+.|++++|.+.|++..+.  .| +...|+.+-..|.+.|++++|+..|++..+
T Consensus        77 ~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~  139 (723)
T 4gyw_A           77 ADAYSNMGNTLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALK  139 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344555555555555555555555544432  12 344555555555555555555555555444

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.07  E-value=0.13  Score=33.49  Aligned_cols=75  Identities=12%  Similarity=-0.024  Sum_probs=60.1

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      ..+...|.++-..+.-.|++++|...+++....+  |+...|..+=..+.-.|++++|...|++-..-.  |...||..
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~--P~~~t~~~  348 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLR--PGANTLYW  348 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CSHHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCcChHHH
Confidence            4577778777777777799999999999998875  888888777788889999999999998876643  55556543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=96.03  E-value=0.098  Score=30.65  Aligned_cols=64  Identities=8%  Similarity=0.033  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDES-DKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+-.+-..+.+.|++++|...|++..... -.| ....+..+..+|.+.|++++|+..|++..+.
T Consensus         5 ~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   70 (225)
T 2yhc_A            5 NEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   70 (225)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            344555667888999999999999998642 112 2457777889999999999999999998764

>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=96.00  E-value=0.082  Score=29.51  Aligned_cols=66  Identities=8%  Similarity=0.132  Sum_probs=53.4

Q ss_pred             cHHHHHHHHHH-HHhcCCH--HHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKF-LGKNGNS--LKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~-~~~~g~~--~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...+..+-.. +.+.|++  ++|...+++..... +-+...+..+...|...|++++|...|++..+..
T Consensus        77 ~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A           77 NAELYAALATVLYYQASQHMTAQTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            45566666667 7788998  99999999887653 2357788888999999999999999999987653

>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=96.00  E-value=0.19  Score=33.60  Aligned_cols=62  Identities=3%  Similarity=-0.146  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ...|..+-..+.+.|++++|...+++..+.. +-+...|..+-..|...|++++|.+.+++..
T Consensus        23 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al   84 (568)
T 2vsy_A           23 FVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLLQQAS   84 (568)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3344444444444455555555444444321 1133444444444444444444444444443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=96.00  E-value=0.072  Score=30.06  Aligned_cols=65  Identities=8%  Similarity=-0.019  Sum_probs=49.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCC--chHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDK--VNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~--p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ....++.+-..+...|++++|...+++....    +-.  .....+..+-..+...|++++|...+++..+
T Consensus        65 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  135 (203)
T 3gw4_A           65 EHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLV  135 (203)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            4566777888888999999999988876542    212  2355677888888999999999999988653

>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=95.98  E-value=0.19  Score=33.56  Aligned_cols=79  Identities=9%  Similarity=0.005  Sum_probs=60.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...|..+-..|.+.|++++|...+++..+.. +-+...|..+-..|.+.|++++|.+.+++..+..- .+...+..+..
T Consensus        56 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~  133 (568)
T 2vsy_A           56 HPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLP-EEPYITAQLLN  133 (568)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            56778888888999999999999999887642 23577888888999999999999999998876532 23455555544


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      .
T Consensus       134 ~  134 (568)
T 2vsy_A          134 W  134 (568)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=95.97  E-value=0.12  Score=31.55  Aligned_cols=66  Identities=11%  Similarity=0.085  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHhc-CCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            9 ISSYSSYIKFLGKN-GNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         9 ~~~~~~ll~~~~~~-g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..+|+.+-..|.+. |++++|...|++-.+.    +-.+ ...+++.+-..+.+.|++++|+..|++..+..
T Consensus       117 a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  188 (292)
T 1qqe_A          117 ANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSS  188 (292)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            45778888888886 9999999999987642    1111 14578888999999999999999999988754

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=95.97  E-value=0.045  Score=29.34  Aligned_cols=64  Identities=14%  Similarity=0.040  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCC-chHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDK-VNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~-p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..++..+-..+...|++++|...+++....    +-. .-..++..+-..+...|++++|...+++..+
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~   77 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLL   77 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            456777788888999999999998877542    111 1124778888888999999999999988654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=95.95  E-value=0.067  Score=32.74  Aligned_cols=64  Identities=9%  Similarity=0.089  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchH------HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNV------FICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~------~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+|+.+-..+.+.|++++|...|++.....-....      ..|..+..++...|++++|+..|++..+
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            356888889999999999999999998865432221      2677778889999999999999998764

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=95.89  E-value=0.079  Score=28.43  Aligned_cols=78  Identities=15%  Similarity=0.091  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ...+...=..|.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|+..|++..+.+- .+...|..+-.+
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~   90 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS-KFIKGYIRKAAC   90 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh-hhhHHHHHHHHH
Confidence            3556666678889999999999999887542 23788999999999999999999999999876532 234455444443

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=95.84  E-value=0.21  Score=33.06  Aligned_cols=64  Identities=16%  Similarity=0.200  Sum_probs=49.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN--VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+...+.+.|++++|..+|++..+.  .|+  ...|......+.+.|+.++|.++|++..+.
T Consensus       320 ~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~  385 (530)
T 2ooe_A          320 NMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  385 (530)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            5677888888888888888888888888764  343  347777777777788888888888877654

>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=95.83  E-value=0.096  Score=28.87  Aligned_cols=77  Identities=14%  Similarity=0.052  Sum_probs=58.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHH-HHHHHHcCCCccHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKL-FDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~-~~~m~~~g~~p~~~~~~~l   85 (94)
                      +...|..+-..|.+.|++++|...|++..+.  .| +...|..+-..|.+.|+.+++.+. +++..+-. +-+...|...
T Consensus        64 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~-P~~~~~~~l~  140 (150)
T 4ga2_A           64 DPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLF-PGSPAVYKLK  140 (150)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHS-TTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhC-cCCHHHHHHH
Confidence            6788899999999999999999999988764  35 578899999999999998876665 57765532 1245555544


Q ss_pred             HH
Q 034447           86 YQ   87 (94)
Q Consensus        86 l~   87 (94)
                      -.
T Consensus       141 ~~  142 (150)
T 4ga2_A          141 EQ  142 (150)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>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=95.76  E-value=0.16  Score=30.99  Aligned_cols=79  Identities=10%  Similarity=-0.052  Sum_probs=61.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      +...+..+-..+.+.|++++|...|++..... +-+...|..+-.+|.+.|++++|+..+++..+..- -+...+..+-.
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            55677788888999999999999999887642 22788899999999999999999999999876532 24445544444


Q ss_pred             H
Q 034447           88 S   88 (94)
Q Consensus        88 ~   88 (94)
                      +
T Consensus        81 ~   81 (281)
T 2c2l_A           81 C   81 (281)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=95.74  E-value=0.092  Score=28.06  Aligned_cols=63  Identities=16%  Similarity=0.064  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+..+-..+...|++++|...+++....    +-.+ ....+..+-..+...|++++|...+++..+
T Consensus        50 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  117 (164)
T 3ro3_A           50 IAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLA  117 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            47778888899999999999999887532    1111 256788888889999999999999988654

>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=95.74  E-value=0.17  Score=31.19  Aligned_cols=63  Identities=6%  Similarity=-0.020  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh----CCCCchH-HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD----ESDKVNV-FICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ..+++.+-..|.+.|++++|...|++...    .+..++. ..+..+...+...|++++|...|++..
T Consensus       155 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          155 AELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            35677777888888888888888887764    2222222 366666677777788888888888876

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=95.73  E-value=0.14  Score=30.82  Aligned_cols=61  Identities=8%  Similarity=0.087  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC-ch--HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDK-VN--VFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      .+...-..+.+.|++++|...|++..+..-. |.  ...+..+...+...|++++|...+++..
T Consensus         7 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al   70 (338)
T 3ro2_A            7 ELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDL   70 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444455666778888888888887764211 11  4677777888888888888888887754

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=95.64  E-value=0.17  Score=32.50  Aligned_cols=65  Identities=12%  Similarity=0.097  Sum_probs=52.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC--------CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE--------SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~--------~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+..||.+=..+...|+.++|.+.|++-.+.        .-+-...+|+.+-..|...|++++|...+++..+
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~  122 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKH  122 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            4567899888999999999999999875431        1123568899999999999999999999988653

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=95.64  E-value=0.14  Score=32.20  Aligned_cols=64  Identities=9%  Similarity=0.113  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh----CCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD----ESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+++.+=..|.+.|++++|...+++...    .+-+....++..+-..+.+.|++++|...+++..+
T Consensus       222 ~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  289 (378)
T 3q15_A          222 AISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLD  289 (378)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34667777788888999999998887765    13333577888888889999999999999988765

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=95.63  E-value=0.18  Score=30.66  Aligned_cols=64  Identities=17%  Similarity=0.236  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh----CCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITD----ESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+|+.+-..|...|++++|...|++...    .+-.+  ...+|+.+-..|.+.|++++|+..+++..+
T Consensus       155 ~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~  224 (293)
T 2qfc_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIE  224 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHH
Confidence            45888899999999999999999998762    22222  236888999999999999999999988654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=95.62  E-value=0.13  Score=28.95  Aligned_cols=65  Identities=6%  Similarity=-0.011  Sum_probs=53.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhh----CCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITD----ESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ....++.+-..+...|++++|...+++...    .+..| ...++..+-..+...|++++|...+++..+
T Consensus        25 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   94 (203)
T 3gw4_A           25 ASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERE   94 (203)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            567788888899999999999999988764    22333 567788888899999999999999988654

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=95.60  E-value=0.11  Score=31.81  Aligned_cols=62  Identities=16%  Similarity=0.062  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..+..+-..+.+.|++++|...|++....  .| +...+..+...+.+.|++++|...+++....
T Consensus       118 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~  180 (287)
T 3qou_A          118 ELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ  180 (287)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG
T ss_pred             hhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh
Confidence            44555666778889999999999988754  24 6778888899999999999999999887554

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=95.56  E-value=0.11  Score=27.63  Aligned_cols=64  Identities=9%  Similarity=-0.030  Sum_probs=54.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+=.++.+.|++++|...|++..+..  | +...+..+-..+...|++++|+..+++..+.
T Consensus        50 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           50 REEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66778888888999999999999999887642  4 6778888999999999999999999998753

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=95.52  E-value=0.23  Score=31.30  Aligned_cols=64  Identities=16%  Similarity=0.045  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+++.+=..|...|++++|...|++..+.    +-.+ ...+++.+-..|...|++++|+..+++..+
T Consensus       182 ~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~  250 (378)
T 3q15_A          182 IQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAK  250 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            567788888899999999999999877542    2222 345788888899999999999999998765

>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=95.47  E-value=0.2  Score=30.50  Aligned_cols=62  Identities=15%  Similarity=0.221  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC-ch----HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDK-VN----VFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~----~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|..+-..+...+++++|...+++....... ++    ..+|+.+-..|...|++++|+..|++..+
T Consensus       117 ~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~  183 (293)
T 3u3w_A          117 WQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILK  183 (293)
T ss_dssp             HHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3444666666778999999999888763222 22    44688888899999999999999988763

>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=95.45  E-value=0.18  Score=33.14  Aligned_cols=64  Identities=16%  Similarity=0.042  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...|..+-.+|.+.|++++|...+++..+.. +-+...|..+-.+|...|++++|+..|++..+.
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l  380 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  380 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            5778888899999999999999999887643 237888999999999999999999999998764

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=95.44  E-value=0.11  Score=27.09  Aligned_cols=59  Identities=15%  Similarity=0.024  Sum_probs=47.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCch-H---HHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKVN-V---FICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~-~---~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .+-..+.+.|++++|...|+...+..  |+ .   ..+..+-.++...|++++|...|++..+..
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~   69 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY   69 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            34456778999999999999987642  32 2   477778888999999999999999987753

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=95.38  E-value=0.27  Score=30.94  Aligned_cols=64  Identities=9%  Similarity=0.045  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+++.+-..|...|++++|...+++..+.    +-.+ ...++..+-..|...|++++|+..+++..+
T Consensus       184 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~  252 (383)
T 3ulq_A          184 LQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIA  252 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            457778888899999999999999877532    2112 335788889999999999999999998765

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=95.37  E-value=0.1  Score=31.41  Aligned_cols=65  Identities=17%  Similarity=0.076  Sum_probs=45.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhh----CCCC-chHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITD----ESDK-VNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~-p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ....+..+-..+.+.|++++|...+++...    .+-. ....++..+...+...|++++|...+++..+
T Consensus       222 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  291 (338)
T 3ro2_A          222 ERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLA  291 (338)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            356677777788888888888877776542    2211 2377777778888888888888887777643

>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=95.34  E-value=0.29  Score=31.59  Aligned_cols=60  Identities=13%  Similarity=0.194  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCC-HHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGK-FESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~-~~~a~~~~~~m~~   72 (94)
                      .|+.+-..+.+.|++++|...+++....  .| +...|+.+-..+...|+ +++|+..|++..+
T Consensus        99 a~~~lg~~~~~~g~~~~Al~~~~~al~l--~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~  160 (382)
T 2h6f_A           99 VYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE  160 (382)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHH
Confidence            3444444444445555555555544432  12 34444444444445553 5555555544443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=95.27  E-value=0.23  Score=29.52  Aligned_cols=64  Identities=9%  Similarity=0.039  Sum_probs=53.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-h---HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-N---VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~---~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+-.+-..+.+.|++++|...|++.....  | +   ...+..+-.+|.+.|++++|+..|++..+.
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   81 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQI   81 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence            55566666777889999999999999998642  3 2   677888889999999999999999998875

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=95.25  E-value=0.19  Score=29.38  Aligned_cols=60  Identities=8%  Similarity=0.040  Sum_probs=47.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCC-CCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDES-DKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~-~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +-..|.+.|++++|...|++..+.- -.| ....+..+..++.+.|+.++|.+.++.+...+
T Consensus       153 ~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          153 VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            3456778999999999999987642 111 23578889999999999999999999988764

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=95.24  E-value=0.13  Score=32.31  Aligned_cols=61  Identities=16%  Similarity=-0.001  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|+.+-.+|.+.|++++|...+++..+.. +-+...|..+-.+|...|++++|+..|++..+
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            67788888999999999999999887642 23788999999999999999999999998754

>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=95.19  E-value=0.2  Score=28.33  Aligned_cols=71  Identities=17%  Similarity=0.240  Sum_probs=54.3

Q ss_pred             HHHHhcC-CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           17 KFLGKNG-NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        17 ~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..+-+.. +..+..+-++.+....+-|+.....+.+++|-+..++.-|.++|+-.+.+- .+....|.-+++-
T Consensus        60 ~~F~~~~iD~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~lqE  131 (152)
T 2y69_E           60 TYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQE  131 (152)
T ss_dssp             HHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHHH
T ss_pred             HHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHHHH
Confidence            3333444 566777778888888899999999999999999999999999999986542 2334456666653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=95.18  E-value=0.13  Score=32.11  Aligned_cols=62  Identities=13%  Similarity=0.054  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      ..++..+-..|.+.|++++|...+++....    +-.+ ...++..+-..|...|++++|...+++.
T Consensus       267 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  333 (406)
T 3sf4_A          267 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  333 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            345555566666666666666666655421    1111 1445556666666666666666666654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=95.07  E-value=0.13  Score=32.34  Aligned_cols=63  Identities=14%  Similarity=0.020  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CC-CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE----SD-KVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..|..+-..|...|++++|...+++....    +- +.....+..+-..|...|++++|...+++..+
T Consensus        87 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  154 (411)
T 4a1s_A           87 AIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLT  154 (411)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46778888888999999999998877542    21 23567788888889999999999999888654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=95.03  E-value=0.29  Score=30.77  Aligned_cols=63  Identities=6%  Similarity=0.100  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC-ch--HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDK-VN--VFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+..+-..+.+.|++++|...|++..+..-. +.  ...|..+-..|...|++++|+..+++..+
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  114 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLT  114 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34445566778899999999999998875321 11  25788889999999999999999988754

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=94.84  E-value=0.31  Score=28.89  Aligned_cols=65  Identities=11%  Similarity=0.014  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--CCchHHHHHHHHHHHHh--------cCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDES--DKVNVFICNLILSCLVR--------NGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~--~~p~~~t~~~li~~~~~--------~g~~~~a~~~~~~m~~~   73 (94)
                      ...+..+-..|.+.|++++|...|+...+..  -+.....+..+-.++..        .|++++|+..|++..+.
T Consensus        52 ~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~  126 (261)
T 3qky_A           52 ADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR  126 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Confidence            5667778888999999999999999988641  11235567777778888        99999999999998765

>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=94.83  E-value=0.17  Score=31.16  Aligned_cols=63  Identities=17%  Similarity=0.139  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+++.+-..|.+ |++++|...|++-...    +-.+ -..+++.+-..|.+.|++++|+..|++..+
T Consensus       116 a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  183 (307)
T 2ifu_A          116 AMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKS  183 (307)
T ss_dssp             HHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3567777777777 9999999988876532    1111 246788888889999999999999988765

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=94.76  E-value=0.24  Score=27.22  Aligned_cols=80  Identities=10%  Similarity=0.130  Sum_probs=58.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC--------C---------CCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE--------S---------DKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~--------~---------~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      ....+...=..+.+.|++++|...|++....        .         -+-+...|..+-.+|.+.|++++|+..+++.
T Consensus        10 ~a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~a   89 (162)
T 3rkv_A           10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEV   89 (162)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            3456667777888999999999999987653        0         1224578888999999999999999999998


Q ss_pred             HHcCCCccHHHHHHHHHH
Q 034447           71 KQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        71 ~~~g~~p~~~~~~~ll~~   88 (94)
                      .+.. +.+...|..+-.+
T Consensus        90 l~~~-p~~~~a~~~~g~~  106 (162)
T 3rkv_A           90 LKRE-ETNEKALFRRAKA  106 (162)
T ss_dssp             HHHS-TTCHHHHHHHHHH
T ss_pred             HhcC-CcchHHHHHHHHH
Confidence            7753 2244555444444

>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=94.60  E-value=0.48  Score=32.73  Aligned_cols=66  Identities=14%  Similarity=0.103  Sum_probs=54.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...+..+-..+.+.|++++|...|++..+.. +-+...|..+-..+...|++++|+..|++..+..
T Consensus       432 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~  497 (681)
T 2pzi_A          432 SVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTF  497 (681)
T ss_dssp             CSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            55677788888999999999999999887642 2267788888889999999999999999987653

>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=94.59  E-value=0.57  Score=30.72  Aligned_cols=77  Identities=10%  Similarity=0.039  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch----------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVN----------------VFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----------------~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...|..+=..+.+.|++++|...|++.....  |+                ...|..+-.+|.+.|++++|+..+++..+
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  345 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG  345 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            4567777788899999999999999887531  32                68899999999999999999999999877


Q ss_pred             cCCCccHHHHHHHHHH
Q 034447           73 SGLTPDAVTYNTVYQS   88 (94)
Q Consensus        73 ~g~~p~~~~~~~ll~~   88 (94)
                      ..- .+...|..+-.+
T Consensus       346 ~~p-~~~~a~~~~g~a  360 (457)
T 1kt0_A          346 LDS-ANEKGLYRRGEA  360 (457)
T ss_dssp             HST-TCHHHHHHHHHH
T ss_pred             cCC-ccHHHHHHHHHH
Confidence            532 244455444433

>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=94.56  E-value=0.54  Score=30.32  Aligned_cols=78  Identities=8%  Similarity=-0.006  Sum_probs=62.9

Q ss_pred             cHHHHHHHHHHHHhcCC-HHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGN-SLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~-~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      +...|+.+-..+.+.|+ +++|...|++.....  | +...|..+-..+...|++++|+..|++..+..- -+...|..+
T Consensus       130 ~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP-~~~~a~~~l  206 (382)
T 2h6f_A          130 NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDA-KNYHAWQHR  206 (382)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCc-cCHHHHHHH
Confidence            56788888889999997 999999999998643  4 788899999999999999999999999987542 245555544


Q ss_pred             HHH
Q 034447           86 YQS   88 (94)
Q Consensus        86 l~~   88 (94)
                      -.+
T Consensus       207 g~~  209 (382)
T 2h6f_A          207 QWV  209 (382)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

>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=94.52  E-value=0.33  Score=27.63  Aligned_cols=79  Identities=9%  Similarity=0.017  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCc--------------hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDES-DKV--------------NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p--------------~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ...+..+-..+.+.|++++|...|++..... -.|              ....|..+-.+|.+.|++++|+..+++..+.
T Consensus        38 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~  117 (198)
T 2fbn_A           38 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI  117 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            3456667778889999999999999887531 112              1378888899999999999999999998775


Q ss_pred             CCCccHHHHHHHHHH
Q 034447           74 GLTPDAVTYNTVYQS   88 (94)
Q Consensus        74 g~~p~~~~~~~ll~~   88 (94)
                      .- .+...|..+-.+
T Consensus       118 ~p-~~~~~~~~lg~~  131 (198)
T 2fbn_A          118 DK-NNVKALYKLGVA  131 (198)
T ss_dssp             ST-TCHHHHHHHHHH
T ss_pred             Cc-ccHHHHHHHHHH
Confidence            31 244444444333

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.49  E-value=0.22  Score=25.57  Aligned_cols=66  Identities=9%  Similarity=-0.004  Sum_probs=49.7

Q ss_pred             ccHHHHHHHHHHHHhcCC---HHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            7 TSISSYSSYIKFLGKNGN---SLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~---~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .|...+..+-.++.-.++   .++|..++++-...  .| +......+-..+.+.|++++|+..|+++.+..
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            355556665566654433   79999999988764  35 66777777788899999999999999998764

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=94.47  E-value=0.48  Score=29.41  Aligned_cols=67  Identities=9%  Similarity=0.084  Sum_probs=50.4

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC-ch--HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDK-VN--VFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .+....+...-..+.+.|++++|...|++.....-. |.  ...|..+...+...|++++|...+++..+
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   75 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLT   75 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            445566667777788899999999999988765211 11  46788888889999999999998887643

>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=94.44  E-value=0.56  Score=29.99  Aligned_cols=78  Identities=9%  Similarity=0.007  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC--------------CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE--------------SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~--------------~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..+..+-..+.+.|++++|...|++..+.              ...| +...|..+-.+|.+.|++++|+..+++..+..
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            45677778888999999999999987651              0223 67888999999999999999999999988753


Q ss_pred             CCccHHHHHHHHHH
Q 034447           75 LTPDAVTYNTVYQS   88 (94)
Q Consensus        75 ~~p~~~~~~~ll~~   88 (94)
                      - -+...|..+-.+
T Consensus       304 p-~~~~a~~~lg~~  316 (370)
T 1ihg_A          304 P-SNTKALYRRAQG  316 (370)
T ss_dssp             T-TCHHHHHHHHHH
T ss_pred             c-hhHHHHHHHHHH
Confidence            2 244555444444

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=94.43  E-value=0.34  Score=29.43  Aligned_cols=61  Identities=15%  Similarity=-0.027  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCC----CCc-hHHHHHHHHHHHHhcCCHHHH-HHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDES----DKV-NVFICNLILSCLVRNGKFESS-LKLFDKI   70 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~----~~p-~~~t~~~li~~~~~~g~~~~a-~~~~~~m   70 (94)
                      .+|+.+-..|.+.|++++|...+++..+..    ... -..+|..+-..|.+.|+.++| ...+++.
T Consensus       197 ~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          197 KVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            688889999999999999999999876421    111 267888889999999999999 7767664

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=94.41  E-value=0.51  Score=31.03  Aligned_cols=60  Identities=12%  Similarity=0.074  Sum_probs=47.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCC---CC----chHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDES---DK----VNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~---~~----p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...+.-+.+.|++++|..++++..+.-   +.    .-..+++.+...|...|++++|+.++++..+
T Consensus       291 l~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~  357 (429)
T 3qwp_A          291 LKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTME  357 (429)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            344566777899999999999886421   11    2467899999999999999999999998753

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.32  E-value=0.25  Score=25.56  Aligned_cols=66  Identities=11%  Similarity=0.068  Sum_probs=53.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDE------SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~------~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...+-.+=..+.+.|+++.|..-|++-.+.      .-.+....+..+-.++.+.|+++.|+..+++..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            4556667778888999999999988876542      12356788899999999999999999999998763

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.30  E-value=0.38  Score=27.48  Aligned_cols=68  Identities=21%  Similarity=0.145  Sum_probs=57.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      +...++..|+...+.|.-++..++..+... +-+|+....-.+..+|.+-|+..++.+++.+.-++|++
T Consensus        90 ~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           90 LNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            345677889999999999999999999643 34567777788899999999999999999999999975

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=93.93  E-value=0.41  Score=29.23  Aligned_cols=70  Identities=17%  Similarity=0.119  Sum_probs=50.2

Q ss_pred             HHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-ccHHHHHHHHHHh
Q 034447           19 LGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT-PDAVTYNTVYQSD   89 (94)
Q Consensus        19 ~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~~~~~ll~~~   89 (94)
                      +.+.+..++|...+++..... +.+...+..+-..+...|++++|+..|++..+..-. .+...+..+...+
T Consensus       195 l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~  265 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEIL  265 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHH
T ss_pred             HHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHH
Confidence            556777788888887776542 236788888889999999999999999998775421 2345566666653

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=93.89  E-value=0.49  Score=27.30  Aligned_cols=72  Identities=6%  Similarity=0.115  Sum_probs=52.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHH----------------HHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNL----------------ILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~----------------li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      ..-..+.+.|++++|...|++....  .| +...|..                +-..|.+.|++++|+..|++..+..- 
T Consensus         9 ~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-   85 (208)
T 3urz_A            9 QKVSAAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAP-   85 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-
Confidence            3444567899999999999988764  25 4455666                88889999999999999999877541 


Q ss_pred             ccHHHHHHHHHH
Q 034447           77 PDAVTYNTVYQS   88 (94)
Q Consensus        77 p~~~~~~~ll~~   88 (94)
                      -+...|..+-..
T Consensus        86 ~~~~~~~~lg~~   97 (208)
T 3urz_A           86 NNVDCLEACAEM   97 (208)
T ss_dssp             TCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH
Confidence            244555444443

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=93.65  E-value=0.41  Score=25.63  Aligned_cols=75  Identities=16%  Similarity=0.263  Sum_probs=57.7

Q ss_pred             HHHHHHHHhcC-CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           13 SSYIKFLGKNG-NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        13 ~~ll~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      .-....+-+.. +..+..+-++.+....+-|+.....+.+++|-+..++.-|.++|+-.+.+- .+....|..+++-
T Consensus        13 aRy~~~F~~~~iD~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lqE   88 (109)
T 1v54_E           13 ARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQE   88 (109)
T ss_dssp             HHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHHH
T ss_pred             HHHHHHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHHH
Confidence            33444455555 678888889999999999999999999999999999999999999886542 2233456666653

>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=93.60  E-value=0.74  Score=30.45  Aligned_cols=69  Identities=12%  Similarity=-0.010  Sum_probs=53.2

Q ss_pred             HHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           18 FLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        18 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      .+.+.|++++|.+.+++..+.. +-+...|..+-.+|.+.|++++|+..+++..+..- -+...|..+-.+
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~   83 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAAS   83 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            4567899999999999887642 23688999999999999999999999999887632 245555555444

>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=93.40  E-value=0.72  Score=35.43  Aligned_cols=61  Identities=13%  Similarity=0.150  Sum_probs=49.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +..+|..+=.++-+.|++++|.+.|.+-      -|...|.-++.++.+.|++++|.+++..-++..
T Consensus      1104 ~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~ 1164 (1630)
T 1xi4_A         1104 EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA 1164 (1630)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc
Confidence            4567788888888899999999998653      367788889999999999999999998765544

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=93.29  E-value=1.1  Score=30.00  Aligned_cols=54  Identities=6%  Similarity=0.065  Sum_probs=42.7

Q ss_pred             HHhcCCHHHHHHHHHHHhhC---CC---Cc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           19 LGKNGNSLKALEIYNSITDE---SD---KV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        19 ~~~~g~~~~a~~~~~~m~~~---~~---~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +-..|++++|..++++..+.   -+   .| -..+++.|...|...|++++|+.++++..+
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~  379 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVD  379 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            45679999999998877532   11   23 567899999999999999999999988643

>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=92.94  E-value=0.65  Score=25.88  Aligned_cols=63  Identities=11%  Similarity=0.048  Sum_probs=37.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      +...+..+-..+.+.|++++|...|++..+..=.+ +...+..+...+...|+.++|...|++.
T Consensus       107 ~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A          107 NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHH
Confidence            34555566666666666676666666665442111 2445666666666666666666666654

>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=92.92  E-value=0.76  Score=26.63  Aligned_cols=64  Identities=13%  Similarity=0.071  Sum_probs=45.4

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC----CHHHHHHHHHHHHHcC
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG----KFESSLKLFDKIKQSG   74 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g----~~~~a~~~~~~m~~~g   74 (94)
                      -|...+..+=..|...+++++|...|++-.+.|   +...+..|-..|.. +    +.++|+..|++-.+.|
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g   83 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG   83 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC
Confidence            355566666667777888888888888887765   44555555555655 5    7888888888887665

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.89  E-value=1.1  Score=28.34  Aligned_cols=64  Identities=13%  Similarity=0.017  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CC-CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SD-KVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~-~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..++..+-..|...|++++|..++++....    +- +-...+|..+.+.|...|++++|..++++...
T Consensus       135 ~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  203 (434)
T 4b4t_Q          135 HSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAART  203 (434)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHH
Confidence            456778888999999999999999877532    11 22466899999999999999999999988653

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=92.89  E-value=0.93  Score=28.19  Aligned_cols=61  Identities=10%  Similarity=-0.044  Sum_probs=41.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhC----CCC--c-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDE----SDK--V-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~--p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ++.+-..+...|++++|...+++....    +-.  | ....+..+-..+...|++++|...+++..+
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  163 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIE  163 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            455566677788888888887766532    221  2 344566667777888888888888877654

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=92.87  E-value=1.1  Score=28.16  Aligned_cols=77  Identities=10%  Similarity=0.050  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHH------------------HHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVF------------------ICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~------------------t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      ...+..+=..+.+.|++++|...|++....  .|+..                  .|..+-.+|.+.|++++|+..+++.
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~a  256 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIV  256 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            345566666777889999999999987643  25433                  7888899999999999999999998


Q ss_pred             HHcCCCccHHHHHHHHHH
Q 034447           71 KQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        71 ~~~g~~p~~~~~~~ll~~   88 (94)
                      .+..- .+...|..+-.+
T Consensus       257 l~~~p-~~~~a~~~lg~a  273 (338)
T 2if4_A          257 LTEEE-KNPKALFRRGKA  273 (338)
T ss_dssp             HHHCT-TCHHHHHHHHHH
T ss_pred             HHhCC-CCHHHHHHHHHH
Confidence            76531 245555555444

>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=92.85  E-value=0.55  Score=30.99  Aligned_cols=51  Identities=18%  Similarity=0.139  Sum_probs=40.4

Q ss_pred             cCCHHHHHHHHHHHhh---CCC---Cc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           22 NGNSLKALEIYNSITD---ESD---KV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        22 ~g~~~~a~~~~~~m~~---~~~---~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|++++|..++++..+   .-+   .| -..+++.|...|...|++++|+.++++..+
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~  368 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIK  368 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Confidence            4788999999987653   112   23 457899999999999999999999998753

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=92.75  E-value=1.1  Score=27.89  Aligned_cols=64  Identities=8%  Similarity=0.073  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...+..+-..+...|++++|...+++....    +-.....+|..+-..+...|++++|...+++...
T Consensus       135 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~  202 (373)
T 1hz4_A          135 EFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLEN  202 (373)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345666777889999999999999987642    2112356788888889999999999999998764

>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=92.63  E-value=0.75  Score=26.29  Aligned_cols=77  Identities=10%  Similarity=0.075  Sum_probs=56.3

Q ss_pred             cHHHHHHHHHHHHhcCC----------HHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhc-----------CCHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGN----------SLKALEIYNSITDESDKV-NVFICNLILSCLVRN-----------GKFESSLK   65 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~----------~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~-----------g~~~~a~~   65 (94)
                      +...|+.+=.++.+.++          +++|...|++-.+.  .| +...|..+=.+|...           |++++|++
T Consensus        35 ~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~  112 (158)
T 1zu2_A           35 DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQ  112 (158)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHH
Confidence            55666666666666655          45999999988764  35 667888888888876           48999999


Q ss_pred             HHHHHHHcCCCccHHHHHHHHHH
Q 034447           66 LFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        66 ~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      .|++..+.  .|+...|...++.
T Consensus       113 ~~~kAl~l--~P~~~~y~~al~~  133 (158)
T 1zu2_A          113 FFQQAVDE--QPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHh--CCCCHHHHHHHHH
Confidence            99998775  3766677666554

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=92.48  E-value=0.84  Score=25.97  Aligned_cols=67  Identities=15%  Similarity=0.104  Sum_probs=47.4

Q ss_pred             CccHHHHHHHHHHHHhcC---CHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            6 KTSISSYSSYIKFLGKNG---NSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g---~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .++..+--.+--++++..   +.+++..++++..+.. .|  +.-.+=.+--+|.+.|++++|.+.+++..+.
T Consensus        29 ~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~i  100 (152)
T 1pc2_A           29 SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  100 (152)
T ss_dssp             CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            345555555666777777   6779999999988765 23  2222333445669999999999999998764

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=92.33  E-value=1.3  Score=27.72  Aligned_cols=62  Identities=8%  Similarity=-0.058  Sum_probs=34.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITDESDKV--NVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +..+=.++.+.|++++|...|++-......|  ........-.++.+.|+.++|..+|+++...
T Consensus       174 ~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          174 GVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3344445556666666666666665433313  2223444445556666666666666666554

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=92.19  E-value=0.61  Score=24.97  Aligned_cols=46  Identities=9%  Similarity=0.091  Sum_probs=37.1

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILS   52 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~   52 (94)
                      .|+.....+.|++|-+..++..|.++|+..+... .....+|..++.
T Consensus        42 VP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lq   87 (109)
T 1v54_E           42 VPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   87 (109)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHH
Confidence            6899999999999999999999999999988532 223446777665

>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=91.93  E-value=2.3  Score=29.78  Aligned_cols=80  Identities=13%  Similarity=0.024  Sum_probs=63.6

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHcC-CCccHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGK---FESSLKLFDKIKQSG-LTPDAVTY   82 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~---~~~a~~~~~~m~~~g-~~p~~~~~   82 (94)
                      -|..+|..++..+-+.+.++.+..+|+.+... ++.....|...+..-.+.++   ++.+.++|++-.... ..|+...|
T Consensus        64 ~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW  142 (679)
T 4e6h_A           64 TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLW  142 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHH
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            38889999999999999999999999999865 55677888888888888888   999999999987654 24666666


Q ss_pred             HHHHH
Q 034447           83 NTVYQ   87 (94)
Q Consensus        83 ~~ll~   87 (94)
                      ..-++
T Consensus       143 ~~Yl~  147 (679)
T 4e6h_A          143 LSYIT  147 (679)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=91.36  E-value=0.92  Score=24.29  Aligned_cols=64  Identities=13%  Similarity=0.000  Sum_probs=47.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      +-+..+...|++++|..+.+.+.    .||...|-++-.  .+.|..+++..-+.++..+|- |....|..
T Consensus        44 IR~sSLmNrG~Yq~Al~l~~~~c----~pdlepw~ALce--~rlGl~s~le~rL~~la~sg~-p~~q~Fa~  107 (115)
T 2uwj_G           44 IRISSLANQGRYQEALAFAHGNP----WPALEPWFALCE--WHLGLGAALDRRLAGLGGSSD-PALADFAA  107 (115)
T ss_dssp             HHHHHHHHTTCHHHHHGGGTTCC----CGGGHHHHHHHH--HHTTCHHHHHHHHHHHHTCSS-HHHHHHHH
T ss_pred             HHHHHHHcchhHHHHHHhcCCCC----CchHHHHHHHHH--HhcccHHHHHHHHHHHHhCCC-HHHHHHHH
Confidence            33455667888888887776655    599999988866  688888888888888887774 55555543

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=91.32  E-value=1.8  Score=27.42  Aligned_cols=76  Identities=12%  Similarity=0.014  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHhc-----CCHHHHHHHHHHHhhCCCCc--hHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHcCCC--cc
Q 034447            9 ISSYSSYIKFLGKN-----GNSLKALEIYNSITDESDKV--NVFICNLILSCLVRN-GKFESSLKLFDKIKQSGLT--PD   78 (94)
Q Consensus         9 ~~~~~~ll~~~~~~-----g~~~~a~~~~~~m~~~~~~p--~~~t~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~--p~   78 (94)
                      -..|..+-..|.+.     |+.++|.+.|++-.+.  .|  +.-++...-+.++.. |+.+++.+.+++-.+....  |+
T Consensus       199 GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~L--nP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~  276 (301)
T 3u64_A          199 GAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRY--CSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPH  276 (301)
T ss_dssp             HHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHH--CCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSS
T ss_pred             CHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHh--CCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCC
Confidence            46788888889994     9999999999988864  36  367777788888885 9999999999999888766  77


Q ss_pred             HHHHHHHH
Q 034447           79 AVTYNTVY   86 (94)
Q Consensus        79 ~~~~~~ll   86 (94)
                      ....+.+-
T Consensus       277 ~~lan~~~  284 (301)
T 3u64_A          277 NKLLVILS  284 (301)
T ss_dssp             CHHHHHHH
T ss_pred             hhHHHHHH
Confidence            66555543

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=91.11  E-value=1  Score=24.16  Aligned_cols=64  Identities=16%  Similarity=0.088  Sum_probs=46.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNT   84 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   84 (94)
                      +-+..+...|++++|..+.+.+.    .||...|-++-.  .+.|..+++..-+.++..+|- |....|..
T Consensus        45 IR~sSLmNrG~Yq~Al~l~~~~c----~pdlepw~ALce--~rlGl~s~le~rL~~la~sg~-p~~q~Fa~  108 (116)
T 2p58_C           45 IRLSSLMNRGDYASALQQGNKLA----YPDLEPWLALCE--YRLGLGSALESRLNRLARSQD-PRIQTFVN  108 (116)
T ss_dssp             HHHHHHHHTTCHHHHHHHHTTSC----CGGGHHHHHHHH--HHHTCHHHHHHHHHHHTTCCC-HHHHHHHH
T ss_pred             HHHHHHHcchhHHHHHHhcCCCC----CchHHHHHHHHH--HhcccHHHHHHHHHHHHhCCC-HHHHHHHH
Confidence            34456667888888888877665    488888888766  677888888888888877764 55555543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=90.38  E-value=2.4  Score=27.12  Aligned_cols=65  Identities=6%  Similarity=-0.153  Sum_probs=45.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHH--HHHHHHH-HHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVF--ICNLILS-CLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~--t~~~li~-~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+..+-..|.+.|++++|...|++..+....+...  .+..+-. ...+.|+.++|+..|++..+
T Consensus       333 ~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~  400 (472)
T 4g1t_A          333 LFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK  400 (472)
T ss_dssp             TCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            34556777888999999999999999988765444321  1222221 23567899999998887655

>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=90.32  E-value=1.6  Score=24.97  Aligned_cols=61  Identities=16%  Similarity=0.000  Sum_probs=48.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch-------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVN-------------VFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~-------------~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+...=..+.+.|++++|...|++-.+..  |+             ...|+.+-.++.+.|++++|+..+++-.+-
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~--p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l   86 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEIS--HTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHY   86 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHH--TTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            34445556778899999999999876532  32             348999999999999999999999997763

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.99  E-value=2  Score=27.13  Aligned_cols=56  Identities=13%  Similarity=0.048  Sum_probs=42.9

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCc----------------hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKV----------------NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p----------------~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+.+.|++++|.+.|.+..+..-..                ....+..+...|...|++++|.+.+.+..+
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~   83 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTE   83 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45678899999999999887532211                113477888999999999999999988654

>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=88.76  E-value=1.7  Score=30.02  Aligned_cols=60  Identities=8%  Similarity=-0.038  Sum_probs=29.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      +...|..+=.++.+.|++++|...|++..+..  | +...|..+-..+.+.|++++ ++.|++.
T Consensus       466 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~lg~~~~~~g~~~~-~~~~~~a  526 (681)
T 2pzi_A          466 RWRLVWYRAVAELLTGDYDSATKHFTEVLDTF--PGELAPKLALAATAELAGNTDE-HKFYQTV  526 (681)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHHTCCCT-TCHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCChHH-HHHHHHH
Confidence            34455555556666666666666666554321  2 23333344444444444444 4444443

>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=88.67  E-value=6.9  Score=30.42  Aligned_cols=54  Identities=15%  Similarity=0.047  Sum_probs=34.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      +...|..+=..|-..|++++|..+|...         ..|..+..++.+.|++++|.+.+++-
T Consensus      1194 n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA 1247 (1630)
T 1xi4_A         1194 NNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA 1247 (1630)
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh
Confidence            4444555555555666666666666553         46777777777777777777776655

>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=88.33  E-value=2.4  Score=24.45  Aligned_cols=65  Identities=11%  Similarity=0.012  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHh----cCCHHHHHHHHHHHhhCCCC-chHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHc
Q 034447            9 ISSYSSYIKFLGK----NGNSLKALEIYNSITDESDK-VNVFICNLILSCLVR----NGKFESSLKLFDKIKQS   73 (94)
Q Consensus         9 ~~~~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~-p~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~~   73 (94)
                      ...+..+=..|..    .+++++|...|++-.+.|-. -+...+..|-..|..    .+++++|+..|++-.+.
T Consensus        85 ~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~  158 (212)
T 3rjv_A           85 KSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL  158 (212)
T ss_dssp             HHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc
Confidence            3444445455554    67788888888777766532 125666666667766    67888888888887665

>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=88.30  E-value=2.4  Score=24.38  Aligned_cols=70  Identities=13%  Similarity=0.168  Sum_probs=51.4

Q ss_pred             cCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHhhccc
Q 034447           22 NGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSDHITW   93 (94)
Q Consensus        22 ~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~   93 (94)
                      .+++++|.++|+.+.+.+-++ ...|-....==.+.|+...|.+++.+-...+-.| .....+.|+-...|+
T Consensus        73 i~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~-~~~le~a~~nl~~~~  142 (161)
T 4h7y_A           73 IQEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP-LEMLEIALRNLNLQK  142 (161)
T ss_dssp             HHCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC-HHHHHHHHHHHHTTC
T ss_pred             hcCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc-HHHHHHHHHhhhcCC
Confidence            378999999999997654444 5555555554467899999999999998887665 445667776655554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=88.07  E-value=3.4  Score=25.81  Aligned_cols=67  Identities=6%  Similarity=-0.156  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCch--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcc
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVN--VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPD   78 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   78 (94)
                      ..-.+-..+.+.+++++|...|+...... .|.  ...+..+=.++.+.|++++|++.|++.......|.
T Consensus       137 ~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~  205 (282)
T 4f3v_A          137 VAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEA  205 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCcc
Confidence            33344447778888888888887554432 121  23566666778899999999999998875444254

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=87.59  E-value=2.2  Score=24.15  Aligned_cols=46  Identities=9%  Similarity=0.091  Sum_probs=37.5

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILS   52 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~   52 (94)
                      .|+.....+.|++|-+..++..|.++|+..+... .+....|..++.
T Consensus        85 VPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~lq  130 (152)
T 2y69_E           85 VPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ  130 (152)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHHH
Confidence            6899999999999999999999999999988542 233456777665

>2ion_A PDCD4, programmed cell death 4, PDCD4; alpha-helical, antitumor protein; 1.57A {Mus musculus} SCOP: a.118.1.14 PDB: 2ios_A 2iol_A

Probab=87.43  E-value=2.6  Score=23.82  Aligned_cols=70  Identities=14%  Similarity=0.106  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCCccHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG--KFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      ..+.+|.=|...|+.++|.++++++..-.+ ....+..++..++-+.+  ..+.+.+++..+.+.|+.+....
T Consensus        11 ki~~lL~EY~~~~D~~EA~~cl~EL~~p~f-~~e~V~~~i~~alE~~~~~~re~~~~LL~~L~~~~~is~~q~   82 (152)
T 2ion_A           11 EIDMLLKEYLLSGDISEAEHCLKELEVPHF-HHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQM   82 (152)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGG-HHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHhCCCcc-hHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcCHHHH
Confidence            456789999999999999999999974322 34566667677776643  34567788888888887654443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=87.42  E-value=1.8  Score=22.01  Aligned_cols=60  Identities=8%  Similarity=0.098  Sum_probs=41.8

Q ss_pred             HHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           27 KALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        27 ~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ++...|++..+.. +-+...|..+-..|...|++++|+..|++..+..- .+...|..+-..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~   62 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDP-TYSVAWKWLGKT   62 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC-CcHHHHHHHHHH
Confidence            4566666665432 23678889999999999999999999999877542 234445444433

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=86.85  E-value=4.8  Score=26.24  Aligned_cols=47  Identities=21%  Similarity=0.279  Sum_probs=19.7

Q ss_pred             CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHh----cCCHHHHHHHHHHHHH
Q 034447           23 GNSLKALEIYNSITDESDKVNVFICNLILSCLVR----NGKFESSLKLFDKIKQ   72 (94)
Q Consensus        23 g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~   72 (94)
                      ++.++|...|++..+.|   +...+..+-..|..    .++.++|+..|++-.+
T Consensus       165 ~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~  215 (490)
T 2xm6_A          165 RDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSAT  215 (490)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHH
Confidence            34444444444444332   23333333333433    4444444444444433

>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=86.85  E-value=2.4  Score=22.84  Aligned_cols=63  Identities=14%  Similarity=0.086  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHh----cCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCC
Q 034447           10 SSYSSYIKFLGK----NGNSLKALEIYNSITDESDKVNVFICNLILSCLVR----NGKFESSLKLFDKIKQSGL   75 (94)
Q Consensus        10 ~~~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~----~g~~~~a~~~~~~m~~~g~   75 (94)
                      ..+..+=..|..    .+++++|...|++-.+.|   +...+..|-..|..    .++.++|...|++-.+.|.
T Consensus        58 ~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           58 NGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            334444444444    556666666666665553   33444445555555    5666666666666665553

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=86.22  E-value=5.2  Score=26.06  Aligned_cols=15  Identities=13%  Similarity=0.155  Sum_probs=6.0

Q ss_pred             cCCHHHHHHHHHHHh
Q 034447           22 NGNSLKALEIYNSIT   36 (94)
Q Consensus        22 ~g~~~~a~~~~~~m~   36 (94)
                      .+++++|...|++-.
T Consensus        92 ~~~~~~A~~~~~~a~  106 (490)
T 2xm6_A           92 PQDYAQAVIWYKKAA  106 (490)
T ss_dssp             CCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH
Confidence            334444444444333

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.16  E-value=4.9  Score=26.33  Aligned_cols=62  Identities=6%  Similarity=-0.003  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhC--CCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDE--SDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~--~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+-..|.+.|++++|.+++.++...  +..--+..+-.+|+.+...+++..+...+++...
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~  196 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNS  196 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3456778899999999999999999853  3345677888899999999999999999988753

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=84.79  E-value=1.9  Score=29.66  Aligned_cols=45  Identities=11%  Similarity=0.115  Sum_probs=30.5

Q ss_pred             hcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447           21 KNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus        21 ~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +.|++++|.++.+.+      .+...|..+-..+.+.++++.|++.|.++.
T Consensus       664 ~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~  708 (814)
T 3mkq_A          664 KVGQLTLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAH  708 (814)
T ss_dssp             HHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             hcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHcc
Confidence            344555555544333      356788888888888888888888887764

>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=83.79  E-value=2.4  Score=27.41  Aligned_cols=42  Identities=12%  Similarity=0.049  Sum_probs=35.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CCCCchHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITD-----ESDKVNVFICNL   49 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~t~~~   49 (94)
                      +...|..+|.++.+.|+..+|.+.|+...+     .|+.|...+-..
T Consensus       204 ~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l  250 (388)
T 2ff4_A          204 REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  250 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            778899999999999999999999998753     589887766443

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A

Probab=83.71  E-value=3.8  Score=22.38  Aligned_cols=70  Identities=14%  Similarity=0.106  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCCccHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG--KFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      ..+.+|.=|...|+.++|.++++++..-.+ ....+..++..++-+.+  ..+.+.+++..+.+.|+.+....
T Consensus         9 ki~~ll~EY~~~~D~~Ea~~cl~eL~~p~f-~~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~~~~~is~~q~   80 (129)
T 2nsz_A            9 EIDMLLKEYLLSGDISEAEHCLKELEVPHF-HHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQM   80 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGG-HHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhCCCcc-HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcCHHHH
Confidence            456788999999999999999999974322 34566666677776654  24677888888888887654443

>3eiq_C Programmed cell death protein 4; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Mus musculus}

Probab=82.10  E-value=8.1  Score=25.02  Aligned_cols=75  Identities=13%  Similarity=0.100  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCC--HHHHHHHHHHHHHcCCCccHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGK--FESSLKLFDKIKQSGLTPDAVTYNTV   85 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~--~~~a~~~~~~m~~~g~~p~~~~~~~l   85 (94)
                      ...+.+|.=|...|+.++|.++++++..-.+. ...+..++..+.-+.++  .+...+++..+.+.|+.+.......+
T Consensus       218 kki~~lL~EY~~s~D~~EA~~ci~EL~~p~fh-he~V~~av~~aLE~~~~~~re~~~~LL~~L~~~glls~~q~~~Gf  294 (358)
T 3eiq_C          218 KEIDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGY  294 (358)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHCCTTCH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHccCCcch-HHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            34678899999999999999999999754333 34556666666665443  45688888888888876655444333

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=81.40  E-value=3.1  Score=19.72  Aligned_cols=48  Identities=13%  Similarity=0.056  Sum_probs=34.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHh
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVR   56 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   56 (94)
                      +...+..+-..+.+.|++++|...+++..... +-+...+..+-..+.+
T Consensus        42 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~   89 (91)
T 1na3_A           42 NAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQK   89 (91)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHh
Confidence            56678888889999999999999999887642 1245555555444443

---

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	94
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.99
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.19
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.18
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.13
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.07
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.05
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.03
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	97.03
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.03
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.02
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	96.8
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.8
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.67
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.67
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.65
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.62
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.6
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.34
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.32
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.17
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	96.06
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.05
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.97
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.9
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.61
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	95.4
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.27
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	94.96
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	94.51
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	94.43
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	94.35
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	94.28
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.74
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	93.61
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.44
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.3
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	92.67
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	92.13
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	91.86
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	91.44
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	91.38
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	90.76
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	90.75
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	89.64
d1ug3a1	193	Eukaryotic initiation factor eIF4G {Human (Homo sa	87.59
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	87.44
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	87.08
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	86.44
d1khda1	69	Anthranilate phosphoribosyltransferase (TrpD) {Pec	85.11
d1fkma2	188	Ypt/Rab-GAP domain of gyp1p {Baker's yeast (Saccha	83.93
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	82.21
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	81.31

>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=97.99  E-value=7e-05  Score=42.33  Aligned_cols=71  Identities=10%  Similarity=0.134  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCccHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ-----SGLTPDAVT   81 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~   81 (94)
                      ..+..+...+.+.|++++|...++...... +-+...|..++.++.+.|+.++|++.|++..+     -|+.|+..+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            456778889999999999999999997642 23899999999999999999999999999754     499998866

>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=97.19  E-value=0.0042  Score=33.57  Aligned_cols=66  Identities=12%  Similarity=-0.003  Sum_probs=51.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|..+-..|.+.|++++|...|++..+.. +-+...|..+..++...|++++|...+++..+..
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~~  108 (159)
T d1a17a_          43 NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKVK  108 (159)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             hhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            56777778888888888888888888877542 2366788888888888888888888888877653

>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=97.18  E-value=0.0043  Score=33.50  Aligned_cols=73  Identities=11%  Similarity=-0.000  Sum_probs=57.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..=..|.+.|++++|...|++..... +-+...|..+-.+|...|++++|++.|++..+.. +-+...|..+-.+
T Consensus        15 ~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~   87 (159)
T d1a17a_          15 TQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS   87 (159)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHH
Confidence            33456789999999999999988653 3388889999999999999999999999988754 2245666665555

>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=97.13  E-value=0.0047  Score=34.01  Aligned_cols=62  Identities=10%  Similarity=0.053  Sum_probs=45.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      +...|+.+-.+|.+.|++++|...|++..+.  .| +..+|..+-.+|...|++++|+..|++..
T Consensus        37 ~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          37 VAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            5666777777778888888888888777643  35 56677777777888888888888777654

>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=97.07  E-value=0.005  Score=32.26  Aligned_cols=72  Identities=17%  Similarity=0.119  Sum_probs=53.0

Q ss_pred             ccHHHHHHHHHHHHhcCC---HHHHHHHHHHHhhCCCCch-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHH
Q 034447            7 TSISSYSSYIKFLGKNGN---SLKALEIYNSITDESDKVN-VFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAV   80 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~---~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   80 (94)
                      .+..++..+-.++.+.++   +++|..++++.....-.|+ ..+|..+-.+|.+.|++++|++.|++..+..  |+-.
T Consensus        31 ~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~~~--P~~~  106 (122)
T d1nzna_          31 VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQTE--PQNN  106 (122)
T ss_dssp             CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCH
T ss_pred             CCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhC--cCCH
Confidence            356667777777776554   4569999999877654444 3467778889999999999999999988743  5433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.05  E-value=0.005  Score=33.26  Aligned_cols=65  Identities=18%  Similarity=0.059  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..+|+.+-.+|.+.|++++|...++...+.. +-+..+|..+-.++...|++++|+..|++..+-.
T Consensus        67 ~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~  131 (153)
T d2fbna1          67 ISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN  131 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            4577778888999999999999999887643 3488999999999999999999999999987653

>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=97.03  E-value=0.007  Score=33.29  Aligned_cols=79  Identities=10%  Similarity=-0.040  Sum_probs=61.9

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-cHHHHHHH
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP-DAVTYNTV   85 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~l   85 (94)
                      |++..+...=..|.+.|++++|...|++..... +-+...|+-+-.+|.+.|++++|+..|++..+-  .| +..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            566666666778899999999999999876542 347888999999999999999999999998753  34 45555555


Q ss_pred             HHH
Q 034447           86 YQS   88 (94)
Q Consensus        86 l~~   88 (94)
                      -.+
T Consensus        79 g~~   81 (201)
T d2c2la1          79 GQC   81 (201)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

>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=97.03  E-value=0.0095  Score=35.22  Aligned_cols=66  Identities=2%  Similarity=-0.057  Sum_probs=46.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...+..+-..|.+.|++++|...|++..+.. +-+..+|..+...|.+.|++++|+..++...+..
T Consensus        32 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~   97 (388)
T d1w3ba_          32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK   97 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccccccccccccccccc
Confidence            45566677777778888888888887776532 1255677777777888888888888877776654

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.03  E-value=0.0061  Score=33.46  Aligned_cols=65  Identities=17%  Similarity=-0.056  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      ..+|+.+-.+|.+.|++++|...++...... +-+...|..+-.+|...|++++|+..|++..+..
T Consensus        62 ~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  126 (170)
T d1p5qa1          62 LASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY  126 (170)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            3567778888999999999999999887643 2388999999999999999999999999987743

>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=97.02  E-value=0.0032  Score=32.26  Aligned_cols=71  Identities=10%  Similarity=-0.069  Sum_probs=53.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      +-..+.+.|++++|...|++.....  | +...|..+-.++.+.|++++|+..|++..+..- -+...|..+-..
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~la~~   93 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVS   93 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhccccccccccc-ccccchHHHHHH
Confidence            3445778899999999999987642  5 688889999999999999999999999776531 134444444333

>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=96.80  E-value=0.017  Score=34.09  Aligned_cols=77  Identities=17%  Similarity=0.224  Sum_probs=49.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-cHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTP-DAVTYNTV   85 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~l   85 (94)
                      +...+..+...+.+.|++++|...|++..+.  .| +..+|..+-..|.+.|++++|+..|++..+.  .| +...|..+
T Consensus       304 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l  379 (388)
T d1w3ba_         304 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNM  379 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHH
T ss_pred             cchhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            4556666666777777777777777766542  24 4556667777777777777777777776543  24 34455555


Q ss_pred             HHH
Q 034447           86 YQS   88 (94)
Q Consensus        86 l~~   88 (94)
                      -..
T Consensus       380 g~~  382 (388)
T d1w3ba_         380 GNT  382 (388)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

>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=96.80  E-value=0.0057  Score=31.99  Aligned_cols=55  Identities=15%  Similarity=0.138  Sum_probs=47.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..+.+.|++++|...|++..+.+ +-+...|..+-.+|.+.|++++|+..+++..+
T Consensus        12 ~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~   66 (128)
T d1elra_          12 NDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIE   66 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHH
Confidence            46788999999999999888653 23788999999999999999999999999765

>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=96.67  E-value=0.011  Score=30.30  Aligned_cols=65  Identities=17%  Similarity=0.019  Sum_probs=48.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|..+-.+|.+.|++++|...++...+.. +.+...|..+-.++...|++++|+..|++..+.
T Consensus        36 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          36 NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  100 (117)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             chhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            55667777777778888888888888776542 246777777888888888888888888887653

>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=96.67  E-value=0.015  Score=31.61  Aligned_cols=65  Identities=9%  Similarity=-0.073  Sum_probs=55.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      +...|+.+-.++.+.|++++|...+++..+.. +-+...|..+-.++...|++++|+..|++..+-
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            44567777788999999999999999987643 237889999999999999999999999998774

>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=96.65  E-value=0.016  Score=32.39  Aligned_cols=66  Identities=8%  Similarity=-0.085  Sum_probs=51.0

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .|+...|..+=..|.+.|++++|...|++-.+.. +-+...|.-+-.+|.+.|++++|+..|++-..
T Consensus        33 ~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~   98 (192)
T d1hh8a_          33 DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALI   98 (192)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            5667777778888888888888888888877543 23677777788888888888888888887653

>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=96.62  E-value=0.013  Score=34.43  Aligned_cols=64  Identities=9%  Similarity=0.132  Sum_probs=37.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...+..+-..+...|++++|...|++..... +-+...|..+-..|.+.|++++|++.|++..+
T Consensus       171 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  234 (323)
T d1fcha_         171 DPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALE  234 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHH
Confidence            44555555566666666666666666654321 11455566666666666666666666666554

>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=96.60  E-value=0.013  Score=30.07  Aligned_cols=70  Identities=13%  Similarity=0.028  Sum_probs=55.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQS   88 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   88 (94)
                      ..+.+.|++++|..+|++..+.. +-+...|..+-.+|.+.|++++|+..+++..+.+- .+...|..+-.+
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~g~~   80 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAA   80 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhcc-chhhHHHHHHHH
Confidence            45778899999999999987642 33778899999999999999999999999887542 355555544444

>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=96.34  E-value=0.031  Score=31.64  Aligned_cols=55  Identities=15%  Similarity=0.158  Sum_probs=25.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           16 IKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        16 l~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      =..|-+.|++++|...|++..+.  .| +..+|+.+-.+|.+.|++++|+..|++..+
T Consensus        44 G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   99 (259)
T d1xnfa_          44 GVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLE   99 (259)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHH
Confidence            33444445555555555444432  12 344444444445555555555555544443

>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=96.32  E-value=0.038  Score=32.35  Aligned_cols=63  Identities=10%  Similarity=0.036  Sum_probs=53.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      +...|..+-..|.+.|++++|.+.|++..+.  .| +..+|..+-.+|.+.|++++|++.|++..+
T Consensus       205 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         205 DYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4677888888999999999999999988754  24 567888899999999999999999988665

>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=96.17  E-value=0.04  Score=31.17  Aligned_cols=65  Identities=14%  Similarity=0.037  Sum_probs=55.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +..+|+.+=.+|.+.|++++|...|++..+..  | +..+|..+-..+...|++++|.+.|++..+..
T Consensus        70 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~  135 (259)
T d1xnfa_          70 MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD  135 (259)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH--hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc
Confidence            66788899999999999999999999988642  4 46678888899999999999999999987654

>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=96.06  E-value=0.056  Score=31.88  Aligned_cols=67  Identities=16%  Similarity=0.211  Sum_probs=50.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|.......-+.|+++.|..+|+......-......|...+....+.|+.+.|.++|++..+.+
T Consensus        98 ~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~  164 (308)
T d2onda1          98 NMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA  164 (308)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST
T ss_pred             CHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC
Confidence            4556677777777888888888888888764333335578888888888888888888888877654

>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=96.05  E-value=0.037  Score=30.77  Aligned_cols=65  Identities=15%  Similarity=0.097  Sum_probs=50.0

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVY   86 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   86 (94)
                      ..+...|+++.|.+.|++..    +|+..+|.-+=.+|...|++++|++.|++-.+-+- -+...|..+=
T Consensus        13 ~~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp-~~~~a~~~~g   77 (192)
T d1hh8a_          13 VLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRG   77 (192)
T ss_dssp             HHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhh-hhhhhHHHHH
Confidence            44567899999999998753    46778888899999999999999999999876542 2344444433

>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=95.97  E-value=0.023  Score=29.55  Aligned_cols=65  Identities=17%  Similarity=0.177  Sum_probs=49.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCcc
Q 034447           13 SSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNG---KFESSLKLFDKIKQSGLTPD   78 (94)
Q Consensus        13 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p~   78 (94)
                      ..++..+...+++++|.+.|++-...+ +.+..++.-+-.++.+++   ++++|+.++++..+.+-.|+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~   70 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEE   70 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCch
Confidence            567888999999999999999887643 236677777888887755   45569999999887654343

>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=95.90  E-value=0.046  Score=29.58  Aligned_cols=63  Identities=16%  Similarity=0.028  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      ..|+.+-.+|.+.|++++|...++...... +.+...|..+-.++...|++++|+..|++..+-
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            446667778889999999999999887642 348889999999999999999999999998764

>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=95.61  E-value=0.047  Score=27.58  Aligned_cols=62  Identities=8%  Similarity=-0.025  Sum_probs=54.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKI   70 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m   70 (94)
                      +...|..+-.++.+.|++++|...|++..+.. +-+...|..+-..|...|+.++|++.+++.
T Consensus        49 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          49 REEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            67888889999999999999999999887642 236889999999999999999999999875

>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=95.40  E-value=0.11  Score=30.53  Aligned_cols=49  Identities=10%  Similarity=0.024  Sum_probs=23.6

Q ss_pred             CCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           23 GNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        23 g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      |+.+.|..+|+..... .+-+...|...++-..+.|+.+.|..+|++-.+
T Consensus       183 ~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~  231 (308)
T d2onda1         183 KDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLT  231 (308)
T ss_dssp             CCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            4455555555544432 222344455555555555555555555555433

>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=95.27  E-value=0.049  Score=32.08  Aligned_cols=53  Identities=17%  Similarity=0.167  Sum_probs=42.6

Q ss_pred             HhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           20 GKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        20 ~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+.|++++|...+++-.+.. +-|...+..+...++..|++++|...+++..+.
T Consensus         7 L~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l   59 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL   59 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            45688999999888877542 237888889999999999999999988887664

>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=94.96  E-value=0.091  Score=27.07  Aligned_cols=68  Identities=12%  Similarity=0.163  Sum_probs=53.6

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-----CCch-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            7 TSISSYSSYIKFLGKNGNSLKALEIYNSITDES-----DKVN-VFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         7 p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-----~~p~-~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .+...|..+-.+|.+.|++++|...+++..+..     ..++ ..+|..+-..+...+++++|+..|++-....
T Consensus        36 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~~  109 (128)
T d1elra_          36 TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEH  109 (128)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             ccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence            367888999999999999999999999876421     1111 3577788888899999999999998876544

>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=94.51  E-value=0.19  Score=28.81  Aligned_cols=64  Identities=6%  Similarity=-0.114  Sum_probs=50.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHh----hCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSIT----DESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~----~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ....+..+-.++...|++++|...+++..    ..+..| ....+..+-..|...|++++|.+.+++-.
T Consensus       250 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         250 LQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             GHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34566677888999999999999998775    235555 45677888888999999999999998753

>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=94.43  E-value=0.14  Score=30.38  Aligned_cols=66  Identities=9%  Similarity=0.089  Sum_probs=44.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      +...|+.+-..+.+.|++++|...+++..+.. +-+...|+.+...+.+.|++++|++.+++..+.+
T Consensus       111 ~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~  176 (315)
T d2h6fa1         111 NYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED  176 (315)
T ss_dssp             CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC
T ss_pred             hhhHHHHHhHHHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC
Confidence            45566666666667777777777777766531 1256777777777777777777777777776654

>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=94.35  E-value=0.049  Score=30.15  Aligned_cols=39  Identities=13%  Similarity=0.080  Sum_probs=34.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHh-----hCCCCchHHH
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSIT-----DESDKVNVFI   46 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~-----~~~~~p~~~t   46 (94)
                      +...|..++.+|.+.|+.++|.+.|+.+.     +.|+.|...+
T Consensus       100 ~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2         100 REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            78899999999999999999999999984     3688887665

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=94.28  E-value=0.16  Score=26.90  Aligned_cols=63  Identities=11%  Similarity=-0.071  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-----CCCc-----hHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDE-----SDKV-----NVFICNLILSCLVRNGKFESSLKLFDKIK   71 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~~~p-----~~~t~~~li~~~~~~g~~~~a~~~~~~m~   71 (94)
                      ...|+.+-.+|.+.|++++|..-+++....     ...+     ....|+.+-.+|...|++++|+..|++..
T Consensus        55 a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          55 AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            567889999999999999999988877531     1111     23356777888999999999999998854

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.74  E-value=0.18  Score=25.56  Aligned_cols=71  Identities=17%  Similarity=0.253  Sum_probs=54.2

Q ss_pred             HHHHHhcC-CHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 034447           16 IKFLGKNG-NSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQ   87 (94)
Q Consensus        16 l~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~   87 (94)
                      ...+-+.. +..+..+-++.+....+-|+...-.+.+++|-+..++.-|.++|+-.+.+- .++...|.-+++
T Consensus        12 ~~~F~~~~iD~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yilq   83 (105)
T d1v54e_          12 VTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             HHHhcCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHHH
Confidence            33344444 677888888888888999999999999999999999999999999887542 223445655654

>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=93.61  E-value=0.3  Score=28.33  Aligned_cols=63  Identities=8%  Similarity=-0.011  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           10 SSYSSYIKFLGKNGNSLKALEIYNSITDE----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        10 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ..|...-..|-..+++++|.+.|.+..+.    +-++ -..+|.-+-.+|.+.|++++|...+++..+
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~  105 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQ  105 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhH
Confidence            45777888888899999999999887542    2222 356888899999999999999999987543

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.44  E-value=0.18  Score=24.56  Aligned_cols=61  Identities=10%  Similarity=0.110  Sum_probs=47.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhC-----CCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           14 SYIKFLGKNGNSLKALEIYNSITDE-----SDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        14 ~ll~~~~~~g~~~~a~~~~~~m~~~-----~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      -+=..+.+.|++++|...|++-.+.     .-.+ ...+++.+-.++.+.|++++|+..+++..+-.
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            4445678899999999998876532     1112 35688899999999999999999999987753

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.30  E-value=0.28  Score=26.31  Aligned_cols=67  Identities=21%  Similarity=0.157  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      ...++..|+...+.|.-++..++.+.+.+. -+|+....-.+-.+|.+-|...++-.++.+.-+.|+.
T Consensus        86 se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          86 NEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            356678899999999999999999997663 3466677778899999999999999999999999875

>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=92.67  E-value=0.45  Score=27.15  Aligned_cols=58  Identities=17%  Similarity=0.186  Sum_probs=43.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCC-Cc---hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447           15 YIKFLGKNGNSLKALEIYNSITDESD-KV---NVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus        15 ll~~~~~~g~~~~a~~~~~~m~~~~~-~p---~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      .-..+...|++++|.+++++-.+..= .+   ....+..+-..|...|++++|...+++..+
T Consensus        18 rA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   79 (366)
T d1hz4a_          18 RAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQ   79 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33456688999999999998765311 11   145677788889999999999999998754

>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=92.13  E-value=0.43  Score=25.60  Aligned_cols=71  Identities=14%  Similarity=0.120  Sum_probs=50.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhC-----CCC---------chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDE-----SDK---------VNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTY   82 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~-----~~~---------p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~   82 (94)
                      ..+.+.|++++|...|.+....     +..         .-..+|+-+..+|.+.|++++|+..+++..+.. +.+...|
T Consensus        21 ~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~   99 (170)
T d1p5qa1          21 TVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGL   99 (170)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhh
Confidence            4678899999999999877532     111         124667778888999999999999999987754 1255555


Q ss_pred             HHHHHH
Q 034447           83 NTVYQS   88 (94)
Q Consensus        83 ~~ll~~   88 (94)
                      ..+-.+
T Consensus       100 ~~~g~~  105 (170)
T d1p5qa1         100 SRRGEA  105 (170)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444444

>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=91.86  E-value=0.62  Score=26.92  Aligned_cols=83  Identities=8%  Similarity=0.075  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC-----chH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-cc---
Q 034447            9 ISSYSSYIKFLGKNGNSLKALEIYNSITDESDK-----VNV-FICNLILSCLVRNGKFESSLKLFDKIKQSGLT-PD---   78 (94)
Q Consensus         9 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-----p~~-~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~---   78 (94)
                      ..+|..+-..+.+.|++++|...|++.......     ... ..+..++-.+...|+++.|.+.+++..+.... ++   
T Consensus       158 ~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre  237 (290)
T d1qqea_         158 NKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRE  237 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------
T ss_pred             hhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHH
Confidence            345777888889999999999999887653221     111 22334455667789999999998887654311 22   


Q ss_pred             HHHHHHHHHHhhc
Q 034447           79 AVTYNTVYQSDHI   91 (94)
Q Consensus        79 ~~~~~~ll~~~~~   91 (94)
                      ......++.++..
T Consensus       238 ~~~l~~l~~a~~~  250 (290)
T d1qqea_         238 SNFLKSLIDAVNE  250 (290)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHh
Confidence            2234555555543

>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=91.44  E-value=0.72  Score=26.84  Aligned_cols=30  Identities=27%  Similarity=0.212  Sum_probs=27.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 034447            8 SISSYSSYIKFLGKNGNSLKALEIYNSITD   37 (94)
Q Consensus         8 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~   37 (94)
                      |...+..+...++..|++++|...++...+
T Consensus        29 d~~ar~~La~lL~~~G~~e~A~~~l~~a~~   58 (264)
T d1zbpa1          29 DASLRSSFIELLCIDGDFERADEQLMQSIK   58 (264)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            778899999999999999999999888764

>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=91.38  E-value=0.5  Score=24.84  Aligned_cols=64  Identities=14%  Similarity=0.093  Sum_probs=47.9

Q ss_pred             HHHHHHHHH--HHHhcCCHHHHHHHHHHHhhC--CCC---------chHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 034447            9 ISSYSSYIK--FLGKNGNSLKALEIYNSITDE--SDK---------VNVFICNLILSCLVRNGKFESSLKLFDKIKQ   72 (94)
Q Consensus         9 ~~~~~~ll~--~~~~~g~~~~a~~~~~~m~~~--~~~---------p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~   72 (94)
                      ...|..+-.  .+.+.|++++|...|++-.+.  ...         .....|+.+-.+|.+.|++++|..-+++..+
T Consensus         7 a~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~   83 (156)
T d2hr2a1           7 VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   83 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhh
Confidence            456676644  455679999999999988642  111         1357889999999999999999998888653

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.76  E-value=0.46  Score=24.85  Aligned_cols=50  Identities=10%  Similarity=0.129  Sum_probs=37.3

Q ss_pred             CCHHHHHHHHHHHhhCCCCchH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 034447           23 GNSLKALEIYNSITDESDKVNV-FICNLILSCLVRNGKFESSLKLFDKIKQS   73 (94)
Q Consensus        23 g~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~~~~g~~~~a~~~~~~m~~~   73 (94)
                      .+.+++..++++..+.+ +.+. -.+--|--+|.+.|++++|.+.++...+.
T Consensus        52 ~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i  102 (124)
T d2pqrb1          52 NDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  102 (124)
T ss_dssp             HHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            56788999999887543 2233 34445566788999999999999998764

>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=90.75  E-value=0.31  Score=24.69  Aligned_cols=46  Identities=9%  Similarity=0.091  Sum_probs=36.8

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 034447            6 KTSISSYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILS   52 (94)
Q Consensus         6 ~p~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~   52 (94)
                      .|+.....+.|++|-+..++..|.++|+..+... .++...|..++.
T Consensus        38 VPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yilq   83 (105)
T d1v54e_          38 VPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   83 (105)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHHH
Confidence            6889999999999999999999999999887432 234456666654

>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=89.64  E-value=0.75  Score=24.10  Aligned_cols=71  Identities=10%  Similarity=0.086  Sum_probs=51.9

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCC---------------CchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHH
Q 034447           17 KFLGKNGNSLKALEIYNSITDESD---------------KVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVT   81 (94)
Q Consensus        17 ~~~~~~g~~~~a~~~~~~m~~~~~---------------~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~   81 (94)
                      ..+.+.|++++|...|.+....--               .....+|+-+..+|.+.|++++|+..+++..+.+ +.+..+
T Consensus        25 ~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka  103 (153)
T d2fbna1          25 NEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKA  103 (153)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhh
Confidence            466788999999999987653210               0124577788889999999999999999987653 235666


Q ss_pred             HHHHHHH
Q 034447           82 YNTVYQS   88 (94)
Q Consensus        82 ~~~ll~~   88 (94)
                      |-.+-.+
T Consensus       104 ~~~~g~~  110 (153)
T d2fbna1         104 LYKLGVA  110 (153)
T ss_dssp             HHHHHHH
T ss_pred             hHHhHHH
Confidence            6655555

>d1ug3a1 a.118.1.14 (A:1235-1427) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Eukaryotic initiation factor eIF4G
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.59  E-value=0.98  Score=25.10  Aligned_cols=69  Identities=16%  Similarity=0.075  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHcCCCccHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRN-GKFESSLKLFDKIKQSGLTPDAV   80 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~~~   80 (94)
                      ....++.=|-..++.++|...++++..-.+. ...+...+..+.-+. ..-+.+.+++..+.++|+.+...
T Consensus        12 k~~~il~Ey~~~~D~~Ea~~~l~el~~p~~~-~~~V~~~i~~~le~~~~~re~~~~Ll~~L~~~~~is~~~   81 (193)
T d1ug3a1          12 KSKAIIEEYLHLNDMKEAVQCVQELASPSLL-FIFVRHGVESTLERSAIAREHMGQLLHQLLCAGHLSTAQ   81 (193)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHTTCCGGGH-HHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHTTSSCHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCchhH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            4567888888999999999999998753333 333344444433221 13345667788888887765443

>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=87.44  E-value=1.2  Score=23.56  Aligned_cols=76  Identities=9%  Similarity=0.027  Sum_probs=53.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhh--------------CCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447           12 YSSYIKFLGKNGNSLKALEIYNSITD--------------ESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus        12 ~~~ll~~~~~~g~~~~a~~~~~~m~~--------------~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      +...-..+.+.|++++|...|.+...              ..+.| +...|..+-.++.+.|++++|+..+++..+.. +
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p  108 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-P  108 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-T
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-h
Confidence            44555667788999999998876632              11123 55677778888999999999999999987653 2


Q ss_pred             ccHHHHHHHHHH
Q 034447           77 PDAVTYNTVYQS   88 (94)
Q Consensus        77 p~~~~~~~ll~~   88 (94)
                      .+...|..+-.+
T Consensus       109 ~~~~a~~~~g~~  120 (169)
T d1ihga1         109 SNTKALYRRAQG  120 (169)
T ss_dssp             TCHHHHHHHHHH
T ss_pred             hhhhHHHhHHHH
Confidence            345555444444

>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=87.08  E-value=1.8  Score=25.37  Aligned_cols=60  Identities=12%  Similarity=0.179  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcC-CHHHHHHHHHHHHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNG-KFESSLKLFDKIKQ   72 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g-~~~~a~~~~~~m~~   72 (94)
                      .|+-+-..+.+.+.+++|..++++..+.  .| +...|+..-..+...| ++++|+..+++..+
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~  106 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE  106 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            3333434444445555555555555442  23 3334444444444433 35555555555433

>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=86.44  E-value=1.3  Score=23.02  Aligned_cols=69  Identities=13%  Similarity=0.078  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHH--HHHHHHHHHHHcCCCccHH
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFE--SSLKLFDKIKQSGLTPDAV   80 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~--~a~~~~~~m~~~g~~p~~~   80 (94)
                      ....++.=|-..|+.++|...++++...... ...++.++..+.-+.+.-.  .+.+++..+..+|+.+...
T Consensus         9 k~~~ll~EY~~~~D~~Ea~~~l~eL~~p~~~-~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~~~~~is~~~   79 (129)
T d2nsza1           9 EIDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQ   79 (129)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHTCGGGH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCchhh-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            4568899999999999999999999753332 4566666666666655543  3577999999988765444

>d1khda1 a.46.2.1 (A:12-80) Anthranilate phosphoribosyltransferase (TrpD) {Pectobacterium carotovorum [TaxId: 554]}

class: All alpha proteins
fold: Methionine synthase domain-like
superfamily: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
family: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
domain: Anthranilate phosphoribosyltransferase (TrpD)
species: Pectobacterium carotovorum [TaxId: 554]

Probab=85.11  E-value=1  Score=20.65  Aligned_cols=65  Identities=9%  Similarity=0.076  Sum_probs=48.0

Q ss_pred             HHHHHHHHHHhcCC--HHHHHHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447           11 SYSSYIKFLGKNGN--SLKALEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus        11 ~~~~ll~~~~~~g~--~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      ||..+|.-.....+  .+++..+++.+....+ +|...=.-|+....+.-..++...+.+-|.+.+.+
T Consensus         1 t~~~il~kl~~g~~Ls~ee~~~~~~~i~~g~~-~d~qiaafL~al~~kg~t~dEi~g~~~am~~~~~~   67 (69)
T d1khda1           1 THQPILEKLFKSQSMTQEESHQLFAAIVRGEL-EDSQLAAALISMKMRGERPEEIAGAASALLADAQP   67 (69)
T ss_dssp             CCHHHHHHHHTTCCCCHHHHHHHHHHHTTTCS-CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTSCC
T ss_pred             CHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCC
Confidence            56777877776654  6888899999886544 66666666666666667888888888999887653

>d1fkma2 a.69.2.1 (A:443-630) Ypt/Rab-GAP domain of gyp1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Left-handed superhelix
superfamily: Ypt/Rab-GAP domain of gyp1p
family: Ypt/Rab-GAP domain of gyp1p
domain: Ypt/Rab-GAP domain of gyp1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.93  E-value=1.6  Score=23.95  Aligned_cols=46  Identities=15%  Similarity=0.302  Sum_probs=41.0

Q ss_pred             HHHHHHHhhCCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 034447           29 LEIYNSITDESDKVNVFICNLILSCLVRNGKFESSLKLFDKIKQSG   74 (94)
Q Consensus        29 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g   74 (94)
                      .++++.+.+.|+.|..+++.-++-.+.+.=..+.+.++++.+..+|
T Consensus        21 p~L~~hl~~~~i~~~~~~~rW~~~lf~~~~~~~~~~rlWD~~~~~~   66 (188)
T d1fkma2          21 ADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSET   66 (188)
T ss_dssp             HHHHHHHHHTTCCTHHHHHHHHHTTTGGGSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCeeeeeHHHHHHHhhccCCHHHHHHHHHHHHhCC
Confidence            4678888899999999999999999999999999999999987654

>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=82.21  E-value=2.2  Score=22.43  Aligned_cols=77  Identities=10%  Similarity=0.057  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhh---CCCC-----------chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITD---ESDK-----------VNVFICNLILSCLVRNGKFESSLKLFDKIKQSGLT   76 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~---~~~~-----------p~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   76 (94)
                      .+.-.=..+.+.|++++|...|++-..   ....           .....|+-+-.+|.+.|++++|+..+++..+.. +
T Consensus        17 ~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p   95 (168)
T d1kt1a1          17 IVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-S   95 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-c
Confidence            344445667889999999999977542   1111           123445667778899999999999999987643 2


Q ss_pred             ccHHHHHHHHHH
Q 034447           77 PDAVTYNTVYQS   88 (94)
Q Consensus        77 p~~~~~~~ll~~   88 (94)
                      .+...|-.+-.+
T Consensus        96 ~~~~a~~~~~~~  107 (168)
T d1kt1a1          96 ANEKGLYRRGEA  107 (168)
T ss_dssp             TCHHHHHHHHHH
T ss_pred             chHHHHHHHHHH
Confidence            345555444444

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.31  E-value=4.4  Score=25.26  Aligned_cols=77  Identities=8%  Similarity=-0.025  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHh
Q 034447           11 SYSSYIKFLGKNGNSLKALEIYNSITDESDKV-NVFICNLILSCLVRNGKFESSLKLFDKIKQSGLTPDAVTYNTVYQSD   89 (94)
Q Consensus        11 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~   89 (94)
                      .+..+=+.+...|++++|...|++-.+.  .| +...|+-+-..+...|+..+|...|.+-.... +|-..++..|...+
T Consensus       154 ~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~  230 (497)
T d1ya0a1         154 CLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKAL  230 (497)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH
Confidence            4555666777889999999999887754  35 66899999999999999999999998877654 35667777776654


Q ss_pred             h
Q 034447           90 H   90 (94)
Q Consensus        90 ~   90 (94)
                      .
T Consensus       231 ~  231 (497)
T d1ya0a1         231 S  231 (497)
T ss_dssp             H
T ss_pred             H
Confidence            3