Citrus Sinensis ID: 042276

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-
Protein Sequence
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHccccccEEEHHHHHHHHcccccHHHHHHHHHHHHHccccccEEEEEEEEccccccccc
Coil and Loop (DISEMBL)
MDEANGLAELMIqrgvnpdtstcnalmdgfcLADRFDRARELLVSMgskgckqdafshsilinggsarirk
Flexible Loop (DISEMBL)
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMgskgckqdafshsilinggsarirk
Low Complexity Region (SEG)
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK
Disordered region (IsUnstruct)
**********MIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI*********
Disordered Region (DISOPRED)
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI**
Disordered Region (DISEMBL)
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK
Disordered Region (DISPRO)
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK
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	71	2.2.26 [Sep-21-2011]
Q9CAN5	614	Pentatricopeptide repeat-	yes	no	0.873	0.100	0.435	7e-10
Q9ASZ8	621	Pentatricopeptide repeat-	no	no	0.873	0.099	0.483	1e-09
Q9LPX2	644	Pentatricopeptide repeat-	no	no	0.873	0.096	0.467	1e-09
Q9CAM8	629	Pentatricopeptide repeat-	no	no	0.873	0.098	0.451	1e-09
Q9SXD8	634	Pentatricopeptide repeat-	no	no	0.873	0.097	0.419	4e-09
Q6NQ83	619	Pentatricopeptide repeat-	no	no	0.816	0.093	0.475	7e-09
Q76C99	791	Protein Rf1, mitochondria	N/A	no	0.859	0.077	0.451	9e-09
Q9FMD3	504	Pentatricopeptide repeat-	no	no	0.901	0.126	0.437	1e-08
Q0WKV3	637	Pentatricopeptide repeat-	no	no	0.873	0.097	0.451	1e-08
Q9C8T7	559	Pentatricopeptide repeat-	no	no	0.873	0.110	0.419	1e-08

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

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 41/62 (66%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + MIQR ++P+  T N+L++GFC+ DR D A+++   M SK C  D  +++ LI
Sbjct: 328 EAEKLFDEMIQRSIDPNIVTYNSLINGFCMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLI 387

Query: 63  NG 64
           NG
Sbjct: 388 NG 389

Arabidopsis thaliana (taxid: 3702)

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

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + MIQRG++PDT T  +L+DGFC  ++ D+A  +L  M SKGC  +  + +ILI
Sbjct: 335 EAEELHKEMIQRGISPDTVTYTSLIDGFCKENQLDKANHMLDLMVSKGCGPNIRTFNILI 394

Query: 63  NG 64
           NG
Sbjct: 395 NG 396

Arabidopsis thaliana (taxid: 3702)

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

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 43/62 (69%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA+ L + M+QRG+ P+T T N+L+DGFC  +R + A +++  M SKGC  D  + +ILI
Sbjct: 351 EADQLLKEMMQRGIAPNTITYNSLIDGFCKENRLEEAIQMVDLMISKGCDPDIMTFNILI 410

Query: 63  NG 64
           NG
Sbjct: 411 NG 412

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAM8|PP100_ARATH Pentatricopeptide repeat-containing protein At1g63150 OS=Arabidopsis thaliana GN=At1g63150 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 41/62 (66%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L E MIQR ++PDT T N L++GFC+ +R D A+++   M SK C  +  +++ LI
Sbjct: 346 EAEKLHEEMIQRSIDPDTITYNLLINGFCMHNRLDEAKQMFKFMVSKDCLPNIQTYNTLI 405

Query: 63  NG 64
           NG
Sbjct: 406 NG 407

Arabidopsis thaliana (taxid: 3702)

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

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 41/62 (66%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + MI+R ++PD  T N+L++GFC+ DR D+A+++   M SK C  D  +++ LI
Sbjct: 348 EAEKLYDDMIKRSIDPDIFTYNSLVNGFCMHDRLDKAKQMFEFMVSKDCFPDVVTYNTLI 407

Query: 63  NG 64
            G
Sbjct: 408 KG 409

Arabidopsis thaliana (taxid: 3702)

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

 Score = 59.3 bits (142), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 38/61 (62%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L   MI RG+ PDT T N+L+DGFC  +    A ++   M SKGC+ D  ++SILI
Sbjct: 333 EAKELYNEMITRGIAPDTITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILI 392

Query: 63  N 63
           N
Sbjct: 393 N 393

Arabidopsis thaliana (taxid: 3702)

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

 Score = 58.9 bits (141), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           E+  L ELM++ GV P+  T N L++G+CLA + D A +LL  M S G K +  ++S LI
Sbjct: 494 ESEKLFELMVRIGVKPNVITYNTLINGYCLAGKMDEAMKLLSGMVSVGLKPNTVTYSTLI 553

Query: 63  NG 64
           NG
Sbjct: 554 NG 555

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

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q9FMD3|PP389_ARATH Pentatricopeptide repeat-containing protein At5g16640, mitochondrial OS=Arabidopsis thaliana GN=At5g16640 PE=2 SV=1

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 38/64 (59%)

Query: 1   MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI 60
           + EA    E MI+R ++PD  T + L+ G C+  R D A E+   M SKGC  D  ++SI
Sbjct: 272 VSEAEEFYEEMIRRSLDPDIVTYSLLIYGLCMYSRLDEAEEMFGFMVSKGCFPDVVTYSI 331

Query: 61  LING 64
           LING
Sbjct: 332 LING 335

Arabidopsis thaliana (taxid: 3702)

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

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + MI RG+ PDT T  +L+DGFC  +  D+A +++  M SKGC  +  + +ILI
Sbjct: 351 EAEELHKEMIHRGIAPDTITYTSLIDGFCKENHLDKANQMVDLMVSKGCDPNIRTFNILI 410

Query: 63  NG 64
           NG
Sbjct: 411 NG 412

Arabidopsis thaliana (taxid: 3702)

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

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 41/62 (66%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + MI+R ++PD  T N+L++GFC+ DR D+A+++   M SK C  D  +++ LI
Sbjct: 273 EAEKLHDDMIKRSIDPDIFTYNSLINGFCMHDRLDKAKQMFEFMVSKDCFPDLDTYNTLI 332

Query: 63  NG 64
            G
Sbjct: 333 KG 334

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	71
359479583	627	PREDICTED: pentatricopeptide repeat-cont	0.873	0.098	0.625	2e-14
449462477	597	PREDICTED: pentatricopeptide repeat-cont	0.845	0.100	0.532	2e-11
449520323	605	PREDICTED: pentatricopeptide repeat-cont	0.845	0.099	0.532	2e-11
449520325	605	PREDICTED: pentatricopeptide repeat-cont	0.957	0.112	0.470	3e-10
449462479	580	PREDICTED: pentatricopeptide repeat-cont	0.957	0.117	0.470	3e-10
449529622	618	PREDICTED: pentatricopeptide repeat-cont	0.845	0.097	0.516	3e-10
255547572	594	pentatricopeptide repeat-containing prot	0.901	0.107	0.453	2e-09
224133106	487	predicted protein [Populus trichocarpa]	0.901	0.131	0.421	5e-09
221554580	688	PPR protein [Raphanus sativus]	0.943	0.097	0.434	1e-08
238908350	683	non restoring pentatricopeptide repeat [	0.943	0.098	0.434	1e-08

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

 Score = 82.8 bits (203), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/64 (62%), Positives = 49/64 (76%)

Query: 1   MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI 60
           M+EAN L +LMIQRG +PDT T N L+DGFCL  R D AR+L VSM SKG + DA S+++
Sbjct: 324 MEEANHLLKLMIQRGESPDTFTYNTLIDGFCLEGRIDDARDLFVSMESKGIETDAVSYNV 383

Query: 61  LING 64
           LING
Sbjct: 384 LING 387

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/62 (53%), Positives = 44/62 (70%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L E+MIQRG+ P+  T N+L++GFCL    + AREL VSM SKGC+ D   +++LI
Sbjct: 322 EAKDLLEVMIQRGIVPNLLTYNSLIEGFCLVGDLNSARELFVSMPSKGCEPDVICYTVLI 381

Query: 63  NG 64
           NG
Sbjct: 382 NG 383

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/62 (53%), Positives = 44/62 (70%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L E+MIQRG+ P+  T N+L++GFCL    + AREL VSM SKGC+ D   +++LI
Sbjct: 330 EAKDLLEVMIQRGIVPNLLTYNSLIEGFCLVGDLNSARELFVSMPSKGCEPDVICYTVLI 389

Query: 63  NG 64
           NG
Sbjct: 390 NG 391

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/68 (47%), Positives = 46/68 (67%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L  +MI+ G+ PD  T N+L++GFC+    + AREL VSM SKGC+ D  S+++LI
Sbjct: 303 EAKKLLGVMIESGIVPDLVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDVISYNVLI 362

Query: 63  NGGSARIR 70
           NG S  ++
Sbjct: 363 NGYSKTLK 370

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/68 (47%), Positives = 46/68 (67%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L  +MI+ G+ PD  T N+L++GFC+    + AREL VSM SKGC+ D  S+++LI
Sbjct: 278 EAKKLLGVMIESGIVPDLVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDVISYNVLI 337

Query: 63  NGGSARIR 70
           NG S  ++
Sbjct: 338 NGYSKTLK 345

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/62 (51%), Positives = 43/62 (69%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L E+MIQRG+ P+  T N+L+DGFC+    + AREL +SM SKG + D  S++ LI
Sbjct: 325 EAKKLLEVMIQRGIVPNLITYNSLIDGFCMVGDLNSARELFLSMPSKGLEPDEISYTTLI 384

Query: 63  NG 64
           NG
Sbjct: 385 NG 386

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547572|ref|XP_002514843.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223545894|gb|EEF47397.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score = 66.2 bits (160), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/64 (45%), Positives = 42/64 (65%)

Query: 1   MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI 60
           + EA  +  LMI+RG+ P+  T N+LMDG+CL  + D AR++   M +KGC  D  S++I
Sbjct: 400 VSEAQSIINLMIERGLRPNVVTYNSLMDGYCLHSQMDEARKVFDIMVNKGCAPDVLSYNI 459

Query: 61  LING 64
           LI G
Sbjct: 460 LIKG 463

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133106|ref|XP_002327962.1| predicted protein [Populus trichocarpa] gi|222837371|gb|EEE75750.1| predicted protein [Populus trichocarpa]

 Score = 65.1 bits (157), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 46/64 (71%)

Query: 1   MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI 60
           + EA G+ ++MI++GV P+ +T N+LM+G+CL ++   AR +  +M +KGC  +  S++I
Sbjct: 310 LSEAQGIIKIMIEKGVEPNYATYNSLMNGYCLQNKVFEARMVFDAMITKGCMPNVVSYNI 369

Query: 61  LING 64
           LING
Sbjct: 370 LING 373

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|221554580|gb|ACM24117.1| PPR protein [Raphanus sativus]

 Score = 63.5 bits (153), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 44/69 (63%), Gaps = 2/69 (2%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + M+ RG+ P+T T N+++DGFC  DR D A ++   M +KGC  D F+ + LI
Sbjct: 343 EAAELYDEMLPRGIIPNTITYNSMIDGFCKQDRLDAAEDMFYLMATKGCSPDVFTFTTLI 402

Query: 63  NG--GSARI 69
           +G  G+ RI
Sbjct: 403 DGYCGAKRI 411

Source: Raphanus sativus

Species: Raphanus sativus

Genus: Raphanus

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|238908350|emb|CAZ40335.1| non restoring pentatricopeptide repeat [Raphanus sativus]

 Score = 63.5 bits (153), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 44/69 (63%), Gaps = 2/69 (2%)

Query: 3   EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
           EA  L + M+ RG+ P+T T N+++DGFC  DR D A ++   M +KGC  D F+ + LI
Sbjct: 341 EAAELYDEMLPRGIIPNTITYNSMIDGFCKQDRLDAAEDMFYLMATKGCSPDVFTFTTLI 400

Query: 63  NG--GSARI 69
           +G  G+ RI
Sbjct: 401 DGYCGAKRI 409

Source: Raphanus sativus

Species: Raphanus sativus

Genus: Raphanus

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	71
TAIR|locus:2026654	257	AT1G63630 [Arabidopsis thalian	0.901	0.249	0.437	2.2e-09
TAIR|locus:2195047	621	AT1G12620 [Arabidopsis thalian	0.873	0.099	0.483	4e-09
TAIR|locus:2038451	323	AT1G63230 [Arabidopsis thalian	0.901	0.198	0.437	4.3e-09
TAIR|locus:1009023134	644	AT1G12775 [Arabidopsis thalian	0.873	0.096	0.467	5.5e-09
TAIR|locus:2015228	614	AT1G63080 [Arabidopsis thalian	0.873	0.100	0.435	1.1e-08
TAIR|locus:2015213	629	AT1G63150 [Arabidopsis thalian	0.873	0.098	0.451	1.8e-08
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.859	0.098	0.475	3.7e-08
TAIR|locus:2034760	637	AT1G12300 [Arabidopsis thalian	0.873	0.097	0.451	3.9e-08
TAIR|locus:2026207	548	AT1G62680 [Arabidopsis thalian	0.873	0.113	0.435	4e-08
TAIR|locus:2203916	634	AT1G62590 [Arabidopsis thalian	0.873	0.097	0.419	4.9e-08

TAIR|locus:2026654 AT1G63630 [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 28/64 (43%), Positives = 40/64 (62%)

Query:     1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI 60
             + EA  + + M++  + P T T N+++DGFC  DR D A+ +L SM SKGC  D  + S 
Sbjct:    96 VSEAEEIYKEMLRWSIFPTTITYNSMIDGFCKQDRVDDAKRMLDSMASKGCSPDVVTFST 155

Query:    61 LING 64
             LING
Sbjct:   156 LING 159

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 145 (56.1 bits), Expect = 4.0e-09, P = 4.0e-09
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L + MIQRG++PDT T  +L+DGFC  ++ D+A  +L  M SKGC  +  + +ILI
Sbjct:   335 EAEELHKEMIQRGISPDTVTYTSLIDGFCKENQLDKANHMLDLMVSKGCGPNIRTFNILI 394

Query:    63 NG 64
             NG
Sbjct:   395 NG 396

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2038451 AT1G63230 [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 4.3e-09, P = 4.3e-09
 Identities = 28/64 (43%), Positives = 40/64 (62%)

Query:     1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI 60
             + EA  +   M++RG+ P T T N+++DGFC  DR + A+ +L SM SK C  D  + S 
Sbjct:   162 VSEAEEIYGDMLRRGIFPTTITYNSMIDGFCKQDRLNDAKRMLDSMASKSCSPDVVTFST 221

Query:    61 LING 64
             LING
Sbjct:   222 LING 225

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 144 (55.7 bits), Expect = 5.5e-09, P = 5.5e-09
 Identities = 29/62 (46%), Positives = 43/62 (69%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA+ L + M+QRG+ P+T T N+L+DGFC  +R + A +++  M SKGC  D  + +ILI
Sbjct:   351 EADQLLKEMMQRGIAPNTITYNSLIDGFCKENRLEEAIQMVDLMISKGCDPDIMTFNILI 410

Query:    63 NG 64
             NG
Sbjct:   411 NG 412

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 141 (54.7 bits), Expect = 1.1e-08, P = 1.1e-08
 Identities = 27/62 (43%), Positives = 41/62 (66%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L + MIQR ++P+  T N+L++GFC+ DR D A+++   M SK C  D  +++ LI
Sbjct:   328 EAEKLFDEMIQRSIDPNIVTYNSLINGFCMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLI 387

Query:    63 NG 64
             NG
Sbjct:   388 NG 389

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 139 (54.0 bits), Expect = 1.8e-08, P = 1.8e-08
 Identities = 28/62 (45%), Positives = 41/62 (66%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L E MIQR ++PDT T N L++GFC+ +R D A+++   M SK C  +  +++ LI
Sbjct:   346 EAEKLHEEMIQRSIDPDTITYNLLINGFCMHNRLDEAKQMFKFMVSKDCLPNIQTYNTLI 405

Query:    63 NG 64
             NG
Sbjct:   406 NG 407

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 136 (52.9 bits), Expect = 3.7e-08, P = 3.7e-08
 Identities = 29/61 (47%), Positives = 38/61 (62%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L   MI RG+ PDT T N+L+DGFC  +    A ++   M SKGC+ D  ++SILI
Sbjct:   333 EAKELYNEMITRGIAPDTITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILI 392

Query:    63 N 63
             N
Sbjct:   393 N 393

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 136 (52.9 bits), Expect = 3.9e-08, P = 3.9e-08
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L + MI RG+ PDT T  +L+DGFC  +  D+A +++  M SKGC  +  + +ILI
Sbjct:   351 EAEELHKEMIHRGIAPDTITYTSLIDGFCKENHLDKANQMVDLMVSKGCDPNIRTFNILI 410

Query:    63 NG 64
             NG
Sbjct:   411 NG 412

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2026207 AT1G62680 [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 4.0e-08, P = 4.0e-08
 Identities = 27/62 (43%), Positives = 39/62 (62%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L E M++  ++PD  T ++L++G CL DR D A ++   M SKGC  D  S++ LI
Sbjct:   278 EAKELFEEMVRMSIDPDIVTYSSLINGLCLHDRIDEANQMFDLMVSKGCLADVVSYNTLI 337

Query:    63 NG 64
             NG
Sbjct:   338 NG 339

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 135 (52.6 bits), Expect = 4.9e-08, P = 4.9e-08
 Identities = 26/62 (41%), Positives = 41/62 (66%)

Query:     3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
             EA  L + MI+R ++PD  T N+L++GFC+ DR D+A+++   M SK C  D  +++ LI
Sbjct:   348 EAEKLYDDMIKRSIDPDIFTYNSLVNGFCMHDRLDKAKQMFEFMVSKDCFPDVVTYNTLI 407

Query:    63 NG 64
              G
Sbjct:   408 KG 409

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	71
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-14
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-07
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	8e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-05
pfam01535	31	pfam01535, PPR, PPR repeat	3e-04

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

 Score = 58.6 bits (143), Expect = 9e-14
 Identities = 18/47 (38%), Positives = 29/47 (61%)

Query: 18 PDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING 64
          PD  T N L+DG+C   + + A +L   M  +G K + +++SILI+G
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDG 47

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

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

 Score = 42.0 bits (100), Expect = 2e-07
 Identities = 17/33 (51%), Positives = 20/33 (60%)

Query: 14 RGVNPDTSTCNALMDGFCLADRFDRARELLVSM 46
          +G+ PD  T N L+DG C A R D A ELL  M
Sbjct: 1  KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 41.0 bits (96), Expect = 8e-06
 Identities = 15/48 (31%), Positives = 25/48 (52%)

Query: 15  GVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI 62
            + P  ST NAL+   C  ++  +A E+L  M   G   +  ++SIL+
Sbjct: 714 KLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL 761

Length = 1060

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

 Score = 37.8 bits (89), Expect = 1e-05
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 1  MDEANGLAELMIQRGVNPDTSTCNALMDGFC 31
          ++EA  L   M +RG+ P+  T + L+DG C
Sbjct: 19 VEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 37.1 bits (87), Expect = 2e-05
 Identities = 14/34 (41%), Positives = 18/34 (52%)

Query: 22 TCNALMDGFCLADRFDRARELLVSMGSKGCKQDA 55
          T N L+DG C A R + A EL   M  +G + D 
Sbjct: 2  TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 33.6 bits (78), Expect = 3e-04
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 21 STCNALMDGFCLADRFDRARELLVSMGSKGC 51
           T N+L+ G+C A + + A EL   M  KG 
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	71
PF13041	50	PPR_2: PPR repeat family	99.9
PLN03218	1060	maturation of RBCL 1; Provisional	99.75
PLN03218	1060	maturation of RBCL 1; Provisional	99.75
PLN03077	857	Protein ECB2; Provisional	99.69
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.69
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.67
PF12854	34	PPR_1: PPR repeat	99.64
PLN03077	857	Protein ECB2; Provisional	99.64
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.41
PF13812	34	PPR_3: Pentatricopeptide repeat domain	99.32
PF13041	50	PPR_2: PPR repeat family	99.28
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	99.22
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.13
PF12854	34	PPR_1: PPR repeat	98.97
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.87
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.71
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.34
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.22
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.19
KOG3941	406	consensus Intermediate in Toll signal transduction	98.08
PRK11788	389	tetratricopeptide repeat protein; Provisional	97.91
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.81
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.76
PRK11788	389	tetratricopeptide repeat protein; Provisional	97.74
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.65
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.25
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	97.14
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	97.03
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	97.03
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.03
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.8
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	96.72
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	96.67
PF13812	34	PPR_3: Pentatricopeptide repeat domain	96.67
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.55
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.5
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	96.41
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.21
PRK15359	144	type III secretion system chaperone protein SscB;	96.16
COG3629	280	DnrI DNA-binding transcriptional activator of the	96.06
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	95.85
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.83
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	95.81
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.75
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.64
PF13428	44	TPR_14: Tetratricopeptide repeat	95.6
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.38
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	95.31
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	95.2
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	95.16
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	95.13
PF13762	145	MNE1: Mitochondrial splicing apparatus component	95.11
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	95.07
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	94.8
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	94.72
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	94.57
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	94.55
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	94.54
PF03704	146	BTAD: Bacterial transcriptional activator domain;	94.43
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	94.41
PRK12370	553	invasion protein regulator; Provisional	94.37
KOG2003	840	consensus TPR repeat-containing protein [General f	94.34
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	94.27
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	94.19
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	94.15
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.04
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	93.96
PRK14574	822	hmsH outer membrane protein; Provisional	93.83
KOG1915	677	consensus Cell cycle control protein (crooked neck	93.79
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	93.77
KOG4570	418	consensus Uncharacterized conserved protein [Funct	93.76
PRK10370	198	formate-dependent nitrite reductase complex subuni	93.67
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	93.65
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.43
PRK10564	303	maltose regulon periplasmic protein; Provisional	93.41
PRK12370	553	invasion protein regulator; Provisional	93.38
PF13371	73	TPR_9: Tetratricopeptide repeat	93.35
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	93.26
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	93.18
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	92.98
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	92.77
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	92.71
PF13929	292	mRNA_stabil: mRNA stabilisation	92.7
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	92.52
PRK15359	144	type III secretion system chaperone protein SscB;	92.49
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	92.45
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.32
KOG4340	459	consensus Uncharacterized conserved protein [Funct	92.32
PF13371	73	TPR_9: Tetratricopeptide repeat	92.18
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	92.13
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	92.09
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	91.99
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	91.86
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	91.84
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	91.78
PRK11189	296	lipoprotein NlpI; Provisional	91.7
COG4783	484	Putative Zn-dependent protease, contains TPR repea	91.62
PF13431	34	TPR_17: Tetratricopeptide repeat	91.6
PRK11639	169	zinc uptake transcriptional repressor; Provisional	91.48
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	91.33
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	91.23
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	91.22
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.15
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	91.09
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	91.09
PRK14574	822	hmsH outer membrane protein; Provisional	90.96
KOG3941	406	consensus Intermediate in Toll signal transduction	90.83
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	90.64
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	90.62
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	90.46
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	90.41
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	90.26
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	90.19
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	90.16
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	90.15
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	89.85
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	89.84
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	89.81
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	89.66
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	89.62
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	89.46
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	89.46
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	89.21
KOG1129	478	consensus TPR repeat-containing protein [General f	89.13
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	89.1
smart00299	140	CLH Clathrin heavy chain repeat homology.	89.09
KOG2047	835	consensus mRNA splicing factor [RNA processing and	89.06
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	88.97
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	88.81
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	88.77
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	88.76
PF10579	80	Rapsyn_N: Rapsyn N-terminal myristoylation and lin	88.72
COG4783	484	Putative Zn-dependent protease, contains TPR repea	88.21
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	88.08
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	88.01
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	87.53
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	87.49
PF02607	79	B12-binding_2: B12 binding domain; InterPro: IPR00	87.46
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	87.34
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	87.33
PF07443	55	HARP: HepA-related protein (HARP); InterPro: IPR01	87.27
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	87.06
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	87.0
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	86.27
TIGR02552	135	LcrH_SycD type III secretion low calcium response	86.15
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	85.92
PRK09462	148	fur ferric uptake regulator; Provisional	85.86
cd08326	84	CARD_CASP9 Caspase activation and recruitment doma	85.69
COG5210	496	GTPase-activating protein [General function predic	85.37
smart00777	125	Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region	85.34
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	85.22
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	85.14
PF09454	65	Vps23_core: Vps23 core domain; InterPro: IPR017916	84.8
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	84.53
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	84.48
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	84.37
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	84.31
KOG4567	370	consensus GTPase-activating protein [General funct	84.06
KOG2003	840	consensus TPR repeat-containing protein [General f	83.95
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	83.73
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	83.63
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	83.36
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	83.08
COG2405	157	Predicted nucleic acid-binding protein, contains P	82.33
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	82.2
COG3629	280	DnrI DNA-binding transcriptional activator of the	82.2
cd08318	86	Death_NMPP84 Death domain of Nuclear Matrix Protei	82.0
PRK10803	263	tol-pal system protein YbgF; Provisional	81.82
COG4003	98	Uncharacterized protein conserved in archaea [Func	81.27
PF09868	128	DUF2095: Uncharacterized protein conserved in arch	80.91
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	80.71
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	80.53
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	80.06

>PF13041 PPR_2: PPR repeat family

Probab=99.90  E-value=1.2e-23  Score=93.99  Aligned_cols=50  Identities=40%  Similarity=0.735  Sum_probs=49.1

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276           18 PDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus        18 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      ||+.+||++|++|++.|++++|+++|++|.++|+.||..||+++|++|||
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            89999999999999999999999999999999999999999999999986

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.75  E-value=7.6e-18  Score=109.50  Aligned_cols=67  Identities=25%  Similarity=0.249  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +|.++|++|.+.|+.||..+||++|++|++.|++++|+++|++|.+.|+.||..||++||.+|++.|
T Consensus       490 ~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G  556 (1060)
T PLN03218        490 AMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSG  556 (1060)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCC
Confidence            4455555555555555555555555555555555555555555555555555555555555555544

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.75  E-value=1e-17  Score=108.95  Aligned_cols=70  Identities=19%  Similarity=0.292  Sum_probs=67.6

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +++|.++|++|.+.|+.||..+||++|.+|++.|++++|.++|++|.+.|+.||..||+++|++|++.|+
T Consensus       453 ~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~  522 (1060)
T PLN03218        453 IDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQ  522 (1060)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcC
Confidence            3679999999999999999999999999999999999999999999999999999999999999999886

>PLN03077 Protein ECB2; Provisional

Probab=99.69  E-value=1.3e-16  Score=102.04  Aligned_cols=69  Identities=19%  Similarity=0.148  Sum_probs=65.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHh-hCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMG-SKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|+.|. +.|+.||..+|++++++|+++|+
T Consensus       571 ~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~  640 (857)
T PLN03077        571 SMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGK  640 (857)
T ss_pred             HHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCC
Confidence            6799999999999999999999999999999999999999999998 67999999999999999999986

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

Probab=99.69  E-value=1.7e-16  Score=99.83  Aligned_cols=69  Identities=22%  Similarity=0.202  Sum_probs=54.8

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-CCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGS-KGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|+.|.+ .|+.|+..+|++++++|+++|+
T Consensus       408 ~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~  477 (697)
T PLN03081        408 TKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGL  477 (697)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCC
Confidence            56778888888888888888888888888888888888888888865 5788888888888888887775

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

Probab=99.67  E-value=2.9e-16  Score=98.79  Aligned_cols=69  Identities=22%  Similarity=0.175  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|++|.+.|+.||..||+++|.+|++.|++++|.+++..|.+.|+.||..+|++||++|++.|+
T Consensus       307 ~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~  375 (697)
T PLN03081        307 EEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGR  375 (697)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCC
Confidence            456666666666666666666666666666666666666666666666666666666666666666554

>PF12854 PPR_1: PPR repeat

Probab=99.64  E-value=4.5e-16  Score=64.32  Aligned_cols=34  Identities=50%  Similarity=0.822  Sum_probs=32.5

Q ss_pred             cCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           14 RGVNPDTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        14 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      +|+.||..|||++|++||+.|++++|+++|++|+
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            5899999999999999999999999999999995

>PLN03077 Protein ECB2; Provisional

Probab=99.64  E-value=1.5e-15  Score=97.19  Aligned_cols=69  Identities=20%  Similarity=0.048  Sum_probs=54.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|++|.+.|+.||..||+++|.+|++.|+++.|.+++..|.+.|+.||..+||+||.+|++.|+
T Consensus       270 ~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~  338 (857)
T PLN03077        270 LEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGS  338 (857)
T ss_pred             HHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCC
Confidence            567777888877788888888888888888888888888888888777888888888888888877765

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.41  E-value=5e-13  Score=54.72  Aligned_cols=35  Identities=40%  Similarity=0.642  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDA   55 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   55 (71)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999984

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=99.32  E-value=4e-12  Score=51.92  Aligned_cols=33  Identities=33%  Similarity=0.353  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQ   53 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p   53 (71)
                      .+||++|++|++.|+++.|+++|++|++.|+.|
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

>PF13041 PPR_2: PPR repeat family

Probab=99.28  E-value=7.1e-12  Score=55.54  Aligned_cols=32  Identities=41%  Similarity=0.717  Sum_probs=30.2

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHh
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCL   32 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~   32 (71)
                      +++|.++|++|.++|+.||..||+++|++|||
T Consensus        19 ~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen   19 FEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            37899999999999999999999999999986

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

Probab=99.22  E-value=1.9e-11  Score=48.85  Aligned_cols=31  Identities=32%  Similarity=0.663  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGC   51 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~   51 (71)
                      ++||++|++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4899999999999999999999999999875

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=99.13  E-value=4.1e-10  Score=68.53  Aligned_cols=67  Identities=22%  Similarity=0.258  Sum_probs=61.1

Q ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHH----HHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            4 ANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDR----ARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~----a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .+++..+|.+..+.||..|||+++.+.++.|+++.    |.+++.+|++-|++|+..+|-.+|..+++.++
T Consensus       257 ~K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~d  327 (625)
T KOG4422|consen  257 GKKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESD  327 (625)
T ss_pred             cHHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCC
Confidence            47899999999999999999999999999998876    66789999999999999999999999987653

>PF12854 PPR_1: PPR repeat

Probab=98.97  E-value=6.3e-10  Score=45.70  Aligned_cols=22  Identities=32%  Similarity=0.582  Sum_probs=20.7

Q ss_pred             CCCCccHHHHHHHHHHHHhccc
Q 042276           49 KGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        49 ~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +|+.||..|||+||++||+.|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~   22 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGR   22 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCC
Confidence            5899999999999999999987

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

Probab=98.87  E-value=7.6e-08  Score=49.28  Aligned_cols=66  Identities=12%  Similarity=0.152  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHhcCC-CcCHHHHHHHHHHHHhcC--------CHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            3 EANGLAELMIQRGV-NPDTSTCNALMDGFCLAD--------RFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         3 ~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~g--------~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ....+++.++..|+ -|++.+||.++.+-++..        ++-..+.++++|..+++.|+..||++++..+.+.
T Consensus        43 ~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen   43 IINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHh
Confidence            34578899999999 999999999999998753        2335788999999999999999999999998764

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 [, , ].

>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=98.71  E-value=1.2e-07  Score=53.42  Aligned_cols=65  Identities=25%  Similarity=0.242  Sum_probs=56.0

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhc----------------CCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLA----------------DRFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~----------------g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ...+..|.+-|+.-|..+|+.||+.+=+.                .+-+-|++++++|...|+.||..|+..|++.|++.
T Consensus        72 ~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~  151 (228)
T PF06239_consen   72 YAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRK  151 (228)
T ss_pred             HHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccc
Confidence            44567889999999999999999997642                24456999999999999999999999999999875


Q ss_pred             c
Q 042276           69 I   69 (71)
Q Consensus        69 ~   69 (71)
                      +
T Consensus       152 s  152 (228)
T PF06239_consen  152 S  152 (228)
T ss_pred             c
Confidence            5

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

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

Probab=98.34  E-value=3.8e-06  Score=51.52  Aligned_cols=65  Identities=20%  Similarity=0.219  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      ++..++..=...|+-||..+||.+|+.+.+.|++..|.++...|...+...+..|+..-+.+|.+
T Consensus       121 ~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~  185 (429)
T PF10037_consen  121 ELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYK  185 (429)
T ss_pred             HHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHH
Confidence            45555555556777788888888888888888888888877777766666677777777766654

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 [].

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.22  E-value=6.1e-06  Score=50.93  Aligned_cols=66  Identities=14%  Similarity=0.099  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      +.|.+++++-.......+..+||.+|.+-.-.-    ..++..+|....+.||..|+|+++++..+.|++
T Consensus       224 ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~----~K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F  289 (625)
T KOG4422|consen  224 ERARELYKEHRAAKGKVYREAFNGLIGASSYSV----GKKLVAEMISQKMTPNLFTFNALLSCAAKFGKF  289 (625)
T ss_pred             HHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhc----cHHHHHHHHHhhcCCchHhHHHHHHHHHHhcch
Confidence            567777777776666777777777776544322    267788888888999999999999999988753

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

Probab=98.19  E-value=7.6e-06  Score=50.23  Aligned_cols=70  Identities=21%  Similarity=0.074  Sum_probs=56.8

Q ss_pred             hHHHHHHHHHHhc--CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQR--GVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~--~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      +++..++-.....  ....-..|.+++|..|.+.|..+.++.+++.=..-|+-||.+|+|.||+.+.+.|.|
T Consensus        83 d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~  154 (429)
T PF10037_consen   83 DEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNY  154 (429)
T ss_pred             HHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccH
Confidence            4455555555543  222345566799999999999999999999999999999999999999999998864

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 [].

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

Probab=98.08  E-value=2.7e-05  Score=46.05  Aligned_cols=65  Identities=22%  Similarity=0.190  Sum_probs=55.3

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhcC----------------CHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLAD----------------RFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g----------------~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ...++.|++-|+..|..+|+.+|+.+=|-.                +-+-+++++++|..+|+.||..+=..|+++|.+.
T Consensus        92 y~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~  171 (406)
T KOG3941|consen   92 YTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRW  171 (406)
T ss_pred             HHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccc
Confidence            345678899999999999999999876532                2345899999999999999999999999999875


Q ss_pred             c
Q 042276           69 I   69 (71)
Q Consensus        69 ~   69 (71)
                      +
T Consensus       172 ~  172 (406)
T KOG3941|consen  172 N  172 (406)
T ss_pred             c
Confidence            5

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=97.91  E-value=7.9e-05  Score=44.36  Aligned_cols=23  Identities=17%  Similarity=0.133  Sum_probs=8.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHH
Q 042276           24 NALMDGFCLADRFDRARELLVSM   46 (71)
Q Consensus        24 ~~li~~~~~~g~~~~a~~~~~~m   46 (71)
                      +.+..+|.+.|++++|.+.++.+
T Consensus       253 ~~l~~~~~~~g~~~~A~~~l~~~  275 (389)
T PRK11788        253 PKLMECYQALGDEAEGLEFLRRA  275 (389)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHH
Confidence            33333333333333333333333

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

Probab=97.81  E-value=6.6e-05  Score=49.62  Aligned_cols=65  Identities=17%  Similarity=0.096  Sum_probs=52.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.|+.++.+|++.|++-+.+-|-.+|-+   .++...++.+++.|.+.|+.|+..|+...+-.+.++|
T Consensus       221 d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~  285 (1088)
T KOG4318|consen  221 DGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNG  285 (1088)
T ss_pred             hhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcch
Confidence            5678888888888888888888888766   7777888888888888888888888888777766644

>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=97.76  E-value=0.0003  Score=32.20  Aligned_cols=57  Identities=30%  Similarity=0.356  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILI   62 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li   62 (71)
                      ++|.++|+...+.  .| +...+-.+..++.+.|++++|.++++.....  .|+...|..++
T Consensus         8 ~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    8 DEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             HHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            6789999999766  44 7778888999999999999999999999877  56655555554

...

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=97.74  E-value=0.00029  Score=41.97  Aligned_cols=68  Identities=15%  Similarity=-0.037  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+++.+.. +.+...+..+...+.+.|++++|.++|+++...+-.....+++.+..+|.+.|+
T Consensus       197 ~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~  264 (389)
T PRK11788        197 DAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGD  264 (389)
T ss_pred             HHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCC
Confidence            45777777776542 224566777777888888888888888888765322224567777777777665

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

Probab=97.65  E-value=5.9e-05  Score=49.84  Aligned_cols=64  Identities=17%  Similarity=0.199  Sum_probs=52.2

Q ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC------------------------CCccHHHHHHH
Q 042276            6 GLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG------------------------CKQDAFSHSIL   61 (71)
Q Consensus         6 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g------------------------~~p~~~~~~~l   61 (71)
                      .++..+...|+.|+.+||-.+|.-||..|+.+.|- +|.-|+-+.                        -+|...||+.|
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~L   89 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNL   89 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHH
Confidence            46778889999999999999999999999999888 666665321                        35777888888


Q ss_pred             HHHHHhccc
Q 042276           62 INGGSARIR   70 (71)
Q Consensus        62 i~~~~~~~~   70 (71)
                      +++|...|+
T Consensus        90 l~ayr~hGD   98 (1088)
T KOG4318|consen   90 LKAYRIHGD   98 (1088)
T ss_pred             HHHHHhccc
Confidence            888887775

>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=97.25  E-value=0.0061  Score=31.95  Aligned_cols=56  Identities=18%  Similarity=0.212  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CCCCccHHHHHH
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS-----KGCKQDAFSHSI   60 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~~~   60 (71)
                      +|..+.......  .| |...|-.+|.++...|+..+|.++|+.+..     .|+.|+..+-..
T Consensus        80 ~a~~~~~~~l~~--dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~l  141 (146)
T PF03704_consen   80 EALRLLQRALAL--DPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRAL  141 (146)
T ss_dssp             HHHHHHHHHHHH--STT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHH
T ss_pred             HHHHHHHHHHhc--CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHHH
Confidence            455555555543  55 899999999999999999999999998863     499998876543

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

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=97.14  E-value=0.00038  Score=27.46  Aligned_cols=19  Identities=42%  Similarity=0.726  Sum_probs=17.3

Q ss_pred             hHHHHHHHHHHhcCCCcCH
Q 042276            2 DEANGLAELMIQRGVNPDT   20 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~   20 (71)
                      ++|.++|++|.+.|+.||.
T Consensus        17 ~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756        17 EEALELFKEMLERGIEPDV   35 (35)
T ss_pred             HHHHHHHHHHHHcCCCCCC
Confidence            6899999999999999984

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.

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

Probab=97.03  E-value=0.011  Score=38.07  Aligned_cols=65  Identities=23%  Similarity=0.003  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            4 ANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         4 a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      |...++...+.  .| +..++..+-..+.+.|++++|..+|+++.+.+.. +..++..+..++.+.|++
T Consensus       822 A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~g~~  887 (899)
T TIGR02917       822 ALEYAEKALKL--APNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLALALLATGRK  887 (899)
T ss_pred             HHHHHHHHHhh--CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHHHcCCH
Confidence            44444444432  22 4555666677778888999999999999877543 888888888888888763

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

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

Probab=97.03  E-value=0.0084  Score=38.54  Aligned_cols=27  Identities=7%  Similarity=-0.140  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ..+..+...+.+.|++++|.+.|+.+.
T Consensus       704 ~~~~~~~~~~~~~g~~~~A~~~~~~~~  730 (899)
T TIGR02917       704 LGFELEGDLYLRQKDYPAAIQAYRKAL  730 (899)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            333334444444444444444444443

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.

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

Probab=97.03  E-value=0.012  Score=30.73  Aligned_cols=54  Identities=13%  Similarity=0.020  Sum_probs=47.6

Q ss_pred             cCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCccHHHHHHHHHHHHh
Q 042276           14 RGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK-GCKQDAFSHSILINGGSA   67 (71)
Q Consensus        14 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~   67 (71)
                      ....|+..+-.+++.+|+..+++..|+++.+...+. ++..+..+|..|++....
T Consensus        46 spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v  100 (126)
T PF12921_consen   46 SPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYV  100 (126)
T ss_pred             CCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            446789999999999999999999999999999765 888889999999988754

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

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

Probab=96.80  E-value=0.0098  Score=26.87  Aligned_cols=46  Identities=20%  Similarity=0.152  Sum_probs=37.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+..  | +...+..+=..+.+.|++++|..+|++..+.
T Consensus        14 ~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen   14 DEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            67889999998764  5 7888888888899999999999999998754

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

Probab=96.72  E-value=0.019  Score=29.73  Aligned_cols=46  Identities=9%  Similarity=0.032  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-CccHHHHHHHHHHHHh
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGSKGC-KQDAFSHSILINGGSA   67 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~~~~~li~~~~~   67 (71)
                      |-...|.-+...+++....-+|+.++..|+ .|+..+|+.++.+.++
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~   73 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAK   73 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHH
Confidence            334556677777999999999999999999 9999999999998875

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 [, , ].

>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=96.67  E-value=0.038  Score=32.65  Aligned_cols=67  Identities=18%  Similarity=0.055  Sum_probs=46.5

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +++|..+|+++.+ .+.++..+.|.+..++...|++++|.+++.+..+.. .-|..+..-++-.....|
T Consensus       183 ~~~A~y~f~El~~-~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~g  249 (290)
T PF04733_consen  183 YQDAFYIFEELSD-KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLG  249 (290)
T ss_dssp             CCHHHHHHHHHHC-CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh-ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhC
Confidence            3678999999754 467789999999999999999999999999976542 124455555555544444

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=96.67  E-value=0.0019  Score=25.44  Aligned_cols=17  Identities=41%  Similarity=0.559  Sum_probs=15.5

Q ss_pred             hHHHHHHHHHHhcCCCc
Q 042276            2 DEANGLAELMIQRGVNP   18 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p   18 (71)
                      ++|..+|++|.+.|+.|
T Consensus        18 ~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen   18 DAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHHhCCCC
Confidence            67899999999999987

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

Probab=96.55  E-value=0.0038  Score=29.85  Aligned_cols=66  Identities=17%  Similarity=0.139  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhcCC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH-HHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGV-NPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA-FSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~   70 (71)
                      ++|..+++.+.+..- .|+...+-.+-.++.+.|++++|..+++. .+.  .|+. ...-.+-.+|.+.|+
T Consensus         6 ~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~--~~~~~~~~~l~a~~~~~l~~   73 (84)
T PF12895_consen    6 ENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKL--DPSNPDIHYLLARCLLKLGK   73 (84)
T ss_dssp             HHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTH--HHCHHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCC--CCCCHHHHHHHHHHHHHhCC
Confidence            578889999976532 23455555578899999999999999998 222  2323 333344455556655

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

Probab=96.50  E-value=0.038  Score=28.24  Aligned_cols=67  Identities=13%  Similarity=-0.013  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.|+.....+ +.+...|..+-..+.+.|++++|..+++...... ..+...+..+-..+...|+
T Consensus        34 ~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~  100 (135)
T TIGR02552        34 DEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGE  100 (135)
T ss_pred             HHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCC
Confidence            45667777665542 2266777777777778888888888888776553 3345555555555555554

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

>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=96.41  E-value=0.0072  Score=34.53  Aligned_cols=35  Identities=31%  Similarity=0.242  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHH
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFD   37 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~   37 (71)
                      -|..++++|...|+-||..++..+++.|++.+.+-
T Consensus       121 c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~  155 (228)
T PF06239_consen  121 CAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPM  155 (228)
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHH
Confidence            47899999999999999999999999999988654

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

>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=96.21  E-value=0.055  Score=28.30  Aligned_cols=52  Identities=8%  Similarity=-0.016  Sum_probs=42.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHh---------------hCCCCccHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMG---------------SKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~---------------~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      |..++.++|-++++.|+++...++.+..=               .....|+..+..+++.+|+.+|+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~   67 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGD   67 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhccc
Confidence            45688999999999999999999886541               12467999999999999988775

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

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=96.16  E-value=0.074  Score=28.08  Aligned_cols=66  Identities=8%  Similarity=-0.139  Sum_probs=38.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+.....  .| +...|..+-.++.+.|++++|...|+...... ..+..++..+-.++.+.|+
T Consensus        41 ~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~  107 (144)
T PRK15359         41 SRAVIDFSWLVMA--QPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGE  107 (144)
T ss_pred             HHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCC
Confidence            3556666665433  33 56666666666777777777777777776542 2244555555445544443

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

Probab=96.06  E-value=0.13  Score=30.52  Aligned_cols=61  Identities=15%  Similarity=0.120  Sum_probs=49.1

Q ss_pred             HHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CCCCccHHHHHHHHHHHH
Q 042276            4 ANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS-----KGCKQDAFSHSILINGGS   66 (71)
Q Consensus         4 a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~~~li~~~~   66 (71)
                      +.+.++++...  .| +...|..+|.+|.+.|+...|++.|+++.+     .|+.|...+......+..
T Consensus       172 ~~~~l~~Li~~--dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~~~~~  238 (280)
T COG3629         172 VIEHLERLIEL--DPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYEEILR  238 (280)
T ss_pred             HHHHHHHHHhc--CccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhc
Confidence            34445555433  55 899999999999999999999999999875     599999999888777643

>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=95.85  E-value=0.061  Score=24.49  Aligned_cols=67  Identities=13%  Similarity=-0.010  Sum_probs=45.9

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+++..+.. +.+...+..+-..+...+++++|.+.|....... ..+..++..+...+...|+
T Consensus        17 ~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   83 (100)
T cd00189          17 DEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGK   83 (100)
T ss_pred             HHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHh
Confidence            56777787776542 2244677778888889999999999999887653 2233566666666655443

>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=95.83  E-value=0.16  Score=31.46  Aligned_cols=66  Identities=12%  Similarity=-0.052  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH-HHHHHHHHHHHhcccC
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA-FSHSILINGGSARIRK   71 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~~   71 (71)
                      +|.+++++..+. .+-|....+...+-+.+.++.+.|+.+.+++.+.  .|+. .+|..|..+|.+.|++
T Consensus       218 ~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~  284 (395)
T PF09295_consen  218 EAIRLLNEALKE-NPQDSELLNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDF  284 (395)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCH
Confidence            344455554432 1124445555555567788888888888888765  4654 4888888888887764

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

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

Probab=95.81  E-value=0.11  Score=29.96  Aligned_cols=67  Identities=16%  Similarity=-0.053  Sum_probs=42.8

Q ss_pred             hHHHHHHHHHHh-cCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQ-RGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~-~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      +++..+++.... ....++...|..+-..+.+.|++++|++.+++..+.  .| |....+.++..+...|+
T Consensus       127 ~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~  195 (280)
T PF13429_consen  127 DEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGD  195 (280)
T ss_dssp             HHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCC
Confidence            345566666543 223457777888888888888888888888888766  35 45667777776665553

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

Probab=95.75  E-value=0.038  Score=22.31  Aligned_cols=26  Identities=15%  Similarity=0.085  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      +|+.+=..|.+.|++++|+++|++..
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            46778889999999999999999854

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

Probab=95.64  E-value=0.21  Score=30.34  Aligned_cols=66  Identities=11%  Similarity=-0.149  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+..+.  .| +...|..+-.++.+.|++++|+..+++..... ..+...|..+-.+|...|+
T Consensus        19 ~~Ai~~~~~Al~~--~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088         19 ALAVDLYTQAIDL--DPNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCC
Confidence            4566667666643  33 56666666667777777777777777776542 1244555555555555554

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.60  E-value=0.055  Score=22.75  Aligned_cols=28  Identities=21%  Similarity=0.095  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +|..+-..|.+.|++++|+++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5667778899999999999999999876

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

Probab=95.38  E-value=0.039  Score=24.93  Aligned_cols=39  Identities=15%  Similarity=0.064  Sum_probs=30.9

Q ss_pred             HhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcccC
Q 042276           31 CLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIRK   71 (71)
Q Consensus        31 ~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~   71 (71)
                      .+.|++++|+++|++....  .| |...+-.+..+|.+.|++
T Consensus         2 l~~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~   41 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQY   41 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-H
T ss_pred             hhccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCH
Confidence            4679999999999999876  34 677777888888888763

...

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=95.31  E-value=0.21  Score=27.03  Aligned_cols=30  Identities=17%  Similarity=0.245  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ...+..+-..+.+.|++++|...+++....
T Consensus       169 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  198 (234)
T TIGR02521       169 PESLLELAELYYLRGQYKDARAYLERYQQT  198 (234)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            344555555555566666666666555444

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.

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

Probab=95.20  E-value=0.1  Score=22.72  Aligned_cols=38  Identities=8%  Similarity=-0.021  Sum_probs=31.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276           27 MDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus        27 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      +....+.|...++..++++|.+.|+..+...|..++.-
T Consensus         9 L~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen    9 LLLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            44456788888999999999999999999988887753

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=95.16  E-value=0.24  Score=26.81  Aligned_cols=29  Identities=10%  Similarity=-0.018  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ...+..+-..+...|++++|.+.+++..+
T Consensus        65 ~~~~~~la~~~~~~~~~~~A~~~~~~al~   93 (234)
T TIGR02521        65 YLAYLALALYYQQLGELEKAEDSFRRALT   93 (234)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44445555555555555555555555544

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.

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

Probab=95.13  E-value=0.19  Score=25.63  Aligned_cols=57  Identities=11%  Similarity=0.086  Sum_probs=39.2

Q ss_pred             HHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276            7 LAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus         7 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      -++.+....+.|+..+..+.+.+|-+.+++..|.++|+..+.+- .+....|.-+++-
T Consensus        32 glN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lqE   88 (108)
T PF02284_consen   32 GLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQE   88 (108)
T ss_dssp             HHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHHH
T ss_pred             HHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHHH
Confidence            34444556678999999999999999999999999999997541 2222377776654

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 ....

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=95.11  E-value=0.14  Score=27.59  Aligned_cols=50  Identities=12%  Similarity=0.068  Sum_probs=43.6

Q ss_pred             CHHHHHHHHHHHHhcCC-HHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276           19 DTSTCNALMDGFCLADR-FDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      +..+|++++.+.++... --.+..+|.-|++.+.++++.-|..+|+++.+.
T Consensus        78 ~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g  128 (145)
T PF13762_consen   78 DNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRG  128 (145)
T ss_pred             ccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC
Confidence            66789999999988776 556888999999988999999999999998763

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=95.07  E-value=0.43  Score=29.30  Aligned_cols=64  Identities=9%  Similarity=0.059  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++.+..+.+.++  .| |....-++=..+.+.+++++|.+.|+...+.  .|+..+|..+-..+-+.|+
T Consensus       312 ~al~~~e~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~  376 (398)
T PRK10747        312 QLEKVLRQQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHK  376 (398)
T ss_pred             HHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCC
Confidence            455556666544  45 5566777777888999999999999999876  6888888888888777665

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=94.80  E-value=0.61  Score=30.60  Aligned_cols=20  Identities=20%  Similarity=0.275  Sum_probs=9.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHh
Q 042276           28 DGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        28 ~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ..+.+.|++++|+..+++..
T Consensus       220 ~~l~~~g~~~eA~~~~~~al  239 (656)
T PRK15174        220 DTLCAVGKYQEAIQTGESAL  239 (656)
T ss_pred             HHHHHCCCHHHHHHHHHHHH
Confidence            34444444444444444444

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

Probab=94.72  E-value=0.29  Score=25.67  Aligned_cols=67  Identities=18%  Similarity=0.144  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHHhcCCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD--TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+......-.|+  ....--+-..+...|++++|+..++.......  ....+...=.++.+.|+
T Consensus        65 ~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~  133 (145)
T PF09976_consen   65 DEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGD  133 (145)
T ss_pred             HHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCC
Confidence            466677777766542222  12233344555667777777777755332222  22334444444444444

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

Probab=94.57  E-value=0.13  Score=20.76  Aligned_cols=29  Identities=28%  Similarity=0.359  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ..+++.+-..|...|++++|+.++++...
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            35788889999999999999999998864

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

Probab=94.55  E-value=0.17  Score=29.23  Aligned_cols=65  Identities=15%  Similarity=0.127  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            4 ANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +.+++....+.. +.|...|..+-.++...|+.++|+..|++..+.. ..|......+..++...|+
T Consensus       199 ~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~  263 (280)
T PF13429_consen  199 AREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGR  263 (280)
T ss_dssp             HHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT----
T ss_pred             HHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-ccccccccccccccccccc
Confidence            334444443332 3345556666666777777777777777765531 2255555566666655554

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=94.54  E-value=0.29  Score=24.79  Aligned_cols=58  Identities=10%  Similarity=0.081  Sum_probs=43.5

Q ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276            6 GLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus         6 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      +-++.+....+.|+..+..+.+++|-+-+++..|.++|+..+.+. ..+...|.-+++-
T Consensus        28 r~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~-~~~~~~y~~~lqe   85 (103)
T cd00923          28 RGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC-GAHKEIYPYILQE   85 (103)
T ss_pred             HHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cCchhhHHHHHHH
Confidence            334444556678999999999999999999999999999887431 2244567666653

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.

>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=94.43  E-value=0.35  Score=25.25  Aligned_cols=49  Identities=18%  Similarity=0.162  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .+...+...+...|++++|.++.+.+.... +.|...|-.+|.+|...|+
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~  111 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGR  111 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcC
Confidence            345556667778999999999999998662 3378899999999999886

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

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=94.41  E-value=0.28  Score=24.12  Aligned_cols=69  Identities=7%  Similarity=-0.030  Sum_probs=43.1

Q ss_pred             hHHHHHHHHHHhcCC-Cc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--CCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGV-NP-DTSTCNALMDGFCLADRFDRARELLVSMGSKG--CKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|..+.+..- .| ....+..+-..+.+.|++++|.+.|+......  .......+..+-..+.+.|+
T Consensus        19 ~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~   91 (119)
T TIGR02795        19 ADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGD   91 (119)
T ss_pred             HHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCC
Confidence            567888888865421 11 13456667888889999999999999987642  11123345555555554443

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.

>PRK12370 invasion protein regulator; Provisional

Probab=94.37  E-value=0.75  Score=29.49  Aligned_cols=45  Identities=9%  Similarity=-0.063  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +|...|++..+.  .| +...+..+-..+...|++++|...+++..+.
T Consensus       356 ~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l  401 (553)
T PRK12370        356 VGSLLFKQANLL--SPISADIKYYYGWNLFMAGQLEEALQTINECLKL  401 (553)
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            444555554433  23 3444444555555556666666666655544

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

Probab=94.34  E-value=0.69  Score=29.88  Aligned_cols=55  Identities=11%  Similarity=0.147  Sum_probs=45.0

Q ss_pred             cCCCcCHHHHHHHHHHHH-hcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           14 RGVNPDTSTCNALMDGFC-LADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        14 ~~~~p~~~~~~~li~~~~-~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .=+.|+..-|-.||..|. +.|++..|++++++.- +.+.-|..+.-.|+..+...|
T Consensus       653 aliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~h-rkfpedldclkflvri~~dlg  708 (840)
T KOG2003|consen  653 ALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIH-RKFPEDLDCLKFLVRIAGDLG  708 (840)
T ss_pred             HhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHH-HhCccchHHHHHHHHHhcccc
Confidence            346899999999998877 5799999999999984 446678888888888877655

>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=94.27  E-value=0.086  Score=28.10  Aligned_cols=24  Identities=33%  Similarity=0.587  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHH
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMD   28 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~   28 (71)
                      +|..+|..|..+|-+||  .|+.|+.
T Consensus       113 DaY~VF~kML~~G~pPd--dW~~Ll~  136 (140)
T PF11663_consen  113 DAYAVFRKMLERGNPPD--DWDALLK  136 (140)
T ss_pred             cHHHHHHHHHhCCCCCc--cHHHHHH
Confidence            44555555555555554  2444443

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 [].

>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=94.19  E-value=0.066  Score=28.53  Aligned_cols=32  Identities=16%  Similarity=0.144  Sum_probs=25.9

Q ss_pred             hcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276           32 LADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus        32 ~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      +.|.-..|..+|+.|.++|-.||  .|+.|+...
T Consensus       107 ~ygsk~DaY~VF~kML~~G~pPd--dW~~Ll~~a  138 (140)
T PF11663_consen  107 AYGSKTDAYAVFRKMLERGNPPD--DWDALLKEA  138 (140)
T ss_pred             hhccCCcHHHHHHHHHhCCCCCc--cHHHHHHHh
Confidence            34566679999999999999987  488888764

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 [].

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=94.15  E-value=0.93  Score=29.78  Aligned_cols=44  Identities=5%  Similarity=0.003  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +|...++.+...  .| +...+..+-..+.+.|++++|...+++...
T Consensus        94 ~A~~~l~~~l~~--~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~  138 (656)
T PRK15174         94 AVLQVVNKLLAV--NVCQPEDVLLVASVLLKSKQYATVADLAEQAWL  138 (656)
T ss_pred             HHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444444332  22 233444444444445555555555554443

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

Probab=94.04  E-value=0.18  Score=22.59  Aligned_cols=41  Identities=10%  Similarity=-0.032  Sum_probs=31.2

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276           28 DGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus        28 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ..+.+.|++++|.+.|++..+..  | +...+..+-.++...|+
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~   46 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGR   46 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCC
Confidence            45778999999999999998874  5 55666666666666665

>TIGR00540 hemY_coli hemY protein

Probab=93.96  E-value=0.86  Score=28.05  Aligned_cols=65  Identities=14%  Similarity=0.014  Sum_probs=44.0

Q ss_pred             HHHHHHHHHhcCCCcC-H--HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            4 ANGLAELMIQRGVNPD-T--STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~-~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +.+.++...+.  .|+ .  ....++=..+.+.|++++|.+.|+........||...+..+-..+.+.|+
T Consensus       318 ~~~~~e~~lk~--~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~  385 (409)
T TIGR00540       318 LEKLIEKQAKN--VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGD  385 (409)
T ss_pred             HHHHHHHHHHh--CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCC
Confidence            34444444332  453 3  44556667778899999999999964444447888888888888877665

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

>PRK14574 hmsH outer membrane protein; Provisional

Probab=93.83  E-value=0.88  Score=30.89  Aligned_cols=69  Identities=12%  Similarity=-0.020  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-----CCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG-----CKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-----~~p~~~~~~~li~~~~~~~~   70 (71)
                      .++.+.++.+...+......+--++-++|...+++++|+.+++......     ..++......|.-++..+++
T Consensus       309 ~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~  382 (822)
T PRK14574        309 ADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQ  382 (822)
T ss_pred             HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhccc
Confidence            4677888888888777667788889999999999999999999986532     12344445667777777665

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

Probab=93.79  E-value=0.42  Score=30.84  Aligned_cols=56  Identities=13%  Similarity=0.070  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSIL   61 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   61 (71)
                      ..|.++|....+-  .|+...|++.|+-=.+...++.|..++.+..-.  .|++.+|--.
T Consensus       158 ~gaRqiferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wiky  213 (677)
T KOG1915|consen  158 AGARQIFERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKY  213 (677)
T ss_pred             HHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHH
Confidence            4577788777654  899999999999999999999999999988654  4887776543

>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=93.77  E-value=1  Score=29.16  Aligned_cols=65  Identities=11%  Similarity=-0.027  Sum_probs=48.1

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+...  +.|+...|..+-.+|.+.|++++|++.+....+.  .| +...|..+-.++...|+
T Consensus       144 ~~Ai~~y~~al~--~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l--~p~~~~a~~~~a~a~~~lg~  209 (615)
T TIGR00990       144 NKAIKLYSKAIE--CKPDPVYYSNRAACHNALGDWEKVVEDTTAALEL--DPDYSKALNRRANAYDGLGK  209 (615)
T ss_pred             HHHHHHHHHHHh--cCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHcCC
Confidence            567778877664  3677788888888899999999999999988765  34 44566666666665554

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.76  E-value=0.34  Score=29.70  Aligned_cols=46  Identities=26%  Similarity=0.249  Sum_probs=33.9

Q ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            4 ANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +..++..=++-|+-||.++++.+|+.+.+.++..+|.++...|...
T Consensus       119 ~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  119 AIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             HHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            3344444456788888888888888888888888888877766543

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

Probab=93.67  E-value=0.67  Score=25.86  Aligned_cols=46  Identities=9%  Similarity=0.118  Sum_probs=32.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|.+++++..+.  .| +..++..+-..+.+.|++++|+..++.+.+.
T Consensus       127 ~~A~~~l~~al~~--dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        127 PQTREMIDKALAL--DANEVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHHHHHh--CCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            4566666666654  44 5666677777777888888888888887655

>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=93.65  E-value=1.1  Score=28.94  Aligned_cols=28  Identities=4%  Similarity=-0.218  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ...+..+-..+.+.|++++|+..|++..
T Consensus       433 ~~~~~~la~~~~~~g~~~eA~~~~~~al  460 (615)
T TIGR00990       433 IFSHIQLGVTQYKEGSIASSMATFRRCK  460 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3334444444444455555555544443

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=93.43  E-value=0.35  Score=21.81  Aligned_cols=29  Identities=10%  Similarity=0.028  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      .+|..+=..+.+.|++++|+..|++..+.
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~   32 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIEL   32 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            34444444455555555555555555443

...

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=93.41  E-value=0.34  Score=29.13  Aligned_cols=39  Identities=18%  Similarity=0.121  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHH
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSH   58 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~   58 (71)
                      ..-||..|+...+.||+++|++++++.++.|..--..+|
T Consensus       257 e~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tF  295 (303)
T PRK10564        257 ESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTF  295 (303)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHH
Confidence            455789999999999999999999999999965444444

>PRK12370 invasion protein regulator; Provisional

Probab=93.38  E-value=1.3  Score=28.41  Aligned_cols=45  Identities=16%  Similarity=0.025  Sum_probs=20.7

Q ss_pred             hHHHHHHHHHHhcCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNPD-TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|...++...+.  .|+ ...+..+...+...|++++|+..+++...
T Consensus       389 ~eAi~~~~~Al~l--~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~  434 (553)
T PRK12370        389 EEALQTINECLKL--DPTRAAAGITKLWITYYHTGIDDAIRLGDELRS  434 (553)
T ss_pred             HHHHHHHHHHHhc--CCCChhhHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            3455555555433  232 11222233334445666666666665543

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=93.35  E-value=0.37  Score=21.92  Aligned_cols=52  Identities=19%  Similarity=0.128  Sum_probs=39.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFS   57 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~   57 (71)
                      ++|.++++.+...  .| +...|...=..+.+.|++++|.+.|+...+.  .|+...
T Consensus        12 ~~A~~~~~~~l~~--~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~--~p~~~~   64 (73)
T PF13371_consen   12 EEALEVLERALEL--DPDDPELWLQRARCLFQLGRYEEALEDLERALEL--SPDDPD   64 (73)
T ss_pred             HHHHHHHHHHHHh--CcccchhhHHHHHHHHHhccHHHHHHHHHHHHHH--CCCcHH
Confidence            5677888888765  34 6777777777888999999999999999866  344433

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=93.26  E-value=1.3  Score=30.66  Aligned_cols=45  Identities=11%  Similarity=-0.113  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +|...+++..+.  .|+...|..+-..+.+.|++++|+..|++....
T Consensus       594 eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l  638 (987)
T PRK09782        594 LALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALEL  638 (987)
T ss_pred             HHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            444445444433  345555555555666666666666666665544

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=93.18  E-value=1.2  Score=27.35  Aligned_cols=30  Identities=10%  Similarity=0.145  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ......+...|.+.|++++|.+++..+.+.
T Consensus       187 ~~al~ll~~~~~~~gdw~~a~~~l~~l~k~  216 (398)
T PRK10747        187 PEVLRLAEQAYIRTGAWSSLLDILPSMAKA  216 (398)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHc
Confidence            444444444444444444444444444444

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

Probab=92.98  E-value=0.099  Score=35.64  Aligned_cols=66  Identities=14%  Similarity=0.107  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|.+....  .| |...-|.+=-+++..|++.+|.++|.+-++.+. -+..+|--+-++|..+|+
T Consensus       629 ~KAlq~y~kvL~~--dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~q  695 (1018)
T KOG2002|consen  629 EKALQLYGKVLRN--DPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQ  695 (1018)
T ss_pred             HHHHHHHHHHHhc--CcchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHH
Confidence            3566666666543  33 667777776677777777777777777776532 122334444444444443

>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=92.77  E-value=0.76  Score=27.29  Aligned_cols=67  Identities=12%  Similarity=-0.053  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHH---HHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNAL---MDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~l---i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      +.|.+.++.|.+.  ..|....+..   +....-.+.+.+|.-+|+++... +.+++.+.+.+.-++...|+|
T Consensus       148 dlA~k~l~~~~~~--~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~  217 (290)
T PF04733_consen  148 DLAEKELKNMQQI--DEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHY  217 (290)
T ss_dssp             HHHHHHHHHHHCC--SCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-H
T ss_pred             HHHHHHHHHHHhc--CCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCH
Confidence            5677888888654  4454443322   22222234788899999998654 456777777777777666653

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.

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=92.71  E-value=0.47  Score=21.36  Aligned_cols=45  Identities=18%  Similarity=0.143  Sum_probs=36.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcC-CHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLAD-RFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~   48 (71)
                      ++|...|.+..+.  .| +...|..+=.++.+.| ++++|++.++...+
T Consensus        20 ~~A~~~~~~ai~~--~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen   20 EEAIEYFEKAIEL--DPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHH--STTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            5788888888775  45 6788888888899999 79999999988764

...

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.70  E-value=1.3  Score=26.55  Aligned_cols=65  Identities=3%  Similarity=-0.029  Sum_probs=52.9

Q ss_pred             HHHHHHH-hcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCccHHHHHHHHHHHHhccc
Q 042276            6 GLAELMI-QRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK-GCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         6 ~~~~~m~-~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++.+.+. ..+-.++..+--++|..+++.+++..-+++....... +..-|...|...|+...+.|+
T Consensus       187 EvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD  253 (292)
T PF13929_consen  187 EVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGD  253 (292)
T ss_pred             HHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCC
Confidence            3444443 3456778889999999999999999999998888755 666799999999999988875

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=92.52  E-value=0.58  Score=23.60  Aligned_cols=45  Identities=13%  Similarity=0.005  Sum_probs=32.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           25 ALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        25 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .+++.+...+..-.|.++++.+.+.+..++..|..-.|+.+.+.|
T Consensus         5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~G   49 (116)
T cd07153           5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAG   49 (116)
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC
Confidence            355556666666778888888887776677777777777776655

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=92.49  E-value=0.88  Score=23.98  Aligned_cols=54  Identities=11%  Similarity=-0.072  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHS   59 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   59 (71)
                      ++|...|+.....  .| +...+..+-.++.+.|++++|...|+...+.  .|+..-|.
T Consensus        75 ~~A~~~y~~Al~l--~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~--~p~~~~~~  129 (144)
T PRK15359         75 TTAINFYGHALML--DASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKM--SYADASWS  129 (144)
T ss_pred             HHHHHHHHHHHhc--CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHH
Confidence            5778888888764  45 7888888888999999999999999999776  45543333

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=92.45  E-value=2  Score=28.72  Aligned_cols=50  Identities=10%  Similarity=-0.066  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA   55 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   55 (71)
                      ++|..+++++...  .| +...+..+...+...|++++|++.+++....  .|+.
T Consensus       376 ~eA~~~l~~al~~--~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l--~Pd~  426 (765)
T PRK10049        376 PQAEMRARELAYN--APGNQGLRIDYASVLQARGWPRAAENELKKAEVL--EPRN  426 (765)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh--CCCC
Confidence            5778888887654  34 6778888888888899999999999888765  3653

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.32  E-value=1.2  Score=26.72  Aligned_cols=63  Identities=16%  Similarity=0.158  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHh--cC----CHHHHHHHHHHHhhCC---CCccHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCL--AD----RFDRARELLVSMGSKG---CKQDAFSHSILING   64 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~--~g----~~~~a~~~~~~m~~~g---~~p~~~~~~~li~~   64 (71)
                      ++...+++.|++.|+.-+..+|-+.......  ..    ....|..+|+.|++..   -.++..++..++..
T Consensus        79 ~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~  150 (297)
T PF13170_consen   79 KEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM  150 (297)
T ss_pred             HHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc
Confidence            4567888899999999888888774433333  33    3345888999998753   12455677777654

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.32  E-value=0.68  Score=28.38  Aligned_cols=49  Identities=12%  Similarity=0.162  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHh-cCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC
Q 042276            2 DEANGLAELMIQ-RGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCK   52 (71)
Q Consensus         2 ~~a~~~~~~m~~-~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   52 (71)
                      +.|.+-|++-.+ .|.. +...||..+. ..+.++.+.|++...+..++|++
T Consensus       161 EaAvqkFqaAlqvsGyq-pllAYniALa-Hy~~~qyasALk~iSEIieRG~r  210 (459)
T KOG4340|consen  161 EAAVQKFQAALQVSGYQ-PLLAYNLALA-HYSSRQYASALKHISEIIERGIR  210 (459)
T ss_pred             HHHHHHHHHHHhhcCCC-chhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhh
Confidence            567788888876 4444 5678888774 55678899999999998888754

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.18  E-value=0.59  Score=21.24  Aligned_cols=42  Identities=12%  Similarity=-0.078  Sum_probs=29.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           28 DGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        28 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ..|.+.+++++|+++++.+.... +.+...|...-..+.+.|+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~   44 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGR   44 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhcc
Confidence            46788999999999999998773 1244455545555555554

>TIGR00540 hemY_coli hemY protein

Probab=92.13  E-value=1.8  Score=26.69  Aligned_cols=49  Identities=8%  Similarity=0.186  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCK   52 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~   52 (71)
                      ++|...++.+.+.  .| +......+...+.+.|++++|.+++....+.+..
T Consensus       170 ~~Al~~l~~l~~~--~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~  219 (409)
T TIGR00540       170 HAARHGVDKLLEM--APRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF  219 (409)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC
Confidence            4677778887766  35 6677888888888999999999999988887644

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.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=92.09  E-value=1.1  Score=24.15  Aligned_cols=64  Identities=11%  Similarity=-0.060  Sum_probs=40.9

Q ss_pred             hHHHHHHHHHHhcCCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNPD--TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~   67 (71)
                      ++|...|++..+..-.++  ...+..+-..+.+.|++++|...+.+....  .| +...+..+-..+..
T Consensus        52 ~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~  118 (172)
T PRK02603         52 AEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIAVIYHK  118 (172)
T ss_pred             HHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHH
Confidence            567777777765433332  467777778888889999999988887764  23 33444444444433

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=91.99  E-value=2.2  Score=29.87  Aligned_cols=45  Identities=16%  Similarity=0.206  Sum_probs=24.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|...|++..+.  .| +...+..+...+...|++++|++.++...+
T Consensus       620 ~~A~~~y~~al~~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~  665 (1157)
T PRK11447        620 AAARAAYQRVLTR--EPGNADARLGLIEVDIAQGDLAAARAQLAKLPA  665 (1157)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            3455555555443  23 455555566666666666666666665543

>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=91.86  E-value=0.51  Score=21.82  Aligned_cols=51  Identities=18%  Similarity=0.025  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----C-CCcc-HHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSK----G-CKQD-AFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g-~~p~-~~~~~~li~~~~~~~~   70 (71)
                      ..+++.+=..|...|++++|++.|++..+.    | -.|+ ..++..+-..+.+.|+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~   61 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGD   61 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCC
Confidence            467888889999999999999999998753    2 1122 3445555555554443

...

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=91.84  E-value=0.49  Score=24.15  Aligned_cols=48  Identities=10%  Similarity=-0.053  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .-..+++...+.+..-.|.++++.|.+.|...+..|..--|+.+.+.|
T Consensus         9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~G   56 (120)
T PF01475_consen    9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAG   56 (120)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCC
Confidence            345677777777778889999999998888888888777778877765

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

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

Probab=91.78  E-value=0.51  Score=30.33  Aligned_cols=50  Identities=12%  Similarity=0.128  Sum_probs=38.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCccHHHHHHHHHHHHhc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKG-CKQDAFSHSILINGGSAR   68 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~   68 (71)
                      -...|+..|+.-.+..-++.|..+|-++++.| ..+++..++++|.-++..
T Consensus       396 ~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~  446 (660)
T COG5107         396 LTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATG  446 (660)
T ss_pred             hhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcC
Confidence            35677778887777777888888888888887 567788888888777653

>PRK11189 lipoprotein NlpI; Provisional

Probab=91.70  E-value=1.7  Score=25.62  Aligned_cols=64  Identities=17%  Similarity=-0.065  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc-HHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD-AFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~   70 (71)
                      +|...|.+..+.  .| +...|+.+=..+...|++++|...|+...+.  .|+ ..+|..+-..+...|+
T Consensus        82 ~A~~~~~~Al~l--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~  147 (296)
T PRK11189         82 LARNDFSQALAL--RPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIALYYGGR  147 (296)
T ss_pred             HHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCC
Confidence            444555554433  34 4666777767777777777777777776653  342 3444444444444443

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

Probab=91.62  E-value=2.4  Score=27.18  Aligned_cols=65  Identities=12%  Similarity=0.006  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHhcCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNPD-TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +|.+.++.+...  .|+ ...+-.+=.++.+.|++.+|..+++.-... ..-|...|..|-.+|...|.
T Consensus       358 ~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~  423 (484)
T COG4783         358 EAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGN  423 (484)
T ss_pred             HHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCc
Confidence            455555555443  443 344444445566666666666666666543 13356677777777766553

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.60  E-value=0.28  Score=19.55  Aligned_cols=24  Identities=21%  Similarity=0.383  Sum_probs=21.4

Q ss_pred             Cc-CHHHHHHHHHHHHhcCCHHHHH
Q 042276           17 NP-DTSTCNALMDGFCLADRFDRAR   40 (71)
Q Consensus        17 ~p-~~~~~~~li~~~~~~g~~~~a~   40 (71)
                      .| |...|+-+=..+.+.|++++|+
T Consensus         9 ~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    9 NPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            56 7999999999999999999986

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=91.48  E-value=1.4  Score=24.13  Aligned_cols=59  Identities=14%  Similarity=-0.031  Sum_probs=44.2

Q ss_pred             HHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           10 LMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        10 ~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .+++.|+.++..-- +++..+......-.|.++++.+.+.+..++..|..--|+.+.+.|
T Consensus        16 ~L~~~GlR~T~qR~-~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~G   74 (169)
T PRK11639         16 LCAQRNVRLTPQRL-EVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQG   74 (169)
T ss_pred             HHHHcCCCCCHHHH-HHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCC
Confidence            34667877654443 566666666667789999999999988888888777788887765

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=91.33  E-value=1.3  Score=23.63  Aligned_cols=62  Identities=15%  Similarity=0.006  Sum_probs=48.5

Q ss_pred             HHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            7 LAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         7 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +...++++|++++.. --.+++.+.+.+..-.|.++++.+.+.+...+..|..--++.+.+.|
T Consensus         8 ~~~~lk~~glr~T~q-R~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~G   69 (145)
T COG0735           8 AIERLKEAGLRLTPQ-RLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAG   69 (145)
T ss_pred             HHHHHHHcCCCcCHH-HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCC
Confidence            445567788876543 45678888888888999999999999887788888777778887765

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

Probab=91.23  E-value=2  Score=25.46  Aligned_cols=45  Identities=16%  Similarity=0.173  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +|...+++..+.. +.+...+..+-..+...|++++|...+++...
T Consensus       132 ~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~  176 (355)
T cd05804         132 RAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRD  176 (355)
T ss_pred             HHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhh
Confidence            4555555554432 22345555555566666666666666666544

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.

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

Probab=91.22  E-value=2.2  Score=25.98  Aligned_cols=60  Identities=17%  Similarity=0.062  Sum_probs=44.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      ++|...++.....  .| +...|..+-.+|.+.|++++|+..|+...+.  .|+......++.-|
T Consensus        53 ~eAl~~~~~Al~l--~P~~~~a~~~lg~~~~~lg~~~eA~~~~~~al~l--~P~~~~~~~~l~~~  113 (356)
T PLN03088         53 TEAVADANKAIEL--DPSLAKAYLRKGTACMKLEEYQTAKAALEKGASL--APGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            5677777777654  45 6777888888899999999999999999875  45555555555444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.15  E-value=0.27  Score=30.09  Aligned_cols=38  Identities=18%  Similarity=0.101  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           33 ADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        33 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .=++++++.++..-.+-|+-||.++++.+|+.+.+.+.
T Consensus       113 ky~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n  150 (418)
T KOG4570|consen  113 KYDPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKEN  150 (418)
T ss_pred             ccChHHHHHHHhCcchhccccchhhHHHHHHHHHhccc
Confidence            34678999999999999999999999999999998764

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=91.09  E-value=1.3  Score=23.08  Aligned_cols=43  Identities=9%  Similarity=0.172  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVS   45 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~   45 (71)
                      ++..+|..|.++|+.- ...-|...-..+.+.|++.+|.++|+.
T Consensus        81 ~~~~if~~l~~~~IG~~~A~fY~~wA~~le~~~~~~~A~~I~~~  124 (126)
T PF08311_consen   81 DPREIFKFLYSKGIGTKLALFYEEWAEFLEKRGNFKKADEIYQL  124 (126)
T ss_dssp             HHHHHHHHHHHHTTSTTBHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCccHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence            4566777777666655 355555555556667777777777653

This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.

>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=91.09  E-value=1.1  Score=27.87  Aligned_cols=45  Identities=20%  Similarity=0.188  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +.|.++.++..+.  .| +..+|..|..+|.+.|+++.|+-.++.|.-
T Consensus       251 ~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  251 ELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             HHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            4677777777654  67 566999999999999999999999998874

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

>PRK14574 hmsH outer membrane protein; Provisional

Probab=90.96  E-value=2.9  Score=28.59  Aligned_cols=45  Identities=11%  Similarity=0.126  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +|.++++++.+.  .| +...+..+...+.+.++.++|++.++.....
T Consensus       120 ~Aiely~kaL~~--dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~  165 (822)
T PRK14574        120 QALALWQSSLKK--DPTNPDLISGMIMTQADAGRGGVVLKQATELAER  165 (822)
T ss_pred             HHHHHHHHHHhh--CCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc
Confidence            455555555443  22 2344444455555555555555555555443

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

Probab=90.83  E-value=1.7  Score=26.57  Aligned_cols=51  Identities=18%  Similarity=0.042  Sum_probs=42.2

Q ss_pred             CcCHHHHHHHHHHHHhc-----CCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276           17 NPDTSTCNALMDGFCLA-----DRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus        17 ~p~~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      ..|-.+|-+++.-|...     +.++-....++.|.+-|++-|..+|+.||+.+=|
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPK  119 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPK  119 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcc
Confidence            34778888888888754     5677777889999999999999999999998765

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

Probab=90.64  E-value=1.8  Score=23.89  Aligned_cols=36  Identities=17%  Similarity=0.152  Sum_probs=31.8

Q ss_pred             cCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276           14 RGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        14 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ....|+..+|..++..+...|+.++|.++..++..-
T Consensus       138 l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~l  173 (193)
T PF11846_consen  138 LRRRPDPNVYQRYALALALLGDPEEARQWLARARRL  173 (193)
T ss_pred             HHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            345899999999999999999999999999998754

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

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

Probab=90.62  E-value=0.28  Score=18.65  Aligned_cols=22  Identities=14%  Similarity=0.214  Sum_probs=18.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhC
Q 042276           28 DGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        28 ~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ..+.+.|++++|.+.|++..+.
T Consensus         8 ~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    8 RCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHH
Confidence            3466789999999999998765

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

Probab=90.46  E-value=2.5  Score=27.80  Aligned_cols=48  Identities=15%  Similarity=0.122  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSA   67 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~   67 (71)
                      ..+|...|+.-.+..-+..|..+|.+.++.+..+ +++.++++|.-+|.
T Consensus       366 tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs  414 (656)
T KOG1914|consen  366 TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS  414 (656)
T ss_pred             ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc
Confidence            3455555555555555666666666666655555 55566666665553

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=90.41  E-value=2.7  Score=27.15  Aligned_cols=49  Identities=8%  Similarity=-0.105  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ...|.++--.....|++++|...+++.....  |+...|..+-+.+...|+
T Consensus       420 ~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~  468 (517)
T PRK10153        420 PRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGD  468 (517)
T ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCC
Confidence            3444444333344455555555555555443  455555555555544443

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=90.26  E-value=2.8  Score=26.76  Aligned_cols=49  Identities=8%  Similarity=-0.130  Sum_probs=23.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH----HHHHHHHHHHHhcc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA----FSHSILINGGSARI   69 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~li~~~~~~~   69 (71)
                      +...|+.+=.+|.+.|++++|+..|++-.+.  .||.    .+|..+-.+|.+.|
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LG  126 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYRE  126 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcC
Confidence            3444555555555555555555555554433  2332    23444444444444

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=90.19  E-value=4.1  Score=27.35  Aligned_cols=64  Identities=6%  Similarity=-0.021  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc-HHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD-AFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~   69 (71)
                      ++|....+.....  .| +....+.+=.++.+.|+.++|..+|++....  .|+ ..++..+=.++-+.|
T Consensus       137 eeA~~~~~~~l~~--~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G  202 (694)
T PRK15179        137 EAGRAEIELYFSG--GSSSAREILLEAKSWDEIGQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRG  202 (694)
T ss_pred             HHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcC
Confidence            3444444444433  34 2333333344444566666666666666552  222 444444444444443

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=90.16  E-value=4.1  Score=27.34  Aligned_cols=28  Identities=18%  Similarity=0.077  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ..+..+...+.+.|++++|...+++..+
T Consensus        84 ~a~~~la~~l~~~g~~~eA~~~l~~~l~  111 (765)
T PRK10049         84 DYQRGLILTLADAGQYDEALVKAKQLVS  111 (765)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3334444444444455555544444443

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

Probab=90.15  E-value=2.7  Score=25.23  Aligned_cols=47  Identities=19%  Similarity=0.152  Sum_probs=40.3

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|.-+|++|-++ ..|+..+-|.+..++...+++++|+.++++...+
T Consensus       190 qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  190 QDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             hhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            5788899998642 5789999999999999999999999999998765

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=89.85  E-value=4.4  Score=27.20  Aligned_cols=46  Identities=17%  Similarity=0.128  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|..+++...+.  .| +......+...+.+.+++++|+..+++....
T Consensus       103 ~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~  149 (694)
T PRK15179        103 DEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG  149 (694)
T ss_pred             HHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc
Confidence            5566666665543  55 4555666666666777777777766666655

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

Probab=89.84  E-value=2.4  Score=26.22  Aligned_cols=48  Identities=8%  Similarity=0.047  Sum_probs=39.4

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +.|.+.++...+.+-..-..+-..+..+|.+.|++++.+..+.++.+.
T Consensus       231 ~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         231 QKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             HHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            567778888877765556778888999999999999999999888765

>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=89.81  E-value=0.61  Score=17.26  Aligned_cols=21  Identities=29%  Similarity=0.197  Sum_probs=17.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHH
Q 042276           24 NALMDGFCLADRFDRARELLV   44 (71)
Q Consensus        24 ~~li~~~~~~g~~~~a~~~~~   44 (71)
                      ..+-..+...|++++|+.+++
T Consensus         5 ~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    5 LALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHcCCHHHHHHHHh
Confidence            345567889999999999876

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

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=89.66  E-value=5.3  Score=27.95  Aligned_cols=36  Identities=11%  Similarity=-0.180  Sum_probs=18.2

Q ss_pred             cCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           33 ADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        33 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .|++++|...+++..+.  .|+...|..+-..+.+.|+
T Consensus       589 ~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~  624 (987)
T PRK09782        589 PGQPELALNDLTRSLNI--APSANAYVARATIYRQRHN  624 (987)
T ss_pred             CCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCC
Confidence            35555555555555433  3444555555555444443

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

Probab=89.62  E-value=0.9  Score=20.75  Aligned_cols=30  Identities=13%  Similarity=0.296  Sum_probs=23.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      |-.--=-+|.++.+.|++++|.++.+++..
T Consensus        22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~~   51 (62)
T PF14689_consen   22 DFLNHLQVIYGLLQLGKYEEAKEYIKELSK   51 (62)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            445555679999999999999999998864

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=89.46  E-value=1.8  Score=22.22  Aligned_cols=34  Identities=15%  Similarity=0.142  Sum_probs=26.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276           27 MDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus        27 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      +..+.+.|++++|..+.+.+    +.||...|-.|-.+
T Consensus        46 lsSLmNrG~Yq~Al~l~~~~----~~pdlepw~ALce~   79 (115)
T TIGR02508        46 LSSLMNRGDYQSALQLGNKL----CYPDLEPWLALCEW   79 (115)
T ss_pred             HHHHHccchHHHHHHhcCCC----CCchHHHHHHHHHH
Confidence            34566888888888877766    58999999887554

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.

>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=89.46  E-value=1.2  Score=19.95  Aligned_cols=47  Identities=13%  Similarity=0.036  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+....... +.+..++..+...+...|+++.|...+....+.
T Consensus        51 ~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          51 EEALEDYEKALELD-PDNAKAYYNLGLAYYKLGKYEEALEAYEKALEL   97 (100)
T ss_pred             HHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHhHHHHHHHHHHHHcc
Confidence            56777787776543 224568888888999999999999999887643

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=89.21  E-value=2.2  Score=22.81  Aligned_cols=64  Identities=8%  Similarity=-0.133  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHHhcCCCc--CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP--DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGS   66 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~   66 (71)
                      ++|...|+......-.|  ...+|..+=..+.+.|++++|+..++...... .....++..+-..+.
T Consensus        52 ~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~i~~  117 (168)
T CHL00033         52 AEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAVICH  117 (168)
T ss_pred             HHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHH
Confidence            56777777775443222  23577777778888999999999988887541 122344555544444

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

Probab=89.13  E-value=3.6  Score=25.72  Aligned_cols=54  Identities=13%  Similarity=-0.029  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHS   59 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   59 (71)
                      .+|.+.|+.-..+  .|.+-||-.+-++|-+.++++.|+.+|.+-.+.  .|-.+||-
T Consensus       240 r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l  293 (478)
T KOG1129|consen  240 RRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYL  293 (478)
T ss_pred             hhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhh
Confidence            3556666655544  677888889999999999999999999887655  46556654

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=89.10  E-value=2.4  Score=23.12  Aligned_cols=47  Identities=11%  Similarity=0.139  Sum_probs=33.1

Q ss_pred             hHHHHHHHHHHhc-CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC
Q 042276            2 DEANGLAELMIQR-GVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG   50 (71)
Q Consensus         2 ~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   50 (71)
                      +++..+++.|.-. =-.|...++-..|  +.+.|++++|+++|++..+.+
T Consensus        27 ~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        27 YDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccC
Confidence            4667777777543 1122455666665  668999999999999998775

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

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=89.09  E-value=2  Score=22.23  Aligned_cols=28  Identities=7%  Similarity=0.050  Sum_probs=13.9

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhc
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLA   33 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~   33 (71)
                      ...++.+...+ ..+....|.++..|++.
T Consensus        27 ~~yLe~~~~~~-~~~~~~~~~li~ly~~~   54 (140)
T smart00299       27 IPYLESALKLN-SENPALQTKLIELYAKY   54 (140)
T ss_pred             HHHHHHHHccC-ccchhHHHHHHHHHHHH
Confidence            33444444443 24555566666666554

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

Probab=89.06  E-value=2.1  Score=28.81  Aligned_cols=45  Identities=11%  Similarity=0.087  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHH
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGS   66 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~   66 (71)
                      ...|++|-+-|-+.|.++.|.++|.+-...-  ..+.-|+.+.++|+
T Consensus       248 g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya  292 (835)
T KOG2047|consen  248 GFLWCSLADYYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYA  292 (835)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHH
Confidence            6789999999999999999999999887652  24455667777665

>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=88.97  E-value=2.1  Score=23.56  Aligned_cols=35  Identities=11%  Similarity=0.159  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD   54 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   54 (71)
                      ...+..+-+-|++.|+.+.|++.|.++......|.
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~   70 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPG   70 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHH
Confidence            45677888889999999999999999987644443

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.

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

Probab=88.81  E-value=2.1  Score=25.92  Aligned_cols=48  Identities=10%  Similarity=0.074  Sum_probs=34.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           17 NPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        17 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      -|+..-|-..|.++++.++|++-.++...  ++    +++.|...+..|.+.|+
T Consensus       205 v~dkrfw~lki~aLa~~~~w~eL~~fa~s--kK----sPIGyepFv~~~~~~~~  252 (319)
T PF04840_consen  205 VPDKRFWWLKIKALAENKDWDELEKFAKS--KK----SPIGYEPFVEACLKYGN  252 (319)
T ss_pred             CcHHHHHHHHHHHHHhcCCHHHHHHHHhC--CC----CCCChHHHHHHHHHCCC
Confidence            46788888888888888888887776543  11    45777777777776664

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

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

Probab=88.77  E-value=2.6  Score=23.14  Aligned_cols=60  Identities=15%  Similarity=0.174  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHHhcCCCc---CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP---DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      +++..+++.+...  +|   ...++-..+  +.+.|++.+|+++|++....+  |...--..|+..|..
T Consensus        27 ~D~e~lL~ALrvL--RP~~~e~~~~~~~l--~i~r~~w~dA~rlLr~l~~~~--~~~p~~kALlA~CL~   89 (160)
T PF09613_consen   27 DDAEALLDALRVL--RPEFPELDLFDGWL--HIVRGDWDDALRLLRELEERA--PGFPYAKALLALCLY   89 (160)
T ss_pred             HHHHHHHHHHHHh--CCCchHHHHHHHHH--HHHhCCHHHHHHHHHHHhccC--CCChHHHHHHHHHHH
Confidence            4667777777543  44   345555555  568999999999999987663  443334455555543

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

Probab=88.76  E-value=3.4  Score=28.56  Aligned_cols=65  Identities=20%  Similarity=0.035  Sum_probs=47.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ++|..+++.....+.. |..|-.++-.+|-+.++.++|..++++....  .|+..-...+..+|++.+
T Consensus        60 ~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFmayvR~~  124 (932)
T KOG2053|consen   60 DEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMAYVREK  124 (932)
T ss_pred             hhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHHHHHHH
Confidence            4566666666544433 7888888888888888999998888887654  577777777777777644

>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=88.72  E-value=1.8  Score=21.08  Aligned_cols=41  Identities=5%  Similarity=-0.010  Sum_probs=27.7

Q ss_pred             hHHHHHHHHHHhcCCCc--CHHHHHHHHHHHHhcCCHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP--DTSTCNALMDGFCLADRFDRAREL   42 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~   42 (71)
                      ++|...|....++-..|  --.+...++.+|+.-|++.+++++
T Consensus        23 ~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~~L~f   65 (80)
T PF10579_consen   23 QQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYREMLAF   65 (80)
T ss_pred             HHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35677777776544333  245677778888888888887764

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

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

Probab=88.21  E-value=5.1  Score=25.81  Aligned_cols=65  Identities=18%  Similarity=0.059  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH-HHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA-FSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~   70 (71)
                      ++|...++++...  .| |+.-+....+.+.+.++.++|.+.++.+...  .|+. ..+-.+-..+.+.|+
T Consensus       323 d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~  389 (484)
T COG4783         323 DEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGK  389 (484)
T ss_pred             chHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCC
Confidence            5788888887654  55 6777777788899999999999999999876  4653 333334444444443

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

Probab=88.08  E-value=3.1  Score=26.12  Aligned_cols=48  Identities=13%  Similarity=-0.092  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      -.+.++=.-|.+.+.+.+|.+.|+.-.+.  .|+..+|+-+-.+|.+.|+
T Consensus       329 ~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~  376 (400)
T COG3071         329 LLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGE  376 (400)
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCC
Confidence            44444544566677777777777744433  5677777777666666554

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=88.01  E-value=7.1  Score=27.56  Aligned_cols=53  Identities=19%  Similarity=0.039  Sum_probs=41.8

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           17 NPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        17 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +++...+..+-..+.+.|++++|++.|++..+.. ..+...+..+...+...|+
T Consensus       600 p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~  652 (1157)
T PRK11447        600 PPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGD  652 (1157)
T ss_pred             CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCC
Confidence            3466677778888999999999999999998762 2356788888888877765

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=87.53  E-value=1.5  Score=18.77  Aligned_cols=25  Identities=28%  Similarity=0.396  Sum_probs=21.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCC
Q 042276           26 LMDGFCLADRFDRARELLVSMGSKG   50 (71)
Q Consensus        26 li~~~~~~g~~~~a~~~~~~m~~~g   50 (71)
                      +-.+|.+.|+.+.|.+++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            4568999999999999999998655

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.

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

Probab=87.49  E-value=1.1  Score=17.22  Aligned_cols=29  Identities=10%  Similarity=0.076  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      .+|..+=..+...|++++|+..|++..+.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            35677778899999999999999998754

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 ....

>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2

Probab=87.46  E-value=1.9  Score=20.12  Aligned_cols=37  Identities=19%  Similarity=0.141  Sum_probs=24.5

Q ss_pred             cCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           33 ADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        33 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .++.+.+.+++++....|..|.......+..+.-+-|
T Consensus        14 ~~d~~~~~~~~~~~l~~g~~~~~i~~~~l~p~m~~iG   50 (79)
T PF02607_consen   14 AGDEEEAEALLEEALAQGYPPEDIIEEILMPAMEEIG   50 (79)
T ss_dssp             TT-CCHHHHHHHHHHHCSSSTTHHHHHTHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence            5677777777777777777777666666666655433

1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=87.34  E-value=3.1  Score=22.37  Aligned_cols=52  Identities=4%  Similarity=-0.245  Sum_probs=36.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc--HHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD--AFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~   70 (71)
                      ....+..+-..+.+.|++++|...|++..+..-.+.  ...+..+-..+.+.|+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~   87 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGE   87 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCC
Confidence            455666677778889999999999999976532222  3566666666666665

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

Probab=87.33  E-value=4  Score=24.18  Aligned_cols=30  Identities=27%  Similarity=0.189  Sum_probs=15.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      |...||.+=-+|-+.|++++|..-|.+..+
T Consensus       133 d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~  162 (257)
T COG5010         133 DWEAWNLLGAALDQLGRFDEARRAYRQALE  162 (257)
T ss_pred             ChhhhhHHHHHHHHccChhHHHHHHHHHHH
Confidence            455555555555555555555555555543

>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP)

Probab=87.27  E-value=0.19  Score=22.66  Aligned_cols=30  Identities=20%  Similarity=0.287  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHh
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCL   32 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~   32 (71)
                      +...+|..|.++..+|....||-.|.-|..
T Consensus        10 ~lI~vFK~~pSr~YD~~Tr~W~F~L~Dy~~   39 (55)
T PF07443_consen   10 ELIAVFKQMPSRNYDPKTRKWNFSLEDYST   39 (55)
T ss_pred             HHHHHHHcCcccccCccceeeeeeHHHHHH
Confidence            456778888888888877777777665543

This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus

>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=87.06  E-value=6.3  Score=25.59  Aligned_cols=60  Identities=12%  Similarity=0.023  Sum_probs=39.2

Q ss_pred             hHHHHHHHHHHhcCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPD-TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      ++|...+.+-  ...-+| .......-..+.+.|+.++|..+++.+..++  |+...|-..+..+
T Consensus        21 ~~AL~~L~~~--~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~   81 (517)
T PF12569_consen   21 EEALEHLEKN--EKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEA   81 (517)
T ss_pred             HHHHHHHHhh--hhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHH
Confidence            3455555442  222344 4445555677889999999999999999884  6666665555444

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 [], [].

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=87.00  E-value=6.1  Score=25.33  Aligned_cols=47  Identities=13%  Similarity=0.091  Sum_probs=37.9

Q ss_pred             ChHHHHHHHHHHhcCCCcCH----HHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            1 MDEANGLAELMIQRGVNPDT----STCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +++|...|+.-.+.  .|+.    .+|..+-.+|.+.|+.++|+..+++..+.
T Consensus        91 yeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         91 VKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            36788888877655  5653    46899999999999999999999998764

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=86.27  E-value=2.7  Score=20.50  Aligned_cols=48  Identities=8%  Similarity=-0.024  Sum_probs=36.2

Q ss_pred             hHHHHHHHHHHhcC--CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRG--VNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~--~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+......  ......++..+-..+.+.|++++|.+.+++..+.
T Consensus        56 ~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        56 ADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            56888888886542  1112456777777888999999999999999877

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.

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

Probab=86.15  E-value=3.1  Score=21.07  Aligned_cols=55  Identities=13%  Similarity=-0.090  Sum_probs=39.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHS   59 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~   59 (71)
                      ++|...++...... +.+...+..+-..+...|++++|...|+...+.  .|+...+.
T Consensus        68 ~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~  122 (135)
T TIGR02552        68 EEAIDAYALAAALD-PDDPRPYFHAAECLLALGEPESALKALDLAIEI--CGENPEYS  122 (135)
T ss_pred             HHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--ccccchHH
Confidence            46677777765542 335677777777888999999999999988876  35555443

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

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

Probab=85.92  E-value=4.5  Score=24.36  Aligned_cols=66  Identities=14%  Similarity=-0.026  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHH----HHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNAL----MDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~l----i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      +-|.+.++.|.+-.   +-.|-+-+    |+-..-.+...+|.-+|++|.++ ..|+..+.+-...++...|+|
T Consensus       154 d~A~~~lk~mq~id---ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~  223 (299)
T KOG3081|consen  154 DLAEKELKKMQQID---EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRY  223 (299)
T ss_pred             HHHHHHHHHHHccc---hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCH
Confidence            34566666665432   34444434    44444456789999999999764 568888888887777766653

>PRK09462 fur ferric uptake regulator; Provisional

Probab=85.86  E-value=3.7  Score=21.80  Aligned_cols=60  Identities=8%  Similarity=0.002  Sum_probs=43.3

Q ss_pred             HHHHhcCCCcCHHHHHHHHHHHHhc-CCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            9 ELMIQRGVNPDTSTCNALMDGFCLA-DRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         9 ~~m~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.+.+.|++++.. -..++..+... +..-.|.++++.+.+.+...+..|..-.|+.+.+.|
T Consensus         6 ~~l~~~glr~T~q-R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~G   66 (148)
T PRK09462          6 TALKKAGLKVTLP-RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAG   66 (148)
T ss_pred             HHHHHcCCCCCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCC
Confidence            3456677775543 34555666654 467799999999999887778888888888887765

>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9

Probab=85.69  E-value=2.9  Score=20.37  Aligned_cols=58  Identities=21%  Similarity=0.290  Sum_probs=39.9

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ..+++.+.+.|+    .|..-.-..-+...+.+.+.++++.+..+|    ..+|....+++-..|+
T Consensus        19 ~~v~~~L~~~~V----lt~~~~e~I~~~~tr~~q~~~LLd~L~~RG----~~AF~~F~~aL~~~~~   76 (84)
T cd08326          19 KYLWDHLLSRGV----FTPDMIEEIQAAGSRRDQARQLLIDLETRG----KQAFPAFLSALRETGQ   76 (84)
T ss_pred             HHHHHHHHhcCC----CCHHHHHHHHcCCCHHHHHHHHHHHHHhcC----HHHHHHHHHHHHhcCc
Confidence            456777776653    333333333456677889999999999996    6778888888766654

Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt

>COG5210 GTPase-activating protein [General function prediction only]

Probab=85.37  E-value=7.5  Score=24.88  Aligned_cols=59  Identities=12%  Similarity=0.006  Sum_probs=49.0

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHH
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILIN   63 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~   63 (71)
                      -+++..|...++.+...++.-++..+.+.-.++.+.++++.+--.|+.-....+.+++.
T Consensus       362 p~l~~hl~~~~~~~~~~~~~w~l~lF~~~~p~e~~lriwD~lf~eg~~~l~~~~~~~l~  420 (496)
T COG5210         362 PELYEHLLREGVVLLMFAFRWFLTLFVREFPLEYALRIWDCLFLEGSSMLFQLALAILK  420 (496)
T ss_pred             HHHHHHHHHcCCchhhhhHHHHHHHHHhcCCHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            46788899999999999999999999999999999999999988876554444444443

>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1

Probab=85.34  E-value=3.9  Score=21.50  Aligned_cols=16  Identities=38%  Similarity=0.405  Sum_probs=7.5

Q ss_pred             HHHHHHHHhhCCCCcc
Q 042276           39 ARELLVSMGSKGCKQD   54 (71)
Q Consensus        39 a~~~~~~m~~~g~~p~   54 (71)
                      +.++|..|..+|+-..
T Consensus        82 p~~if~~L~~~~IG~~   97 (125)
T smart00777       82 PRELFQFLYSKGIGTK   97 (125)
T ss_pred             HHHHHHHHHHCCcchh
Confidence            3445555555544433

Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.

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

Probab=85.22  E-value=2.1  Score=27.76  Aligned_cols=45  Identities=13%  Similarity=0.081  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHHhcC-CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRG-VNPDTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus         2 ~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      +.|..+|-+..+.+ +.+++.+++++|.-++ .|++..|.++|+-=.
T Consensus       414 ~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl  459 (660)
T COG5107         414 EAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGL  459 (660)
T ss_pred             HHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHH
Confidence            56788999998887 7889999999998777 466788888887543

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=85.14  E-value=8.1  Score=25.04  Aligned_cols=55  Identities=13%  Similarity=-0.087  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSI   60 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~   60 (71)
                      ++|...++.....+  |+...|..+-..+...|++++|.+.+++....  .|...||..
T Consensus       437 ~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~P~~pt~~~  491 (517)
T PRK10153        437 DEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--RPGENTLYW  491 (517)
T ss_pred             HHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCCchHHH
Confidence            57788888877664  78889999999999999999999999888654  344445543

>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes

Probab=84.80  E-value=2.8  Score=19.45  Aligned_cols=51  Identities=12%  Similarity=0.024  Sum_probs=39.5

Q ss_pred             CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276           16 VNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus        16 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      +.|+...++-++...++..-.++++..+.+..++|. .+..+|---+..+++
T Consensus         4 v~~~~~l~~Ql~el~Aed~AieDtiy~L~~al~~g~-I~~d~~lK~vR~LaR   54 (65)
T PF09454_consen    4 VVAEDPLSNQLYELVAEDHAIEDTIYYLDRALQRGS-IDLDTFLKQVRSLAR   54 (65)
T ss_dssp             EE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-S-HHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHH
Confidence            356778899999999999999999999999999985 455666655555554

ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=84.53  E-value=6.7  Score=23.62  Aligned_cols=60  Identities=12%  Similarity=0.043  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      .++..+|++....  +| |+.+-.-+=..+...|++.+|...++.|...  -|....+..+|..-
T Consensus       210 a~a~~ll~~al~~--D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~--lp~~~~rr~~ie~~  270 (287)
T COG4235         210 AKARALLRQALAL--DPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDL--LPADDPRRSLIERS  270 (287)
T ss_pred             HHHHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--CCCCCchHHHHHHH
Confidence            3677888888755  66 4555555566788999999999999999876  34446666666543

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

Probab=84.48  E-value=4.4  Score=26.77  Aligned_cols=45  Identities=13%  Similarity=0.070  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ..|..+|.+..+.+..+ ++.+++++|.-+|.. +.+.|.++|+-=.
T Consensus       383 kaaR~iF~kaR~~~r~~hhVfVa~A~mEy~csk-D~~~AfrIFeLGL  428 (656)
T KOG1914|consen  383 KAARKIFKKAREDKRTRHHVFVAAALMEYYCSK-DKETAFRIFELGL  428 (656)
T ss_pred             HHHHHHHHHHhhccCCcchhhHHHHHHHHHhcC-ChhHHHHHHHHHH
Confidence            46788999998877777 899999999988854 5578888887543

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

Probab=84.37  E-value=8.3  Score=28.41  Aligned_cols=63  Identities=17%  Similarity=-0.032  Sum_probs=44.3

Q ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            4 ANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .+++|+...+.  +-.-..|..|..-|.+.+.+++|-++++.|.++= .-....|......+.++.
T Consensus      1516 l~kVFeRAcqy--cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF-~q~~~vW~~y~~fLl~~n 1578 (1710)
T KOG1070|consen 1516 LKKVFERACQY--CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKF-GQTRKVWIMYADFLLRQN 1578 (1710)
T ss_pred             HHHHHHHHHHh--cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHh-cchhhHHHHHHHHHhccc
Confidence            45566655433  3345678888888999999999999999997651 245667777777776543

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=84.31  E-value=3  Score=23.05  Aligned_cols=56  Identities=9%  Similarity=-0.046  Sum_probs=45.7

Q ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            6 GLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         6 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      +..+.+.+.++.|+...|..+|+.+.+.|+    ...+..+...++-||.......+-.+
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~----~~~L~qllq~~Vi~DSk~lA~~LLs~   70 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQ----FSQLHQLLQYHVIPDSKPLACQLLSL   70 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCC----HHHHHHHHhhcccCCcHHHHHHHHHh
Confidence            445556678999999999999999999997    78888998988888888777666443

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

Probab=84.06  E-value=7.7  Score=23.93  Aligned_cols=58  Identities=10%  Similarity=0.001  Sum_probs=46.7

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      .++|+.|...++.|--.+|.=+.-.+.+.=.+.+++.+++.+......     |..|+..||.
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            578899999999998888887777788888889999999998755332     7777777774

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

Probab=83.95  E-value=3.9  Score=26.68  Aligned_cols=53  Identities=11%  Similarity=0.044  Sum_probs=36.9

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAF   56 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   56 (71)
                      ++|...|++..+.  .||..+---++-++.-.|+.+...+.|..|..-...||..
T Consensus       293 ~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~ddd  345 (840)
T KOG2003|consen  293 DDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDD  345 (840)
T ss_pred             hhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcc
Confidence            5677777777655  6776555555556666888888888999888765555443

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

Probab=83.73  E-value=9.7  Score=24.82  Aligned_cols=53  Identities=15%  Similarity=0.046  Sum_probs=41.7

Q ss_pred             cCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276           14 RGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus        14 ~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      ..+.| |...|.+|=++|.+.+++++|++.|.+....|- .+...|..|-+.+-+
T Consensus       425 ~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d-te~~~l~~LakLye~  478 (559)
T KOG1155|consen  425 LELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD-TEGSALVRLAKLYEE  478 (559)
T ss_pred             HhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc-cchHHHHHHHHHHHH
Confidence            44567 899999999999999999999999999987762 244667666666543

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=83.63  E-value=1.8  Score=16.44  Aligned_cols=27  Identities=11%  Similarity=0.019  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +|..+=..+.+.|++++|.+.|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            455666778899999999999998764

...

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=83.36  E-value=7.7  Score=23.34  Aligned_cols=56  Identities=13%  Similarity=0.122  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCC---HHHHHHHHHHHhhCCCCccHHHH
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADR---FDRARELLVSMGSKGCKQDAFSH   58 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~~~~   58 (71)
                      ....+++.+...|+.. |..-+-+-|-+++....   ...+.++++.+.+.|+++....|
T Consensus       161 ~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~y  220 (297)
T PF13170_consen  161 RMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHY  220 (297)
T ss_pred             HHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccc
Confidence            3444555555555544 33333333333333221   22455555555555555544443

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

Probab=83.08  E-value=2.8  Score=29.23  Aligned_cols=69  Identities=10%  Similarity=-0.036  Sum_probs=49.6

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCccHHHHHHHHHHHHhccc
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK-GCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +.+|..+|.+..+... -+.-+|--+-++|...|++..|+++|+...+. .-.-+......|-.++.+.|+
T Consensus       662 ~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~  731 (1018)
T KOG2002|consen  662 FSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGK  731 (1018)
T ss_pred             chHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhh
Confidence            3578889999876543 13456667788899999999999999988654 433456666777676666554

>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]

Probab=82.33  E-value=4.9  Score=21.85  Aligned_cols=40  Identities=8%  Similarity=0.003  Sum_probs=32.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276           26 LMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus        26 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      ++..+.+.|...+...++++|.++|+..+...|+-++.-.
T Consensus       115 vL~~ak~kgLisk~Kpild~LI~~GF~iS~~~~eeiL~~~  154 (157)
T COG2405         115 VLALAKSKGLISKDKPILDELIEKGFRISRSILEEILRKL  154 (157)
T ss_pred             HHHHHHHcCcccchHHHHHHHHHhcCcccHHHHHHHHHHh
Confidence            3444556788888999999999999999999998887643

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=82.20  E-value=6.5  Score=21.73  Aligned_cols=28  Identities=11%  Similarity=-0.070  Sum_probs=12.8

Q ss_pred             HHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           42 LLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        42 ~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.+.+.+.++.|+...|..+|+.+.+.|
T Consensus        16 YirSl~~~~i~~~~~L~~lli~lLi~~~   43 (167)
T PF07035_consen   16 YIRSLNQHNIPVQHELYELLIDLLIRNG   43 (167)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHcC
Confidence            3334444444444444444444444444

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

Probab=82.20  E-value=8.6  Score=23.08  Aligned_cols=50  Identities=16%  Similarity=0.037  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ..+...++..+...|+.+.+.+.++++.... .-|...|..+|.+|.+.|+
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~  202 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGR  202 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCC
Confidence            4556667777888899999999999998762 3488999999999998875

>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84

Probab=82.00  E-value=4.4  Score=19.67  Aligned_cols=35  Identities=23%  Similarity=0.134  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           34 DRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        34 g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +..+.+.+++..-.++.-  ...|...|+.++.+.|+
T Consensus        44 ~~~eq~~~mL~~W~~r~g--~~AT~~~L~~aL~~~~~   78 (86)
T cd08318          44 DIKMQAKQLLVAWQDREG--SQATPETLITALNAAGL   78 (86)
T ss_pred             CHHHHHHHHHHHHHHhcC--ccccHHHHHHHHHHcCc
Confidence            345667777777765521  34677778877776653

Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=81.82  E-value=8.4  Score=22.70  Aligned_cols=46  Identities=17%  Similarity=0.085  Sum_probs=30.3

Q ss_pred             hHHHHHHHHHHhcCCCcCH----HHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDT----STCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+.+.+.  .|+.    ..+--+-..|...|++++|...|+...+.
T Consensus       160 ~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~  209 (263)
T PRK10803        160 DDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN  209 (263)
T ss_pred             HHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4566677777654  3322    34444555677888888888888888754

>COG4003 Uncharacterized protein conserved in archaea [Function unknown]

Probab=81.27  E-value=4.4  Score=19.98  Aligned_cols=26  Identities=19%  Similarity=0.295  Sum_probs=23.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCC
Q 042276           25 ALMDGFCLADRFDRARELLVSMGSKG   50 (71)
Q Consensus        25 ~li~~~~~~g~~~~a~~~~~~m~~~g   50 (71)
                      ++++-+.++.--++|+++++-|.++|
T Consensus        36 tV~D~L~rCdT~EEAlEii~yleKrG   61 (98)
T COG4003          36 TVIDFLRRCDTEEEALEIINYLEKRG   61 (98)
T ss_pred             hHHHHHHHhCcHHHHHHHHHHHHHhC
Confidence            46777889999999999999999987

>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095); InterPro: IPR018662 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=80.91  E-value=6.3  Score=20.66  Aligned_cols=39  Identities=13%  Similarity=0.077  Sum_probs=28.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276           25 ALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus        25 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      ++|+-.-++...++|+++.+-|.++| +.+...-+.|-..
T Consensus        66 tViD~lrRC~T~EEALEVInylek~G-EIt~e~A~eLr~~  104 (128)
T PF09868_consen   66 TVIDYLRRCKTDEEALEVINYLEKRG-EITPEEAKELRSI  104 (128)
T ss_pred             hHHHHHHHhCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            46777889999999999999999988 3444444444333

>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=80.71  E-value=0.7  Score=23.99  Aligned_cols=38  Identities=13%  Similarity=0.272  Sum_probs=25.3

Q ss_pred             HHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 042276            7 LAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLV   44 (71)
Q Consensus         7 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~   44 (71)
                      .++.+...+-.-+....+.++..|++.++.+..+++++
T Consensus        29 yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   29 YLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             CHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            34555544444567777888888888877777777766

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.

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

Probab=80.53  E-value=8.3  Score=27.77  Aligned_cols=50  Identities=18%  Similarity=0.075  Sum_probs=41.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      |...|.-+++...+.|.+++-.+.+.-.++...+|...+  .||-+|++.+|
T Consensus      1132 Dps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~AyAkt~r 1181 (1666)
T KOG0985|consen 1132 DPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFAYAKTNR 1181 (1666)
T ss_pred             CcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHHHHHhch
Confidence            778899999999999999999998888888877777654  67778887665

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=80.06  E-value=6.2  Score=20.07  Aligned_cols=28  Identities=21%  Similarity=0.224  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      .-|+.++.-|...|.-++|++++.+...
T Consensus        40 ~~~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen   40 GKYQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             CCHHHHHHHHHccCccHHHHHHHHHHhc
Confidence            5689999999999999999999999987

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.

---

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	71
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-07
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-06

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 45.6 bits (106), Expect = 1e-07
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 3/67 (4%)

Query: 1   MDEANGLAEL---MIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFS 57
           +  A+ L  +     Q+         NA+M G+     F     +L  +   G   D  S
Sbjct: 143 LPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS 202

Query: 58  HSILING 64
           ++  +  
Sbjct: 203 YAAALQC 209

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 41.7 bits (96), Expect = 3e-06
 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 1/64 (1%)

Query: 1   MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRA-RELLVSMGSKGCKQDAFSHS 59
             E   +  ++   G+ PD  +  A +      D+        L  M  +G K  A   +
Sbjct: 181 FKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTA 240

Query: 60  ILIN 63
           +L++
Sbjct: 241 VLLS 244

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	71
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.86
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.85
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.85
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.72
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	98.54
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	98.54
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	97.68
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	97.68
2gw1_A	514	Mitochondrial precursor proteins import receptor;	97.64
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	97.62
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.62
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	97.62
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	97.53
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	97.46
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	97.33
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	97.32
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.29
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	97.25
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.23
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	97.22
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.2
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.19
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	97.18
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.18
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.13
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.1
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	97.09
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	97.08
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	97.07
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	97.07
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	97.07
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	97.06
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.03
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	96.99
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	96.99
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	96.99
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	96.99
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.95
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	96.95
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	96.92
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	96.92
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	96.87
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	96.86
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	96.85
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.82
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	96.81
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.81
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	96.75
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	96.74
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	96.73
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.73
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.73
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.71
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	96.71
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	96.71
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	96.7
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.7
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	96.67
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	96.64
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	96.58
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	96.57
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	96.52
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	96.47
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	96.45
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	96.43
3u4t_A	272	TPR repeat-containing protein; structural genomics	96.42
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	96.34
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	96.28
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	96.26
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.25
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.24
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	96.22
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	96.2
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.2
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	96.15
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	96.13
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	96.11
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	96.1
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.06
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	96.04
2gw1_A	514	Mitochondrial precursor proteins import receptor;	96.02
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	95.96
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.96
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	95.95
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	95.93
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	95.88
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	95.87
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	95.83
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.74
3u4t_A	272	TPR repeat-containing protein; structural genomics	95.71
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	95.67
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.66
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	95.64
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	95.61
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	95.55
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	95.51
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	95.51
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	95.45
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	95.42
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	95.32
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	95.21
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	95.16
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	95.14
2l6j_A	111	TPR repeat-containing protein associated with HSP;	95.13
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	95.1
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	95.01
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	95.01
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.0
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	94.97
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.95
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	94.86
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	94.85
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	94.81
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	94.81
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	94.78
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	94.67
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	94.62
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	94.61
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	94.48
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	94.42
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	94.36
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	94.34
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	94.33
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	94.33
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	94.21
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	94.17
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	94.13
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	94.11
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	94.06
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	93.89
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	93.89
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	93.86
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	93.8
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	93.66
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	93.54
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	93.51
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	93.43
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	93.34
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	93.3
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	93.26
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	93.21
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	93.19
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	93.19
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	93.16
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	93.15
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	93.14
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	92.92
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	92.92
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	92.9
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	92.78
4aez_C	223	MAD3, mitotic spindle checkpoint component MAD3; c	92.77
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	92.25
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	92.14
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	91.97
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	91.97
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	91.85
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	91.62
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	91.6
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	91.58
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	91.3
1pc2_A	152	Mitochondria fission protein; unknown function; NM	91.18
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	91.12
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	90.93
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	90.89
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	90.88
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	90.56
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	90.44
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	90.08
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	89.92
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	89.89
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	89.69
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	89.49
4ets_A	162	Ferric uptake regulation protein; metal binding pr	89.37
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	89.25
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	89.12
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	89.09
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	88.98
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	88.92
2b7e_A	59	PRE-mRNA processing protein PRP40; structural prot	88.78
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	88.78
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	88.16
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	88.03
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	87.78
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	87.77
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	87.71
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	87.69
4g1t_A	472	Interferon-induced protein with tetratricopeptide	87.31
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	86.9
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	86.59
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	86.59
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	86.58
4g1t_A	472	Interferon-induced protein with tetratricopeptide	86.15
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	85.98
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	85.84
2yru_A	118	Steroid receptor RNA activator 1; SRAP, structural	85.8
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	85.71
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	85.46
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	84.86
2w57_A	150	Ferric uptake regulation protein; gene regulation,	84.57
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	84.42
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	84.23
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	84.12
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	83.61
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	83.43
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	83.06
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	82.95
2p58_C	116	Putative type III secretion protein YSCG; type III	82.93
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	81.56
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	80.74

>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=99.86  E-value=2.1e-21  Score=117.47  Aligned_cols=68  Identities=16%  Similarity=0.044  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +|.++|++|.+.|+.||..|||++|++|++.|++++|+++|++|.+.|+.||..|||+||.+|++.|+
T Consensus        88 ~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~  155 (501)
T 4g26_A           88 RGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGD  155 (501)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCC
Confidence            45555555555555555555555555555555555555555555555555555555555555555543

>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=99.85  E-value=3.7e-21  Score=116.46  Aligned_cols=69  Identities=17%  Similarity=0.209  Sum_probs=67.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|++|.+.|+.||..|||++|.+|++.|++++|.++|++|.+.|+.||..||++||++|++.|+
T Consensus       122 ~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~  190 (501)
T 4g26_A          122 EMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKN  190 (501)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999986

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

Probab=99.85  E-value=1.7e-21  Score=124.89  Aligned_cols=70  Identities=17%  Similarity=0.126  Sum_probs=65.9

Q ss_pred             ChHHHHHHHHHH---hcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            1 MDEANGLAELMI---QRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         1 ~~~a~~~~~~m~---~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +++|.++|++|.   ..|+.||++|||+||++||+.|++++|.++|++|.+.|+.||.+|||+||+++|+.|+
T Consensus       143 leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI~glcK~G~  215 (1134)
T 3spa_A          143 LPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQ  215 (1134)
T ss_dssp             HHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhCCC
Confidence            368999998886   4689999999999999999999999999999999999999999999999999999875

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

Probab=99.72  E-value=3.3e-18  Score=109.95  Aligned_cols=68  Identities=18%  Similarity=0.214  Sum_probs=62.5

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCH-HHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRF-DRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      +++|.++|++|.+.|+.||++|||++|+++|+.|+. ++|.++|++|..+|+.||..+|++++++..+.
T Consensus       181 ~~eA~~Lf~eM~~~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~  249 (1134)
T 3spa_A          181 FKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA  249 (1134)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH
Confidence            368999999999999999999999999999999984 78999999999999999999999888776553

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

Probab=98.54  E-value=4.8e-07  Score=54.52  Aligned_cols=68  Identities=12%  Similarity=-0.184  Sum_probs=48.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCcc--HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK----GCKQD--AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~~~~~li~~~~~~~~   70 (71)
                      ++|.++|+++.+.. +.+..+|+.+...+.+.|++++|+++|+++.+.    +..|+  ..+|..+..+|.+.|+
T Consensus       458 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~  531 (597)
T 2xpi_A          458 LLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKM  531 (597)
T ss_dssp             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcC
Confidence            46777777776542 226777788888888888888888888777654    66676  6677777777777665

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

Probab=98.54  E-value=4.7e-07  Score=54.56  Aligned_cols=69  Identities=14%  Similarity=-0.018  Sum_probs=60.6

Q ss_pred             hHHHHHHHHHHhc----CCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQR----GVNPD--TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~----~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      ++|.++|+++.+.    +..|+  ..+|+.+..+|.+.|++++|+++|+++.+.+ ..+..+|..+..+|.+.|++
T Consensus       492 ~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~  566 (597)
T 2xpi_A          492 QTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIALVYLHKKIP  566 (597)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCH
Confidence            6789999999765    77887  7899999999999999999999999998764 34789999999999998874

>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=97.68  E-value=0.00063  Score=39.13  Aligned_cols=67  Identities=15%  Similarity=-0.029  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+++.+.. +.+..+|+.+...+.+.|++++|.+.++++.+.. ..+..++..+...+.+.|+
T Consensus       288 ~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  354 (388)
T 1w3b_A          288 AEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGK  354 (388)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCC
Confidence            34555555554431 2355566666666666666666666666665431 2234556666666665554

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

Probab=97.68  E-value=0.00054  Score=38.78  Aligned_cols=67  Identities=13%  Similarity=0.050  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|..+|+++.+. .+.+...|+.+-.++.+.|++++|+..|++..... .-+..++..+...+...|+
T Consensus       183 ~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~~~l~~l~~~~~~~g~  249 (291)
T 3mkr_A          183 QDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHPETLINLVVLSQHLGK  249 (291)
T ss_dssp             HHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            4677777777665 23467777878778888888888888888876542 1255667777666666554

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

Probab=97.64  E-value=0.00034  Score=41.19  Aligned_cols=66  Identities=8%  Similarity=-0.039  Sum_probs=55.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.++.+..  |+..+|..+..++.+.|++++|+..|+++.+.. ..+..+|..+..++.+.|+
T Consensus        23 ~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~   88 (514)
T 2gw1_A           23 DDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGK   88 (514)
T ss_dssp             HHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhh
Confidence            57888999998764  789999999999999999999999999998763 2356788888888887775

>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=97.62  E-value=0.00073  Score=32.54  Aligned_cols=65  Identities=14%  Similarity=0.001  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +|...++++.... +.+...+..+...+.+.|++++|.+.++++.+.. ..+..++..+...+.+.|
T Consensus        53 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  117 (136)
T 2fo7_A           53 EAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQG  117 (136)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHc
Confidence            3444444443321 1134444444455555555555555555554331 113344444444444443

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

Probab=97.62  E-value=0.00084  Score=32.05  Aligned_cols=67  Identities=15%  Similarity=0.036  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+.+..... +.+..++..+...+.+.|++++|..+|+++.... ..+..++..+...+.+.|+
T Consensus        26 ~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~   92 (125)
T 1na0_A           26 DEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGD   92 (125)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcC
Confidence            46777777776542 2356777788888888888888888888887642 2355667777766666554

>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=97.62  E-value=0.00098  Score=32.08  Aligned_cols=67  Identities=15%  Similarity=0.023  Sum_probs=52.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|..+++++.+.. +.+...+..+...+.+.|++++|..+++++.... ..+...+..+...+.+.|+
T Consensus        18 ~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~   84 (136)
T 2fo7_A           18 DEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGD   84 (136)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcC
Confidence            57888898887653 2367888889999999999999999999998653 2356677778777777665

>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=97.53  E-value=0.001  Score=38.27  Aligned_cols=66  Identities=15%  Similarity=-0.037  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+.+.+.  .| +..+|+.+...+.+.|++++|++.|+++.+.. ..+..+|..+...+.+.|+
T Consensus       254 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  320 (388)
T 1w3b_A          254 DLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGN  320 (388)
T ss_dssp             HHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCC
Confidence            3455566665543  23 45566666666666666666666666665542 3355666666666665554

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

Probab=97.46  E-value=0.0015  Score=36.92  Aligned_cols=63  Identities=13%  Similarity=-0.032  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHHhcCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD-TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.++++...+..|+ ...+..+-..+.+.|++++|++.+++      ..+...+..+...+.+.|+
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~  145 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDR  145 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCC
Confidence            345566666655554453 33333333555566666666666655      2345555555555555554

>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=97.33  E-value=0.0017  Score=37.76  Aligned_cols=67  Identities=6%  Similarity=-0.196  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|..+|+++.+.. +.+..+|..+...+.+.|++++|+..|+++.+.+ ..+..+|..+...|.+.|+
T Consensus        43 ~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  109 (450)
T 2y4t_A           43 ADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGK  109 (450)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCC
Confidence            46777777776541 2367778888888888888888888888887653 2246677777777776665

>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=97.32  E-value=0.00077  Score=41.05  Aligned_cols=55  Identities=11%  Similarity=-0.033  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      ++|...|..+         ..|.-+.+.+.+.|++++|.+.++++.      ++.+|..++.+|...|+|
T Consensus       139 eeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA~------~~~~Wk~v~~aCv~~~ef  193 (449)
T 1b89_A          139 DAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVCFACVDGKEF  193 (449)
T ss_dssp             TTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHcC------CchhHHHHHHHHHHcCcH
Confidence            4566666654         478888888888888888888888872      678888888888887753

>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=97.29  E-value=0.0037  Score=33.66  Aligned_cols=29  Identities=14%  Similarity=0.136  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ...+..+...+.+.|++++|+++|++...
T Consensus       105 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~  133 (252)
T 2ho1_A          105 ARVLNNYGGFLYEQKRYEEAYQRLLEASQ  133 (252)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence            44444444444444555555555444444

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

Probab=97.25  E-value=0.0032  Score=35.82  Aligned_cols=66  Identities=17%  Similarity=-0.113  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +|...|++..+.. +.+..+|+.+-..+.+.|++++|+..|++..+.. ..+..+|..+-..|.+.|+
T Consensus       231 ~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  296 (365)
T 4eqf_A          231 RAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGA  296 (365)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCC
Confidence            3444444443321 1134455555555555555555555555554431 1124444444444444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.23  E-value=0.0027  Score=32.91  Aligned_cols=66  Identities=14%  Similarity=0.049  Sum_probs=50.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+.....  .| +...|..+=.++.+.|++++|+..|++..+.. .-+...|..+=.+|.+.|+
T Consensus        53 ~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~  119 (151)
T 3gyz_A           53 EEAEVFFRFLCIY--DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQCQLRLKA  119 (151)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCC
Confidence            5788888888765  45 68888888888999999999999999987652 1245667777777777665

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=97.22  E-value=0.0042  Score=32.58  Aligned_cols=27  Identities=11%  Similarity=-0.203  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ..+..+-..+.+.|++++|+..|+++.
T Consensus       114 ~~~~~l~~~~~~~~~~~~A~~~~~~~~  140 (225)
T 2vq2_A          114 IANLNKGICSAKQGQFGLAEAYLKRSL  140 (225)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            333344444444444444444444443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.20  E-value=0.0055  Score=31.24  Aligned_cols=65  Identities=14%  Similarity=-0.097  Sum_probs=48.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.|++..+.  .| +..+|..+=..+.+.|++++|+..|++..+.  .| +..+|..+-..+.+.|+
T Consensus        48 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~  114 (150)
T 4ga2_A           48 DLAKKYICTYINV--QERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCKNDV  114 (150)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCC
Confidence            5677778777654  44 6788888888888899999999988888765  34 45667777777766654

>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=97.19  E-value=0.0043  Score=33.41  Aligned_cols=66  Identities=11%  Similarity=-0.114  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +|...+++..+.+..| +...+..+...+.+.|++++|.+.|++..+.. ..+...+..+...+.+.|
T Consensus       123 ~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g  189 (252)
T 2ho1_A          123 EAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKER  189 (252)
T ss_dssp             HHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcC
Confidence            4455555554422233 34455555555555555555555555554432 113444444544444444

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

Probab=97.18  E-value=0.0033  Score=35.80  Aligned_cols=68  Identities=16%  Similarity=0.022  Sum_probs=55.0

Q ss_pred             hHHHHHHHHHHhcCCC-cCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVN-PDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+++..+..-. ++..+|..+-..+.+.|++++|++.|++..+.. ..+..+|..+...|.+.|+
T Consensus       194 ~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  262 (365)
T 4eqf_A          194 EGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDR  262 (365)
T ss_dssp             HHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            5788888888765321 268899999999999999999999999998752 3367889999999888776

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.18  E-value=0.005  Score=30.61  Aligned_cols=66  Identities=11%  Similarity=-0.113  Sum_probs=48.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+..+.  .| +...|..+-.++.+.|++++|+..|++..+.. ..+...|..+-.++.+.|+
T Consensus        30 ~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~   96 (126)
T 4gco_A           30 PTAMRHYNEAVKR--DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVAMRE   96 (126)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHHCCC
Confidence            5677888877654  34 67888888888889999999999998887652 2245667777777766665

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.13  E-value=0.0012  Score=32.17  Aligned_cols=68  Identities=13%  Similarity=-0.023  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHHhcCC-Cc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGV-NP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.+. .| +...|..+-..+.+.|++++|+..|++..+.. .-+...+..+-.++.+.|+
T Consensus         7 ~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~   76 (117)
T 3k9i_A            7 AQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGR   76 (117)
T ss_dssp             CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCC
Confidence            345555555554321 12 45556666666666666666666666665542 1134444445444444443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.10  E-value=0.0052  Score=30.80  Aligned_cols=66  Identities=8%  Similarity=-0.135  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+.....  .| +...|..+-..+.+.|++++|+..|+...... .-+...|..+-.++...|+
T Consensus        35 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~  101 (142)
T 2xcb_A           35 DDAQKIFQALCML--DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGD  101 (142)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCC
Confidence            4677777777654  34 67777777778888888888888888887652 1244556666666665554

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=97.09  E-value=0.0016  Score=34.91  Aligned_cols=67  Identities=16%  Similarity=0.011  Sum_probs=53.4

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--CCcc----HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG--CKQD----AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~----~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+..  .+..+|..+-..+.+.|++++|++.+++..+..  ..|+    ..+|..+-..+.+.|+
T Consensus        22 ~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   94 (258)
T 3uq3_A           22 DEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGD   94 (258)
T ss_dssp             HHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHccc
Confidence            57889999998776  788999999999999999999999999987642  1122    4777777777777665

>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=97.08  E-value=0.0057  Score=34.61  Aligned_cols=67  Identities=12%  Similarity=-0.121  Sum_probs=53.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+++.+.. +.+..+|..+-..+.+.|++++|++.|++..+.. ..+..++..+...+.+.|+
T Consensus        81 ~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~  147 (368)
T 1fch_A           81 PNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESL  147 (368)
T ss_dssp             HHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCC
Confidence            57888888887652 2378889999999999999999999999998763 3367788888888877765

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=97.07  E-value=0.0066  Score=32.64  Aligned_cols=63  Identities=11%  Similarity=-0.026  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~   69 (71)
                      +|...|++..+..  .+...+..+-..+.+.|++++|+..|++..+.  .| +...+..+-..+.+.|
T Consensus       136 ~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~la~~~~~~g  199 (217)
T 2pl2_A          136 KAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQ--APKDLDLRVRYASALLLKG  199 (217)
T ss_dssp             HHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTC--
T ss_pred             HHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcc
Confidence            4444444444433  34444455555555555555555555555433  12 3334444444444433

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=97.07  E-value=0.009  Score=31.29  Aligned_cols=68  Identities=7%  Similarity=-0.119  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhc-CCHHHHHHHHHHHhhCCCCcc-HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLA-DRFDRARELLVSMGSKGCKQD-AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~   70 (71)
                      ++|...++...+.. +.+..++..+...+.+. |++++|...++++.+.+..|+ ...|..+...+.+.|+
T Consensus        59 ~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  128 (225)
T 2vq2_A           59 DKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQ  128 (225)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCC
Confidence            34555555554431 12455566666666666 666666666666655322332 3445555555554443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=97.07  E-value=0.0075  Score=32.42  Aligned_cols=65  Identities=15%  Similarity=-0.054  Sum_probs=54.1

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...++...+.  .| +...|..+=..+.+.|++++|+..|++..+..  .+...+..+-..+...|+
T Consensus       101 ~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~  166 (217)
T 2pl2_A          101 EQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGR  166 (217)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCC
Confidence            5788888888765  45 67888888889999999999999999998876  678888888888877775

>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=97.06  E-value=0.0047  Score=35.95  Aligned_cols=66  Identities=8%  Similarity=-0.007  Sum_probs=48.8

Q ss_pred             hHHHHHHHHHHhcCCCcC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD-----TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+.+.+.  .|+     ...|..+...+.+.|++++|+..++++.... ..+..+|..+..+|.+.|+
T Consensus       274 ~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~  344 (450)
T 2y4t_A          274 TDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALKDRAEAYLIEEM  344 (450)
T ss_dssp             HHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcC
Confidence            4677788887653  343     4577888888888999999999998887652 2357788888888877765

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.03  E-value=0.0066  Score=29.18  Aligned_cols=66  Identities=12%  Similarity=0.003  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +++...|++..+.  .| +...|..+-..+.+.|++++|+..|++..... ..+...|..+-..+.+.|+
T Consensus         2 ~~a~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~   68 (115)
T 2kat_A            2 QAITERLEAMLAQ--GTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGD   68 (115)
T ss_dssp             CCHHHHHHHHHTT--TCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCC
Confidence            4566667666543  34 57777777778888888888888888877652 1245566666666665554

>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=96.99  E-value=0.0098  Score=33.62  Aligned_cols=67  Identities=16%  Similarity=0.048  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhcCCC-cCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVN-PDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +|...|+++.+..-. ++..++..+-..+.+.|++++|+..|++..... ..+..+|..+...+.+.|+
T Consensus       199 ~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~  266 (368)
T 1fch_A          199 EVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQ  266 (368)
T ss_dssp             HHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCC
Confidence            455555555443111 135555556666666666666666666655431 1234455555555554443

>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=96.99  E-value=0.0092  Score=30.18  Aligned_cols=65  Identities=12%  Similarity=-0.092  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +|...++...+.. +.+...+..+...+.+.|++++|.+.+++..+.. ..+...+..+...+.+.|
T Consensus        94 ~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  158 (186)
T 3as5_A           94 LAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMG  158 (186)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcC
Confidence            3444444443321 1244455555555555555555555555554432 123344444444444443

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=96.99  E-value=0.0059  Score=33.09  Aligned_cols=49  Identities=6%  Similarity=-0.338  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ..+|..+-..+.+.|++++|...|++..+.. ..+..+|..+-..+.+.|
T Consensus        43 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~   91 (275)
T 1xnf_A           43 AQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAG   91 (275)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHcc
Confidence            4444444444445555555555555444331 113344444444444433

>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=96.99  E-value=0.0071  Score=30.81  Aligned_cols=66  Identities=8%  Similarity=-0.136  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+.....  .| +...|..+=.++.+.|++++|+..|++..... .-+...|..+-.++...|+
T Consensus        38 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~  104 (148)
T 2vgx_A           38 EDAHXVFQALCVL--DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQXGE  104 (148)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHc--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCC
Confidence            4667777776554  34 66777777777778888888888888876542 1244556666556655554

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=96.95  E-value=0.0099  Score=30.33  Aligned_cols=66  Identities=11%  Similarity=-0.030  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .| +...|..+-..+.+.|++++|+..|++..+.. .-+...|..+-.++.+.|+
T Consensus        28 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~   94 (164)
T 3sz7_A           28 SKAIDLYTQALSI--APANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLARFDMAD   94 (164)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccC
Confidence            4677777777654  34 67778888888888888888888888887652 1245667766666666654

>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=96.95  E-value=0.0061  Score=33.75  Aligned_cols=45  Identities=13%  Similarity=0.028  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +|...|++..+.. +.+..+|..+-..+.+.|++++|.+.|++..+
T Consensus       224 ~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  268 (327)
T 3cv0_A          224 EALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIY  268 (327)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            4444555444321 11344555555555555555555555555543

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=96.92  E-value=0.0088  Score=28.81  Aligned_cols=66  Identities=14%  Similarity=-0.088  Sum_probs=37.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .| +...+..+-..+.+.|++++|+..+++..+.. ..+...|..+-..+.+.|+
T Consensus        33 ~~A~~~~~~al~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~   99 (133)
T 2lni_A           33 PQAMKHYTEAIKR--NPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKD   99 (133)
T ss_dssp             HHHHHHHHHHHTT--CTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhh
Confidence            4556666665543  23 55666666666667777777777776665542 1234555555555555443

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=96.92  E-value=0.009  Score=32.37  Aligned_cols=67  Identities=16%  Similarity=-0.103  Sum_probs=53.9

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.. +.+..+|..+-..+.+.|++++|.+.|++..+.. ..+..+|..+-..+.+.|+
T Consensus        60 ~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~  126 (275)
T 1xnf_A           60 ALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGR  126 (275)
T ss_dssp             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhcc
Confidence            57888888887652 2268899999999999999999999999998752 2256788888888887775

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=96.87  E-value=0.0085  Score=27.91  Aligned_cols=69  Identities=10%  Similarity=-0.072  Sum_probs=51.3

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCC-ccHHHHHHHHHHHHhc-ccC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCK-QDAFSHSILINGGSAR-IRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~~~~~li~~~~~~-~~~   71 (71)
                      ++|...|+...+.. +.+...|..+-..+.+.|++++|...|++..+..-. .+...|..+-..+.+. |++
T Consensus        23 ~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~~~~   93 (112)
T 2kck_A           23 TESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALRYIEGKE   93 (112)
T ss_dssp             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHTTCSSCS
T ss_pred             HHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHHhCCH
Confidence            56788888876542 226778888888999999999999999999876311 1467777777777777 653

>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=96.86  E-value=0.01  Score=28.81  Aligned_cols=66  Identities=15%  Similarity=-0.044  Sum_probs=47.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+..+.  .| +...|..+-.++.+.|++++|+..|++..+.. .-+...|..+-.++...|+
T Consensus        21 ~~A~~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~   87 (126)
T 3upv_A           21 PNAVKAYTEMIKR--APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKE   87 (126)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhC
Confidence            4677777777654  34 67888888888889999999999998887652 1245666666666666554

>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=96.85  E-value=0.013  Score=29.65  Aligned_cols=67  Identities=15%  Similarity=0.085  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+++..+.. +.+...+..+...+.+.|++++|.+.+++..+.. ..+...+..+...+.+.|+
T Consensus        59 ~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~  125 (186)
T 3as5_A           59 DRGTELLERSLADA-PDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGR  125 (186)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCc
Confidence            35556666655431 2245666666666677777777777777665542 2244555555555555443

>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=96.82  E-value=0.0074  Score=28.89  Aligned_cols=68  Identities=13%  Similarity=0.048  Sum_probs=49.7

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC--Ccc----HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGC--KQD----AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~--~p~----~~~~~~li~~~~~~~~   70 (71)
                      ++|...|....... +.+...+..+-..+.+.|++++|...+++.....-  .++    ..+|..+-..+.+.|+
T Consensus        21 ~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~   94 (131)
T 1elr_A           21 DTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEK   94 (131)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhcc
Confidence            56778888876642 33678888888999999999999999999876521  122    5667777777766664

>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=96.81  E-value=9.8e-05  Score=44.89  Aligned_cols=44  Identities=7%  Similarity=0.003  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +.+.+.++.+|.+.|+++++.++++       .|+..+|..+-..|.+.|+
T Consensus        94 ~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~  137 (449)
T 1b89_A           94 SYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKM  137 (449)
T ss_dssp             ---------------CHHHHTTTTT-------CC----------------C
T ss_pred             chhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCC
Confidence            3444444444444444444444442       1333444444444444443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=96.81  E-value=0.0099  Score=28.75  Aligned_cols=65  Identities=15%  Similarity=0.072  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHHhcCCCcC-H---HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc----HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD-T---STCNALMDGFCLADRFDRARELLVSMGSKGCKQD----AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-~---~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+...+.  .|+ .   ..+..+-..+.+.|++++|...|+......  |+    ..++..+-.++.+.|+
T Consensus        19 ~~A~~~~~~~~~~--~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~   91 (129)
T 2xev_A           19 DDASQLFLSFLEL--YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGK   91 (129)
T ss_dssp             HHHHHHHHHHHHH--CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHH--CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCC
Confidence            4667777777654  232 2   356666667778888888888888876642  32    3445555555555554

>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=96.75  E-value=0.011  Score=27.65  Aligned_cols=67  Identities=10%  Similarity=-0.106  Sum_probs=41.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+...... +.+...+..+-..+.+.|++++|...+++..+.. ..+...+..+-..+.+.|+
T Consensus        21 ~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~   87 (118)
T 1elw_A           21 DDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNR   87 (118)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhh
Confidence            45666666665431 2256667777777777788888888777776542 1245556666666655554

>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=96.74  E-value=0.021  Score=31.56  Aligned_cols=29  Identities=21%  Similarity=0.163  Sum_probs=13.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      +..++..+...+.+.|++++|.+.+++..
T Consensus       171 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~  199 (327)
T 3cv0_A          171 DAQLHASLGVLYNLSNNYDSAAANLRRAV  199 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            34444444444444455555555444444

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=96.73  E-value=0.021  Score=30.48  Aligned_cols=67  Identities=13%  Similarity=-0.084  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+++..+.. +.+..+|..+-..+.+.|++++|+..|++..+.. ..+..+|..+-..+.+.|+
T Consensus       156 ~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~  222 (258)
T 3uq3_A          156 PNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKE  222 (258)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhh
Confidence            35566666665432 2256666777777777777777777777776542 2235556666666655554

>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=96.73  E-value=0.014  Score=28.48  Aligned_cols=67  Identities=12%  Similarity=-0.129  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|....... +.+...|..+-..+.+.|++++|...++...+.. .-+...|..+-.++.+.|+
T Consensus        26 ~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~   92 (137)
T 3q49_B           26 PEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMES   92 (137)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHHhh
Confidence            46777777776542 2257778888888888888888888888887653 2245667777666666654

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=96.73  E-value=0.021  Score=30.33  Aligned_cols=65  Identities=12%  Similarity=-0.047  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +|...+++..+.. +.+...+..+...+.+.|++++|.+.+++..+.. ..+...+..+...+.+.|
T Consensus       109 ~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  173 (243)
T 2q7f_A          109 EAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEG  173 (243)
T ss_dssp             HHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcC
Confidence            3444444443321 1134444444444555555555555555444321 113334444444444333

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=96.71  E-value=0.014  Score=28.72  Aligned_cols=65  Identities=17%  Similarity=0.020  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+...+.  .| +...|..+=..+.+.|++++|+..|++..+.  .| +...+..+-.++.+.|+
T Consensus        34 ~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~la~~~~~~g~  100 (121)
T 1hxi_A           34 AEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTNEHN  100 (121)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCC
Confidence            5677888887764  45 6788888888889999999999999998765  34 45666666666666554

>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=96.71  E-value=0.021  Score=30.46  Aligned_cols=67  Identities=10%  Similarity=-0.179  Sum_probs=43.7

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|....+..-.++...+..+-..+.+.|++++|++.|++..+.  .| +...|..+-..+.+.|+
T Consensus        24 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~   91 (228)
T 4i17_A           24 AVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKSAAYRDMKN   91 (228)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHccc
Confidence            467777777766543356666666777777788888888888877654  23 44556666666655554

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.71  E-value=0.015  Score=28.53  Aligned_cols=66  Identities=9%  Similarity=-0.107  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHhcCCCcC----HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD----TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .|+    ...|..+-..+.+.|++++|+..++...+.. ..+...|..+-.++.+.|+
T Consensus        45 ~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~  114 (148)
T 2dba_A           45 GGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRRSQALEKLGR  114 (148)
T ss_dssp             HHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHHHHHHHHcCC
Confidence            4566777766644  454    5677777777778888888888888776542 1245555555555555443

>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=96.70  E-value=0.0098  Score=31.28  Aligned_cols=64  Identities=9%  Similarity=-0.022  Sum_probs=48.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+.    +.|+...|..+-..+.+.|++++|++.|++..... ..+...|..+-..+.+.|+
T Consensus        23 ~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~   86 (213)
T 1hh8_A           23 KGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   86 (213)
T ss_dssp             HHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHccc
Confidence            3555555544    46788899999999999999999999999987653 2356677777777777665

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=96.70  E-value=0.022  Score=30.23  Aligned_cols=30  Identities=3%  Similarity=0.160  Sum_probs=14.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +..++..+...+.+.|++++|.+.+++..+
T Consensus        90 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  119 (243)
T 2q7f_A           90 AATAYYGAGNVYVVKEMYKEAKDMFEKALR  119 (243)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            344444444445555555555555554443

>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=0.0092  Score=35.42  Aligned_cols=68  Identities=6%  Similarity=-0.017  Sum_probs=52.0

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +++|...|++..+.. +.+..+|..+-..+.+.|++++|++.|++..+.. ..+..+|..+...+.+.|+
T Consensus        41 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~  108 (537)
T 3fp2_A           41 FNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGN  108 (537)
T ss_dssp             CC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCC
Confidence            357788888887652 2378899999999999999999999999998753 2356777777777777665

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=96.64  E-value=0.015  Score=27.66  Aligned_cols=29  Identities=3%  Similarity=-0.086  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ...+..+-..+.+.|++++|...|++..+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  108 (131)
T 2vyi_A           80 SKAYGRMGLALSSLNKHVEAVAYYKKALE  108 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHh
Confidence            34444444444455555555555544443

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=96.58  E-value=0.031  Score=31.44  Aligned_cols=66  Identities=11%  Similarity=-0.033  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH-H-HHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA-F-SHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~-~~~~li~~~~~~~~   70 (71)
                      ++|..+|+.-.+. +.| +...|..+...+.+.|++++|..+|++..+.  .|+. . .|..+...+.+.|+
T Consensus        81 ~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~  149 (308)
T 2ond_A           81 DEAANIYERAIST-LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEG  149 (308)
T ss_dssp             HHHHHHHHHHHTT-TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHH-hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcC
Confidence            4566666666542 245 5668888888888888888888888888764  4532 2 67777766665543

>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=96.57  E-value=0.0088  Score=32.30  Aligned_cols=68  Identities=15%  Similarity=-0.071  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CCCc-cHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK------GCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      +|.+++.......-+....++..+-..+...|++++|+..+++....      +-.| ...+|..+-..+...|+
T Consensus        26 ~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  100 (283)
T 3edt_B           26 QALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGK  100 (283)
T ss_dssp             HHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhcc
Confidence            44444444432222235788899999999999999999999998754      2233 45667777777777665

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=96.52  E-value=0.039  Score=31.03  Aligned_cols=67  Identities=13%  Similarity=-0.002  Sum_probs=47.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCc--cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKG-CKQ--DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p--~~~~~~~li~~~~~~~~   70 (71)
                      ++|..+|+...+.  .| +...|..+...+.+.|++++|..+|++..... ..|  +...|..++....+.|+
T Consensus       186 ~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~  256 (308)
T 2ond_A          186 SVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGD  256 (308)
T ss_dssp             HHHHHHHHHHHHH--HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCC
Confidence            3566777776543  23 67888888888888899999999999988763 455  35567777766655553

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=96.47  E-value=0.042  Score=30.63  Aligned_cols=67  Identities=7%  Similarity=-0.120  Sum_probs=49.1

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+++..+.. +.+...+..+-..+.+.|++++|...+++..+.. ..+..+|..+...+.+.|+
T Consensus       137 ~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~  203 (359)
T 3ieg_A          137 TAAITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGD  203 (359)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            46777777776542 2367788888888889999999999999887653 3366777777777766654

>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=96.45  E-value=0.023  Score=31.42  Aligned_cols=68  Identities=7%  Similarity=-0.130  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--------CCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG--------CKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--------~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+++..+.. +.+..++..+...+.+.|++++|...+++..+..        ...+..+|..+-..+.+.|+
T Consensus       176 ~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~  251 (330)
T 3hym_B          176 KLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKK  251 (330)
T ss_dssp             HHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcC
Confidence            35566666665432 2256677777777777777777777777765421        12234566666666665554

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=96.43  E-value=0.0087  Score=32.88  Aligned_cols=47  Identities=17%  Similarity=0.200  Sum_probs=36.5

Q ss_pred             hHHHHHHHHHHhc------CCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQR------GVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~------~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|...+++....      +..| ...++..+-..+.+.|++++|.+.|++..+
T Consensus       170 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          170 EEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4677777777543      2234 466888899999999999999999999875

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=96.42  E-value=0.018  Score=31.25  Aligned_cols=66  Identities=11%  Similarity=-0.071  Sum_probs=34.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc--HHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD--AFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~   69 (71)
                      ++|...|++..+.  .| +...+..+-..+.+.|++++|++.+++..+.+-.|+  ..+|..+-..+.+.|
T Consensus        20 ~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~   88 (272)
T 3u4t_A           20 AEAIEVFNKLEAK--KYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKG   88 (272)
T ss_dssp             HHHHHHHHHHHHT--TCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcc
Confidence            4566666666543  23 344566666666666677777766666665321121  122445544444444

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=96.34  E-value=0.028  Score=31.37  Aligned_cols=67  Identities=6%  Similarity=-0.191  Sum_probs=47.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.. +.+..++..+-..+.+.|++++|+..|++..+.. .-+...|..+-..+.+.|+
T Consensus        20 ~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~   86 (359)
T 3ieg_A           20 ADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGK   86 (359)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCC
Confidence            56778888876542 2257788888888888888888888888887652 1255667777777666654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=96.28  E-value=0.035  Score=33.42  Aligned_cols=63  Identities=14%  Similarity=0.015  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ++|...|++..+.  .| +...|..+-..|.+.|++++|++.|++..+.  .|+...+..+-..+...
T Consensus       120 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~~~~~~  183 (474)
T 4abn_A          120 PEAEVLLSKAVKL--EPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSMVLRQL  183 (474)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHHHHHHh
Confidence            6788888888765  44 5788999999999999999999999998876  47767777776666655

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

Probab=96.26  E-value=0.028  Score=26.47  Aligned_cols=63  Identities=16%  Similarity=0.102  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGS   66 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~   66 (71)
                      ++|...++++.+.. +.+..++..+...+.+.|++++|...|+++.+.. ..+...+..+-..+.
T Consensus        60 ~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~  122 (125)
T 1na0_A           60 DEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQ  122 (125)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            57888888887642 3367889999999999999999999999997652 123444544444443

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.25  E-value=0.027  Score=26.30  Aligned_cols=46  Identities=11%  Similarity=0.040  Sum_probs=38.1

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+.  .| +...|..+-..+.+.|++++|+..|++..+.
T Consensus        21 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A           21 REAVHCYDQLITA--QPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            5678888887654  34 6788888888999999999999999999865

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.24  E-value=0.032  Score=26.88  Aligned_cols=64  Identities=13%  Similarity=0.030  Sum_probs=47.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCccHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK-GCKQDAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~   67 (71)
                      ++|...|++..+.  .| +...+..+-.++.+.|++++|+..|++.... .-.|+...|...+..+.+
T Consensus        44 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~ai~~~~~  109 (117)
T 3k9i_A           44 RKAEAVLANGVKQ--FPNHQALRVFYAMVLYNLGRYEQGVELLLKIIAETSDDETIQSYKQAILFYAD  109 (117)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHTHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh--CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHH
Confidence            5788888888765  34 5788888888999999999999999988754 334455556666655543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=96.22  E-value=0.031  Score=26.54  Aligned_cols=67  Identities=6%  Similarity=-0.135  Sum_probs=51.1

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+...... +.+...+..+-..+.+.|++++|.+.++...... ..+...|..+-..+.+.|+
T Consensus        29 ~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   95 (131)
T 2vyi_A           29 EAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSSLNK   95 (131)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHhCC
Confidence            57888888887642 2367888889999999999999999999988652 2246677777777776665

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=96.20  E-value=0.044  Score=28.14  Aligned_cols=65  Identities=12%  Similarity=-0.159  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .+...+......  .| +...+..+-..+.+.|++++|++.|++..+.. +-+..+|..+-..+.+.|+
T Consensus        91 ~a~~~~~~a~~~--~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~  156 (184)
T 3vtx_A           91 AAIDALQRAIAL--NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGL  156 (184)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHh--CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCC
Confidence            344444444432  23 56666667777777777777777777776542 1245566666666666554

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.20  E-value=0.027  Score=26.56  Aligned_cols=64  Identities=19%  Similarity=0.049  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-CCCccHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK-GCKQDAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~   67 (71)
                      ++|...|+...+.  .| +...|..+-..|.+.|++++|.+.|++..+. .-.++.....-+-..+.+
T Consensus        24 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~l~~~l~~   89 (100)
T 3ma5_A           24 SRALALFEELVET--DPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSELQDAKLK   89 (100)
T ss_dssp             HHHHHHHHHHHHH--STTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHHHHHHHHH
Confidence            4677777777654  33 4667777777888888888888888777643 123455555555444443

>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=96.15  E-value=0.064  Score=29.61  Aligned_cols=48  Identities=10%  Similarity=-0.088  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ..+..+-..+.+.|++++|.+.+++..+.. ..+...+..+...+.+.|
T Consensus       160 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~  207 (330)
T 3hym_B          160 LPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNG  207 (330)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcc
Confidence            334444444555555555555555554331 123344444444444443

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=96.13  E-value=0.033  Score=29.66  Aligned_cols=44  Identities=11%  Similarity=0.066  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +|...|++..+.  .| +...|..+-..+.+.|++++|+..|++..+
T Consensus        72 ~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  116 (208)
T 3urz_A           72 KAYLFYKELLQK--APNNVDCLEACAEMQVCRGQEKDALRMYEKILQ  116 (208)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            444444444433  23 445555555555555555555555555544

>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=96.11  E-value=0.044  Score=27.33  Aligned_cols=30  Identities=3%  Similarity=-0.147  Sum_probs=15.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +..++..+-..+.+.|++++|...+++..+
T Consensus        46 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~   75 (166)
T 1a17_A           46 NAIYYGNRSLAYLRTECYGYALGDATRAIE   75 (166)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444444555555555555555555443

>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=96.10  E-value=0.016  Score=31.22  Aligned_cols=69  Identities=16%  Similarity=-0.009  Sum_probs=49.3

Q ss_pred             hHHHHHHHHHHhc------CCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CCCc-cHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQR------GVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK------GCKQ-DAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~------~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~~~~~li~~~~~   67 (71)
                      ++|...+.+....      +-.| ...+++.+-..+...|++++|++.|++....      .-.| ...+|..+-..+..
T Consensus        60 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~  139 (283)
T 3edt_B           60 KEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQN  139 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHH
Confidence            4667777776543      2233 5778899999999999999999999998754      1123 45667777777777


Q ss_pred             ccc
Q 042276           68 RIR   70 (71)
Q Consensus        68 ~~~   70 (71)
                      .|+
T Consensus       140 ~g~  142 (283)
T 3edt_B          140 QGK  142 (283)
T ss_dssp             TTC
T ss_pred             cCC
Confidence            665

>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=96.06  E-value=0.077  Score=29.67  Aligned_cols=66  Identities=15%  Similarity=-0.059  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+..+.  .| +...|..+-..+.+.|++++|+..+++..+.. .-+...+..+-.++.+.|+
T Consensus        21 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~   87 (281)
T 2c2l_A           21 PEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMES   87 (281)
T ss_dssp             HHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            5677778777654  44 67888888888889999999999999887652 2255667777677766665

>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=96.04  E-value=0.055  Score=27.88  Aligned_cols=65  Identities=18%  Similarity=0.053  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            4 ANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         4 a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      |...++...+.  .| +...+..+-..+.+.|++++|...|++..+..-.+ +...+..+...+...|+
T Consensus        93 a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~  159 (176)
T 2r5s_A           93 ELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQ  159 (176)
T ss_dssp             HHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCC
Confidence            44555555443  55 57888888889999999999999999998764222 35578888888877765

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

Probab=96.02  E-value=0.03  Score=32.96  Aligned_cols=67  Identities=12%  Similarity=-0.220  Sum_probs=44.8

Q ss_pred             hHHHHHHHHHHh-----cCCC-------c-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            2 DEANGLAELMIQ-----RGVN-------P-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         2 ~~a~~~~~~m~~-----~~~~-------p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ++|...|+++.+     ..-.       | +..++..+-..+.+.|++++|...|++..+..  |+...|..+...+.+.
T Consensus       206 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~  283 (514)
T 2gw1_A          206 DKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADR  283 (514)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHC
Confidence            456667776655     2111       2 45677777777888888888888888887653  3366677777777666


Q ss_pred             cc
Q 042276           69 IR   70 (71)
Q Consensus        69 ~~   70 (71)
                      |+
T Consensus       284 ~~  285 (514)
T 2gw1_A          284 ND  285 (514)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=95.96  E-value=0.027  Score=30.87  Aligned_cols=69  Identities=14%  Similarity=-0.008  Sum_probs=49.3

Q ss_pred             hHHHHHHHHHHhc-------CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC------CCCc-cHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQR-------GVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK------GCKQ-DAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~-------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~~~~~li~~~~~   67 (71)
                      ++|...+++..+.       .......++..+-..+...|++++|...+++....      +-.| ...++..+-..+..
T Consensus        44 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~  123 (311)
T 3nf1_A           44 EVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGK  123 (311)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence            4677777777542       22335778888999999999999999999998754      2223 45667777777776


Q ss_pred             ccc
Q 042276           68 RIR   70 (71)
Q Consensus        68 ~~~   70 (71)
                      .|+
T Consensus       124 ~g~  126 (311)
T 3nf1_A          124 RGK  126 (311)
T ss_dssp             TTC
T ss_pred             cCc
Confidence            665

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=95.96  E-value=0.035  Score=24.96  Aligned_cols=64  Identities=16%  Similarity=0.099  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      ++|...|++..+.. +.+...+..+-..+.+.|++++|...|++..+.. .-+...+..+-..+.+
T Consensus        26 ~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~   89 (91)
T 1na3_A           26 DEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQK   89 (91)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHh
Confidence            46777777776542 2257778888888889999999999998887652 1244555555555443

>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=95.95  E-value=0.022  Score=28.17  Aligned_cols=46  Identities=11%  Similarity=0.118  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|.+..+.  .| +...|+.+=.+|.+.|++++|++.|++..+.
T Consensus        25 ~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~   71 (127)
T 4gcn_A           25 EKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEV   71 (127)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            5788888887764  45 6888998989999999999999999988754

>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=95.93  E-value=0.072  Score=31.59  Aligned_cols=28  Identities=11%  Similarity=0.097  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ..+|..+-..+.+.|++++|...|++..
T Consensus       310 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~  337 (537)
T 3fp2_A          310 PPTYYHRGQMYFILQDYKNAKEDFQKAQ  337 (537)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            3444444444444444444444444443

>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=95.88  E-value=0.079  Score=33.99  Aligned_cols=65  Identities=14%  Similarity=-0.133  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.|++..+.  .| +...|+.+=..+.+.|++++|++.|++..+.  .| +...|..+...+.+.|+
T Consensus        94 ~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~  160 (723)
T 4gyw_A           94 QGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCD  160 (723)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhccc
Confidence            3455555555433  33 4555666666666666666666666665543  23 34455555555555544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=95.87  E-value=0.051  Score=25.99  Aligned_cols=65  Identities=9%  Similarity=-0.136  Sum_probs=48.1

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~   69 (71)
                      ++|...+++..+.. +.+...+..+-..+.+.|++++|.+.|++..+.  .| +...+..+-..+.+.|
T Consensus        67 ~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           67 QLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDL--DSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhc
Confidence            57788888887642 226788888889999999999999999998765  23 3455666666665544

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=95.83  E-value=0.078  Score=28.18  Aligned_cols=47  Identities=11%  Similarity=0.017  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ..+.+-..+.+.|++++|+..|++..+.  .| +...|..+-..+...|+
T Consensus        56 ~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~  103 (208)
T 3urz_A           56 LATELALAYKKNRNYDKAYLFYKELLQK--APNNVDCLEACAEMQVCRGQ  103 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCC
Confidence            3444566677888888888888887765  23 45666666666665554

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.74  E-value=0.055  Score=25.46  Aligned_cols=51  Identities=20%  Similarity=-0.048  Sum_probs=40.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +...|..+-..+.+.|++++|+..|++..+.. .-+...|..+-.+|.+.|+
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~   56 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDR   56 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCC
Confidence            67788888889999999999999999998763 1245677777777777765

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=95.71  E-value=0.1  Score=28.21  Aligned_cols=68  Identities=6%  Similarity=-0.187  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHhcCCCc--CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP--DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...++...+..-.|  ...+|..+-..+.+.|++++|++.|++..+.. ..+..+|..+-..+.+.|+
T Consensus        54 ~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~  123 (272)
T 3u4t_A           54 DLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGN  123 (272)
T ss_dssp             HHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccC
Confidence            46677777776533222  23346777777778888888888888776642 1244566666666666554

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=95.67  E-value=0.11  Score=31.36  Aligned_cols=58  Identities=14%  Similarity=0.123  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILIN   63 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~   63 (71)
                      ++|..+|+.+.+.  .| +...|...+..+.+.|++++|.++|++....  .|+...|...+.
T Consensus        29 ~~a~~~~e~al~~--~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw~~~~~   87 (530)
T 2ooe_A           29 DKARKTYERLVAQ--FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLWKCYLS   87 (530)
T ss_dssp             HHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHHHHHHH
Confidence            5678888888754  45 7888999999999999999999999999876  377766666554

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=95.66  E-value=0.091  Score=31.78  Aligned_cols=70  Identities=10%  Similarity=-0.120  Sum_probs=50.6

Q ss_pred             hHHHHHHHHHHh---cCCCcC----HHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CC-CCccH-HHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQ---RGVNPD----TSTCNALMDGFCLADRFDRARELLVSMGS-----KG-CKQDA-FSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~---~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g-~~p~~-~~~~~li~~~~~   67 (71)
                      ++|..++++..+   .-+.|+    ..+++.+-.+|...|++++|+.++++...     .| -.|++ .+|+-|-..|..
T Consensus       315 ~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~  394 (433)
T 3qww_A          315 SELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMG  394 (433)
T ss_dssp             HHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHh
Confidence            466777776643   334442    57889999999999999999999998864     23 34544 568888888888


Q ss_pred             cccC
Q 042276           68 RIRK   71 (71)
Q Consensus        68 ~~~~   71 (71)
                      +|++
T Consensus       395 qg~~  398 (433)
T 3qww_A          395 LENK  398 (433)
T ss_dssp             TTCH
T ss_pred             ccCH
Confidence            7764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=95.64  E-value=0.086  Score=27.00  Aligned_cols=46  Identities=17%  Similarity=0.058  Sum_probs=33.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+.  .| +..+|..+-..+.+.|++++|...+......
T Consensus        22 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~   68 (184)
T 3vtx_A           22 DGAIRAYKKVLKA--DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL   68 (184)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            5677777777654  34 5777777777888888888888887777654

>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=95.61  E-value=0.059  Score=27.55  Aligned_cols=30  Identities=3%  Similarity=-0.005  Sum_probs=16.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      +...|..+-..+...|++++|...|++..+
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   72 (177)
T 2e2e_A           43 NSEQWALLGEYYLWQNDYSNSLLAYRQALQ   72 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445555555555555555555555555543

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=95.55  E-value=0.084  Score=26.24  Aligned_cols=60  Identities=12%  Similarity=0.085  Sum_probs=45.7

Q ss_pred             HHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            5 NGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         5 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      .+-++.+-...+.|+..+..+.+.+|-+.+++..|.++|+..+.+. .+....|.-+++-+
T Consensus        30 rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lqEl   89 (109)
T 1v54_E           30 RKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQEL   89 (109)
T ss_dssp             HHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHHHH
T ss_pred             HHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHHHH
Confidence            3344455556789999999999999999999999999999997552 33345677776643

>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=95.51  E-value=0.15  Score=29.35  Aligned_cols=50  Identities=12%  Similarity=-0.165  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ..+|..+-.++.+.|++++|+..|++..+.. ..+...|..+-.+|.+.|+
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~  245 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVND  245 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCC
Confidence            3556666666666666666666666665432 1244455555555544443

>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=95.51  E-value=0.045  Score=27.75  Aligned_cols=65  Identities=9%  Similarity=-0.023  Sum_probs=46.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+.....  ..| +...+-.+=..|.+.|++++|++.|++..+.  .| +..+|..+-..+.+.|+
T Consensus        14 e~ai~~~~~a~~--~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A           14 ERYIASVQGSTP--SPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             HHHHHHHHHHSC--SHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhcc--cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCc
Confidence            345555554432  244 4556666778899999999999999999875  34 56778888777777765

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=95.45  E-value=0.14  Score=31.02  Aligned_cols=66  Identities=11%  Similarity=-0.071  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.+++..+.  .| +..+|..+-..+.+.|++++|++.+++..+.. .-+..+|..+-.+|.+.|+
T Consensus        23 ~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~   89 (477)
T 1wao_1           23 ENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGK   89 (477)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            3555555555443  33 45666666666666666666666666665541 1134455555555544443

>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=95.42  E-value=0.1  Score=29.11  Aligned_cols=69  Identities=7%  Similarity=-0.057  Sum_probs=44.6

Q ss_pred             hHHHHHHHHHHhcCCC-cC----HHHHHHHHHHHHhcCCHHHHHHHHHHHhh----C-CCCccH-HHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVN-PD----TSTCNALMDGFCLADRFDRARELLVSMGS----K-GCKQDA-FSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~-p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~-g~~p~~-~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+....... ++    ..+++.+-..|.+.|++++|+..|++..+    . +-.+.. .+|..+-..|.+.|+
T Consensus       132 ~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~  211 (293)
T 3u3w_A          132 EYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSR  211 (293)
T ss_dssp             HHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhH
Confidence            4677777777653222 22    33688888888899999999998888873    1 222222 356666666666654

>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=95.32  E-value=0.13  Score=33.08  Aligned_cols=64  Identities=14%  Similarity=-0.073  Sum_probs=31.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~   69 (71)
                      ++|...|++..+.  .| +..+|+.+=..+.+.|++++|+..|++..+.  .| +..+|..+-..+.+.|
T Consensus        26 ~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~~l~~~g   91 (723)
T 4gyw_A           26 EEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQ   91 (723)
T ss_dssp             HHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcC
Confidence            3455555554433  23 3455555555555555555555555555443  22 2344444444444444

>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=95.21  E-value=0.18  Score=30.78  Aligned_cols=28  Identities=18%  Similarity=0.039  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ...|..+-..+.+.|++++|.+.|++..
T Consensus        57 ~~~~~~lg~~~~~~g~~~~A~~~~~~al   84 (568)
T 2vsy_A           57 PEAVARLGRVRWTQQRHAEAAVLLQQAS   84 (568)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3334444444444444444444444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=95.16  E-value=0.11  Score=26.73  Aligned_cols=53  Identities=8%  Similarity=-0.100  Sum_probs=41.2

Q ss_pred             CCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276           16 VNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus        16 ~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      +.| +...+..+=..+.+.|++++|+..|++....  .| +...|..+-.++.+.|+
T Consensus        31 l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~   85 (151)
T 3gyz_A           31 IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIY--DFYNVDYIMGLAAIYQIKEQ   85 (151)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHcc
Confidence            345 4667777777888999999999999999876  34 56778877777777765

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=95.14  E-value=0.25  Score=29.78  Aligned_cols=64  Identities=9%  Similarity=-0.031  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH--HHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA--FSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~~~~~li~~~~~~~   69 (71)
                      +|..+|+.-.+. +.| +...|..+...+.+.|++++|..+|++..+.  .|+.  ..|......+.+.|
T Consensus       304 ~A~~~~~~Al~~-~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~  370 (530)
T 2ooe_A          304 EAANIYERAIST-LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAE  370 (530)
T ss_dssp             HHHHHHHHHTTT-TCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhc
Confidence            566666666532 245 6888888888888889999999999988774  4542  46776666555443

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=95.13  E-value=0.095  Score=24.35  Aligned_cols=51  Identities=6%  Similarity=-0.149  Sum_probs=39.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +...|..+-..+.+.|++++|++.|++..+.. ..+...|..+-.++.+.|+
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~   53 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGE   53 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcC
Confidence            45667777888999999999999999987652 2256677777777777665

>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=95.10  E-value=0.1  Score=24.65  Aligned_cols=62  Identities=10%  Similarity=0.114  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHhcC--CCcC----HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRG--VNPD----TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         2 ~~a~~~~~~m~~~~--~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      ++|...+.......  ..++    ..+|..+-..+.+.|++++|.+.|+...+..  |+...+..+-...
T Consensus        55 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~  122 (131)
T 1elr_A           55 NKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQQAE  122 (131)
T ss_dssp             HHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHHHHH
Confidence            46777777775432  1122    7788888889999999999999999998753  5655555544433

>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=95.01  E-value=0.12  Score=30.56  Aligned_cols=45  Identities=9%  Similarity=0.012  Sum_probs=21.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCC-HHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADR-FDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~   48 (71)
                      ++|...++...+.  .| +...|+.+-..+.+.|+ +++|+..|++..+
T Consensus       114 ~~Al~~~~~al~l--~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~  160 (382)
T 2h6f_A          114 ERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE  160 (382)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHH
Confidence            3444445444432  23 34445555445555553 5555555555544

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=95.01  E-value=0.077  Score=31.93  Aligned_cols=29  Identities=7%  Similarity=-0.052  Sum_probs=13.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      +...|..+-..|.+.|++++|++.|++..
T Consensus       257 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al  285 (474)
T 4abn_A          257 NPDLHLNRATLHKYEESYGEALEGFSQAA  285 (474)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444444444444444444444443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.00  E-value=0.11  Score=24.73  Aligned_cols=62  Identities=15%  Similarity=-0.095  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCccHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKG-CKQDAFSHSILINGG   65 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~   65 (71)
                      ++|...|+...+.  .| +...|..+-..+.+.|++++|...|++..... -..+......+...+
T Consensus        36 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~l~~~l   99 (115)
T 2kat_A           36 DAALPHLRAALDF--DPTYSVAWKWLGKTLQGQGDRAGARQAWESGLAAAQSRGDQQVVKELQVFL   99 (115)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccccHHHHHHHHHHH
Confidence            5778888887764  34 57788888899999999999999999987541 112444444444443

>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=94.97  E-value=0.15  Score=25.95  Aligned_cols=46  Identities=9%  Similarity=0.138  Sum_probs=27.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...++...+.  .| +...+..+-..+.+.|++++|...|++..+.
T Consensus        98 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           98 AQTRAMIDKALAL--DSNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            4556666665543  23 3555666666666667777777766666544

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.95  E-value=0.18  Score=29.97  Aligned_cols=45  Identities=16%  Similarity=0.223  Sum_probs=38.1

Q ss_pred             Cc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CCCCccHHHHHHH
Q 042276           17 NP-DTSTCNALMDGFCLADRFDRARELLVSMGS-----KGCKQDAFSHSIL   61 (71)
Q Consensus        17 ~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~~~l   61 (71)
                      .| +...|-.+|.++.+.|+..+|++.|+....     .|+.|+..+-...
T Consensus       201 ~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~  251 (388)
T 2ff4_A          201 HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALN  251 (388)
T ss_dssp             STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            45 888999999999999999999999999864     4999998765443

>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=94.86  E-value=0.31  Score=28.83  Aligned_cols=67  Identities=6%  Similarity=-0.102  Sum_probs=51.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      ++|...|++..+.  .| +...|+.+=..+.+.|++++|+..|++..+.. .-+...|..+-.++.+.|++
T Consensus       149 ~eAl~~~~~al~l--~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~  216 (382)
T 2h6f_A          149 HEEMNYITAIIEE--QPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLW  216 (382)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCCh
Confidence            5677888887764  44 68888888888999999999999999998752 12667787777777776654

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=94.85  E-value=0.24  Score=27.67  Aligned_cols=65  Identities=17%  Similarity=0.072  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC-CCccHHHHHHHHHHHHhccc
Q 042276            4 ANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKG-CKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         4 a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~   70 (71)
                      |...+++....  .| +...+..+-..+.+.|++++|+..|++..+.. -..+...+..+...+...|+
T Consensus       204 a~~~l~~al~~--~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          204 EIQQLQQQVAE--NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCT
T ss_pred             cHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCC
Confidence            45555555543  44 68888889999999999999999999998763 12236678888888877665

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=94.81  E-value=0.23  Score=30.52  Aligned_cols=70  Identities=6%  Similarity=-0.121  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHHh---cCCCc----CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-----C-CCccH-HHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQ---RGVNP----DTSTCNALMDGFCLADRFDRARELLVSMGSK-----G-CKQDA-FSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~---~~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g-~~p~~-~~~~~li~~~~~   67 (71)
                      ++|..++++..+   .-+.|    ...+++.+-..|...|++++|+.++++....     | -.|++ .+++.|-..|..
T Consensus       326 ~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~  405 (490)
T 3n71_A          326 HEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWH  405 (490)
T ss_dssp             HHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            456666666532   22333    3678899999999999999999999887641     2 33443 568888888888


Q ss_pred             cccC
Q 042276           68 RIRK   71 (71)
Q Consensus        68 ~~~~   71 (71)
                      .|++
T Consensus       406 ~G~~  409 (490)
T 3n71_A          406 AGHI  409 (490)
T ss_dssp             TTCH
T ss_pred             CCCH
Confidence            7763

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=94.81  E-value=0.12  Score=23.79  Aligned_cols=46  Identities=13%  Similarity=0.106  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHH-HHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTS-TCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+.  .| +.. .|..+=..+.+.|++++|.+.|++..+.
T Consensus        17 ~~A~~~~~~al~~--~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A           17 ENALQALEEFLQT--EPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHHHHHH--CSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            5788888888765  44 556 7888888899999999999999999865

>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=94.78  E-value=0.16  Score=25.21  Aligned_cols=47  Identities=13%  Similarity=-0.080  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+....+.. +.+...|..+-..+.+.|++++|...|++..+.
T Consensus        64 ~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~  110 (166)
T 1a17_A           64 GYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKV  110 (166)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            46777777776542 236788888888999999999999999999765

>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=94.67  E-value=0.21  Score=26.06  Aligned_cols=49  Identities=10%  Similarity=-0.120  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ..|..+-..+.+.|++++|+..++...+.. ..+...|..+-.++...|+
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~  137 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGF  137 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccc
Confidence            556666666667777777777777766541 1244455555555544443

>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=94.62  E-value=0.21  Score=28.68  Aligned_cols=64  Identities=8%  Similarity=-0.023  Sum_probs=48.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARI   69 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~   69 (71)
                      ++|...++...+.  .| +...|..+-.++.+.|++++|+..|++..+.  .| +...+..+-..+.+.|
T Consensus       213 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~  278 (336)
T 1p5q_A          213 SAAIESCNKALEL--DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIR  278 (336)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHH
Confidence            5677888887664  34 7888999999999999999999999999875  34 4556666666665544

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=94.61  E-value=0.3  Score=28.10  Aligned_cols=48  Identities=6%  Similarity=-0.109  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .|+.+-.++.+.|++++|+..++...+.. .-+...|..+-.+|...|+
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~  279 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQ  279 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            55666666667777777777777665542 1245556666556655554

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=94.48  E-value=0.37  Score=28.09  Aligned_cols=45  Identities=16%  Similarity=0.004  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|..+|+++.+.  .|+..+-..++.++.+.|++++|++.++.+.+
T Consensus       195 q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          195 TSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             THHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5789999998655  45544445555588899999999999997764

>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=94.42  E-value=0.21  Score=25.17  Aligned_cols=54  Identities=9%  Similarity=-0.027  Sum_probs=40.1

Q ss_pred             CCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           16 VNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        16 ~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ..| +...+..+-..+.+.|++++|+..|+...... ..+...|..+-.++.+.|+
T Consensus        16 ~~p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~   70 (148)
T 2vgx_A           16 ISSDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQ   70 (148)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             CCHhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhh
Confidence            345 56667777788899999999999999987652 2266677777667766665

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=94.36  E-value=0.16  Score=23.32  Aligned_cols=47  Identities=13%  Similarity=-0.006  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHhcCCCc--CHHHHHHHHHHHHhc-CCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP--DTSTCNALMDGFCLA-DRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+.. +.  +...+..+-..+.+. |++++|.+.++.....
T Consensus        57 ~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           57 EEAVDCYNYVINVI-EDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHHHHHHHHHHHTS-CCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHhC-cccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhc
Confidence            57888888887652 22  578888999999999 9999999999999866

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=94.34  E-value=0.19  Score=24.92  Aligned_cols=46  Identities=9%  Similarity=-0.120  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+.....  .| +...|..+-.++...|++++|...|+...+.
T Consensus        69 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           69 EQALQSYSYGALM--DINEPRFPFHAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5778888888765  34 6777888888999999999999999998764

>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=94.33  E-value=0.26  Score=25.80  Aligned_cols=58  Identities=12%  Similarity=0.092  Sum_probs=44.9

Q ss_pred             HHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            7 LAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         7 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      -++.+....+.|+..+..+.+.+|-+.+++..|.++|+..+.+ +.+....|.-+++-+
T Consensus        75 glN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~lqEl  132 (152)
T 2y69_E           75 GMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQEL  132 (152)
T ss_dssp             HHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHHH
T ss_pred             HHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHHHHH
Confidence            3344445668899999999999999999999999999999755 234455677776643

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=94.33  E-value=0.22  Score=28.99  Aligned_cols=47  Identities=9%  Similarity=-0.038  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHhcCCC-cCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            3 EANGLAELMIQRGVN-PDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +|.+++.+-...+-. -+...+-..+..+.+.|+++.|.+.++.|.+.
T Consensus       118 eAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~  165 (310)
T 3mv2_B          118 KSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA  165 (310)
T ss_dssp             HHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            444444444332211 13444555555555666666666666665443

>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=94.21  E-value=0.47  Score=28.57  Aligned_cols=70  Identities=6%  Similarity=-0.118  Sum_probs=49.4

Q ss_pred             hHHHHHHHHHHh---cCCCc----CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CC-CCccH-HHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQ---RGVNP----DTSTCNALMDGFCLADRFDRARELLVSMGS-----KG-CKQDA-FSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~---~~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g-~~p~~-~~~~~li~~~~~   67 (71)
                      ++|..+++...+   .-+.|    ...+++.+..+|...|++++|+.++++...     .| -.|++ .+++.|-..|..
T Consensus       304 ~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~  383 (429)
T 3qwp_A          304 EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLH  383 (429)
T ss_dssp             HHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHh
Confidence            456677776653   22333    356888999999999999999999998864     12 34544 567778778877


Q ss_pred             cccC
Q 042276           68 RIRK   71 (71)
Q Consensus        68 ~~~~   71 (71)
                      .|++
T Consensus       384 ~g~~  387 (429)
T 3qwp_A          384 QGMF  387 (429)
T ss_dssp             TTCH
T ss_pred             cCCH
Confidence            7763

>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=94.17  E-value=0.34  Score=26.39  Aligned_cols=11  Identities=9%  Similarity=0.147  Sum_probs=4.0

Q ss_pred             CCHHHHHHHHH
Q 042276           34 DRFDRARELLV   44 (71)
Q Consensus        34 g~~~~a~~~~~   44 (71)
                      +++++|++.|+
T Consensus        92 ~~~~~A~~~~~  102 (273)
T 1ouv_A           92 QNTNKALQYYS  102 (273)
T ss_dssp             CCHHHHHHHHH
T ss_pred             cCHHHHHHHHH
Confidence            33333333333

>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=94.13  E-value=0.29  Score=25.49  Aligned_cols=68  Identities=12%  Similarity=-0.117  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC--------------CCc-cHHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG--------------CKQ-DAFSHSILINGGS   66 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--------------~~p-~~~~~~~li~~~~   66 (71)
                      ++|...|++..+.. +.+...|..+-..+.+.|++++|+..|+...+..              ..| +...+..+-..+.
T Consensus        54 ~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  132 (213)
T 1hh8_A           54 TEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYA  132 (213)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHH
Confidence            56788888876542 2367889999999999999999999999998642              122 2256666666666


Q ss_pred             hccc
Q 042276           67 ARIR   70 (71)
Q Consensus        67 ~~~~   70 (71)
                      +.|+
T Consensus       133 ~~g~  136 (213)
T 1hh8_A          133 KKEE  136 (213)
T ss_dssp             HTTC
T ss_pred             HccC
Confidence            6654

>4a1g_A Mitotic checkpoint serine/threonine-protein kinas; cell cycle, transferase, spindle assembly checkpoint, mitosi repeat, KNL1, KMN network; 2.60A {Homo sapiens} PDB: 2lah_A

Probab=94.11  E-value=0.3  Score=25.69  Aligned_cols=54  Identities=9%  Similarity=0.124  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA   55 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   55 (71)
                      +++..+|..|..+|+.- -..-|-..-..+-..|++.+|.++|+.=.+++-+|-.
T Consensus        82 ~dp~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~~A~P~~  136 (152)
T 4a1g_A           82 SDLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASAVLQRGIQNQAEPRE  136 (152)
T ss_dssp             SCHHHHHHHHHTTTTTTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHH
T ss_pred             CCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHH
Confidence            35788999999999887 4667777777788899999999999999998877743

>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=94.06  E-value=0.56  Score=28.57  Aligned_cols=64  Identities=14%  Similarity=0.031  Sum_probs=49.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ++|.+.+++..+.  .| +...+..+-..+.+.|++++|.+.|++..+.. .-+...+..+...+.+.
T Consensus        74 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~  138 (568)
T 2vsy_A           74 AEAAVLLQQASDA--APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRL  138 (568)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHh
Confidence            5778888887664  34 67888889899999999999999999987652 22456777777777766

>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=93.89  E-value=0.3  Score=30.81  Aligned_cols=66  Identities=9%  Similarity=-0.063  Sum_probs=46.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcccC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIRK   71 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~   71 (71)
                      ++|...|++..+.  .| +...|..+=..+.+.|++++|+..|++..+.  .| +...|..+-..+.+.|++
T Consensus       450 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~  517 (681)
T 2pzi_A          450 AKATRKLDDLAER--VGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNT  517 (681)
T ss_dssp             HHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHhcc--CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCCh
Confidence            4677777777654  34 5677777777888888999999888888765  23 446666666666666653

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=93.89  E-value=0.4  Score=26.75  Aligned_cols=69  Identities=10%  Similarity=-0.120  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhc----CCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHH------HHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQR----GVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAF------SHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.    +-.+ ...+++.+-..+.+.|++++|+..|++..+........      .|..+-.++...|+
T Consensus       135 ~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~  214 (292)
T 1qqe_A          135 AKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATD  214 (292)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCC
Confidence            4566666665432    1111 14568888889999999999999999998753222211      34555455555443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.86  E-value=0.25  Score=23.92  Aligned_cols=50  Identities=6%  Similarity=-0.134  Sum_probs=39.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc----HHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD----AFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~   70 (71)
                      +...+..+-..+.+.|++++|.+.|++..+.  .|+    ...|..+-..+.+.|+
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~   80 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLED   80 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHcc
Confidence            6778888888999999999999999999875  455    5667777666666654

>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=93.80  E-value=0.26  Score=23.76  Aligned_cols=52  Identities=6%  Similarity=-0.084  Sum_probs=40.7

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           18 PDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        18 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .+...|..+-..+.+.|++++|+..|+...... ..+...|..+-..+.+.|+
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~   58 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQ   58 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcC
Confidence            367888888899999999999999999987653 2246677777777766665

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=93.66  E-value=0.48  Score=26.45  Aligned_cols=46  Identities=15%  Similarity=0.095  Sum_probs=32.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+.  .| +...+..+-..+.+.|++++|...+++....
T Consensus       134 ~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~  180 (287)
T 3qou_A          134 TDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ  180 (287)
T ss_dssp             HHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG
T ss_pred             HHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh
Confidence            4566777776554  44 5667777777788888888888888776543

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=93.54  E-value=0.45  Score=25.77  Aligned_cols=46  Identities=9%  Similarity=-0.036  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHHhcCCCc-C---HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-D---TSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+...+.  .| +   ...+..+-..+.+.|++++|+..|+...+.
T Consensus        32 ~~A~~~~~~~l~~--~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   81 (261)
T 3qky_A           32 DRAIEYFKAVFTY--GRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQI   81 (261)
T ss_dssp             HHHHHHHHHHGGG--CSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence            5788888888765  34 3   567777778888999999999999999875

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=93.51  E-value=0.28  Score=23.22  Aligned_cols=46  Identities=22%  Similarity=0.289  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|..++++..+.  .| ++.....+=..+.+.|++++|+..++.+.+.
T Consensus        26 ~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A           26 DEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            4677788777664  56 5666666667788999999999999999876

>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=93.43  E-value=0.53  Score=26.15  Aligned_cols=69  Identities=7%  Similarity=-0.086  Sum_probs=44.1

Q ss_pred             hHHHHHHHHHHhc-CCCcCH----HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCC-Ccc----HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQR-GVNPDT----STCNALMDGFCLADRFDRARELLVSMGSKGC-KQD----AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~-~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~----~~~~~~li~~~~~~~~   70 (71)
                      ++|..++++..+. ...|+.    ..+..+-..+...+++++|+..|++...... .++    ..+|+.+-..|.+.|+
T Consensus        92 ~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~  170 (293)
T 3u3w_A           92 KEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGY  170 (293)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCC
Confidence            4677778777653 223332    2344566667778899999999999986322 223    2357777777766664

>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=93.34  E-value=0.56  Score=28.15  Aligned_cols=49  Identities=6%  Similarity=-0.179  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ...|..+-.++.+.|++++|+..|++..+.. .-+...|..+-.+|.+.|
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g  365 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMN  365 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHcc
Confidence            3555555555666666666666666655431 113444544444444444

>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=93.30  E-value=0.51  Score=25.65  Aligned_cols=60  Identities=13%  Similarity=0.029  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCL----ADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      ++|...|+...+.+   +...+..+-..+.+    .+++++|++.|++..+.+   +..++..+-..|..
T Consensus        23 ~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~   86 (273)
T 1ouv_A           23 TQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLGNLYYS   86 (273)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhC
Confidence            56788888877632   56777778888888    999999999999998876   56666666666654

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=93.26  E-value=0.24  Score=24.12  Aligned_cols=46  Identities=15%  Similarity=-0.073  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+...+.  .| +...+..+-..+.+.|++++|+..|++..+.
T Consensus        68 ~~A~~~~~~al~l--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           68 GLAIIALNHARML--DPKDIAVHAALAVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4677788877654  45 6778888889999999999999999998764

>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=93.21  E-value=0.48  Score=25.05  Aligned_cols=52  Identities=12%  Similarity=-0.097  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      |...+...=..+.+.|++++|++.|++..+..-.++...+..+-..+.+.|+
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~   57 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKK   57 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhc
Confidence            5567777777888999999999999999876533666676666666666654

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=93.19  E-value=0.57  Score=25.83  Aligned_cols=53  Identities=17%  Similarity=0.183  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA   55 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   55 (71)
                      ++..+|..|..+|+.- -..-|-..-..+-..|++.+|.++|+.=.+++-+|-.
T Consensus        97 ~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A~P~~  150 (202)
T 3esl_A           97 ESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYN  150 (202)
T ss_dssp             HHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHH
T ss_pred             CHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHH
Confidence            7889999999998887 4677777777788899999999999999988877743

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=93.19  E-value=0.26  Score=21.91  Aligned_cols=51  Identities=14%  Similarity=0.006  Sum_probs=38.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +...+..+-..+.+.|++++|+..|++..+.. ..+...+..+-..+.+.|+
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~   58 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGD   58 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhh
Confidence            45677777788899999999999999987653 2255667777667766654

>2wvi_A Mitotic checkpoint serine/threonine-protein kinase BUB1 beta; tumor suppressor, TPR, apoptosis, cell division, cell cycle, kinetochore, transferase; 1.80A {Homo sapiens} PDB: 3si5_A

Probab=93.16  E-value=0.5  Score=25.16  Aligned_cols=55  Identities=7%  Similarity=0.109  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHhcCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHH
Q 042276            2 DEANGLAELMIQRGVNPD-TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAF   56 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   56 (71)
                      +++..+|..|..+|+.-. ..-|-..-..+-..|++.+|.++|+.-.+++-+|-..
T Consensus        77 ~~p~~if~~L~~~~IG~~~AlfY~~wA~~lE~~~~~~~A~~Iy~~Gi~~~A~P~~~  132 (164)
T 2wvi_A           77 NEPLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPLER  132 (164)
T ss_dssp             SCHHHHHHHHHHTTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHHH
T ss_pred             CCHHHHHHHHHHCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHH
Confidence            456789999999998874 6667777777778999999999999999998888543

>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=93.15  E-value=0.37  Score=25.42  Aligned_cols=61  Identities=13%  Similarity=0.096  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhc-----------CCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLA-----------DRFDRARELLVSMGSKGCKQDAFSHSILINGGS   66 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~-----------g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~   66 (71)
                      ++|...|++..+.  .| +..+|..+=.+|.+.           |++++|++.|++..+.  .|+...|.--+...-
T Consensus        63 ~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~~~~  135 (158)
T 1zu2_A           63 QEAITKFEEALLI--DPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMTA  135 (158)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHH
Confidence            4777778777655  55 577888888888876           4899999999999876  577777766665543

>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=93.14  E-value=0.41  Score=28.96  Aligned_cols=46  Identities=13%  Similarity=-0.073  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+++..+.  .| +..+|..+-.+|.+.|++++|++.|++..+.
T Consensus        57 ~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~  103 (477)
T 1wao_1           57 GYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFRAALRDYETVVKV  103 (477)
T ss_dssp             HHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5788888888765  44 6788888999999999999999999998765

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=92.92  E-value=0.27  Score=26.86  Aligned_cols=67  Identities=13%  Similarity=0.051  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHhcCCCcC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD-----TSTCNALMDGFCLADRFDRARELLVSMGSK----GCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .|+     ...+..+-..+...|++++|.+.+++....    +-.| ...++..+-..+...|+
T Consensus        22 ~~A~~~~~~al~~--~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   98 (338)
T 3ro2_A           22 RAGVSFFEAAVQV--GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGN   98 (338)
T ss_dssp             HHHHHHHHHHHHH--CCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhh--CcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHccC
Confidence            5788888888765  332     467888888899999999999998886542    2222 23455666666655554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=92.92  E-value=0.41  Score=23.45  Aligned_cols=55  Identities=5%  Similarity=-0.088  Sum_probs=41.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc-HHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD-AFSHSI   60 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~   60 (71)
                      ++|...|+...+.  .| +...|..+-.++.+.|++++|++.|++..+.  .|+ ...+..
T Consensus        64 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~l--~P~~~~a~~~  120 (126)
T 4gco_A           64 QRALDDCDTCIRL--DSKFIKGYIRKAACLVAMREWSKAQRAYEDALQV--DPSNEEAREG  120 (126)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHh--hhhhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcCCHHHHHH
Confidence            5677778777654  44 6788999999999999999999999999875  454 333433

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=92.90  E-value=0.23  Score=28.47  Aligned_cols=67  Identities=13%  Similarity=0.050  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHhcCCCcC-H----HHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPD-T----STCNALMDGFCLADRFDRARELLVSMGSK----GCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .|+ .    .+|..+-..+...|++++|+..+++..+.    +-.| ...++..+-..+...|+
T Consensus        65 ~~A~~~~~~al~~--~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~  141 (411)
T 4a1s_A           65 RAGVAFFQAAIQA--GTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGR  141 (411)
T ss_dssp             HHHHHHHHHHHHH--CCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--cccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCC
Confidence            5678888888765  332 2    57788888888999999999998887643    2122 33556666666655554

>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=92.78  E-value=0.72  Score=27.01  Aligned_cols=49  Identities=6%  Similarity=-0.164  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ..+|+.+-.++.+.|++++|++.+++..+.. .-+...|..+-.+|.+.|
T Consensus       273 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g  321 (370)
T 1ihg_A          273 LSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLK  321 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHcc
Confidence            4555555555556666666666666655431 113444444444444444

>4aez_C MAD3, mitotic spindle checkpoint component MAD3; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}

Probab=92.77  E-value=0.71  Score=25.83  Aligned_cols=53  Identities=15%  Similarity=0.120  Sum_probs=44.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD   54 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   54 (71)
                      +++..+|..|..+|+.- -..-|-..-..+-..|++.+|..+|+.=.+++-+|-
T Consensus       131 ~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~~A~P~  184 (223)
T 4aez_C          131 DEPVELFSFLAHHHIGQESSIFYEEYANYFESRGLFQKADEVYQKGKRMKAKPF  184 (223)
T ss_dssp             SCHHHHHHHHHHTTCSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCBSH
T ss_pred             CCHHHHHHHHHHCCcchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccH
Confidence            35678999999999887 466777777778889999999999999998887774

>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=92.25  E-value=0.48  Score=22.64  Aligned_cols=46  Identities=17%  Similarity=0.103  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...++...+.  .| +...|..+-..+.+.|++++|...|++..+.
T Consensus        55 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           55 PEAIADCNKAIEK--DPNFVRAYIRKATAQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHHh
Confidence            5677788877654  44 6788888889999999999999999998765

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=92.14  E-value=0.48  Score=22.48  Aligned_cols=46  Identities=13%  Similarity=0.063  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHHhcCCCc-C---HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-D---TSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+...+.  .| +   ...+..+-..+.+.|++++|...|+...+.
T Consensus        56 ~~A~~~~~~~~~~--~p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           56 QLAEAQFRDLVSR--YPTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHHHHH--CTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5788888888764  33 2   566777778899999999999999999875

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=91.97  E-value=0.9  Score=25.19  Aligned_cols=69  Identities=9%  Similarity=-0.108  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHHh----cCCCc--CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCcc-HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQ----RGVNP--DTSTCNALMDGFCLADRFDRARELLVSMGSK----GCKQD-AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~----~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+    ..-.+  ...+++.+-..|.+.|++++|+..+++..+.    +.... ..+|..+-..+.+.|+
T Consensus       172 ~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~  251 (293)
T 2qfc_A          172 KKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEY  251 (293)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCC
Confidence            467777777652    11112  2368888888999999999999999987643    11111 4566666666666664

>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=91.97  E-value=0.71  Score=23.98  Aligned_cols=62  Identities=11%  Similarity=-0.049  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~   67 (71)
                      ++|...++...+.  .| +...+..+-.++.+.|++++|++.|++..+.  .| +...+..+-..+..
T Consensus       105 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~  168 (198)
T 2fbn_A          105 PKAIDHASKVLKI--DKNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELCVNK  168 (198)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHH
Confidence            4677777777654  34 6788888888999999999999999998765  34 44555555554443

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=91.85  E-value=0.5  Score=27.12  Aligned_cols=50  Identities=4%  Similarity=-0.194  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CC-CccHHHHHHHHHHHHhccc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSK----GC-KQDAFSHSILINGGSARIR   70 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~-~p~~~~~~~li~~~~~~~~   70 (71)
                      .+++.+=..|.+.|++++|++.|++..+.    +- .....++..+-..+.+.|+
T Consensus       225 ~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~  279 (383)
T 3ulq_A          225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGK  279 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCC
Confidence            45666666677777777777777776541    22 2234455555555555544

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=91.62  E-value=0.52  Score=24.14  Aligned_cols=30  Identities=13%  Similarity=0.099  Sum_probs=20.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ...+++.+-..+...|++++|...+++...
T Consensus        65 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   94 (203)
T 3gw4_A           65 EHRALHQVGMVERMAGNWDAARRCFLEERE   94 (203)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            355666666677777888887777776654

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=91.60  E-value=0.7  Score=23.22  Aligned_cols=46  Identities=17%  Similarity=0.036  Sum_probs=38.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+...+.  .| +...|..+-..+.+.|++++|...|++..+.
T Consensus        62 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           62 EKAAEDAELATVV--DPKYSKAWSRLGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            5778888888765  34 6888999999999999999999999998764

>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=91.58  E-value=0.86  Score=27.33  Aligned_cols=63  Identities=6%  Similarity=-0.013  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSAR   68 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~   68 (71)
                      ++|...++...+.  .| +...|..+=.+|.+.|++++|+..|++..+.  .| +...+..+-.++.+.
T Consensus       334 ~~A~~~~~~al~~--~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~  398 (457)
T 1kt0_A          334 TKAVECCDKALGL--DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKA  398 (457)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHH
Confidence            4677777777654  34 6888888889999999999999999999865  34 345555555555443

>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=91.30  E-value=0.69  Score=22.55  Aligned_cols=49  Identities=6%  Similarity=-0.152  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ...+.-+=..+.+.|++++|++.|++..+.  .| +...|+.+-.+|.+.|+
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~   57 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKK   57 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhh
Confidence            345555666788999999999999998865  34 56777777777777765

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=91.18  E-value=0.71  Score=24.25  Aligned_cols=49  Identities=10%  Similarity=0.151  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHHhcCCCc---CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc
Q 042276            2 DEANGLAELMIQRGVNP---DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD   54 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~   54 (71)
                      +++..+|++..+.. .|   ....|+.-+ ++.+.+++++|.+.++...+.  +|+
T Consensus        52 ~~gI~lLe~ll~~~-~p~~~rd~lY~LAv-~~~kl~~Y~~A~~y~~~lL~i--eP~  103 (152)
T 1pc2_A           52 RKGIVLLEELLPKG-SKEEQRDYVFYLAV-GNYRLKEYEKALKYVRGLLQT--EPQ  103 (152)
T ss_dssp             HHHHHHHHHHHHHS-CHHHHHHHHHHHHH-HHHHTSCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHHHHHHHHhcC-CccchHHHHHHHHH-HHHHccCHHHHHHHHHHHHhc--CCC
Confidence            35677777776653 23   122343333 557888888888888887765  454

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=91.12  E-value=0.8  Score=22.95  Aligned_cols=50  Identities=6%  Similarity=-0.039  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ...|..+-.++.+.|++++|+..++...+.. ..+...|..+-.++...|+
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~  112 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWK  112 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhc
Confidence            3556666666667777777777777665542 1244555555555555544

>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=90.93  E-value=0.73  Score=23.52  Aligned_cols=46  Identities=13%  Similarity=0.030  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ++|...|++..+..-.+ +...+..+...+...|+.++|...|++..
T Consensus       125 ~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A          125 EEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             HHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHH
Confidence            57888888887663322 36688999999999999999999998764

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=90.89  E-value=0.68  Score=26.24  Aligned_cols=67  Identities=15%  Similarity=0.048  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHhcCCCc-C----HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC----CCCcc-HHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-D----TSTCNALMDGFCLADRFDRARELLVSMGSK----GCKQD-AFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .| +    ..+|..+-..+...|++++|...+++....    +-.|. ..++..+-..+...|+
T Consensus        26 ~~A~~~~~~al~~--~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~  102 (406)
T 3sf4_A           26 RAGVSFFEAAVQV--GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGN  102 (406)
T ss_dssp             HHHHHHHHHHHHH--CCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhc--CcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCC
Confidence            5778888888765  33 2    357788888888999999999998886532    22222 3455566666655554

>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=90.88  E-value=1.2  Score=24.73  Aligned_cols=50  Identities=4%  Similarity=-0.122  Sum_probs=39.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      +...+..+-..+.+.|++++|+..|++....  .| +...|..+-..+.+.|+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~   53 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQ   53 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcC
Confidence            4566777778889999999999999999875  34 66777777777777665

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=90.56  E-value=0.71  Score=26.51  Aligned_cols=28  Identities=7%  Similarity=-0.027  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      .+++.+=..|.+.|++++|++.|++...
T Consensus       223 ~~~~~lg~~y~~~~~~~~A~~~~~~al~  250 (378)
T 3q15_A          223 ISLLNIANSYDRSGDDQMAVEHFQKAAK  250 (378)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3455555556666666666666666554

>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=90.44  E-value=0.83  Score=25.62  Aligned_cols=29  Identities=17%  Similarity=0.092  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ..+++.+-..+.+.|++++|+..|++...
T Consensus       155 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~  183 (307)
T 2ifu_A          155 AELIGKASRLLVRQQKFDEAAASLQKEKS  183 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34566666666677777777777766654

>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=90.08  E-value=2  Score=25.80  Aligned_cols=41  Identities=5%  Similarity=-0.108  Sum_probs=25.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHH
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSIL   61 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   61 (71)
                      +..+|.++-..+...|++++|...+++....+  |+...|..+
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~ll  316 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLL  316 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHH
Confidence            56666666555555677777777777766654  565555433

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=89.92  E-value=0.39  Score=23.29  Aligned_cols=28  Identities=14%  Similarity=0.169  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      .++..+-..+...|++++|.+.+++...
T Consensus        50 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~   77 (164)
T 3ro3_A           50 IAYSNLGNAYIFLGEFETASEYYKKTLL   77 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4677777778888888888888887654

>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=89.89  E-value=1.9  Score=27.28  Aligned_cols=67  Identities=3%  Similarity=-0.263  Sum_probs=48.3

Q ss_pred             hHHHHHHHHHHh------cCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQ------RGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~------~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.+++...      ....| +...+..+-..+.+.|++++|++.|++..+.  .| +...|..+=.++.+.|+
T Consensus       408 ~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~  482 (681)
T 2pzi_A          408 VQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAER--VGWRWRLVWYRAVAELLTGD  482 (681)
T ss_dssp             HHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc--CcchHHHHHHHHHHHHHcCC
Confidence            467777777761      12344 6778888888999999999999999999865  23 55677766666666654

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=89.69  E-value=0.82  Score=23.00  Aligned_cols=46  Identities=15%  Similarity=0.065  Sum_probs=35.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           24 NALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        24 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      -.+++.+...+..-.|.++++.+.+.+-..+..|..-.++.+.+.|
T Consensus        14 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~G   59 (131)
T 2o03_A           14 AAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSG   59 (131)
T ss_dssp             HHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCC
Confidence            3566677777777889999999988876778888877788877765

>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=89.49  E-value=0.87  Score=20.80  Aligned_cols=46  Identities=11%  Similarity=0.041  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+++..+.  .| +...+..+-..+.+.|++++|.+.+++..+.
T Consensus        55 ~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           55 QKAYEDGCKTVDL--KPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence            4677788777654  34 6788888889999999999999999998765

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=89.37  E-value=1.4  Score=23.09  Aligned_cols=64  Identities=9%  Similarity=-0.010  Sum_probs=47.4

Q ss_pred             HHHHHH-HHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC--CCCccHHHHHHHHHHHHhcc
Q 042276            5 NGLAEL-MIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK--GCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         5 ~~~~~~-m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p~~~~~~~li~~~~~~~   69 (71)
                      .+-+.+ +++.|++++. --..++..+.+.+..-.|.++++.+.+.  +-..+..|..--|+.+.+.|
T Consensus        17 ~~~~~~~L~~~g~r~T~-qR~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~G   83 (162)
T 4ets_A           17 LERFKKILRQGGLKYTK-QREVLLKTLYHSDTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAE   83 (162)
T ss_dssp             HHHHHHHHHHHTCCCCH-HHHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCCCH-HHHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCC
Confidence            333444 4568888754 4466777888888888999999999887  66678888777778877765

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=89.25  E-value=1.2  Score=22.23  Aligned_cols=57  Identities=16%  Similarity=0.056  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHH-HHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAF-SHSILI   62 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-~~~~li   62 (71)
                      ++|...+....+.  .| +...|..+-.++...|++++|...|+...+.  .|+.. .....+
T Consensus        80 ~~A~~~~~~al~~--~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~l  138 (162)
T 3rkv_A           80 HEAEETSSEVLKR--EETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAASVVAREM  138 (162)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCHHHHHHHH
Confidence            4667777777654  45 6888888999999999999999999998776  46544 433333

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=89.12  E-value=1.6  Score=23.25  Aligned_cols=46  Identities=11%  Similarity=0.121  Sum_probs=28.1

Q ss_pred             hHHHHHHHHHHhcCCCcC----HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPD----TSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+.+.+.  .|+    ...+..+-.++.+.|++++|.+.++.+...
T Consensus       164 ~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          164 VAVVNRVEGMLRD--YPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             HHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHH--CcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence            3556666666543  232    245666666777777777777777766654

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=89.09  E-value=0.79  Score=23.38  Aligned_cols=57  Identities=12%  Similarity=-0.024  Sum_probs=39.6

Q ss_pred             HhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           12 IQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        12 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ++.|++++ .--..++..+.+.+..-.|.++++.+.+.+-..+..|..--|+.+.+.|
T Consensus         6 r~~g~r~T-~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~G   62 (139)
T 3mwm_A            6 PPVKGRAT-RQRAAVSAALQEVEEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAG   62 (139)
T ss_dssp             ----CHHH-HHHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCccC-HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCC
Confidence            34444432 2335667777777777889999999998877778888888888887766

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=88.98  E-value=0.84  Score=24.88  Aligned_cols=29  Identities=14%  Similarity=0.366  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ..++..+-..+.+.|++++|...+++...
T Consensus       263 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~  291 (338)
T 3ro2_A          263 AQSCYSLGNTYTLLQDYEKAIDYHLKHLA  291 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            44556666666677777777777666643

>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=88.92  E-value=2.3  Score=24.90  Aligned_cols=62  Identities=15%  Similarity=0.088  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSA   67 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~   67 (71)
                      ++|...+++..+.  .| +...|..+-.+|.+.|++++|++.|++..+.  .| +...+..+-..+.+
T Consensus       290 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~  353 (370)
T 1ihg_A          290 QGAVDSCLEALEI--DPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQK  353 (370)
T ss_dssp             HHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            5677788777754  45 6788888888999999999999999998765  34 44555555544443

>2b7e_A PRE-mRNA processing protein PRP40; structural protein; NMR {Saccharomyces cerevisiae} SCOP: a.159.2.1

Probab=88.78  E-value=0.26  Score=21.93  Aligned_cols=34  Identities=15%  Similarity=0.075  Sum_probs=17.6

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHH-HhcCC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGF-CLADR   35 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~-~~~g~   35 (71)
                      ++|...|-+|.+..-.++.-||.-.|... ++.-+
T Consensus         3 eEae~aF~~lL~~~~V~s~wsweqamr~i~i~DPr   37 (59)
T 2b7e_A            3 MEAEKEFITMLKENQVDSTWSFSRIISELGTRDPR   37 (59)
T ss_dssp             THHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHCTH
T ss_pred             hHHHHHHHHHHHHcCCCCCCcHHHHHHHhccCCCc
Confidence            45666666665433333445666666555 44443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=88.78  E-value=1.1  Score=21.15  Aligned_cols=52  Identities=12%  Similarity=0.022  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHhc------CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH
Q 042276            2 DEANGLAELMIQR------GVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDA   55 (71)
Q Consensus         2 ~~a~~~~~~m~~~------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   55 (71)
                      +.|...|++..+.      .-.+...++..+-.++.+.|+++.|...+++..+.  .|+.
T Consensus        22 ~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l--~P~~   79 (104)
T 2v5f_A           22 YHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEH   79 (104)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCCC
Confidence            3455556555432      12346778889999999999999999999999764  4543

>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=88.16  E-value=1.8  Score=22.89  Aligned_cols=44  Identities=14%  Similarity=0.199  Sum_probs=22.7

Q ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCC
Q 042276            4 ANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKG   50 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g   50 (71)
                      |.+.|....+.|   +...+..+=..|.+.+++++|++.|++..+.|
T Consensus         5 A~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g   48 (212)
T 3rjv_A            5 PGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG   48 (212)
T ss_dssp             TTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC
Confidence            444454444443   44444444445555566666666666555544

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=88.03  E-value=1.1  Score=25.43  Aligned_cols=28  Identities=14%  Similarity=0.365  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           20 TSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        20 ~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ..++..+-..+.+.|++++|...+++..
T Consensus       267 ~~~~~~la~~~~~~g~~~~A~~~~~~a~  294 (406)
T 3sf4_A          267 AQSCYSLGNTYTLLQDYEKAIDYHLKHL  294 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence            4455555556666666666666666554

>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=87.78  E-value=2.7  Score=25.24  Aligned_cols=56  Identities=11%  Similarity=-0.058  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSIL   61 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~l   61 (71)
                      ++|...++.....+  |+...|..+=..+.-.|++++|.+.|.+....  .|...||...
T Consensus       294 d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~~~  349 (372)
T 3ly7_A          294 DESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLYWI  349 (372)
T ss_dssp             HHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHHHH
Confidence            57788888888775  78777766666777899999999999888766  4666666543

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=87.77  E-value=2.6  Score=24.18  Aligned_cols=47  Identities=15%  Similarity=0.130  Sum_probs=38.1

Q ss_pred             ChHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            1 MDEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +++|...++...+.  .| +...|..+-.+|...|++++|+..|++..+.
T Consensus       246 ~~~A~~~~~~al~~--~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l  293 (338)
T 2if4_A          246 YDEAIGHCNIVLTE--EEKNPKALFRRGKAKAELGQMDSARDDFRKAQKY  293 (338)
T ss_dssp             CHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            35777888877654  44 6888899999999999999999999998754

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=87.71  E-value=1.2  Score=22.52  Aligned_cols=59  Identities=10%  Similarity=0.031  Sum_probs=43.2

Q ss_pred             HHHhcCCCcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           10 LMIQRGVNPDTSTCNALMDGFCLAD-RFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        10 ~m~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .+++.|++++..= -.++..+...+ ..-.|.++++.+.+.+-..+..|..--++.+.+.|
T Consensus         8 ~l~~~g~r~T~qR-~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~G   67 (136)
T 1mzb_A            8 ELRKAGLKVTLPR-VKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAG   67 (136)
T ss_dssp             HHHHTTCCCCHHH-HHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHCCCCCCHHH-HHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCC
Confidence            4567787766443 45566666666 67789999999998877778888887888877665

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=87.69  E-value=1.8  Score=22.20  Aligned_cols=59  Identities=7%  Similarity=-0.014  Sum_probs=43.3

Q ss_pred             HHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            9 ELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         9 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.+++.|++++..= ..++..+.+.+ .-.|.++++.+.+.+-..+..|..--|+.+.+.|
T Consensus         8 ~~L~~~g~r~T~qR-~~Il~~l~~~~-h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~G   66 (145)
T 3eyy_A            8 SDLRQRGYRLTPQR-QLVLEAVDTLE-HATPDDILGEVRKTASGINISTVYRTLELLEELG   66 (145)
T ss_dssp             HHHHTTTCCCCHHH-HHHHHHHHHHS-SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCCcCHHH-HHHHHHHHhcC-CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCC
Confidence            34567888876543 44555666666 6789999999998877778888877788877765

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=87.31  E-value=3  Score=24.36  Aligned_cols=52  Identities=15%  Similarity=-0.030  Sum_probs=38.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-----C--CCc-cHHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSK-----G--CKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g--~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ....||.+=..+...|+.++|++.|++-.+.     +  ..| ...+|+-+-..|...|+
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~  109 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGR  109 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCC
Confidence            4678998888899999999999999876531     1  233 34678887777777665

>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=86.90  E-value=2.6  Score=30.05  Aligned_cols=49  Identities=12%  Similarity=0.151  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      |...|.-+...+.+.|++++|.+.+...++..  ++....+.+..+|++.+
T Consensus      1133 D~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~ 1181 (1630)
T 1xi4_A         1133 DPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTN 1181 (1630)
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhc
Confidence            56666677777777777777777776655543  22222223555555544

>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=86.59  E-value=2.3  Score=22.37  Aligned_cols=67  Identities=15%  Similarity=-0.043  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHhcCCCcC-------------HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC-----CCCccH-HHH----
Q 042276            2 DEANGLAELMIQRGVNPD-------------TSTCNALMDGFCLADRFDRARELLVSMGSK-----GCKQDA-FSH----   58 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~-------------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~~-~~~----   58 (71)
                      ++|...|+...+.  .|+             ...|+..=.++.+.|++++|+..+++..+.     .+.|+. ..|    
T Consensus        28 eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~  105 (159)
T 2hr2_A           28 DEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAV  105 (159)
T ss_dssp             HHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHH
Confidence            4667777766543  222             338888888999999999999999998764     225643 445    


Q ss_pred             HHHHHHHHhccc
Q 042276           59 SILINGGSARIR   70 (71)
Q Consensus        59 ~~li~~~~~~~~   70 (71)
                      ...=.++.+.|+
T Consensus       106 ~~rG~aL~~lgr  117 (159)
T 2hr2_A          106 YSRALALDGLGR  117 (159)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HhHHHHHHHCCC
Confidence            444444444443

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=86.59  E-value=1.4  Score=19.99  Aligned_cols=60  Identities=10%  Similarity=0.027  Sum_probs=44.0

Q ss_pred             HHHHhcCCCcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            9 ELMIQRGVNPDTSTCNALMDGFCLAD-RFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         9 ~~m~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.|.+.|+..+..- -.++..+.+.+ ..-.+.++++.+.+.+...+..|..-.++.+.+.|
T Consensus         6 ~~l~~~g~~~t~~r-~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~G   66 (83)
T 2fu4_A            6 TALKKAGLKVTLPR-LKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAG   66 (83)
T ss_dssp             HHHHHTTCCCCHHH-HHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCCcCHHH-HHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCC
Confidence            44667888877654 45667777664 56778899999988766667888888888877665

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=86.58  E-value=1.4  Score=25.25  Aligned_cols=26  Identities=15%  Similarity=0.126  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      ++..+-..+.+.|++++|...|++..
T Consensus       265 ~~~~la~~~~~~g~~~~A~~~~~~al  290 (411)
T 4a1s_A          265 ANSNLGNSHIFLGQFEDAAEHYKRTL  290 (411)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55555556666666666666665554

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=86.15  E-value=2.6  Score=24.60  Aligned_cols=30  Identities=7%  Similarity=-0.022  Sum_probs=26.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ...+|+-+-.+|...|++++|...+++..+
T Consensus        93 ~~~~~~nla~~y~~~g~~~~A~~~~~ka~~  122 (472)
T 4g1t_A           93 SLVTWGNYAWVYYHMGRLSDVQIYVDKVKH  122 (472)
T ss_dssp             THHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            467899999999999999999999887754

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=85.98  E-value=2.2  Score=21.65  Aligned_cols=68  Identities=15%  Similarity=0.077  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh----CCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGS----KGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.++.... .......+++.+-..+...|++++|+..+++...    .|..| ...++..+-..+...|+
T Consensus         9 ~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            9 ALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             HHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            355553333322 1122577888888889999999999999998875    22222 23455555555555554

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=85.84  E-value=3  Score=23.02  Aligned_cols=69  Identities=7%  Similarity=-0.036  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHhcC---CCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHhh---C-CCCc--cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRG---VNPD--TSTCNALMDGFCLADRFDRARELLVSMGS---K-GCKQ--DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~---~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~-g~~p--~~~~~~~li~~~~~~~~   70 (71)
                      ++|...+.+..+..   ..+.  ..+|+.+-..|.+.|++++|+..|++..+   . +-.+  ...+|..+-..|.+.|+
T Consensus       132 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~  211 (293)
T 2qfc_A          132 EYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSR  211 (293)
T ss_dssp             HHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhh
Confidence            46677777665321   1222  45888888899999999999999998863   1 1111  12467777777777665

>2yru_A Steroid receptor RNA activator 1; SRAP, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=85.80  E-value=2.2  Score=21.44  Aligned_cols=44  Identities=18%  Similarity=0.068  Sum_probs=34.5

Q ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            6 GLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         6 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      .+|+.+....+.|++..-=.-|....+.++++.|.++...+...
T Consensus        47 ~LfdkLn~~~Ls~~v~~~L~~l~~al~~~dy~~A~~ih~~l~t~   90 (118)
T 2yru_A           47 LLREQWAGGKLSIPVKKRMALLVQELLHHQWDAADDIHRSLMVD   90 (118)
T ss_dssp             HHHHHHHHTCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Confidence            46777777778777666666677777899999999999998764

>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=85.71  E-value=2.9  Score=29.82  Aligned_cols=47  Identities=9%  Similarity=0.027  Sum_probs=38.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      +..+|.-+=.++.+.|++++|.+.|.+-      -|...|.-++..|.+.|+|
T Consensus      1104 ~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGky 1150 (1630)
T 1xi4_A         1104 EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNW 1150 (1630)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCH
Confidence            5788888888999999999999999664      2677888888888888764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=85.46  E-value=2.7  Score=23.36  Aligned_cols=48  Identities=15%  Similarity=-0.093  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHHhcCCCcCH------HHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDT------STCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~------~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..........      ..|..+-.++...|++++|...|++..+.
T Consensus       175 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  228 (292)
T 1qqe_A          175 IEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (292)
T ss_dssp             HHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5788888888765332221      15667777888999999999999998753

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=84.86  E-value=2.6  Score=21.49  Aligned_cols=60  Identities=10%  Similarity=-0.011  Sum_probs=45.1

Q ss_pred             HHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            9 ELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         9 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.+.+.|++++.. --.++..+...+..-.|.++++.+.+.+-..+..|..--|+.+.+.|
T Consensus        11 ~~l~~~g~r~T~q-R~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~G   70 (145)
T 2fe3_A           11 ETLKETGVRITPQ-RHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESG   70 (145)
T ss_dssp             HHHHHTTCCCCHH-HHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCCCCHH-HHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCC
Confidence            4466788876644 34556666667777889999999998877778888888888887765

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=84.57  E-value=2.8  Score=21.56  Aligned_cols=60  Identities=10%  Similarity=0.032  Sum_probs=44.6

Q ss_pred             HHHHhcCCCcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            9 ELMIQRGVNPDTSTCNALMDGFCLAD-RFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         9 ~~m~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.+.+.|++++..= -.++..+...+ ..-.|.++++.+.+.+-..+..|..--|+.+.+.|
T Consensus         6 ~~l~~~g~r~T~qR-~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~G   66 (150)
T 2w57_A            6 QALKDAGLKVTLPR-LKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAG   66 (150)
T ss_dssp             HHHHHTTCCCCHHH-HHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCCCCHHH-HHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCC
Confidence            44667888776543 34566666665 67789999999998877778888888888887765

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=84.42  E-value=4.2  Score=23.38  Aligned_cols=21  Identities=14%  Similarity=-0.064  Sum_probs=11.1

Q ss_pred             HHHhcCCHHHHHHHHHHHhhC
Q 042276           29 GFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus        29 ~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++.+.|+.++|..+|+++...
T Consensus       217 aL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          217 ARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhc
Confidence            344555555555555555443

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=84.23  E-value=3.2  Score=21.98  Aligned_cols=48  Identities=13%  Similarity=0.025  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHhcCC-Cc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGV-NP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+.+.+..- .| ....+..+-..+.+.|++++|+..|++..+.
T Consensus        21 ~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   70 (225)
T 2yhc_A           21 RQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   70 (225)
T ss_dssp             HHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            578889999876421 12 2356777788899999999999999999865

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=84.12  E-value=3  Score=21.47  Aligned_cols=60  Identities=10%  Similarity=0.010  Sum_probs=43.2

Q ss_pred             HHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276            9 ELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus         9 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      +.+.+.|++++. ---.++..+...+..-.|.++++.+.+.+-..+..|..--|+.+.+.|
T Consensus        16 ~~l~~~g~r~T~-qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~G   75 (150)
T 2xig_A           16 MSIKKNGLKNSK-QREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKEN   75 (150)
T ss_dssp             HHHHHCC--CHH-HHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCCCCH-HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCC
Confidence            345667777543 344566677777778899999999988876778888888888887765

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=83.61  E-value=4.5  Score=23.12  Aligned_cols=47  Identities=11%  Similarity=0.016  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHh----cCC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQ----RGV-NPDTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~----~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|...+++..+    .+. +....++..+-..+.+.|++++|...+++..+
T Consensus       241 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          241 EDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            456666666654    133 33577888888999999999999999988764

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=83.43  E-value=4.6  Score=23.11  Aligned_cols=48  Identities=10%  Similarity=-0.042  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHh----cCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQ----RGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~----~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+.+..+    .+-+....++..+-..+.+.|++++|...+++..+.
T Consensus       239 ~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  290 (378)
T 3q15_A          239 QMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDH  290 (378)
T ss_dssp             HHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            456666666644    122224777888888999999999999999998753

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=83.06  E-value=3  Score=20.75  Aligned_cols=33  Identities=9%  Similarity=-0.076  Sum_probs=23.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276           28 DGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus        28 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      ..+.+.|++++|..+.+.+    +.||...|-.|-.+
T Consensus        47 sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce~   79 (115)
T 2uwj_G           47 SSLANQGRYQEALAFAHGN----PWPALEPWFALCEW   79 (115)
T ss_dssp             HHHHHTTCHHHHHGGGTTC----CCGGGHHHHHHHHH
T ss_pred             HHHHcchhHHHHHHhcCCC----CCchHHHHHHHHHH
Confidence            3456788888887765544    48999999887654

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=82.95  E-value=5.2  Score=23.41  Aligned_cols=63  Identities=13%  Similarity=0.078  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHhcCCCcC---HHHHHHHHHHHHh-----cCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHh
Q 042276            3 EANGLAELMIQRGVNPD---TSTCNALMDGFCL-----ADRFDRARELLVSMGSKGCKQDAFSHSILINGGSA   67 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~   67 (71)
                      +|+..++...+.  .|+   ...|.++-..|.+     -|+.+.|.+.|++..+..-.-+..++...-..++.
T Consensus       181 ~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~  251 (301)
T 3u64_A          181 AAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCI  251 (301)
T ss_dssp             HHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHH
Confidence            344444444433  664   6678888888888     48889999998888765311124555555555554

>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=82.93  E-value=3.1  Score=20.75  Aligned_cols=54  Identities=19%  Similarity=0.132  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHH--HHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276            3 EANGLAELMIQRGVNPDTSTCNAL--MDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~l--i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      +|..+-+.+...+.    .-..+|  +..+.+.|++++|..+.+.+    +.||...|-.|-.+
T Consensus        25 EA~tIAdwL~~~~~----~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce~   80 (116)
T 2p58_C           25 EANCIAEWLHLKGE----EEAVQLIRLSSLMNRGDYASALQQGNKL----AYPDLEPWLALCEY   80 (116)
T ss_dssp             HHHHHHHHHHHTTC----HHHHHHHHHHHHHHTTCHHHHHHHHTTS----CCGGGHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCc----HHHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHHHH
Confidence            45555555544432    222333  34466889999998877655    48999999887655

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=81.56  E-value=4.5  Score=21.74  Aligned_cols=50  Identities=16%  Similarity=0.096  Sum_probs=36.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc----HHHHHHHHHHHHhccc
Q 042276           19 DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD----AFSHSILINGGSARIR   70 (71)
Q Consensus        19 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~   70 (71)
                      +...+-..-..+.+.|++++|...|+...+..  |+    ...+..+-.++.+.|+
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~   67 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKE   67 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCc
Confidence            45556666667889999999999999998762  43    4566666666666665

>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=80.74  E-value=3.8  Score=24.82  Aligned_cols=47  Identities=11%  Similarity=-0.037  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHHh---cCC---Cc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQ---RGV---NP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~---~~~---~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|..+++....   .-.   .| ...+++.+=..|...|++++|+.++++..+
T Consensus       357 ~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          357 EGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            456666665532   112   33 367788899999999999999999988764

---

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	71
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.51
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.33
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.28
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.22
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	97.12
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.0
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.74
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.53
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	96.48
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.41
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.05
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.98
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	95.97
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.81
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.79
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.78
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	95.61
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	95.02
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	94.68
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	94.33
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	94.27
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	94.2
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	93.45
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	93.32
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	93.29
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	93.25
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	93.2
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	93.02
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	92.13
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	92.05
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	92.03
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	91.85
d1u9pa1	36	Arc repressor {Salmonella bacteriophage P22 [TaxId	90.41
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	90.37
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	89.82
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	89.04
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	88.76
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	87.91
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	87.68
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	87.36
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	86.64
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	85.61
d1ddfa_	127	Fas {Human (Homo sapiens) [TaxId: 9606]}	83.84
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	82.89
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	82.09
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	81.56

>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=97.51  E-value=0.00036  Score=36.03  Aligned_cols=56  Identities=14%  Similarity=0.161  Sum_probs=46.1

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-----CCCCccHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS-----KGCKQDAFSHS   59 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~~~~   59 (71)
                      ++|...++...+.  .| +...|..++.++.+.|+..+|++.|+++..     .|+.|+..+-.
T Consensus        84 ~~Al~~~~~al~~--~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~~  145 (179)
T d2ff4a2          84 SAVIAELEALTFE--HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  145 (179)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             hHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHHH
Confidence            4667777777654  55 899999999999999999999999999854     59999976643

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.33  E-value=0.0012  Score=31.46  Aligned_cols=66  Identities=12%  Similarity=-0.048  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+..+.  .| +...|+.+=.++.+.|++++|+..+....+.. ..+...|..+-.++...|+
T Consensus        20 ~eAi~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_          20 DDALQCYSEAIKL--DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhc--CCcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccC
Confidence            5778888888765  44 67788888888889999999999998887653 3366777777777776665

>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=97.28  E-value=0.0015  Score=33.03  Aligned_cols=65  Identities=14%  Similarity=-0.072  Sum_probs=52.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+....  .| +...|+.+=.+|.+.|++++|+..|+...+.  .| +..+|..+-.+|.+.|+
T Consensus        21 ~~Ai~~~~kal~~--~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~lg~~~~~l~~   87 (201)
T d2c2la1          21 PEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQLEMES   87 (201)
T ss_dssp             HHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHHHHHHHHCCC
Confidence            6788888887765  34 7888999999999999999999999999764  45 46778888888777765

>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=97.22  E-value=0.0018  Score=32.19  Aligned_cols=66  Identities=11%  Similarity=-0.071  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|.+..+.  .| +...|..+-..+.+.|++++|++.|+...+.. .-+..+|..+..++...|+
T Consensus        27 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          27 ENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhhcccc--chhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCC
Confidence            4677777777654  34 67777777778888888888888888887652 2244677777777766665

>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=97.12  E-value=0.0017  Score=35.17  Aligned_cols=66  Identities=18%  Similarity=0.044  Sum_probs=51.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      ++|.+.++++.+.  .| +...+..+-..+.+.|++++|+..|++..+.. +-+..+|..+-..+.+.|+
T Consensus        16 ~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~   82 (388)
T d1w3ba_          16 EAAERHCMQLWRQ--EPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcc
Confidence            5788889888765  45 67888888889999999999999999987652 1245678888777777665

>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=97.00  E-value=0.0028  Score=29.87  Aligned_cols=65  Identities=17%  Similarity=0.020  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++..+.  .| +..+|..+-..+.+.|++++|+..|++..+.  .| +..+|..+-..|.+.|+
T Consensus        33 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          33 AEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccc--ccccchhhhhhhhhhhhhhhHHHhhccccccccc--ccccccchHHHHHHHHHCCC
Confidence            5788888888765  45 6889999999999999999999999998765  34 56777777777766654

>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=96.74  E-value=0.0079  Score=32.33  Aligned_cols=65  Identities=15%  Similarity=-0.048  Sum_probs=51.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+...+.  .| +..+|..+-..+.+.|++++|...|.+..+.  .| +...|..+...+.+.|+
T Consensus        36 ~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          36 PNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELLAISALRRCLEL--KPDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcc--cccccccccccccccccccc
Confidence            6788999998865  55 6888999999999999999999999998765  23 45667777777766654

>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=96.53  E-value=0.014  Score=30.36  Aligned_cols=65  Identities=18%  Similarity=-0.048  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|+...+.  .| +..+|+.+=.++.+.|++++|++.|++..+.  .| +..+|..+-..+...|+
T Consensus        54 ~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~  120 (259)
T d1xnfa_          54 ALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGR  120 (259)
T ss_dssp             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH--HhhhhhhHHHHHHHHHHHhh
Confidence            4667777776653  44 5777877777888888888888888888764  23 34456666666655554

>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=96.48  E-value=0.014  Score=31.42  Aligned_cols=63  Identities=14%  Similarity=-0.089  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcc
Q 042276            3 EANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARI   69 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~   69 (71)
                      +|...|++..+.  .| +..++..+-..+.+.|++++|.+.|++..+.  .| +..+|..+-..|.+.|
T Consensus       323 ~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~~~~~~~  387 (388)
T d1w3ba_         323 EAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQ  387 (388)
T ss_dssp             HHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcC
Confidence            444444444322  33 3444555555555555555555555555432  23 2344555544444433

>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=96.41  E-value=0.0036  Score=30.13  Aligned_cols=46  Identities=13%  Similarity=0.104  Sum_probs=39.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|.+..+.  .| +...|..+-.+|.+.|++++|+..+++..+.
T Consensus        21 ~~Ai~~y~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l   67 (128)
T d1elra_          21 DTALKHYDKAKEL--DPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEV   67 (128)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHh
Confidence            6788889888765  44 6889999999999999999999999998753

>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=96.05  E-value=0.032  Score=29.82  Aligned_cols=65  Identities=14%  Similarity=-0.087  Sum_probs=35.4

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~   70 (71)
                      ++|...|++....  .| +..+|..+-..+.+.|++++|.+.|++..+.  .| +..+|..+-.+|.+.|+
T Consensus       189 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~  255 (323)
T d1fcha_         189 DKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGA  255 (323)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTC
T ss_pred             hhhhccccccccc--ccccccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCC
Confidence            3455555555433  23 4555666666666666666666666666543  23 34445555555555443

>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=95.98  E-value=0.025  Score=27.09  Aligned_cols=47  Identities=13%  Similarity=0.149  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHhcCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            3 EANGLAELMIQRGVNPD-TSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +|..++++.....-.|+ ..+|..+=.+|.+.|++++|++.|++..+.
T Consensus        54 ~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          54 KGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            35555555544322222 224444455556666666666666666553

>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=95.97  E-value=0.016  Score=29.64  Aligned_cols=64  Identities=9%  Similarity=-0.022  Sum_probs=46.2

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      +.|.+.|.++    .+|+..+|.-+=.++.+.|++++|++.|++..+.. .-+...|..+=.++.+.|+
T Consensus        22 ~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~   85 (192)
T d1hh8a_          22 KGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   85 (192)
T ss_dssp             HHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhcc
Confidence            4566666543    35677888888888899999999999999988653 2255667777666666665

>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=95.81  E-value=0.042  Score=29.72  Aligned_cols=46  Identities=26%  Similarity=0.380  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+++-++.  .| |...+..+...++..|++++|...|+...+.
T Consensus        13 ~eAl~~l~~al~~--~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l   59 (264)
T d1zbpa1          13 QQALELLIEAIKA--SPKDASLRSSFIELLCIDGDFERADEQLMQSIKL   59 (264)
T ss_dssp             HHHHHHHHHHHHT--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            5788888888765  55 8999999999999999999999999999875

>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=95.79  E-value=0.032  Score=28.39  Aligned_cols=50  Identities=12%  Similarity=-0.075  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      ..+..+...+.+.|++++|+..++...... .-+...|..++.+|.+.|++
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~  117 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQ  117 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCH
Confidence            467788888999999999999999998752 23789999999999998873

>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=95.78  E-value=0.031  Score=26.70  Aligned_cols=69  Identities=14%  Similarity=-0.020  Sum_probs=48.1

Q ss_pred             ChHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCC---HHHHHHHHHHHhhCCCCccH-HHHHHHHHHHHhccc
Q 042276            1 MDEANGLAELMIQRGVNPDTSTCNALMDGFCLADR---FDRARELLVSMGSKGCKQDA-FSHSILINGGSARIR   70 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~   70 (71)
                      +++|.+.|+...+.+ +.+..++.-+-.++.+.++   .++|+.+|++.....-.|+. .+|..+=.+|.+.|+
T Consensus        15 l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~   87 (122)
T d1nzna_          15 LLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKE   87 (122)
T ss_dssp             HHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHhh
Confidence            367899999887753 2366777777777877554   45699999999876544442 356666667777665

>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=95.61  E-value=0.063  Score=28.97  Aligned_cols=62  Identities=8%  Similarity=-0.051  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHH
Q 042276            4 ANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGG   65 (71)
Q Consensus         4 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~   65 (71)
                      |..+|+...+...+.+...|.......-+.|+++.|..+|+.+....-......|...+..+
T Consensus        83 a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~  144 (308)
T d2onda1          83 AANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFA  144 (308)
T ss_dssp             HHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHH
Confidence            34444444432222244555555555556666666666666655432111223444444444

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.02  E-value=0.061  Score=25.38  Aligned_cols=58  Identities=12%  Similarity=0.111  Sum_probs=44.7

Q ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Q 042276            6 GLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILING   64 (71)
Q Consensus         6 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~   64 (71)
                      +-++.+....+.|+..+..+.+.+|-+.+++..|.++|+..+.+ +.++...|.-+++-
T Consensus        27 rgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilqe   84 (105)
T d1v54e_          27 KGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE   84 (105)
T ss_dssp             HHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             HHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHHH
Confidence            33444555667899999999999999999999999999999754 23345567666654

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.68  E-value=0.087  Score=25.52  Aligned_cols=59  Identities=10%  Similarity=0.008  Sum_probs=47.4

Q ss_pred             HHHhcCCCcCHHHHHHHHHHHHhc-CCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           10 LMIQRGVNPDTSTCNALMDGFCLA-DRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        10 ~m~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      ++++.|++++. .-..++..+.+. +..-.|.++++.+.+.+..++..|..--|+.+.+.|
T Consensus         6 ~Lr~~GlR~T~-qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~g   65 (134)
T d1mzba_           6 ELRKAGLKVTL-PRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAG   65 (134)
T ss_dssp             HHHHTTCCCCH-HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHcCCCCCH-HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhcc
Confidence            47889999876 456777888776 457889999999999998889988877788877655

>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=94.33  E-value=0.15  Score=27.71  Aligned_cols=46  Identities=2%  Similarity=-0.054  Sum_probs=28.0

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+....+.  .| +...|+.+-..+.+.|++++|++.++...+.
T Consensus       129 ~eAl~~~~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~  175 (315)
T d2h6fa1         129 SQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE  175 (315)
T ss_dssp             TTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            3555566655543  33 5666666666666666666666666666554

>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=94.27  E-value=0.12  Score=25.55  Aligned_cols=52  Identities=6%  Similarity=-0.084  Sum_probs=37.7

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           18 PDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        18 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      |+.....-.=..+.+.|++++|+..|++..+.. +-+...|+.+-.+|.+.|+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~   53 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQ   53 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTC
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhh
Confidence            444444444467889999999999999987652 2366778887777777765

>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=94.20  E-value=0.12  Score=28.10  Aligned_cols=44  Identities=9%  Similarity=-0.012  Sum_probs=19.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcC-CHHHHHHHHHHHh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLAD-RFDRARELLVSMG   47 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g-~~~~a~~~~~~m~   47 (71)
                      ++|..++++..+.  .| +...|+..-..+.+.+ ++++|++.++...
T Consensus        60 ~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al  105 (315)
T d2h6fa1          60 ERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAII  105 (315)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHH
Confidence            3444555554443  33 3444444444444433 3455555555443

>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=93.45  E-value=0.19  Score=24.89  Aligned_cols=45  Identities=13%  Similarity=-0.192  Sum_probs=22.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhcc
Q 042276           23 CNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSARI   69 (71)
Q Consensus        23 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~   69 (71)
                      |+-+-.+|.+.|++++|+..++.....  .| ++.+|..+-.++...|
T Consensus        65 ~~nla~~y~k~~~~~~A~~~~~~al~~--~p~~~~a~~~~g~~~~~~g  110 (170)
T d1p5qa1          65 HLNLAMCHLKLQAFSAAIESCNKALEL--DSNNEKGLSRRGEAHLAVN  110 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhhhcccccchhhhhhhc--cccchhhhHHHHHHHHHhh
Confidence            344444455555555555555555443  22 4444444444444444

>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=93.32  E-value=0.16  Score=23.58  Aligned_cols=52  Identities=8%  Similarity=-0.040  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHH
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAF   56 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   56 (71)
                      ++|...+....+.. +.+...|..+-.++...|++++|+..|+...+.  .|+..
T Consensus        54 ~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~--~p~~~  105 (117)
T d1elwa_          54 QKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH--EANNP  105 (117)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCH
T ss_pred             cccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCH
Confidence            56778888887652 337889999999999999999999999999865  45543

>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=93.29  E-value=0.1  Score=24.10  Aligned_cols=43  Identities=16%  Similarity=-0.029  Sum_probs=35.9

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSM   46 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m   46 (71)
                      ++|...|+...+.  .| +..+|..+-..|.+.|+.++|++.+++.
T Consensus        67 ~~A~~~~~~al~~--~p~~~~a~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          67 GLAIIALNHARML--DPKDIAVHAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhccccccccc--ccccccchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            5677788877654  45 6889999999999999999999999875

>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=93.25  E-value=0.11  Score=24.58  Aligned_cols=43  Identities=7%  Similarity=-0.167  Sum_probs=33.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276           28 DGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus        28 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      ..+.+.|++++|++.|++..+.. ..+...|..+-.+|.+.|++
T Consensus        12 ~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~   54 (128)
T d1elra_          12 NDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDY   54 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCch
Confidence            45788999999999999998763 23577788888888777653

>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=93.20  E-value=0.2  Score=24.33  Aligned_cols=46  Identities=13%  Similarity=-0.073  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|+...+.  .| +..+|..+-.++...|++++|.+.+++..+.
T Consensus        61 ~~A~~~~~kal~~--~p~~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          61 GYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFRAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHH--cccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            5788888888765  35 6789999999999999999999999999876

>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=93.02  E-value=0.23  Score=24.58  Aligned_cols=46  Identities=9%  Similarity=0.030  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...++.....  .| ++.+|.-+-.++.+.|++++|+..|+...+.
T Consensus        79 ~~A~~~~~~al~~--~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          79 SAAIESCNKALEL--DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccccchhhhhhhc--cccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            5677777777655  45 7889999999999999999999999999775

>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=92.13  E-value=0.24  Score=23.99  Aligned_cols=50  Identities=6%  Similarity=0.026  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHHhcCCCc-CH-HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccH
Q 042276            2 DEANGLAELMIQRGVNP-DT-STCNALMDGFCLADRFDRARELLVSMGSKGCKQDA   55 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   55 (71)
                      ++|..+|++....  .| +. -.+--+=-+|.+.|+++.|.+.++...+.  .|+.
T Consensus        55 ~~gI~lLe~~~~~--~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i--eP~n  106 (124)
T d2pqrb1          55 RLGVKILTDIYKE--AESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH--ERNN  106 (124)
T ss_dssp             HHHHHHHHHHHHH--CGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHHHHHHHHHhc--CchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc--CCCc
Confidence            4678888888754  34 32 34344444688999999999999998876  4544

>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=92.05  E-value=0.43  Score=25.50  Aligned_cols=48  Identities=8%  Similarity=0.007  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      +.|..+|+.+.+..-.....+|...+....+.|+++.|.++|.+..+.
T Consensus       116 ~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~  163 (308)
T d2onda1         116 EKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  163 (308)
T ss_dssp             HHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHh
Confidence            466777777765432223557888888888888888888888887765

>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=92.03  E-value=0.3  Score=23.66  Aligned_cols=46  Identities=15%  Similarity=0.045  Sum_probs=31.8

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...+....+.  .| ++.+|.-+-.++.+.|++++|+..|+...+.
T Consensus        84 ~~Al~~~~~al~~--~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1          84 PKAIDHASKVLKI--DKNNVKALYKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             HHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             chhhhhhhccccc--cchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3556666665543  34 6777777777788888888888887777655

>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=91.85  E-value=0.32  Score=23.56  Aligned_cols=50  Identities=10%  Similarity=-0.132  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      .+|+-+-.+|.+.|++++|++.+....+.. ..+..+|..+-.++...|++
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~  117 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFL  117 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCH
Confidence            466777788899999999999999987653 33778888888888877753

>d1u9pa1 a.43.1.1 (A:72-107) Arc repressor {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: Ribbon-helix-helix
superfamily: Ribbon-helix-helix
family: Arc/Mnt-like phage repressors
domain: Arc repressor
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=90.41  E-value=0.19  Score=18.49  Aligned_cols=32  Identities=9%  Similarity=0.036  Sum_probs=22.1

Q ss_pred             HHHHHHHH-hhCCCCccHHHHHHHHHHHHhccc
Q 042276           39 ARELLVSM-GSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        39 a~~~~~~m-~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .+++.+.. .++|...|...|..++..+.+.|+
T Consensus         3 vldlvrkvaeeng~s~ns~iy~~vmes~kkegr   35 (36)
T d1u9pa1           3 VLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR   35 (36)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCcchhHHHHHHHHHHHHHccC
Confidence            44555544 346777788888888888887776

>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=90.37  E-value=0.25  Score=26.52  Aligned_cols=41  Identities=20%  Similarity=0.028  Sum_probs=34.4

Q ss_pred             HHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcccC
Q 042276           30 FCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIRK   71 (71)
Q Consensus        30 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~   71 (71)
                      ..+.|++++|+..+++-.+.. .-|...+..+...++..|+|
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~   46 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDF   46 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCH
Confidence            456899999999999998762 33779999999999998874

>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=89.82  E-value=0.56  Score=22.86  Aligned_cols=47  Identities=4%  Similarity=-0.177  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhcc
Q 042276           22 TCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARI   69 (71)
Q Consensus        22 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~   69 (71)
                      .|+.+-.++.+.|++++|+..+....+.. .-+..+|..+-.++.+.|
T Consensus        79 ~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~  125 (169)
T d1ihga1          79 CVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLK  125 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHcc
Confidence            34444444555555555555555554431 113344444444444433

>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=89.04  E-value=0.66  Score=22.65  Aligned_cols=51  Identities=8%  Similarity=0.017  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAF   56 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~   56 (71)
                      ++|...+......  .| +..+|.-.-.++...|++++|+..|....+.  .|+..
T Consensus        81 ~~Ai~~~~~al~l--~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~  132 (168)
T d1kt1a1          81 TKAVECCDKALGL--DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNK  132 (168)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCH
T ss_pred             ccchhhhhhhhhc--ccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCH
Confidence            4566666666553  34 7888888888899999999999999998765  45443

>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=88.76  E-value=0.51  Score=20.97  Aligned_cols=57  Identities=11%  Similarity=-0.022  Sum_probs=38.6

Q ss_pred             hHHHHHHHHHHhc-----CCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCcc-HHHHHH
Q 042276            2 DEANGLAELMIQR-----GVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQD-AFSHSI   60 (71)
Q Consensus         2 ~~a~~~~~~m~~~-----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~   60 (71)
                      ++|...|++-.+.     ...+ ...+++.+=.++.+.|++++|++.+++..+.  .|+ ..+++-
T Consensus        22 ~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l--~P~~~~a~~N   85 (95)
T d1tjca_          22 YHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEHQRANGN   85 (95)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh--CcCCHHHHHH
Confidence            3566666655431     1122 2567888999999999999999999999876  454 334433

>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=87.91  E-value=0.89  Score=22.77  Aligned_cols=45  Identities=16%  Similarity=-0.010  Sum_probs=37.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|...|++-.+.  .| +...|+-+=.++.+.|++++|++.|++...
T Consensus        53 ~~A~~~~~kAl~l--dp~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~   98 (192)
T d1hh8a_          53 TEAEKAFTRSINR--DKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALI   98 (192)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHH--hhhhhhhHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            5788888888764  45 688888888889999999999999998754

>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=87.68  E-value=0.97  Score=22.92  Aligned_cols=46  Identities=13%  Similarity=0.052  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhC
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSK   49 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~   49 (71)
                      ++|...|++..+.  .| +..++..+-..+.+.|++++|.+.|+...+.
T Consensus        88 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~  134 (259)
T d1xnfa_          88 DAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD  134 (259)
T ss_dssp             HHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhhhhhhHHHHH--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            5788889888764  44 5677888888899999999999999998765

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.36  E-value=0.84  Score=21.87  Aligned_cols=64  Identities=11%  Similarity=-0.054  Sum_probs=41.8

Q ss_pred             ChHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHh----------cCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHHHHHhc
Q 042276            1 MDEANGLAELMIQRGVNP-DTSTCNALMDGFCL----------ADRFDRARELLVSMGSKGCKQ-DAFSHSILINGGSAR   68 (71)
Q Consensus         1 ~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~----------~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~   68 (71)
                      +++|...|+...+.  .| +..++..+=.++.+          .+.+++|+..|++..+.  .| +..+|..+=.+|...
T Consensus        13 fe~A~~~~e~al~~--~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l--~P~~~~a~~~lG~~y~~~   88 (145)
T d1zu2a1          13 FEQIRQDAENTYKS--NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYTSF   88 (145)
T ss_dssp             HHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhh--CCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHh--cchhhHHHhhHHHHHHHc
Confidence            36788888888765  45 56666655555543          34567899999888765  34 556776665555543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.64  E-value=0.94  Score=21.69  Aligned_cols=61  Identities=13%  Similarity=0.092  Sum_probs=41.1

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcC-----------CHHHHHHHHHHHhhCCCCccHHHHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLAD-----------RFDRARELLVSMGSKGCKQDAFSHSILINGGS   66 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g-----------~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~   66 (71)
                      ++|...|+...+.  .| +..+|+.+=.+|...|           .+++|.+.|+...+.  .|+...|-.-+..+.
T Consensus        58 ~~Ai~~~~kAl~l--~P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~~~L~~~~  130 (145)
T d1zu2a1          58 QEAITKFEEALLI--DPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMTA  130 (145)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--cchhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHHHHHHHHH
Confidence            4677777777654  55 6778877766776544           357788888887765  577777666555443

>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=85.61  E-value=2  Score=24.62  Aligned_cols=64  Identities=11%  Similarity=-0.136  Sum_probs=49.3

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhc
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSAR   68 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~   68 (71)
                      ++|...+.+-.+.  .| +..+|+-+=..+...|+..+|...|.+-.... .|...++..|...+.+.
T Consensus       169 ~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~~  233 (497)
T d1ya0a1         169 SQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSKA  233 (497)
T ss_dssp             HHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHh
Confidence            4566666666544  55 67899999889999999999999998887654 56778888888877653

>d1ddfa_ a.77.1.2 (A:) Fas {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DEATH domain
superfamily: DEATH domain
family: DEATH domain, DD
domain: Fas
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.84  E-value=1.4  Score=21.10  Aligned_cols=43  Identities=12%  Similarity=0.013  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Q 042276            3 EANGLAELMIQRGVNPDTSTCNALMDGFCLADRFDRARELLVSMG   47 (71)
Q Consensus         3 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~   47 (71)
                      .+.+++..+..+.  .+..|...|+.++.+.|..+-|.++-+.+.
T Consensus        57 q~~qmL~~W~~~~--G~~at~~~L~~aL~~~~~~dlAeki~~~~~   99 (127)
T d1ddfa_          57 QKVQLLRNWHQLH--GKKEAYDTLIKDLKKANLCTLAEKIQTIIL   99 (127)
T ss_dssp             HHHHHHHHHHHHS--CSSSHHHHHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CchhHHHHHHHHHHHcCcHHHHHHHHHHHh
Confidence            4556666665432  234467777777777777777777665543

>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=82.89  E-value=1.6  Score=21.12  Aligned_cols=58  Identities=16%  Similarity=0.120  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHhcCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCc-cHHHHHHHHH
Q 042276            2 DEANGLAELMIQRGVNP-DTSTCNALMDGFCLADRFDRARELLVSMGSKGCKQ-DAFSHSILIN   63 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~li~   63 (71)
                      ++|...+....+.  .| +..+|.-+=.++.+.|++++|++.|+...+.  .| |...+..+-.
T Consensus        94 ~~Ai~~~~~al~~--~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~  153 (169)
T d1ihga1          94 QGAVDSCLEALEI--DPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLK  153 (169)
T ss_dssp             HHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             chhhhhhhhhhhh--hhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            4677777777654  45 7888999999999999999999999999875  34 4444444433

>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=82.09  E-value=2.1  Score=22.05  Aligned_cols=45  Identities=22%  Similarity=0.290  Sum_probs=34.0

Q ss_pred             hHHHHHHHHHHhcCCCcC------HHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Q 042276            2 DEANGLAELMIQRGVNPD------TSTCNALMDGFCLADRFDRARELLVSMGS   48 (71)
Q Consensus         2 ~~a~~~~~~m~~~~~~p~------~~~~~~li~~~~~~g~~~~a~~~~~~m~~   48 (71)
                      ++|..++++..+.  .|+      ...++.+-..+...|++++|+..|++..+
T Consensus        29 ~~A~~~~~~aL~~--~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   79 (366)
T d1hz4a_          29 DEAERLAKLALEE--LPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQ   79 (366)
T ss_dssp             HHHHHHHHHHHHT--CCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh--CcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5788888887654  232      34666777788899999999999998764

>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=81.56  E-value=1.8  Score=20.95  Aligned_cols=49  Identities=6%  Similarity=-0.168  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHhccc
Q 042276           21 STCNALMDGFCLADRFDRARELLVSMGSKGCKQDAFSHSILINGGSARIR   70 (71)
Q Consensus        21 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~   70 (71)
                      .+|+-+-.+|.+.|++++|+..++...+.. ..+..+|..+-.++...|+
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~  113 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNE  113 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCC
Confidence            345556667889999999999999998752 3366777777777777665