Citrus Sinensis ID: 033570

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110------
Protein Sequence
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF
Secondary Structure (PSIPRED)
cEEEEEcccccEEEEEEEccccHHHHHHHHHHHHcccccccEEEEccccccccccccccccccccEEEEEEEcccccccccHHHHHHHHcccccEEccEEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEcccccEHHHHHHHHHHHHcccHHHEEEEEccEEcccccEcHHHccccccEEEEEEcccccccHHHHHHHHccccHccEEHHHHHccccHHHHHccccccc
Coil and Loop (DISEMBL)
MQIFVKTltgktitlevessdtiDNVKAKiqdkegippdqQRLIFAGkqledgrtladyniqkeSTLHLVLRLRGGIIEPSLMALARKYNqdkmicrkshtrtrnqfpffnfvncf
Flexible Loop (DISEMBL)
mqifvktltgktitlevessdtidnVKAKIqdkegippdqqRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKShtrtrnqfpffnfvncf
Low Complexity Region (SEG)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF
Disordered region (IsUnstruct)
***FVKTLTGKTITLEV************************RLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNC*
Disordered Region (DISOPRED)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF
Disordered Region (DISEMBL)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF
Disordered Region (DISPRO)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF
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	116	2.2.26 [Sep-21-2011]
P49636	128	Ubiquitin-60S ribosomal p	N/A	no	0.879	0.796	0.970	4e-52
Q42202	128	Ubiquitin-60S ribosomal p	yes	no	0.879	0.796	0.960	2e-51
B9DHA6	128	Ubiquitin-60S ribosomal p	yes	no	0.879	0.796	0.960	2e-51
P51423	128	Ubiquitin-60S ribosomal p	N/A	no	0.879	0.796	0.960	2e-51
P0CH35	129	Ubiquitin-60S ribosomal p	yes	no	0.879	0.790	0.960	2e-51
P0CH34	129	Ubiquitin-60S ribosomal p	yes	no	0.879	0.790	0.960	2e-51
P0CH10	128	Ubiquitin-60S ribosomal p	N/A	no	0.879	0.796	0.941	1e-50
P0CH11	128	Ubiquitin-60S ribosomal p	N/A	no	0.879	0.796	0.941	1e-50
P0CH09	128	Ubiquitin-60S ribosomal p	yes	no	0.879	0.796	0.901	4e-48
P0CH08	128	Ubiquitin-60S ribosomal p	yes	no	0.879	0.796	0.901	4e-48

>sp|P49636|RL40_NICSY Ubiquitin-60S ribosomal protein L40 OS=Nicotiana sylvestris GN=UBICEP52-7 PE=2 SV=2

 Score =  202 bits (515), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYAR 102

Ribosomal protein L40 is a component of the 60S subunit of the ribosome.
Nicotiana sylvestris (taxid: 4096)

>sp|Q42202|RL40B_ARATH Ubiquitin-60S ribosomal protein L40-2 OS=Arabidopsis thaliana GN=RPL40B PE=1 SV=2

 Score =  201 bits (510), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYAR 102

Ribosomal protein L40-2 is a component of the 60S subunit of the ribosome.

Arabidopsis thaliana (taxid: 3702)

>sp|B9DHA6|RL40A_ARATH Ubiquitin-60S ribosomal protein L40-1 OS=Arabidopsis thaliana GN=RPL40A PE=1 SV=1

 Score =  201 bits (510), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYAR 102

Ribosomal protein L40-1 is a component of the 60S subunit of the ribosome.

Arabidopsis thaliana (taxid: 3702)

>sp|P51423|RL40_BRARA Ubiquitin-60S ribosomal protein L40 OS=Brassica rapa PE=2 SV=2

 Score =  200 bits (509), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQAKMICRKCYAR 102

Ribosomal protein L40 is a component of the 60S subunit of the ribosome.

Brassica rapa (taxid: 51350)

>sp|P0CH35|RL40B_ORYSJ Ubiquitin-60S ribosomal protein L40-2 OS=Oryza sativa subsp. japonica GN=Ub-CEP52-2 PE=3 SV=1

 Score =  200 bits (509), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQDKMICRKCYAR 102

Ribosomal protein L40-2 is a component of the 60S subunit of the ribosome.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P0CH34|RL40A_ORYSJ Ubiquitin-60S ribosomal protein L40-1 OS=Oryza sativa subsp. japonica GN=Ub-CEP52-1 PE=2 SV=1

 Score =  200 bits (509), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQDKMICRKCYAR 102

Ribosomal protein L40-1 is a component of the 60S subunit of the ribosome.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P0CH10|RL403_CHLRE Ubiquitin-60S ribosomal protein L40 OS=Chlamydomonas reinhardtii GN=UBI3 PE=1 SV=1

 Score =  197 bits (501), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 96/102 (94%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQ+KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQEKMICRKCYAR 102

Ribosomal protein L40 is a component of the 60S subunit of the ribosome.

Chlamydomonas reinhardtii (taxid: 3055)

>sp|P0CH11|RL401_CHLRE Ubiquitin-60S ribosomal protein L40 OS=Chlamydomonas reinhardtii GN=UBI1 PE=1 SV=1

 Score =  197 bits (501), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 96/102 (94%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQ+KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQEKMICRKCYAR 102

Ribosomal protein L40 is a component of the 60S subunit of the ribosome.

Chlamydomonas reinhardtii (taxid: 3055)

>sp|P0CH09|RL402_YEAST Ubiquitin-60S ribosomal protein L40 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPL40B PE=1 SV=1

 Score =  189 bits (480), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYAR 102

Ribosomal protein L40 is a component of the 60S subunit of the ribosome.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P0CH08|RL401_YEAST Ubiquitin-60S ribosomal protein L40 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPL40A PE=1 SV=1

 Score =  189 bits (480), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYAR 102

Ribosomal protein L40 is a component of the 60S subunit of the ribosome.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	116
359482015	228	PREDICTED: LOW QUALITY PROTEIN: ubiquiti	0.879	0.447	0.970	1e-50
255578906	128	ubiquitin, putative [Ricinus communis] g	0.879	0.796	0.970	1e-50
449483218	208	PREDICTED: ubiquitin-60S ribosomal prote	0.879	0.490	0.970	2e-50
302393724	128	RecName: Full=Ubiquitin-60S ribosomal pr	0.879	0.796	0.970	2e-50
118483333	128	unknown [Populus trichocarpa]	0.879	0.796	0.960	3e-50
8698909	108	ubiquitin fusion protein [Pyrus pyrifoli	0.879	0.944	0.960	4e-50
224120992	128	predicted protein [Populus trichocarpa]	0.879	0.796	0.960	4e-50
118483418	120	unknown [Populus trichocarpa]	0.879	0.85	0.960	4e-50
351722530	128	uncharacterized protein LOC100306626 [Gl	0.879	0.796	0.960	5e-50
242036397	129	hypothetical protein SORBIDRAFT_01g04180	0.879	0.790	0.960	5e-50

>gi|359482015|ref|XP_002282071.2| PREDICTED: LOW QUALITY PROTEIN: ubiquitin-60S ribosomal protein L40 [Vitis vinifera]

 Score =  203 bits (517), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 101 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 160

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRK + R
Sbjct: 161 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYAR 202

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578906|ref|XP_002530306.1| ubiquitin, putative [Ricinus communis] gi|255578975|ref|XP_002530340.1| ubiquitin, putative [Ricinus communis] gi|356509194|ref|XP_003523336.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Glycine max] gi|356516113|ref|XP_003526741.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Glycine max] gi|356572584|ref|XP_003554448.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Glycine max] gi|449438865|ref|XP_004137208.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Cucumis sativus] gi|449456437|ref|XP_004145956.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Cucumis sativus] gi|449497417|ref|XP_004160396.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Cucumis sativus] gi|71040673|gb|AAZ20285.1| ubiquitin fusion protein [Arachis hypogaea] gi|147769165|emb|CAN60770.1| hypothetical protein VITISV_012429 [Vitis vinifera] gi|148908659|gb|ABR17437.1| unknown [Picea sitchensis] gi|192910738|gb|ACF06477.1| ubiquitin fusion protein [Elaeis guineensis] gi|223530144|gb|EEF32056.1| ubiquitin, putative [Ricinus communis] gi|223530162|gb|EEF32073.1| ubiquitin, putative [Ricinus communis] gi|284433784|gb|ADB85098.1| ubiquitin C variant [Jatropha curcas] gi|297740140|emb|CBI30322.3| unnamed protein product [Vitis vinifera] gi|330318561|gb|AEC10952.1| ubiquitin fusion protein [Camellia sinensis] gi|388516721|gb|AFK46422.1| unknown [Lotus japonicus]

 Score =  202 bits (515), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYAR 102

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449483218|ref|XP_004156525.1| PREDICTED: ubiquitin-60S ribosomal protein L40-like [Cucumis sativus]

 Score =  202 bits (515), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 81  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 140

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRK + R
Sbjct: 141 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYAR 182

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302393724|sp|P49636.2|RL40_NICSY RecName: Full=Ubiquitin-60S ribosomal protein L40; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=60S ribosomal protein L40; AltName: Full=CEP52; Flags: Precursor gi|170217|gb|AAA34064.1| ubiquitin fusion protein [Nicotiana sylvestris]

 Score =  202 bits (515), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYAR 102

Source: Nicotiana sylvestris

Species: Nicotiana sylvestris

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118483333|gb|ABK93568.1| unknown [Populus trichocarpa]

 Score =  201 bits (512), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ+KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQEKMICRKCYAR 102

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8698909|gb|AAF78520.1|AF195224_1 ubiquitin fusion protein [Pyrus pyrifolia]

 Score =  201 bits (512), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ+KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQEKMICRKCYAR 102

Source: Pyrus pyrifolia

Species: Pyrus pyrifolia

Genus: Pyrus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120992|ref|XP_002318470.1| predicted protein [Populus trichocarpa] gi|224135055|ref|XP_002321972.1| predicted protein [Populus trichocarpa] gi|118484077|gb|ABK93924.1| unknown [Populus trichocarpa] gi|118485427|gb|ABK94570.1| unknown [Populus trichocarpa] gi|118488135|gb|ABK95887.1| unknown [Populus trichocarpa] gi|222859143|gb|EEE96690.1| predicted protein [Populus trichocarpa] gi|222868968|gb|EEF06099.1| predicted protein [Populus trichocarpa] gi|321149957|gb|ADW66126.1| ubiquitin extension protein [Solanum nigrum] gi|399920239|gb|AFP55586.1| ubiquitin [Rosa rugosa]

 Score =  201 bits (512), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ+KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQEKMICRKCYAR 102

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118483418|gb|ABK93609.1| unknown [Populus trichocarpa]

 Score =  201 bits (512), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ+KMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQEKMICRKCYAR 102

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722530|ref|NP_001237759.1| uncharacterized protein LOC100306626 [Glycine max] gi|255629117|gb|ACU14903.1| unknown [Glycine max]

 Score =  201 bits (511), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 100/102 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ+RLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQRRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYAR 102

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242036397|ref|XP_002465593.1| hypothetical protein SORBIDRAFT_01g041800 [Sorghum bicolor] gi|242043942|ref|XP_002459842.1| hypothetical protein SORBIDRAFT_02g012040 [Sorghum bicolor] gi|195605244|gb|ACG24452.1| ubiquitin fusion protein [Zea mays] gi|195605578|gb|ACG24619.1| ubiquitin fusion protein [Zea mays] gi|195606772|gb|ACG25216.1| ubiquitin fusion protein [Zea mays] gi|195611116|gb|ACG27388.1| ubiquitin fusion protein [Zea mays] gi|195617574|gb|ACG30617.1| ubiquitin fusion protein [Zea mays] gi|195638770|gb|ACG38853.1| ubiquitin fusion protein [Zea mays] gi|195639710|gb|ACG39323.1| ubiquitin fusion protein [Zea mays] gi|223943621|gb|ACN25894.1| unknown [Zea mays] gi|241919447|gb|EER92591.1| hypothetical protein SORBIDRAFT_01g041800 [Sorghum bicolor] gi|241923219|gb|EER96363.1| hypothetical protein SORBIDRAFT_02g012040 [Sorghum bicolor] gi|414589037|tpg|DAA39608.1| TPA: Ubiquitin fusion protein [Zea mays] gi|414865712|tpg|DAA44269.1| TPA: Ubiquitin fusion protein [Zea mays] gi|414865715|tpg|DAA44272.1| TPA: Ubiquitin fusion protein [Zea mays]

 Score =  201 bits (511), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQDKMICRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQDKMICRKCYAR 102

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	116
TAIR|locus:2053496	128	UBQ2 "ubiquitin extension prot	0.879	0.796	0.960	5.4e-47
TAIR|locus:2079924	128	UBQ1 "ubiquitin extension prot	0.879	0.796	0.960	5.4e-47
SGD|S000001410	128	RPL40A "Ubiquitin-ribosomal 60	0.879	0.796	0.901	5e-44
SGD|S000001802	128	RPL40B "Ubiquitin-ribosomal 60	0.879	0.796	0.901	5e-44
FB|FBgn0003941	128	RpL40 "Ribosomal protein L40"	0.879	0.796	0.901	8.1e-44
UNIPROTKB|P63048	128	UBA52 "Ubiquitin-60S ribosomal	0.879	0.796	0.901	8.1e-44
UNIPROTKB|P63050	128	UBA52 "Ubiquitin-60S ribosomal	0.879	0.796	0.901	8.1e-44
UNIPROTKB|P62987	128	UBA52 "Ubiquitin-60S ribosomal	0.879	0.796	0.901	8.1e-44
UNIPROTKB|P63053	128	UBA52 "Ubiquitin-60S ribosomal	0.879	0.796	0.901	8.1e-44
POMBASE|SPAC11G7.04	128	ubi1 "ribosomal-ubiquitin fusi	0.879	0.796	0.901	8.1e-44

TAIR|locus:2053496 UBQ2 "ubiquitin extension protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYAR 102

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2079924 UBQ1 "ubiquitin extension protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 98/102 (96%), Positives = 99/102 (97%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYAR 102

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

GO:0016567 "protein ubiquitination" evidence=TAS

SGD|S000001410 RPL40A "Ubiquitin-ribosomal 60S subunit protein L40A fusion protein" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYAR 102

GO:0003735 "structural constituent of ribosome" evidence=IEA;TAS

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0042254 "ribosome biogenesis" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IMP

GO:0031386 "protein tag" evidence=ISS

GO:0002181 "cytoplasmic translation" evidence=TAS

GO:0022625 "cytosolic large ribosomal subunit" evidence=TAS

GO:0006412 "translation" evidence=IEA

SGD|S000001802 RPL40B "Ubiquitin-ribosomal 60S subunit protein L40B fusion protein" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYAR 102

GO:0005840 "ribosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0003735 "structural constituent of ribosome" evidence=IEA;TAS

GO:0005634 "nucleus" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0002181 "cytoplasmic translation" evidence=TAS

GO:0006281 "DNA repair" evidence=IEA

GO:0031386 "protein tag" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=IMP

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=TAS

FB|FBgn0003941 RpL40 "Ribosomal protein L40" [Drosophila melanogaster (taxid:7227)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRILAQKYNCDKMICRKCYAR 102

GO:0006412 "translation" evidence=ISS;TAS

GO:0003735 "structural constituent of ribosome" evidence=ISS;NAS;TAS

GO:0006464 "cellular protein modification process" evidence=ISS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISS;IDA

GO:0005840 "ribosome" evidence=NAS

GO:0005811 "lipid particle" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

UNIPROTKB|P63048 UBA52 "Ubiquitin-60S ribosomal protein L40" [Bos taurus (taxid:9913)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYAR 102

GO:0005634 "nucleus" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

UNIPROTKB|P63050 UBA52 "Ubiquitin-60S ribosomal protein L40" [Canis lupus familiaris (taxid:9615)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYAR 102

GO:0005634 "nucleus" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

UNIPROTKB|P62987 UBA52 "Ubiquitin-60S ribosomal protein L40" [Homo sapiens (taxid:9606)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYAR 102

GO:0003735 "structural constituent of ribosome" evidence=IEA;NAS

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=NAS;TAS

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0006464 "cellular protein modification process" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000080 "G1 phase of mitotic cell cycle" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0000187 "activation of MAPK activity" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002224 "toll-like receptor signaling pathway" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0002755 "MyD88-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0002756 "MyD88-independent toll-like receptor signaling pathway" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0005886 "plasma membrane" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0007179 "transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0007219 "Notch signaling pathway" evidence=TAS

GO:0007220 "Notch receptor processing" evidence=TAS

GO:0007249 "I-kappaB kinase/NF-kappaB cascade" evidence=TAS

GO:0007254 "JNK cascade" evidence=TAS

GO:0008063 "Toll signaling pathway" evidence=TAS

GO:0008543 "fibroblast growth factor receptor signaling pathway" evidence=TAS

GO:0010008 "endosome membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016044 "cellular membrane organization" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0016197 "endosomal transport" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0019221 "cytokine-mediated signaling pathway" evidence=TAS

GO:0030512 "negative regulation of transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0030666 "endocytic vesicle membrane" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0032480 "negative regulation of type I interferon production" evidence=TAS

GO:0033554 "cellular response to stress" evidence=TAS

GO:0034130 "toll-like receptor 1 signaling pathway" evidence=TAS

GO:0034134 "toll-like receptor 2 signaling pathway" evidence=TAS

GO:0034138 "toll-like receptor 3 signaling pathway" evidence=TAS

GO:0034142 "toll-like receptor 4 signaling pathway" evidence=TAS

GO:0035666 "TRIF-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0035872 "nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway" evidence=TAS

GO:0042059 "negative regulation of epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0043123 "positive regulation of I-kappaB kinase/NF-kappaB cascade" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0045087 "innate immune response" evidence=TAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0046788 "egress of virus within host cell" evidence=TAS

GO:0048011 "neurotrophin TRK receptor signaling pathway" evidence=TAS

GO:0050852 "T cell receptor signaling pathway" evidence=TAS

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=TAS

GO:0051403 "stress-activated MAPK cascade" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0061418 "regulation of transcription from RNA polymerase II promoter in response to hypoxia" evidence=TAS

GO:0070423 "nucleotide-binding oligomerization domain containing signaling pathway" evidence=TAS

GO:0071456 "cellular response to hypoxia" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|P63053 UBA52 "Ubiquitin-60S ribosomal protein L40" [Sus scrofa (taxid:9823)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYAR 102

GO:0005634 "nucleus" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

POMBASE|SPAC11G7.04 ubi1 "ribosomal-ubiquitin fusion protein Ubi1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
             IQKESTLHLVLRLRGGIIEPSL ALA KYN +K ICRK + R
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLKALASKYNCEKQICRKCYAR 102

GO:0002181 "cytoplasmic translation" evidence=NAS

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006412 "translation" evidence=ISO

GO:0016567 "protein ubiquitination" evidence=ISM

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

GO:0042254 "ribosome biogenesis" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P46575	RL40_EIMBO	No assigned EC number	0.8725	0.8793	0.7906	N/A	no
P0CG83	UBIQP_HORVU	No assigned EC number	0.9870	0.6637	0.4502	N/A	no
P0CG84	UBI4P_NICSY	No assigned EC number	0.9870	0.6637	0.2042	N/A	no
P0CG85	UBI1P_NICSY	No assigned EC number	0.9870	0.6637	0.1684	N/A	no
P68205	RL40_OPHHA	No assigned EC number	0.9019	0.8793	0.7968	N/A	no
P63052	RL40_FELCA	No assigned EC number	0.9019	0.8793	0.7968	N/A	no
P63053	RL40_PIG	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P63050	RL40_CANFA	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P0DJ25	RL40_TETTS	No assigned EC number	0.8235	0.8793	0.7906	N/A	no
Q42202	RL40B_ARATH	No assigned EC number	0.9607	0.8793	0.7968	yes	no
P14795	RL40_TRYCR	No assigned EC number	0.8529	0.8793	0.7968	N/A	no
P14794	RL40_DICDI	No assigned EC number	0.8823	0.8706	0.7890	yes	no
P0C275	RL40_PONPY	No assigned EC number	0.9019	0.8793	0.7968	N/A	no
P0C276	RL40_SHEEP	No assigned EC number	0.9019	0.8793	0.7968	N/A	no
P0CH09	RL402_YEAST	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P0CH08	RL401_YEAST	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P0CH07	RL402_SCHPO	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P0CH06	RL401_SCHPO	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P0CH05	UBI2P_PETCR	No assigned EC number	0.9870	0.6637	0.1681	N/A	no
P0CH04	UBI1P_PETCR	No assigned EC number	0.9870	0.6637	0.1681	N/A	no
P49632	RL40_CAEEL	No assigned EC number	0.8921	0.8793	0.7968	yes	no
P49633	RL40_ACACA	No assigned EC number	0.8921	0.8793	0.7968	N/A	no
P21899	RL40_TRYBB	No assigned EC number	0.8333	0.8793	0.7968	N/A	no
P40909	RL40_CRYNJ	No assigned EC number	0.9019	0.8793	0.7906	yes	no
B9DHA6	RL40A_ARATH	No assigned EC number	0.9607	0.8793	0.7968	yes	no
P69201	RL40_LEIMA	No assigned EC number	0.8235	0.8793	0.7968	yes	no
P69200	RL40_LEITA	No assigned EC number	0.8039	0.8793	0.7968	N/A	no
P69309	UBIQP_AVEFA	No assigned EC number	0.9870	0.6637	0.2524	N/A	no
P69322	UBIQP_PEA	No assigned EC number	0.9870	0.6637	0.2020	N/A	no
P63048	RL40_BOVIN	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P33190	RL40_TETPY	No assigned EC number	0.8235	0.8793	0.7906	N/A	no
P0CH10	RL403_CHLRE	No assigned EC number	0.9411	0.8793	0.7968	N/A	no
P0CH11	RL401_CHLRE	No assigned EC number	0.9411	0.8793	0.7968	N/A	no
P0CH34	RL40A_ORYSJ	No assigned EC number	0.9607	0.8793	0.7906	yes	no
P0CH35	RL40B_ORYSJ	No assigned EC number	0.9607	0.8793	0.7906	yes	no
P18101	RL40_DROME	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P62987	RL40_HUMAN	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P62986	RL40_RAT	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P62984	RL40_MOUSE	No assigned EC number	0.9019	0.8793	0.7968	yes	no
P49636	RL40_NICSY	No assigned EC number	0.9705	0.8793	0.7968	N/A	no
P0C273	RL40_MACFA	No assigned EC number	0.9019	0.8793	0.7968	N/A	no
P0C224	RL40_NEUCR	No assigned EC number	0.9117	0.8793	0.7968	N/A	no
P51423	RL40_BRARA	No assigned EC number	0.9607	0.8793	0.7968	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pm.C_LG_XV0026 SubName- Full=Putative uncharacterized protein; (129 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	116
cd01803	76	cd01803, Ubiquitin, Ubiquitin	9e-52
smart00213	72	smart00213, UBQ, Ubiquitin homologues	3e-33
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	3e-33
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	7e-32
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	8e-30
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	8e-25
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	2e-20
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	1e-19
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	6e-18
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	6e-17
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	8e-16
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	3e-15
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	1e-14
cd01807	74	cd01807, GDX_N, ubiquitin-like domain of GDX	8e-14
cd01800	76	cd01800, SF3a120_C, Ubiquitin-like domain of Mamma	1e-12
cd01797	78	cd01797, NIRF_N, amino-terminal ubiquitin-like dom	7e-12
cd01810	74	cd01810, ISG15_repeat2, ISG15 ubiquitin-like prote	3e-11
COG5272	57	COG5272, UBI4, Ubiquitin [Posttranslational modifi	4e-11
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	4e-11
cd01794	70	cd01794, DC_UbP_C, dendritic cell derived ubiquiti	5e-08
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	1e-07
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	2e-07
cd01796	71	cd01796, DDI1_N, DNA damage inducible protein 1 ub	1e-06
pfam01020	52	pfam01020, Ribosomal_L40e, Ribosomal L40e family	3e-06
cd01792	80	cd01792, ISG15_repeat1, ISG15 ubiquitin-like prote	5e-06
cd01804	78	cd01804, midnolin_N, Ubiquitin-like domain of midn	2e-05
pfam13881	111	pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUM	7e-05
cd01799	75	cd01799, Hoil1_N, Ubiquitin-like domain of HOIL1	6e-04
pfam13019	163	pfam13019, Telomere_Sde2, Telomere stability and s	0.001
cd01815	75	cd01815, BMSC_UbP_N, Ubiquitin-like domain of BMSC	0.004

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score =  157 bits (398), Expect = 9e-52
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains). Length = 76

>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues

 Score =  110 bits (277), Expect = 3e-33
 Identities = 47/72 (65%), Positives = 57/72 (79%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL GKTITLEV+ SDT+  +K KI +  GIPP+QQRLI+ GK LED RTLADY 
Sbjct: 1  IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYG 60

Query: 61 IQKESTLHLVLR 72
          IQ  ST+HLVLR
Sbjct: 61 IQDGSTIHLVLR 72

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression. Length = 72

>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family

 Score =  110 bits (276), Expect = 3e-33
 Identities = 50/69 (72%), Positives = 57/69 (82%)

Query: 6  KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES 65
          KTL GKTITLEV+ SDT+  +K KI+DKEGIP DQQRLIF+GK LED  TL++Y IQ  S
Sbjct: 1  KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGS 60

Query: 66 TLHLVLRLR 74
          TLHLVLRLR
Sbjct: 61 TLHLVLRLR 69

This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. Length = 69

>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score =  107 bits (268), Expect = 7e-32
 Identities = 42/76 (55%), Positives = 59/76 (77%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          ++  S LHLVL LRGG
Sbjct: 61 LEGGSVLHLVLALRGG 76

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Length = 76

>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL

 Score =  101 bits (254), Expect = 8e-30
 Identities = 46/69 (66%), Positives = 54/69 (78%)

Query: 4  FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK 63
           VKTLTGKT  LEV   DT+  +KAKI  KEG+PP+QQRLI+AGK L+D +TL+DY IQ 
Sbjct: 1  TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQD 60

Query: 64 ESTLHLVLR 72
           STLHLVLR
Sbjct: 61 GSTLHLVLR 69

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways. Length = 69

>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 89.1 bits (221), Expect = 8e-25
 Identities = 38/76 (50%), Positives = 52/76 (68%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQI +KTLTGK  +   E  +T+  VK  +Q+KEGI   Q RLI++GKQ+ D   L+DY 
Sbjct: 1  MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          +   ST+H+VL+LRGG
Sbjct: 61 VVPGSTIHMVLQLRGG 76

Length = 76

>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like

 Score = 77.6 bits (192), Expect = 2e-20
 Identities = 26/72 (36%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIFAGKQLEDGRTLADY 59
          ++I +K   GK + ++V+ + T+  +    + K GIP DQQ RLIF G++L+   T+ADY
Sbjct: 1  IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRGIPADQQVRLIFDGERLDPNDTVADY 60

Query: 60 NIQKESTLHLVL 71
          +I+   T+ +V+
Sbjct: 61 DIEDGDTIDVVI 72

The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localisation, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45). Length = 72

>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 76.8 bits (189), Expect = 1e-19
 Identities = 39/76 (51%), Positives = 50/76 (65%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           M++F++TLTG    L V   +T+ +VKAKIQ  EGIP  QQ LI+   +LED   L DYN
Sbjct: 28  MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYN 87

Query: 61  IQKESTLHLVLRLRGG 76
           I +  TL LVL +RGG
Sbjct: 88  ISEGCTLKLVLAMRGG 103

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown. Length = 103

>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23

 Score = 71.6 bits (176), Expect = 6e-18
 Identities = 28/63 (44%), Positives = 44/63 (69%), Gaps = 2/63 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLAD 58
          M+I  KTL  +T  +EV+  DT+  +K KI++++G   PP+QQ+LI++GK L+D  TL +
Sbjct: 1  MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEE 60

Query: 59 YNI 61
          Y I
Sbjct: 61 YKI 63

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL). Length = 77

>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein

 Score = 68.8 bits (169), Expect = 6e-17
 Identities = 32/72 (44%), Positives = 50/72 (69%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          ++I VKTL  +T T  VE   T+ ++K KI ++ GIP +QQRLI++G+ L+D  TL++Y 
Sbjct: 1  IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYK 60

Query: 61 IQKESTLHLVLR 72
          ++   T+HLV R
Sbjct: 61 VEDGHTIHLVKR 72

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. Length = 72

>gnl|CDD|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 66.3 bits (162), Expect = 8e-16
 Identities = 30/76 (39%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FV+     T TLEV   +T+ ++KA +   EGI  + Q L+ AG  LED  TL    
Sbjct: 1  MQLFVRAQ--NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCG 58

Query: 61 IQKESTLHLVLRLRGG 76
          +++  TL +  RL GG
Sbjct: 59 VEELCTLEVAGRLLGG 74

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8. Length = 74

>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 64.9 bits (158), Expect = 3e-15
 Identities = 32/69 (46%), Positives = 41/69 (59%)

Query: 4  FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK 63
           VK   GKT+ L V S  T+ ++K K+  K G+PP+QQRL+  GK L D  TL DY +Q 
Sbjct: 1  KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQD 60

Query: 64 ESTLHLVLR 72
             L LV R
Sbjct: 61 GDELVLVPR 69

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate. Length = 69

>gnl|CDD|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein

 Score = 63.2 bits (154), Expect = 1e-14
 Identities = 27/70 (38%), Positives = 46/70 (65%)

Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          ++V+T TG T  +EV+    I  +K  +  ++G+PPDQ R+IFAGK+L +  T+ + ++ 
Sbjct: 1  VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLG 60

Query: 63 KESTLHLVLR 72
          ++S LH V R
Sbjct: 61 QQSILHAVRR 70

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain. Length = 70

>gnl|CDD|176402 cd01807, GDX_N, ubiquitin-like domain of GDX

 Score = 61.1 bits (148), Expect = 8e-14
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M + VK L G+  +L+V   +++  +K  + +   +P +QQRL+F GK L D + L+DY+
Sbjct: 1  MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYS 60

Query: 61 IQKESTLHLVLR 72
          I   + L+LV+R
Sbjct: 61 IGPNAKLNLVVR 72

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown. Length = 74

>gnl|CDD|176395 cd01800, SF3a120_C, Ubiquitin-like domain of Mammalian splicing factor SF3a_120

 Score = 57.9 bits (140), Expect = 1e-12
 Identities = 23/69 (33%), Positives = 42/69 (60%)

Query: 8  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
          L G+ +   ++ SD +  +K KI ++ G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 5  LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTII 64

Query: 68 HLVLRLRGG 76
          HL L+ RGG
Sbjct: 65 HLQLKERGG 73

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus. Length = 76

>gnl|CDD|176392 cd01797, NIRF_N, amino-terminal ubiquitin-like domain of Np95 and NIRF

 Score = 56.4 bits (136), Expect = 7e-12
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 2/74 (2%)

Query: 1  MQIFVKTLTGK-TITLEVESSDT-IDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ GK T T++  S  T ++ ++ KIQ+   + P+ QRL + GKQ+EDG TL D
Sbjct: 1  MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFD 60

Query: 59 YNIQKESTLHLVLR 72
          YN+     + L++R
Sbjct: 61 YNVGLNDIIQLLVR 74

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation. Length = 78

>gnl|CDD|176405 cd01810, ISG15_repeat2, ISG15 ubiquitin-like protein, second repeat of 2

 Score = 54.5 bits (131), Expect = 3e-11
 Identities = 24/74 (32%), Positives = 42/74 (56%)

Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          I V+   G++   EV+ + T+  +K ++  +E +  DQ  L F G+ +ED   L +Y ++
Sbjct: 1  ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLK 60

Query: 63 KESTLHLVLRLRGG 76
             T+ + LRLRGG
Sbjct: 61 PGCTVFMNLRLRGG 74

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. Length = 74

>gnl|CDD|227597 COG5272, UBI4, Ubiquitin [Posttranslational modification, protein turnover, chaperones]

 Score = 53.7 bits (129), Expect = 4e-11
 Identities = 10/56 (17%), Positives = 19/56 (33%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL 56
              +K  TG     E + +   D    K   ++    ++  L+   + LE  R  
Sbjct: 1  DAKPIKKATGGAAKPESQLAKAKDTRPEKQYAEQDSQLNEMALMDCERNLEASRIS 56

Length = 57

>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 58.0 bits (140), Expect = 4e-11
 Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          M +  KTL  +   +++E  +T+  +K KI+ ++G    P  QQ+LI++GK L D +T+ 
Sbjct: 1  MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVK 60

Query: 58 DYNI 61
          +Y I
Sbjct: 61 EYKI 64

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 378

>gnl|CDD|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein

 Score = 46.0 bits (109), Expect = 5e-08
 Identities = 25/67 (37%), Positives = 39/67 (58%)

Query: 5  VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKE 64
          V+  TGK + L V S DT+  +K ++Q  EG+ P  QR  F+GK L D   L +  IQK+
Sbjct: 3  VRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKD 62

Query: 65 STLHLVL 71
            + +++
Sbjct: 63 YVVQVIV 69

DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis. Length = 70

>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2

 Score = 45.2 bits (107), Expect = 1e-07
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K   +E+    ++ + K  +  K     +Q  LIFAGK L+D  TL  +N
Sbjct: 1  IKVTVKTPKDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHN 59

Query: 61 IQKESTLHLVLR 72
          I+   T+HLV++
Sbjct: 60 IKDGLTVHLVIK 71

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein. Length = 71

>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69
          G++  L + S  T  ++K  +    G+ P  Q+LIF GK+ +D  TL    ++  S + L
Sbjct: 9  GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVML 68

Query: 70 V 70
          +
Sbjct: 69 L 69

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP). Length = 71

>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like domain

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADYNIQ 62
            T +L+V+    ++N KA  + + GIP  QQ+LI+ G++L ++ R LA Y ++
Sbjct: 9  ETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVK 62

DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1. Length = 71

>gnl|CDD|110049 pfam01020, Ribosomal_L40e, Ribosomal L40e family

 Score = 41.1 bits (96), Expect = 3e-06
 Identities = 13/26 (50%), Positives = 20/26 (76%)

Query: 77  IIEPSLMALARKYNQDKMICRKSHTR 102
           ++EP+L ALA+KYN +K +CR  + R
Sbjct: 1   VMEPTLAALAKKYNCEKKVCRDCYAR 26

Bovine L40 has been identified as a secondary RNA binding protein. L40 is fused to a ubiquitin protein. Length = 52

>gnl|CDD|176387 cd01792, ISG15_repeat1, ISG15 ubiquitin-like protein, first repeat of 2

 Score = 41.1 bits (96), Expect = 5e-06
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 5  VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLEDGRTLADYNIQ 62
          VK L G    + +  S T+  +K +I  K G+P  QQRL      + L+DG  L    + 
Sbjct: 7  VKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLG 66

Query: 63 KESTLHLVLR 72
            ST+ LV++
Sbjct: 67 PGSTVLLVVQ 76

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. Length = 80

>gnl|CDD|176399 cd01804, midnolin_N, Ubiquitin-like domain of midnolin

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M + + + TG    L V   +T++ +K +I  +  +P ++  L+    +L  G  L D  
Sbjct: 2  MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLG 60

Query: 61 IQKESTLHLVLRLRGGII 78
          +   S L LV  +  G++
Sbjct: 61 LGDGSKLTLVPTVEAGLM 78

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain. Length = 78

>gnl|CDD|206052 pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUMO-like

 Score = 38.8 bits (91), Expect = 7e-05
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 13/68 (19%)

Query: 18 ESSDTIDNVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLADYNI------QKE 64
            + T+ ++K K+     +DKE  P  P+  +LI AGK LE+ +TL +  +         
Sbjct: 21 SPATTVADLKEKVLAQWPKDKEEGPKSPNDVKLINAGKILENNKTLGECRLPAGETPGGV 80

Query: 65 STLHLVLR 72
            +H+V+R
Sbjct: 81 IVMHVVVR 88

Length = 111

>gnl|CDD|176394 cd01799, Hoil1_N, Ubiquitin-like domain of HOIL1

 Score = 35.6 bits (82), Expect = 6e-04
 Identities = 16/51 (31%), Positives = 23/51 (45%)

Query: 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          TI L V    T+  +K K+    G PP  QR +   +   D  TL  + I+
Sbjct: 14 TIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRWVIGQRLARDQETLYSHGIR 64

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Length = 75

>gnl|CDD|205200 pfam13019, Telomere_Sde2, Telomere stability and silencing

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 11/87 (12%)

Query: 1  MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQL--ED 52
          + + V +  G     T++L + S+ T+ ++  K+  +       Q +    + +QL    
Sbjct: 1  INVLVSSFPGLGLPPTLSLTLPSTATVSDLIDKLSRRLPESLTSQLILTTTSNRQLSPSS 60

Query: 53 GRTLADYNIQKEST---LHLVLRLRGG 76
             L+        T   L L  RL GG
Sbjct: 61 DLPLSSLLSSSADTFLSLRLSPRLCGG 87

Sde2 has been identified in fission yeast as an important factor in telomere formation and maintenance. This is a more N-terminal domain on these nuclear proteins, and is essential for telomeric silencing and genomic stability. Length = 163

>gnl|CDD|176410 cd01815, BMSC_UbP_N, Ubiquitin-like domain of BMSC-UbP

 Score = 33.2 bits (76), Expect = 0.004
 Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 3/48 (6%)

Query: 26 VKAKIQDKEGIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72
          + A++ D   +P P+   LI  G++L+D +TL  Y IQ  ST+H++ +
Sbjct: 30 IAAQLPDS--LPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILRK 75

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain. Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	116
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.94
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.87
PTZ00044	76	ubiquitin; Provisional	99.86
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.86
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.86
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.85
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.85
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.84
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.83
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.83
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.83
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.82
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.81
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.79
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.79
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.79
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.78
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.78
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.76
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.75
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.75
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.74
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.73
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.72
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.68
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.68
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.65
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.63
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.58
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.58
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.57
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.56
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.52
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.47
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.46
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.45
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.34
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	99.25
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	99.24
PLN02560	308	enoyl-CoA reductase	99.21
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	99.17
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	99.11
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	99.08
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	99.03
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.94
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.9
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.85
PF13019	162	Telomere_Sde2: Telomere stability and silencing	98.82
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.74
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.74
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	98.71
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.5
PF01020	52	Ribosomal_L40e: Ribosomal L40e family; InterPro: I	98.38
KOG4495	110	consensus RNA polymerase II transcription elongati	98.28
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	98.19
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	98.07
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	98.03
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	97.96
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.84
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.79
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.68
COG5417	81	Uncharacterized small protein [Function unknown]	97.68
KOG1639	297	consensus Steroid reductase required for elongatio	97.65
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.63
PRK04136	48	rpl40e 50S ribosomal protein L40e; Provisional	97.63
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.62
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	97.48
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	97.4
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	97.36
KOG0013	231	consensus Uncharacterized conserved protein [Funct	97.36
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	97.12
PRK08364	70	sulfur carrier protein ThiS; Provisional	97.09
PRK06437	67	hypothetical protein; Provisional	97.09
PRK06488	65	sulfur carrier protein ThiS; Validated	97.06
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	96.93
KOG4583	391	consensus Membrane-associated ER protein involved	96.9
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	96.84
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	96.75
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	96.62
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	96.44
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	96.43
PF12754	309	Blt1: Cell-cycle control medial ring component; In	96.33
PRK05863	65	sulfur carrier protein ThiS; Provisional	96.26
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	96.26
PRK08053	66	sulfur carrier protein ThiS; Provisional	96.25
PRK05659	66	sulfur carrier protein ThiS; Validated	96.09
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	96.06
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	96.04
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	95.93
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	95.86
PF14453	57	ThiS-like: ThiS-like ubiquitin	95.86
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	95.79
PRK07696	67	sulfur carrier protein ThiS; Provisional	95.72
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	95.66
PRK06083	84	sulfur carrier protein ThiS; Provisional	95.65
PRK07440	70	hypothetical protein; Provisional	95.65
TIGR01683	64	thiS thiamine biosynthesis protein ThiS. This mode	95.46
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	95.43
PRK06944	65	sulfur carrier protein ThiS; Provisional	95.38
KOG0012	380	consensus DNA damage inducible protein [Replicatio	95.31
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	95.12
COG1552	50	RPL40A Ribosomal protein L40E [Translation, riboso	95.05
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	94.63
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	94.27
COG2104	68	ThiS Sulfur transfer protein involved in thiamine	94.17
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	94.02
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	93.74
cd06396	81	PB1_NBR1 The PB1 domain is an essential part of NB	93.56
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	93.27
cd05992	81	PB1 The PB1 domain is a modular domain mediating s	93.18
PRK11130	81	moaD molybdopterin synthase small subunit; Provisi	92.68
smart00455	70	RBD Raf-like Ras-binding domain.	92.59
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	92.59
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	92.33
PTZ00380	121	microtubule-associated protein (MAP); Provisional	91.69
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	91.52
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	91.26
PF10407	73	Cytokin_check_N: Cdc14 phosphatase binding protein	89.67
cd06410	97	PB1_UP2 Uncharacterized protein 2. The PB1 domain	89.29
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	89.21
cd06398	91	PB1_Joka2 The PB1 domain is present in the Nicotia	88.91
PF14732	87	UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquiti	88.74
PF02196	71	RBD: Raf-like Ras-binding domain; InterPro: IPR003	88.62
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	87.68
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	87.39
PF08825	84	E2_bind: E2 binding domain; InterPro: IPR014929 E1	87.11
PF14533	213	USP7_C2: Ubiquitin-specific protease C-terminal; P	87.08
cd01787	85	GRB7_RA RA (RAS-associated like) domain of Grb7. G	86.87
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	86.74
cd01766	82	Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-f	85.48
PF00788	93	RA: Ras association (RalGDS/AF-6) domain; InterPro	84.87
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	84.36
cd01611	112	GABARAP Ubiquitin domain of GABA-receptor-associat	84.35
KOG2507	506	consensus Ubiquitin regulatory protein UBXD2, cont	83.67
PF00276	91	Ribosomal_L23: Ribosomal protein L23; InterPro: IP	83.65
cd01768	87	RA RA (Ras-associating) ubiquitin domain. The RA (	83.32
PF02991	104	Atg8: Autophagy protein Atg8 ubiquitin like; Inter	83.14
PF06234	85	TmoB: Toluene-4-monooxygenase system protein B (Tm	82.14
PRK05738	92	rplW 50S ribosomal protein L23; Reviewed	82.01
KOG2982	418	consensus Uncharacterized conserved protein [Funct	82.0
PF08337	539	Plexin_cytopl: Plexin cytoplasmic RasGAP domain; I	81.91
PF02017	78	CIDE-N: CIDE-N domain; InterPro: IPR003508 This do	81.48
cd01764	94	Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Rel	80.44

>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=5.2e-28  Score=151.53  Aligned_cols=110  Identities=88%  Similarity=1.197  Sum_probs=107.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+++++...|++..+++.|++||..+|..|..+.|+|++.|+|+|+|+.|.|..++++||+..-++|+++.++.||.+.+
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG~i~~   80 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcCCCCh
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHcCCCcccccccccccccCCCccccccC
Q 033570           81 SLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        81 ~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      +++..+.++|.++.+||+||.+   ..|+|  -||
T Consensus        81 ~~aalAmK~~~D~lICRkCYAR---~g~~A--e~C  110 (128)
T KOG0003|consen   81 SLAALAMKYNCDKLICRKCYAR---LGPRA--ENC  110 (128)
T ss_pred             hHHHHHHHhccchHHHHHHHHh---cCcHH--HHh
Confidence            9999999999999999999999   99999  787

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.87  E-value=2.1e-21  Score=116.57  Aligned_cols=74  Identities=41%  Similarity=0.618  Sum_probs=71.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+||..  +.+.++|++++||++||++|++..|+|++.|+|+|+|+.|+|+.+|++|+|+++++|+++++++||
T Consensus         1 mqi~vk~~--~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~GG   74 (74)
T cd01793           1 MQLFVRAQ--NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLGG   74 (74)
T ss_pred             CEEEEECC--CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            89999984  688999999999999999999999999999999999999999999999999999999999999887

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.

>PTZ00044 ubiquitin; Provisional

Probab=99.86  E-value=3.6e-21  Score=115.82  Aligned_cols=76  Identities=50%  Similarity=0.822  Sum_probs=74.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+||..+|+.+.+.+++++||++||++|++..|+|++.|+|+|+|+.|+|+.+|++|++.++++|++++++.||
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~gg   76 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG   76 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEccCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999998876

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.86  E-value=4e-21  Score=115.29  Aligned_cols=73  Identities=36%  Similarity=0.653  Sum_probs=71.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.++|++++||++||++|+++.|+|+++|+|+|+|+.|.|+.+|++|||+++++|++++++
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999874

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.

>cd01803 Ubiquitin Ubiquitin

Probab=99.86  E-value=5.8e-21  Score=114.54  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=74.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|.|+|+.|+|+.+|++||+.+|++|++++++.||
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~gg   76 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999998887

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.85  E-value=1e-20  Score=113.43  Aligned_cols=76  Identities=55%  Similarity=0.965  Sum_probs=74.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|.|+..+|+.+.+++++++||++||++|++..|+|+++|+|+|+|+.|.|+.+|++|++.+|++|+++++.+||
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~gg   76 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRGG   76 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEccCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999998876

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.85  E-value=8.5e-21  Score=120.61  Aligned_cols=76  Identities=51%  Similarity=0.763  Sum_probs=74.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|+|+++++|+++++++||
T Consensus        28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~GG  103 (103)
T cd01802          28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRGG  103 (103)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999886

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.84  E-value=1.4e-20  Score=114.13  Aligned_cols=75  Identities=25%  Similarity=0.491  Sum_probs=72.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+...|+.+.+++++++||++||+.|+++.++++++|+|+|.|+.|+|+ +|++|||++|++|+++..+.+|
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~~~   76 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVEAG   76 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecccc
Confidence            89999999999999999999999999999999999999999999999999998 9999999999999999998887

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.83  E-value=2.6e-20  Score=111.57  Aligned_cols=71  Identities=24%  Similarity=0.378  Sum_probs=68.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|+|++..|+.+.+++++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|++..
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            78999999999999999999999999999999999999999999999999999999999999999999863

UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2

Probab=99.83  E-value=3.7e-20  Score=111.08  Aligned_cols=74  Identities=32%  Similarity=0.618  Sum_probs=71.6

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+||.+.|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|.|+.+|++|||+++++++++.++.||
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~gg   74 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLRGG   74 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEccCC
Confidence            67999999999999999999999999999999999999999999999999999999999999999999998876

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF

Probab=99.83  E-value=7.4e-20  Score=110.94  Aligned_cols=74  Identities=36%  Similarity=0.634  Sum_probs=70.4

Q ss_pred             CEEEEEcCCCCE-EEEE-ecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKT-ITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~-~~i~-v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+||..+|+. +.++ +++++||++||++|++..|+|++.|+|+|+|+.|+|+.+|++|||+++++|++++++.
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~   76 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQD   76 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            899999999997 6885 8999999999999999999999999999999999999999999999999999999864

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.82  E-value=1.2e-19  Score=109.25  Aligned_cols=73  Identities=38%  Similarity=0.705  Sum_probs=70.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCC--CCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i--~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.+++++++||.+||+.|++..|+  |+++|+|+|+|+.|+|+.+|++||+++|++|+++++.
T Consensus         1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~   75 (77)
T cd01805           1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSK   75 (77)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEec
Confidence            899999999999999999999999999999999999  9999999999999999999999999999999998874

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.81  E-value=3.3e-19  Score=105.83  Aligned_cols=72  Identities=44%  Similarity=0.704  Sum_probs=69.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++||+++|++|+++.+
T Consensus         1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809           1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            899999999999999999999999999999999999999999999999999999999999999999998764

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein

Probab=99.79  E-value=5e-19  Score=105.03  Aligned_cols=70  Identities=39%  Similarity=0.733  Sum_probs=67.3

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+..+|+.+.+++++++||++||++|+++.|+|+++|+|+|+|++|+|+.+|++|||+++++|+++.|
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            5789999999999999999999999999999999999999999999999999999999999999999864

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2

Probab=99.79  E-value=6.8e-19  Score=107.09  Aligned_cols=73  Identities=32%  Similarity=0.431  Sum_probs=70.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEE--EECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L--~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.++++++.||.+||++|++..++|+++|+|  .|+|+.|.|+.+|++||+++|++|+++++.
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~   77 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN   77 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence            7899999999999999999999999999999999999999999  899999999999999999999999999884

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.79  E-value=9.1e-19  Score=104.11  Aligned_cols=68  Identities=37%  Similarity=0.581  Sum_probs=65.6

Q ss_pred             EEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         4 ~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .|+..+|+.+.+++++++||.+||++|++..|+|++.|+|+|+|++|+|+.+|++|+|+++++|++++
T Consensus         2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794           2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             eEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            57889999999999999999999999999999999999999999999999999999999999999986

DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.

>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade

Probab=99.78  E-value=1.2e-18  Score=102.87  Aligned_cols=68  Identities=56%  Similarity=0.962  Sum_probs=65.0

Q ss_pred             EcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         6 k~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |..+|+.+.+++++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++|||++|++|+++++.
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999999875

There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2

Probab=99.78  E-value=2.3e-18  Score=102.44  Aligned_cols=71  Identities=34%  Similarity=0.489  Sum_probs=67.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.|+|+...|+ ..+++++++||.+||+.|++..|+++++|+|+|+|+.|.|+.+|++||+++|++|+++++
T Consensus         1 ~~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808           1 IKVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            68999999997 589999999999999999999999999999999999999999999999999999999864

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120

Probab=99.76  E-value=3.8e-18  Score=102.84  Aligned_cols=70  Identities=33%  Similarity=0.656  Sum_probs=67.0

Q ss_pred             CCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         8 ~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      .+|+.+.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|++.+|++|+++++.+||.
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~gg~   74 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERGGR   74 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCCCc
Confidence            3688999999999999999999999999999999999999999999999999999999999999998875

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.75  E-value=7.3e-18  Score=101.22  Aligned_cols=70  Identities=23%  Similarity=0.400  Sum_probs=66.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE---CCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~---~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |.|.|++ +|+.+.+++++++||++||++|++.+++|+++|+|+|   .|+.+.|+.+|++|++++|+.|+++.
T Consensus         1 ~~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lmG   73 (74)
T cd01813           1 VPVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMMG   73 (74)
T ss_pred             CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEEe
Confidence            6899998 7889999999999999999999999999999999996   89999999999999999999998863

The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

Probab=99.75  E-value=6.1e-18  Score=102.37  Aligned_cols=71  Identities=24%  Similarity=0.251  Sum_probs=63.8

Q ss_pred             CEEEEEcCCCCEEEE--EecCCCCHHHHHHHHHHhhC--CCCCceEEEECCEEcCCCCccccCC--CCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITL--EVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYN--IQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i--~v~~~~TV~~LK~~I~~~~~--i~~~~q~L~~~g~~L~d~~tL~~~g--i~~g~~I~v~~   71 (116)
                      |.|+||+++++.+.+  ++++++||.+||++|++..+  .++++|+|+|+|++|+|+.+|++|+  +.++.+||+++
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            579999999998554  55899999999999999875  4579999999999999999999996  99999999986

Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.74  E-value=1.4e-17  Score=98.72  Aligned_cols=70  Identities=29%  Similarity=0.469  Sum_probs=66.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|.|++. |+.+.+++++++||.+||++|++.+|+|+++|+|.|+|+.|.|+.+|++||+++|++|+++.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            68999995 88999999999999999999999999999999999999999999999999999999998864

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain

Probab=99.73  E-value=1.7e-17  Score=98.85  Aligned_cols=68  Identities=35%  Similarity=0.543  Sum_probs=63.8

Q ss_pred             EEEEcC-CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCC-CccccCCCCCCCEEEEE
Q 033570            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLV   70 (116)
Q Consensus         3 v~Vk~~-~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~-~tL~~~gi~~g~~I~v~   70 (116)
                      |+|+.. +|+.+.+++++++||++||++|++..|+|++.|+|+|+|+.|.|+ .+|++|||++|++|++.
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            578898 899999999999999999999999999999999999999999887 68999999999999874

DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.72  E-value=8.8e-17  Score=99.27  Aligned_cols=76  Identities=18%  Similarity=0.467  Sum_probs=73.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|.|++.+|+...+.|.+++|+..||++++++.|+|++.|+|+|+|+.|.++.|+.+|++.++++|++++++.||
T Consensus        12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~GG   87 (87)
T cd01763          12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTGG   87 (87)
T ss_pred             EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEecccC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999887

Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.

>smart00213 UBQ Ubiquitin homologues

Probab=99.68  E-value=2.5e-16  Score=90.98  Aligned_cols=64  Identities=61%  Similarity=0.864  Sum_probs=61.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES   65 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~   65 (116)
                      |+|.|++.+ +.+.+++++++||++||++|++.+++|+++|+|+|+|+.|.|+.+|++||+++|+
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            899999998 7899999999999999999999999999999999999999999999999999875

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression

>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]

Probab=99.68  E-value=3.5e-17  Score=109.02  Aligned_cols=107  Identities=71%  Similarity=0.919  Sum_probs=96.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC---
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI---   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~---   77 (116)
                      |+|+|+...++...+++.+++||..+|..|+...|||+++|+|+|.|+.|.|..+|+||+|+.-++|+++++++||.   
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~kkr   80 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGAKKR   80 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCcccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999994   


Q ss_pred             ---CCCchHHHHHHcCCCcccccccccccccCC
Q 033570           78 ---IEPSLMALARKYNQDKMICRKSHTRTRNQF  107 (116)
Q Consensus        78 ---~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~  107 (116)
                         ....|+...+.....+..-+.||+.+++..
T Consensus        81 kkk~~~~pk~~~~~~kk~~l~~~~y~kvd~ngk  113 (156)
T KOG0004|consen   81 KKKSYTTPKKIKSKHKKVSLAVLKYYKVDENGK  113 (156)
T ss_pred             cccccccccccCCCccccccCCccceeeccCcc
Confidence               345566666666666778889999887763

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.65  E-value=6.5e-16  Score=117.27  Aligned_cols=73  Identities=30%  Similarity=0.601  Sum_probs=70.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhC---CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+||+.+|+.+.|+|++++||.+||++|++..|   +++++|+|+|+|++|+|+.+|++|+|+++++|++++..
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k   76 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSK   76 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEecc
Confidence            89999999999999999999999999999999998   99999999999999999999999999999999988764

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.63  E-value=3.4e-16  Score=88.63  Aligned_cols=70  Identities=54%  Similarity=0.911  Sum_probs=67.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |.|.|+++.|+.+.++++|+++|+.+|+.++++.|+||..|+|+|.|+.+.|+.+-.+|.+.-||+++++
T Consensus         1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999874

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.58  E-value=1.6e-14  Score=86.91  Aligned_cols=69  Identities=29%  Similarity=0.372  Sum_probs=60.2

Q ss_pred             EEEEE--cCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcC-CCCccccCCCC-CCCEEEEEE
Q 033570            2 QIFVK--TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQ-KESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk--~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~-d~~tL~~~gi~-~g~~I~v~~   71 (116)
                      ++.|.  ...|.++.+++++++||++||++|++..|+|++.|+| |.|+.|. |+.+|++||+. +|+++++.+
T Consensus         2 ~~~~~~~~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           2 NVSVEDAQSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             EEEEeccccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            34443  3467889999999999999999999999999999999 9999885 67999999998 889998864

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=99.58  E-value=3.9e-15  Score=114.45  Aligned_cols=76  Identities=36%  Similarity=0.546  Sum_probs=71.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      ++|+||+.++ ++.|.|..+.||.+||+.|++++++++++++|+|.|++|+|+.+|..|||++|.+||++++...+.
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~~   91 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPRP   91 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCCC
Confidence            4799999888 899999999999999999999999999999999999999999999999999999999999866443

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.57  E-value=1.9e-14  Score=84.13  Aligned_cols=67  Identities=67%  Similarity=0.992  Sum_probs=63.5

Q ss_pred             EEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         5 Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+..+|+.+.+.+++++||++||++|++.+++|+++|+|.|+|+.|+|+.+|.+|++.+++.|++..
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            6777899999999999999999999999999999999999999999999999999999999998864

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.56  E-value=5.7e-15  Score=88.38  Aligned_cols=56  Identities=32%  Similarity=0.555  Sum_probs=50.4

Q ss_pred             EecC-CCCHHHHHHHHHHhh--CCC-CCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570           16 EVES-SDTIDNVKAKIQDKE--GIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        16 ~v~~-~~TV~~LK~~I~~~~--~i~-~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      +|+| ++||.+||++|+++.  +++ +++|+|+|.|+.|+|+.+|++|||++|++|+++.
T Consensus        15 ~~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          15 DVSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             CcCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            4444 789999999999996  464 8899999999999999999999999999999985

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins

Probab=99.52  E-value=6.8e-14  Score=83.09  Aligned_cols=71  Identities=34%  Similarity=0.633  Sum_probs=65.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC-CceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~-~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.++++ +.++|.|+|+.|+++.|++++|+.+|++|+|++
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            78999999999999999999999999999999999999 999999999999999999999999999999874

SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.47  E-value=2e-13  Score=85.09  Aligned_cols=63  Identities=27%  Similarity=0.305  Sum_probs=57.9

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCC-CCccccCCCCCCCEEEEEEecC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d-~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      ...+.|++++||.+||..|.++++++|.+|+|+++|+.|.| ..+|++|||.++++|.+.+..+
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~LlideP   79 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEP   79 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecCC
Confidence            46788999999999999999999999999999999998865 7899999999999999998743

The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.46  E-value=1.6e-13  Score=87.52  Aligned_cols=76  Identities=22%  Similarity=0.289  Sum_probs=64.4

Q ss_pred             EEEEEcCCCCEE-EEEecCCCCHHHHHHHHHHhhC-------CCCCceEEEECCEEcCCCCccccCC------CCCCCEE
Q 033570            2 QIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKEG-------IPPDQQRLIFAGKQLEDGRTLADYN------IQKESTL   67 (116)
Q Consensus         2 ~v~Vk~~~g~~~-~i~v~~~~TV~~LK~~I~~~~~-------i~~~~q~L~~~g~~L~d~~tL~~~g------i~~g~~I   67 (116)
                      .|.++..+|..+ .+.+++++||.+||++|++.++       .+++.|+|+|.|+.|.|+.+|++|+      +....++
T Consensus         6 e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~Tm   85 (113)
T cd01814           6 EIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITM   85 (113)
T ss_pred             EEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEE
Confidence            566777788765 5788899999999999997773       4599999999999999999999999      6667899


Q ss_pred             EEEEecCCCC
Q 033570           68 HLVLRLRGGI   77 (116)
Q Consensus        68 ~v~~~~~gg~   77 (116)
                      ||+++....+
T Consensus        86 Hvvlr~~~~~   95 (113)
T cd01814          86 HVVVQPPLAD   95 (113)
T ss_pred             EEEecCCCCC
Confidence            9999876543

NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=99.45  E-value=2.8e-13  Score=99.88  Aligned_cols=74  Identities=38%  Similarity=0.657  Sum_probs=70.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhC--CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~--i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+||++.++.|.+++.|++||.++|+.|+...|  +|.+.|+|+|+|++|.|+.++.+|+++++..|++++...
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~   76 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKD   76 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecC
Confidence            89999999999999999999999999999999999  899999999999999999999999999999988888654

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B

Probab=99.34  E-value=1.1e-11  Score=76.02  Aligned_cols=70  Identities=21%  Similarity=0.379  Sum_probs=58.5

Q ss_pred             EEEEEcCC-CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE-ECCE-----Ec-CCCCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLT-GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGK-----QL-EDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~-g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~~g~-----~L-~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .|.|.+.. .......+++++||.+||++++..+|++++.|+|. |.|+     .| +|+.+|++||+.+|..|+|+-
T Consensus         3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVvD   80 (84)
T cd01789           3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVID   80 (84)
T ss_pred             EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEEe
Confidence            46666643 33355679999999999999999999999999995 7877     45 678899999999999999874

Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A

Probab=99.25  E-value=4.2e-11  Score=73.71  Aligned_cols=71  Identities=27%  Similarity=0.530  Sum_probs=57.2

Q ss_pred             EEEEEcCCC--CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEEC----CE---Ec-CCCCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----GK---QL-EDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~g--~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~----g~---~L-~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .|.|.+...  ......+++++||++||.+|+..+|+|++.|+|.+.    +.   .+ +|+.+|++||+.+|.+|+|.=
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D   82 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVD   82 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEe
Confidence            567777654  478899999999999999999999999999999875    22   24 468899999999999999874


Q ss_pred             e
Q 033570           72 R   72 (116)
Q Consensus        72 ~   72 (116)
                      .
T Consensus        83 ~   83 (87)
T PF14560_consen   83 T   83 (87)
T ss_dssp             -
T ss_pred             C
Confidence            3

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A

Probab=99.24  E-value=1.4e-10  Score=74.49  Aligned_cols=76  Identities=29%  Similarity=0.461  Sum_probs=57.2

Q ss_pred             EEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCC-------CCCceEEEECCEEcCCCCccccCCCCCCC------EE
Q 033570            2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGI-------PPDQQRLIFAGKQLEDGRTLADYNIQKES------TL   67 (116)
Q Consensus         2 ~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i-------~~~~q~L~~~g~~L~d~~tL~~~gi~~g~------~I   67 (116)
                      .|.++..+|. ...+..++++||.+||+.|...+.-       .++.+||+|.|+.|+|..+|+++++..|+      ++
T Consensus         4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vm   83 (111)
T PF13881_consen    4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVM   83 (111)
T ss_dssp             EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEE
T ss_pred             EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEE
Confidence            5666777898 6789999999999999999988731       34578999999999999999999987766      57


Q ss_pred             EEEEecCCCC
Q 033570           68 HLVLRLRGGI   77 (116)
Q Consensus        68 ~v~~~~~gg~   77 (116)
                      ||+++.....
T Consensus        84 Hlvvrp~~~~   93 (111)
T PF13881_consen   84 HLVVRPNAPE   93 (111)
T ss_dssp             EEEE-SSSSS
T ss_pred             EEEecCCCCC
Confidence            7788755443

>PLN02560 enoyl-CoA reductase

Probab=99.21  E-value=7.3e-11  Score=87.81  Aligned_cols=69  Identities=32%  Similarity=0.560  Sum_probs=61.1

Q ss_pred             CEEEEEcCCCCEE---EEEecCCCCHHHHHHHHHHhhCC-CCCceEEEEC---C----EEcCCCCccccCCCCCCCEEEE
Q 033570            1 MQIFVKTLTGKTI---TLEVESSDTIDNVKAKIQDKEGI-PPDQQRLIFA---G----KQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         1 m~v~Vk~~~g~~~---~i~v~~~~TV~~LK~~I~~~~~i-~~~~q~L~~~---g----~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      |+|+|+..+|+..   .+++++++||++||++|+++.++ ++++|+|.+.   |    ..|+|+.+|+++|+++|++|++
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            8999998888886   69999999999999999999986 8999999973   3    3788999999999999998644

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=99.17  E-value=2.1e-10  Score=73.20  Aligned_cols=78  Identities=29%  Similarity=0.431  Sum_probs=66.1

Q ss_pred             CEEEEEcCCCCE-EEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCC-------CCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKT-ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-------QKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~-~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi-------~~g~~I~v~~~   72 (116)
                      |.++++....++ +.+++.++.||.+||++|+..+..||++|+|+..+.+|+|+++|++||+       .+..+|-+.++
T Consensus         1 MdvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r   80 (119)
T cd01788           1 MDVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR   80 (119)
T ss_pred             CceEEEEEecceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence            566666665444 5679999999999999999999999999999977788999999999999       56888888888


Q ss_pred             cCCCCC
Q 033570           73 LRGGII   78 (116)
Q Consensus        73 ~~gg~~   78 (116)
                      ...|.+
T Consensus        81 ~~d~~f   86 (119)
T cd01788          81 SSDDTF   86 (119)
T ss_pred             cCCCCc
Confidence            766653

Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.

>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]

Probab=99.11  E-value=1.9e-10  Score=94.98  Aligned_cols=74  Identities=34%  Similarity=0.579  Sum_probs=69.9

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .|.||+++.++..|.|...+||.+||.+|+++.+|+.+.|+|+|+|++|.|++++.+|+| +|-+||++-|.+.+
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverppp~   77 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERPPPQ   77 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeeccCCCC
Confidence            478999999999999999999999999999999999999999999999999999999999 99999999885544

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=99.08  E-value=6.4e-10  Score=66.97  Aligned_cols=69  Identities=26%  Similarity=0.327  Sum_probs=54.8

Q ss_pred             CEEEEEcCC-CCEEEEEe-cCCCCHHHHHHHHHHhhC-CCCCceEEE--ECCEEcCCCCccccCCCCCCCEEEE
Q 033570            1 MQIFVKTLT-GKTITLEV-ESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         1 m~v~Vk~~~-g~~~~i~v-~~~~TV~~LK~~I~~~~~-i~~~~q~L~--~~g~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      ++|.++..+ .....+++ +++.||.+||..|++..+ +++++|+|.  +.|+.|.|+.+|.++|+.+|++|++
T Consensus         1 ~~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801           1 LEILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CeeeccccCcCceeecccCCCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            356666655 33322444 578999999999999986 578999886  7899999999999999999999876

Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.

>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=99.03  E-value=5.6e-09  Score=60.58  Aligned_cols=72  Identities=83%  Similarity=1.130  Sum_probs=67.2

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      +.+....|+...+.+.+..++..+|.+|+...++++..|++.+.|+.|.|+.+|.+|+|..++++++..+..
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~   73 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLR   73 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecC
Confidence            456677899999999999999999999999999999999999999999999999999999999999988765

>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway

Probab=98.94  E-value=2e-09  Score=65.43  Aligned_cols=69  Identities=29%  Similarity=0.434  Sum_probs=43.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC---EEc--CCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQL--EDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g---~~L--~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |-|.|++.+| .+.+++++++|+.+|+++|++.+++|...+.|..+.   ..+  .+..+|+++||+.|+.|++.
T Consensus         5 milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen    5 MILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             -EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             EEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            5688888776 578899999999999999999999999988886322   234  45889999999999999874

Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.

>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]

Probab=98.90  E-value=5.5e-10  Score=64.32  Aligned_cols=70  Identities=26%  Similarity=0.405  Sum_probs=64.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      +++.+.+.-|+...+.+.+++||+++|..|+.++|..++.+.|.-.+.+++|+-+|++|.|.+|..+.+.
T Consensus         2 iev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    2 IEVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             ceehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            3677788889999999999999999999999999999999999888889999999999999999887764

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.85  E-value=3.7e-08  Score=54.54  Aligned_cols=66  Identities=45%  Similarity=0.659  Sum_probs=59.7

Q ss_pred             EcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         6 k~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      +..++....+.+.++.|+.+|+..|.++++++++.+.|.++|..+.+...+.++++.+++.|++..
T Consensus         3 ~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           3 KLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             EecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            344678888999999999999999999999999999999999999998888899999999998864

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=98.82  E-value=5.7e-08  Score=65.94  Aligned_cols=109  Identities=27%  Similarity=0.376  Sum_probs=78.6

Q ss_pred             CEEEEEcCCC----CEEEEEecCCCCHHHHHHHHHHhhCCCCCce-EEEE-CCEEc--CCCCccccCCCCCC----CEEE
Q 033570            1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIF-AGKQL--EDGRTLADYNIQKE----STLH   68 (116)
Q Consensus         1 m~v~Vk~~~g----~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q-~L~~-~g~~L--~d~~tL~~~gi~~g----~~I~   68 (116)
                      |+|.|++.+|    .++.+.++++.||.+|+..|.+..+++...+ .|.+ .++.|  .++..++++.-.+.    .++.
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~~l~   80 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFITLR   80 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCceEEE
Confidence            7899999999    5788999999999999999999999988874 3443 34444  45666666654333    3688


Q ss_pred             EEEecCCCCCC--CchHHHHHHc----CCCcccccccccccccCCCcc
Q 033570           69 LVLRLRGGIIE--PSLMALARKY----NQDKMICRKSHTRTRNQFPFF  110 (116)
Q Consensus        69 v~~~~~gg~~~--~~~~~~~~~~----~~~~~~c~~~~~~~~~~~~~~  110 (116)
                      +..++.||++.  .-++.++.+.    ....-.||+.-.+ |+++++.
T Consensus        81 l~~rl~GGKGGFGs~Lr~~g~~~s~~k~~n~dscRdL~GR-Rlr~v~~  127 (162)
T PF13019_consen   81 LSLRLRGGKGGFGSQLRAAGGRMSSKKTTNFDSCRDLSGR-RLRTVNE  127 (162)
T ss_pred             EEEeccCCCccHHHHHHHHHHHhhcccCCCcccccCCCCc-ChhhhHH
Confidence            88999999854  3344444333    2223489999888 8877653

>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2

Probab=98.74  E-value=1.1e-07  Score=56.45  Aligned_cols=71  Identities=28%  Similarity=0.411  Sum_probs=62.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE---CCE--EcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGK--QLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~---~g~--~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      ++|+|+..++....+.|+|..+|..+|++|....+++ ..|+|.|   +|+  .|.+..+|++|||-+...|.++-.
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~-g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT   76 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCS-GLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLET   76 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCcc-cceEEEeecCCcccccccccccHhhhcceeccEEEEEec
Confidence            5899999999999999999999999999999999987 5999987   333  578999999999998888877644

OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.

>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]

Probab=98.74  E-value=3.6e-08  Score=76.03  Aligned_cols=74  Identities=24%  Similarity=0.429  Sum_probs=67.0

Q ss_pred             EEEEEcCCCCEEEEE-ecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            2 QIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~-v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .|.|++ .|+.+.++ ++.++|+..||.++...+|++|++|+++++|..+.|+..+..++|++|.+++++.....+
T Consensus         5 ~v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e~~   79 (473)
T KOG1872|consen    5 TVIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAEAG   79 (473)
T ss_pred             eEeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeecccccc
Confidence            367777 78888887 999999999999999999999999999999999999999999999999999998775544

>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]

Probab=98.71  E-value=2.5e-07  Score=57.81  Aligned_cols=76  Identities=17%  Similarity=0.441  Sum_probs=70.1

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      .+.|+..++....+.|.-+++...|....+++.|++...++++|+|+.+.+..|-.+++..+|+.|.++....||-
T Consensus        22 ~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q~gG~   97 (99)
T KOG1769|consen   22 NLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQTGGF   97 (99)
T ss_pred             EEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeecccCC
Confidence            5667776778889999999999999999999999999999999999999999999999999999999999888774

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=98.50  E-value=3.4e-07  Score=68.04  Aligned_cols=70  Identities=30%  Similarity=0.592  Sum_probs=60.3

Q ss_pred             CEEEEEcCC---CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLT---GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~---g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |.+.|....   ...+.+.|+.+.+|.+||+.++...|+|+++.+++|.|+.|.++.++..+.+...+.++++
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~   73 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIM   73 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceeecccccccchhhhh
Confidence            566676642   2347889999999999999999999999999999999999999999998888777777766

>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.38  E-value=9.6e-08  Score=52.66  Aligned_cols=33  Identities=67%  Similarity=0.941  Sum_probs=25.1

Q ss_pred             CCCchHHHHHHcCCCcccccccccccccCCCccccccC
Q 033570           78 IEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      +.|++...+.++|.++|+||+||.+   ++|+|  |||
T Consensus         2 iePsl~~la~K~n~~k~ICrkCyar---l~~~A--~nC   34 (52)
T PF01020_consen    2 IEPSLRALAQKYNCDKMICRKCYAR---LPPRA--TNC   34 (52)
T ss_dssp             --HHHHHHHHHHHTS-EEETTT--E---E-TTS--SS-
T ss_pred             cChHHHHHHHHHcccceecccccCc---CCCCc--cce
Confidence            4688999999999999999999999   99999  999

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 family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.

>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]

Probab=98.28  E-value=1.5e-06  Score=53.96  Aligned_cols=63  Identities=30%  Similarity=0.449  Sum_probs=51.4

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC--EEcCCCCccccCCCCC
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG--KQLEDGRTLADYNIQK   63 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g--~~L~d~~tL~~~gi~~   63 (116)
                      |.++++-...+ ++.++..++.||.+||.+++..+.-|++.|+|+...  .+|+|.++|+++|..+
T Consensus         1 ~~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~gfts   66 (110)
T KOG4495|consen    1 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGFTS   66 (110)
T ss_pred             CceeeeeeecceeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhccccc
Confidence            44555555444 466799999999999999999999999999998744  4789999999998754

>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []

Probab=98.19  E-value=5.7e-06  Score=49.88  Aligned_cols=68  Identities=24%  Similarity=0.405  Sum_probs=49.5

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC------ceEEE-ECCEEcCCCCccccCCCCCCCEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD------QQRLI-FAGKQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~------~q~L~-~~g~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      +|+|...+|+.+.+.++.+.+|.+|...|.+.++.+..      ...|. -+|..|+++.+|+++||.+|+.+.+
T Consensus         4 rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen    4 RVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            57777755688999999999999999999998876322      24555 5789999999999999999999876

Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly

Probab=98.07  E-value=2.5e-05  Score=45.57  Aligned_cols=63  Identities=19%  Similarity=0.252  Sum_probs=46.6

Q ss_pred             cCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEE
Q 033570            7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         7 ~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      ..+++.+.+.+.|++++.++-+...++++++++...|.|+++.|+-+.++.-.|+.+|+.+.+
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence            457889999999999999999999999999999999999999999999999999999998864

TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.

>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast

Probab=98.03  E-value=0.00011  Score=44.34  Aligned_cols=69  Identities=23%  Similarity=0.351  Sum_probs=58.9

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCc-eEEE--ECCEEcCC-C-CccccCCCCCCCEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--FAGKQLED-G-RTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~--~~g~~L~d-~-~tL~~~gi~~g~~I~v~   70 (116)
                      +|.|+.++|+.+.-...+++||.+|..-|......+... ..|+  |-.+.+.+ + .+|+++|+.++++|+|.
T Consensus         8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v~   81 (82)
T PF00789_consen    8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIVE   81 (82)
T ss_dssp             EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEEE
Confidence            688999999999999999999999999999988776664 7776  66777765 3 79999999999998764

The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....

>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]

Probab=97.96  E-value=1.9e-05  Score=48.58  Aligned_cols=76  Identities=17%  Similarity=0.371  Sum_probs=68.1

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      .+.|...+|..+.+.|..+++...|-...+.+.|-..+..|++|+|+.++.+++-++++..+++.|.++....||.
T Consensus        26 nLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~eQvGG~  101 (103)
T COG5227          26 NLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVTEQVGGA  101 (103)
T ss_pred             ceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchHHHHHHHHhcCc
Confidence            3556666788899999999999999999999999999999999999999999999999999999998887777764

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.84  E-value=0.00024  Score=42.75  Aligned_cols=68  Identities=22%  Similarity=0.260  Sum_probs=56.1

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcCC---CCccccCCCCCCCEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~d---~~tL~~~gi~~g~~I~v   69 (116)
                      +|.||.++|+.+......++||++|.+-|....+.......|+  |-.+.+.+   +.+|.+.|+.+.+++.|
T Consensus         6 ~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        6 RLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             EEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            6889999999999999999999999999976666666667776  56667753   57999999988888765

Present in FAF1 and Shp1p.

>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi

Probab=97.79  E-value=8.5e-05  Score=46.64  Aligned_cols=57  Identities=21%  Similarity=0.339  Sum_probs=44.0

Q ss_pred             EEEEcCC-CCEEEEEec--CCCCHHHHHHHHHHhhC--CCCCceEEEECCEEcCCCCccccC
Q 033570            3 IFVKTLT-GKTITLEVE--SSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADY   59 (116)
Q Consensus         3 v~Vk~~~-g~~~~i~v~--~~~TV~~LK~~I~~~~~--i~~~~q~L~~~g~~L~d~~tL~~~   59 (116)
                      |+|+..+ -..+.++++  .+.||..||++|.+...  ..-.+++|+|+|+.|.|+..|+.-
T Consensus         3 l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen    3 LTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             EEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhh
Confidence            5566654 234667777  78999999999999984  344478999999999998887764

They contain a characteristic GFDRL sequence motif.

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.68  E-value=0.00073  Score=40.69  Aligned_cols=67  Identities=16%  Similarity=0.324  Sum_probs=55.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcCC---CCccccCCCCCCCEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~d---~~tL~~~gi~~g~~I~v   69 (116)
                      +|.|+.++|+...-..+.++|+.++.+-|....+-. ....|+  |-.+.+.+   +.+|.+.|+.+..+++|
T Consensus         6 ~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           6 RIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            588999999999889999999999999998765433 556666  67777853   57999999999888876

SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.68  E-value=0.00054  Score=40.74  Aligned_cols=64  Identities=19%  Similarity=0.263  Sum_probs=54.9

Q ss_pred             EcCCCCEEEEEecCCCCHHHHHHHHHHhhCCC---C--CceEEEECCEEcCCCCccccCCCCCCCEEEE
Q 033570            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIP---P--DQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         6 k~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~---~--~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      +..+|.++.+.++...++..|...+.+...+.   .  ..+++.-++++|.++..|.+|+|.+|+.+.+
T Consensus        12 t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417          12 TNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             EecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            55579999999999999999999999887652   2  2467888999999999999999999999865

>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]

Probab=97.65  E-value=0.00014  Score=52.67  Aligned_cols=74  Identities=27%  Similarity=0.335  Sum_probs=54.4

Q ss_pred             CEEEEEcCCCC-E-EEEEecCCCCHHHHHHHHHHh-hCCCCCceEE----EECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGK-T-ITLEVESSDTIDNVKAKIQDK-EGIPPDQQRL----IFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~-~-~~i~v~~~~TV~~LK~~I~~~-~~i~~~~q~L----~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |.|++.+.++. . ...+.+...|+.|+++.+.++ ..+.+.++++    .-+|++|.|+++|+++|..+|.+|  .++-
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i--~vKD   78 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATI--YVKD   78 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEE--EEec
Confidence            78999988752 2 336778889999999777665 4565544433    358999999999999999999766  4554


Q ss_pred             CCC
Q 033570           74 RGG   76 (116)
Q Consensus        74 ~gg   76 (116)
                      .|.
T Consensus        79 LGp   81 (297)
T KOG1639|consen   79 LGP   81 (297)
T ss_pred             cCC
Confidence            444

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.63  E-value=0.00095  Score=39.80  Aligned_cols=66  Identities=15%  Similarity=0.265  Sum_probs=51.9

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC---CCCccccCCCCCCCEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHL   69 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~---d~~tL~~~gi~~g~~I~v   69 (116)
                      +|.|+.++|+...-....++||++|.+-|.....- .....|+  |-.+.+.   .+.+|.+.|+.+ +.+.+
T Consensus         4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~-s~~~~   74 (77)
T cd01767           4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFPRRVLTDLDYELTLQEAGLVN-EVVFQ   74 (77)
T ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCCCccCCCCCccCcHHHcCCcc-ceEEE
Confidence            58899999999999999999999999999876543 4556666  5566674   478999999994 44433

The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.

>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional

Probab=97.63  E-value=2.8e-05  Score=42.26  Aligned_cols=27  Identities=26%  Similarity=0.278  Sum_probs=24.7

Q ss_pred             HHHHHcCCCcccccccccccccCCCccccccC
Q 033570           84 ALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        84 ~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      ..+.+++.++++||+||.+   ++|.|  |||
T Consensus         5 ~~A~k~~~~k~ICrkC~AR---np~~A--~~C   31 (48)
T PRK04136          5 EEAEKRVFNKKICMRCNAR---NPWRA--TKC   31 (48)
T ss_pred             HHHHHHhhcccchhcccCC---CCccc--ccc
Confidence            4577889999999999999   99999  999

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.62  E-value=0.0008  Score=40.61  Aligned_cols=66  Identities=23%  Similarity=0.323  Sum_probs=53.0

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCC-CCCceEEE--ECCEEcCC-CCccccCCCCCCCEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI-PPDQQRLI--FAGKQLED-GRTLADYNIQKESTL   67 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i-~~~~q~L~--~~g~~L~d-~~tL~~~gi~~g~~I   67 (116)
                      +|.|+.++|+.+......++||++|.+-|....+- ......|.  |-.+.|.| +.+|.+.|+.+...+
T Consensus         6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~v~   75 (79)
T cd01770           6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLNAVIV   75 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcCcEEE
Confidence            68899999999999999999999999999987643 23456776  66777755 889999999864443

p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=97.48  E-value=0.0022  Score=39.09  Aligned_cols=68  Identities=16%  Similarity=0.334  Sum_probs=57.8

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC---CCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~---d~~tL~~~gi~~g~~I~v~   70 (116)
                      +|.|+.++|+...-....++++.+|..-+.. .|.+++..+|+  |--+.+.   .+.+|.+.|+.+..++.|-
T Consensus         7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq   79 (82)
T cd01773           7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ   79 (82)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEe
Confidence            6899999999999999999999999999988 57788888887  5566653   3579999999999998774

Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=97.40  E-value=0.0027  Score=38.39  Aligned_cols=68  Identities=21%  Similarity=0.329  Sum_probs=57.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC---CCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~---d~~tL~~~gi~~g~~I~v~   70 (116)
                      +|.|+.++|+...-....++++++|-.-|... |.++...+|+  |--+.+.   .+.+|.+.|+.+..++.|-
T Consensus         6 ~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~Ve   78 (80)
T cd01771           6 KLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-GYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLILE   78 (80)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence            68899999999988999999999999999875 7777788887  5566664   3679999999999888764

Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=97.36  E-value=0.0035  Score=38.33  Aligned_cols=68  Identities=12%  Similarity=0.177  Sum_probs=55.3

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEEC--CEEcC--------CCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLE--------DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~--g~~L~--------d~~tL~~~gi~~g~~I~v~   70 (116)
                      +|.|+.++|+...-....++||++|..-|.. .+..++...|+.+  -+.+.        .+.||.+.|+.+..++.|.
T Consensus         6 ~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~V~   83 (85)
T cd01774           6 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFVQ   83 (85)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEEe
Confidence            6889999999998899999999999999964 4556678888754  36664        3679999999988887663

Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.36  E-value=0.00062  Score=48.11  Aligned_cols=66  Identities=27%  Similarity=0.413  Sum_probs=58.4

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      .++.+.+.+...+|+.++|..+.++-++.+-.|++.++|..|.|...|.+++|..|...++-+...
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqviVl  220 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVIVL  220 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEEEec
Confidence            456688888999999999999999999999999999999999999999999999997766655443

>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]

Probab=97.12  E-value=0.0026  Score=44.95  Aligned_cols=73  Identities=15%  Similarity=0.273  Sum_probs=55.7

Q ss_pred             EEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE-ECC-----EEcC-CCCccccCCCCCCCEEEEEEec
Q 033570            2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAG-----KQLE-DGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         2 ~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~~g-----~~L~-d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      +|.|.+.... ......+++.||.+||.+++..+|.+++.+.|. |.|     ..|+ ++..|..|+..+|-.||++=..
T Consensus         3 ~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihviD~~   82 (234)
T KOG3206|consen    3 RVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVIDSN   82 (234)
T ss_pred             EEEEecccccchhhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEEecC
Confidence            4555553222 244578899999999999999999999999886 544     2454 4889999999999999987553


Q ss_pred             C
Q 033570           74 R   74 (116)
Q Consensus        74 ~   74 (116)
                      .
T Consensus        83 ~   83 (234)
T KOG3206|consen   83 A   83 (234)
T ss_pred             c
Confidence            3

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=97.09  E-value=0.0097  Score=34.92  Aligned_cols=65  Identities=14%  Similarity=0.225  Sum_probs=47.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      +|.+... +....+++++..||.+|-+.+    +++++...+..+|+.+..     +.-+++|+.|.++.-..||
T Consensus         6 ~v~vng~-~~~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii~~V~GG   70 (70)
T PRK08364          6 RVKVIGR-GIEKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALE-----DDPVKDGDYVEVIPVVSGG   70 (70)
T ss_pred             EEEEecc-ccceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCC-----CcCcCCCCEEEEEccccCC
Confidence            4445332 124667888889999988766    677777788899999864     4446679999988777765

>PRK06437 hypothetical protein; Provisional

Probab=97.09  E-value=0.01  Score=34.60  Aligned_cols=63  Identities=19%  Similarity=0.398  Sum_probs=48.0

Q ss_pred             EEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         5 Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ++-.+++...++++...||.+|-+.+    +++++..-+..+|+.+.     .+.-+++|+.|.++.-..||
T Consensus         5 ~~v~g~~~~~~~i~~~~tv~dLL~~L----gi~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~~V~GG   67 (67)
T PRK06437          5 IRVKGHINKTIEIDHELTVNDIIKDL----GLDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILEVFSGG   67 (67)
T ss_pred             EEecCCcceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECC-----CceEcCCCCEEEEEecccCC
Confidence            33334566778888889999877654    88888898899999997     44456679999988776665

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=97.06  E-value=0.009  Score=34.41  Aligned_cols=65  Identities=18%  Similarity=0.389  Sum_probs=47.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|.|   +|+.+.+  + ..|+.+|.+.+    +++++...+..+++.++ ....++.-+.+|+.|.++.-..||
T Consensus         1 m~i~~---Ng~~~~~--~-~~tl~~Ll~~l----~~~~~~vavavN~~iv~-~~~~~~~~L~dgD~Ieiv~~V~GG   65 (65)
T PRK06488          1 MKLFV---NGETLQT--E-ATTLALLLAEL----DYEGNWLATAVNGELVH-KEARAQFVLHEGDRIEILSPMQGG   65 (65)
T ss_pred             CEEEE---CCeEEEc--C-cCcHHHHHHHc----CCCCCeEEEEECCEEcC-HHHcCccccCCCCEEEEEEeccCC
Confidence            56666   5566665  3 45899888765    66666677889999886 334556667889999999887776

>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain

Probab=96.93  E-value=0.0054  Score=37.67  Aligned_cols=44  Identities=14%  Similarity=0.278  Sum_probs=39.0

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC---CceEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP---DQQRLIF   45 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~---~~q~L~~   45 (116)
                      ...++.+.|+.+.+.+.+++++.+|++.|++++|+..   ....|.|
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y   48 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY   48 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE
Confidence            3567889999999999999999999999999999876   4777877

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is

>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]

Probab=96.90  E-value=0.00038  Score=52.30  Aligned_cols=59  Identities=24%  Similarity=0.408  Sum_probs=46.8

Q ss_pred             EEEEEcCCCCE--EEEEecCCCCHHHHHHHHHHhhCC-C-CCceEEEECCEEcCCCCccccCC
Q 033570            2 QIFVKTLTGKT--ITLEVESSDTIDNVKAKIQDKEGI-P-PDQQRLIFAGKQLEDGRTLADYN   60 (116)
Q Consensus         2 ~v~Vk~~~g~~--~~i~v~~~~TV~~LK~~I~~~~~i-~-~~~q~L~~~g~~L~d~~tL~~~g   60 (116)
                      .+.||+.+.+.  ..|+.+..+||++||..++..+-- | ..+|||+|.|+.|.|+..|.+.-
T Consensus        11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~l   73 (391)
T KOG4583|consen   11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDWL   73 (391)
T ss_pred             EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHHH
Confidence            56788877544  566777789999999999988742 2 35899999999999998888763

>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A

Probab=96.84  E-value=0.012  Score=36.25  Aligned_cols=68  Identities=19%  Similarity=0.242  Sum_probs=47.0

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--E--CCE-EcC-CCCccccCCCCCCCEEEEEEecCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--F--AGK-QLE-DGRTLADYNIQKESTLHLVLRLRGGIIE   79 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~--~g~-~L~-d~~tL~~~gi~~g~~I~v~~~~~gg~~~   79 (116)
                      ..+....+..+||+.+...+.+.+.+ ..+.||.  |  ++. .|. .+.||.+.||.+|.+|.+-.+...|.++
T Consensus        14 ~~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn~DGtWP   87 (88)
T PF14836_consen   14 SVLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERNEDGTWP   87 (88)
T ss_dssp             EEEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--TTS--T
T ss_pred             cHhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeeccCCCCC
Confidence            35667889999999999999999999 5666765  3  222 464 4789999999999999999998888654

>PF15044 CLU_N: Mitochondrial function, CLU-N-term

Probab=96.75  E-value=0.0036  Score=37.52  Aligned_cols=57  Identities=23%  Similarity=0.312  Sum_probs=47.4

Q ss_pred             ecCCCCHHHHHHHHHHhhC-CCCCceEEEECCEEcCCCCccccC-CCCCCCEEEEEEec
Q 033570           17 VESSDTIDNVKAKIQDKEG-IPPDQQRLIFAGKQLEDGRTLADY-NIQKESTLHLVLRL   73 (116)
Q Consensus        17 v~~~~TV~~LK~~I~~~~~-i~~~~q~L~~~g~~L~d~~tL~~~-gi~~g~~I~v~~~~   73 (116)
                      |+++++|.++++.+..... ..-....|.++|..|++...|+++ |+++|..+.++-.+
T Consensus         1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve~p   59 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVEEP   59 (76)
T ss_pred             CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEecC
Confidence            5688999999999998754 355678899999999998888888 58889999988653

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=96.62  E-value=0.021  Score=33.78  Aligned_cols=60  Identities=13%  Similarity=0.228  Sum_probs=46.0

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCC----CCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGI----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i----~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ...++++...||.+|.+.+...++-    ......+..+|+....     +.-+++|+.|.++....||
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~-----~~~l~~gD~v~i~ppv~GG   80 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRL-----DTPLKDGDEVAIIPPVSGG   80 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCC-----CcccCCCCEEEEeCCCCCC
Confidence            3567887789999999999987642    2345677789998873     3457789999999887776

MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.

>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain

Probab=96.44  E-value=0.038  Score=32.69  Aligned_cols=58  Identities=26%  Similarity=0.350  Sum_probs=46.0

Q ss_pred             EEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCC-CCceEEEE----CCE--EcCCCCccccCCCC
Q 033570            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLIF----AGK--QLEDGRTLADYNIQ   62 (116)
Q Consensus         5 Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~-~~~q~L~~----~g~--~L~d~~tL~~~gi~   62 (116)
                      |+.++|....+.+++++|+.+|-+.|.++.++. .+..-|.+    +|.  -|+.+++|.++...
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~   65 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKK   65 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBT
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCC
Confidence            567889999999999999999999999999984 44557777    222  36778889988776

The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=96.43  E-value=0.024  Score=34.01  Aligned_cols=71  Identities=18%  Similarity=0.275  Sum_probs=48.2

Q ss_pred             CEEEEEcCC------C-CEEEEEecCCCCHHHHHHHHHHhhC-CCC--CceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-IPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~------g-~~~~i~v~~~~TV~~LK~~I~~~~~-i~~--~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |+|.|+...      | ....++++...|+.+|.+.+..... +..  ....+..+|+...++.     -+++|+.|.+.
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~~~~-----~l~dgDeVai~   76 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTTESA-----ALKDGDELAII   76 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcCCCc-----CcCCCCEEEEe
Confidence            556665432      3 4467788888999999999977651 111  1234667888875443     45679999998


Q ss_pred             EecCCC
Q 033570           71 LRLRGG   76 (116)
Q Consensus        71 ~~~~gg   76 (116)
                      ....||
T Consensus        77 PpvsGG   82 (82)
T PLN02799         77 PPISGG   82 (82)
T ss_pred             CCCCCC
Confidence            887776

>PF12754 Blt1: Cell-cycle control medial ring component; InterPro: IPR024737 During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localise with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localise to similar interphase structures

Probab=96.33  E-value=0.00096  Score=49.68  Aligned_cols=76  Identities=18%  Similarity=0.428  Sum_probs=0.0

Q ss_pred             EEEEEcCCCCEEEEEec---C--CCCHHHHHHHHHH----------hhCCCCCceE-----EEECCEEcCCCCccccCCC
Q 033570            2 QIFVKTLTGKTITLEVE---S--SDTIDNVKAKIQD----------KEGIPPDQQR-----LIFAGKQLEDGRTLADYNI   61 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~---~--~~TV~~LK~~I~~----------~~~i~~~~q~-----L~~~g~~L~d~~tL~~~gi   61 (116)
                      .|++|+..+..+.+.++   +  +.||.+||..+++          ..++|.+.++     |+|+.+++.|.++|.+..-
T Consensus        80 tV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kkPv~~~ktl~e~l~  159 (309)
T PF12754_consen   80 TVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKKPVGDSKTLAEVLA  159 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCccCCCcCcHHHHHh
Confidence            45666665555544322   3  5789999999999          8899999999     9999999989889888754


Q ss_pred             C-------CCCEEEEEEecCCCC
Q 033570           62 Q-------KESTLHLVLRLRGGI   77 (116)
Q Consensus        62 ~-------~g~~I~v~~~~~gg~   77 (116)
                      .       .+..+.+.+...||.
T Consensus       160 ~~~~~l~~~~~~vE~gvMVlGGa  182 (309)
T PF12754_consen  160 DSESRLLSGGKEVEFGVMVLGGA  182 (309)
T ss_dssp             -----------------------
T ss_pred             cccchhccCCceEEEEEEEECCc
Confidence            3       466777777777775

Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase[].; PDB: 2LO0_A.

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=96.26  E-value=0.047  Score=31.46  Aligned_cols=65  Identities=20%  Similarity=0.329  Sum_probs=46.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|   +|+.+  ++++..|+.+|-+.    .++++...-+.+++..+..+. ...+ +++|+.|.++.-..||
T Consensus         1 m~i~v---NG~~~--~~~~~~tl~~ll~~----l~~~~~~vav~~N~~iv~r~~-~~~~-L~~gD~ieIv~~VgGG   65 (65)
T PRK05863          1 MIVVV---NEEQV--EVDEQTTVAALLDS----LGFPEKGIAVAVDWSVLPRSD-WATK-LRDGARLEVVTAVQGG   65 (65)
T ss_pred             CEEEE---CCEEE--EcCCCCcHHHHHHH----cCCCCCcEEEEECCcCcChhH-hhhh-cCCCCEEEEEeeccCC
Confidence            56666   45544  44567788877655    488888999999999875421 2235 8999999998877776

>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis

Probab=96.26  E-value=0.028  Score=34.05  Aligned_cols=38  Identities=18%  Similarity=0.344  Sum_probs=35.0

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEE
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ   49 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~   49 (116)
                      .+.|.++++.+..+|.++|.++.++|++.++|.|....
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~   49 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEA   49 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCC
Confidence            78899999999999999999999999999999996553

PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain

>PRK08053 sulfur carrier protein ThiS; Provisional

Probab=96.25  E-value=0.093  Score=30.26  Aligned_cols=66  Identities=15%  Similarity=0.256  Sum_probs=46.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|   +|+.+  +++...|+.+|.+.+    +.+.....+-.+++.++.+ ..++.-+++|+.|.++.-..||
T Consensus         1 m~i~v---Ng~~~--~~~~~~tl~~ll~~l----~~~~~~vaVavN~~iv~r~-~w~~~~L~~gD~Ieii~~v~GG   66 (66)
T PRK08053          1 MQILF---NDQPM--QCAAGQTVHELLEQL----NQLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQVIAGG   66 (66)
T ss_pred             CEEEE---CCeEE--EcCCCCCHHHHHHHc----CCCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEEEccCC
Confidence            56666   44544  456677899888654    5555678888999998532 3444457889999998887776

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=96.09  E-value=0.097  Score=29.95  Aligned_cols=66  Identities=20%  Similarity=0.379  Sum_probs=46.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|   +|+.  ++++...|+.+|-..    .++++...-+.++|..+.-+ ...+.-+++|+.|.++.-..||
T Consensus         1 m~i~v---NG~~--~~~~~~~tl~~lL~~----l~~~~~~vav~vNg~iv~r~-~~~~~~l~~gD~vei~~~vgGG   66 (66)
T PRK05659          1 MNIQL---NGEP--RELPDGESVAALLAR----EGLAGRRVAVEVNGEIVPRS-QHASTALREGDVVEIVHALGGG   66 (66)
T ss_pred             CEEEE---CCeE--EEcCCCCCHHHHHHh----cCCCCCeEEEEECCeEeCHH-HcCcccCCCCCEEEEEEEecCC
Confidence            55555   4554  456667888887654    47888888888999888633 3344446789999998877765

>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats)

Probab=96.06  E-value=0.044  Score=33.50  Aligned_cols=60  Identities=20%  Similarity=0.333  Sum_probs=42.7

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +...++=..+++.||..++.+.++..+...+...+..|.++++|-+.+++-...+.+.+.
T Consensus         5 I~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQ   64 (88)
T PF11620_consen    5 IMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQ   64 (88)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEE
T ss_pred             EEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEEE
Confidence            344566677999999999999999999999999998899999999999987777777665

This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.

>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function

Probab=96.04  E-value=0.055  Score=31.43  Aligned_cols=65  Identities=23%  Similarity=0.473  Sum_probs=52.0

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhC---CCCCceEEE-ECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~---i~~~~q~L~-~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      +|+...++..++..+.-..++--+..+   -|++...|. -+|..|+-++.+++||+.++-++++.++.
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLKA   72 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLKA   72 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEeec
Confidence            678888888888887766665555543   577777776 57889998999999999999999988874

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal

Probab=95.93  E-value=0.11  Score=30.95  Aligned_cols=60  Identities=17%  Similarity=0.294  Sum_probs=45.2

Q ss_pred             EEEEEecCC-CCHHHHHHHHHHhhC-C--CCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           12 TITLEVESS-DTIDNVKAKIQDKEG-I--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        12 ~~~i~v~~~-~TV~~LK~~I~~~~~-i--~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ...++++.+ .||.+|++.+.+.+. +  ......+..+++...+     +.-+++|+.|.+.....||
T Consensus        17 ~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~PpvsGG   80 (80)
T TIGR01682        17 EETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFIPPVSGG   80 (80)
T ss_pred             eEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCC-----CcCcCCCCEEEEeCCCCCC
Confidence            356788876 899999999998874 1  1234567789998775     3456779999999887776

The C-terminal Gly-Gly of this model is critical to function.

>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer

Probab=95.86  E-value=0.058  Score=31.53  Aligned_cols=63  Identities=14%  Similarity=0.249  Sum_probs=49.8

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCC--CCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i--~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ...+.+....||.+|.+.+...+.-  ......+..+|+...+  ...+.-+++|+.|.++....||
T Consensus        13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~--~~~~~~l~~gD~V~i~ppvsGG   77 (77)
T PF02597_consen   13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD--DGLDTPLKDGDEVAILPPVSGG   77 (77)
T ss_dssp             EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEEESTSTS
T ss_pred             CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEECCCCCC
Confidence            5667888899999999999888731  2367788899999977  3555556789999998887776

ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=95.86  E-value=0.051  Score=30.81  Aligned_cols=56  Identities=18%  Similarity=0.303  Sum_probs=40.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|.|..     -.+++..+.|+.+||..+....      --++++|-+..++..|.+     |+.|++..|
T Consensus         1 M~I~vN~-----k~~~~~~~~tl~~lr~~~k~~~------DI~I~NGF~~~~d~~L~e-----~D~v~~Ikk   56 (57)
T PF14453_consen    1 MKIKVNE-----KEIETEENTTLFELRKESKPDA------DIVILNGFPTKEDIELKE-----GDEVFLIKK   56 (57)
T ss_pred             CEEEECC-----EEEEcCCCcCHHHHHHhhCCCC------CEEEEcCcccCCccccCC-----CCEEEEEeC
Confidence            5666633     3567888889999999875432      246899999988877765     888877643

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=95.79  E-value=0.079  Score=30.38  Aligned_cols=58  Identities=21%  Similarity=0.390  Sum_probs=43.4

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .++++...||.+|.+.+    +++++.+.+..+|+.+..+ ...+.-+++|+.|.+..-..||
T Consensus         8 ~~~~~~~~tv~~ll~~l----~~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii~~v~GG   65 (65)
T cd00565           8 PREVEEGATLAELLEEL----GLDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIVTAVGGG   65 (65)
T ss_pred             EEEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEEEeccCC
Confidence            34556678999888776    5777888888999988543 3334457789999999887776

ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.

>PRK07696 sulfur carrier protein ThiS; Provisional

Probab=95.72  E-value=0.16  Score=29.46  Aligned_cols=66  Identities=18%  Similarity=0.255  Sum_probs=46.5

Q ss_pred             CEEEEEcCCCCEEEEEecCC-CCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~-~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|   +|+.+  +++.. .||.+|-+.    .++++...-+-++|..++.+ ...+.-+++|+.|.++.-..||
T Consensus         1 m~I~v---NG~~~--~~~~~~~tv~~lL~~----l~~~~~~vav~vN~~iv~r~-~w~~~~L~~gD~iEIv~~VgGG   67 (67)
T PRK07696          1 MNLKI---NGNQI--EVPESVKTVAELLTH----LELDNKIVVVERNKDILQKD-DHTDTSVFDGDQIEIVTFVGGG   67 (67)
T ss_pred             CEEEE---CCEEE--EcCCCcccHHHHHHH----cCCCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEEEecCC
Confidence            55665   55544  44444 578776653    47788888888999998543 4555567889999998877765

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)

Probab=95.66  E-value=0.092  Score=31.85  Aligned_cols=47  Identities=11%  Similarity=0.140  Sum_probs=37.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC-CceEEEECCE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGK   48 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~-~~q~L~~~g~   48 (116)
                      |+|.+.- +|..+.+.++++++..+|++.|++++++.. ..+.|.|...
T Consensus         1 ~~vK~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dd   48 (82)
T cd06407           1 VRVKATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDD   48 (82)
T ss_pred             CEEEEEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECC
Confidence            3444443 667889999999999999999999999865 6778888544

The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte

>PRK06083 sulfur carrier protein ThiS; Provisional

Probab=95.65  E-value=0.13  Score=31.44  Aligned_cols=57  Identities=12%  Similarity=0.242  Sum_probs=42.9

Q ss_pred             EEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .+++...||.+|-+.    .++++...-+-++|..+.- ...++.-+++|+.|.++--..||
T Consensus        28 ~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~iVpr-~~w~~t~L~egD~IEIv~~VgGG   84 (84)
T PRK06083         28 IQVDISSSLAQIIAQ----LSLPELGCVFAINNQVVPR-SEWQSTVLSSGDAISLFQAIAGG   84 (84)
T ss_pred             EEcCCCCcHHHHHHH----cCCCCceEEEEECCEEeCH-HHcCcccCCCCCEEEEEEEecCC
Confidence            344566788877665    3788888888899999843 35666678889999998877776

>PRK07440 hypothetical protein; Provisional

Probab=95.65  E-value=0.15  Score=29.85  Aligned_cols=61  Identities=20%  Similarity=0.334  Sum_probs=44.7

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      +|+.  +++....||.+|-+.    .++++...-+-++|+.+.-+ ...+.-+++|+.|.++.-..||
T Consensus        10 NG~~--~~~~~~~tl~~lL~~----l~~~~~~vav~~N~~iv~r~-~w~~~~L~~gD~IEIv~~v~GG   70 (70)
T PRK07440         10 NGET--RTCSSGTSLPDLLQQ----LGFNPRLVAVEYNGEILHRQ-FWEQTQVQPGDRLEIVTIVGGG   70 (70)
T ss_pred             CCEE--EEcCCCCCHHHHHHH----cCCCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEEEecCC
Confidence            5554  556677888887653    47788888899999998532 4455557789999998877776

>TIGR01683 thiS thiamine biosynthesis protein ThiS

Probab=95.46  E-value=0.14  Score=29.21  Aligned_cols=61  Identities=20%  Similarity=0.391  Sum_probs=44.0

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      +|+.  ++++...|+.+|.+.+    +++++...+..+|+.+..+ ...++-+++|+.|.++.-..||
T Consensus         4 Ng~~--~~~~~~~tv~~ll~~l----~~~~~~v~v~vN~~iv~~~-~~~~~~L~~gD~veii~~V~GG   64 (64)
T TIGR01683         4 NGEP--VEVEDGLTLAALLESL----GLDPRRVAVAVNGEIVPRS-EWDDTILKEGDRIEIVTFVGGG   64 (64)
T ss_pred             CCeE--EEcCCCCcHHHHHHHc----CCCCCeEEEEECCEEcCHH-HcCceecCCCCEEEEEEeccCC
Confidence            4444  4456677899888765    5667788888999988432 3344557789999999887776

This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=95.43  E-value=0.18  Score=30.50  Aligned_cols=62  Identities=13%  Similarity=0.286  Sum_probs=45.0

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhCC------C-----CCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEGI------P-----PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~i------~-----~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ....++++ ..||.+|.+.+.+.+.-      .     ...+.+..+|+....+..   ..+++|+.|.+.....||
T Consensus        16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~PpvsGG   88 (88)
T TIGR01687        16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIFPPVSGG   88 (88)
T ss_pred             ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEeCCCcCC
Confidence            34567776 88999999999887641      1     123667789998765432   557889999999888776

Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.

>PRK06944 sulfur carrier protein ThiS; Provisional

Probab=95.38  E-value=0.24  Score=28.15  Aligned_cols=65  Identities=22%  Similarity=0.283  Sum_probs=43.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|   +|+  .+++++..|+.+|.+.+    +++ ....+.++|.....+ ...+.-+++|+.|.++....||
T Consensus         1 m~i~v---Ng~--~~~~~~~~tl~~ll~~l----~~~-~~~~v~vN~~~v~~~-~~~~~~L~~gD~vei~~~v~GG   65 (65)
T PRK06944          1 MDIQL---NQQ--TLSLPDGATVADALAAY----GAR-PPFAVAVNGDFVART-QHAARALAAGDRLDLVQPVAGG   65 (65)
T ss_pred             CEEEE---CCE--EEECCCCCcHHHHHHhh----CCC-CCeEEEECCEEcCch-hcccccCCCCCEEEEEeeccCC
Confidence            55555   444  34566778999888766    333 346777899987532 2333346789999999887776

>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]

Probab=95.31  E-value=0.032  Score=42.51  Aligned_cols=72  Identities=21%  Similarity=0.320  Sum_probs=60.2

Q ss_pred             CEEEEEcC--CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCC--CCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED--GRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~--~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d--~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.++|...  ....+.+++..+..+..|+..++...|++....-++|+++++.+  +..+.++|+++++.+.+-.+
T Consensus         1 M~~tvs~~l~~~~~~~i~v~~dg~L~nl~aL~~~d~g~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~lr~k   76 (380)
T KOG0012|consen    1 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTGIVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLALRCK   76 (380)
T ss_pred             CeEEEEEEecceeeeccccccccchhhHHHHHHHHhCcccchhhcccCCCccccchhhhhhhcccccceeEeccCC
Confidence            45555444  55668899999999999999999999999999999999999875  57899999999998866554

>smart00666 PB1 PB1 domain

Probab=95.12  E-value=0.16  Score=30.10  Aligned_cols=45  Identities=16%  Similarity=0.336  Sum_probs=37.4

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK   48 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~   48 (116)
                      |.++. ++....+.++++.|..+|+.+|.+.++.+.....|.|...
T Consensus         4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~De   48 (81)
T smart00666        4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDE   48 (81)
T ss_pred             EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECC
Confidence            44444 5677889999999999999999999998877888888643

Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.

>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]

Probab=95.05  E-value=0.0076  Score=32.88  Aligned_cols=27  Identities=37%  Similarity=0.490  Sum_probs=22.2

Q ss_pred             HHHHHcCCCcccccccccccccCCCccccccC
Q 033570           84 ALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        84 ~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      ..+.+....+.+|++||.+   +++.|  +.|
T Consensus         5 ~~a~~r~~~kkIC~rC~Ar---np~~A--~kC   31 (50)
T COG1552           5 AEAEKRLFNKKICRRCYAR---NPPRA--TKC   31 (50)
T ss_pred             HHHHHHHhhHHHHHHhcCC---CCcch--hHH
Confidence            3455667778899999999   99999  887

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=94.63  E-value=0.31  Score=38.50  Aligned_cols=71  Identities=14%  Similarity=0.162  Sum_probs=56.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCC------CCceEEE-ECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP------PDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~------~~~q~L~-~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      +|+|...+ +..++-++.+.+|.+|--.|-+..+-.      .....|. .+|.+|+.+.+|.+.||.||+.+++....
T Consensus         4 RVtV~~~~-~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p~~   81 (452)
T TIGR02958         4 RVTVLAGR-RAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVPAS   81 (452)
T ss_pred             EEEEeeCC-eeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEeeCC
Confidence            57777644 558888999999999999998887641      2234444 57889999999999999999999998753

Members of this family are the 12-transmembrane domain protein snm4, where snm stands for secretion in mycocbacteria. This system acts on Mycobacterium tuberculosis related pair of virulence factors ESAT-6 and CFP-10 and on other homologs. The system is conserved in many Actinobacteria, including the non-pathogenic Mycobacterium smegmatis.

>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional

Probab=94.27  E-value=0.41  Score=36.26  Aligned_cols=69  Identities=19%  Similarity=0.233  Sum_probs=51.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~   79 (116)
                      |+|+|   +|+.  +++....||.+|-+.    .+++++.+-+.+||+.+.- ....+.-+++|+.|.++.-..||.+.
T Consensus         1 M~I~V---NGk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNgeIVpr-~~w~~t~LkeGD~IEII~~VgGGs~~   69 (326)
T PRK11840          1 MRIRL---NGEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLEIVPR-SEYGQVALEEGDELEIVHFVGGGSDL   69 (326)
T ss_pred             CEEEE---CCEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCEECCH-HHcCccccCCCCEEEEEEEecCCCCC
Confidence            56666   4454  556677888887755    4888889999999999853 34556668889999999999999753

>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]

Probab=94.17  E-value=0.63  Score=27.23  Aligned_cols=58  Identities=19%  Similarity=0.413  Sum_probs=43.4

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .++++...|+.+|-..+    +++++..-+.++|..+..+ ...+.-+++|+.|.++--..||
T Consensus        11 ~~e~~~~~tv~dLL~~l----~~~~~~vav~vNg~iVpr~-~~~~~~l~~gD~ievv~~v~GG   68 (68)
T COG2104          11 EVEIAEGTTVADLLAQL----GLNPEGVAVAVNGEIVPRS-QWADTILKEGDRIEVVRVVGGG   68 (68)
T ss_pred             EEEcCCCCcHHHHHHHh----CCCCceEEEEECCEEccch-hhhhccccCCCEEEEEEeecCC
Confidence            45666668999887654    8888888899999998643 3455556778999988776665

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA

Probab=94.02  E-value=0.5  Score=28.98  Aligned_cols=53  Identities=19%  Similarity=0.282  Sum_probs=39.8

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCcccc
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD   58 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~   58 (116)
                      +|.+.. .|....+.++++.+..+|..+|.+++++. ..+++.|...  .|--++++
T Consensus         4 kVKv~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE--GD~iti~s   56 (86)
T cd06408           4 RVKVHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD--GDMITMGD   56 (86)
T ss_pred             EEEEEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC--CCCccccC
Confidence            344443 56788899999999999999999999995 5777777665  44444443

NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is

>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein

Probab=93.74  E-value=0.42  Score=28.80  Aligned_cols=36  Identities=11%  Similarity=0.250  Sum_probs=32.7

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g   47 (116)
                      ++.+.+++..+..+|..+|++++..+++..+|.|..
T Consensus         8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~   43 (78)
T cd06411           8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRA   43 (78)
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecC
Confidence            467899999999999999999999999999999853

p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo

>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62

Probab=93.56  E-value=0.33  Score=29.45  Aligned_cols=35  Identities=17%  Similarity=0.318  Sum_probs=30.1

Q ss_pred             CCCEEEEEecC--CCCHHHHHHHHHHhhCCCCCceEEEE
Q 033570            9 TGKTITLEVES--SDTIDNVKAKIQDKEGIPPDQQRLIF   45 (116)
Q Consensus         9 ~g~~~~i~v~~--~~TV~~LK~~I~~~~~i~~~~q~L~~   45 (116)
                      +|....+.+++  +++..+|++.|+..++++  .+.|.|
T Consensus         8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKY   44 (81)
T cd06396           8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKY   44 (81)
T ss_pred             CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEE
Confidence            67788899988  789999999999999998  666655

A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.

>smart00295 B41 Band 4

Probab=93.27  E-value=1.6  Score=29.82  Aligned_cols=72  Identities=28%  Similarity=0.373  Sum_probs=51.3

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEEC---C---EEcCCCCccccCCCC-CCCEEEEEEec
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFA---G---KQLEDGRTLADYNIQ-KESTLHLVLRL   73 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~~---g---~~L~d~~tL~~~gi~-~g~~I~v~~~~   73 (116)
                      .+.|..++|....+.+++.+|+.++.+.++.+.|++.. ..-|.+-   +   .-++...+|.+.... ....+++..+.
T Consensus         5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~fr~r~   84 (207)
T smart00295        5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLYFRVKF   84 (207)
T ss_pred             EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEEEEEEE
Confidence            57788889999999999999999999999999998532 3344431   1   235556677776654 34456665553

1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.

>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity

Probab=93.18  E-value=0.56  Score=27.52  Aligned_cols=46  Identities=22%  Similarity=0.337  Sum_probs=35.8

Q ss_pred             EEEEEcCCCCEEEEEec-CCCCHHHHHHHHHHhhCCCCCceEEEECCE
Q 033570            2 QIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGK   48 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~-~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~   48 (116)
                      .|.++. +|....+.++ .+.|..+|+.+|.+.++.+.....+.|...
T Consensus         2 ~vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~   48 (81)
T cd05992           2 RVKVKY-GGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDE   48 (81)
T ss_pred             cEEEEe-cCCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCC
Confidence            344554 4567888888 899999999999999998766777777543

A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.

>PRK11130 moaD molybdopterin synthase small subunit; Provisional

Probab=92.68  E-value=1.3  Score=26.38  Aligned_cols=57  Identities=11%  Similarity=0.209  Sum_probs=37.9

Q ss_pred             EEecC-CCCHHHHHHHHHHhhC-----CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           15 LEVES-SDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        15 i~v~~-~~TV~~LK~~I~~~~~-----i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      +++++ ..||.+|++.+.+++.     ......++..++....++.     -+++|+.|.+.....||
T Consensus        19 ~~v~~~~~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~~~~~~~-----~l~dgDeVai~PPVsGG   81 (81)
T PRK11130         19 LELAADFPTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLVSFDH-----PLTDGDEVAFFPPVTGG   81 (81)
T ss_pred             EEecCCCCCHHHHHHHHHHhCccHHhhhcCCCEEEEECCEEcCCCC-----CCCCCCEEEEeCCCCCC
Confidence            44443 4799999999988762     1223345556776543333     46789999998887776

>smart00455 RBD Raf-like Ras-binding domain

Probab=92.59  E-value=0.99  Score=26.41  Aligned_cols=45  Identities=20%  Similarity=0.279  Sum_probs=39.7

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g   47 (116)
                      ..|--++|+...+.+.|..|+.++-..+-++.|+.++...+...|
T Consensus         2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g   46 (70)
T smart00455        2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRG   46 (70)
T ss_pred             eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence            346678999999999999999999999999999999988887744

>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins

Probab=92.59  E-value=0.65  Score=27.46  Aligned_cols=44  Identities=20%  Similarity=0.397  Sum_probs=34.9

Q ss_pred             EEEEcCCCCEEE-EEecCCCCHHHHHHHHHHhhCCCCCceEEEECC
Q 033570            3 IFVKTLTGKTIT-LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (116)
Q Consensus         3 v~Vk~~~g~~~~-i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g   47 (116)
                      |.+.. ++.... +.+..+.+..+|+..|++.++.+....+|.|..
T Consensus         4 vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D   48 (84)
T PF00564_consen    4 VKVRY-GGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKD   48 (84)
T ss_dssp             EEEEE-TTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEE
T ss_pred             EEEEE-CCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeC
Confidence            33433 344555 899999999999999999999988888999843

The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....

>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases

Probab=92.33  E-value=0.8  Score=27.07  Aligned_cols=44  Identities=20%  Similarity=0.272  Sum_probs=38.3

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEEC
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~   46 (116)
                      +.|..++|+...+.+.|.+|+.++-..+.++.|+.++..-+...
T Consensus         2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~   45 (72)
T cd01760           2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLL   45 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEe
Confidence            45777899999999999999999999999999998887766544

The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.

>PTZ00380 microtubule-associated protein (MAP); Provisional

Probab=91.69  E-value=0.23  Score=32.34  Aligned_cols=58  Identities=17%  Similarity=0.269  Sum_probs=42.9

Q ss_pred             EEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCC---CCCCEEEEEEe
Q 033570           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI---QKESTLHLVLR   72 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi---~~g~~I~v~~~   72 (116)
                      +-|+.+.||+++...|..+.+++++.+-|..++.+...+.+++++--   .++.-+++...
T Consensus        45 llVP~d~tV~qF~~iIRkrl~l~~~k~flfVnn~lp~~s~~mg~lYe~~KDeDGFLYi~Ys  105 (121)
T PTZ00380         45 LALPRDATVAELEAAVRQALGTSAKKVTLAIEGSTPAVTATVGDIADACKRDDGFLYVSVR  105 (121)
T ss_pred             EEcCCCCcHHHHHHHHHHHcCCChhHEEEEECCccCCccchHHHHHHHhcCCCCeEEEEEc
Confidence            36999999999999999999999888655567766666777776521   23445666554

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=91.52  E-value=1.8  Score=34.02  Aligned_cols=70  Identities=21%  Similarity=0.261  Sum_probs=54.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhC--CCCCceEEEE----CCEE--cCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIF----AGKQ--LEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~--i~~~~q~L~~----~g~~--L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |-+.+++..|. ..+++.++++.+.|-.+|-.-+.  ..|+.+.+.-    +|..  +..++++.++|++.|.++++-.
T Consensus         1 Mi~rfRsk~G~-~Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~y   78 (571)
T COG5100           1 MIFRFRSKEGQ-RRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY   78 (571)
T ss_pred             CeEEEecCCCc-eeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEe
Confidence            67888887775 77899999999988888877653  4666777663    3332  3457899999999999999876

>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]

Probab=91.26  E-value=0.51  Score=36.36  Aligned_cols=65  Identities=20%  Similarity=0.311  Sum_probs=51.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCC-CCCceEEE--ECCEEcCC-CCccccCCCCCCCE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI-PPDQQRLI--FAGKQLED-GRTLADYNIQKEST   66 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i-~~~~q~L~--~~g~~L~d-~~tL~~~gi~~g~~   66 (116)
                      .|.|+..+|......++...||.+++..|...-.- +...+.|+  |--+.|.| +.||++.|+.+...
T Consensus       307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvl  375 (380)
T KOG2086|consen  307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVL  375 (380)
T ss_pred             eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcccCCcchhHHhccchhhhh
Confidence            47888899999999999999999999999987654 34455555  56777865 78999999876543

>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus

Probab=89.67  E-value=2  Score=25.50  Aligned_cols=62  Identities=15%  Similarity=0.333  Sum_probs=41.5

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhC-CCCCc--eEEE----ECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEG-IPPDQ--QRLI----FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~-i~~~~--q~L~----~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      +.|..-.+++.|+++|+..|.+++. +.|..  ..+.    -.|-.|+.+..+++. ..++++|.++++.
T Consensus         3 kKFLhlt~~~~tl~~L~~eI~~~f~kLYP~~~~~~I~~LQD~~~cDLD~d~~V~DV-f~~~~~vrvi~~n   71 (73)
T PF10407_consen    3 KKFLHLTDPNNTLSQLKEEIEERFKKLYPNEPELEILSLQDSDGCDLDPDFLVKDV-FNSNNVVRVILKN   71 (73)
T ss_pred             cEEEEEeCCCCcHHHHHHHHHHHHHHHCCCCCCceEEEeecCCCCCCCcccEeeee-eccCCEEEEEecC
Confidence            4566678899999999999999875 33332  2221    234456667777765 3467777777653

This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].

>cd06410 PB1_UP2 Uncharacterized protein 2

Probab=89.29  E-value=2.5  Score=26.45  Aligned_cols=39  Identities=18%  Similarity=0.240  Sum_probs=32.9

Q ss_pred             EcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE
Q 033570            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (116)
Q Consensus         6 k~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~   45 (116)
                      +-.+|++..+.|+.+.|..+|+.++.+.++++.. +.|.|
T Consensus        18 ~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky   56 (97)
T cd06410          18 RYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKY   56 (97)
T ss_pred             EEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEE
Confidence            4457888899999999999999999999998765 55555

The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.

>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]

Probab=89.21  E-value=1.7  Score=32.16  Aligned_cols=68  Identities=18%  Similarity=0.283  Sum_probs=54.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC--C-CCccccCCCCCCCEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--D-GRTLADYNIQKESTLHL   69 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~--d-~~tL~~~gi~~g~~I~v   69 (116)
                      +|.|+.++|+++...+.+..++.+++.-|....+.......|.  |--..+.  | .++|..+++.+.+++.+
T Consensus       212 rlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~t~fPR~tf~edD~~KpLq~L~L~Psa~lil  284 (290)
T KOG2689|consen  212 RLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHTGFPRVTFTEDDELKPLQELDLVPSAVLIL  284 (290)
T ss_pred             EEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeecCCCceecccccccccHHHhccccchheec
Confidence            5789999999999999999999999999999988766566554  3344443  2 57899999988887644

>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein

Probab=88.91  E-value=3.8  Score=25.28  Aligned_cols=40  Identities=13%  Similarity=0.305  Sum_probs=31.7

Q ss_pred             CCCEEEEEecC-----CCCHHHHHHHHHHhhCCCC-CceEEEECCE
Q 033570            9 TGKTITLEVES-----SDTIDNVKAKIQDKEGIPP-DQQRLIFAGK   48 (116)
Q Consensus         9 ~g~~~~i~v~~-----~~TV~~LK~~I~~~~~i~~-~~q~L~~~g~   48 (116)
                      +|....|.++.     +.+..+|+++|++.+++++ ....|.|...
T Consensus         8 ~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~De   53 (91)
T cd06398           8 GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDE   53 (91)
T ss_pred             CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECC
Confidence            55566677774     7999999999999999987 5778888543

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module

>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B

Probab=88.74  E-value=0.77  Score=28.04  Aligned_cols=55  Identities=16%  Similarity=0.289  Sum_probs=29.8

Q ss_pred             EecC-CCCHHHHHHHHHH-hhCCCCCce----EEEECCEE----cCCCCccccCCCCCCCEEEEE
Q 033570           16 EVES-SDTIDNVKAKIQD-KEGIPPDQQ----RLIFAGKQ----LEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus        16 ~v~~-~~TV~~LK~~I~~-~~~i~~~~q----~L~~~g~~----L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      .++. .+|+++|-+.|-+ +.|+....+    .++|....    -..+++|+++||.+|+.+.+.
T Consensus         3 ~~d~~~~TL~~lv~~Vlk~~Lg~~~P~v~~~~~ilyd~de~~~~~~l~k~L~elgi~~gs~L~v~   67 (87)
T PF14732_consen    3 KVDTKKMTLGDLVEKVLKKKLGMNEPDVSVGGTILYDSDEEEYDDNLPKKLSELGIVNGSILTVD   67 (87)
T ss_dssp             EE-TTT-BHHHHHHHCCCCCS--SSEEEEES-EEEE-SSSSSSTTCTTSBGGGGT--TT-EEEEE
T ss_pred             EEechhCcHHHHHHHHHHhccCCCCCEEEeCCCEEEcCCcchhhhcccCChhHcCCCCCCEEEEE
Confidence            3444 6899999997654 677644333    34443332    112578999999999988764

>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras

Probab=88.62  E-value=3.4  Score=24.17  Aligned_cols=56  Identities=20%  Similarity=0.241  Sum_probs=40.1

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE--CCEEcCCCCcccc
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLAD   58 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~--~g~~L~d~~tL~~   58 (116)
                      +.|.-++|+...+.+.|..||.+.-..+-++.++.++...+..  ..+.|+-+...+.
T Consensus         3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~~~d~~~   60 (71)
T PF02196_consen    3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDWDQDSSS   60 (71)
T ss_dssp             EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-TTSBGGG
T ss_pred             EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccCCCceee
Confidence            4567789999999999999999999999999999888766554  3445654444443

It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.

>KOG4250 consensus TANK binding protein kinase TBK1 [Signal transduction mechanisms]

Probab=87.68  E-value=1.9  Score=35.97  Aligned_cols=42  Identities=24%  Similarity=0.460  Sum_probs=37.7

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEc
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL   50 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L   50 (116)
                      +...+.+.++++.|+..|+..|...+|+|.+.|.|+|.|...
T Consensus       323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~~  364 (732)
T KOG4250|consen  323 QATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGLS  364 (732)
T ss_pred             cceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCcc
Confidence            456688999999999999999999999999999999987753

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=87.39  E-value=4.5  Score=24.39  Aligned_cols=54  Identities=19%  Similarity=0.366  Sum_probs=41.0

Q ss_pred             CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE-ECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus        10 g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +..+.+.+++..||.++-+.    .|+|..+..++ .+|+..+-+     +-+++|+.|.+...
T Consensus        22 ~~~~~~~~~~~~tvkd~IEs----LGVP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~P~   76 (81)
T PF14451_consen   22 GGPFTHPFDGGATVKDVIES----LGVPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVYPV   76 (81)
T ss_pred             CCceEEecCCCCcHHHHHHH----cCCChHHeEEEEECCEECCCc-----ccCCCCCEEEEEec
Confidence            44577889999999988765    49998888665 699987554     44567999988754

>PF08825 E2_bind: E2 binding domain; InterPro: IPR014929 E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades

Probab=87.11  E-value=1.6  Score=26.56  Aligned_cols=56  Identities=16%  Similarity=0.294  Sum_probs=37.6

Q ss_pred             EEecCCCCHHHHHHHHHHhhCCCCCc-------eEEEECCE-EcC-----C-CCccccCCCCCCCEEEEEE
Q 033570           15 LEVESSDTIDNVKAKIQDKEGIPPDQ-------QRLIFAGK-QLE-----D-GRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~i~~~~-------q~L~~~g~-~L~-----d-~~tL~~~gi~~g~~I~v~~   71 (116)
                      +++++++|+.+|.+.+.+.-.+....       -.|++.+- .|.     + +++|.++ +.+|..|.|.=
T Consensus         1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~VtD   70 (84)
T PF08825_consen    1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVTD   70 (84)
T ss_dssp             EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEEE
T ss_pred             CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEEC
Confidence            57899999999999999984433332       23433332 121     1 6789999 89999988753

This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains []. ; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0045116 protein neddylation; PDB: 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H 1YOV_B 3FN1_A ....

>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A

Probab=87.08  E-value=4.1  Score=28.84  Aligned_cols=48  Identities=21%  Similarity=0.329  Sum_probs=30.7

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCCCCC---ceEEE--ECCEE---cCCCCccccC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGIPPD---QQRLI--FAGKQ---LEDGRTLADY   59 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i~~~---~q~L~--~~g~~---L~d~~tL~~~   59 (116)
                      .+.+-|+.+.||.+|.+.+.++.+++.+   .+++.  ++++.   +..+.+|.++
T Consensus        35 ~~~~~vpk~~tV~Dll~~l~~k~~~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l   90 (213)
T PF14533_consen   35 EYELLVPKTGTVSDLLEELQKKVGFSEEGTGKLRLWEVSNHKIYKILSEDEPISSL   90 (213)
T ss_dssp             EEEE--BTT-BHHHHHHHHHTT----TT----EEEEEEETTEEEEEE-TTSBGGGS
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCcCCcCcEEEEEeECCEEEeecCCCCchhhc
Confidence            4778999999999999999999998655   45554  67774   5667788776

>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7

Probab=86.87  E-value=5.2  Score=24.46  Aligned_cols=56  Identities=23%  Similarity=0.283  Sum_probs=41.0

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCce-EEE------ECCEEcCCCCcccc
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLI------FAGKQLEDGRTLAD   58 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q-~L~------~~g~~L~d~~tL~~   58 (116)
                      |.|-..+|....+.|+..+|++++-+.++.+.++....- .|+      .-.+.+.|+..|.+
T Consensus         5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~~P~l~lER~~EDHE~vvd   67 (85)
T cd01787           5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEHLPHLQLERLFEDHELVVE   67 (85)
T ss_pred             EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEecchhhhhhhccchHHHHH
Confidence            556677899999999999999999999999998765543 333      12334667665443

Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.

>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown

Probab=86.74  E-value=1.7  Score=28.31  Aligned_cols=57  Identities=19%  Similarity=0.432  Sum_probs=39.4

Q ss_pred             EecC-CCCHHHHHHHHHHhhC----CCC------CceEEEE----------------CC-EEc---CCCCccccCCCCCC
Q 033570           16 EVES-SDTIDNVKAKIQDKEG----IPP------DQQRLIF----------------AG-KQL---EDGRTLADYNIQKE   64 (116)
Q Consensus        16 ~v~~-~~TV~~LK~~I~~~~~----i~~------~~q~L~~----------------~g-~~L---~d~~tL~~~gi~~g   64 (116)
                      .|+. +.||.+|++.+.+...    ++|      +.++|.+                .. ..|   +++.+|.++||.+.
T Consensus        21 ~vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~~~~~~tL~~~gv~nE  100 (122)
T PF10209_consen   21 NVDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDVSDDDKTLKELGVENE  100 (122)
T ss_pred             cCCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeecCCCCCcHHHcCCCcc
Confidence            5787 8999999999988753    332      2234432                12 356   67888999999998


Q ss_pred             CEEEEEEe
Q 033570           65 STLHLVLR   72 (116)
Q Consensus        65 ~~I~v~~~   72 (116)
                      ..|.+..+
T Consensus       101 TEiSfF~~  108 (122)
T PF10209_consen  101 TEISFFNM  108 (122)
T ss_pred             ceeeeeCH
Confidence            88866543

>cd01766 Ufm1 Urm1-like ubiquitin domain

Probab=85.48  E-value=5.8  Score=23.66  Aligned_cols=61  Identities=21%  Similarity=0.268  Sum_probs=48.8

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCceEEE-ECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      .+.|+++......-.-.++++++|+..--++ -.|--+...++-+..-++.|+.+.+..|-+
T Consensus        19 vlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvGINP~qtAGnvflkhgselrliPRDr   80 (82)
T cd01766          19 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRLIPRDR   80 (82)
T ss_pred             EEeccccCchHHHHHHHHHhcCCCccceeEEecCccccChhhcccceeeecCCEeeeccccc
Confidence            4688888888888888899999998866665 456667778888888889999988877644

Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.

>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []

Probab=84.87  E-value=6.1  Score=23.40  Aligned_cols=42  Identities=29%  Similarity=0.290  Sum_probs=32.5

Q ss_pred             EEEEcCCCC----EEEEEecCCCCHHHHHHHHHHhhCC--CCCceEEE
Q 033570            3 IFVKTLTGK----TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLI   44 (116)
Q Consensus         3 v~Vk~~~g~----~~~i~v~~~~TV~~LK~~I~~~~~i--~~~~q~L~   44 (116)
                      |.|-..++.    ...+.|++++|+.++-..+.+++++  .+....|.
T Consensus         5 lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~   52 (93)
T PF00788_consen    5 LRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLV   52 (93)
T ss_dssp             EEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEE
T ss_pred             EEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEE
Confidence            344444555    7789999999999999999999998  44456663

This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....

>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=84.36  E-value=0.62  Score=36.88  Aligned_cols=59  Identities=24%  Similarity=0.264  Sum_probs=49.8

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      .++.+.+.|-.+|...|++++|++-..++.+.+|++|.-.++|.+.|++......+++.
T Consensus        53 l~k~sL~i~Gselqa~iakklgi~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~  111 (568)
T KOG2561|consen   53 LKKCSLHITGSELQALIAKKLGIKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG  111 (568)
T ss_pred             hhhcccccccHHHHHHHHHHcCCchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence            45566677789999999999999988999999999999999999999987766555443

>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein

Probab=84.35  E-value=2.5  Score=27.11  Aligned_cols=58  Identities=14%  Similarity=0.145  Sum_probs=40.8

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCc-eEEEECCEEcCCCCccccC----CCCCCCEEEEEEe
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY----NIQKESTLHLVLR   72 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~~~g~~L~d~~tL~~~----gi~~g~~I~v~~~   72 (116)
                      .+-|+.+.||+++...|..+.++.++. +-|..++.....+.+++++    +. ++..+++...
T Consensus        44 KflVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~~p~~~~~~~~lY~~~kd-~DGfLyl~Ys  106 (112)
T cd01611          44 KYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPTSATMSQLYEEHKD-EDGFLYMTYS  106 (112)
T ss_pred             eEEecCCCCHHHHHHHHHHHhCCCccceEEEEECCccCCchhHHHHHHHHhCC-CCCEEEEEEe
Confidence            356999999999999999999987775 4455566544556777665    32 2456666544

GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.

>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]

Probab=83.67  E-value=2.6  Score=33.21  Aligned_cols=75  Identities=15%  Similarity=0.290  Sum_probs=60.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcCC---CCccccCCCCCCCEEEEEEecCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~d---~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      +|.|+.++|..+.=..+.+.-+..++..+.+.-++....+.|-  |--++..+   +++|.++.+.+...+.|+.+..+.
T Consensus       316 rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~i~~g~f~LatpyPRReft~eDy~KtllEl~L~psaalvvlpk~r~t  395 (506)
T KOG2507|consen  316 RLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQTIGLGAFDLATPYPRREFTDEDYDKTLLELRLFPSAALVVLPKKRAT  395 (506)
T ss_pred             EEEEecCCccchhhcCCcchHHHHHHHHHHhcccccccceeeccccccccccchhhhhhHHHhccCCcceEEEEecCCcc
Confidence            6889999999888888888888899999998877777776664  77777643   679999999999888887765443

>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=83.65  E-value=3.7  Score=25.18  Aligned_cols=40  Identities=23%  Similarity=0.346  Sum_probs=34.4

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEE-EECCEEc
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL-IFAGKQL   50 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L-~~~g~~L   50 (116)
                      ..+.|.|+++.|=.++|+.|++.+|+.+...+. .+.|+.-
T Consensus        21 n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~k   61 (91)
T PF00276_consen   21 NQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKK   61 (91)
T ss_dssp             SEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEE
T ss_pred             CEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCce
Confidence            568999999999999999999999999888754 4777754

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 domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....

>cd01768 RA RA (Ras-associating) ubiquitin domain

Probab=83.32  E-value=7.3  Score=23.09  Aligned_cols=35  Identities=29%  Similarity=0.448  Sum_probs=29.2

Q ss_pred             CCEEEEEecCCCCHHHHHHHHHHhhCCC--CCceEEE
Q 033570           10 GKTITLEVESSDTIDNVKAKIQDKEGIP--PDQQRLI   44 (116)
Q Consensus        10 g~~~~i~v~~~~TV~~LK~~I~~~~~i~--~~~q~L~   44 (116)
                      +....+.|+.++|..++-..+.+++++.  +....|+
T Consensus        12 ~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~   48 (87)
T cd01768          12 GTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALV   48 (87)
T ss_pred             ccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEE
Confidence            5667899999999999999999999986  4555554

The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.

>PF02991 Atg8: Autophagy protein Atg8 ubiquitin like; InterPro: IPR004241 Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules

Probab=83.14  E-value=4  Score=25.85  Aligned_cols=45  Identities=16%  Similarity=0.193  Sum_probs=34.5

Q ss_pred             EEecCCCCHHHHHHHHHHhhCCCCCc-eEEEECCEEcCCCCccccC
Q 033570           15 LEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY   59 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~~~g~~L~d~~tL~~~   59 (116)
                      +-|+.+.||++|...|..+..++++. +-|..++.....+.++++.
T Consensus        37 fLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~~lp~~s~tm~el   82 (104)
T PF02991_consen   37 FLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNNTLPSTSSTMGEL   82 (104)
T ss_dssp             EEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTTBESSTTSBHHHH
T ss_pred             EEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcCcccchhhHHHHH
Confidence            45889999999999999999997664 5566688666778888765

The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N terminus and the C terminus of Atg19. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [] Related proteins that belong to this group include the human ganglioside expression factor and a symbiosis-related fungal protein.; PDB: 3ECI_A 3D32_B 1GNU_A 1KM7_A 1KLV_A 1KOT_A 3DOW_A 1KJT_A 1V49_A 2ZJD_C ....

>PF06234 TmoB: Toluene-4-monooxygenase system protein B (TmoB); InterPro: IPR009355 This family consists of several Toluene-4-monooxygenase system protein B (TmoB) sequences

Probab=82.14  E-value=9.2  Score=23.39  Aligned_cols=60  Identities=23%  Similarity=0.389  Sum_probs=43.5

Q ss_pred             EEEEecCCCCHHHHHHHHHHhh-C--CC--CC-ceEEEECC--EEcCCCCccccCCCCCCCEEEEEEe
Q 033570           13 ITLEVESSDTIDNVKAKIQDKE-G--IP--PD-QQRLIFAG--KQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~-~--i~--~~-~q~L~~~g--~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      ..+.|+.++|+.++-++++.+. |  ++  ++ ..++.++|  ..+..+.++++.||.+-+.|.+...
T Consensus        17 ~Lv~VDt~dTmdqVA~k~A~HsVGrRV~~~pg~~lrVr~~g~~~~~p~~~tVaeagl~P~e~vev~~~   84 (85)
T PF06234_consen   17 QLVPVDTEDTMDQVAAKVAHHSVGRRVAPRPGAPLRVRRQGDTQPFPRSMTVAEAGLQPMEWVEVRFE   84 (85)
T ss_dssp             EEEEEETT-BHHHHHHHHHTTTTTTSS---TTSEEEEEETTTSSEE-TT-BGGGHT--TTEEEEEEEE
T ss_pred             EEEEeCCCCcHHHHHHHHhhhhcceecCCCCCCEEEEEecCCCccCCCccEehhcCCCcceEEEEEEc
Confidence            4578999999999999998864 4  32  33 45677888  8999999999999999999887653

Pseudomonas mendocina KR1 metabolises toluene as a carbon source. The initial step of the pathway is hydroxylation of toluene to form p-cresol by a multicomponent toluene-4-monooxygenase (T4MO) system [].; PDB: 3N1Y_C 3RNG_C 3RNA_C 3RN9_C 3RNC_C 3N1X_C 3RNE_C 3RNF_C 3N1Z_C 3N20_C ....

>PRK05738 rplW 50S ribosomal protein L23; Reviewed

Probab=82.01  E-value=6.2  Score=24.32  Aligned_cols=40  Identities=20%  Similarity=0.263  Sum_probs=33.9

Q ss_pred             CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEE-EECCEE
Q 033570           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL-IFAGKQ   49 (116)
Q Consensus        10 g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L-~~~g~~   49 (116)
                      ...+.|.|+++.|=.++|+.|++.+++++...+- ...|+.
T Consensus        20 ~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~   60 (92)
T PRK05738         20 QNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKT   60 (92)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCce
Confidence            4578999999999999999999999999988854 456554

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.00  E-value=2.3  Score=32.53  Aligned_cols=56  Identities=13%  Similarity=0.182  Sum_probs=44.2

Q ss_pred             EEecCCCCHHHHHHHHHHhhCCCCCceEEEE---CCEEc-----CCCCccccCCCCCCCEEEEE
Q 033570           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQL-----EDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~---~g~~L-----~d~~tL~~~gi~~g~~I~v~   70 (116)
                      .-|+-.-||-+|+..+..+.|+.+.+++|.|   .|+.-     +...+|-.|.|.+|+.+.+-
T Consensus       352 ~~I~~~~TV~D~~~~Ld~~VGvk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq  415 (418)
T KOG2982|consen  352 GLICMTRTVLDFMKILDPKVGVKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ  415 (418)
T ss_pred             eEEEeehHHHHHHHHhccccccccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence            3455566999999999999999999999987   44432     23667899999999988653

>PF08337 Plexin_cytopl: Plexin cytoplasmic RasGAP domain; InterPro: IPR013548 This domain is found at C terminus of various plexins (e

Probab=81.91  E-value=3.7  Score=33.31  Aligned_cols=64  Identities=36%  Similarity=0.500  Sum_probs=42.3

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEE--EC--CE-EcCCC-------------CccccCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLI--FA--GK-QLEDG-------------RTLADYNIQKE   64 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~--~~--g~-~L~d~-------------~tL~~~gi~~g   64 (116)
                      ..+.+.|-..+||.+.|++|-...  +.|      ++++-|.  .+  |. +|.|.             .||+.|+|.+|
T Consensus       202 ~~i~VkVLdCDTItQVKeKiLDavyk~~p~S~rp~~~d~dLEwr~~~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  281 (539)
T PF08337_consen  202 EEIPVKVLDCDTITQVKEKILDAVYKNTPYSQRPRADDVDLEWRQGRGGRLILQDEDSTSKVEGGWKRLNTLAHYKVPDG  281 (539)
T ss_dssp             TCEEEEEETTSBHHHHHHHHHHHHTTTS-GGGS--GGGEEEEEEETTSEEEEESSSSTTSEEETTEEE--BHHHHT--TT
T ss_pred             ceEEEEEEecCcccHHHHHHHHHHHcCCCCCCCCCccccceeeecCCCCcccccCCCCCcccCCCceEeccHhhcCCCCC
Confidence            457889989999999999998763  222      3444443  22  33 56552             24899999999


Q ss_pred             CEEEEEEecC
Q 033570           65 STLHLVLRLR   74 (116)
Q Consensus        65 ~~I~v~~~~~   74 (116)
                      +++.++.+..
T Consensus       282 a~vaLv~k~~  291 (539)
T PF08337_consen  282 ATVALVPKQH  291 (539)
T ss_dssp             EEEEEEES--
T ss_pred             ceEEEeeccc
Confidence            9999998864

g. P51805 from SWISSPROT). Plexins are receptors for semaphorins, and plexin signalling is important in pathfinding and patterning of both neurons and developing blood vessels [, ]. The cytoplasmic region, which has been called a SEX domain [], and is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins []. ; PDB: 3H6N_A 4E71_A 4E74_A 3IG3_A 2REX_C 2JPH_A 2R2O_A 3HM6_X 3SU8_X 3SUA_E ....

>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease

Probab=81.48  E-value=9.2  Score=22.97  Aligned_cols=62  Identities=18%  Similarity=0.381  Sum_probs=39.9

Q ss_pred             EEcCC-CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE--CCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            5 VKTLT-GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         5 Vk~~~-g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~--~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.+.+ ...+-|..   .++.+|+.+..+.++++.+..+|+.  .|..++|+.-...+  . ..++.|++.
T Consensus         7 v~~~~r~~k~Gv~A---~sL~eL~~K~~~~l~~~~~~~~lvL~eDGT~VddEeyF~tL--p-~nT~lm~L~   71 (78)
T PF02017_consen    7 VRNHDRSVKKGVAA---SSLEELLEKACDKLQLPEEPVRLVLEEDGTEVDDEEYFQTL--P-DNTVLMLLE   71 (78)
T ss_dssp             EEETTSSCEEEEEE---SSHHHHHHHHHHHHT-SSSTCEEEETTTTCBESSCHHHCCS--S-SSEEEEEEE
T ss_pred             EecCCCCceEeEEc---CCHHHHHHHHHHHhCCCCcCcEEEEeCCCcEEccHHHHhhC--C-CCCEEEEEC
Confidence            44433 23344555   3799999999999999988888776  78888766443332  2 345545544

The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.

>cd01764 Urm1 Urm1-like ubuitin domain

Probab=80.44  E-value=7.4  Score=24.01  Aligned_cols=56  Identities=14%  Similarity=0.295  Sum_probs=35.0

Q ss_pred             EecCCCCHHHHHHHHHHhhCCCCCceE-------------EEECCEEcCCCCcc--ccCCCCCCCEEEEEEecCCC
Q 033570           16 EVESSDTIDNVKAKIQDKEGIPPDQQR-------------LIFAGKQLEDGRTL--ADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        16 ~v~~~~TV~~LK~~I~~~~~i~~~~q~-------------L~~~g~~L~d~~tL--~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .+....||.+|-+.+.+.+.  ..+..             ++.||+..   ..+  .++-+++|+.|.+.....||
T Consensus        24 ~~~~~~tV~dll~~L~~~~~--~~~~~lf~~~g~lr~~i~VlvN~~di---~~l~g~~t~L~dgD~v~i~P~v~GG   94 (94)
T cd01764          24 DGEKPVTVGDLLDYVASNLL--EERPDLFIEGGSVRPGIIVLINDTDW---ELLGEEDYILEDGDHVVFISTLHGG   94 (94)
T ss_pred             cCCCCCcHHHHHHHHHHhCc--hhhhhhEecCCcccCCEEEEECCccc---cccCCcccCCCCcCEEEEECCCCCC
Confidence            34356799999999988762  22222             22333321   122  24567889999999877765

Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	116
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		3e-49
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		4e-47
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		1e-45
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		3e-38
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-38
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		4e-38
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		5e-38
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		5e-38
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		7e-38
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		1e-37
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		2e-37
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		2e-37
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		2e-37
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		2e-37
3jvz_X	81	E2~ubiquitin-Hect Length = 81		3e-37
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		3e-37
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		3e-37
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		3e-37
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		3e-37
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		3e-37
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		3e-37
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		4e-37
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		4e-37
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		4e-37
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		5e-37
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		6e-37
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		6e-37
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		7e-37
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		7e-37
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		9e-37
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		9e-37
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		1e-36
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		1e-36
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		1e-36
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-36
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		2e-36
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		2e-36
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		2e-36
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		2e-36
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		2e-36
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		2e-36
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		3e-36
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		5e-36
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		5e-36
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		7e-36
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		8e-36
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		1e-35
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		1e-35
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		1e-35
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		4e-35
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		4e-35
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		4e-35
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		4e-35
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		9e-35
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		1e-34
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		1e-34
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		1e-34
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-34
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		2e-34
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-34
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		4e-34
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		4e-34
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		5e-34
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		1e-32
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		6e-32
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		3e-31
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		1e-30
4hk2_A	78	U7ub25.2540 Length = 78		4e-30
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		4e-26
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		1e-22
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		4e-22
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		3e-21
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-20
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-20
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		2e-20
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		2e-20
1ndd_B	76	Structure Of Nedd8 Length = 76		3e-20
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		3e-20
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		3e-20
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		1e-19
2dzi_A	81	2dziSOLUTION STRUCTURE OF THE N-Terminal Ubiquitin-		1e-10
2zeq_A	78	Crystal Structure Of Ubiquitin-Like Domain Of Murin		3e-08
2hj8_A	88	Solution Nmr Structure Of The C-Terminal Domain Of		4e-08
2knb_A	81	Solution Nmr Structure Of The Parkin Ubl Domain In		4e-08
3b1l_X	76	Crystal Structure Of Parkin Ubiquitin-Like Domain R		4e-08
1iyf_A	81	Solution Structure Of Ubiquitin-Like Domain Of Huma		5e-08
3sdl_C	164	Crystal Structure Of Human Isg15 In Complex With Ns		8e-08
3r66_C	164	Crystal Structure Of Human Isg15 In Complex With Ns		9e-08
3rt3_B	159	Complex Of Influenza Virus Protein With Host Anti-V		9e-08
2l7r_A	93	Solution Nmr Structure Of N-Terminal Ubiquitin-Like		1e-07
3phx_B	79	Otu Domain Of Crimean Congo Hemorrhagic Fever Virus		3e-07
2faz_A	78	Ubiquitin-Like Domain Of Human Nuclear Zinc Finger		3e-07
3pse_B	156	Structure Of A Viral Otu Domain Protease Bound To I		4e-07
3izr_p	53	Localization Of The Large Subunit Ribosomal Protein		5e-07
1zkh_A	86	Solution Structure Of A Human Ubiquitin-Like Domain		8e-07
1wy8_A	89	Solution Structure Of The N-Terminal Ubiquitin-Like		2e-06
1z2m_A	155	Crystal Structure Of Isg15, The Interferon-Induced		2e-06
1wh3_A	87	Solution Structure Of C-Terminal Ubiquitin Like Dom		3e-06
1we7_A	115	Solution Structure Of Ubiquitin-Like Domain In Sf3a		4e-06
1wx9_A	86	Solution Structure Of The N-Terminal Ubiquitin-Like		5e-06
4dwf_A	90	Crystal Structure Of A Hla-B Associated Transcript		6e-06
4eew_A	88	Crystal Structure Of The Ubl Domain Of Bag6 Length		1e-05
1ttn_A	106	Solution Structure Of The Ubiquitin-Like Domain Of		1e-05
3m63_B	101	Crystal Structure Of Ufd2 In Complex With The Ubiqu		2e-05
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		3e-05
2bwe_S	77	The Crystal Structure Of The Complex Between The Ub		3e-05
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		4e-05
1oqy_A	368	Structure Of The Dna Repair Protein Hhr23a Length =		2e-04
3izs_p	52	Localization Of The Large Subunit Ribosomal Protein		2e-04
3zey_9	153	High-resolution Cryo-electron Microscopy Structure		3e-04
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		5e-04

>pdb|3U5E|MM Chain m, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 60s Subunit, Ribosome A Length = 128

Iteration: 1
 Score =  189 bits (480), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 96/102 (94%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYAR 102

>pdb|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score =  182 bits (462), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 85/102 (83%), Positives = 96/102 (94%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTI LEVE+SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLE+GRTLADYN
Sbjct: 1   MQIFVKTLTGKTIALEVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEEGRTLADYN 60
Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGG++EP+L ALA+KYN +K +CR+ + R
Sbjct: 61  IQKESTLHLVLRLRGGVMEPTLEALAKKYNWEKKVCRRCYAR 102

>pdb|4A18|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 129

Iteration: 1
 Score =  177 bits (449), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 84/102 (82%), Positives = 95/102 (93%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITL+VE+SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGG +EP++ ALA+KYN +K +CR  + R
Sbjct: 61  IQKESTLHLVLRLRGGGMEPTIAALAKKYNCEKKVCRDCYAR 102

>pdb|3OLM|D Chain D, Structure And Function Of A Ubiquitin Binding Site Within The Catalytic Domain Of A Hect Ubiquitin Ligase Length = 79

Iteration: 1
 Score =  153 bits (386), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

>pdb|3U5G|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome B Length = 152

Iteration: 1
 Score =  152 bits (384), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|1OTR|B Chain B, Solution Structure Of A Cue-Ubiquitin Complex Length = 76

Iteration: 1
 Score =  152 bits (384), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score =  152 bits (384), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|4II3|B Chain B, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme 1 (uba1) In Complex With Ubiquitin And Atp/mg Length = 96

Iteration: 1
 Score =  152 bits (384), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 21 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 81 IQKESTLHLVLRLRGG 96

>pdb|4HCN|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Ubiquitin Length = 98

Iteration: 1
 Score =  151 bits (382), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 82
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 83 IQKESTLHLVLRLRGG 98

>pdb|1YX5|B Chain B, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Length = 98

Iteration: 1
 Score =  150 bits (380), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|3B08|A Chain A, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With Linear Di- Ubiquitin Length = 152

Iteration: 1
 Score =  150 bits (379), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/77 (94%), Positives = 76/77 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGGI 77
          IQKESTLHLVLRLRGG+
Sbjct: 61 IQKESTLHLVLRLRGGM 77

>pdb|2JWZ|A Chain A, Mutations In The Hydrophobic Core Of Ubiquitin Differentially Affect Its Recognition By Receptor Proteins Length = 76

Iteration: 1
 Score =  150 bits (378), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLH VLRLRGG
Sbjct: 61 IQKESTLHSVLRLRGG 76

>pdb|3U30|A Chain A, Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin Length = 172

Iteration: 1
 Score =  150 bits (378), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/77 (94%), Positives = 76/77 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80
Query: 61 IQKESTLHLVLRLRGGI 77
          IQKESTLHLVLRLRGG+
Sbjct: 81 IQKESTLHLVLRLRGGM 97

>pdb|2ZVN|A Chain A, Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group Length = 154

Iteration: 1
 Score =  150 bits (378), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/77 (94%), Positives = 76/77 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLRGGI 77
          IQKESTLHLVLRLRGG+
Sbjct: 63 IQKESTLHLVLRLRGGM 79

>pdb|3JVZ|X Chain X, E2~ubiquitin-Hect Length = 81

Iteration: 1
 Score =  149 bits (377), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 6  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 65
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 66 IQKESTLHLVLRLRGG 81

>pdb|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score =  149 bits (377), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 63 IQKESTLHLVLRLRGG 78

>pdb|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

Iteration: 1
 Score =  149 bits (377), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 64
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 65 IQKESTLHLVLRLRGG 80

>pdb|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

Iteration: 1
 Score =  149 bits (377), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

>pdb|2W9N|A Chain A, Crystal Structure Of Linear Di-Ubiquitin Length = 152

Iteration: 1
 Score =  149 bits (377), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 77  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 136
Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 137 IQKESTLHLVLRLRGG 152

>pdb|2LD9|A Chain A, Backbone Structure Of Ubiquitin Determined Using Backbone Amide Noes And Backbone N-H And N-C Rdcs Length = 77

Iteration: 1
 Score =  149 bits (377), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 62 IQKESTLHLVLRLRGG 77

>pdb|1AAR|A Chain A, Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2) Length = 76

Iteration: 1
 Score =  149 bits (376), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|3DVG|X Chain X, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 80

Iteration: 1
 Score =  149 bits (376), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

>pdb|2ZNV|C Chain C, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 77

Iteration: 1
 Score =  149 bits (376), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|3VDZ|A Chain A, Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-Dse3-Ubiquitin At 2.4 Angstroms Length = 111

Iteration: 1
 Score =  149 bits (376), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

>pdb|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score =  149 bits (375), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

>pdb|4II2|B Chain B, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1) In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg Length = 83

Iteration: 1
 Score =  149 bits (375), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFV+TLTG+TITLEVESSDTIDNV+A+IQD+EGIPPDQQRLIFAG+QLEDGRTLADYN
Sbjct: 8  MQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDGRTLADYN 67
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 68 IQRESTLHLVLRLRGG 83

>pdb|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score =  148 bits (374), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 64 IQRESTLHLVLRLRGG 79

>pdb|2ZNV|B Chain B, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 76

Iteration: 1
 Score =  148 bits (374), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

>pdb|1ZGU|B Chain B, Solution Structure Of The Human Mms2-Ubiquitin Complex Length = 76

Iteration: 1
 Score =  148 bits (374), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAG+QLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin Length = 76

Iteration: 1
 Score =  148 bits (373), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|3Q3F|A Chain A, Engineering Domain-Swapped Binding Interfaces By Mutually Exclusive Folding: Insertion Of Ubiquitin Into Position 103 Of Barnase Length = 189

Iteration: 1
 Score =  148 bits (373), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 2   QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
           QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYNI
Sbjct: 107 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 166
Query: 62  QKESTLHLVLRLRGG 76
           QKESTLHLVLRLRGG
Sbjct: 167 QKESTLHLVLRLRGG 181

>pdb|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score =  148 bits (373), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 70/75 (93%), Positives = 74/75 (98%)
Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
          QIF KTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLI+AGKQLEDGRTL+DYNI
Sbjct: 11 QIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNI 70
Query: 62 QKESTLHLVLRLRGG 76
          Q+ESTLHLVLRLRGG
Sbjct: 71 QRESTLHLVLRLRGG 85

>pdb|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score =  147 bits (371), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

>pdb|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

Iteration: 1
 Score =  147 bits (371), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

>pdb|2O6V|D Chain D, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score =  147 bits (371), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAG+QLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

>pdb|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

Iteration: 1
 Score =  147 bits (371), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

>pdb|1CMX|B Chain B, Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases Length = 76

Iteration: 1
 Score =  147 bits (371), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

>pdb|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score =  147 bits (371), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPP QQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPQQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|1S1Q|B Chain B, Tsg101(Uev) Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score =  147 bits (370), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
          QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYNI
Sbjct: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 61
Query: 62 QKESTLHLVLRLRGG 76
          QKESTLHLVLRLRGG
Sbjct: 62 QKESTLHLVLRLRGG 76

>pdb|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

Iteration: 1
 Score =  147 bits (370), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 62 IQKESTLHLVLRLRG 76

>pdb|2K6D|B Chain B, Cin85 Sh3-C Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score =  146 bits (369), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

>pdb|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score =  146 bits (368), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAG QLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGXQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score =  145 bits (366), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 71/75 (94%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL++YN
Sbjct: 9  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSEYN 68
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 69 IQKESTLHLVLRLRG 83

>pdb|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score =  145 bits (366), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQ EDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQXEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKEST HLVLRLRGG
Sbjct: 61 IQKESTXHLVLRLRGG 76

>pdb|1YJ1|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin Length = 76

Iteration: 1
 Score =  145 bits (365), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKE IPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEXIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|2FCS|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group Length = 76

Iteration: 1
 Score =  145 bits (365), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKE IPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEQIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score =  144 bits (363), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/74 (95%), Positives = 73/74 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 293
Query: 61  IQKESTLHLVLRLR 74
           IQKESTLHLVLRLR
Sbjct: 294 IQKESTLHLVLRLR 307

>pdb|2ZCB|A Chain A, Crystal Structure Of Ubiquitin P37aP38A Length = 76

Iteration: 1
 Score =  144 bits (363), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGI  DQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIAADQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score =  144 bits (362), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 73/81 (90%), Positives = 75/81 (92%), Gaps = 5/81 (6%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRT 55
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEG     IPPDQQRLIFAGKQLEDGRT
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIFAGKQLEDGRT 60
Query: 56 LADYNIQKESTLHLVLRLRGG 76
          L+DYNIQKESTLHLVLRLRGG
Sbjct: 61 LSDYNIQKESTLHLVLRLRGG 81

>pdb|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score =  142 bits (359), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 70/73 (95%), Positives = 72/73 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRL 73
          IQKESTLHLVLRL
Sbjct: 61 IQKESTLHLVLRL 73

>pdb|2GBK|A Chain A, Crystal Structure Of The 9-10 Moad Insertion Mutant Of Ubiquitin Length = 83

Iteration: 1
 Score =  142 bits (359), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 73/83 (87%), Positives = 75/83 (90%), Gaps = 7/83 (8%)
Query: 1  MQIFVKTLT-------GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG 53
          MQIFVKTLT       GKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDG
Sbjct: 1  MQIFVKTLTQVRELVGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 60
Query: 54 RTLADYNIQKESTLHLVLRLRGG 76
          RTL+DYNIQKESTLHLVLRLRGG
Sbjct: 61 RTLSDYNIQKESTLHLVLRLRGG 83

>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score =  142 bits (359), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 66/76 (86%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+F+KTLTGKT+T+EVE SDT++N KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQVFLKTLTGKTVTIEVEPSDTVENFKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKEST+HLVLRLRGG
Sbjct: 61 IQKESTIHLVLRLRGG 76

>pdb|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score =  141 bits (356), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 71/76 (93%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTG TITLEVESSDTIDNVK+KIQ   GIPPDQQ LIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGATITLEVESSDTIDNVKSKIQAAPGIPPDQQELIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>pdb|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural Specificity Length = 76

Iteration: 1
 Score =  141 bits (355), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FVKTLTGKT+T+E+E SDT++N+KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQLFVKTLTGKTLTVELEPSDTVENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          +QKEST+HLVLRLRGG
Sbjct: 61 LQKESTIHLVLRLRGG 76

>pdb|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score =  141 bits (355), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 69/72 (95%), Positives = 71/72 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLR 72
          IQKESTLHLVLR
Sbjct: 61 IQKESTLHLVLR 72

>pdb|4GSW|A Chain A, Crystal Structure Of Ubiquitin From Entamoeba Histolytica To 2.15 Angstrom Length = 80

Iteration: 1
 Score =  141 bits (355), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE +D+ID +KAKIQ+KEGIPPDQQRLIFAGKQLE+G+TL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score =  140 bits (353), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 70/70 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLV 70
          IQKESTLHLV
Sbjct: 61 IQKESTLHLV 70

>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score =  140 bits (352), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 66/76 (86%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+F+KTLTGKT T+E+E SDTI+N+KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 69
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 70 IQKESTLHLVLRLRGG 85

>pdb|3V6E|B Chain B, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin Length = 91

Iteration: 1
 Score =  140 bits (352), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 68/74 (91%), Positives = 71/74 (95%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFV TL+GK ITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 18 MQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 77
Query: 61 IQKESTLHLVLRLR 74
          IQKESTLHLVLRLR
Sbjct: 78 IQKESTLHLVLRLR 91

>pdb|2GBJ|A Chain A, Crystal Structure Of The 9-10 8 Glycine Insertion Mutant Of Ubiquitin. Length = 84

Iteration: 1
 Score =  139 bits (350), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 73/84 (86%), Positives = 75/84 (89%), Gaps = 8/84 (9%)
Query: 1  MQIFVKTLTG--------KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED 52
          MQIFVKTLTG        KTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLED
Sbjct: 1  MQIFVKTLTGGGGGGGGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED 60
Query: 53 GRTLADYNIQKESTLHLVLRLRGG 76
          GRTL+DYNIQKESTLHLVLRLRGG
Sbjct: 61 GRTLSDYNIQKESTLHLVLRLRGG 84

>pdb|2GBM|A Chain A, Crystal Structure Of The 35-36 8 Glycine Insertion Mutant Of Ubiquitin Length = 84

Iteration: 1
 Score =  139 bits (350), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 73/84 (86%), Positives = 75/84 (89%), Gaps = 8/84 (9%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--------IPPDQQRLIFAGKQLED 52
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEG        IPPDQQRLIFAGKQLED
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLED 60
Query: 53 GRTLADYNIQKESTLHLVLRLRGG 76
          GRTL+DYNIQKESTLHLVLRLRGG
Sbjct: 61 GRTLSDYNIQKESTLHLVLRLRGG 84

>pdb|3V6C|B Chain B, Crystal Structure Of Usp2 In Complex With Mutated Ubiquitin Length = 91

Iteration: 1
 Score =  139 bits (349), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 68/74 (91%), Positives = 70/74 (94%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFV TLTG  ITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 77
Query: 61 IQKESTLHLVLRLR 74
          IQKESTLHLVLRLR
Sbjct: 78 IQKESTLHLVLRLR 91

>pdb|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score =  134 bits (337), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 69/76 (90%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVK LTGKT TLEVE SDTI+NVKAKIQDK G PPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKCLTGKTNTLEVEPSDTIENVKAKIQDKIGYPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLH V RLRGG
Sbjct: 62 IQKESTLHCVRRLRGG 77

>pdb|4I6L|B Chain B, Crystal Structure Of Otub1 In Complex With Ubiquitin Variant Length = 76

Iteration: 1
 Score =  132 bits (331), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 65/74 (87%), Positives = 70/74 (94%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQ+L+FA KQLEDGRTL+DYN
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQKLLFARKQLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLR 74
          I KES L+LVLRLR
Sbjct: 63 IHKESFLYLVLRLR 76

>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein Length = 82

Iteration: 1
 Score =  129 bits (325), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 60/77 (77%), Positives = 69/77 (89%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTIT++V+ +DT+  VKAKI DKEGIPPDQQRLIF GKQLED   ++DYN
Sbjct: 6  MQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEGIPPDQQRLIFGGKQLEDSNAMSDYN 65
Query: 61 IQKESTLHLVLRLRGGI 77
          +QKESTLHLVLRLRGG+
Sbjct: 66 VQKESTLHLVLRLRGGV 82

>pdb|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score =  128 bits (321), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 63/67 (94%), Positives = 65/67 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTL 67
          IQK STL
Sbjct: 64 IQKWSTL 70

>pdb|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score =  125 bits (315), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 64/76 (84%), Positives = 67/76 (88%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVK  TGKT TLEVE SDTI+NVKAKIQDK GIPPDQQ LIFAGK+LEDGRTL+DYN
Sbjct: 3  MQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLGIPPDQQWLIFAGKRLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTL  V RLRGG
Sbjct: 63 IQKESTLRGVRRLRGG 78

>pdb|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score =  112 bits (281), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 54/66 (81%), Positives = 58/66 (87%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M+I VKTL G+TI LEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKEST 66
          I   S 
Sbjct: 64 IHNHSA 69

>pdb|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score =  100 bits (250), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 48/76 (63%), Positives = 60/76 (78%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +DTID +K ++++KEGIPP QQRLI+AGKQL D +T  DYN
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          I+  S LHLVL LRGG
Sbjct: 61 IEGGSVLHLVLALRGG 76

>pdb|1GJZ|A Chain A, Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin Length = 53

Iteration: 1
 Score = 99.8 bits (247), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 49/51 (96%), Positives = 50/51 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 51
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLE
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 53

>pdb|3DBH|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190ala-Nedd8ala72arg) Length = 88

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 44/76 (57%), Positives = 59/76 (77%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 72
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVLRLRGG
Sbjct: 73 ILGGSVLHLVLRLRGG 88

>pdb|3DBL|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190wt-Nedd8ala72gln) Length = 88

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 59/76 (77%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 72
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL+LRGG
Sbjct: 73 ILGGSVLHLVLQLRGG 88

>pdb|4HCP|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Nedd8 Length = 78

Iteration: 1
 Score = 94.0 bits (232), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 3  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 62
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 63 ILGGSVLHLVLALRGG 78

>pdb|2BKR|B Chain B, Nedd8 Nedp1 Complex Length = 77

Iteration: 1
 Score = 93.6 bits (231), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 2  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 61
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 62 ILGGSVLHLVLALRGG 77

>pdb|4F8C|B Chain B, Structure Of The Cif:nedd8 Complex - Yersinia Pseudotuberculosis Cycle Inhibiting Factor In Complex With Human Nedd8 Length = 88

Iteration: 1
 Score = 93.6 bits (231), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

>pdb|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

>pdb|3GZN|I Chain I, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8 And Mln4924 Length = 82

Iteration: 1
 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 7  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 66
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 67 ILGGSVLHLVLALRGG 82

>pdb|2NVU|I Chain I, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex Length = 81

Iteration: 1
 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 6  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 65
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 66 ILGGSVLHLVLALRGG 81

>pdb|3DQV|A Chain A, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 81

Iteration: 1
 Score = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/74 (56%), Positives = 56/74 (75%)
Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ  D +T ADY I 
Sbjct: 8  IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQXNDEKTAADYKIX 67
Query: 63 KESTLHLVLRLRGG 76
            S LHLVL LRGG
Sbjct: 68 GGSVLHLVLALRGG 81

>pdb|2DZI|A Chain A, 2dziSOLUTION STRUCTURE OF THE N-Terminal Ubiquitin-Like Domain In Human Ubiquitin-Like Protein 4a (Gdx) Length = 81

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 46/72 (63%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+ VK L G+  +L+V   + +  +K  + +K  +P  QQRL+F GK L DG+ L+DY+
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYS 67
Query: 61 IQKESTLHLVLR 72
          I   S L+LV++
Sbjct: 68 IGPNSKLNLVVK 79

>pdb|2ZEQ|A Chain A, Crystal Structure Of Ubiquitin-Like Domain Of Murine Parkin Length = 78

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 48/74 (64%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCD 62
Query: 61 IQKESTLHLVLRLR 74
          ++++S +H+V R R
Sbjct: 63 LEQQSIVHIVQRPR 76

>pdb|2HJ8|A Chain A, Solution Nmr Structure Of The C-Terminal Domain Of The Interferon Alpha-Inducible Isg15 Protein From Homo Sapiens. Northeast Structural Genomics Target Hr2873b Length = 88

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 45/77 (58%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64
Query: 61 IQKESTLHLVLRLRGGI 77
          ++  ST+ + LRLRGG+
Sbjct: 65 LKPLSTVFMNLRLRGGL 81

>pdb|2KNB|A Chain A, Solution Nmr Structure Of The Parkin Ubl Domain In Complex With The Endophilin-A1 Sh3 Domain Length = 81

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 48/72 (66%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L++  T+ + +
Sbjct: 6  MIVFVRFNSSYGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELQNHLTVQNCD 65
Query: 61 IQKESTLHLVLR 72
          ++++S +H+V R
Sbjct: 66 LEQQSIVHIVQR 77

>pdb|3B1L|X Chain X, Crystal Structure Of Parkin Ubiquitin-Like Domain R33q Mutant Length = 76

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 48/74 (64%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCD 60
Query: 61 IQKESTLHLVLRLR 74
          ++++S +H+V R R
Sbjct: 61 LEQQSIVHIVQRPR 74

>pdb|1IYF|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Human Parkin Length = 81

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 46/72 (63%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 6  MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD 65
Query: 61 IQKESTLHLVLR 72
          + ++S +H+V R
Sbjct: 66 LDQQSIVHIVQR 77

>pdb|3SDL|C Chain C, Crystal Structure Of Human Isg15 In Complex With Ns1 N-Terminal Region From Influenza B Virus, Northeast Structural Genomics Consortium Target Ids Hx6481, Hr2873, And Or2 Length = 164

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 89  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 148
Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 149 LKPLSTVFMNLRLRGG 164

>pdb|3R66|C Chain C, Crystal Structure Of Human Isg15 In Complex With Ns1 N-Terminal Region From Influenza Virus B, Northeast Structural Genomics Consortium Target Ids Hx6481, Hr2873, And Or2 Length = 164

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 89  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 148
Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 149 LKPLSTVFMNLRLRGG 164

>pdb|3RT3|B Chain B, Complex Of Influenza Virus Protein With Host Anti-Viral Factor Length = 159

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 142 LKPLSTVFMNLRLRGG 157

>pdb|2L7R|A Chain A, Solution Nmr Structure Of N-Terminal Ubiquitin-Like Domain Of Fubi, A Ribosomal Protein S30 Precursor From Homo Sapiens. Northeast Structural Genomics Consortium (Nesg) Target Hr6166 Length = 93

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FV+    +  T EV   +T+  +KA +   EGI P+ Q ++ AG  LED  TL    
Sbjct: 20 MQLFVRAQ--ELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCG 77
Query: 61 IQKESTLHLVLRLRGG 76
          ++  +TL +  R+ GG
Sbjct: 78 VEALTTLEVAGRMLGG 93

>pdb|3PHX|B Chain B, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In Complex With Isg15 Length = 79

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64
Query: 61 IQKESTLHLVLRLRG 75
          ++  ST+ + LRLRG
Sbjct: 65 LKPLSTVFMNLRLRG 79

>pdb|2FAZ|A Chain A, Ubiquitin-Like Domain Of Human Nuclear Zinc Finger Protein Np95 Length = 78

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 1  MQIFVKTLTGK-TITLEVESSDT-IDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G+ T T++  S  T ++ ++ KIQ+   + P  QRL + GKQ+EDG TL D
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 62
Query: 59 YNIQKESTLHLVLR 72
          Y ++   T+ L++R
Sbjct: 63 YEVRLNDTIQLLVR 76

>pdb|3PSE|B Chain B, Structure Of A Viral Otu Domain Protease Bound To Interferon- Stimulated Gene 15 (Isg15) Length = 156

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LNILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLRG 75
           ++  ST+ + LRLRG
Sbjct: 142 LKPLSTVFMNLRLRG 156

>pdb|3IZR|PP Chain p, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 53

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/26 (84%), Positives = 23/26 (88%)
Query: 77  IIEPSLMALARKYNQDKMICRKSHTR 102
           IIEPSL ALARKYNQDKMICRK + R
Sbjct: 1   IIEPSLQALARKYNQDKMICRKCYAR 26

>pdb|1ZKH|A Chain A, Solution Structure Of A Human Ubiquitin-Like Domain In Sf3a1 Length = 86

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 8  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
          L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVI 78
Query: 68 HLVLRLRG 75
          HL L+ RG
Sbjct: 79 HLALKERG 86

>pdb|1WY8|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like Domain In Human Np95ICBP90-Like Ring Finger Protein (Nirf) Length = 89

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 1  MQIFVKTLTG-KTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G KT T+E V    TI+ ++ ++     + P+ QRL + GKQLE+G TL D
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 67
Query: 59 YNIQKESTLHLVLRLRGG 76
          Y++     + L++R   G
Sbjct: 68 YDVGLNDIIQLLVRPDSG 85

>pdb|1Z2M|A Chain A, Crystal Structure Of Isg15, The Interferon-Induced Ubiquitin Cross Reactive Protein Length = 155

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLR 74
           ++  ST+ + LRLR
Sbjct: 142 LKPLSTVFMNLRLR 155

>pdb|1WH3|A Chain A, Solution Structure Of C-Terminal Ubiquitin Like Domain Of Human 2'-5'-Oligoadenylate Synthetase-Like Protain (P59 Oasl) Length = 87

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+FVK   G +    +  +  I  +K +I+D++G+P  QQ+L F G+ L+D   L  Y 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYG 67
Query: 61 IQKESTLHL 69
          IQ   TL L
Sbjct: 68 IQDSDTLIL 76

>pdb|1WE7|A Chain A, Solution Structure Of Ubiquitin-Like Domain In Sf3a120 Length = 115

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 39/69 (56%)
Query: 8   LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
           L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 43  LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVI 102
Query: 68  HLVLRLRGG 76
           HL L+ R G
Sbjct: 103 HLALKERSG 111

>pdb|1WX9|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like Domain In The Human Bat3 Protein Length = 86

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 8  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 67
Query: 61 IQKESTLHLVLRLRGG 76
          +  +  +HLV R   G
Sbjct: 68 VGGK-VIHLVERAPSG 82

>pdb|4DWF|A Chain A, Crystal Structure Of A Hla-B Associated Transcript 3 (Bat3) From Homo Sapiens At 1.80 A Resolution Length = 90

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQXNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 65
Query: 61 IQKESTLHLVLR 72
          +  +  +HLV R
Sbjct: 66 VGGK-VIHLVER 76

>pdb|4EEW|A Chain A, Crystal Structure Of The Ubl Domain Of Bag6 Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 77
Query: 61 IQKESTLHLVLR 72
          +  +  +HLV R
Sbjct: 78 VGGK-VIHLVER 88

>pdb|1TTN|A Chain A, Solution Structure Of The Ubiquitin-Like Domain Of Human Dc- Ubp From Dendritic Cells Length = 106

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 40/70 (57%)
Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
          Q+ ++  TGK + L V S+DT+ ++K ++   EG+ P  QR  F+G+ L D     +  I
Sbjct: 25 QLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKI 84
Query: 62 QKESTLHLVL 71
           K+  + +++
Sbjct: 85 PKDYVVQVIV 94

>pdb|3M63|B Chain B, Crystal Structure Of Ufd2 In Complex With The Ubiquitin-Like (Ubl) Domain Of Dsk2 Length = 101

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70
          + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y+IQ   ++HLV
Sbjct: 42 VNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLV 97

>pdb|1UEL|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Hhr23b Complexed With Ubiquitin-Interacting Motif Of Proteasome Subunit S5a Length = 95

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 50/88 (56%), Gaps = 3/88 (3%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ ++G    P   Q+LI+AGK L D   L 
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60
Query: 58 DYNIQKESTLHLVLRLRGGIIEPSLMAL 85
          +Y I +++ + +++     +  P+   L
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVSTPAPATL 88

>pdb|2BWE|S Chain S, The Crystal Structure Of The Complex Between The Uba And Ubl Domains Of Dsk2 Length = 77

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70
          + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y+IQ   ++HLV
Sbjct: 18 VNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLV 73

>pdb|1P1A|A Chain A, Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ ++G    P   Q+LI+AGK L D   L 
Sbjct: 4  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 63
Query: 58 DYNI 61
          +Y I
Sbjct: 64 EYKI 67

>pdb|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a Length = 368

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADY 59
          I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + DY
Sbjct: 10 ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 69
Query: 60 NI-QKESTLHLVLRLRGG 76
           I +K   + +V + + G
Sbjct: 70 RIDEKNFVVVMVTKTKAG 87

>pdb|3IZS|PP Chain p, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 52

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/26 (69%), Positives = 20/26 (76%)
Query: 77  IIEPSLMALARKYNQDKMICRKSHTR 102
           IIEPSL ALA KYN DK +CRK + R
Sbjct: 1   IIEPSLKALASKYNCDKSVCRKCYAR 26

>pdb|3ZEY|9 Chain 9, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 153

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          MQ+F+++ TG T  +E  ++DT+  ++AK     G         F G  L E+  TLA+ 
Sbjct: 1  MQLFLRSATGATSVVEASAADTVGTLRAKA----GFDDTSSIFFFGGFCLREESATLAEC 56
Query: 60 NIQKESTLHLVL 71
           +Q+ ST+ +++
Sbjct: 57 GLQQGSTVQVMI 68

>pdb|2WYQ|A Chain A, The Crystal Structure Of The Ubiquitin-Like (Ubl) Domain Of Hhr23a (Human Homologue A Of Rad23) Length = 85

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADY 59
          I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + DY
Sbjct: 8  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67
Query: 60 NI-QKESTLHLVLRLRGG 76
           I +K   + +V + + G
Sbjct: 68 RIDEKNFVVVMVTKTKAG 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	116
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	3e-55
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	2e-54
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	3e-53
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	3e-53
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	6e-53
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	8e-53
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	1e-52
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	1e-52
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	5e-52
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	8e-52
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	1e-51
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	5e-51
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	5e-51
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	7e-51
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	9e-51
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	1e-50
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	1e-50
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	6e-50
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	8e-50
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	4e-49
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	7e-49
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-48
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	3e-48
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	4e-48
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	3e-18
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	8e-48
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	9e-48
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	2e-47
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	2e-47
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	3e-05
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	2e-47
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	4e-47
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	6e-46
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	1e-45
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	2e-45
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	5e-45
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	6e-45
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	7e-45
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	1e-44
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	4e-43
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	3e-41
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	4e-07
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	9e-40
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	3e-19
1we6_A	111	Splicing factor, putative; structural genomics, ub	1e-39
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-39
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-35
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	6e-39
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	1e-37
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	8e-37
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-37
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	2e-37
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	1e-33
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	2e-32
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	1e-27
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	5e-23
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	6e-21
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	3e-17
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	3e-17
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	7e-17
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	2e-16
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	2e-15
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	2e-15
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	3e-15
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	4e-15
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	4e-15
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	8e-14
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	1e-13
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	7e-13
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	2e-10
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	3e-08
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	3e-08
2kj6_A	97	Tubulin folding cofactor B; methods development, N	1e-07
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	2e-07
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	4e-07
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	2e-06
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	3e-06
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	4e-06
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	1e-05
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	1e-05
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	3e-05
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	6e-05
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	1e-04
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	2e-04
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	3e-04

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Length = 76

 Score =  165 bits (420), Expect = 3e-55
 Identities = 43/76 (56%), Positives = 58/76 (76%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B Length = 88

 Score =  163 bits (415), Expect = 2e-54
 Identities = 43/76 (56%), Positives = 58/76 (76%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score =  161 bits (409), Expect = 3e-53
 Identities = 22/80 (27%), Positives = 41/80 (51%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            Q+ ++  TGK + L V S+DT+ ++K ++   EG+ P  QR  F+G+ L D     +  
Sbjct: 24  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELK 83

Query: 61  IQKESTLHLVLRLRGGIIEP 80
           I K+  + +++        P
Sbjct: 84  IPKDYVVQVIVSQPVQNPTP 103

>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G* 2noq_F 1s1h_G 3iz6_F Length = 225

 Score =  163 bits (413), Expect = 3e-53
 Identities = 5/76 (6%), Positives = 19/76 (25%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M      +  +     VE    +       ++ +    + +       +  + +  +  +
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD 60

Query: 61 IQKESTLHLVLRLRGG 76
            +      V    G 
Sbjct: 61 YVQVRQPIFVAHTAGR 76

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Length = 85

 Score =  159 bits (405), Expect = 6e-53
 Identities = 71/81 (87%), Positives = 74/81 (91%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63

Query: 61 IQKESTLHLVLRLRGGIIEPS 81
          IQK STL L+LRLRGG    S
Sbjct: 64 IQKWSTLFLLLRLRGGGGGGS 84

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score =  159 bits (405), Expect = 8e-53
 Identities = 66/79 (83%), Positives = 76/79 (96%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+F+KTLTGKT T+E+E SDTI+N+KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 69

Query: 61 IQKESTLHLVLRLRGGIIE 79
          IQKESTLHLVLRLRGG ++
Sbjct: 70 IQKESTLHLVLRLRGGGLD 88

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score =  159 bits (404), Expect = 1e-52
 Identities = 62/81 (76%), Positives = 69/81 (85%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M+I VKTL G+TI LEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63

Query: 61 IQKESTLHLVLRLRGGIIEPS 81
          I   S L+L+L+LRGG    S
Sbjct: 64 IHNHSALYLLLKLRGGGGGGS 84

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Length = 88

 Score =  159 bits (403), Expect = 1e-52
 Identities = 44/76 (57%), Positives = 59/76 (77%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 72

Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVLRLRGG
Sbjct: 73 ILGGSVLHLVLRLRGG 88

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ... Length = 76

 Score =  157 bits (399), Expect = 5e-52
 Identities = 72/76 (94%), Positives = 75/76 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A Length = 90

 Score =  157 bits (398), Expect = 8e-52
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 65

Query: 61 IQKESTLHLVLRLRGGIIEPS 81
          +  +  +HLV R       PS
Sbjct: 66 VGGK-VIHLVERAPPQTHLPS 85

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 87

 Score =  156 bits (397), Expect = 1e-51
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+FVK   G +    +  +  I  +K +I+D++G+P  QQ+L F G+ L+D   L  Y 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYG 67

Query: 61 IQKESTLHLVLRLRGG 76
          IQ   TL L  +   G
Sbjct: 68 IQDSDTLILSKKKGSG 83

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Length = 96

 Score =  155 bits (394), Expect = 5e-51
 Identities = 72/76 (94%), Positives = 74/76 (97%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61

Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRG 
Sbjct: 62 IQKESTLHLVLRLRGY 77

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 95

 Score =  155 bits (394), Expect = 5e-51
 Identities = 25/93 (26%), Positives = 52/93 (55%), Gaps = 3/93 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ ++G    P   Q+LI+AGK L D   L 
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 58 DYNIQKESTLHLVLRLRGGIIEPSLMALARKYN 90
          +Y I +++ + +++     +  P+   L   ++
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVSTPAPATLEHHHH 93

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score =  155 bits (394), Expect = 7e-51
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95

Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score =  155 bits (393), Expect = 9e-51
 Identities = 70/82 (85%), Positives = 76/82 (92%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           QIF KTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLI+AGKQLEDGRTL+DYN
Sbjct: 10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYN 69

Query: 61 IQKESTLHLVLRLRGGIIEPSL 82
          IQ+ESTLHLVLRLRGG +  + 
Sbjct: 70 IQRESTLHLVLRLRGGSMGGAA 91

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score =  154 bits (392), Expect = 1e-50
 Identities = 75/97 (77%), Positives = 81/97 (83%), Gaps = 6/97 (6%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGGI------IEPSLMALARKYNQ 91
          IQKESTLHLVLRLRGG       ++    AL   ++ 
Sbjct: 61 IQKESTLHLVLRLRGGRDPNSSSVDKLAAALEHHHHH 97

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A Length = 76

 Score =  153 bits (390), Expect = 1e-50
 Identities = 25/75 (33%), Positives = 48/75 (64%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCD 60

Query: 61 IQKESTLHLVLRLRG 75
          ++++S +H+V R R 
Sbjct: 61 LEQQSIVHIVQRPRR 75

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens} Length = 88

 Score =  152 bits (386), Expect = 6e-50
 Identities = 28/78 (35%), Positives = 45/78 (57%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64

Query: 61 IQKESTLHLVLRLRGGII 78
          ++  ST+ + LRLRGG+ 
Sbjct: 65 LKPLSTVFMNLRLRGGLE 82

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score =  152 bits (385), Expect = 8e-50
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 77

Query: 61 IQKESTLHLVLR 72
          +  +  +HLV R
Sbjct: 78 VGGK-VIHLVER 88

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score =  150 bits (380), Expect = 4e-49
 Identities = 29/73 (39%), Positives = 46/73 (63%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+ VK L G+  +L+V   + +  +K  + +K  +P  QQRL+F GK L DG+ L+DY+
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYS 67

Query: 61 IQKESTLHLVLRL 73
          I   S L+LV++ 
Sbjct: 68 IGPNSKLNLVVKP 80

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 89

 Score =  149 bits (379), Expect = 7e-49
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 2/78 (2%)

Query: 1  MQIFVKTLTG-KTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G KT T+E V    TI+ ++ ++     + P+ QRL + GKQLE+G TL D
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 67

Query: 59 YNIQKESTLHLVLRLRGG 76
          Y++     + L++R   G
Sbjct: 68 YDVGLNDIIQLLVRPDSG 85

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score =  149 bits (377), Expect = 1e-48
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FV+    +  T EV   +T+  +KA +   EGI P+ Q ++ AG  LED  TL    
Sbjct: 20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCG 77

Query: 61 IQKESTLHLVLRLRGG 76
          ++  +TL +  R+ GG
Sbjct: 78 VEALTTLEVAGRMLGG 93

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p Length = 128

 Score =  149 bits (377), Expect = 3e-48
 Identities = 92/102 (90%), Positives = 96/102 (94%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTR 102
           IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRK + R
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYAR 102

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score =  150 bits (381), Expect = 4e-48
 Identities = 76/101 (75%), Positives = 80/101 (79%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHT 101
           IQKESTLHLVLRLRGG  E              +I +    
Sbjct: 61  IQKESTLHLVLRLRGGGGETIKFVADGDIGSGSVIIKPFVD 101

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score = 74.6 bits (183), Expect = 3e-18
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 12/96 (12%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED---GRTLA 57
              FV      + ++ ++    +++ +  I+ +   P D   L F  K L D   G +L+
Sbjct: 80  TIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVD---LTFGAKYLLDIIKGSSLS 136

Query: 58  D---YNIQKESTLHLVLRLRGGIIEPSLMALARKYN 90
           D     +  E+       L+ G ++     LA K+N
Sbjct: 137 DRVGIRLSSEAPALFQFDLKSGFLQ---FFLAPKFN 169

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score =  146 bits (371), Expect = 8e-48
 Identities = 27/75 (36%), Positives = 43/75 (57%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64

Query: 61 IQKESTLHLVLRLRG 75
          ++  ST+ + LRLRG
Sbjct: 65 LKPLSTVFMNLRLRG 79

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Length = 77

 Score =  146 bits (371), Expect = 9e-48
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 1  MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59
          M + +   +G+    + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY 62

Query: 60 NIQKESTLHLVLR 72
          +IQ   ++HLV  
Sbjct: 63 HIQDGHSVHLVKS 75

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score =  146 bits (371), Expect = 2e-47
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 18 IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 76

Query: 61 IQKESTLHLVLRLRGG 76
          ++   T+HLV++ +  
Sbjct: 77 VRDGLTVHLVIKRQHR 92

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score =  146 bits (371), Expect = 2e-47
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 1  MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59
          M + +   +G+    + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y
Sbjct: 27 MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY 86

Query: 60 NIQKESTLHLVLR 72
          +IQ   ++HLV  
Sbjct: 87 HIQDGHSVHLVKS 99

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 38.9 bits (91), Expect = 3e-05
 Identities = 5/22 (22%), Positives = 9/22 (40%)

Query: 48 KQLEDGRTLADYNIQKESTLHL 69
          K       ++DY+I     L+ 
Sbjct: 2  KHHHHHHPMSDYDIPTTENLYF 23

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score =  145 bits (369), Expect = 2e-47
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRTLADY 59
          M+  V+ L G +  LEV+  DT+  VK KI+  + IP  +Q LI  G   L +  T+   
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQC 70

Query: 60 NIQKESTLHLVL 71
           I   S + L +
Sbjct: 71 QIVPTSDIQLEV 82

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A Length = 115

 Score =  146 bits (370), Expect = 4e-47
 Identities = 21/75 (28%), Positives = 39/75 (52%)

Query: 2   QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
                 L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+
Sbjct: 37  DKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNM 96

Query: 62  QKESTLHLVLRLRGG 76
              + +HL L+ R G
Sbjct: 97  ASGAVIHLALKERSG 111

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score =  142 bits (361), Expect = 6e-46
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M++ VKT   K     V  + ++   K +I  +     DQ  LIFAGK L+D  TL+ + 
Sbjct: 26 MKVTVKTPKEK-EEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHG 84

Query: 61 IQKESTLHLVLR 72
          I    T+HLV++
Sbjct: 85 IHDGLTVHLVIK 96

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A Length = 85

 Score =  141 bits (357), Expect = 1e-45
 Identities = 24/80 (30%), Positives = 47/80 (58%), Gaps = 4/80 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          + I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + 
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 65

Query: 58 DYNIQKESTLHLVL-RLRGG 76
          DY I +++ + +++ + + G
Sbjct: 66 DYRIDEKNFVVVMVTKTKAG 85

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 100

 Score =  141 bits (357), Expect = 2e-45
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 81

Query: 61 IQKESTLHLVLRLR 74
          ++   T+HLV++ +
Sbjct: 82 VRDGLTVHLVIKRQ 95

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 96

 Score =  140 bits (354), Expect = 5e-45
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT         +  +  +   K +I        D+  LIF GK L D   L+   
Sbjct: 18 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRG 76

Query: 61 IQKESTLHLVLRLRGG 76
          I   ST+H+V+R   G
Sbjct: 77 ILDGSTVHVVVRSHSG 92

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score =  141 bits (356), Expect = 6e-45
 Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++ VKT   K     V  + ++   K  I  +     DQ  LIFAGK L+D  TL  + 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHG 91

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYN 90
           I    T+HLV++           A A +++
Sbjct: 92  IHDGLTVHLVIKRDPNSSSVDKYAAALEHH 121

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 78

 Score =  139 bits (352), Expect = 7e-45
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 1  MQIFVKTLTGKTIT--LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G+       +     ++ ++ KIQ+   + P  QRL + GKQ+EDG TL D
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 62

Query: 59 YNIQKESTLHLVLRL 73
          Y ++   T+ L++R 
Sbjct: 63 YEVRLNDTIQLLVRQ 77

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score =  142 bits (358), Expect = 1e-44
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+ VKTL G+T    +E   ++ ++K++I    G   D   L+  G    +   + D  
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVTDD- 59

Query: 61 IQKESTLHLVLRLRGG 76
               T +L L+L GG
Sbjct: 60 ----VTYYLSLKLLGG 71

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 106

 Score =  135 bits (342), Expect = 4e-43
 Identities = 16/72 (22%), Positives = 37/72 (51%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + +  K    + + L++E S+TI   K K+         Q +LI++GK L+D +T+++  
Sbjct: 2  VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECG 61

Query: 61 IQKESTLHLVLR 72
          ++    +  ++ 
Sbjct: 62 LKDGDQVVFMVS 73

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score =  137 bits (345), Expect = 3e-41
 Identities = 71/74 (95%), Positives = 73/74 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 293

Query: 61  IQKESTLHLVLRLR 74
           IQKESTLHLVLRLR
Sbjct: 294 IQKESTLHLVLRLR 307

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score = 46.0 bits (108), Expect = 4e-07
 Identities = 7/48 (14%), Positives = 15/48 (31%), Gaps = 1/48 (2%)

Query: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKEST-LHLVLRLRGG 76
               +G    +  + F G  L +   L   + +++   L   L     
Sbjct: 100 FFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYN 147

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score =  130 bits (327), Expect = 9e-40
 Identities = 72/76 (94%), Positives = 74/76 (97%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 165

Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 166 IQKESTLHLVLRLRGG 181

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 77.7 bits (191), Expect = 3e-19
 Identities = 13/70 (18%), Positives = 22/70 (31%), Gaps = 7/70 (10%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLA--D 58
                    GK+I       D   N + K+  K G    +  + +        R L   D
Sbjct: 40  KGNLADVAPGKSIG-----GDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSD 94

Query: 59  YNIQKESTLH 68
           + I K +  +
Sbjct: 95  WLIYKTTDHY 104

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 111

 Score =  127 bits (320), Expect = 1e-39
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 1   MQIFVKT-LTGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
           +++       G+ + + V+S S+ + ++K KI  +  IP ++Q+L      L+D  +LA 
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAH 89

Query: 59  YNIQKESTLHLVLRLRGG 76
           YN+     L L LR R G
Sbjct: 90  YNVGAGEILTLSLRERSG 107

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score =  128 bits (323), Expect = 1e-39
 Identities = 28/76 (36%), Positives = 44/76 (57%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141

Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 142 LKPLSTVFMNLRLRGG 157

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score =  118 bits (297), Expect = 1e-35
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLAD 58
            + VK L G    + + SS ++  +KA+I  K G+   QQRL    +G  L+D   LA 
Sbjct: 3  WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLAS 62

Query: 59 YNIQKESTLHLV 70
            +   ST+ LV
Sbjct: 63 QGLGPGSTVLLV 74

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score =  124 bits (314), Expect = 6e-39
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          + + VK    K  T+EV+ ++T+ ++K KI   E  P  + +L ++G +L +D R L +Y
Sbjct: 16 IHVTVKFP-SKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEY 74

Query: 60 NIQKESTLHLVLR 72
           I + S + + L+
Sbjct: 75 GITEFSEIVVFLK 87

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score =  123 bits (310), Expect = 1e-37
 Identities = 73/77 (94%), Positives = 76/77 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGGI 77
          IQKESTLHLVLRLRGG+
Sbjct: 61 IQKESTLHLVLRLRGGM 77

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score =  121 bits (304), Expect = 8e-37
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 77  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 136

Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 137 IQKESTLHLVLRLRGG 152

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score =  124 bits (312), Expect = 1e-37
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 97  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 156

Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 157 IQKESTLHLVLRLRGG 172

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score =  123 bits (309), Expect = 2e-37
 Identities = 73/77 (94%), Positives = 76/77 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80

Query: 61 IQKESTLHLVLRLRGGI 77
          IQKESTLHLVLRLRGG+
Sbjct: 81 IQKESTLHLVLRLRGGM 97

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana} Length = 85

 Score =  110 bits (278), Expect = 1e-33
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VK   GK+I L V    T+ ++K+++Q    + P  Q+LIF GK L +  TL   +
Sbjct: 13 IKLTVK-FGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSD 71

Query: 61 IQKESTLHLV 70
          +   + L L+
Sbjct: 72 VGSGAKLMLM 81

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A Length = 368

 Score =  115 bits (289), Expect = 2e-32
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          + I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + 
Sbjct: 8  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 67

Query: 58 DYNIQKESTLHLVLRLRGG 76
          DY I +++ + +++     
Sbjct: 68 DYRIDEKNFVVVMVTKTKA 86

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 102

 Score = 96.6 bits (240), Expect = 1e-27
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 1  MQIFVKT----LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRT 55
          M I V      LT  T +L+V     + N +   + + G+P ++ ++++  + L +D  +
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCS 67

Query: 56 LADYNIQKESTLHLVLRLRGGIIEPS 81
          L  Y ++    + L+ +   G+  P 
Sbjct: 68 LGSYGLKDGDMVVLLQKDNVGLRTPG 93

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 100

 Score = 84.8 bits (209), Expect = 5e-23
 Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADY 59
          M  F      + + + +E + T+  +K  ++++  IP  +  L  +    +ED   L   
Sbjct: 9  MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSL 68

Query: 60 NIQKESTLHLVLRLRGGIIEPS 81
          ++ K ++L+++          S
Sbjct: 69 HLPKNNSLYVLTPDLPPPSSSS 90

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 79.7 bits (196), Expect = 6e-21
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + +    +   TI L V    T+ ++K  +    G PP  Q+ +   +   D  TL  + 
Sbjct: 27 VSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHG 86

Query: 61 IQKE-STLHLVL 71
          +++   + +L L
Sbjct: 87 VRQNGDSAYLYL 98

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 69.8 bits (171), Expect = 3e-17
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + +         ++V    T   +K KI    G+PP  Q++++ G  + + +TL +  
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIK 75

Query: 61 IQKESTLHLV 70
          +   + + +V
Sbjct: 76 VTSGAKIMVV 85

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A Length = 118

 Score = 70.4 bits (172), Expect = 3e-17
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 1  MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59
          M +F+     K TI  + + S T+  +K  ++     PP++QRL    + L+DG+TL + 
Sbjct: 1  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGEC 60

Query: 60 NI-------QKESTLHLVLRLRG 75
                   Q  +T+ L  R   
Sbjct: 61 GFTSQTARPQAPATVGLAFRADD 83

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 93

 Score = 68.8 bits (168), Expect = 7e-17
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 1  MQIFVKT--LTGKTITLEVESSDTIDNVKAKIQDK--EGIPPDQQRLIFAGKQLEDGRTL 56
          + + VK+     + + L  +   ++ ++KA +     E   P+ QRLI++GK L D + L
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCL 67

Query: 57 ADYNIQKES--TLHLVLRLRGG 76
           D   ++E    LHLV  ++ G
Sbjct: 68 RDLLPKQEKRHVLHLVCNVKSG 89

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1 Length = 96

 Score = 67.6 bits (165), Expect = 2e-16
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            + VK    K   +E+ + +     KA++    G+ P +Q+++  G  L+D     +  
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIK 66

Query: 61 IQKESTLHLV 70
          ++   T+ ++
Sbjct: 67 MKNGMTVLMM 76

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 66.2 bits (161), Expect = 2e-15
 Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 8/89 (8%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKI--------QDKEGIPPDQQRLIFAGKQLED 52
           + + +  ++GKT       +D+  ++   +        ++++   P+  RLI+ G+ L  
Sbjct: 18  INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 77

Query: 53  GRTLADYNIQKESTLHLVLRLRGGIIEPS 81
             TL    +    T  + L  R  + EP+
Sbjct: 78  NVTLGALKLPFGKTTVMHLVARETLPEPN 106

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1 Length = 122

 Score = 65.7 bits (160), Expect = 2e-15
 Identities = 17/102 (16%), Positives = 38/102 (37%), Gaps = 13/102 (12%)

Query: 1   MQIFVK---TLTGKTITLE--VESSDTIDNVKAKIQDKEGIPPDQQRLI-------FAGK 48
           M        T       +E    +  +++++K K++   G   D  R+          G+
Sbjct: 3   MTEVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGE 62

Query: 49  QLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYN 90
             +  ++L D  ++    +H V  + GG  +    ++  KY 
Sbjct: 63  LTDGAKSLKDLGVRDGYRIHAV-DVTGGNEDFKDESMVEKYE 103

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1 Length = 116

 Score = 65.5 bits (159), Expect = 3e-15
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 10/82 (12%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD-------KEGIP-PDQQRLIFAGKQLED 52
          + + +  ++GKT       +D+  ++   + D       +E +  P+  RLI+ G+ L  
Sbjct: 17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 76

Query: 53 GRTLADYNIQ--KESTLHLVLR 72
            TL    +   K + +HLV R
Sbjct: 77 NVTLGALKLPFGKTTVMHLVAR 98

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1 Length = 107

 Score = 64.8 bits (157), Expect = 4e-15
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 1  MQIFVKTLTGKTITLEVE--------SSDTIDNVKAKIQDKEGI---PPDQQRLIFAGKQ 49
          +++  + L  K+I    E           +I  +K  I  K       P+   LI+ G++
Sbjct: 17 VKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRK 76

Query: 50 LEDGRTLADYNIQKESTLHLVLR 72
          L+D +TL  Y IQ  ST+H++ +
Sbjct: 77 LKDDQTLDFYGIQPGSTVHVLRK 99

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A Length = 93

 Score = 64.6 bits (157), Expect = 4e-15
 Identities = 16/69 (23%), Positives = 34/69 (49%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V    GK + ++    D++ + K  +  + G  P++  L   G  L+D  +L DY 
Sbjct: 22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYE 81

Query: 61 IQKESTLHL 69
          +  ++ L L
Sbjct: 82 VHDQTNLEL 90

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1 Length = 100

 Score = 61.3 bits (148), Expect = 8e-14
 Identities = 16/69 (23%), Positives = 30/69 (43%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++      GK + ++  + DTI ++K  I  + G   ++  L       +D  +L DY 
Sbjct: 29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYE 88

Query: 61 IQKESTLHL 69
          I     L L
Sbjct: 89 IHDGMNLEL 97

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 60.7 bits (147), Expect = 1e-13
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 1  MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDK--EGIPPDQQRLIFAGKQLEDGRTL 56
          + + +K    K    T+    + T+  +K  + +          QRL+++G+ L D   L
Sbjct: 24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQL 83

Query: 57 AD--YNIQKESTLHLV 70
           D      +   +HLV
Sbjct: 84 KDILRKQDEYHMVHLV 99

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 58.9 bits (142), Expect = 7e-13
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          + + +K L            DT+  +K+K    +     Q +LI+ G+ L +  RTL+  
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSL 64

Query: 60 NIQKESTLHLVLR 72
          NI     +H    
Sbjct: 65 NITNNCVIHCHRS 77

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A Length = 90

 Score = 52.2 bits (125), Expect = 2e-10
 Identities = 15/74 (20%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 1  MQIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTL 56
          + I VK   G+  ++  +   DT+ ++K  ++   G+ P++Q+L+     GK  E+   L
Sbjct: 8  LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKL 66

Query: 57 ADYNIQKESTLHLV 70
              ++  + + ++
Sbjct: 67 GALKLKPNTKIMMM 80

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 105

 Score = 46.9 bits (111), Expect = 3e-08
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 16/91 (17%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIF 45
          M + V  + G+ + + V  + T+ ++K  IQ    +  +++                L  
Sbjct: 8  MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 46 AGKQL-EDGRTLADYNIQKESTLHLVLRLRG 75
          AG++L ED + L DY I+    +  + +L  
Sbjct: 68 AGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQ 98

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus} Length = 86

 Score = 46.4 bits (110), Expect = 3e-08
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTL 56
          ++  K   G  +   + S   +  ++ +I    GI P  QR++  +  + L+      TL
Sbjct: 2  RVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITL 61

Query: 57 ADYNIQKESTL 67
           D  IQ    L
Sbjct: 62 GDLPIQSGDML 72

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 97

 Score = 44.9 bits (106), Expect = 1e-07
 Identities = 12/72 (16%), Positives = 23/72 (31%), Gaps = 7/72 (9%)

Query: 6  KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-------FAGKQLEDGRTLAD 58
            L   +         +++ VK K+  K G   +   L              +D R L  
Sbjct: 22 ANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGF 81

Query: 59 YNIQKESTLHLV 70
          ++      LH++
Sbjct: 82 FSPFDGFRLHII 93

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei} Length = 110

 Score = 45.3 bits (107), Expect = 2e-07
 Identities = 12/77 (15%), Positives = 34/77 (44%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + + V    G  +   ++S   +  +      K+GI  +  R +F G  +++ +T  +  
Sbjct: 27  VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELG 86

Query: 61  IQKESTLHLVLRLRGGI 77
           ++ +  +  ++   GG+
Sbjct: 87  MEDDDVIDAMVEQTGGL 103

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 92

 Score = 43.6 bits (102), Expect = 4e-07
 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 6/68 (8%)

Query: 9  TGKTITLEVESSD-----TIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADYNIQ 62
          + +   L V S        + ++   +++  G+P   Q+LIF GK L E    L+   IQ
Sbjct: 15 SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQ 74

Query: 63 KESTLHLV 70
              + L+
Sbjct: 75 DGCRVMLI 82

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster} Length = 320

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 16/110 (14%), Positives = 40/110 (36%), Gaps = 8/110 (7%)

Query: 10  GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKEST 66
           GK   +++   DT++ ++ +I  K  + P++Q+L+   + GK   D   ++   ++    
Sbjct: 14  GKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFK 73

Query: 67  LHLVLRLRGGIIEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNCF 116
           L +V     G  E  +       +    +          +    +     
Sbjct: 74  LMMV-----GSTEADIEDACSLPDNIGEVVDDFDDADEREESVAHSAVYL 118

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1 Length = 91

 Score = 41.7 bits (98), Expect = 3e-06
 Identities = 13/77 (16%), Positives = 34/77 (44%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 6  INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 65

Query: 61 IQKESTLHLVLRLRGGI 77
          ++ E T+ +  +  GG+
Sbjct: 66 MEDEDTIDVFQQQTGGV 82

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 126

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 13/67 (19%)

Query: 19  SSDTIDNVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLADYNIQ------KES 65
            + T+  +K  +     ++KE  P    + +LI AGK LE+ +T+ DY           +
Sbjct: 36  DATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVT 95

Query: 66  TLHLVLR 72
           T+H++++
Sbjct: 96  TMHVIIQ 102

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 7/58 (12%)

Query: 20 SDTIDNVKAKIQDKEGIPPDQQRLI-------FAGKQLEDGRTLADYNIQKESTLHLV 70
          S TI   K K++   G P     L        F  K  ++   L  Y +     +H++
Sbjct: 28 SLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVI 85

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C Length = 97

 Score = 39.9 bits (93), Expect = 1e-05
 Identities = 14/76 (18%), Positives = 36/76 (47%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V       I  +V+ +  +  +K     ++G+P +  R +F G+++ D  T  +  
Sbjct: 22 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELG 81

Query: 61 IQKESTLHLVLRLRGG 76
          +++E  + +     GG
Sbjct: 82 MEEEDVIEVYQEQTGG 97

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 104

 Score = 39.1 bits (91), Expect = 3e-05
 Identities = 12/76 (15%), Positives = 32/76 (42%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 25  INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 84

Query: 61  IQKESTLHLVLRLRGG 76
           ++ E T+ +  +   G
Sbjct: 85  MEDEDTIDVFQQQTSG 100

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1 Length = 94

 Score = 38.3 bits (89), Expect = 6e-05
 Identities = 16/82 (19%), Positives = 37/82 (45%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 8  INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 67

Query: 61 IQKESTLHLVLRLRGGIIEPSL 82
          ++ E T+ +  +  GG+ E SL
Sbjct: 68 MEDEDTIDVFQQQTGGVPESSL 89

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 88

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 5/66 (7%)

Query: 9  TGKTIT--LEVESSDTIDNVKAKI-QDKEGIPPDQQ--RLIFAGKQLEDGRTLADYNIQK 63
          T + +    +VE   TI  +K    +      P +Q  RL   GK L+D   L    +  
Sbjct: 20 TREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGT 79

Query: 64 ESTLHL 69
           +TL+ 
Sbjct: 80 TATLYF 85

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster} Length = 95

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 6/55 (10%)

Query: 22 TIDNVKAKIQDKEGIPPDQQRL-IFAGKQL-----EDGRTLADYNIQKESTLHLV 70
          T+  +K K++   G      ++ +F G         +   L  Y       LH+V
Sbjct: 39 TVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV 93

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A Length = 93

 Score = 36.0 bits (83), Expect = 3e-04
 Identities = 13/76 (17%), Positives = 33/76 (43%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 18 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 77

Query: 61 IQKESTLHLVLRLRGG 76
          ++ E T+ +  +  GG
Sbjct: 78 MEDEDTIDVFQQQTGG 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	116
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.96
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.91
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.89
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.89
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.88
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.88
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.88
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.88
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.88
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.87
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.87
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.87
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.87
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.86
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.86
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.86
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.86
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.85
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.85
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.85
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.85
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.85
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.85
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.84
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.84
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.84
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.84
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.84
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.84
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.84
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.84
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.83
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.83
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.83
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.83
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.82
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.82
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.82
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.82
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.71
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.82
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.82
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.82
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.82
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.81
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.81
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.8
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.8
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.8
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.8
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.8
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.79
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.79
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.78
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.78
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.78
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.78
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.78
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.77
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.77
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.77
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.77
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.76
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.76
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.75
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.75
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.75
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.74
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.74
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.74
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.74
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.74
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.74
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.73
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.69
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.68
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.66
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.66
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.66
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.65
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.65
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.63
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.61
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.6
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.6
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.59
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.58
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.57
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.56
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.55
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.54
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.54
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.52
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.5
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.48
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.39
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.3
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	99.2
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	99.16
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	99.1
2pjh_A	80	Protein NPL4, nuclear protein localization protein	99.03
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.93
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.89
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.71
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.62
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	98.57
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	98.56
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.48
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	98.42
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.29
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	98.17
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	98.07
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.92
2ayj_A	56	50S ribosomal protein L40E; Zn-binding, beta-stran	97.81
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.68
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	97.48
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	97.28
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	97.27
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	97.26
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	97.26
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	97.08
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	96.92
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	96.73
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	96.45
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	96.44
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	96.28
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	96.24
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	96.22
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	96.18
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	96.01
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	95.45
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	95.39
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	95.16
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	95.11
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	95.08
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	94.92
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	94.82
2cu3_A	64	Unknown function protein; thermus thermophilus HB8	94.65
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	94.42
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	94.0
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	93.96
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	93.93
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	93.81
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	93.53
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	93.3
2g1e_A	90	Hypothetical protein TA0895; MOAD, molybdopterin,	93.01
1rws_A	77	Hypothetical protein PF1061; residual dipolar coup	92.78
1wgy_A	104	RAP guanine nucleotide exchange factor 5; ubiquiti	92.73
3u52_E	119	Phenol hydroxylase component PHO; 4-helix bundle,	92.61
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	92.27
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	91.59
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	91.52
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	91.4
1y8x_B	98	Ubiquitin-activating enzyme E1C; ubiquitin-conjuga	91.33
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	91.29
2inc_C	83	TOUB protein; DIIRON, 4-helix bundle, carboxylate	90.88
2kmc_A	102	Fermitin family homolog 1; kindlin, cytoskeleton,	90.72
3ge3_C	84	Toluene-4-monooxygenase system protein B; DIIRON h	90.72
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	90.23
2l52_A	99	Methanosarcina acetivorans SAMP1 homolog; beta-grA	89.92
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	89.12
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	89.05
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	88.43
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	88.42
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	88.27
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	87.48
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	86.78
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	86.12
1j0g_A	92	Hypothetical protein 1810045K17; ubiquitin-like fo	85.01
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	83.73
3h9d_A	119	ATG8, microtubule-associated protein 1A/1B, light	83.15
2dhz_A	120	RAP guanine nucleotide exchange factor (GEF)- like	82.37
3qa8_A	676	MGC80376 protein; kinase ubiquitin-like domain, ph	82.28
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	82.11
3r8s_T	93	50S ribosomal protein L23; protein biosynthesis, R	81.65
2zjd_A	130	Microtubule-associated proteins 1A/1B light chain	80.28

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=99.96  E-value=3.4e-31  Score=173.36  Aligned_cols=110  Identities=86%  Similarity=1.191  Sum_probs=33.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+|+|++.+|+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++..||.+++
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~GG~~~~   80 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEP   80 (128)
T ss_dssp             ----------------------------------------------------------------------------CCCH
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCCCCCCh
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHcCCCcccccccccccccCCCccccccC
Q 033570           81 SLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        81 ~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      +.+..+.+++..+++|++||.+   ++|.|  +||
T Consensus        81 sl~~la~k~n~~~~ic~~~~~~---~~~~~--~~~  110 (128)
T 3u5e_m           81 SLKALASKYNCDKSVCRKCYAR---LPPRA--TNC  110 (128)
T ss_dssp             HHHHHHHHHHTSCEEETTTCCE---ECTTC--SSC
T ss_pred             hHHHHHHHhhcceEeecccccc---CCchh--hcc
Confidence            9999999999999999999999   99999  888

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B

Probab=99.91  E-value=1.2e-23  Score=129.22  Aligned_cols=84  Identities=51%  Similarity=0.795  Sum_probs=73.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||+..+
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~Gg~~~~   80 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGGLR   80 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC------
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCCCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998776


Q ss_pred             chHH
Q 033570           81 SLMA   84 (116)
Q Consensus        81 ~~~~   84 (116)
                      +...
T Consensus        81 ~~~~   84 (88)
T 4fbj_B           81 QKHH   84 (88)
T ss_dssp             ----
T ss_pred             cccc
Confidence            6543

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.89  E-value=1e-22  Score=123.49  Aligned_cols=81  Identities=77%  Similarity=1.057  Sum_probs=72.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|+++++|++++++.||+.++
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG~g~~   83 (85)
T 3n3k_B            4 MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGGGGGG   83 (85)
T ss_dssp             CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC------
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998665


Q ss_pred             c
Q 033570           81 S   81 (116)
Q Consensus        81 ~   81 (116)
                      +
T Consensus        84 ~   84 (85)
T 3n3k_B           84 S   84 (85)
T ss_dssp             -
T ss_pred             C
Confidence            3

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} SCOP: d.15.1.1

Probab=99.89  E-value=1.7e-22  Score=122.43  Aligned_cols=81  Identities=88%  Similarity=1.139  Sum_probs=74.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.++++|++++++.||+..+
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~GG~ggg   83 (85)
T 3mtn_B            4 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGGGGGG   83 (85)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCCC----
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcCCCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999998665


Q ss_pred             c
Q 033570           81 S   81 (116)
Q Consensus        81 ~   81 (116)
                      +
T Consensus        84 ~   84 (85)
T 3mtn_B           84 S   84 (85)
T ss_dssp             -
T ss_pred             C
Confidence            4

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.88  E-value=2.9e-22  Score=120.27  Aligned_cols=75  Identities=36%  Similarity=0.595  Sum_probs=72.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+|++.+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++++|
T Consensus         5 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~G   79 (79)
T 3phx_B            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (79)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCBC
T ss_pred             EEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999875

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A

Probab=99.88  E-value=4e-22  Score=118.21  Aligned_cols=76  Identities=57%  Similarity=0.952  Sum_probs=72.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|++.+|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++.+||
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC--
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999887

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.88  E-value=2.4e-22  Score=122.59  Aligned_cols=80  Identities=33%  Similarity=0.481  Sum_probs=77.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|.++++|++++++.||++++
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG~~~g   87 (87)
T 1wh3_A            8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGPSSG   87 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCSCCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999998764

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...

Probab=99.88  E-value=6.9e-22  Score=117.20  Aligned_cols=76  Identities=95%  Similarity=1.320  Sum_probs=74.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++||+.+|++|+++++..||
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG   76 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999987

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.88  E-value=4.7e-22  Score=122.04  Aligned_cols=78  Identities=85%  Similarity=1.232  Sum_probs=70.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~   78 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++.+||+.
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~GG~~   87 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGL   87 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC-------
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999999964

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.87  E-value=6.2e-22  Score=123.70  Aligned_cols=76  Identities=97%  Similarity=1.333  Sum_probs=74.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
T Consensus        23 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~GG   98 (98)
T 4hcn_B           23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   98 (98)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999987

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: d.15.1.1 PDB: 3dbr_I 3dbl_I

Probab=99.87  E-value=4.8e-22  Score=121.32  Aligned_cols=76  Identities=58%  Similarity=0.975  Sum_probs=74.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|.++++|++++++.||
T Consensus        13 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   88 (88)
T 3dbh_I           13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRGG   88 (88)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999987

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=99.87  E-value=2.5e-24  Score=144.44  Aligned_cols=106  Identities=70%  Similarity=0.889  Sum_probs=24.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC---
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI---   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~---   77 (116)
                      |+|+|++.+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|++++++.||.   
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GGgKkr   80 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGKKR   80 (152)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCCCcCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999983   


Q ss_pred             ---CCCchHHHHHHcCCCcccccccccccccC
Q 033570           78 ---IEPSLMALARKYNQDKMICRKSHTRTRNQ  106 (116)
Q Consensus        78 ---~~~~~~~~~~~~~~~~~~c~~~~~~~~~~  106 (116)
                         ....|+...++++..+++.+++|+++++.
T Consensus        81 kKk~~t~Pkk~~~~~~~~~~~~~~~~~~~~~~  112 (152)
T 3u5c_f           81 KXXXXXXXXXXXXXXXXXXXXVLSYYKVDAEG  112 (152)
T ss_dssp             -CCCCCCCSCCCCCCCCCCCCCCCCSEECSSS
T ss_pred             ccccccccccccccccccccceeeEEEEccCC
Confidence               45678888899999999999999998764

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A

Probab=99.87  E-value=1.4e-21  Score=121.26  Aligned_cols=77  Identities=94%  Similarity=1.256  Sum_probs=73.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++..||.
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~gG~   78 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYA   78 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC--
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999985

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A

Probab=99.86  E-value=2.2e-21  Score=119.12  Aligned_cols=77  Identities=32%  Similarity=0.546  Sum_probs=71.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~   78 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+| +|++|+++.+.+++..
T Consensus         6 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~~~~   82 (90)
T 4dwf_A            6 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPPQTH   82 (90)
T ss_dssp             EEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC---
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCCCCC
Confidence            7999999999999999999999999999999999999999999999999999999999999 8999999999877653

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=99.86  E-value=3.3e-21  Score=118.92  Aligned_cols=70  Identities=23%  Similarity=0.433  Sum_probs=68.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |+|+|+++.|+++.++++|++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|+|++|++|++.
T Consensus        22 IqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~   91 (93)
T 3plu_A           22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   91 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999999999999986

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.86  E-value=5.2e-21  Score=117.12  Aligned_cols=77  Identities=36%  Similarity=0.607  Sum_probs=74.1

Q ss_pred             CEEEEEcCCC-CEEEE-EecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTG-KTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g-~~~~i-~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+| +.+.+ +|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|.+|++|++++++.||+
T Consensus         8 m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~gG~   86 (89)
T 1wy8_A            8 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDSGP   86 (89)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCCCSS
T ss_pred             EEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCCCCC
Confidence            7899999999 69999 59999999999999999999999999999999999999999999999999999999999985

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B

Probab=99.86  E-value=2.1e-21  Score=116.45  Aligned_cols=76  Identities=18%  Similarity=0.448  Sum_probs=73.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|++.+|+.+.++|++++||.+||+.|+++.|+|++.|+|+|+|+.|.|+.+|++|+|.+|++|+++++..||
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~GG   79 (79)
T 2uyz_B            4 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   79 (79)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC-
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999887

>3vdz_A Ubiquitin-40S ribosomal protein S27A; gadolinium, MRI contrast agent, peptide-based contrast agent lanthanide binding TAG; 2.40A {Synthetic construct} PDB: 2ojr_A

Probab=99.85  E-value=5.2e-21  Score=122.11  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|.|+.+|++|+|.+|++|+++++++||
T Consensus        36 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~GG  111 (111)
T 3vdz_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC-
T ss_pred             EEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999987

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.85  E-value=1.5e-21  Score=119.71  Aligned_cols=78  Identities=36%  Similarity=0.601  Sum_probs=70.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~   78 (116)
                      |+|+|++.+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..||+-
T Consensus         5 m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~gg~~   82 (88)
T 2hj8_A            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGLE   82 (88)
T ss_dssp             EEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC------
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCcc
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999999874

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.85  E-value=5.3e-21  Score=117.81  Aligned_cols=74  Identities=92%  Similarity=1.261  Sum_probs=71.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++
T Consensus        18 m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rlr   91 (91)
T 3v6c_B           18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   91 (91)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEecC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999998863

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.85  E-value=8.3e-21  Score=118.40  Aligned_cols=77  Identities=95%  Similarity=1.295  Sum_probs=74.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..||+
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~   77 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGR   77 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999885

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.85  E-value=6.4e-21  Score=118.42  Aligned_cols=76  Identities=28%  Similarity=0.452  Sum_probs=73.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCC-CccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~-~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|++.++ .+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+ .+|++|||++|++|+++++++||+
T Consensus        16 ~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~gg~   92 (94)
T 2kan_A           16 IHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINRA   92 (94)
T ss_dssp             EEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCSSC
T ss_pred             EEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCCCC
Confidence            6899999887 899999999999999999999999999999999999999999 999999999999999999999885

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.85  E-value=1.5e-20  Score=116.72  Aligned_cols=77  Identities=29%  Similarity=0.573  Sum_probs=72.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHh---hCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~---~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|++.+|+.+.++|++++||.+||++|++.   .|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+...+.
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~~~~   80 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAV   80 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCCCCC
Confidence            899999999999999999999999999999999   78999999999999999999999999999999999998765543

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.84  E-value=8.1e-21  Score=117.64  Aligned_cols=74  Identities=36%  Similarity=0.620  Sum_probs=71.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|++  |+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++++||
T Consensus        20 m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~GG   93 (93)
T 2l7r_A           20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLGG   93 (93)
T ss_dssp             CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCCC
T ss_pred             EEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            7999998  7899999999999999999999999999999999999999999999999999999999999999987

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.84  E-value=8.4e-21  Score=115.64  Aligned_cols=72  Identities=33%  Similarity=0.489  Sum_probs=70.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEE-cCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~-L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+. |+|+.+|++|||.+|++|+++++
T Consensus        11 ~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~   83 (84)
T 2kk8_A           11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVS   83 (84)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEEC
T ss_pred             eEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEc
Confidence            8999999999999999999999999999999999999999999999999 99999999999999999999876

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.84  E-value=6.3e-21  Score=121.61  Aligned_cols=80  Identities=31%  Similarity=0.421  Sum_probs=76.5

Q ss_pred             CEEEEEcC---CCCEEEEEecC-CCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTL---TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~---~g~~~~i~v~~-~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+.+   +|+.+.++|++ ++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++++||
T Consensus        28 i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r~~GG  107 (111)
T 1we6_A           28 ATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             EEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             EEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCC
Confidence            68999998   78899999998 999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 033570           77 IIEP   80 (116)
Q Consensus        77 ~~~~   80 (116)
                      +.|+
T Consensus       108 k~h~  111 (111)
T 1we6_A          108 PSSG  111 (111)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8774

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C

Probab=99.84  E-value=9.1e-21  Score=118.25  Aligned_cols=76  Identities=18%  Similarity=0.448  Sum_probs=74.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|++.+|+.+.+.|.+++||.+||++|+++.|+|++.|+|+|+|+.|.|+.+|++|+|.+|++|++++++.||
T Consensus        22 m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~GG   97 (97)
T 1wyw_B           22 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   97 (97)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999987

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.84  E-value=2.6e-20  Score=126.77  Aligned_cols=77  Identities=96%  Similarity=1.296  Sum_probs=74.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||+
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~GG~   77 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC--
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEecccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999985

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.84  E-value=1.4e-20  Score=116.35  Aligned_cols=77  Identities=29%  Similarity=0.465  Sum_probs=72.7

Q ss_pred             CEEEEEcCCCC--EEEEEecCCCCHHHHHHHHHHhh--CCCCCceEEEECCEEcCCCCccccC--CCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~--~~~i~v~~~~TV~~LK~~I~~~~--~i~~~~q~L~~~g~~L~d~~tL~~~--gi~~g~~I~v~~~~~   74 (116)
                      |+|+|++.+++  .+.+++++++||.+||++|++.+  ++|+++|+|+|+|+.|+|+.+|++|  +|+++++|+++++..
T Consensus         8 m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~~~   87 (93)
T 1wgd_A            8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVK   87 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCC
T ss_pred             EEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeCCC
Confidence            78999999888  57777889999999999999998  9999999999999999999999999  999999999999999


Q ss_pred             CCC
Q 033570           75 GGI   77 (116)
Q Consensus        75 gg~   77 (116)
                      ||+
T Consensus        88 gg~   90 (93)
T 1wgd_A           88 SGP   90 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            985

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.84  E-value=1.8e-20  Score=121.99  Aligned_cols=87  Identities=29%  Similarity=0.329  Sum_probs=69.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      |+|+|+.. |+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..+|+..+
T Consensus        33 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~gg~~~~  111 (125)
T 1j8c_A           33 IKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPNSSSV  111 (125)
T ss_dssp             EEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC--------
T ss_pred             EEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCCCCCCc
Confidence            78999998 89999999999999999999999999999999999999999999999999999999999999999998777


Q ss_pred             chHHHHHH
Q 033570           81 SLMALARK   88 (116)
Q Consensus        81 ~~~~~~~~   88 (116)
                      +...++.+
T Consensus       112 ~~~~~~~~  119 (125)
T 1j8c_A          112 DKYAAALE  119 (125)
T ss_dssp             --------
T ss_pred             chhhhhhh
Confidence            66666544

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.84  E-value=2.5e-20  Score=111.46  Aligned_cols=73  Identities=36%  Similarity=0.643  Sum_probs=70.0

Q ss_pred             CEEEEEcCCCCEE-EEE-ecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTI-TLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~-~i~-v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|++.+|+.+ .++ +++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|++++++
T Consensus         3 m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~   77 (78)
T 2faz_A            3 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             EEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            7999999999885 899 999999999999999999999999999999999999999999999999999999875

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.83  E-value=4.4e-20  Score=117.72  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||.+|++|++++++.||
T Consensus        36 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~GG  111 (111)
T 2ojr_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCCC-
T ss_pred             EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999987

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.83  E-value=2.7e-20  Score=113.74  Aligned_cols=71  Identities=35%  Similarity=0.627  Sum_probs=68.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+|++.+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++||| +|++|+++.|
T Consensus        18 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i-~g~~i~lv~R   88 (88)
T 4eew_A           18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             EEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcHHHcCC-CCcEEEEEEC
Confidence            7899999999999999999999999999999999999999999999999999999999999 8999999875

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.83  E-value=1.5e-20  Score=119.10  Aligned_cols=75  Identities=21%  Similarity=0.426  Sum_probs=70.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+||..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++++...
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~   76 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKK   76 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC--
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999998544

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=3.4e-20  Score=111.33  Aligned_cols=73  Identities=40%  Similarity=0.690  Sum_probs=70.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|++++++
T Consensus         8 m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A            8 MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             EEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999875

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.82  E-value=2.6e-20  Score=116.67  Aligned_cols=71  Identities=23%  Similarity=0.324  Sum_probs=68.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|+|+++.|+.+.++|++++||.+||++|+++.|+|+++|+|+|+|++|+|+.+|++|+|.++++|+++.
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            78999999999999999999999999999999999999999999999999999999999999999999863

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.82  E-value=2.2e-20  Score=115.98  Aligned_cols=77  Identities=27%  Similarity=0.345  Sum_probs=73.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~   78 (116)
                      |+|+|+.. |+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++.+..+|+-
T Consensus        18 m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~g~~   94 (96)
T 1wx8_A           18 IRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSGPS   94 (96)
T ss_dssp             EEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSCSS
T ss_pred             EEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCCCC
Confidence            78999998 899999999999999999999999999999999999999999999999999999999999999988853

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A

Probab=99.82  E-value=1.1e-19  Score=110.14  Aligned_cols=74  Identities=30%  Similarity=0.531  Sum_probs=69.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHh---hCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~---~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++.   .|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..
T Consensus         6 m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A            6 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             EEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            789999999999999999999999999999998   78999999999999999999999999999999999998643

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.82  E-value=9.6e-20  Score=122.20  Aligned_cols=77  Identities=36%  Similarity=0.589  Sum_probs=72.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||.
T Consensus        82 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~GG~  158 (159)
T 3rt3_B           82 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGG  158 (159)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC---
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999983

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=99.71  E-value=7.7e-22  Score=117.45  Aligned_cols=75  Identities=33%  Similarity=0.588  Sum_probs=72.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+|++.+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++++|
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999876

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.82  E-value=1.4e-19  Score=107.65  Aligned_cols=71  Identities=34%  Similarity=0.574  Sum_probs=68.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+|++ +|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.+
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            6899999 8999999999999999999999999999999999999999999999999999999999999865

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.82  E-value=8.6e-20  Score=115.39  Aligned_cols=78  Identities=33%  Similarity=0.465  Sum_probs=73.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~   79 (116)
                      |+|+|+..+|+ +.++|++++||.+||++|++..++++++|+|+|+|+.|+|+.+|++|+|.+|++|+++.+..+|+..
T Consensus        18 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~~~~~   95 (106)
T 1wx7_A           18 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAMG   95 (106)
T ss_dssp             EEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCCSCC
T ss_pred             EEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCCCCC
Confidence            78999998875 7899999999999999999999999999999999999999999999999999999999999988754

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.82  E-value=3.3e-20  Score=113.75  Aligned_cols=73  Identities=22%  Similarity=0.429  Sum_probs=68.7

Q ss_pred             CEEEEEcCCCCEEEEEec--CCCCHHHHHHHH-HHhhCCCCCceEEEECCEEcCCCCccccCCC-CCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVE--SSDTIDNVKAKI-QDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~--~~~TV~~LK~~I-~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi-~~g~~I~v~~~~   73 (116)
                      |+|+||+.+|+.+.++|+  +++||.+||++| ++..|+|+++|+|+|+|+.|+|+.+|++|+| .+|++|++..+.
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            899999999998888755  999999999999 9999999999999999999999999999999 699999999874

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.9e-19  Score=115.33  Aligned_cols=77  Identities=91%  Similarity=1.265  Sum_probs=74.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      ++|.|+..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+++||.
T Consensus        10 ~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG~   86 (114)
T 2kdi_A           10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGS   86 (114)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSSC
T ss_pred             EEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCCc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999985

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.81  E-value=9.7e-20  Score=114.25  Aligned_cols=76  Identities=34%  Similarity=0.469  Sum_probs=72.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+ +.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..+|.
T Consensus        23 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~p   98 (100)
T 1yqb_A           23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRA   98 (100)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCSC
T ss_pred             EEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCCC
Confidence            78999998886 78999999999999999999999999999999999999999999999999999999999988764

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.81  E-value=8e-20  Score=126.26  Aligned_cols=77  Identities=94%  Similarity=1.252  Sum_probs=75.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|+++++|++++++.||+
T Consensus       106 MqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG~  182 (189)
T 3q3f_A          106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG  182 (189)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCCC
T ss_pred             eeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999985

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.80  E-value=1.7e-19  Score=112.83  Aligned_cols=73  Identities=21%  Similarity=0.423  Sum_probs=67.9

Q ss_pred             CEEEEEcCCCCEEEE--EecCCCCHHHHHHHH-HHhhCCCCCceEEEECCEEcCCCCccccCCC-CCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITL--EVESSDTIDNVKAKI-QDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i--~v~~~~TV~~LK~~I-~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi-~~g~~I~v~~~~   73 (116)
                      |+|+||+.+|+.+.+  +|++++||.+||++| ++..|+|+++|+|+|+|+.|.|+.+|++|+| ++|++|+++++.
T Consensus        20 m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvsk   96 (98)
T 4a20_A           20 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   96 (98)
T ss_dssp             EEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeC
Confidence            789999999998776  666999999999999 8888999999999999999999999999999 999999999874

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A

Probab=99.80  E-value=2.3e-19  Score=115.01  Aligned_cols=79  Identities=28%  Similarity=0.538  Sum_probs=72.9

Q ss_pred             CEEEEEcCC----------CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLT----------GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~----------g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      ++|.|+.++          |+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|.|+.+|++|+|.+|++|+++
T Consensus        26 i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i~lv  105 (115)
T 1we7_A           26 VSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLA  105 (115)
T ss_dssp             EEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSCEEEEE
T ss_pred             EEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCCEEEEE
Confidence            357777753          6789999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCCC
Q 033570           71 LRLRGGIIE   79 (116)
Q Consensus        71 ~~~~gg~~~   79 (116)
                      ++++||+.+
T Consensus       106 ~rl~GGk~~  114 (115)
T 1we7_A          106 LKERSGPSS  114 (115)
T ss_dssp             ECCCSCCSC
T ss_pred             EEcCCCCCC
Confidence            999999765

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.80  E-value=4.6e-19  Score=111.29  Aligned_cols=74  Identities=32%  Similarity=0.446  Sum_probs=70.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+|+.. |+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+.++
T Consensus        26 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~~   99 (101)
T 2klc_A           26 MKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQN   99 (101)
T ss_dssp             EEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSS
T ss_pred             EEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            68999998 889999999999999999999999999999999999999999999999999999999999988654

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.80  E-value=2.1e-19  Score=113.70  Aligned_cols=76  Identities=28%  Similarity=0.492  Sum_probs=72.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||.+|++..|+|+++|+|+|+|+.|.|+.+|++|||.+|++|+++.+...+
T Consensus        24 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~~~   99 (106)
T 1ttn_A           24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQ   99 (106)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999987655

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.80  E-value=2e-19  Score=113.09  Aligned_cols=77  Identities=19%  Similarity=0.384  Sum_probs=71.9

Q ss_pred             CEEEEEcCCC----CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCC-CccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g----~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~-~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+|+...+    +.+.++|++++||.+||++|++..++|+++|+|+|+|+.|.|+ .+|++|+|++|++|+++.+..|
T Consensus         8 m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~~g   87 (102)
T 1v5o_A            8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNV   87 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCC
T ss_pred             EEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECCCC
Confidence            7899999754    7899999999999999999999999999999999999999887 6999999999999999999888


Q ss_pred             CC
Q 033570           76 GI   77 (116)
Q Consensus        76 g~   77 (116)
                      |.
T Consensus        88 g~   89 (102)
T 1v5o_A           88 GL   89 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            85

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=99.79  E-value=3.3e-19  Score=114.57  Aligned_cols=77  Identities=27%  Similarity=0.421  Sum_probs=71.0

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCC-------CCCEEEEEEe
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ-------KESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~-------~g~~I~v~~~   72 (116)
                      |+++|+...++ ++.++|.+++||.+||++|+.+.|+|++.|+|+|+|+.|+|+.+|++|||.       .+++|+++++
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr   80 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEB
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEec
Confidence            78888887776 488999999999999999999999999999999999999999999999999       7999999999


Q ss_pred             cCCCCC
Q 033570           73 LRGGII   78 (116)
Q Consensus        73 ~~gg~~   78 (116)
                       .||.+
T Consensus        81 -~~g~f   85 (118)
T 2fnj_B           81 -ADDTF   85 (118)
T ss_dssp             -SSSCB
T ss_pred             -CCCce
Confidence             77753

>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.79  E-value=4.7e-19  Score=110.95  Aligned_cols=75  Identities=23%  Similarity=0.290  Sum_probs=67.6

Q ss_pred             EEEEEcCC----CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            2 QIFVKTLT----GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         2 ~v~Vk~~~----g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      .|.|+..+    ++.+.++|++++||.+||+.|+++.|+|++.|+|+|+|+.|+|+.+|++|+|++|++| +++++.|..
T Consensus        17 ti~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti-~vl~lrg~~   95 (100)
T 1wju_A           17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKA-MVLELKQSS   95 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEE-EEECCCCCC
T ss_pred             EEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEE-EEEEECCCC
Confidence            35666666    6789999999999999999999999999999999999999999999999999999999 677766654

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.78  E-value=2e-19  Score=113.69  Aligned_cols=77  Identities=23%  Similarity=0.360  Sum_probs=70.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC---------------CceEEEECCEEcC-CCCccccCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP---------------DQQRLIFAGKQLE-DGRTLADYNIQKE   64 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~---------------~~q~L~~~g~~L~-d~~tL~~~gi~~g   64 (116)
                      |+|+|+..+|+.+.++|++++||.+||+.|+++.++|+               +.|+|+|+|+.|. |+.+|++|||.+|
T Consensus         8 M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI~~g   87 (105)
T 1v2y_A            8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNR   87 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSS
T ss_pred             EEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCCCCC
Confidence            89999999999999999999999999999999999876               3569999999996 6799999999999


Q ss_pred             CEEEEEEecCCCC
Q 033570           65 STLHLVLRLRGGI   77 (116)
Q Consensus        65 ~~I~v~~~~~gg~   77 (116)
                      ++|+++.++.|..
T Consensus        88 ~~l~lv~~lr~~~  100 (105)
T 1v2y_A           88 DEVSFIKKLGQKS  100 (105)
T ss_dssp             EEEEEEECSCSCC
T ss_pred             CEEEEEehhccCC
Confidence            9999999987753

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=118.57  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.++++|+++++..+|
T Consensus        21 m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg   96 (172)
T 3u30_A           21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   96 (172)
T ss_dssp             EEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeeccccc
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999988877

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=99.78  E-value=1.8e-18  Score=114.61  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+++||
T Consensus        77 ~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~r~~GG  152 (152)
T 3b08_A           77 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  152 (152)
T ss_dssp             EEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC-
T ss_pred             cceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHhCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            6789999999999999999999999999999999999999999999999999999999999999999999999987

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.78  E-value=5.1e-21  Score=131.89  Aligned_cols=101  Identities=23%  Similarity=0.254  Sum_probs=20.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCC-
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE-   79 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~-   79 (116)
                      |+|+|++++|+++.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|+     ++++|+|+++++||..+ 
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLrGG~~kr   75 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLLGGKKKK   75 (189)
T ss_dssp             ----------------------------------------------------------------------------CCCC
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCccc-----CCCEEEEEEecCCCcccc
Confidence            899999999999999999999999999999999999999999999999999999999     89999999999999764 


Q ss_pred             -----CchHHHHHHcCCCcccccccccccccC
Q 033570           80 -----PSLMALARKYNQDKMICRKSHTRTRNQ  106 (116)
Q Consensus        80 -----~~~~~~~~~~~~~~~~c~~~~~~~~~~  106 (116)
                           ..|+...++++..++..+.+|+++++.
T Consensus        76 kK~~~~tPK~~k~~kKkvkl~~Lk~y~Vd~~G  107 (189)
T 2xzm_9           76 KKKSYTTKKKTKHRHVHTKLGALAFYKLENNG  107 (189)
T ss_dssp             CCCCCCSSSCCCCCCCCCCCSCCCCEEEETTT
T ss_pred             cccccCCCccccccccccCCceeeEEEECCCc
Confidence                 245555666677778889999987743

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*

Probab=99.78  E-value=1.7e-18  Score=111.02  Aligned_cols=76  Identities=29%  Similarity=0.431  Sum_probs=70.6

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCC-------CCEEEEEEe
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK-------ESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~-------g~~I~v~~~   72 (116)
                      |.|+++...++ ++.+++.+++||.+||++|+...|+|+++|+|+|+|+.|+|+.+|++|||.+       +++|+++++
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr   80 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEEC
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEe
Confidence            78888888777 5778999999999999999999999999999999999999999999999999       999999999


Q ss_pred             cCCCC
Q 033570           73 LRGGI   77 (116)
Q Consensus        73 ~~gg~   77 (116)
                      . +|.
T Consensus        81 ~-~~~   84 (118)
T 4ajy_B           81 A-DDT   84 (118)
T ss_dssp             C-SSC
T ss_pred             c-CCC
Confidence            7 554

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.77  E-value=1.8e-18  Score=112.31  Aligned_cols=78  Identities=24%  Similarity=0.393  Sum_probs=70.1

Q ss_pred             CEEEEEcCCCCEE-EEEecCCCCHHHHHHHHHHh-----hCCCC--CceEEEECCEEcCCCCccccCCCCCC------CE
Q 033570            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDK-----EGIPP--DQQRLIFAGKQLEDGRTLADYNIQKE------ST   66 (116)
Q Consensus         1 m~v~Vk~~~g~~~-~i~v~~~~TV~~LK~~I~~~-----~~i~~--~~q~L~~~g~~L~d~~tL~~~gi~~g------~~   66 (116)
                      |+|.||..+|+.+ .+++++++||.+||++|++.     .++|+  ++|+|+|+|+.|+|+.+|++|+|..+      ++
T Consensus        17 ~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v~t   96 (126)
T 1se9_A           17 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTT   96 (126)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEE
T ss_pred             EEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCcEE
Confidence            6899999999888 69999999999999999654     46776  79999999999999999999999988      68


Q ss_pred             EEEEEecCCCCC
Q 033570           67 LHLVLRLRGGII   78 (116)
Q Consensus        67 I~v~~~~~gg~~   78 (116)
                      ++++++++||..
T Consensus        97 mhlVlrl~g~~k  108 (126)
T 1se9_A           97 MHVIIQAPVTEK  108 (126)
T ss_dssp             EEEEECCCSSCC
T ss_pred             EEEEeccCCccc
Confidence            999999988753

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=118.50  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=69.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
T Consensus        97 ~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rlrgG  172 (172)
T 3u30_A           97 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  172 (172)
T ss_dssp             EEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBSGGGTCCTTCEEEECC-----
T ss_pred             ccceeecccCcceeEEecCCCCHHHHHHHHHHHhCCCceeEEEEECCccCCCCCcHHHhCCCCCCEEEEEEecCCC
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999999887

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.77  E-value=7.9e-19  Score=114.10  Aligned_cols=77  Identities=23%  Similarity=0.359  Sum_probs=69.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHH------hhCC--CCCceEEEECCEEcCCCCccccCCCCCCC--EEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD------KEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKES--TLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~------~~~i--~~~~q~L~~~g~~L~d~~tL~~~gi~~g~--~I~v~   70 (116)
                      |.|+|+...|+++.++|++++||.+||++|++      +.++  ++++|+|+|+|+.|+|+.+|++|+|..++  +|+++
T Consensus        18 m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlhlv   97 (125)
T 2gow_A           18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   97 (125)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            68999999999999999999999999999999      4566  48899999999999999999999999776  78889


Q ss_pred             EecCCCC
Q 033570           71 LRLRGGI   77 (116)
Q Consensus        71 ~~~~gg~   77 (116)
                      +++.++.
T Consensus        98 ~r~~~~~  104 (125)
T 2gow_A           98 ARETLPE  104 (125)
T ss_dssp             ECSCCSS
T ss_pred             ecCCCCc
Confidence            9887664

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=99.77  E-value=4.6e-18  Score=112.60  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..+|
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~   76 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTC
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecccc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999887765

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.76  E-value=4.4e-18  Score=114.04  Aligned_cols=73  Identities=33%  Similarity=0.428  Sum_probs=70.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE-E-CCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-F-AGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~-~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++.+|+|+++|+|+ | +|+.|+|+.+|++|+|.+|++|+++++.
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~   77 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   77 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECC
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccC
Confidence            79999999999999999999999999999999999999999999 9 7999999999999999999999999983

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.76  E-value=5.6e-19  Score=110.97  Aligned_cols=71  Identities=34%  Similarity=0.574  Sum_probs=67.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|.|++ +|+.+.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.+
T Consensus        29 i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~g~tI~lv~~   99 (101)
T 3m63_B           29 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   99 (101)
T ss_dssp             CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCC
T ss_pred             EEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            5688887 8888999999999999999999999999999999999999999999999999999999999865

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.75  E-value=1.4e-17  Score=106.94  Aligned_cols=77  Identities=23%  Similarity=0.363  Sum_probs=68.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHh------hCC--CCCceEEEECCEEcCCCCccccCCCCCC--CEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK------EGI--PPDQQRLIFAGKQLEDGRTLADYNIQKE--STLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~------~~i--~~~~q~L~~~g~~L~d~~tL~~~gi~~g--~~I~v~   70 (116)
                      |+|+|+...|+.+.++|++++||.+||++|++.      .++  |+++|+|+|.|+.|+|+.+|++|+|..+  ++||++
T Consensus        17 m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLv   96 (116)
T 1wgh_A           17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   96 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            789999999999999999999999999999994      354  6999999999999999999999999766  578888


Q ss_pred             EecCCCC
Q 033570           71 LRLRGGI   77 (116)
Q Consensus        71 ~~~~gg~   77 (116)
                      ++..+..
T Consensus        97 lr~~~~~  103 (116)
T 1wgh_A           97 ARETLPE  103 (116)
T ss_dssp             ECSSCSS
T ss_pred             ccCCCCC
Confidence            8876553

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.75  E-value=6.1e-18  Score=104.74  Aligned_cols=74  Identities=26%  Similarity=0.377  Sum_probs=69.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCC-CccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~-~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..   +++|+|+|+|+.|.|+ .+|++|||.+|++|+++.+.++..
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~~~   82 (95)
T 1wia_A            8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGAA   82 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCCCC
Confidence            7899999999999999999999999999999987   8999999999999998 999999999999999999865543

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.75  E-value=1.2e-17  Score=105.37  Aligned_cols=73  Identities=23%  Similarity=0.240  Sum_probs=67.7

Q ss_pred             CEEEEEcCCC--CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCC-CCCCEEEEEEec
Q 033570            1 MQIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g--~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi-~~g~~I~v~~~~   73 (116)
                      |+|+|++..+  ..+.++|+|++||.+||++|+++.|+|++.|||+|+|+.++|+.+|++||| .+|+++++++-.
T Consensus        25 l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~~  100 (105)
T 4dbg_A           25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLS  100 (105)
T ss_dssp             EEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEECC
T ss_pred             EEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEEe
Confidence            6899999874  678999999999999999999999999999999999999999999999999 599999998753

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A

Probab=99.74  E-value=5.8e-18  Score=104.11  Aligned_cols=73  Identities=21%  Similarity=0.408  Sum_probs=68.4

Q ss_pred             CEEEEEcCCCCEEEE-EecCCCCHHHHHHHHHHhhCCCCCceEEE---ECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i-~v~~~~TV~~LK~~I~~~~~i~~~~q~L~---~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+|++ .|+.+.+ ++++++||.+||++|++.+|+|+++|+|+   |+|+.|+|+.+|++|+|++|++|+++....
T Consensus         8 m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~~   84 (90)
T 1v5t_A            8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRE   84 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCS
T ss_pred             EEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecCc
Confidence            7899997 7888999 99999999999999999999999999999   999999999999999999999999986543

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.74  E-value=1.3e-17  Score=101.61  Aligned_cols=70  Identities=29%  Similarity=0.452  Sum_probs=64.9

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +.++..+|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++..
T Consensus        14 ~~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           14 KLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             EEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            3455668999999999999999999999999999999999999999999999999999999999998764

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.74  E-value=1.7e-17  Score=102.16  Aligned_cols=73  Identities=23%  Similarity=0.429  Sum_probs=67.1

Q ss_pred             CEEEEEcCCCCEEEEEecCC-----CCHHHHHHHHHHhhCCCCCceEEEECCEEcCC-CCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTITLEVESS-----DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~-----~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d-~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+|++ .|+.+.++++++     +||.+||++|++.+|+|+++|+|+|+|+.|.| +.+|++|||++|++|+++.+..
T Consensus         8 ~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~~~   86 (92)
T 1wxv_A            8 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKKN   86 (92)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCCS
T ss_pred             EEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEecCC
Confidence            6899998 588899999995     99999999999999999999999999999988 6689999999999999987643

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.74  E-value=1.3e-17  Score=105.63  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=68.3

Q ss_pred             CEEEEEcCCC---CEEEEEecC---------CCCHHHHHHHHHHhh--CCCCCc-eEEEECCEEcCCCCccccCCCCCCC
Q 033570            1 MQIFVKTLTG---KTITLEVES---------SDTIDNVKAKIQDKE--GIPPDQ-QRLIFAGKQLEDGRTLADYNIQKES   65 (116)
Q Consensus         1 m~v~Vk~~~g---~~~~i~v~~---------~~TV~~LK~~I~~~~--~i~~~~-q~L~~~g~~L~d~~tL~~~gi~~g~   65 (116)
                      |+|+||+.++   +.+.+++++         ++||.+||++|++..  ++|+++ |+|+|+|+.|+|+.+|++|+|++|+
T Consensus        13 ~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~g~   92 (107)
T 1x1m_A           13 WHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGS   92 (107)
T ss_dssp             CCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTC
T ss_pred             eEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCCCC
Confidence            7899999988   788998554         599999999999999  999999 9999999999999999999999999


Q ss_pred             EEEEEEecC
Q 033570           66 TLHLVLRLR   74 (116)
Q Consensus        66 ~I~v~~~~~   74 (116)
                      +|+++.+..
T Consensus        93 ~i~lv~~~~  101 (107)
T 1x1m_A           93 TVHVLRKSW  101 (107)
T ss_dssp             EEEEEESSC
T ss_pred             EEEEEeCCC
Confidence            999998754

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.74  E-value=4.5e-18  Score=106.50  Aligned_cols=70  Identities=24%  Similarity=0.383  Sum_probs=63.7

Q ss_pred             CEEEEEcCCCC--EEEEEecCCCCHHHHHHHHHHhh-CCC-CCceEEEECCEEcCCCCccccC--CCCCCCEEEEE
Q 033570            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKE-GIP-PDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~--~~~i~v~~~~TV~~LK~~I~~~~-~i~-~~~q~L~~~g~~L~d~~tL~~~--gi~~g~~I~v~   70 (116)
                      |+|+||+.+|+  .+.+++++++||.+||++|++++ |.| +++|+|+|+|+.|+|+.+|++|  +|.++++|+++
T Consensus        24 m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             EEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            78999999887  57899999999999999999974 555 5999999999999999999999  99999999874

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.6e-17  Score=106.13  Aligned_cols=74  Identities=16%  Similarity=0.305  Sum_probs=68.0

Q ss_pred             EEEEE-cCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            2 QIFVK-TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         2 ~v~Vk-~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      .|.|+ ...++.+.++++++.||.+||+.+++.+++|++.|+|+|+|+.|+|+.+|++|||++|.+||++++...
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~   91 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTN   91 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESC
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCC
Confidence            45555 667889999999999999999999999999999999999999999999999999999999999998543

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.73  E-value=6.7e-18  Score=105.10  Aligned_cols=72  Identities=17%  Similarity=0.287  Sum_probs=67.0

Q ss_pred             CEEEEEcCCCCEE-EEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~-~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |+|+|++ .|+.+ .+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ +|++|+|++|++|+++....
T Consensus         8 m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~~   80 (96)
T 1wgg_A            8 YSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             EEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             EEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            6899996 67889 6999999999999999999999999999999999999999 99999999999999987643

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.69  E-value=2.1e-17  Score=102.62  Aligned_cols=71  Identities=18%  Similarity=0.328  Sum_probs=65.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+. .++.+.+++++++||.+||++|++.+++|+++|+|+|+|+.| |+.+|++|+|+++++|+++...
T Consensus        18 ~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVP-EDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeC-CcCcHHHCCCCCCCEEEEEecc
Confidence            6788985 688899999999999999999999999999999999999999 5559999999999999998654

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.68  E-value=1.5e-16  Score=116.91  Aligned_cols=73  Identities=96%  Similarity=1.295  Sum_probs=69.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|+++++|++++++
T Consensus       234 MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRL  306 (307)
T 3ai5_A          234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  306 (307)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC--
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999875

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.2e-16  Score=98.06  Aligned_cols=69  Identities=23%  Similarity=0.303  Sum_probs=62.9

Q ss_pred             CEEEEEcCCCCEE--EE-EecCCCCHHHHHHHHHHh-hCCCCCceEEEEC--CEEcCCCCccccCCCCCCCEEEE
Q 033570            1 MQIFVKTLTGKTI--TL-EVESSDTIDNVKAKIQDK-EGIPPDQQRLIFA--GKQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         1 m~v~Vk~~~g~~~--~i-~v~~~~TV~~LK~~I~~~-~~i~~~~q~L~~~--g~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      |+|+|++..|+.+  .+ +|++++||.+||+.|++. .++|+++|+|.|.  |+.|+|+.+|++|+|.++++|++
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            7899999987664  58 999999999999999995 7999999999976  99999999999999999999765

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=99.66  E-value=1.7e-16  Score=119.23  Aligned_cols=77  Identities=31%  Similarity=0.567  Sum_probs=71.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHH---hhCCCCCceEEEECCEEcCCCCccccCCCCCCCEE-EEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD---KEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL-HLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~---~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I-~v~~~~~gg   76 (116)
                      |+|+||+.+|+.+.|+|++++||.+||++|++   +.|+|+++|+|+|+|+.|+|+.+|++|+|++|++| +++.+..++
T Consensus         8 M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~~~   87 (368)
T 1oqy_A            8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAG   87 (368)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCCSS
T ss_pred             EEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCCCC
Confidence            88999999999999999999999999999999   56799999999999999999999999999999998 677777776


Q ss_pred             C
Q 033570           77 I   77 (116)
Q Consensus        77 ~   77 (116)
                      +
T Consensus        88 ~   88 (368)
T 1oqy_A           88 Q   88 (368)
T ss_dssp             S
T ss_pred             C
Confidence            5

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=2e-16  Score=99.07  Aligned_cols=75  Identities=19%  Similarity=0.262  Sum_probs=66.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE--CCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~--~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |.++++.+.|+.+.++|++++||.+||++|++++|+||++|+|++  .|+ |+|+.+|++|+|++|++|+++.....+
T Consensus         9 m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~~~~   85 (100)
T 2dzm_A            9 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPDLPP   85 (100)
T ss_dssp             EEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSSSCC
T ss_pred             eEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecCCCC
Confidence            556666778999999999999999999999999999999999986  565 899999999999999999998875443

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.65  E-value=5.7e-16  Score=96.21  Aligned_cols=70  Identities=14%  Similarity=0.222  Sum_probs=61.6

Q ss_pred             CEEEEEcCCCC--EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEEC--CE---Ec-CCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GK---QL-EDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~--~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~--g~---~L-~d~~tL~~~gi~~g~~I~v~   70 (116)
                      +.|.|+...++  .+.+++++++||.+||++|++.+|+|++.|+|+|.  |+   .| +|+.+|++|+|.+|++|+|+
T Consensus        16 v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           16 IKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             EEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             EEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            35778776553  78899999999999999999999999999999997  55   34 88999999999999999986

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.65  E-value=1.2e-15  Score=94.67  Aligned_cols=77  Identities=17%  Similarity=0.411  Sum_probs=74.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.|++++.++|+|.|+.|.++.|+++|++.+|++|+++.+..||.
T Consensus         8 i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG~   84 (94)
T 2io1_B            8 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV   84 (94)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEESC
T ss_pred             EEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999985

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.63  E-value=6.8e-16  Score=94.26  Aligned_cols=72  Identities=17%  Similarity=0.266  Sum_probs=62.4

Q ss_pred             EEEEEcC--CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE-------CCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            2 QIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-------AGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         2 ~v~Vk~~--~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~-------~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +|.|...  +.+.+.+.+++++||++||++|+..+|+|++.|+|+|       .|+.|+|+.+|++|+|.+|++|||+-.
T Consensus         4 ~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~   83 (86)
T 4b6w_A            4 KVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDL   83 (86)
T ss_dssp             EEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeC
Confidence            3455432  4566789999999999999999999999999999997       478899999999999999999999865


Q ss_pred             c
Q 033570           73 L   73 (116)
Q Consensus        73 ~   73 (116)
                      .
T Consensus        84 ~   84 (86)
T 4b6w_A           84 Q   84 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=99.61  E-value=7.3e-15  Score=90.54  Aligned_cols=77  Identities=17%  Similarity=0.411  Sum_probs=74.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.|++++.++|+|.|+.|.++.|.+++++.+|++|+++....||.
T Consensus         6 i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~gg~   82 (91)
T 2io0_B            6 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV   82 (91)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCc
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999885

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.60  E-value=2.5e-15  Score=93.61  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=61.1

Q ss_pred             EEEEEcCCC--CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC---EE----cCCCCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~g--~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g---~~----L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .|.|++...  ..+.+++++++||++||++|++.+|+|++.|+|+|.|   +.    ++|+.+|++|+|.+|++|+|+-
T Consensus        16 ~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihlvd   94 (97)
T 2kj6_A           16 HLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHIID   94 (97)
T ss_dssp             EEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEEEE
T ss_pred             EEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEEEe
Confidence            566776443  4688999999999999999999999999999999987   33    4889999999999999999874

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.60  E-value=8e-16  Score=97.36  Aligned_cols=72  Identities=21%  Similarity=0.252  Sum_probs=65.6

Q ss_pred             CEEEEEcCCCCEEEEEec-CCCCHHHHHHHHHHhhCCCCCceEEEECCE-----------E----cCCCCccccCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-----------Q----LEDGRTLADYNIQKE   64 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~-~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~-----------~----L~d~~tL~~~gi~~g   64 (116)
                      |.|.|++.+|+. .++|+ +++||.+||++|++++++|++.|+|.+.|+           .    ++|+.+|++|||++|
T Consensus         8 M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G   86 (107)
T 1wf9_A            8 TMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHG   86 (107)
T ss_dssp             EEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTT
T ss_pred             EEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCC
Confidence            789999999865 78999 999999999999999999999999999888           3    578999999999999


Q ss_pred             CEEEEEEec
Q 033570           65 STLHLVLRL   73 (116)
Q Consensus        65 ~~I~v~~~~   73 (116)
                      ++|+++...
T Consensus        87 ~~L~l~~~~   95 (107)
T 1wf9_A           87 SMVYLAYEG   95 (107)
T ss_dssp             CEEECCCSS
T ss_pred             CEEEEEeCC
Confidence            999988763

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.59  E-value=3.8e-15  Score=92.26  Aligned_cols=72  Identities=19%  Similarity=0.278  Sum_probs=62.3

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC---EE----cCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g---~~----L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +.|.|++.... .+.+++++++||.+||++|++..|+|+++|+|+|.|   +.    ++|+.+|++|||.+|++|+|+-.
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d~   87 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH   87 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCC
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEEC
Confidence            35777775543 688999999999999999999999999999999976   43    58999999999999999988753

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=99.58  E-value=1.6e-14  Score=89.32  Aligned_cols=76  Identities=17%  Similarity=0.403  Sum_probs=70.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |.|.|++.+|+.+.+.|.+++++..|+..++++.|++++.++|+|.|+.|.++.|+++|++.+|++|+++.+..||
T Consensus        18 i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG   93 (93)
T 2d07_B           18 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   93 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC---
T ss_pred             EEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeeccCC
Confidence            5788999899999999999999999999999999999999999999999999999999999999999999998886

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.57  E-value=4e-15  Score=90.57  Aligned_cols=71  Identities=24%  Similarity=0.352  Sum_probs=63.1

Q ss_pred             CEEEEEcCCCCEEEEE-ecCCCCHHHHHHHHHHhhCCCCCceEEEEC--CEEcC---CCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLE---DGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~-v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~--g~~L~---d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|.|++.+|+. .+. +++++||.+||+.|+++.|+|+++|+|.|+  ++.|+   |+.+|++|||.+|++|++...
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~~   77 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEED   77 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCCC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEeC
Confidence            899999999964 477 999999999999999999999999999986  47774   688999999999999988754

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=99.56  E-value=1.5e-14  Score=93.47  Aligned_cols=73  Identities=14%  Similarity=0.223  Sum_probs=63.2

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC---E----EcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---K----QLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g---~----~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.|.|++..+. .+.+++++++||.+||++|++..|+|+++|+|+|.|   +    +++|+.+|++|||.+|++|+|+..
T Consensus         7 v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd~   86 (122)
T 1t0y_A            7 YDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDV   86 (122)
T ss_dssp             EEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEEC
T ss_pred             EEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEeC
Confidence            36778775543 688999999999999999999999999999999977   3    247899999999999999999875


Q ss_pred             c
Q 033570           73 L   73 (116)
Q Consensus        73 ~   73 (116)
                      .
T Consensus        87 ~   87 (122)
T 1t0y_A           87 T   87 (122)
T ss_dssp             T
T ss_pred             C
Confidence            3

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.55  E-value=1.9e-14  Score=90.69  Aligned_cols=78  Identities=15%  Similarity=0.348  Sum_probs=74.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~   78 (116)
                      |.|.|++.+|+.+.+.|.+++++..|+..++++.|++++.++|+|.|+.|.++.|+.+|++.+|++|+++.++.||..
T Consensus        25 I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG~~  102 (104)
T 1wz0_A           25 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTSGPS  102 (104)
T ss_dssp             EEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCCCSS
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCCC
Confidence            578999989999999999999999999999999999999999999999999999999999999999999999999864

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.54  E-value=8.3e-15  Score=108.34  Aligned_cols=73  Identities=22%  Similarity=0.440  Sum_probs=66.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE---ECCEEcCCCCccccCCCCCCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~---~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      |.|+|++ +|+.+.+++++++||++||++|++.+|+|+++|+|+   |+|+.|+|+.+|++|||++|++|+++....
T Consensus         6 i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~~   81 (320)
T 3shq_A            6 VVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGSTE   81 (320)
T ss_dssp             EEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCCC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccch
Confidence            5788997 789999999999999999999999999999999999   899999999999999999999999986543

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=99.54  E-value=7.3e-14  Score=82.39  Aligned_cols=70  Identities=16%  Similarity=0.384  Sum_probs=67.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.|++++.++|+|.|+.|.++.|.+++++.+|++|++.
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   71 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            6789999999999999999999999999999999999999999999999999999999999999999986

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=99.52  E-value=8.1e-14  Score=88.01  Aligned_cols=75  Identities=13%  Similarity=0.339  Sum_probs=69.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |.|.|++ +|+...+.|.+++++..|+..++++.|++++.++|+|.|+.|.++.|.++|++.+|++|+++.++.||
T Consensus        32 I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~GG  106 (106)
T 2eke_C           32 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG  106 (106)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC---
T ss_pred             EEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeecccC
Confidence            5788999 99999999999999999999999999999999999999999999999999999999999999998886

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.50  E-value=4.3e-14  Score=89.83  Aligned_cols=77  Identities=16%  Similarity=0.428  Sum_probs=73.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |.|.|++.+|+.+.+.|.+++++..|+..++++.|++++.++|+|.|+.|.++.|+++|++.+|++|+++....||-
T Consensus        27 I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~Gg~  103 (110)
T 2k8h_A           27 VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTGGL  103 (110)
T ss_dssp             EEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCCC-
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccCcc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999998884

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.48  E-value=4e-13  Score=80.59  Aligned_cols=70  Identities=10%  Similarity=0.274  Sum_probs=66.8

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |+|.|++.+|+ .+.+.|.+++++..|+..++++.|++++.++|+|.|+.|.++.|.+++++.+|++|++.
T Consensus         8 i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A            8 LRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             EEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             EEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            57899999996 89999999999999999999999999999999999999999999999999999999985

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.39  E-value=2.1e-12  Score=80.09  Aligned_cols=71  Identities=17%  Similarity=0.238  Sum_probs=60.9

Q ss_pred             EEEEEc---CCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC-------EEc-CCCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKT---LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG-------KQL-EDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~---~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g-------~~L-~d~~tL~~~gi~~g~~I~v~   70 (116)
                      .|.|+.   .+++.+...+++++||++||.+|++.+|+|+..|+|.|.+       ..| +|..+|+.|++.+|++|+|.
T Consensus        11 ~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V~   90 (97)
T 1wjn_A           11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             EEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEEE
Confidence            566665   3577889999999999999999999999999999999863       225 57889999999999999998


Q ss_pred             Ee
Q 033570           71 LR   72 (116)
Q Consensus        71 ~~   72 (116)
                      ..
T Consensus        91 d~   92 (97)
T 1wjn_A           91 WS   92 (97)
T ss_dssp             CC
T ss_pred             ec
Confidence            74

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=99.30  E-value=3.3e-11  Score=76.87  Aligned_cols=75  Identities=17%  Similarity=0.416  Sum_probs=70.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |.|.|++.+|....+.|.+++++..|+..++++.|+++..++|+|.|+.|.++.|..++++.+|++|.++....|
T Consensus        41 I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q~G  115 (115)
T 3kyd_D           41 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQCG  115 (115)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeeccC
Confidence            468888888999999999999999999999999999999999999999999999999999999999999987543

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=99.20  E-value=1.3e-10  Score=80.55  Aligned_cols=76  Identities=13%  Similarity=0.315  Sum_probs=71.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|.|+. +|+...+.|.+++++..|+..++++.|+++..++++|.|+.|.++.|..++++.+|++|+++..+.||.
T Consensus        30 I~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~gg~  105 (200)
T 3pge_A           30 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGG  105 (200)
T ss_dssp             EEEEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSCCC
T ss_pred             EEEEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCcCc
Confidence            4677875 888999999999999999999999999999999999999999999999999999999999999998885

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=99.16  E-value=1e-10  Score=80.44  Aligned_cols=76  Identities=12%  Similarity=0.326  Sum_probs=71.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |.|.|+. +|..+.+.|.+++++..|+..++++.|+++..++++|+|+.|.++.|..++++.+|++|+++....||.
T Consensus        58 InLKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG~  133 (207)
T 3tix_A           58 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGL  133 (207)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTTG
T ss_pred             EEEEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            4577764 888999999999999999999999999999999999999999999999999999999999999999995

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*

Probab=99.10  E-value=1.5e-09  Score=64.30  Aligned_cols=70  Identities=16%  Similarity=0.316  Sum_probs=64.4

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .+.+++.....+.+.|.++.+|.+|-.....+.+++++ .++|.|.|..|+.+.++.+|++.+|+.|.+++
T Consensus        11 ~~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           11 TLLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEEESSSCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHhhhccCCCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            45667766677999999999999999999999999999 99999999999999999999999999999875

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=99.03  E-value=1.4e-10  Score=69.59  Aligned_cols=69  Identities=14%  Similarity=0.229  Sum_probs=57.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEE---c--CCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ---L--EDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~---L--~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |.|.|++.+| .+.+++++++|+.+|+++|++.++++++.+.+.++-.+   |  .++.+|+++||++|++|++.
T Consensus         5 m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            5 IIIRVQSPDG-VKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             EEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            6788999887 57788999999999999999999999888777654443   3  36789999999999999875

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.93  E-value=1.1e-10  Score=81.31  Aligned_cols=77  Identities=13%  Similarity=0.329  Sum_probs=1.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~   78 (116)
                      |.|.| ..+|+...+.|.+++++..|++.++++.|++++.++++|+|+.+.++.|..++++.+|++|+++....||..
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG~~   98 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGLT   98 (227)
T ss_dssp             ---------------------------------------------------------------------------CCC
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCCch
Confidence            56777 567888999999999999999999999999999999999999999999999999999999999999999953

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.89  E-value=1.5e-08  Score=62.72  Aligned_cols=70  Identities=13%  Similarity=0.295  Sum_probs=64.7

Q ss_pred             CEEEEEcCCCC-EEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      +.|.|+..+|. .+.+.|..++++..|....+++.|++++.++++|.|..|.++.|..++++.+|++|.+.
T Consensus        26 I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           26 LQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             EEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            36778887884 78999999999999999999999999999999999999999999999999999999875

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=98.71  E-value=7.5e-08  Score=67.12  Aligned_cols=75  Identities=13%  Similarity=0.320  Sum_probs=69.8

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      .|.|++ .++...+.+..++++..|++..+++.|++++.+++.|.|+.+.++.+..++.+.++++|.+..+..||.
T Consensus        23 ~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~Gg~   97 (209)
T 3uf8_A           23 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGS   97 (209)
T ss_dssp             EEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTTCC
T ss_pred             EEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCCCChHHhhhcccccchhhccccccc
Confidence            566776 677889999999999999999999999999999999999999999999999999999999999988874

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.62  E-value=3.8e-07  Score=55.98  Aligned_cols=71  Identities=14%  Similarity=0.294  Sum_probs=65.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +.|.|++ +|....+.+..++....|....+++.|++++.++++|.|..+.++.|-.++++.+|++|.++.-
T Consensus        22 IniKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~~   92 (95)
T 2l76_A           22 FPLKIRC-RADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVVL   92 (95)
T ss_dssp             EEEEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEEC
T ss_pred             EEEEEEc-CCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEEe
Confidence            3577775 6888999999999999999999999999999999999999999999999999999999998764

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=98.57  E-value=6.5e-09  Score=77.65  Aligned_cols=76  Identities=13%  Similarity=0.346  Sum_probs=0.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      +.|.|++ +|+...+.|..++++..|++..+++.|++++.++++|+|+.+.++.|.+++++.+|++|++.....||-
T Consensus        22 I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~g~~   97 (360)
T 3ix6_A           22 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGM   97 (360)
T ss_dssp             ----------------------------------------------------------------------------C
T ss_pred             EEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccCchH
Confidence            3566766 577788999999999999999999999999999999999999999999999999999999999999984

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=98.56  E-value=4.1e-07  Score=55.31  Aligned_cols=73  Identities=18%  Similarity=0.186  Sum_probs=68.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |.|+|-..+++...+.|.|++++.++-+...+++|+.+++..|.|+++.|+-+.++.-.|+.+|+.+.++...
T Consensus        10 m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s   82 (90)
T 2al3_A           10 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVS   82 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEcc
Confidence            6789999999999999999999999999999999999999999999999988999999999999999998653

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.48  E-value=1e-06  Score=54.09  Aligned_cols=64  Identities=20%  Similarity=0.299  Sum_probs=49.6

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEc--CCCCccccCCCCC-CCEEEEEEe
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL--EDGRTLADYNIQK-ESTLHLVLR   72 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L--~d~~tL~~~gi~~-g~~I~v~~~   72 (116)
                      .+..+.+.+.+++|+..||++|++++|||++.|+|+|.|+.+  +...+...|.-+. ..-|.+..+
T Consensus        22 ~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~Tt~~~Pl~L~s~   88 (94)
T 4efo_A           22 QMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSL   88 (94)
T ss_dssp             TTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCCCBTTBCEEEEEC
T ss_pred             cceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccccCCCCccccCCCCCCCCCEEEEec
Confidence            467789999999999999999999999999999999999865  4455666665432 334544433

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=98.42  E-value=2.8e-08  Score=74.81  Aligned_cols=75  Identities=12%  Similarity=0.308  Sum_probs=0.0

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      .|.|+. .+....+.|..++++..|++..+++.|+++..+++.|+|+.+.++.|..++++.+|++|.++....||.
T Consensus        32 ~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~gg~  106 (389)
T 4da1_A           32 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIGGE  106 (389)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             EEEEec-CCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecccccc
Confidence            455665 667778999999999999999999999999999999999999999999999999999999999999885

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.29  E-value=2.5e-06  Score=50.99  Aligned_cols=68  Identities=15%  Similarity=0.224  Sum_probs=57.2

Q ss_pred             EEEEEc--CCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-----ceEEEECCEEcCCCCccccCCCCCCCEEEE
Q 033570            2 QIFVKT--LTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-----QQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (116)
Q Consensus         2 ~v~Vk~--~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-----~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v   69 (116)
                      .|++..  ..++.+.+.++...||..|++.+.+.++++..     .+++.-++..|.+...|++|+|++|+.+.+
T Consensus         6 ~ITidl~~y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A            6 DITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             EEEEECTTTTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEeeccCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            456653  47899999999999999999999999987542     245667888999999999999999999875

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=98.17  E-value=4.4e-06  Score=53.99  Aligned_cols=70  Identities=26%  Similarity=0.377  Sum_probs=55.9

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEE------------------------------------
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLI------------------------------------   44 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~------------------------------------   44 (116)
                      .+.|+.++|+...+.|+.+.+|++++..|..++|++.. ..-|.                                    
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~kL~   92 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQKLH   92 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCSCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccccccccccccCchhhccccccccchhHHHHHHHHhc
Confidence            37899999999999999999999999999999998643 22222                                    


Q ss_pred             E--CCEEcCCCCccccCCCCCCCEEEEEE
Q 033570           45 F--AGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        45 ~--~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .  .+.-|+++.+|.++||.++++|.+-.
T Consensus        93 ~dd~~~WLD~srtL~EQGI~e~~tllLRr  121 (128)
T 2kc2_A           93 TDDELNWLDHGRTLREQGVEEHETLLLRR  121 (128)
T ss_dssp             CSSSEEEECSSSCHHHHTCCTTSEEEEEE
T ss_pred             ccCCCCcccCCCcHHHcCCCCCCEEEEEE
Confidence            1  12346778999999999999976544

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A

Probab=98.07  E-value=4.4e-05  Score=45.57  Aligned_cols=69  Identities=19%  Similarity=0.358  Sum_probs=58.4

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC---CCCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~---d~~tL~~~gi~~g~~I~v~~   71 (116)
                      +|.|+.++|+.+.-....++||.+|..-|.. .+.++..+.|+  |-.+.+.   .+.+|.++|+.+.++|.|--
T Consensus         9 ~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~ve~   82 (84)
T 3qx1_A            9 KLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEA   82 (84)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEEe
Confidence            6889999999888889999999999999988 56777888888  5567773   47899999999999987753

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A

Probab=97.92  E-value=0.0001  Score=46.18  Aligned_cols=71  Identities=17%  Similarity=0.269  Sum_probs=60.7

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC--C-CCccccCCCCCCCEEEEEEe
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--D-GRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~--d-~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +|.||.++|+.+.-....++||.+|.+-|....+.+.....|+  |-.+.+.  | +++|.++|+.+..++++...
T Consensus        15 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~~   90 (109)
T 2dzk_A           15 RIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPA   90 (109)
T ss_dssp             EEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEECC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEEC
Confidence            6889999999999899999999999999999988777778887  5677775  3 78999999999888877654

>2ayj_A 50S ribosomal protein L40E; Zn-binding, beta-strand protein, structural genomics, PSI, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: g.41.8.7

Probab=97.81  E-value=2.2e-06  Score=47.35  Aligned_cols=32  Identities=19%  Similarity=0.311  Sum_probs=28.7

Q ss_pred             CCchHHHHHHcCCCcccccccccccccCCCccccccC
Q 033570           79 EPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        79 ~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      .++....+.+++.++++||+||.+   ++|.|  |||
T Consensus         5 e~~~~~lA~k~~~~k~ICrkC~AR---np~~A--~~C   36 (56)
T 2ayj_A            5 DPAKLQIVQQRVFLKKVCRKCGAL---NPIRA--TKC   36 (56)
T ss_dssp             CSCCSSTTTTCSCCCEEETTTCCE---ECTTC--SSC
T ss_pred             chhHHHHHHHHHhchhhhccccCc---CCccc--ccc
Confidence            456677788999999999999999   99999  999

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2

Probab=97.68  E-value=0.00025  Score=45.45  Aligned_cols=69  Identities=20%  Similarity=0.354  Sum_probs=58.5

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEc--CC-CCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL--ED-GRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L--~d-~~tL~~~gi~~g~~I~v~~   71 (116)
                      +|.||.++|..+.-....++||.+|..-|... +.++....|+  |-.+.|  .| +.+|.++|+.+..+|+|..
T Consensus        45 ~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~~  118 (124)
T 1wj4_A           45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE  118 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEEE
Confidence            68899999998888999999999999999887 7777788887  567777  33 7899999999988877654

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=97.48  E-value=0.0023  Score=36.71  Aligned_cols=66  Identities=21%  Similarity=0.270  Sum_probs=50.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|.... ....++++...|+.+|.+.+    ++++....+..+|..+..+.     -+++|+.|.++....||
T Consensus         5 m~i~vNg~~-~~~~~~~~~~~tv~~Ll~~l----~~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii~~V~GG   70 (70)
T 1ryj_A            5 MKFTVITDD-GKKILESGAPRRIKDVLGEL----EIPIETVVVKKNGQIVIDEE-----EIFDGDIIEVIRVIYGG   70 (70)
T ss_dssp             EEEEEEETT-EEEEEEESSCCBHHHHHHHT----TCCTTTEEEEETTEECCTTS-----BCCTTCEEEEEECTTCC
T ss_pred             EEEEEeCcc-CceeEECCCCCcHHHHHHHh----CCCCCCEEEEECCEECCCcc-----cCCCCCEEEEEeccccC
Confidence            567776643 23456788888999998876    56677778889999997665     46779999998877776

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=97.28  E-value=0.00096  Score=38.90  Aligned_cols=66  Identities=14%  Similarity=0.367  Sum_probs=51.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|+-.+.....+++++..||.+|-+.    ++++++..-+..||+.+..+..      .+|+.|.++--..||
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~~----Lgl~~~~VvV~vNG~~v~~d~~------l~GD~VeIv~~V~G~   66 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVRA----VDLSPHEVTVLVDGRPVPEDQS------VEVDRVKVLRLIKGG   66 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHHT----TCCCSSCCCEECCCCCCCTTSS------SCCCCEEECSSCSCC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHHH----cCCCcceEEEEECCEECCHHHC------CCCCEEEEEEeeccc
Confidence            89999987555566899999999987655    5999998878889998876652      248888887666666

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A

Probab=97.27  E-value=0.0011  Score=42.55  Aligned_cols=66  Identities=21%  Similarity=0.370  Sum_probs=54.1

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhh-CCCCCceEEE--ECCEEcCC-CCccccCCCCCCCEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLI--FAGKQLED-GRTLADYNIQKESTL   67 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~-~i~~~~q~L~--~~g~~L~d-~~tL~~~gi~~g~~I   67 (116)
                      +|.|+..+|..+.-....++||.+|..-|.... +.....+.|+  |-.+.|.| +.+|.++|+.+..+|
T Consensus        54 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psavl  123 (127)
T 1s3s_G           54 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIV  123 (127)
T ss_dssp             CEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceEE
Confidence            588999999998889999999999999999864 3445677777  56788875 789999999985443

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.26  E-value=0.0017  Score=40.50  Aligned_cols=70  Identities=19%  Similarity=0.252  Sum_probs=57.6

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC--CCCccccCCCCCCCEEEEEEe
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--DGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~--d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +|.|+.++|+.+.-....++||.+|..-|... +..+....|+  |-.+.|.  .+.+|.++|+.+..+|.|...
T Consensus        25 ~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve~~   98 (109)
T 2cr5_A           25 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEEK   98 (109)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEEC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEEeC
Confidence            68899999998888889999999999999865 5556677886  5567775  378999999999988877654

>3jyu_A Ubiquitin carboxyl-terminal hydrolase; domain in ubiquitin-specific peptidases (DUSP), proto- oncogene, ubiquitin-fold, UBL, protease, thioesterase; HET: 1PS; 2.37A {Mus musculus}

Probab=97.26  E-value=0.0017  Score=45.58  Aligned_cols=68  Identities=19%  Similarity=0.273  Sum_probs=57.0

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEE-C----CEEcCC-CCccccCCCCCCCEEEEEEecCCCCCCC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF-A----GKQLED-GRTLADYNIQKESTLHLVLRLRGGIIEP   80 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~-~----g~~L~d-~~tL~~~gi~~g~~I~v~~~~~gg~~~~   80 (116)
                      +.+.++..+|+.+|++.+.+.++++++ ..||.. .    ...|.| +.+|.++++.++..|.+-.+...|..+.
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~~dg~WP~  228 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQNEDGTWPR  228 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECCTTSCCCC
T ss_pred             EEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEecCCCCCCc
Confidence            456779999999999999999999987 688873 2    335665 6899999999999999999988886653

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=97.08  E-value=0.0028  Score=44.04  Aligned_cols=67  Identities=22%  Similarity=0.381  Sum_probs=55.2

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEE--E-CCE--EcCC-CCccccCCCCCCCEEEEEEecCCCCCC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLI--F-AGK--QLED-GRTLADYNIQKESTLHLVLRLRGGIIE   79 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~--~-~g~--~L~d-~~tL~~~gi~~g~~I~v~~~~~gg~~~   79 (116)
                      +.+.++..+||.+|++.+.+.++++++ ..||.  + .++  .|.+ +.+|.++++.++..|.+-.+...|..+
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~~dg~WP  215 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWP  215 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECCCC-CCC
T ss_pred             eEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEecCCCCCC
Confidence            557889999999999999999999987 67775  3 333  5665 679999999999999999998888654

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.92  E-value=0.0018  Score=38.77  Aligned_cols=62  Identities=13%  Similarity=0.239  Sum_probs=55.1

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE---CCEEcCCCCccccCCCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQK   63 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~---~g~~L~d~~tL~~~gi~~   63 (116)
                      ++.|.-...+...+.|+|..++.+|--.|.++-.+.++...|..   .+..|+-+++|.+|||.+
T Consensus        12 RLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~d~~~~e~LdLskSLndlgirE   76 (91)
T 2daj_A           12 RVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE   76 (91)
T ss_dssp             EEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEESCSSCCCBCCTTSCHHHHTCSE
T ss_pred             EEEEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEecCCCCCcccchhcchhhhhhhh
Confidence            67788877788999999999999999999999999999998874   455788899999999986

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=96.73  E-value=0.0069  Score=36.36  Aligned_cols=57  Identities=11%  Similarity=0.152  Sum_probs=42.5

Q ss_pred             EEecCC-CCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           15 LEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        15 i~v~~~-~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ++++.. .||.+|.+.+    ++++....+..||+.+..+ ...+.-+++|+.|.++....||
T Consensus        30 ~el~~~~~Tv~dLL~~L----~~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~~~V~GG   87 (87)
T 1tyg_B           30 VKWKKDTGTIQDLLASY----QLENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVHFVGGG   87 (87)
T ss_dssp             ECCSSSCCBHHHHHHHT----TCTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEEECCC-
T ss_pred             EECCCCCCcHHHHHHHh----CCCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEEcccccC
Confidence            445665 8999998876    5677778888999988543 3445567889999999887765

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=96.44  E-value=0.022  Score=32.70  Aligned_cols=71  Identities=15%  Similarity=0.331  Sum_probs=48.8

Q ss_pred             CEEEEEcCCC-CEEEEEecCCCCHHHHHHHHHHhhCCCC--CceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g-~~~~i~v~~~~TV~~LK~~I~~~~~i~~--~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |.|+|+-... +...+++ ...||.+|.+.+....++..  ....+..||+.+.+    .+.-+++|+.|.+.....||
T Consensus         1 M~v~V~~fa~l~~~~~e~-~~~tv~~ll~~L~~~~~l~~~l~~~~vavN~~~v~~----~~~~l~~gDeV~i~PpvsGG   74 (74)
T 3rpf_C            1 MMVEVRFFGPIKEENFFI-KANDLKELRAILQEKEGLKEWLGVCAIALNDHLIDN----LNTPLKDGDVISLLPPVCGG   74 (74)
T ss_dssp             CEEEEEECTTCCCCCEEE-ECSSHHHHHHHHHTCTTTTTTTTTCEEEESSSEECC----TTCCCCTTCEEEEECCBCCC
T ss_pred             CEEEEEEEeecceeEEee-CCCcHHHHHHHHHHCcCHHHHhhccEEEECCEEcCC----CCcCCCCCCEEEEECCCCCC
Confidence            7788877642 1134666 56799999999987543321  45677788887543    23457789999999888776

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=96.28  E-value=0.056  Score=32.62  Aligned_cols=71  Identities=13%  Similarity=0.298  Sum_probs=48.1

Q ss_pred             CEEEEEcCC------C-CEEEEEecCCCCHHHHHHHHHHhhC-C----------CCCceEEEECCEEcCCCCccccCCCC
Q 033570            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-I----------PPDQQRLIFAGKQLEDGRTLADYNIQ   62 (116)
Q Consensus         1 m~v~Vk~~~------g-~~~~i~v~~~~TV~~LK~~I~~~~~-i----------~~~~q~L~~~g~~L~d~~tL~~~gi~   62 (116)
                      |+|.|+...      | ....+++++..||.+|.+.+...+. +          ......+..||+....     +.-++
T Consensus        10 ~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~-----~~~L~   84 (98)
T 1vjk_A           10 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEELK   84 (98)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCBCC
T ss_pred             EEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCC-----CCCCC
Confidence            556665542      3 4567888888999999999987642 1          1245677889988764     44577


Q ss_pred             CCCEEEEEEecCCC
Q 033570           63 KESTLHLVLRLRGG   76 (116)
Q Consensus        63 ~g~~I~v~~~~~gg   76 (116)
                      +|+.|.+.....||
T Consensus        85 dGDeV~i~ppv~GG   98 (98)
T 1vjk_A           85 DGDVVGVFPPVSGG   98 (98)
T ss_dssp             TTCEEEEESCC---
T ss_pred             CCCEEEEECCCCCC
Confidence            89999988776665

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=96.24  E-value=0.033  Score=33.10  Aligned_cols=59  Identities=19%  Similarity=0.370  Sum_probs=51.0

Q ss_pred             EEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      ..++=..++..||..++.+.+++.+...+...+..|.++++|.+.+++-...+.+.+..
T Consensus         7 qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqi   65 (89)
T 2juo_A            7 QAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQV   65 (89)
T ss_dssp             EEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEE
T ss_pred             hhccccCcHHHHHHHHHHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEE
Confidence            34556678999999999999999999999999999999999999999877777766653

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=96.22  E-value=0.0096  Score=33.51  Aligned_cols=66  Identities=15%  Similarity=0.263  Sum_probs=46.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|   +|+.  ++++...||.+|.+.+    ++++....+..+|+.+..+ ...+.-+++|+.|.++....||
T Consensus         1 m~i~v---Ng~~--~~~~~~~tv~~ll~~l----~~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~~~V~GG   66 (66)
T 1f0z_A            1 MQILF---NDQA--MQCAAGQTVHELLEQL----DQRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLFQVIAGG   66 (66)
T ss_dssp             CCEEE---SSCE--ECCCTTCCHHHHHHHH----TCCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEEESCCCC
T ss_pred             CEEEE---CCEE--EEcCCCCcHHHHHHHc----CCCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEEeecccC
Confidence            55555   4554  4556778999998877    5667778888999988542 2333456789999998877665

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2

Probab=96.18  E-value=0.016  Score=34.48  Aligned_cols=45  Identities=11%  Similarity=0.208  Sum_probs=38.6

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK   48 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~   48 (116)
                      .|.|...  -++.|.|+++.+..+|+++|.++.+++++..+|.|...
T Consensus         7 ~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~   51 (83)
T 1oey_A            7 TLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPR   51 (83)
T ss_dssp             EEEEESS--SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCT
T ss_pred             EEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCC
Confidence            4555553  57889999999999999999999999999999999654

>2k5p_A THis protein, thiamine-biosynthesis protein; NESG, GMR137, structural genomics, PSI-2, protein structure initiative; NMR {Geobacter metallireducens gs-15} PDB: 3cwi_A

Probab=96.01  E-value=0.011  Score=34.63  Aligned_cols=67  Identities=16%  Similarity=0.334  Sum_probs=50.0

Q ss_pred             CEEEEEcCCCCEEEEEec--CCCCHHHHHHHHHHhhCCC-CCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVE--SSDTIDNVKAKIQDKEGIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~--~~~TV~~LK~~I~~~~~i~-~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+|   +|+..  +++  ...||.+|-+.+    +++ +...-+..||..+..+ ...+.-+++|+.|.++.-..||.
T Consensus         1 M~I~v---NGe~~--e~~~~~~~Tl~~LL~~l----~~~~~~~vAVavNg~iVpr~-~~~~~~L~dGD~IEIv~~VgGG~   70 (78)
T 2k5p_A            1 MNLTV---NGKPS--TVDGAESLNVTELLSAL----KVAQAEYVTVELNGEVLERE-AFDATTVKDGDAVEFLYFMGGGK   70 (78)
T ss_dssp             CEEEE---TTEEE--ECSSCSCEEHHHHHHHH----TCSCTTTCCEEETTEECCTT-HHHHCEECSSBCEEECCCCCCSC
T ss_pred             CEEEE---CCEEE--EcCCCCCCcHHHHHHHc----CCCCCCcEEEEECCEECChH-HcCcccCCCCCEEEEEeeecCCC
Confidence            66666   45544  455  668999987755    677 7778888999998544 45556677899999998888885

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=95.45  E-value=0.15  Score=29.90  Aligned_cols=61  Identities=16%  Similarity=0.281  Sum_probs=45.6

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhC-C-----C-----CCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEG-I-----P-----PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~-i-----~-----~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ....++++...||.+|.+.+...+. +     .     .....+..||+....+     .-+++|+.|.+.....||
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~~~~~~l~~~g~l~~~~~v~VN~~~v~~~-----~~l~~gDeV~i~Ppv~GG   89 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAALG-----EATAAGDELALFPPVSGG   89 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGGGHHHHBCTTSCBCTTSEEEETTEECCTT-----SBCCTTCEEEEECCCSCC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcHHHHHHhccCCcccccEEEEECCEECCCC-----cccCCCCEEEEECCCCCC
Confidence            5577888888899999999988752 1     1     0136778899988653     346779999999887776

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=95.39  E-value=0.13  Score=32.10  Aligned_cols=63  Identities=38%  Similarity=0.494  Sum_probs=45.0

Q ss_pred             CCEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEEE----CCEEcCCC-------------CccccCCCCCC
Q 033570           10 GKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGKQLEDG-------------RTLADYNIQKE   64 (116)
Q Consensus        10 g~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~~----~g~~L~d~-------------~tL~~~gi~~g   64 (116)
                      +..+.+.|-..+||.+.|++|-..+  |.|      ++++-|-+    .|++|.|.             .||+.|+|.+|
T Consensus        23 ~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  102 (111)
T 4e71_A           23 VDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRVNTLMHYNVRDG  102 (111)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCEECCSSCTTSCC---CCCCCBHHHHTCCTT
T ss_pred             CCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCccccccCccceecCcceEecchhhcCCCCC
Confidence            4557788888999999999998764  333      45566654    35566652             25889999999


Q ss_pred             CEEEEEEe
Q 033570           65 STLHLVLR   72 (116)
Q Consensus        65 ~~I~v~~~   72 (116)
                      +++.++.+
T Consensus       103 atl~l~~~  110 (111)
T 4e71_A          103 ATLILSKV  110 (111)
T ss_dssp             CEEEEEEC
T ss_pred             CEEEEEeC
Confidence            99987654

>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D

Probab=95.16  E-value=0.095  Score=30.15  Aligned_cols=59  Identities=5%  Similarity=0.128  Sum_probs=41.9

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhC-----CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~-----i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ...++ .+..||.+|.+.+.....     ++.....+..||+....+     .-+++|+.|.+.....||
T Consensus        18 ~~~~~-~~~~tv~~ll~~L~~~~p~~~~~l~~~~~~v~vN~~~v~~~-----~~l~~gD~V~i~Ppv~GG   81 (81)
T 1fm0_D           18 ATEVA-ADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFD-----HPLTDGDEVAFFPPVTGG   81 (81)
T ss_dssp             EEEEC-SCCSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCTT-----CBCCTTCEEEEECCCCCC
T ss_pred             eEEEc-CCCCCHHHHHHHHHHHChhHHHHhcCCCEEEEECCEECCCC-----CCCCCCCEEEEeCCCCCC
Confidence            44555 567799999999876531     233456788899987543     356789999998877766

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=95.11  E-value=0.054  Score=30.96  Aligned_cols=60  Identities=13%  Similarity=0.212  Sum_probs=43.3

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhCCCCCce--EEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ--RLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q--~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ....++++...||.+|.+.+..... .....  .+..||+....+     .-+++|+.|.+.....||
T Consensus        16 ~~~~~~~~~~~tv~~ll~~l~~~~p-~~~~v~~~v~vNg~~v~~~-----~~L~~gD~V~i~ppv~GG   77 (77)
T 2q5w_D           16 AQEDIVLEQALTVQQFEDLLFERYP-QINNKKFQVAVNEEFVQKS-----DFIQPNDTVALIPPVSGG   77 (77)
T ss_dssp             SEEECCCSSCEEHHHHHHHHHHHCG-GGTTCCCEEEETTEEECTT-----SEECTTCEEEEECSCCCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCc-chhcceEEEEECCEECCCC-----CCcCCCCEEEEECCCCCC
Confidence            3456677777899999999887642 11334  788899988754     346679999988777665

>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis} PDB: 3dwm_A

Probab=95.08  E-value=0.21  Score=29.54  Aligned_cols=74  Identities=15%  Similarity=0.196  Sum_probs=47.9

Q ss_pred             CEEEEEcCC------CCEEEEEecCCCCHHHHHHHHHHhhCC------C-------CCceEEEECCEEcCCCCccccCCC
Q 033570            1 MQIFVKTLT------GKTITLEVESSDTIDNVKAKIQDKEGI------P-------PDQQRLIFAGKQLEDGRTLADYNI   61 (116)
Q Consensus         1 m~v~Vk~~~------g~~~~i~v~~~~TV~~LK~~I~~~~~i------~-------~~~q~L~~~g~~L~d~~tL~~~gi   61 (116)
                      |+|+|+-..      |....+++ +..||.+|.+.+.+++.-      .       .....+..||+......- .+.-+
T Consensus         1 M~v~V~~fa~lr~~~g~~~~~~~-~~~Tv~~ll~~L~~~~p~l~~~l~~~~~~g~~~~~~~v~VN~~~v~~~~~-~~~~L   78 (93)
T 3dwg_C            1 MNVTVSIPTILRPHTGGQKSVSA-SGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGG-LATAI   78 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEE-CCSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTG-GGCBC
T ss_pred             CEEEEEEeHHHHHHhCCCeEEec-CCCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCC-CCcCC
Confidence            667776542      32234664 457999999999887520      1       113677789987754222 23457


Q ss_pred             CCCCEEEEEEecCCC
Q 033570           62 QKESTLHLVLRLRGG   76 (116)
Q Consensus        62 ~~g~~I~v~~~~~gg   76 (116)
                      ++|+.|.+.....||
T Consensus        79 ~~gDeV~i~Ppv~GG   93 (93)
T 3dwg_C           79 ADGDSVTILPAVAGG   93 (93)
T ss_dssp             CTTCEEEEEECCTTC
T ss_pred             CCCCEEEEECCCCCC
Confidence            889999999888776

>2r2o_A Plexin-B1; effector domain, structural genomics, structural GEN consortium, SGC, glycoprotein, membrane, phosphorylation, R secreted, transmembrane; 2.00A {Homo sapiens} PDB: 2rex_A* 2jph_A

Probab=94.92  E-value=0.2  Score=32.42  Aligned_cols=64  Identities=33%  Similarity=0.530  Sum_probs=46.0

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEEE----CCE-EcCCC-------------CccccCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGK-QLEDG-------------RTLADYNIQKE   64 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~~----~g~-~L~d~-------------~tL~~~gi~~g   64 (116)
                      ..+.+.|-..+||.+.|++|-..+  +.|      ++++-|-+    .|+ .|.|.             .||+.|+|.+|
T Consensus        41 ~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~~~wkrLNTL~HY~V~Dg  120 (138)
T 2r2o_A           41 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  120 (138)
T ss_dssp             CCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBHHHHTCCTT
T ss_pred             CceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCceEeeccCCcccccCCceeecchhccCCCCC
Confidence            457888999999999999998874  343      34555543    344 36552             26999999999


Q ss_pred             CEEEEEEecC
Q 033570           65 STLHLVLRLR   74 (116)
Q Consensus        65 ~~I~v~~~~~   74 (116)
                      +++.++.+..
T Consensus       121 a~l~l~~~~~  130 (138)
T 2r2o_A          121 ATVALVPCLT  130 (138)
T ss_dssp             CEEEEEEC--
T ss_pred             CEEEEEECCC
Confidence            9999887743

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=94.82  E-value=0.21  Score=36.88  Aligned_cols=74  Identities=22%  Similarity=0.346  Sum_probs=55.4

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhC----CCCCceEEEE------CCEEcCCCCccccCCCCCCCEEEEE--
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG----IPPDQQRLIF------AGKQLEDGRTLADYNIQKESTLHLV--   70 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~----i~~~~q~L~~------~g~~L~d~~tL~~~gi~~g~~I~v~--   70 (116)
                      +.|... +.+-.+..++++||.+....|.+++.    .++++.-|..      +|.=|.+..+|..|++.+++.+...  
T Consensus         6 ~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~~~   84 (371)
T 3ivf_A            6 LKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRKK   84 (371)
T ss_dssp             EEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             EEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeeccCc
Confidence            445444 56678999999999999999988874    3566666665      3444777889999999999987664  


Q ss_pred             -----EecCCCC
Q 033570           71 -----LRLRGGI   77 (116)
Q Consensus        71 -----~~~~gg~   77 (116)
                           +.+.+|.
T Consensus        85 ~~~~~V~l~dg~   96 (371)
T 3ivf_A           85 QRPLKIRMLDGT   96 (371)
T ss_dssp             EEEEEEECTTSC
T ss_pred             eeEEEEECcCCC
Confidence                 5566664

>2cu3_A Unknown function protein; thermus thermophilus HB8, structural genomics, riken structu genomics/proteomics initiative, RSGI, NPPSFA; 1.70A {Thermus thermophilus} SCOP: d.15.3.2 PDB: 2htm_E

Probab=94.65  E-value=0.14  Score=28.38  Aligned_cols=60  Identities=13%  Similarity=0.315  Sum_probs=42.9

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      +|+.+.  + +..||.+|.+.+    ++++....+..+|+.+..+ ...+.-+++|+.|.++....||
T Consensus         5 Ng~~~~--~-~~~tv~~ll~~l----~~~~~~v~vavN~~~v~~~-~~~~~~L~dgD~v~i~~~V~GG   64 (64)
T 2cu3_A            5 NGEPRP--L-EGKTLKEVLEEM----GVELKGVAVLLNEEAFLGL-EVPDRPLRDGDVVEVVALMQGG   64 (64)
T ss_dssp             TTEEEC--C-TTCCHHHHHHHH----TBCGGGEEEEETTEEEEGG-GCCCCCCCTTCEEEEEECCCC-
T ss_pred             CCEEEE--c-CCCcHHHHHHHc----CCCCCcEEEEECCEECCcc-ccCCcCCCCCCEEEEEeecccC
Confidence            555544  4 568999998877    5666777888999987533 3344457789999998877765

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=94.42  E-value=0.061  Score=34.49  Aligned_cols=34  Identities=21%  Similarity=0.323  Sum_probs=30.7

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEEEC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~   46 (116)
                      ..+.|..++|+.+|+..|++.+|+|++.|+|...
T Consensus        58 ~~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW~~   91 (130)
T 2kvr_A           58 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPM   91 (130)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEEC
T ss_pred             ceEEEeccCcHHHHHHHHHHHhCCCcccEEEEEe
Confidence            4678889999999999999999999999999853

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=94.00  E-value=0.7  Score=29.45  Aligned_cols=65  Identities=26%  Similarity=0.401  Sum_probs=47.2

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEEE----CCE-EcCC-C------------CccccCCCC
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGK-QLED-G------------RTLADYNIQ   62 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~~----~g~-~L~d-~------------~tL~~~gi~   62 (116)
                      ++..+.+.|-..+||.+.|++|-..+  +.|      ++++.|-+    .|. .|.| +            .||+.|+|.
T Consensus        15 ~~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~~krLNTL~HY~V~   94 (127)
T 3h6n_A           15 GMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIP   94 (127)
T ss_dssp             CCCCEEEEEETTSBHHHHHHHHHHHHSTTSCGGGSCCGGGEEEEEECSSSCEEECCSSSTTSCEETTEECCCBTTTTTCC
T ss_pred             CCCceeeeeeccCchhhhhHHHHHHHhccCCcccCCCCcccceEEecCCCCceEeecCCCcceecCceeEeccccccCCC
Confidence            44567888889999999999998764  333      45666665    233 3654 1            258899999


Q ss_pred             CCCEEEEEEec
Q 033570           63 KESTLHLVLRL   73 (116)
Q Consensus        63 ~g~~I~v~~~~   73 (116)
                      +|+++.++.+.
T Consensus        95 dgatv~l~~~~  105 (127)
T 3h6n_A           95 EGASLAMSLID  105 (127)
T ss_dssp             TTCEEEEEECC
T ss_pred             CCCEEEEEEcc
Confidence            99999888663

>1ef1_A Moesin; membrane, FERM domain, tail domain, membrane protein; 1.90A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1sgh_A 1j19_A 2emt_A 2ems_A 2d10_A 2d11_A 2yvc_A 2d2q_A 2zpy_A 1gc7_A 1gc6_A 1ni2_A

Probab=93.96  E-value=0.51  Score=33.45  Aligned_cols=71  Identities=17%  Similarity=0.270  Sum_probs=52.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEE---CCE--EcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF---AGK--QLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~---~g~--~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.+.|..++| +..+.+++.+|+.+|-+.|.++.|+... ..-|.+   +|.  -|+.+..+.+.++..+....+..+
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~fr   78 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFR   78 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCCCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEEE
Confidence            4678888888 6779999999999999999999998543 345554   343  367788888876655554444443

>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A

Probab=93.93  E-value=0.68  Score=33.21  Aligned_cols=70  Identities=11%  Similarity=0.125  Sum_probs=51.9

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC-CceEEEE--CCEE--cCCCCccccCCCCCCCEEEEEEe
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIF--AGKQ--LEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~-~~q~L~~--~g~~--L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      .+.|..++| .+.+.+++.+|+.+|-+.|.++.|+.. +..-|.|  .|..  |+.+..|.+.++..+....+..+
T Consensus        24 ~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~fr   98 (314)
T 1h4r_A           24 TVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   98 (314)
T ss_dssp             EEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             EEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCCCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEEE
Confidence            567888888 788999999999999999999999853 3445554  4443  77788888887655554444443

>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.3.3 PDB: 1xo3_A

Probab=93.81  E-value=0.53  Score=29.29  Aligned_cols=74  Identities=18%  Similarity=0.196  Sum_probs=46.2

Q ss_pred             CEEEEEcCC------C--CEEEEEecC---CCCHHHHHHHHHHhhC-CC----------CCceEEEECCEEcCCCCcc--
Q 033570            1 MQIFVKTLT------G--KTITLEVES---SDTIDNVKAKIQDKEG-IP----------PDQQRLIFAGKQLEDGRTL--   56 (116)
Q Consensus         1 m~v~Vk~~~------g--~~~~i~v~~---~~TV~~LK~~I~~~~~-i~----------~~~q~L~~~g~~L~d~~tL--   56 (116)
                      |+|+|+...      |  +.+.++++.   ..||.+|...+.+.+. ..          ...+.++.||+...   .|  
T Consensus        12 M~v~V~~~~~Lr~~~g~~~~~~vel~~~~~~~TV~~Ll~~L~~~~~~~~~~lf~~~g~lr~~i~VlVN~~di~---~l~g   88 (114)
T 1wgk_A           12 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWE---LLGE   88 (114)
T ss_dssp             EEEEEEECTTTGGGTTTCSEEEEEECCCSSCCBHHHHHHHHTTTTCCSCHHHHCCSSSCCSSEEEEESSSBHH---HHCT
T ss_pred             cEEEEEEchHHHHHhCCceEEEEEeCCCCCCCCHHHHHHHHHHHccchhHhhCccCCcccCCeEEEECCeeee---ccCC
Confidence            567776653      3  356788884   3699999999998761 10          01123334444210   11  


Q ss_pred             ccCCCCCCCEEEEEEecCCCC
Q 033570           57 ADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus        57 ~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      -++-+++|+.|.++....||.
T Consensus        89 ldt~L~dGDeV~iip~vaGG~  109 (114)
T 1wgk_A           89 LDYQLQDQDSILFISTLHGGS  109 (114)
T ss_dssp             TTCBCCSSEEEEEEECSCCCC
T ss_pred             cCcCCCCCCEEEEeCCCCCCC
Confidence            235578899999998888884

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A

Probab=93.53  E-value=0.44  Score=28.51  Aligned_cols=46  Identities=13%  Similarity=0.221  Sum_probs=36.8

Q ss_pred             EEEEcC-CCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEECCE
Q 033570            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFAGK   48 (116)
Q Consensus         3 v~Vk~~-~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~~g~   48 (116)
                      |.||.. +|....+.++++.+..+|.+++.+.++++.+ .+.+.|...
T Consensus         7 vkvK~~~~gdi~~~~v~~~i~~~~L~~kv~~~~~~~~~~~f~lky~DE   54 (89)
T 1vd2_A            7 VRVKAYYRGDIMITHFEPSISFEGLCNEVRDMCSFDNEQLFTMKWIDE   54 (89)
T ss_dssp             EEEEEESSSCEEEEEECTTCCHHHHHHHHHHHTTCCSSCCEEEEECCS
T ss_pred             EEEEEEeCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCeEEEEEECC
Confidence            344443 5678889999999999999999999998754 478888765

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=93.30  E-value=0.7  Score=34.01  Aligned_cols=71  Identities=27%  Similarity=0.399  Sum_probs=54.0

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCC-CCceEEEECC---------EEcCCCCccccCCCCCCCEEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLIFAG---------KQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~-~~~q~L~~~g---------~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      .+.|..++|....+.+++.+|+.++-+.|.++.|+. .+..-|.+..         .-|+.++++.+.+......+.+.+
T Consensus        87 ~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~~~~~wL~~~k~l~~q~~~~~~~l~frv  166 (371)
T 3ivf_A           87 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDDELNWLDHGRTLREQGVEEHETLLLRR  166 (371)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTCSCGGGEEEECCC----------CCCTTSBTGGGTCCTTCEEEEEE
T ss_pred             EEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCCCCccccEEEEEecccccchHHHHHhcCchhHhhCCCCCceEEEEE
Confidence            577888999999999999999999999999999984 4455666532         124556777777766666776655


Q ss_pred             e
Q 033570           72 R   72 (116)
Q Consensus        72 ~   72 (116)
                      +
T Consensus       167 K  167 (371)
T 3ivf_A          167 K  167 (371)
T ss_dssp             C
T ss_pred             E
Confidence            5

>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A

Probab=93.01  E-value=0.62  Score=27.09  Aligned_cols=61  Identities=13%  Similarity=0.245  Sum_probs=41.5

Q ss_pred             EEecCCCCHHHHHHHHHHhhC------C-----CCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           15 LEVESSDTIDNVKAKIQDKEG------I-----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        15 i~v~~~~TV~~LK~~I~~~~~------i-----~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ++++...||.+|.+.+.....      +     ......+..||+..... .-.+.-+++|+.|.++....||
T Consensus        19 ~~~~~~~tv~~ll~~l~~~~p~~~~~~l~~~~g~~~~v~v~vN~~~v~~~-~~~~~~l~~gD~V~i~ppv~GG   90 (90)
T 2g1e_A           19 ETFNGISKISELLERLKVEYGSEFTKQMYDGNNLFKNVIILVNGNNITSM-KGLDTEIKDDDKIDLFPPVAGG   90 (90)
T ss_dssp             EEESSCCBHHHHHHHHHHHSCHHHHHHHCCSSCSTTTCEEEESSSBGGGT-CSSSCBCCTTCEEEEECCTTCC
T ss_pred             EEcCCCCcHHHHHHHHHHHCcchhhhccccccCcCcceEEEECCEEcccc-CCCCcCCCCCCEEEEeCCCCCC
Confidence            456666899999999987742      1     01456777899876422 1233457789999998777765

>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown FUN; NMR {Pyrococcus furiosus} SCOP: d.15.3.2 PDB: 1sf0_A

Probab=92.78  E-value=0.035  Score=32.15  Aligned_cols=54  Identities=11%  Similarity=0.260  Sum_probs=39.9

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .+++++..||.+|.+.+    +++.....+..+|+..+.+     .-+++|+.|.++....||
T Consensus        24 ~~~~~~~~Tv~dLl~~L----~~~~~~v~VavNg~~v~~~-----~~L~dGD~V~i~ppv~GG   77 (77)
T 1rws_A           24 EIEWREGMKVRDILRAV----GFNTESAIAKVNGKVVLED-----DEVKDGDFVEVIPVVSGG   77 (77)
T ss_dssp             CCCCCSSCCHHHHHHTT----TCSSCSSCEEETTEEECSS-----SCCCSSCCCBCSCCCCCC
T ss_pred             EEECCCCCcHHHHHHHh----CCCCcCEEEEECCEECCCC-----CCcCCCCEEEEEcccccC
Confidence            34566778999988766    4666777788999988765     446679988877766665

>1wgy_A RAP guanine nucleotide exchange factor 5; ubiquitin fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=92.73  E-value=1  Score=27.73  Aligned_cols=69  Identities=10%  Similarity=0.207  Sum_probs=49.2

Q ss_pred             EEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE---ECCEE--cCCCCccccCCCCCCCEEEEEEec
Q 033570            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQ--LEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         5 Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~---~~g~~--L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |-..+...+.+.+..+.|+.+++..++++.+...+++.|+   ++|..  |+++..--.-.+.-+..|++..+.
T Consensus        14 Vy~~Dhsy~tvr~~v~~sa~eIl~~va~kl~~~~e~l~Lv~v~ssGEk~~lqp~d~si~tsL~~NgRLfvc~kd   87 (104)
T 1wgy_A           14 VYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRKD   87 (104)
T ss_dssp             EECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEECC
T ss_pred             EEeccCceEEEEEeccchHHHHHHHHHHHhcCCccceEEEEEccCCcEeecCCcceEEEeeccccceEEEeehH
Confidence            4445666778889999999999999999999876677776   67773  554333222234557788887763

>3u52_E Phenol hydroxylase component PHO; 4-helix bundle, dioxygen, hydrocarbons, oxidore; HET: MPO EPE; 1.95A {Pseudomonas stutzeri} PDB: 2inn_E* 2inp_E

Probab=92.61  E-value=0.88  Score=28.60  Aligned_cols=65  Identities=14%  Similarity=0.145  Sum_probs=50.2

Q ss_pred             EEEEEecCCCCHHHHHHHHHHh-hC-------CCCCceEEEECCEEcC--CCCccccCCCCCCCEEEEEEecCCC
Q 033570           12 TITLEVESSDTIDNVKAKIQDK-EG-------IPPDQQRLIFAGKQLE--DGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~-~~-------i~~~~q~L~~~g~~L~--d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .+.+.++|+++.++|-+.+-.. ++       |+.+...+..+|++..  .+++|.+.|+...+.|.+.-.-..|
T Consensus        39 p~~~p~pP~mpFg~lv~~vl~~~~~~hPDfa~idws~v~W~l~g~pftPD~~kSLaenG~~HKs~lrf~TPgL~G  113 (119)
T 3u52_E           39 PFALLVQPGMTFSALVDEILKPATAAHPDSAKADFLNAEWLLNDEPFTPKADASLKEQGIDHKSMLTVTTPGLKG  113 (119)
T ss_dssp             CEEEEECTTSBHHHHHHHTHHHHTTTSTTGGGCCTTSSEEEETTEEECCCTTSBTTTTTCCTTEEEEEECTTCCC
T ss_pred             ceeecCCCCCCHHHHHHHhcchhhhcCCccccCCcchheEEECCccCCCChhhhHHHcCCCchheEEEeCCCcCc
Confidence            3678999999999988776553 33       5666778889999884  3889999999999998776544333

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=92.27  E-value=0.86  Score=28.62  Aligned_cols=63  Identities=30%  Similarity=0.477  Sum_probs=44.8

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEEE-C---CE-EcCC-C------------CccccCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-A---GK-QLED-G------------RTLADYNIQKE   64 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~~-~---g~-~L~d-~------------~tL~~~gi~~g   64 (116)
                      ..+.+.|-..+||.+.|++|-..+  +.|      ++++-|-+ .   |+ .|.| +            .||+.|+|.+|
T Consensus        27 ~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  106 (117)
T 4e74_A           27 PEVPVKILNCDTITQVKEKILDAIFKNVPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPDG  106 (117)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCTT
T ss_pred             CceEeeeecCCchHHHHHHHHHHHhcCCCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCCC
Confidence            347788888999999999998764  333      34555554 2   23 3544 1            25889999999


Q ss_pred             CEEEEEEec
Q 033570           65 STLHLVLRL   73 (116)
Q Consensus        65 ~~I~v~~~~   73 (116)
                      +++.++.+.
T Consensus       107 atl~l~~~~  115 (117)
T 4e74_A          107 SVVALVSKQ  115 (117)
T ss_dssp             CEEEEEECC
T ss_pred             CEEEEEeCC
Confidence            999988764

>3qij_A Protein 4.1; cytoskeleton, structural genomics, structural genomics conso SGC; 1.80A {Homo sapiens} PDB: 1gg3_A 3bin_A 2he7_A 2rq1_A

Probab=91.59  E-value=1.1  Score=32.06  Aligned_cols=72  Identities=10%  Similarity=0.038  Sum_probs=51.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC-CceEEEEC---CE--EcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFA---GK--QLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~-~~q~L~~~---g~--~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.+.|..++|....+.|++.+|+.+|-..|.++.|+.. +..-|.+.   |.  -|+.++.+.+........+.+.++
T Consensus        18 ~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~~~~~~~l~frvk   95 (296)
T 3qij_A           18 GHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNVK   95 (296)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTCSSGGGEEEEEEEETTEEEECCTTSBHHHHC---CCEEEEEES
T ss_pred             EEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCCCCcceeEEEEEcCCCccchhccchhHHHhcCCCCcEEEEEEE
Confidence            56889999999999999999999999999999999853 33455542   32  366677777664433445555554

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=91.52  E-value=0.96  Score=25.12  Aligned_cols=63  Identities=13%  Similarity=0.105  Sum_probs=42.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.+.|..++|+.  .+++...|+.+|-..+....+  ....-...+|+..+-+..|     .+|+.|.++-.
T Consensus         1 m~i~i~~p~g~~--~~~~~g~T~~dla~~i~~~l~--~~~vaa~vNg~lvdl~~~L-----~~~~~Veivt~   63 (73)
T 2kmm_A            1 MEVMVFTPKGEI--KRLPQGATALDFAYSLHSDLG--DHCIGAKVNHKLVPLSYVL-----NSGDQVEVLSS   63 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHHH--HTEEEEEETTEECCTTCBC-----CSSSBEEEEEC
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhccc--cceEEEEECCEEeCCCcCc-----CCCCEEEEEEC
Confidence            788898888875  566677899998887743321  1223345789877655444     45788877654

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=91.40  E-value=1.4  Score=34.72  Aligned_cols=71  Identities=15%  Similarity=0.276  Sum_probs=52.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCC-CceEEEEC---CE--EcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFA---GK--QLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~-~~q~L~~~---g~--~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.+.|..++| ++.+.|++.+|+.+|-..|....|+.. ..+-|.|.   |.  -|+.+.++.+.++..+..+.+..+
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~FR   81 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGLREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKFR   81 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCCCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEEE
Confidence            3577888888 678999999999999999999999853 34556552   22  466678888877666655544444

>1y8x_B Ubiquitin-activating enzyme E1C; ubiquitin-conjugating enzyme E2 M, ligase; 2.40A {Homo sapiens} SCOP: c.111.1.2 PDB: 3fn1_A

Probab=91.33  E-value=0.52  Score=28.69  Aligned_cols=59  Identities=12%  Similarity=0.264  Sum_probs=40.0

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCCCCCce----------EEEECCE--EcC------CCCccccCCCCCCCEEEEE
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQ----------RLIFAGK--QLE------DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q----------~L~~~g~--~L~------d~~tL~~~gi~~g~~I~v~   70 (116)
                      ...+.+++++|+.+|.+.+.+.-.+....=          +-+|...  .|.      -+++|.++|+.+|+.|+|.
T Consensus         6 ~~~l~v~~~~TL~~lid~L~~~p~~qlk~PSltt~~~~~~k~LYmq~pp~Lee~Tr~NL~k~l~eLgl~~g~ei~Vt   82 (98)
T 1y8x_B            6 PQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVA   82 (98)
T ss_dssp             CCCEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEE
T ss_pred             cEEEEECCchhHHHHHHHHHhChHhhccCCeeeeecCCCCCeEEEeCcHHHHHHhHhhhhCCHHHhCCCCCCEEEEE
Confidence            456899999999999999999543322211          2223222  122      1567999999999998885

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=91.29  E-value=0.86  Score=29.04  Aligned_cols=57  Identities=23%  Similarity=0.334  Sum_probs=41.6

Q ss_pred             EEEecC----CCCHHHHHHHHHHhhCCCCCceEEEE--CCEEc-----CC--CCccccCCCCCCCEEEEEE
Q 033570           14 TLEVES----SDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQL-----ED--GRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        14 ~i~v~~----~~TV~~LK~~I~~~~~i~~~~q~L~~--~g~~L-----~d--~~tL~~~gi~~g~~I~v~~   71 (116)
                      .+.|++    ..|+.+|-+.+..++|.. +.+.+.-  ..+.|     +|  +++|+++|+++|+.+.+.=
T Consensus         9 vl~v~~~dl~~~TL~dLV~~l~~~~gy~-~eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~D   78 (127)
T 3onh_A            9 VIKLSSDCLNKMKLSDFVVLIREKYSYP-QDISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFSD   78 (127)
T ss_dssp             EEEECHHHHHHCBHHHHHHHHHHHHTCC-SSEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEEE
T ss_pred             EEEeCcccccccCHHHHHHHHHHhcCCC-CcEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEEc
Confidence            355654    479999999998899986 3666653  34444     23  6799999999999987763

>2inc_C TOUB protein; DIIRON, 4-helix bundle, carboxylate bridge, metalloenzyme, oxidoreductase; HET: P6G; 1.85A {Pseudomonas stutzeri} SCOP: d.15.12.1 PDB: 2ind_C* 3n20_C* 1t0r_C 1t0s_C 1t0q_C* 3n1x_C 3n1y_C* 3n1z_C* 2rdb_C* 3rn9_C* 3rna_C 3rnb_C 3rnc_C 3rne_C 3rnf_C* 3rng_C

Probab=90.88  E-value=1.5  Score=25.78  Aligned_cols=60  Identities=20%  Similarity=0.335  Sum_probs=49.0

Q ss_pred             EEEEecCCCCHHHHHHHHHHhh-C--C--CCC-ceEEEECC--EEcCCCCccccCCCCCCCEEEEEEe
Q 033570           13 ITLEVESSDTIDNVKAKIQDKE-G--I--PPD-QQRLIFAG--KQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~-~--i--~~~-~q~L~~~g--~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      ..+.|+.++|+.++-++++.+. |  +  .+. -.+..++|  +.+..+.++++.||.+-+.|.+...
T Consensus        15 ~LV~VDt~dTmdqVA~kvA~HsVGrRV~p~p~~~~rVr~~G~~~~~pr~~tvae~gl~P~e~vev~~~   82 (83)
T 2inc_C           15 QLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFM   82 (83)
T ss_dssp             EEEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEEE
T ss_pred             EEEEecCCCcHHHHHHHHhhhhcceecCCCCCCeEEEEecCCccCCCCCCEeeccCCCCceEEEEEEc
Confidence            4578999999999999998863 3  3  223 46777999  8999999999999999999988653

>2kmc_A Fermitin family homolog 1; kindlin, cytoskeleton, integrin, N-terminal, talin, cell adhesion, cell junction, cell membrane, cell projection; NMR {Mus musculus}

Probab=90.72  E-value=1.8  Score=26.37  Aligned_cols=71  Identities=23%  Similarity=0.238  Sum_probs=54.8

Q ss_pred             EEEEEcCCC---CEEEEEecCCCCHHHHHHHHHHhhCCC--CCceEEEEC---CEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            2 QIFVKTLTG---KTITLEVESSDTIDNVKAKIQDKEGIP--PDQQRLIFA---GKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         2 ~v~Vk~~~g---~~~~i~v~~~~TV~~LK~~I~~~~~i~--~~~q~L~~~---g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +|+|...+.   ....+.|..+.-|+.+-.+|-+...++  .++--|-.-   -.+|.-..+|..|||..++.+++...
T Consensus        21 ~V~V~d~~~~~~~~~~lrV~GdlHIGGvmlklVEki~i~~dWSDhaLWW~~k~~WLlkt~~tLDkygiqADa~L~ftp~   99 (102)
T 2kmc_A           21 VVRVDHANGEQQTEITLRVSGDLHIGGVMLKLVEQMNIAQDWSDYALWWEQKRCWLLKTHWTLDKCGVQADANLLFTPQ   99 (102)
T ss_dssp             EEEEECTTSSCEEEEEEEECSCCBHHHHHHHHHHHHCCSSCCSSEEEEETTTTEEECCTTSBHHHHTCCTTSCEEEEEC
T ss_pred             EEEEecCCcccCccEEEEEeeccccchhhhhhhhhcccccchHHhhhhhhhhchhhhhhhhhhhhhceeeeeeeeccCC
Confidence            577888654   447889999999999999998887764  445555543   23688899999999999999887754

>3ge3_C Toluene-4-monooxygenase system protein B; DIIRON hydroxylase, effector protein, T201A, aromatic hydrocarbons catabolism, FAD, flavoprotein; 1.52A {Pseudomonas mendocina} SCOP: d.15.12.0 PDB: 3dhh_C* 3dhg_C* 3dhi_C 3ge8_C 3i5j_C 3i63_C 3q14_C 3q2a_C* 3q3m_C* 3q3n_C* 3q3o_C* 3rmk_C* 3ri7_C*

Probab=90.72  E-value=1.6  Score=25.72  Aligned_cols=59  Identities=15%  Similarity=0.229  Sum_probs=49.1

Q ss_pred             EEEEecCCCCHHHHHHHHHHhh-C--C--CCCceEEEECCEE--cCCCCccccCCCCCCCEEEEEE
Q 033570           13 ITLEVESSDTIDNVKAKIQDKE-G--I--PPDQQRLIFAGKQ--LEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~-~--i--~~~~q~L~~~g~~--L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      ..+.|+.++|+.++-++++... |  +  .+.-.+..++|..  |.++.++++.||.+-+.|.+..
T Consensus        17 ~Lv~VDt~dtmdqVA~k~A~h~VGrrv~p~pg~lrVr~~G~~~~~Pr~mtVaeaGl~Pme~vev~~   82 (84)
T 3ge3_C           17 QLVVVDLNDSMDQVAEKVAYHCVNRRVAPREGVMRVRKHRSTELFPRDMTIAESGLNPTEVIDVVF   82 (84)
T ss_dssp             EEEEEETTCBHHHHHHHHHHTTBTTTBCCCSSCEEEEETTCSCBCCTTCBHHHHCCCTTCEEEEEE
T ss_pred             EEEEecCCCcHHHHHHHHhhhhcceeeCCCCCcEEEEECCCcccCCCCCEeeccCCCcceEEEEEE
Confidence            4578999999999999998864 4  3  2346788899997  9999999999999999998764

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=90.23  E-value=1.9  Score=31.40  Aligned_cols=52  Identities=19%  Similarity=0.281  Sum_probs=41.1

Q ss_pred             CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE-Ec-CCCCccccCCC
Q 033570           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-QL-EDGRTLADYNI   61 (116)
Q Consensus        10 g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~-~L-~d~~tL~~~gi   61 (116)
                      -....+.+.+..|+.++++.+++.++++++.|.+++.+. .. +...+...+.-
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~~~~~~~~~~~~~~~~  374 (396)
T 4eut_A          321 MTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPK  374 (396)
T ss_dssp             TEEEEEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSSEECCCSSCBTTSSCC
T ss_pred             ceEEEEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCCCCCCCCCCccccCCC
Confidence            345678889999999999999999999999999999884 33 33555555544

>2l52_A Methanosarcina acetivorans SAMP1 homolog; beta-grAsp fold, protein binding, E1-like, SAMP activator, ELSA, adenylation, ubiquitin; NMR {Methanosarcina acetivorans}

Probab=89.92  E-value=2  Score=25.66  Aligned_cols=72  Identities=14%  Similarity=0.286  Sum_probs=44.7

Q ss_pred             CEEEEEcCC------C-CEEEEEecCCCCHHHHHHHHHHhhC-CCC---------Cce-------EEEECCEEcCCCCcc
Q 033570            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-IPP---------DQQ-------RLIFAGKQLEDGRTL   56 (116)
Q Consensus         1 m~v~Vk~~~------g-~~~~i~v~~~~TV~~LK~~I~~~~~-i~~---------~~q-------~L~~~g~~L~d~~tL   56 (116)
                      |+|+|+-..      | +...+  + ..||.+|.+.+...+. +..         ..+       .+..||+..... .-
T Consensus         4 m~v~V~~fa~lr~~~g~~~~~l--~-~~tv~~ll~~L~~~~p~l~~~l~~~g~l~~~v~~~~~~~~v~VNg~~v~~~-~~   79 (99)
T 2l52_A            4 AEVKVKLFANLREAAGTPELPL--S-GEKVIDVLLSLTDKYPALKYVIFEKGDEKSEILILCGSINILINGNNIRHL-EG   79 (99)
T ss_dssp             CEEEEEECTHHHHHHSSSEEEE--E-CSSHHHHHHHHHHHCGGGTTTSBCSCCTTSSCCCBCSSCEEEETTSCGGGT-TS
T ss_pred             eEEEEEEeHHHHHHhCCCeEEE--e-CCcHHHHHHHHHHHChhHHHHHhcccccccceeccccccEEEECCEEcccc-CC
Confidence            566776553      2 23444  4 5799999999987742 111         123       677888866322 12


Q ss_pred             ccCCCCCCCEEEEEEecCCC
Q 033570           57 ADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        57 ~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .+.-+++|+.|.+.....||
T Consensus        80 ~~~~L~~gD~V~i~ppv~GG   99 (99)
T 2l52_A           80 LETLLKDSDEIGILPPVSGG   99 (99)
T ss_dssp             TTSCCCTTEEEEEECCCSCC
T ss_pred             CCCCCCCCCEEEEECCCCCC
Confidence            23356789999998777665

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=89.12  E-value=0.14  Score=31.81  Aligned_cols=74  Identities=16%  Similarity=0.275  Sum_probs=41.9

Q ss_pred             CEEEEEcCC------CCEEEEEecC----CCCHHHHHHHHHHhhCCCCCceEEE-ECC--E------EcCCCCcc-----
Q 033570            1 MQIFVKTLT------GKTITLEVES----SDTIDNVKAKIQDKEGIPPDQQRLI-FAG--K------QLEDGRTL-----   56 (116)
Q Consensus         1 m~v~Vk~~~------g~~~~i~v~~----~~TV~~LK~~I~~~~~i~~~~q~L~-~~g--~------~L~d~~tL-----   56 (116)
                      |+|.|+...      |+...++++.    ..||.+|-..+.+.+.-  .+-.|. -+|  .      +|-++..+     
T Consensus         5 m~v~V~f~g~l~~l~g~~~~v~l~~~~g~~~TV~dLl~~L~~~~~~--~r~~lf~~~g~~~lrpgIlVLVNg~d~e~l~g   82 (110)
T 2k9x_A            5 NHITVQFAGGCELLFAKQTSLQLDGVVPTGTNLNGLVQLLKTNYVK--ERPDLLVDQTGQTLRPGILVLVNSCDAEVVGG   82 (110)
T ss_dssp             SCCEEEEESSCGGGTTSCSEECCCCSCGGGCCHHHHHHHHTTTTCC--SCHHHHBCSSSSSBCTTEEEEESSSBHHHHTS
T ss_pred             cEEEEEEEecHHHHhCCeEEEEeCCcCCCCccHHHHHHHHHHHccc--cchhhEecCCCcccCCCeEEEECCeeeeccCC
Confidence            445555443      3445667763    35999999999887521  121221 112  1      12222222     


Q ss_pred             ccCCCCCCCEEEEEEecCCC
Q 033570           57 ADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        57 ~~~gi~~g~~I~v~~~~~gg   76 (116)
                      -++-+++|+.|.+.....||
T Consensus        83 ldt~L~dgD~V~fistlhg~  102 (110)
T 2k9x_A           83 MDYVLNDGDTVEFISTLHGG  102 (110)
T ss_dssp             SCCCCCSSCEEEEEECCCCC
T ss_pred             cccCCCCcCEEEEeCCCccc
Confidence            24568899999888877776

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=89.05  E-value=2.9  Score=26.52  Aligned_cols=61  Identities=33%  Similarity=0.506  Sum_probs=41.2

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHh----hCCC----CCceEEEE--C--CEEcCC----------C----CccccCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDK----EGIP----PDQQRLIF--A--GKQLED----------G----RTLADYNIQKE   64 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~----~~i~----~~~q~L~~--~--g~~L~d----------~----~tL~~~gi~~g   64 (116)
                      ..+.+.|-..+||.+.|++|-..    .+.|    ++++-|-+  +  +..|.|          .    .||+.|+|.+|
T Consensus        39 ~~v~VkVLdCDTItQVKEKILdavYk~k~~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V~Dg  118 (126)
T 3kuz_A           39 RNISVNVLDCDTIGQAKEKIFQAFLSKNGSPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEISNG  118 (126)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHHHHHSSCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTCCTT
T ss_pred             CceEeeeecCCcHHHHHHHHHHHHhccCCCcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCCCCC
Confidence            45788888999999999999764    2554    33444443  1  123332          1    25788999999


Q ss_pred             CEEEEEE
Q 033570           65 STLHLVL   71 (116)
Q Consensus        65 ~~I~v~~   71 (116)
                      +++.++.
T Consensus       119 atlal~k  125 (126)
T 3kuz_A          119 STIKVFK  125 (126)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEee
Confidence            9997764

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=88.43  E-value=0.59  Score=36.43  Aligned_cols=33  Identities=21%  Similarity=0.340  Sum_probs=30.2

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~   45 (116)
                      ..+.|..++|+.+|++.|++.+|+|+++|||..
T Consensus        38 ~~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW~   70 (530)
T 2ylm_A           38 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   70 (530)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTSCGGGEEEEE
T ss_pred             ceEEEcCcCCHHHHHHHHHHHhCcCcccEEEEE
Confidence            468899999999999999999999999999874

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=88.42  E-value=5.3  Score=31.86  Aligned_cols=64  Identities=28%  Similarity=0.472  Sum_probs=45.4

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEEE----CCE-EcCCC-------------CccccCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGK-QLEDG-------------RTLADYNIQKE   64 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~~----~g~-~L~d~-------------~tL~~~gi~~g   64 (116)
                      ..+.+.|-..+||.++|++|-...  +.|      ++++-|-+    .|+ .|.|.             .||++|+|.+|
T Consensus       247 ~~i~vkVLdCDTItQVKeKiLdavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~Dg  326 (627)
T 3ig3_A          247 AQVPVKVLNCDSITQAKDKLLDTVYKGIPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDWKRVNSLAHYQVTDG  326 (627)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCccceeEeeCCCCceeeccCCccccccCceeEecchhhcCCCCC
Confidence            557788889999999999998764  333      44555543    233 35441             25899999999


Q ss_pred             CEEEEEEecC
Q 033570           65 STLHLVLRLR   74 (116)
Q Consensus        65 ~~I~v~~~~~   74 (116)
                      +++.++.+..
T Consensus       327 a~v~L~p~~~  336 (627)
T 3ig3_A          327 SLVALVPKQV  336 (627)
T ss_dssp             CEEEEEEC--
T ss_pred             ceEEEEeccc
Confidence            9999988753

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=88.27  E-value=2.7  Score=25.00  Aligned_cols=65  Identities=15%  Similarity=0.236  Sum_probs=40.2

Q ss_pred             CEEEEEec--CCCCHHHHHHHHHHhhCCCC---------C----ceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570           11 KTITLEVE--SSDTIDNVKAKIQDKEGIPP---------D----QQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus        11 ~~~~i~v~--~~~TV~~LK~~I~~~~~i~~---------~----~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      +...++++  +..||.+|.+.+.+++.-..         .    ...+..||+...-. .=.+.-+++|+.|.+.....|
T Consensus        20 ~~~~~~l~~~~~~Tv~~L~~~L~~~~~~~~~~l~~~~~~~~lr~~~~v~VN~~~~~~~-~~~d~~L~dgDeVa~~Ppv~G   98 (99)
T 2qjl_A           20 RVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWELE-GEKDYILEDGDIISFTSTLHG   98 (99)
T ss_dssp             CEEEEEECSCSCCBHHHHHHHHHHHTCSSGGGHHHHEETTEECTTEEEEETTEEGGGG-TGGGCBCCTTCEEEEEECTTC
T ss_pred             cEEEEecCCCCCCcHHHHHHHHHHHCchhhHHHhhhccCCccccCeEEEECCEEcccc-CCCCcCcCCCCEEEEECCCCC
Confidence            44667776  67899999999998863111         1    12344566532100 002345778999999887777


Q ss_pred             C
Q 033570           76 G   76 (116)
Q Consensus        76 g   76 (116)
                      |
T Consensus        99 G   99 (99)
T 2qjl_A           99 G   99 (99)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1wgr_A Growth factor receptor-bound protein 7; RA domain, GRB7, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=87.48  E-value=1.5  Score=26.68  Aligned_cols=67  Identities=18%  Similarity=0.249  Sum_probs=45.7

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCc-eEEE--E----CCEEcCCCCccccC----CCCCCCEEEE
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--F----AGKQLEDGRTLADY----NIQKESTLHL   69 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~--~----~g~~L~d~~tL~~~----gi~~g~~I~v   69 (116)
                      |.|-..+|....+.|++++|+.++-+.++++.++..+. ..|+  +    .-+.+.|+..|-+.    .+.....+.+
T Consensus        12 vkvf~~Dgssksi~V~~~~Ta~dv~~~L~~K~~~~~~~~WaLvE~~P~L~~ER~~EDHE~vvevl~~W~~~s~nr~~F   89 (100)
T 1wgr_A           12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDETWGLVECHPHLALERGLEDHESVVEVQAAWPVGGDSRFVF   89 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCCCCCEEEEETTTTEEEEECSSSCHHHHHTTSCSSSCCEEEE
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCCCCCCeEEEEecCCCCcEEeccCchhHHHHHhhCccCCCcEEEE
Confidence            55666789999999999999999999999999875443 3333  1    22457787664443    3444444433

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*

Probab=86.78  E-value=5.6  Score=31.77  Aligned_cols=64  Identities=33%  Similarity=0.530  Sum_probs=44.6

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhh--CCC------CCceEEEE----CCE-EcCCC-------------CccccCCCCCC
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGK-QLEDG-------------RTLADYNIQKE   64 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~--~i~------~~~q~L~~----~g~-~L~d~-------------~tL~~~gi~~g   64 (116)
                      ..+.+.|-..+||.+.|++|-...  |.|      ++++-|-+    .|+ .|.|.             .||+.|+|.+|
T Consensus       274 ~~i~VkVLdCDTItQVKeKiLDavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  353 (644)
T 3hm6_X          274 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  353 (644)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCCC
Confidence            347788888999999999998653  333      34555553    233 35542             36999999999


Q ss_pred             CEEEEEEecC
Q 033570           65 STLHLVLRLR   74 (116)
Q Consensus        65 ~~I~v~~~~~   74 (116)
                      +++.++.+..
T Consensus       354 a~v~L~p~~~  363 (644)
T 3hm6_X          354 ATVALVPCLT  363 (644)
T ss_dssp             CEEEEEEC--
T ss_pred             cEEEEEeccc
Confidence            9999887643

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=86.12  E-value=2.4  Score=25.09  Aligned_cols=39  Identities=10%  Similarity=0.079  Sum_probs=30.0

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK   48 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~   48 (116)
                      ++-.+.+.|+++.+..+|+.+|..+..+. +.+.+.|++.
T Consensus        20 ~DDIiAIrvP~di~~~~L~dKi~~RLk~~-~~~l~~ykde   58 (85)
T 1ip9_A           20 KDDIFALMLKGDTTYKELRSKIAPRIDTD-NFKLQTKLFD   58 (85)
T ss_dssp             TTCCEEEEECSCCCHHHHHHHHHHHHTSS-CEEEEECCSS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHhccc-ceEEEEecCC
Confidence            44578999999999999999999999883 3334445443

>1j0g_A Hypothetical protein 1810045K17; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.6 PDB: 1wxs_A 1l7y_A

Probab=85.01  E-value=3  Score=24.45  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=52.1

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE-CCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~-~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ..+.|++.......-+-.++++++|+...-++- .|--+..+++-+..-++.|+.+.+..|-+-|
T Consensus        26 kvlsVPE~~PftAVlkfaaEeF~vp~~TsAiiT~dGiGInP~QtAGnvFlKhGseLrlIPRDRVG   90 (92)
T 1j0g_A           26 KVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG   90 (92)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHTTCCSSSEEEECTTSCCCCCSSBHHHHHHHTCSEEEEEECCSSC
T ss_pred             eEEecCccCchHHHHHHHHHHcCCCccceEEEecCCcccChhhccchhhhhcCceeEeccccccc
Confidence            357899999898888899999999998776664 4666777888888888899999999886554

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=83.73  E-value=8.4  Score=29.93  Aligned_cols=49  Identities=14%  Similarity=0.187  Sum_probs=37.9

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhCCC---CCceEEE--ECCE---EcCCCCccccCC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEGIP---PDQQRLI--FAGK---QLEDGRTLADYN   60 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~i~---~~~q~L~--~~g~---~L~d~~tL~~~g   60 (116)
                      .+.+-++.+.||++|-+.+.++.+++   .+.+++.  ++++   .++++.+|+.+.
T Consensus       353 ~~~l~vpK~gtV~Dll~~l~k~~~~~~~~~~~lRl~ev~~~ki~ki~~~~~~i~~i~  409 (530)
T 2ylm_A          353 EITLYPDKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLS  409 (530)
T ss_dssp             EEEECCBTTCBHHHHHHHHHTTCCCCTTCCCCEEEEEEETTEEEEEECTTSBGGGSC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCCcCCcccEEEEEEECCEEEEecCCCccccccc
Confidence            46677888999999999999999986   4567765  7887   456777777653

>3h9d_A ATG8, microtubule-associated protein 1A/1B, light chain putative; autophagy, lipidation, ubiquitin-like, S protein; 2.30A {Trypanosoma brucei} SCOP: d.15.1.0

Probab=83.15  E-value=3.2  Score=25.98  Aligned_cols=46  Identities=13%  Similarity=0.152  Sum_probs=36.5

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCc-eEEEECCEEcCCCCccccC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY   59 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~~~g~~L~d~~tL~~~   59 (116)
                      .+-|+.+.||+++...|..+.++++++ +-|..++.....+.+++++
T Consensus        51 KflVp~~~tv~qf~~~iRkrl~l~~~~alFl~Vn~~~p~~~~~m~~l   97 (119)
T 3h9d_A           51 KFLVPSDLTVGQFVSVLRKRVQLEAESALFVYTNDTVLPSSAQMADI   97 (119)
T ss_dssp             EEEEETTCBHHHHHHHHHHHHTCCTTSCCEEEETTEECCTTSBHHHH
T ss_pred             eEEcCCCCCHHHHHHHHHHHhCCCccceEEEEECCcCCCccchHHHH
Confidence            457899999999999999999998775 5565688755567777765

>2dhz_A RAP guanine nucleotide exchange factor (GEF)- like 1; LINK guanine nucleotide exchange factor II, LINK-gefii, RA domain, structural genomics; NMR {Homo sapiens}

Probab=82.37  E-value=3.1  Score=26.15  Aligned_cols=64  Identities=14%  Similarity=0.210  Sum_probs=44.0

Q ss_pred             cCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC------ceEEE---ECCE--EcCCCC--ccccCCCCCCCEEEEEEe
Q 033570            7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD------QQRLI---FAGK--QLEDGR--TLADYNIQKESTLHLVLR   72 (116)
Q Consensus         7 ~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~------~q~L~---~~g~--~L~d~~--tL~~~gi~~g~~I~v~~~   72 (116)
                      ..+...+.+.+..+.|+.+++..++++.+...+      ++.|+   ++|.  .|+++.  ....++  -+..|++..+
T Consensus        16 ~~Dhsy~tvr~~v~~sa~eIl~~va~kl~~~e~~~~~~~~l~Lv~V~ssGEk~vlqp~d~sv~tsL~--~NgRLfvc~k   92 (120)
T 2dhz_A           16 MPDHSYVTIRSRLSASVQDILGSVTEKLQYSEEPAGREDSLILVAVSSSGEKVLLQPTEDCVFTALG--INSHLFACTR   92 (120)
T ss_dssp             CTTSCCCCEEECTTCCHHHHHHHHHHHSTTCSSTTSCCSCCEEEEEETTCCCEECCTTCSCHHHHSC--SSEEEEEECT
T ss_pred             eccCceEEEEEeccccHHHHHHHHHHHhccccccccccCceEEEEEccCCcEeecCCcceEEEeecc--ccceEEEeeh
Confidence            345555678889999999999999999987443      56665   6777  355432  233443  4678887766

>3qa8_A MGC80376 protein; kinase ubiquitin-like domain, phosphorylation, kinase domain ubiquitin-like domain, kinase, substrate binding; 3.60A {Xenopus laevis} PDB: 3qad_A* 3rzf_A*

Probab=82.28  E-value=1.6  Score=35.08  Aligned_cols=50  Identities=30%  Similarity=0.563  Sum_probs=40.0

Q ss_pred             CCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECC-EEcCCCCccccC
Q 033570           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG-KQLEDGRTLADY   59 (116)
Q Consensus        10 g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g-~~L~d~~tL~~~   59 (116)
                      .+...+.+.++.|+.+|+..|++.+|++++.|.+++.+ -.+........+
T Consensus       321 ~~~~~~~i~~~~tl~~l~~~i~~~T~i~~~~q~~~~~~~~~~~p~~~~~~~  371 (676)
T 3qa8_A          321 GRVHTYPVTENENLQNLKSWLQQDTGIPEEEQELLQASGLALNSAQPLTQY  371 (676)
T ss_dssp             SCCCEEECCTTCCHHHHHHHHHTTSCCCSTTCEEESSSSCCCCTTSCGGGS
T ss_pred             cccceeecCCCccHHHHHHHHHHHhCCCHHHHHHHhccCCCCCCCcchhhh
Confidence            45567889999999999999999999999999998754 455555555554

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=82.11  E-value=0.62  Score=24.96  Aligned_cols=24  Identities=13%  Similarity=0.079  Sum_probs=19.6

Q ss_pred             HHcCCCcccccccccccccCCCccccccC
Q 033570           87 RKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        87 ~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      .+...++++|++|+.+   .++.+  ++|
T Consensus         8 e~r~~~k~iCpkC~a~---~~~ga--w~C   31 (51)
T 3j21_g            8 EARIFKKYVCLRCGAT---NPWGA--KKC   31 (51)
T ss_dssp             HHHSSSEEECTTTCCE---ECTTC--SSC
T ss_pred             HHHHhCCccCCCCCCc---CCCCc--eec
Confidence            4566678899999999   88888  777

>3r8s_T 50S ribosomal protein L23; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_T 3j19_T 2wwq_T 3oat_T* 3oas_T* 3ofd_T 3ofc_T 3ofr_T* 3ofz_T* 3og0_T 3ofq_T 3r8t_T 2j28_T 3e1b_M 3e1d_M 3iy9_T 3i1n_T 1p85_R 1p86_R 1vs8_T ...

Probab=81.65  E-value=5.7  Score=23.73  Aligned_cols=39  Identities=28%  Similarity=0.351  Sum_probs=33.9

Q ss_pred             CEEEEEecCCCCHHHHHHHHHHhhCCCCCceE-EEECCEE
Q 033570           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQR-LIFAGKQ   49 (116)
Q Consensus        11 ~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~-L~~~g~~   49 (116)
                      ..+.|.|+++.+=.++|+.+++.+++.+.... +...|+.
T Consensus        28 n~~~F~V~~~AnK~eIK~AVE~lf~VkV~~VnT~~~~gK~   67 (93)
T 3r8s_T           28 NTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKV   67 (93)
T ss_dssp             SEEEEEECSSCCHHHHHHHHHHHSCCCCCEEEEEEECCCB
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHcCCceEEEEEEEeCCce
Confidence            57899999999999999999999999998874 4567764

>2zjd_A Microtubule-associated proteins 1A/1B light chain 3B precursor; autophagy, LC3, microtubule-associated protein 1 light chain 3, cytoplasm, cytoplasmic vesicle, lipoprotein; 1.56A {Homo sapiens} SCOP: d.15.1.3 PDB: 2z0e_B 2zzp_B 2z0d_B 1ugm_A 1v49_A 2k6q_A 3eci_A

Probab=80.28  E-value=4.8  Score=25.57  Aligned_cols=47  Identities=9%  Similarity=0.188  Sum_probs=35.5

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEE-ECCEEc-CCCCccccC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQL-EDGRTLADY   59 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~~g~~L-~d~~tL~~~   59 (116)
                      -.+-|+.+.||+++...|..+.++++++--++ |-+..+ ..+.+++++
T Consensus        55 ~KflVp~~~tv~qf~~~iRkrL~l~~~~alFl~~vn~~~p~~~~~m~~l  103 (130)
T 2zjd_A           55 TKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEV  103 (130)
T ss_dssp             CEEEEETTCBHHHHHHHHHHHHTCCTTCCEEEEETTTEECCTTSBHHHH
T ss_pred             cEEEcCCCCcHHHHHHHHHHHhCCCCCceEEEEEECCccCCccchHHHH
Confidence            34678999999999999999999988765545 655444 456677765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	116
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	3e-41
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	4e-41
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	3e-39
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	4e-38
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	4e-37
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	2e-35
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	2e-35
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	2e-35
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	2e-35
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	9e-35
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	1e-33
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-33
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	4e-32
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	6e-32
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	6e-32
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	6e-32
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	7e-32
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	8e-32
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	2e-30
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	5e-30
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	4e-29
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	7e-28
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	8e-28
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	2e-27
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	4e-27
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	5e-26
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	2e-25
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	1e-24
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	1e-24
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	4e-24
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	5e-24
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	9e-23
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	1e-22
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	7e-22
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	1e-21
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	2e-20
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	2e-20
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	3e-20
d2ayja1	56	g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolob	2e-07

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  129 bits (325), Expect = 3e-41
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+FVK   G +    +  +  I  +K +I+D++G+P  QQ+L F G+ L+D   L  Y 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYG 67

Query: 61 IQKESTLHLVLRLRGG 76
          IQ   TL L  +   G
Sbjct: 68 IQDSDTLILSKKKGSG 83

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  128 bits (324), Expect = 4e-41
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  123 bits (311), Expect = 3e-39
 Identities = 25/75 (33%), Positives = 48/75 (64%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCD 62

Query: 61 IQKESTLHLVLRLRG 75
          ++++S +H+V R R 
Sbjct: 63 LEQQSIVHIVQRPRR 77

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  121 bits (304), Expect = 4e-38
 Identities = 45/73 (61%), Positives = 57/73 (78%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +DTID +K ++++KEGIPP QQRLI+AGKQL D +T  DYN
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYN 60

Query: 61 IQKESTLHLVLRL 73
          I+  S LHLVL L
Sbjct: 61 IEGGSVLHLVLAL 73

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  118 bits (297), Expect = 4e-37
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 4  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 63

Query: 61 IQKESTLHLVLRL 73
          ++  ST+ + LRL
Sbjct: 64 LKPLSTVFMNLRL 76

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  114 bits (288), Expect = 2e-35
 Identities = 21/68 (30%), Positives = 39/68 (57%)

Query: 8  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
          L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVI 78

Query: 68 HLVLRLRG 75
          HL L+ RG
Sbjct: 79 HLALKERG 86

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  115 bits (289), Expect = 2e-35
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 2  QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +F+     K TI  + + S T+  +K  ++     PPD+QRL    + L+DG+TL +  
Sbjct: 1  DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECG 60

Query: 61 I-------QKESTLHLVLRLRGG 76
                  Q  +T+ L  R    
Sbjct: 61 FTSQTARPQAPATVGLAFRADDT 83

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  114 bits (286), Expect = 2e-35
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 60

Query: 61 IQKESTLHLVLR 72
          +     +HLV R
Sbjct: 61 VGG-KVIHLVER 71

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 116

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  115 bits (289), Expect = 2e-35
 Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 8/89 (8%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKI--------QDKEGIPPDQQRLIFAGKQLED 52
           + + +  ++GKT       +D+  ++   +        ++++   P+  RLI+ G+ L  
Sbjct: 17  INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 76

Query: 53  GRTLADYNIQKESTLHLVLRLRGGIIEPS 81
             TL    +    T  + L  R  + EP+
Sbjct: 77  NVTLGALKLPFGKTTVMHLVARETLPEPN 105

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  113 bits (283), Expect = 9e-35
 Identities = 23/84 (27%), Positives = 48/84 (57%), Gaps = 3/84 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ +   +  P   Q+LI+AGK L D   L 
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 58 DYNIQKESTLHLVLRLRGGIIEPS 81
          +Y I +++ + +++     +  P+
Sbjct: 61 EYKIDEKNFVVVMVTKPKAVSTPA 84

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  109 bits (275), Expect = 1e-33
 Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 2/75 (2%)

Query: 1  MQIFVKTLTGK-TITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G+ T T++ +     ++ ++ KIQ+   + P  QRL + GKQ+EDG TL D
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 60

Query: 59 YNIQKESTLHLVLRL 73
          Y ++   T+ L++R 
Sbjct: 61 YEVRLNDTIQLLVRQ 75

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  110 bits (276), Expect = 1e-33
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 16/92 (17%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIF 45
          M + V  + G+ + + V  + T+ ++K  IQ    +  +++                L  
Sbjct: 8  MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 46 AGKQLEDGR-TLADYNIQKESTLHLVLRLRGG 76
          AG++L + R  L DY I+    +  + +L   
Sbjct: 68 AGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQK 99

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  106 bits (265), Expect = 4e-32
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 3/74 (4%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          + I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + 
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 62

Query: 58 DYNIQKESTLHLVL 71
          DY I +++ + +++
Sbjct: 63 DYRIDEKNFVVVMV 76

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  105 bits (264), Expect = 6e-32
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           Q+ ++  TGK + L V S+DT+ ++K ++   EG+ P  QR  F+G+ L D     +  
Sbjct: 4  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELK 63

Query: 61 IQKESTLHLVLRL 73
          I K+  + +++  
Sbjct: 64 IPKDYVVQVIVSQ 76

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  105 bits (263), Expect = 6e-32
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 1  MQIFVKTLTG-KTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G KT T+E V    TI+ ++ ++     + P+ QRL + GKQLE+G TL D
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 60

Query: 59 YNIQKESTLHLVLR 72
          Y++     + L++R
Sbjct: 61 YDVGLNDIIQLLVR 74

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  106 bits (265), Expect = 6e-32
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 6/82 (7%)

Query: 1  MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTL 56
          + + VK+   +   + L  +   ++ ++KA +         P+ QRLI++GK L D + L
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCL 67

Query: 57 ADYNIQKES--TLHLVLRLRGG 76
           D   ++E    LHLV  ++ G
Sbjct: 68 RDLLPKQEKRHVLHLVCNVKSG 89

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  105 bits (264), Expect = 7e-32
 Identities = 16/72 (22%), Positives = 31/72 (43%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++      GK + ++  + DTI ++K  I  + G   ++  L       +D  +L DY 
Sbjct: 29  IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYE 88

Query: 61  IQKESTLHLVLR 72
           I     L L  +
Sbjct: 89  IHDGMNLELYYQ 100

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  104 bits (262), Expect = 8e-32
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I +K+       + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y+
Sbjct: 2  LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYH 60

Query: 61 IQKESTLHLVLR 72
          IQ   ++HLV  
Sbjct: 61 IQDGHSVHLVKS 72

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  101 bits (254), Expect = 2e-30
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADY 59
           + VK L G    + + SS ++  +KA+I  K G+   QQRL    +G  L+D   LA  
Sbjct: 2  DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQ 61

Query: 60 NIQKESTLHLVLR 72
           +   ST+ LV+ 
Sbjct: 62 GLGPGSTVLLVVD 74

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 102

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  101 bits (252), Expect = 5e-30
 Identities = 17/86 (19%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 1  MQIFV----KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRT 55
          M I V    + LT  T +L+V     + N +   + + G+P ++ ++++  +   +D  +
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCS 67

Query: 56 LADYNIQKESTLHLVLRLRGGIIEPS 81
          L  Y ++    + L+ +   G+  P 
Sbjct: 68 LGSYGLKDGDMVVLLQKDNVGLRTPG 93

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 98.8 bits (246), Expect = 4e-29
 Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          + + +K L            DT+  +K+K    +     Q +LI+ G+ L +  RTL+  
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSL 64

Query: 60 NIQKESTLHLVLRLRGG 76
          NI     +H      G 
Sbjct: 65 NITNNCVIHCHRSPPGA 81

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.2 bits (239), Expect = 7e-28
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++ VKT   K     V  + ++   K  I  +     DQ  LIFAGK L+D  TL  + 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHG 91

Query: 61  IQKESTLHLVLR 72
           I    T+HLV++
Sbjct: 92  IHDGLTVHLVIK 103

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 95.4 bits (237), Expect = 8e-28
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLA 57
          + I VK    +     +   DT+ ++K  ++   G+ P++Q+L+     GK  E+   L 
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLG 67

Query: 58 DYNIQKESTLHLVLRLRGG 76
             ++  + + ++     G
Sbjct: 68 ALKLKPNTKIMMMGTRESG 86

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 111

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 95.1 bits (236), Expect = 2e-27
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 1   MQIFVKTLT-GKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
           +++       G+ + + V+S S+ + ++K KI  +  IP ++Q+L      L+D  +LA 
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAH 89

Query: 59  YNIQKESTLHLVLRLRGG 76
           YN+     L L LR R G
Sbjct: 90  YNVGAGEILTLSLRERSG 107

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 93.5 bits (232), Expect = 4e-27
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT         +  +  +   K +I        D+  LIF GK L D   L+   
Sbjct: 11 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRG 69

Query: 61 IQKESTLHLVLR 72
          I   ST+H+V+R
Sbjct: 70 ILDGSTVHVVVR 81

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 91.1 bits (226), Expect = 5e-26
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 14/86 (16%)

Query: 1  MQIFVKTLTGKTIT-LEVESSDTIDNVKAKIQD-----KEGIP--PDQQRLIFAGKQLED 52
          ++I  +   G  I       + T+  +K  +       KE  P    + +LI AGK LE+
Sbjct: 8  LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 67

Query: 53 GRTLADYNI------QKESTLHLVLR 72
           +T+ DY           +T+H++++
Sbjct: 68 SKTVKDYRSPVSNLAGAVTTMHVIIQ 93

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 89.3 bits (221), Expect = 2e-25
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 8  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 66

Query: 61 IQKESTLHLVLRLR 74
          ++   T+HLV++ +
Sbjct: 67 VRDGLTVHLVIKRQ 80

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 87.7 bits (217), Expect = 1e-24
 Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 8/85 (9%)

Query: 1  MQIFVKT-LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-------LED 52
          + +F+ + L           S TI   K K++   G P     L   G          ++
Sbjct: 8  VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQE 67

Query: 53 GRTLADYNIQKESTLHLVLRLRGGI 77
             L  Y +     +H++     G 
Sbjct: 68 DALLGSYPVDDGCRIHVIDHSGSGP 92

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 87.3 bits (216), Expect = 1e-24
 Identities = 11/81 (13%), Positives = 30/81 (37%), Gaps = 11/81 (13%)

Query: 1  MQIFVK---TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE------ 51
          + + +K       + +  ++  S T+  VK  +     +P  +  L +   ++       
Sbjct: 10 LTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIEL 69

Query: 52 --DGRTLADYNIQKESTLHLV 70
            D + L  Y+++    L + 
Sbjct: 70 ENDLQPLQFYSVENGDCLLVR 90

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 86.1 bits (213), Expect = 4e-24
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 7  TLTGKTITLEVESSDTIDNVKAKIQDK--EGIP-PDQQRLIFAGKQLEDGRTLADYNIQK 63
           L    +        +I  +K  I  K  E +P P+   LI+ G++L+D +TL  Y IQ 
Sbjct: 24 QLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQP 83

Query: 64 ESTLHLVLR 72
           ST+H++ +
Sbjct: 84 GSTVHVLRK 92

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 85.5 bits (211), Expect = 5e-24
 Identities = 16/69 (23%), Positives = 35/69 (50%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V    GK + ++  + D++ + K  +  + G  P++  L   G  L+D  +L DY 
Sbjct: 2  IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYE 61

Query: 61 IQKESTLHL 69
          +  ++ L L
Sbjct: 62 VHDQTNLEL 70

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.1 bits (205), Expect = 9e-23
 Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 1  MQIFV--KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          +++F+  +    +   LE     T   +++KI +  G+  +  +++   KQL+ G+TL +
Sbjct: 18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEE 77

Query: 59 YNIQKESTLHLVLRLRGG 76
            +       ++   +  
Sbjct: 78 QGVAHNVKAMVLELKQSS 95

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 82.3 bits (203), Expect = 1e-22
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + +         ++V    T   +K KI    G+PP  Q++++    + + +TL +  
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMY-KGLVPEDKTLREIK 75

Query: 61 IQKESTLHLVLRLRGG 76
          +   + + +V     G
Sbjct: 76 VTSGAKIMVVGSTISG 91

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]} Length = 79

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

 Score = 79.9 bits (197), Expect = 7e-22
 Identities = 10/76 (13%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V       I  +++ +  +  +      ++G   D  R ++ G +++  +T  D +
Sbjct: 5  INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLD 63

Query: 61 IQKESTLHLVLRLRGG 76
          ++    +       GG
Sbjct: 64 MEDNDIIEAHREQIGG 79

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]} Length = 96

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 80.0 bits (197), Expect = 1e-21
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            + VK    K   +E+ + +     KA++    G+ P +Q+++  G  L+D     +  
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIK 66

Query: 61 IQKESTLHLVLRLRGGIIEPS 81
          ++   T+ ++        EPS
Sbjct: 67 MKNGMTVLMMGSADALPEEPS 87

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.3 bits (188), Expect = 2e-20
 Identities = 13/75 (17%), Positives = 35/75 (46%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V       I  +V+ +  +  +K     ++G+P +  R +F G+++ D  T  +  
Sbjct: 3  IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELG 62

Query: 61 IQKESTLHLVLRLRG 75
          +++E  + +     G
Sbjct: 63 MEEEDVIEVYQEQTG 77

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.4 bits (188), Expect = 2e-20
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 1  MQIFVKTLTGKTITLEVE-----SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGR 54
          + + V   + +   L V      S   + ++   +++  G+P   Q+LIF GK L E   
Sbjct: 2  LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMET 60

Query: 55 TLADYNIQKESTLHLVLR 72
           L+   IQ    + L+ +
Sbjct: 61 PLSALGIQDGCRVMLIGK 78

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

 Score = 76.1 bits (187), Expect = 3e-20
 Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 7  TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-------LEDGRTLADY 59
            T   +  +  +  +++++K K++   G   D  R+              +  ++L D 
Sbjct: 12 NATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDL 71

Query: 60 NIQKESTLHLVLRLRG 75
           ++    +H V    G
Sbjct: 72 GVRDGYRIHAVDVTGG 87

>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus solfataricus [TaxId: 2287]} Length = 56

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L40e
domain: Ribosomal protein L40e
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 42.5 bits (100), Expect = 2e-07
 Identities = 5/26 (19%), Positives = 13/26 (50%)

Query: 77  IIEPSLMALARKYNQDKMICRKSHTR 102
           + +P+ + + ++    K +CRK    
Sbjct: 3   LTDPAKLQIVQQRVFLKKVCRKCGAL 28

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	116
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.92
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.9
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.9
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.9
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.88
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.87
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.87
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.86
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.86
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.86
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.85
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.85
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.85
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.84
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.84
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.82
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.82
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.82
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.81
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.81
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.8
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.79
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.78
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.77
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.76
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.76
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.76
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.75
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.74
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.74
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.73
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.68
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.65
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.65
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.58
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.51
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.45
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.44
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	99.16
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.9
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	98.36
d2ayja1	56	Ribosomal protein L40e {Sulfolobus solfataricus [T	97.96
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.93
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.76
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	97.43
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.29
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	95.88
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	94.85
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	94.85
d1wgya_	104	Rap guanine nucleotide exchange factor 5, RapGEF5	94.39
d1zud21	65	Thiamin biosynthesis sulfur carrier protein ThiS {	94.36
d1y8xb1	92	UBA3 {Human (Homo sapiens) [TaxId: 9606]}	94.28
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	93.38
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	92.95
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	92.57
d1fm0d_	81	Molybdopterin synthase subunit MoaD {Escherichia c	91.92
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	90.95
d1v8ca1	87	MoaD-related protein, N-terminal domain {Thermus t	90.32
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	89.26
d2incc1	83	Toluene, o-xylene monooxygenase oxygenase subunit	88.85
d1eo6a_	116	Golgi-associated ATPase enhancer of 16 kD, Gate-16	87.03
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	86.85
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	86.32
d3d32a1	118	GABA(A) receptor associated protein GABARAP {Human	86.12
d2cu3a1	63	Uncharacterised protein TTHA0675 {Thermus thermoph	83.19
d1j0ga_	92	Hypothetical protein 1810045k17 {Mouse (Mus muscul	81.5
d1tygb_	65	Thiamin biosynthesis sulfur carrier protein ThiS {	80.98
d2bkfa1	85	Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Hum	80.79
d2zjda1	119	Microtubule-associated proteins 1A/1B light chain	80.21

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1e-24  Score=129.32  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=74.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+||..+|+.+.++|++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++++++||
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlrgG   76 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTTCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999987

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=1.2e-23  Score=127.65  Aligned_cols=79  Identities=33%  Similarity=0.494  Sum_probs=76.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~   79 (116)
                      |+|+|+.++|+.+.++|++++||.+||++|+++.|+|+++|+|+|+|+.|+|+.+|++|+|.++++|+++.+.++|+.+
T Consensus         8 mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~gp~s   86 (87)
T d1wh3a_           8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGPSS   86 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCSCC
T ss_pred             EEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCCCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999888643

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.90  E-value=2.3e-23  Score=122.55  Aligned_cols=73  Identities=62%  Similarity=0.943  Sum_probs=71.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+||+.+|+++.++|++++||.+||++|+++.|+|++.|+|+|+|+.|.|+.+|++|||++|++|++++|+
T Consensus         1 M~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_           1 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999874

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=1.7e-23  Score=124.60  Aligned_cols=75  Identities=33%  Similarity=0.593  Sum_probs=73.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+|+..+|+++.++|++++||.+||+.|+++.|+|++.|+|+|+|+.|+|+.+|++|+|.++++|+++.|++|
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999876

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.3e-22  Score=120.01  Aligned_cols=73  Identities=34%  Similarity=0.560  Sum_probs=71.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|+++.|+|++.|+|+|+|+.|.|+.+|++|||++|++|++++|+
T Consensus         4 ~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2           4 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999874

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.2e-21  Score=120.41  Aligned_cols=81  Identities=30%  Similarity=0.592  Sum_probs=74.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhC---CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+||..+|+++.++|++++||.+||++|+++.+   +|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++...+.
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~~   80 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAV   80 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCCC
Confidence            99999999999999999999999999999999876   789999999999999999999999999999999999866554


Q ss_pred             CCCc
Q 033570           78 IEPS   81 (116)
Q Consensus        78 ~~~~   81 (116)
                      ..+.
T Consensus        81 ~~~~   84 (95)
T d1uela_          81 STPA   84 (95)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            3333

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=8.1e-22  Score=116.72  Aligned_cols=73  Identities=37%  Similarity=0.647  Sum_probs=69.5

Q ss_pred             CEEEEEcCCCC-EEEEE-ecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGK-TITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~-~~~i~-v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+||+.+|+ .+.++ +++++||++||+.|+++.|+|++.|+|+|+|+.|+|+.+|++|||.++++|++++|.
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            89999999996 67775 999999999999999999999999999999999999999999999999999999885

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=6.8e-22  Score=118.06  Aligned_cols=75  Identities=28%  Similarity=0.503  Sum_probs=72.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+||..+|+.+.++|++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++++.+.
T Consensus         4 ~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p~   78 (80)
T d1ttna1           4 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPV   78 (80)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSS
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999988653

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.7e-21  Score=115.36  Aligned_cols=73  Identities=37%  Similarity=0.622  Sum_probs=69.2

Q ss_pred             CEEEEEcCCC-CEEEE-EecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTG-KTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g-~~~~i-~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|+..+| +.+.+ +|++++||.+||.+|+++.|+|++.|+|+|+|+.|+|+.+|++|||.+|++|++++|+
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            8999999998 46776 6999999999999999999999999999999999999999999999999999999874

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.8e-22  Score=117.86  Aligned_cols=72  Identities=35%  Similarity=0.613  Sum_probs=69.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+||+.+|+.+.++|++++||.+||++|+++.|+|++.|+|+|+|+.|.|+.+|++|+| ++++|+++.+.
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i-~~~ti~lv~r~   72 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERA   72 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBHHHHTC-TTEEEBCCCSS
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCHHHhCC-CCCEEEEEecC
Confidence            8999999999999999999999999999999999999999999999999999999999999 58999988764

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=9.5e-22  Score=115.57  Aligned_cols=70  Identities=23%  Similarity=0.437  Sum_probs=68.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      |+|+|+...|+++.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|||++|++|++.
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~   71 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   71 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999999999999986

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=5e-21  Score=113.22  Aligned_cols=73  Identities=33%  Similarity=0.428  Sum_probs=70.0

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE--CCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~--~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      .+|+||..+|+.+.++|++++||.+||+.|+++.|+|++.|+|+|  .|+.|.|+.+|++|||.+|++|+++++.
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            479999999999999999999999999999999999999999999  6999999999999999999999999864

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=5.7e-21  Score=112.15  Aligned_cols=71  Identities=34%  Similarity=0.558  Sum_probs=67.1

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+|++. +..+.++|++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++.+
T Consensus         2 i~I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~   72 (73)
T d2bwfa1           2 LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             EEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEee
Confidence            68999985 567999999999999999999999999999999999999999999999999999999999875

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.5e-21  Score=115.43  Aligned_cols=74  Identities=34%  Similarity=0.476  Sum_probs=69.6

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |+|+|++.++ .+.++|++++||.+||++|++++|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++++...
T Consensus         8 i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~   81 (84)
T d1yqba1           8 IKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   81 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCC
Confidence            7899999755 5899999999999999999999999999999999999999999999999999999999998654

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4e-21  Score=113.88  Aligned_cols=71  Identities=32%  Similarity=0.587  Sum_probs=68.2

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhC---CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~---i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|+||..+|+.+.++|++++||.+||++|+++.|   +|+++|+|+|+|+.|+|+.+|++|||++|++|++++
T Consensus         3 ~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~v   76 (77)
T d1oqya4           3 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMV   76 (77)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEE
Confidence            78999999999999999999999999999999987   899999999999999999999999999999998875

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=9.3e-21  Score=117.38  Aligned_cols=71  Identities=23%  Similarity=0.324  Sum_probs=68.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|+|++..|+.+.+.|++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++..
T Consensus        29 i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            48999999999999999999999999999999999999999999999999999999999999999999875

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.7e-20  Score=115.91  Aligned_cols=71  Identities=32%  Similarity=0.437  Sum_probs=67.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+|++.++ .+.|+|++++||.+||++|++.+|+|++.|+|+|+|+.|.|+.+|++|||++|++|++++|
T Consensus        33 i~V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          33 IKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             EEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             EEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            6899999765 5789999999999999999999999999999999999999999999999999999999875

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2e-20  Score=116.29  Aligned_cols=77  Identities=22%  Similarity=0.422  Sum_probs=70.8

Q ss_pred             CEEEE----EcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcC-CCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFV----KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~V----k~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~-d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |.|+|    +..++..+.++|++++||.+||+.|+.+.++|++.|+|+|+|+.|. |+.+|++|||++|++|+++.+..+
T Consensus         8 m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~~~   87 (102)
T d1v5oa_           8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNV   87 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCC
T ss_pred             EEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECCCC
Confidence            78888    6777999999999999999999999999999999999999999995 567999999999999999988766


Q ss_pred             CC
Q 033570           76 GI   77 (116)
Q Consensus        76 g~   77 (116)
                      +.
T Consensus        88 ~~   89 (102)
T d1v5oa_          88 GL   89 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=1.1e-20  Score=113.54  Aligned_cols=72  Identities=28%  Similarity=0.356  Sum_probs=67.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|++.++ .+.++|++++||.+||+.|++.+++|++.|+|+|+|+.|.|+.+|++|||++|++|++++|.
T Consensus        11 i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          11 IRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             EEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             EEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            6899999654 57899999999999999999999999999999999999999999999999999999998873

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.81  E-value=1.6e-20  Score=118.30  Aligned_cols=78  Identities=29%  Similarity=0.420  Sum_probs=70.8

Q ss_pred             EEEEEcC-CCCEEEEEecC-CCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCCCC
Q 033570            2 QIFVKTL-TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (116)
Q Consensus         2 ~v~Vk~~-~g~~~~i~v~~-~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~~~   79 (116)
                      +|.|+.. +|+.+.++|.+ ++||.+||++|++++|+|++.|+|+|.|+.|+|+.+|++|+|.+|++|++++|.+||+.+
T Consensus        31 ~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG~~~  110 (111)
T d1we6a_          31 RVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSGPSS  110 (111)
T ss_dssp             EECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCSSCC
T ss_pred             EEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCCCCC
Confidence            3444443 58999999987 899999999999999999999999999999999999999999999999999999999754

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.1e-19  Score=109.75  Aligned_cols=68  Identities=31%  Similarity=0.646  Sum_probs=65.4

Q ss_pred             CCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         8 ~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      .+|+.+.++|++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||.+|++|++++|.+|
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~RG   86 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            47899999999999999999999999999999999999999999999999999999999999999765

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2.7e-20  Score=116.26  Aligned_cols=76  Identities=22%  Similarity=0.396  Sum_probs=70.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceE---------------EEECCEEcCCC-CccccCCCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIFAGKQLEDG-RTLADYNIQKE   64 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~---------------L~~~g~~L~d~-~tL~~~gi~~g   64 (116)
                      |+|+|+..+|+.+.++|++++||.+||++|++.+++|+++|+               |+|+|+.|.|+ .+|++|||.+|
T Consensus         8 M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI~~g   87 (105)
T d1v2ya_           8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNR   87 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSS
T ss_pred             EEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCCCCC
Confidence            899999999999999999999999999999999999999987               99999999765 58999999999


Q ss_pred             CEEEEEEecCCC
Q 033570           65 STLHLVLRLRGG   76 (116)
Q Consensus        65 ~~I~v~~~~~gg   76 (116)
                      ++|+++.++...
T Consensus        88 ~~l~lv~r~~~~   99 (105)
T d1v2ya_          88 DEVSFIKKLGQK   99 (105)
T ss_dssp             EEEEEEECSCSC
T ss_pred             CEEEEEEecCCC
Confidence            999999886543

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=8e-19  Score=107.65  Aligned_cols=74  Identities=24%  Similarity=0.335  Sum_probs=67.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcC-CCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~-d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|+||..+|+.+.++|++++||.+||++|+   .++++.|+|+|+|+.|. |..+|++|+|.+|++|+++++.+++.
T Consensus         8 m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~~~~~   82 (95)
T d1wiaa_           8 INVRLKFLNDTEELAVARPEDTVGTLKSKYF---PGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGAA   82 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHS---SSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHh---cCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcCCCCC
Confidence            7999999999999999999999999999986   45789999999999996 56799999999999999999877664

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=3e-19  Score=109.84  Aligned_cols=71  Identities=18%  Similarity=0.266  Sum_probs=66.7

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|+||+.+++.+.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+ +|++|||++|++|+++..
T Consensus         8 ~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t   78 (96)
T d1wgga_           8 YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGS   78 (96)
T ss_dssp             EEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCC
T ss_pred             eEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEee
Confidence            68999998887788999999999999999999999999999999999999986 799999999999999865

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=6.5e-19  Score=107.06  Aligned_cols=75  Identities=21%  Similarity=0.428  Sum_probs=68.2

Q ss_pred             CEEEEEcCCCCEEEE-EecCCCCHHHHHHHHHHhhCCCCCceEEE---ECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            1 MQIFVKTLTGKTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i-~v~~~~TV~~LK~~I~~~~~i~~~~q~L~---~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      |+|+|++ .|+.+.+ +|++++||.+||++|++.+++|+++|+|+   |.|+.|+|+.+|++|+|++|++|+++.+...|
T Consensus         8 ~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~~~~   86 (90)
T d1v5ta_           8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRESG   86 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCSSS
T ss_pred             EEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeCCCC
Confidence            7899998 6666776 79999999999999999999999999999   58999999999999999999999999876554

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.76  E-value=3.9e-18  Score=105.33  Aligned_cols=75  Identities=25%  Similarity=0.427  Sum_probs=68.3

Q ss_pred             CEEEEEcCCCCEE-EEEecCCCCHHHHHHHHHHh-----hCCC--CCceEEEECCEEcCCCCccccCCCCCCC------E
Q 033570            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDK-----EGIP--PDQQRLIFAGKQLEDGRTLADYNIQKES------T   66 (116)
Q Consensus         1 m~v~Vk~~~g~~~-~i~v~~~~TV~~LK~~I~~~-----~~i~--~~~q~L~~~g~~L~d~~tL~~~gi~~g~------~   66 (116)
                      |+|.+|..+|+.+ .+.+++++||.+||++|++.     .|+|  ++.|+|+|+|+.|.|+.+|++|+|..|+      +
T Consensus         8 i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~~~t   87 (101)
T d1se9a_           8 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTT   87 (101)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEE
T ss_pred             EEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCCceE
Confidence            6899999999976 69999999999999999987     4576  7799999999999999999999999998      9


Q ss_pred             EEEEEecCC
Q 033570           67 LHLVLRLRG   75 (116)
Q Consensus        67 I~v~~~~~g   75 (116)
                      +|+++|.+.
T Consensus        88 mHlVvrpp~   96 (101)
T d1se9a_          88 MHVIIQAPV   96 (101)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999998754

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=3.4e-18  Score=108.22  Aligned_cols=72  Identities=24%  Similarity=0.401  Sum_probs=65.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHH--------HhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEE--EEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQ--------DKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL--HLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~--------~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I--~v~   70 (116)
                      |+|.|+..+|+.+.+.|++++||.+||++|.        ++.++|++.|||+|.|+.|.|+.+|++|+|.+|+++  |++
T Consensus        17 i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~lhlv   96 (116)
T d1wgha_          17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   96 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEE
T ss_pred             EEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCHHHcCCCCCCEEEEEEE
Confidence            5789999999999999999999999999994        567899999999999999999999999999999874  444


Q ss_pred             Ee
Q 033570           71 LR   72 (116)
Q Consensus        71 ~~   72 (116)
                      .+
T Consensus        97 ~r   98 (116)
T d1wgha_          97 AR   98 (116)
T ss_dssp             EC
T ss_pred             eC
Confidence            44

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=8.3e-19  Score=107.61  Aligned_cols=75  Identities=19%  Similarity=0.342  Sum_probs=68.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg~   77 (116)
                      |+|.|++ +++.+.|+|++++||.+||++|++.+++|+++|+|+|+|+ |.|+.+|++|+|++|++|+|+....+|.
T Consensus        18 i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~~~gp   92 (95)
T d1v86a_          18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGSTISGP   92 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSSCCCC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecCCCCC
Confidence            5788886 8889999999999999999999999999999999999997 8899999999999999999997766653

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.3e-18  Score=101.55  Aligned_cols=72  Identities=24%  Similarity=0.409  Sum_probs=65.0

Q ss_pred             CEEEEEcCCCCEEEEEe-----cCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcC-CCCccccCCCCCCCEEEEEEec
Q 033570            1 MQIFVKTLTGKTITLEV-----ESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v-----~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~-d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      |+|+|++ .++.+.++|     ++++||++||++|++.+|+|+++|+|+|+|+.|. |+.+|++|||++|++|+++.+.
T Consensus         2 i~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~   79 (81)
T d1wxva1           2 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   79 (81)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             EEEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEec
Confidence            6789977 678888888     4688999999999999999999999999999996 5789999999999999998764

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.1e-18  Score=106.71  Aligned_cols=72  Identities=18%  Similarity=0.308  Sum_probs=65.4

Q ss_pred             CEEEE--EcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFV--KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~V--k~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |+|++  +...|+.+.++|.+++||.+||.+|+++.++|+++|+|+|+|+.|+|+.+|++|||+++++|+++..
T Consensus        18 i~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~   91 (100)
T d1wjua_          18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLEL   91 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECC
T ss_pred             EEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEc
Confidence            35555  4456899999999999999999999999999999999999999999999999999999999987764

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.2e-17  Score=101.94  Aligned_cols=76  Identities=29%  Similarity=0.458  Sum_probs=66.5

Q ss_pred             CEEEEEcCCCCE--EEEEecCCCCHHHHHHHHHHhhC--CCCCceEEEECCEEcCCCCccccCCCC--CCCEEEEEEecC
Q 033570            1 MQIFVKTLTGKT--ITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQ--KESTLHLVLRLR   74 (116)
Q Consensus         1 m~v~Vk~~~g~~--~~i~v~~~~TV~~LK~~I~~~~~--i~~~~q~L~~~g~~L~d~~tL~~~gi~--~g~~I~v~~~~~   74 (116)
                      |+|+|+.++++.  +.+++++++||.+||++|++.++  +|+++|+|+|+|+.|.|+.+|++|...  ++.+||++.+..
T Consensus         8 i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~~   87 (93)
T d1wgda_           8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVK   87 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCC
T ss_pred             EEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecCC
Confidence            789999997654  88999999999999999999965  899999999999999999999999765  445999998765


Q ss_pred             CC
Q 033570           75 GG   76 (116)
Q Consensus        75 gg   76 (116)
                      .+
T Consensus        88 ~~   89 (93)
T d1wgda_          88 SG   89 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

Probab=99.68  E-value=1.7e-16  Score=93.98  Aligned_cols=74  Identities=14%  Similarity=0.332  Sum_probs=69.2

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .|.|++ +|+...+.|.+++++..|++.++++.+++++.++|+|+|+.|.++.|+++|++.+|++|+++++..||
T Consensus         6 ~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~GG   79 (79)
T d1euvb_           6 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   79 (79)
T ss_dssp             EEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBCC
T ss_pred             EEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            456665 67788899999999999999999999999999999999999999999999999999999999999887

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=2e-16  Score=96.78  Aligned_cols=77  Identities=18%  Similarity=0.248  Sum_probs=68.2

Q ss_pred             CEEEEEcC-CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE-------EcCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~-~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~-------~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.|+|++. ++......+++++||.+||++|+..+|+|++.|+|+|.|+       .++|+.+|++|++.+|++|||+.+
T Consensus         8 v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlvd~   87 (95)
T d1v6ea_           8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH   87 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCC
T ss_pred             EEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEEeC
Confidence            57888885 5556889999999999999999999999999999999776       578999999999999999999988


Q ss_pred             cCCCC
Q 033570           73 LRGGI   77 (116)
Q Consensus        73 ~~gg~   77 (116)
                      .+.+.
T Consensus        88 ~p~~~   92 (95)
T d1v6ea_          88 SGSGP   92 (95)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            76553

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.4e-16  Score=97.59  Aligned_cols=75  Identities=27%  Similarity=0.410  Sum_probs=64.6

Q ss_pred             EEEEEcCCC-CEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCC-------CEEEEEEec
Q 033570            2 QIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKE-------STLHLVLRL   73 (116)
Q Consensus         2 ~v~Vk~~~g-~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g-------~~I~v~~~~   73 (116)
                      +|+|+...+ .++.++|++++||.+||++|+++.|+|++.|+|+|+|+.|.|+.+|++|||.+.       .++.+..+.
T Consensus         1 qifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~~~   80 (103)
T d2c9wb1           1 DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRA   80 (103)
T ss_dssp             CEEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEEE
T ss_pred             CEEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEEec
Confidence            356665554 457899999999999999999999999999999999999999999999999654       478888886


Q ss_pred             CCC
Q 033570           74 RGG   76 (116)
Q Consensus        74 ~gg   76 (116)
                      .|+
T Consensus        81 ~~~   83 (103)
T d2c9wb1          81 DDT   83 (103)
T ss_dssp             TTE
T ss_pred             CCC
Confidence            665

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=4.7e-15  Score=87.25  Aligned_cols=75  Identities=17%  Similarity=0.425  Sum_probs=71.3

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~g   75 (116)
                      |.|.|++.+|+.+.+.|..++++..|+..++++.+++++.++|+|+|+.|.++.|++++++.+|++|+++.+..|
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q~G   77 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   77 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            578899999999999999999999999999999999999999999999999999999999999999999987654

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=2.4e-14  Score=87.65  Aligned_cols=70  Identities=19%  Similarity=0.266  Sum_probs=60.5

Q ss_pred             EEEEEcC---CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE-------EcC-CCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKTL---TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLE-DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~---~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~-------~L~-d~~tL~~~gi~~g~~I~v~   70 (116)
                      .|.|+..   +++.+.+.+++++||.+||.+|+..+|+|++.|+|+|.|+       .|+ |+.+|.+|||.+|++|+|.
T Consensus        11 ti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~   90 (97)
T d1wjna_          11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEE
Confidence            4666654   3677899999999999999999999999999999999876       244 6899999999999999986


Q ss_pred             E
Q 033570           71 L   71 (116)
Q Consensus        71 ~   71 (116)
                      .
T Consensus        91 ~   91 (97)
T d1wjna_          91 W   91 (97)
T ss_dssp             C
T ss_pred             e
Confidence            4

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=99.45  E-value=2.8e-13  Score=81.75  Aligned_cols=73  Identities=15%  Similarity=0.205  Sum_probs=60.5

Q ss_pred             EEEEEcC-CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE-------EcCCCCccccCCCCCCCEEEEEEec
Q 033570            2 QIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         2 ~v~Vk~~-~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~-------~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      .|.|.+. .+......+++++||.+||.+|+..+|+|++.|+|.|.|+       ..+|+.+|++||+.+|++|+|+-+.
T Consensus         6 ~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd~~   85 (90)
T d1t0ya_           6 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVT   85 (90)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECT
T ss_pred             EEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEeCC
Confidence            3455542 2344678899999999999999999999999999998776       4567999999999999999997654


Q ss_pred             C
Q 033570           74 R   74 (116)
Q Consensus        74 ~   74 (116)
                      .
T Consensus        86 ~   86 (90)
T d1t0ya_          86 G   86 (90)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=1.1e-13  Score=83.96  Aligned_cols=56  Identities=34%  Similarity=0.518  Sum_probs=49.9

Q ss_pred             cCCCCHHHHHHHHHHhhC--CC-CCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570           18 ESSDTIDNVKAKIQDKEG--IP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus        18 ~~~~TV~~LK~~I~~~~~--i~-~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      ..++||.+||+.|+++..  +| ++.|+|+|+|+.|.|+.+|++|||.+|++||++.|.
T Consensus        35 ~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r~   93 (94)
T d1x1ma1          35 LGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKS   93 (94)
T ss_dssp             CCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEESS
T ss_pred             CCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEeC
Confidence            346799999999999874  43 689999999999999999999999999999999873

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=2e-10  Score=66.16  Aligned_cols=70  Identities=16%  Similarity=0.384  Sum_probs=66.4

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~   70 (116)
                      +.|.|++.+|+.+.+.|..++++..|....+++.++++..++++|+|..+....|.+++++.+|++|.+.
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            4688899899999999999999999999999999999999999999999999999999999999999874

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.90  E-value=2.3e-09  Score=63.71  Aligned_cols=69  Identities=23%  Similarity=0.297  Sum_probs=55.9

Q ss_pred             EEEEcCCCCEEEEEecC-CCCHHHHHHHHHHhhCCCCCceEEEEC--------------CEEcCC-CCccccCCCCCCCE
Q 033570            3 IFVKTLTGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFA--------------GKQLED-GRTLADYNIQKEST   66 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~-~~TV~~LK~~I~~~~~i~~~~q~L~~~--------------g~~L~d-~~tL~~~gi~~g~~   66 (116)
                      |.|++.+| ...++|+. +.||.+||..|++..++|.+.|.|..+              -..|.| ..+|+++||.+|+.
T Consensus         3 iRiRsrdG-~eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsi   81 (94)
T d1wf9a1           3 LRVRSRDG-LERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSM   81 (94)
T ss_dssp             EEEECSSC-EEEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCE
T ss_pred             EEEEecCC-ceEEEecCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceE
Confidence            67888777 57788864 789999999999999999999999653              223444 56799999999999


Q ss_pred             EEEEEe
Q 033570           67 LHLVLR   72 (116)
Q Consensus        67 I~v~~~   72 (116)
                      |++...
T Consensus        82 vyL~y~   87 (94)
T d1wf9a1          82 VYLAYE   87 (94)
T ss_dssp             EECCCS
T ss_pred             EEEEee
Confidence            988654

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.36  E-value=1.6e-06  Score=49.62  Aligned_cols=70  Identities=19%  Similarity=0.211  Sum_probs=65.9

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.|-.++|+...+.|.|++++.++-+...+++|+.+++..|.|+++.|+-+.++.-.|+.+|+.+.++..
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~~   72 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPV   72 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECS
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeeecCCCCCCEEEEEEc
Confidence            6778889999999999999999999999999999999999999999999999999999999999998753

>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus solfataricus [TaxId: 2287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L40e
domain: Ribosomal protein L40e
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.96  E-value=4e-07  Score=48.69  Aligned_cols=33  Identities=18%  Similarity=0.295  Sum_probs=30.0

Q ss_pred             CCCchHHHHHHcCCCcccccccccccccCCCccccccC
Q 033570           78 IEPSLMALARKYNQDKMICRKSHTRTRNQFPFFNFVNC  115 (116)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~  115 (116)
                      ..++...++.+++.++++||+||.+   ++|+|  |||
T Consensus         4 ~eP~l~~lA~k~~~~k~ICrkC~AR---~p~rA--t~C   36 (56)
T d2ayja1           4 TDPAKLQIVQQRVFLKKVCRKCGAL---NPIRA--TKC   36 (56)
T ss_dssp             CCSCCSSTTTTCSCCCEEETTTCCE---ECTTC--SSC
T ss_pred             cCHHHHHHHHHHhhhhHHHhhcccc---CCccc--ccc
Confidence            3577788889999999999999999   99999  999

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.93  E-value=4.2e-05  Score=44.04  Aligned_cols=68  Identities=21%  Similarity=0.379  Sum_probs=57.8

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC---CCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~---d~~tL~~~gi~~g~~I~v~   70 (116)
                      +|.|+.++|+.+.-....++||.+|..-|... +.++....|+  |-.+.+.   .+.+|.+.|+.+.++|+|-
T Consensus         7 ~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~vq   79 (82)
T d1h8ca_           7 KLRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   79 (82)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-TCCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-CCCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEEE
Confidence            58899999999999999999999999999874 7777788877  5677773   4689999999998888764

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.76  E-value=6.8e-05  Score=43.84  Aligned_cols=65  Identities=20%  Similarity=0.348  Sum_probs=53.5

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhh-CCCCCceEEEE--CCEEcCC-CCccccCCCCCCCEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLIF--AGKQLED-GRTLADYNIQKESTL   67 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~-~i~~~~q~L~~--~g~~L~d-~~tL~~~gi~~g~~I   67 (116)
                      .|.|+.++|+.+......+++|++|.+-+.... +.+.....|+.  --+.|.| +.+|.++|+.+ +.|
T Consensus        16 ~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~-s~v   84 (89)
T d1i42a_          16 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLN-AVI   84 (89)
T ss_dssp             EEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEECCCCSSCSGGGTTCC-SEE
T ss_pred             EEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcccCCCcCcHHHCCCcC-ceE
Confidence            578999999999999999999999999998864 56666788874  4667754 88999999985 444

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Hypothetical protein KIAA0794
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.43  E-value=0.00036  Score=43.07  Aligned_cols=68  Identities=19%  Similarity=0.350  Sum_probs=55.5

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC---CCCccccCCCCCCCEEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~---d~~tL~~~gi~~g~~I~v~   70 (116)
                      +|.||.++|+.+......++||.+|...|... +.......|+  |--+.|.   .+.+|.++|+.+..+|+|-
T Consensus        45 ~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~-~~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-ccCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            68899999999999999999999999999775 4556677776  4555663   4789999999998888654

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.29  E-value=0.0008  Score=39.42  Aligned_cols=70  Identities=17%  Similarity=0.217  Sum_probs=55.4

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE--ECCEEcC--CCCccccCCCCCCCEEEEEEe
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--DGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~--~~g~~L~--d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +|.||.++|+.+.-....++||.+|..-+.... .......|+  |-.+.+.  .+.+|.++|+.+..+|+|--+
T Consensus        18 ~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~~-~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~~~   91 (96)
T d2cr5a1          18 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVG-YHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEEK   91 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHHT-CCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEEC
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHhc-cCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEecC
Confidence            688999999999889999999999999997653 455667776  3445553  378999999999888877544

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.88  E-value=0.056  Score=30.36  Aligned_cols=66  Identities=9%  Similarity=0.222  Sum_probs=47.9

Q ss_pred             CEEEEEcCC------C-CEEEEEecCCCCHHHHHHHHHHhhCC-----------CCCceEEEECCEEcCCCCccccCCCC
Q 033570            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEGI-----------PPDQQRLIFAGKQLEDGRTLADYNIQ   62 (116)
Q Consensus         1 m~v~Vk~~~------g-~~~~i~v~~~~TV~~LK~~I~~~~~i-----------~~~~q~L~~~g~~L~d~~tL~~~gi~   62 (116)
                      |+|+|+...      | ....++++...||.+|.+.+.++++-           .....++..+|+...++..     ++
T Consensus         2 mkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~d~~-----L~   76 (88)
T d1vjka_           2 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEE-----LK   76 (88)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTTCB-----CC
T ss_pred             eEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCCCcC-----cC
Confidence            677877653      3 56788999999999999999887531           1234577788888766544     55


Q ss_pred             CCCEEEEEE
Q 033570           63 KESTLHLVL   71 (116)
Q Consensus        63 ~g~~I~v~~   71 (116)
                      +|+.|.+..
T Consensus        77 ~gDevai~P   85 (88)
T d1vjka_          77 DGDVVGVFP   85 (88)
T ss_dssp             TTCEEEEES
T ss_pred             CCCEEEEeC
Confidence            799887764

>d1oeya_ d.15.2.2 (A:) Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.85  E-value=0.037  Score=31.31  Aligned_cols=43  Identities=12%  Similarity=0.197  Sum_probs=36.7

Q ss_pred             EEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEEC
Q 033570            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (116)
Q Consensus         4 ~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~   46 (116)
                      +||-.-.-++.+.+.+..+..+|.++|++++..+++..+|.|.
T Consensus         7 ~vkVh~~fTVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~   49 (82)
T d1oeya_           7 TLKVHYKYTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYR   49 (82)
T ss_dssp             EEEEESSSEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEEC
T ss_pred             EEEEEEEEEEEEEccCCCCHHHHHHHHHHHhCCChhheEEEec
Confidence            3443333578899999999999999999999999999999995

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.85  E-value=0.083  Score=29.82  Aligned_cols=70  Identities=16%  Similarity=0.249  Sum_probs=51.9

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCC-CCceEEEEC---CEE--cCCCCccccCCCCCCCEEEEEE
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLIFA---GKQ--LEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~-~~~q~L~~~---g~~--L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      |+|.|..+++ .+.+.++..++..+|-..+.+..++. .+-.=|.|.   |..  |+.++.|..+.++.+..+.+..
T Consensus         2 ~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~~l~F   77 (84)
T d1ef1a3           2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKF   77 (84)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcCCcccccceEEEECCCCCeEeccCCCchhhhccCCCCCEEEEE
Confidence            5788999987 48999999999999999999999985 334455553   322  6778888887665555444443

>d1wgya_ d.15.1.5 (A:) Rap guanine nucleotide exchange factor 5, RapGEF5 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: Rap guanine nucleotide exchange factor 5, RapGEF5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.39  E-value=0.16  Score=29.90  Aligned_cols=70  Identities=10%  Similarity=0.213  Sum_probs=51.0

Q ss_pred             EEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEE---ECCEE--cCC-CCccccCCCCCCCEEEEEEecC
Q 033570            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQ--LED-GRTLADYNIQKESTLHLVLRLR   74 (116)
Q Consensus         4 ~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~---~~g~~--L~d-~~tL~~~gi~~g~~I~v~~~~~   74 (116)
                      .|-..++.-..+.+..+.|++++++.++++.+.+.+++.|+   .+|..  |++ +..+.. .+.-++.+++..+-.
T Consensus        13 ~VY~~Dhsy~tlr~~v~~sa~eI~~~vaeKl~~~~e~L~LV~V~SsGEr~~lkp~d~sV~T-sL~lN~rLFvc~~d~   88 (104)
T d1wgya_          13 HVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISK-SLEASGRIYVYRKDL   88 (104)
T ss_dssp             EEECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCC-SSCSSCEEEEEECCS
T ss_pred             EEEecCCcEEEEEeeccCcHHHHHHHHHHHhCCCCCceEEEEEccCCcEEeeCccceeEEe-eeeecceEEEechhh
Confidence            45556677788999999999999999999999988887665   56763  444 333332 345578888887743

>d1zud21 d.15.3.2 (2:2-66) Thiamin biosynthesis sulfur carrier protein ThiS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: ThiS
domain: Thiamin biosynthesis sulfur carrier protein ThiS
species: Escherichia coli [TaxId: 562]

Probab=94.36  E-value=0.16  Score=27.12  Aligned_cols=58  Identities=12%  Similarity=0.186  Sum_probs=44.5

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .+++++..|+.+|-+.    .++++...-+..++..+.- ....+.-+++|+.|.++.-..||
T Consensus         8 ~~~~~~~~tl~~ll~~----l~~~~~~vaV~vN~~ivpk-~~~~~~~L~~gD~ieIv~~v~GG   65 (65)
T d1zud21           8 AMQCAAGQTVHELLEQ----LDQRQAGAALAINQQIVPR-EQWAQHIVQDGDQILLFQVIAGG   65 (65)
T ss_dssp             EECCCTTCBHHHHHHH----HTCCCTTEEEEETTEECCG-GGTTTCBCCTTCEEEEEECCCCC
T ss_pred             EEEcCCCCcHHHHHHH----cCCCCCcEEEEECCEEcCH-HHHhhccCCCCCEEEEEEEecCC
Confidence            3456777899987765    4788888888899998853 24556667889999998877776

>d1y8xb1 c.111.1.2 (B:349-440) UBA3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Activating enzymes of the ubiquitin-like proteins
superfamily: Activating enzymes of the ubiquitin-like proteins
family: Ubiquitin activating enzymes (UBA)
domain: UBA3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.28  E-value=0.046  Score=31.60  Aligned_cols=58  Identities=12%  Similarity=0.287  Sum_probs=40.7

Q ss_pred             EEEecCCCCHHHHHHHHHHhhCCCCC--c--------eEEEECCEE--cCC------CCccccCCCCCCCEEEEEE
Q 033570           14 TLEVESSDTIDNVKAKIQDKEGIPPD--Q--------QRLIFAGKQ--LED------GRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~i~~~--~--------q~L~~~g~~--L~d------~~tL~~~gi~~g~~I~v~~   71 (116)
                      .+++++++|+.+|.+.+.+.-.+...  .        .+-.|...+  |..      .++|.++|+.+|+.|.|.=
T Consensus         4 ~l~~~~~~TL~~li~~L~e~p~~qlk~Psltt~~~g~~ktLYm~~pp~Lee~Tr~NL~k~L~eLgl~dG~ei~VtD   79 (92)
T d1y8xb1           4 NIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD   79 (92)
T ss_dssp             CEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEEC
T ss_pred             eEEcCCCCcHHHHHHHHhhChHhhccCCceeeecCCCccEEEecCcHHHHHHhhhccccCHHHhCCcCCCEEEEec
Confidence            47889999999999999997433222  2        223344333  321      5789999999999998863

>d1xo3a_ d.15.3.3 (A:) C9orf74 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: C9orf74 homolog
domain: C9orf74 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.38  E-value=0.35  Score=27.79  Aligned_cols=73  Identities=19%  Similarity=0.248  Sum_probs=47.7

Q ss_pred             CEEEEEcCCC--------CEEEEEecC---CCCHHHHHHHHHHhhCCCCC-----------ceEEEECCEEcCCCCccc-
Q 033570            1 MQIFVKTLTG--------KTITLEVES---SDTIDNVKAKIQDKEGIPPD-----------QQRLIFAGKQLEDGRTLA-   57 (116)
Q Consensus         1 m~v~Vk~~~g--------~~~~i~v~~---~~TV~~LK~~I~~~~~i~~~-----------~q~L~~~g~~L~d~~tL~-   57 (116)
                      |+|+|+..+|        +.+.++++.   ..||.+|-+.+.+++.-...           .+.+..+|....   -+. 
T Consensus         5 m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~~~~~l~~~~~~lr~~v~v~vN~~di~---~l~g   81 (101)
T d1xo3a_           5 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWE---LLGE   81 (101)
T ss_dssp             CEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCCSCGGGSCCTTSCCSSEEEEETTEEHH---HHTT
T ss_pred             eEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCcchhhhhccCcCeeeeEEEEEcCccee---ccCC
Confidence            7888887542        345666643   47999999999988753211           134455665431   111 


Q ss_pred             -cCCCCCCCEEEEEEecCCC
Q 033570           58 -DYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        58 -~~gi~~g~~I~v~~~~~gg   76 (116)
                       ++.+++|+.|.+.....||
T Consensus        82 l~t~l~dgDeV~~~p~v~GG  101 (101)
T d1xo3a_          82 LDYQLQDQDSILFISTLHGG  101 (101)
T ss_dssp             TSCCCCTTCEEEEEETTCCC
T ss_pred             CccCcCCCCEEEEeCCCCCC
Confidence             4567889999999888776

>d1gg3a3 d.15.1.4 (A:1-81) Erythroid membrane protein 4.1R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.95  E-value=0.22  Score=27.80  Aligned_cols=59  Identities=12%  Similarity=0.142  Sum_probs=43.8

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCc-eEEEEC---CEE--cCCCCccccC
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFA---GKQ--LEDGRTLADY   59 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~~~---g~~--L~d~~tL~~~   59 (116)
                      |+..|..++|..+.+.++..++..+|-+.+.+..++...+ .=|.|-   |..  |+.++.|...
T Consensus         1 ~~C~V~lLD~~~~~~~v~~~~~G~~l~~~Vc~~l~l~E~~YFGL~y~d~~~~~~WLd~~K~i~kq   65 (81)
T d1gg3a3           1 MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQ   65 (81)
T ss_dssp             CEEEEECTTSCEEEEECCTTCCHHHHHHHHHHHHTTCSCCSSSCEEECCSSSCCBCCTTSCHHHH
T ss_pred             CEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCcccccceEEEECCCCceEecccccchhhh
Confidence            7889999999999999999999999999999999985332 223332   221  4455565544

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Bud emergence mediator Bemp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.57  E-value=0.33  Score=27.17  Aligned_cols=44  Identities=16%  Similarity=0.151  Sum_probs=34.7

Q ss_pred             EEEEcC-CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCE
Q 033570            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK   48 (116)
Q Consensus         3 v~Vk~~-~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~   48 (116)
                      |.||.. ++..+.+.++++.+..+|+++|+++++.  +.++|.|...
T Consensus        13 ikVKv~~~~D~~~~~l~~~it~~dL~~kI~~rf~~--~~~~lkY~De   57 (85)
T d1ip9a_          13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDT--DNFKLQTKLF   57 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHTS--SCEEEEECCS
T ss_pred             EEEEEEECCcEEEEEeCCCCCHHHHHHHHHHHhCC--CceEEEEEcC
Confidence            455555 5567889999999999999999999975  4578877643

>d1fm0d_ d.15.3.1 (D:) Molybdopterin synthase subunit MoaD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Escherichia coli [TaxId: 562]

Probab=91.92  E-value=0.31  Score=26.79  Aligned_cols=59  Identities=5%  Similarity=0.162  Sum_probs=42.1

Q ss_pred             EEEEEecCCCCHHHHHHHHHHhhC-----CCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           12 TITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        12 ~~~i~v~~~~TV~~LK~~I~~~~~-----i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ...++++ ..|+.+|++.+.++..     +.....++..+++..+++..     +++|+.|-+.....||
T Consensus        18 ~~~~~~~-~~tv~~l~~~L~~~~~~~~~~l~~~~~~vavn~~~~~~~~~-----l~~gdevAi~PPVsGG   81 (81)
T d1fm0d_          18 ATEVAAD-FPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHP-----LTDGDEVAFFPPVTGG   81 (81)
T ss_dssp             EEEECSC-CSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCTTCB-----CCTTCEEEEECCCCCC
T ss_pred             eEEecCC-CCCHHHHHHHHHHhCchHHHHhcCCcEEEecCceecCCCCC-----cCCCCEEEEECCCCCC
Confidence            4455543 4589999999987643     33456777888887765554     5679999998888776

>d1wgra_ d.15.1.5 (A:) Growth factor receptor-bound protein 7, GRB-7 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: Growth factor receptor-bound protein 7, GRB-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.95  E-value=0.24  Score=28.51  Aligned_cols=53  Identities=21%  Similarity=0.275  Sum_probs=39.1

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCce-EEE--E--CC--EEcCCCCc
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLI--F--AG--KQLEDGRT   55 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q-~L~--~--~g--~~L~d~~t   55 (116)
                      |.|-..+|....+.|++++|+.++-+.+.++.++....- -|+  +  .|  +.|.|+..
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~~~~~f~L~E~~~~~~leR~L~d~E~   71 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDETWGLVECHPHLALERGLEDHES   71 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCCCCCEEEEETTTTEEEEECSSSC
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCCCCCCeEEEEecCCCcceeecCchHh
Confidence            455567899999999999999999999999999854432 232  2  23  56777554

>d1v8ca1 d.15.3.1 (A:1-87) MoaD-related protein, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: MoaD-related protein, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.32  E-value=0.49  Score=26.22  Aligned_cols=61  Identities=18%  Similarity=0.298  Sum_probs=41.5

Q ss_pred             EEEecCCCCHHHHHHHHHHhhC-C---------CCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           14 TLEVESSDTIDNVKAKIQDKEG-I---------PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        14 ~i~v~~~~TV~~LK~~I~~~~~-i---------~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      .++++. .||.+|.+.+.+++. +         ....+.+..+|+...+...+ +.-+++|+.|.++....||
T Consensus        17 e~~v~~-~Tv~~ll~~L~~~~p~l~~~l~~~~~~~~~v~i~vng~~i~~~~~~-~~~l~~gdeV~i~PpvsGG   87 (87)
T d1v8ca1          17 QLELPG-ATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGL-STPLSPGATLDLFPPVAGG   87 (87)
T ss_dssp             EEECCC-SBHHHHHHHHHHHCGGGHHHHEETTEECTTCEEEETTEEGGGTTGG-GCBCCTTCEEEEECSCCSE
T ss_pred             EEEEcC-CCHHHHHHHHHHHCHHHHHHhcccccccceEEEEEcCeeeecccCC-cccCCCCCEEEEECCCCCC
Confidence            356654 599999999988763 1         12345677888877543222 2347889999998887775

>d1h4ra3 d.15.1.4 (A:20-103) Merlin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Merlin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.26  E-value=1  Score=25.03  Aligned_cols=71  Identities=11%  Similarity=0.161  Sum_probs=51.5

Q ss_pred             CEEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEE--CCEE--cCCCCccccCCCCCCCEEEEEEe
Q 033570            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF--AGKQ--LEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         1 m~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~--~g~~--L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      |.|.|..++++ ..+.+++.++..+|-..+.+..++... -.=|.|  .|..  |+.++.|..+.++.+..+.+..+
T Consensus         3 ~~v~V~lLD~~-le~~v~~~a~G~~L~d~Vc~~L~L~E~~YFGL~y~~~~~~~WLd~~k~l~kq~~~~~~~~~~~F~   78 (84)
T d1h4ra3           3 FTVRIVTMDAE-MEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   78 (84)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             EEEEEEEcCCc-EEEEEcCCChHHHHHHHHHHHcCCcccccceEEEecCCceEEccCCCchhhhccCCCCCEEEEEE
Confidence            46788888875 789999999999999999999998533 333443  4443  66788888886666665544433

>d2incc1 d.15.12.1 (C:3-85) Toluene, o-xylene monooxygenase oxygenase subunit TouB {Pseudomonas stutzeri [TaxId: 316]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: TmoB-like
family: TmoB-like
domain: Toluene, o-xylene monooxygenase oxygenase subunit TouB
species: Pseudomonas stutzeri [TaxId: 316]

Probab=88.85  E-value=1.1  Score=24.88  Aligned_cols=59  Identities=22%  Similarity=0.403  Sum_probs=45.4

Q ss_pred             EEEEecCCCCHHHHHHHHHHhh-C--CCC--Cce-EEE--ECCEEcCCCCccccCCCCCCCEEEEEE
Q 033570           13 ITLEVESSDTIDNVKAKIQDKE-G--IPP--DQQ-RLI--FAGKQLEDGRTLADYNIQKESTLHLVL   71 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~-~--i~~--~~q-~L~--~~g~~L~d~~tL~~~gi~~g~~I~v~~   71 (116)
                      ..+.|+.++|+.++-++++.+. |  +.|  +.. +.-  .+|+.+..+.++++.||++-..|.+..
T Consensus        15 qLVaVDt~dtmdqVA~k~A~HsVGRRv~p~P~~~~rvr~~~~ge~~pr~~tv~~~gi~P~e~iev~f   81 (83)
T d2incc1          15 QLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIF   81 (83)
T ss_dssp             EEEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEE
T ss_pred             EEEEEcCCCcHHHHHHHHHHHhhccccCCCCCCccEEEEcCCCcCCCCCCChhhcCCCCceEEEEEE
Confidence            3468999999999999998864 3  422  332 332  378999999999999999999888753

>d1eo6a_ d.15.1.3 (A:) Golgi-associated ATPase enhancer of 16 kD, Gate-16 {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: GABARAP-like
domain: Golgi-associated ATPase enhancer of 16 kD, Gate-16
species: Cow (Bos taurus) [TaxId: 9913]

Probab=87.03  E-value=0.51  Score=28.06  Aligned_cols=60  Identities=13%  Similarity=0.108  Sum_probs=44.4

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCC-ceEEEECCEEcCCCCccccCC---CCCCCEEEEEEe
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFAGKQLEDGRTLADYN---IQKESTLHLVLR   72 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~-~q~L~~~g~~L~d~~tL~~~g---i~~g~~I~v~~~   72 (116)
                      ..+-|+.+.||++|...|..+.+++++ .+-|..++..+..+.+++++-   -.++.-+++...
T Consensus        47 ~KfLVP~dltv~qf~~vIRkrl~l~~~~alflfv~~~l~~~s~~i~~lY~~~KdeDGfLYi~Ys  110 (116)
T d1eo6a_          47 RKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYS  110 (116)
T ss_dssp             CEEEEETTSBHHHHHHHHHHHHTCCTTSCCEEEBTTBCCCTTSBHHHHHHHHCCTTSCEEEEEE
T ss_pred             cEEeecCCCcHHHHHHHHHHHcCCCccceEEEEECCcccchhhhHHHHHHHcCCCCcEEEEEEe
Confidence            456788999999999999999998765 456667888778888888761   124555666544

>d1wxma1 d.15.1.5 (A:8-80) A-Raf proto-oncogene serine/threonine-protein kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: A-Raf proto-oncogene serine/threonine-protein kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.85  E-value=1.4  Score=23.90  Aligned_cols=43  Identities=12%  Similarity=0.047  Sum_probs=38.5

Q ss_pred             EEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE
Q 033570            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (116)
Q Consensus         3 v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~   45 (116)
                      |.|.-++|+...+.+.|..|+.+.-..+.++.|+.++...+..
T Consensus         3 iRv~LPngq~T~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~~   45 (73)
T d1wxma1           3 VKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYR   45 (73)
T ss_dssp             EEEECSSSCEEEEECCSSCBSHHHHHHHHHTTTCCSSSEEEEE
T ss_pred             EEEEcCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            6777889999999999999999999999999999988877753

>d1c1yb_ d.15.1.5 (B:) c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: c-Raf1 RBD
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.32  E-value=1.4  Score=24.14  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=38.6

Q ss_pred             EEEEEcCCCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE
Q 033570            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (116)
Q Consensus         2 ~v~Vk~~~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~   45 (116)
                      .|.|.-++|+...+.+.|..|+.+.-..+.++.|+.++...++.
T Consensus         3 ~iRv~LPngq~T~V~vrpG~tird~L~k~l~kRgl~~~~c~V~~   46 (77)
T d1c1yb_           3 TIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFR   46 (77)
T ss_dssp             EEEEEETTTEEEEEECCTTCBHHHHHHHHHHTTTCCGGGEEEEE
T ss_pred             eEEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            36777889999999999999999999999999999988877753

>d3d32a1 d.15.1.3 (A:1-118) GABA(A) receptor associated protein GABARAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: GABARAP-like
domain: GABA(A) receptor associated protein GABARAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.12  E-value=0.61  Score=27.76  Aligned_cols=60  Identities=10%  Similarity=0.042  Sum_probs=44.2

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCc-eEEEECCEEcCCCCccccCC--C-CCCCEEEEEEe
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADYN--I-QKESTLHLVLR   72 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~-q~L~~~g~~L~d~~tL~~~g--i-~~g~~I~v~~~   72 (116)
                      ..+-|+.+.||++|...|..+.+++++. +-|..++..+..+.+++++-  - .++.-+++...
T Consensus        49 ~KflVp~d~tv~qf~~~iRkrl~l~~~~alflfvn~~~~~~~~ti~~lY~~~kdeDGfLYi~Ys  112 (118)
T d3d32a1          49 KKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYS  112 (118)
T ss_dssp             SEEEEETTCBHHHHHHHHHHHHTCCTTSCCEEEBTTBCCCTTCBHHHHHHHHCCTTSCEEEEEE
T ss_pred             ceEEecCCccHHHHHHHHHHHhCCCccceEEEEECCcccCccccHHHHHHHhCCCCcEEEEEEe
Confidence            3467889999999999999999997775 56667887777788887751  1 23455665544

>d2cu3a1 d.15.3.2 (A:1-63) Uncharacterised protein TTHA0675 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: ThiS
domain: Uncharacterised protein TTHA0675
species: Thermus thermophilus [TaxId: 274]

Probab=83.19  E-value=1.9  Score=22.39  Aligned_cols=56  Identities=13%  Similarity=0.240  Sum_probs=40.2

Q ss_pred             CCCEEEEEecCCCCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEe
Q 033570            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (116)
Q Consensus         9 ~g~~~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~   72 (116)
                      +|+.+.  ++ ..|+.+|-..    .++++...-+-++|..+.- ....+.-+++|+.|.++--
T Consensus         5 NGe~~~--~~-~~tl~~LL~~----l~~~~~~vAV~vN~~ivpr-~~~~~~~l~~gD~iEIv~~   60 (63)
T d2cu3a1           5 NGEPRP--LE-GKTLKEVLEE----MGVELKGVAVLLNEEAFLG-LEVPDRPLRDGDVVEVVAL   60 (63)
T ss_dssp             TTEEEC--CT-TCCHHHHHHH----HTBCGGGEEEEETTEEEEG-GGCCCCCCCTTCEEEEEEC
T ss_pred             CCEEEE--cC-CCCHHHHHHH----cCCCCCcEEEEECCEEcCH-HHcCcccCCCCCEEEEEEe
Confidence            666554  43 5688776654    4777788888999998843 3566777888999997754

>d1j0ga_ d.15.1.6 (A:) Hypothetical protein 1810045k17 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: BM-002-like
domain: Hypothetical protein 1810045k17
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.50  E-value=2.4  Score=23.49  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=51.9

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEEE-CCEEcCCCCccccCCCCCCCEEEEEEecCCC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~~-~g~~L~d~~tL~~~gi~~g~~I~v~~~~~gg   76 (116)
                      ..+.|++.......-+-.++++++++..--++- .|--+...++-+..-++.|+.+.+..|-+-|
T Consensus        26 kvlsVpE~aPftAVlkfaAEeFkV~~~TSAiITndGvGINP~QtAg~vFlKhGselrliPRDRVG   90 (92)
T d1j0ga_          26 KVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG   90 (92)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHTTCCSSSEEEECTTSCCCCCSSBHHHHHHHTCSEEEEEECCSSC
T ss_pred             EEEecCccCchHHHHHHHHHHcCCCccceeEEecCccccChhhccchhhhhcCceeeeccccccc
Confidence            346899988898888899999999988776665 4666777888888888899999998886655

>d1tygb_ d.15.3.2 (B:) Thiamin biosynthesis sulfur carrier protein ThiS {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: ThiS
domain: Thiamin biosynthesis sulfur carrier protein ThiS
species: Bacillus subtilis [TaxId: 1423]

Probab=80.98  E-value=2.4  Score=22.04  Aligned_cols=58  Identities=10%  Similarity=0.134  Sum_probs=41.6

Q ss_pred             CCCEEEEEecCC-CCHHHHHHHHHHhhCCCCCceEEEECCEEcCCCCccccCCCCCCCEEEEEEec
Q 033570            9 TGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (116)
Q Consensus         9 ~g~~~~i~v~~~-~TV~~LK~~I~~~~~i~~~~q~L~~~g~~L~d~~tL~~~gi~~g~~I~v~~~~   73 (116)
                      +|+.  .+++.+ .|+.+|-..    .++++...-+-++|..+.- ....+.-+++|+.|.++--.
T Consensus         5 NG~~--~~~~~~~~tl~~LL~~----l~~~~~~vAVevN~~iv~k-~~~~~~~L~~gD~IEIv~~v   63 (65)
T d1tygb_           5 NGKD--VKWKKDTGTIQDLLAS----YQLENKIVIVERNKEIIGK-ERYHEVELCDRDVIEIVHFV   63 (65)
T ss_dssp             TTEE--ECCSSSCCBHHHHHHH----TTCTTSCCEEEETTEEECG-GGTTTSBCCSSSEEEEEEEC
T ss_pred             CCEE--EEcCCCcccHHHHHHH----cCCCCCcEEEEECCEEcCH-HHcCcccCCCCCEEEEEEee
Confidence            5554  345554 589888544    4788888899999998853 35666678889999987643

>d2bkfa1 d.15.2.2 (A:1-85) Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Next to BRCA1 gene 1 protein, NBR1 (KIAA0049)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.79  E-value=2.7  Score=23.38  Aligned_cols=41  Identities=7%  Similarity=0.165  Sum_probs=30.4

Q ss_pred             EEEEcC-CCCEEEEEec--CCCCHHHHHHHHHHhhCCCCCceEEEE
Q 033570            3 IFVKTL-TGKTITLEVE--SSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (116)
Q Consensus         3 v~Vk~~-~g~~~~i~v~--~~~TV~~LK~~I~~~~~i~~~~q~L~~   45 (116)
                      |+||-. +|.+..+.++  .+++..+|..+|+..++++  .+.|.|
T Consensus         5 vtvKvtf~~dt~RF~ls~~~~~~~~~L~~~i~~rf~l~--~~~lkY   48 (85)
T d2bkfa1           5 VTLNVTFKNEIQSFLVSDPENTTWADIEAMVKVSFDLN--TIQIKY   48 (85)
T ss_dssp             EEEEEEETTEEEEEEESCGGGCCHHHHHHHHHHHHTCS--SEEEEE
T ss_pred             EEEEEEECCceEEEEecCCCCCcHHHHHHHHHHhcCcc--cceEEE
Confidence            455544 5666566654  5788999999999999985  577777

>d2zjda1 d.15.1.3 (A:2-120) Microtubule-associated proteins 1A/1B light chain 3B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: GABARAP-like
domain: Microtubule-associated proteins 1A/1B light chain 3B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.21  E-value=2.2  Score=25.16  Aligned_cols=47  Identities=9%  Similarity=0.181  Sum_probs=35.9

Q ss_pred             EEEEecCCCCHHHHHHHHHHhhCCCCCceEEE-ECCEE-cCCCCccccC
Q 033570           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQ-LEDGRTLADY   59 (116)
Q Consensus        13 ~~i~v~~~~TV~~LK~~I~~~~~i~~~~q~L~-~~g~~-L~d~~tL~~~   59 (116)
                      ..+-|+.+.||+++...|..+.+++++.--++ .+|.. ...+.+++++
T Consensus        49 ~KfLVp~d~tv~qf~~~iRkrl~l~~~~alFlfvn~~~~p~~~~~i~~l   97 (119)
T d2zjda1          49 TKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEV   97 (119)
T ss_dssp             CEEEEETTCBHHHHHHHHHHHHTCCTTCCEEEEETTTEECCTTSBHHHH
T ss_pred             eEEEEecCccHHHHHHHHHHHhCCCCcceEEEEEcCCccCCchhHHHHH
Confidence            34568999999999999999999977655444 56665 4567778765