Citrus Sinensis ID: 033059

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK
Secondary Structure (PSIPRED)
cEEEEEcccccEEEEEEEcccHHHHHHHHHHHHHcccccccEEEEccEEccccccccccccccccEEEccccccccccccHHHHHHHHHccccccEEccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEcccccEHHHHHHHHHHHHcccHHHEEEEEccEEcccccEcHHHccccccEEEEEEcccccccHHHHHHHHcccccccEEHHHHEcccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MQIFVKTltgktitlevessdtiDNVKAKiqdkegippdqQRLIFAGkqledgrtladyniqkeSTLHLVLRLRGGIIEPSLMALARKYNQdkmicrkcyarlhpravncrkkkcghsnqlrpkkkik
Flexible Loop (DISEMBL)
mqifvktltgktitlevessdtidnVKAKIqdkegippdqqRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARlhpravncrkkkcghsnqlrpkkkik
Low Complexity Region (SEG)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK
Disordered region (IsUnstruct)
***FVKTLTGKTITLEV************************RLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCR*****************
Disordered Region (DISOPRED)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLR******
Disordered Region (DISEMBL)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRK****************
Disordered Region (DISPRO)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNC*KKK**************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK
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	128	2.2.26 [Sep-21-2011]
P49636	128	Ubiquitin-60S ribosomal p	N/A	no	1.0	1.0	0.992	3e-70
Q42202	128	Ubiquitin-60S ribosomal p	yes	no	1.0	1.0	0.992	7e-70
B9DHA6	128	Ubiquitin-60S ribosomal p	yes	no	1.0	1.0	0.992	7e-70
P0CH35	129	Ubiquitin-60S ribosomal p	yes	no	1.0	0.992	0.992	8e-70
P0CH34	129	Ubiquitin-60S ribosomal p	yes	no	1.0	0.992	0.992	8e-70
P51423	128	Ubiquitin-60S ribosomal p	N/A	no	1.0	1.0	0.992	9e-70
P0CH10	128	Ubiquitin-60S ribosomal p	N/A	no	1.0	1.0	0.945	6e-67
P0CH11	128	Ubiquitin-60S ribosomal p	N/A	no	1.0	1.0	0.945	6e-67
P49633	128	Ubiquitin-60S ribosomal p	N/A	no	1.0	1.0	0.914	7e-65
P0C276	128	Ubiquitin-60S ribosomal p	N/A	no	1.0	1.0	0.921	1e-64

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

 Score =  263 bits (671), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 128/128 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCR+KKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRRKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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 =  261 bits (668), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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 =  261 bits (668), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  261 bits (667), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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 =  261 bits (667), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  261 bits (667), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ KMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQAKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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

Brassica rapa (taxid: 51350)

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

 Score =  251 bits (642), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 121/128 (94%), Positives = 125/128 (97%)

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

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQ+KMICRKCYARLHPRA NCRKK CGH+NQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQEKMICRKCYARLHPRAKNCRKKSCGHTNQ 120

Query: 121 LRPKKKIK 128
           LRPKKK+K
Sbjct: 121 LRPKKKLK 128

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 =  251 bits (642), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 121/128 (94%), Positives = 125/128 (97%)

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

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQ+KMICRKCYARLHPRA NCRKK CGH+NQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLQALARKYNQEKMICRKCYARLHPRAKNCRKKSCGHTNQ 120

Query: 121 LRPKKKIK 128
           LRPKKK+K
Sbjct: 121 LRPKKKLK 128

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

Chlamydomonas reinhardtii (taxid: 3055)

>sp|P49633|RL40_ACACA Ubiquitin-60S ribosomal protein L40 OS=Acanthamoeba castellanii PE=2 SV=2

 Score =  245 bits (625), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 117/128 (91%), Positives = 122/128 (95%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTI+NVK KIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIENVKQKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGG+IEPSL  LARKYN DK++CRKCYARLHPRAVNCRKKKCGHSN 
Sbjct: 61  IQKESTLHLVLRLRGGVIEPSLQVLARKYNCDKVVCRKCYARLHPRAVNCRKKKCGHSNH 120

Query: 121 LRPKKKIK 128
            RPKKK+K
Sbjct: 121 WRPKKKLK 128

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

Acanthamoeba castellanii (taxid: 5755)

>sp|P0C276|RL40_SHEEP Ubiquitin-60S ribosomal protein L40 OS=Ovis aries GN=UBA52 PE=2 SV=2

 Score =  244 bits (622), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 118/128 (92%), Positives = 123/128 (96%)

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

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query: 121 LRPKKKIK 128
           LRPKKK+K
Sbjct: 121 LRPKKKVK 128

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

Ovis aries (taxid: 9940)

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	128
449483218	208	PREDICTED: ubiquitin-60S ribosomal prote	1.0	0.615	1.0	4e-69
359482015	228	PREDICTED: LOW QUALITY PROTEIN: ubiquiti	1.0	0.561	1.0	7e-69
255578906	128	ubiquitin, putative [Ricinus communis] g	1.0	1.0	1.0	1e-68
302393724	128	RecName: Full=Ubiquitin-60S ribosomal pr	1.0	1.0	0.992	2e-68
224120992	128	predicted protein [Populus trichocarpa]	1.0	1.0	0.992	3e-68
351722530	128	uncharacterized protein LOC100306626 [Gl	1.0	1.0	0.992	4e-68
18404062	128	60S ribosomal protein L40-2 [Arabidopsis	1.0	1.0	0.992	5e-68
225455266	128	PREDICTED: ubiquitin-60S ribosomal prote	1.0	1.0	0.992	5e-68
388518175	128	unknown [Lotus japonicus]	1.0	1.0	0.992	6e-68
357464075	128	Ubiquitin [Medicago truncatula] gi|14640	1.0	1.0	0.992	6e-68

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

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 128/128 (100%), Positives = 128/128 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 81  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 140

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 141 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 200

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 201 LRPKKKIK 208

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  265 bits (676), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 128/128 (100%), Positives = 128/128 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 101 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 160

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 161 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 220

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 221 LRPKKKIK 228

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 =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 128/128 (100%), Positives = 128/128 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  263 bits (671), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 128/128 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCR+KKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRRKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Nicotiana sylvestris

Species: Nicotiana sylvestris

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

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 =  262 bits (670), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 128/128 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQ+KMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQEKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

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 =  262 bits (669), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 128/128 (100%)

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

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18404062|ref|NP_565836.1| 60S ribosomal protein L40-2 [Arabidopsis thaliana] gi|18409639|ref|NP_566969.1| 60S ribosomal protein L40-2 [Arabidopsis thaliana] gi|302425250|sp|Q42202.2|RL40B_ARATH RecName: Full=Ubiquitin-60S ribosomal protein L40-2; AltName: Full=Protein EARLY-RESPONSIVE TO DEHYDRATION 16; AltName: Full=Protein EMBRYO DEFECTIVE 2167; AltName: Full=Protein HAPLESS 4; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=60S ribosomal protein L40-2; AltName: Full=CEP52; Flags: Precursor gi|302595860|sp|B9DHA6.1|RL40A_ARATH RecName: Full=Ubiquitin-60S ribosomal protein L40-1; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=60S ribosomal protein L40-1; AltName: Full=CEP52; Flags: Precursor gi|13430798|gb|AAK26021.1|AF360311_1 putative ubiquitin extension protein UBQ2 [Arabidopsis thaliana] gi|166930|gb|AAA32904.1| ubiquitin extension protein (UBQ1) [Arabidopsis thaliana] gi|166932|gb|AAA32905.1| ubiquitin extension protein (UBQ2) [Arabidopsis thaliana] gi|4886268|emb|CAB43405.1| ubiquitin / ribosomal protein CEP52 [Arabidopsis thaliana] gi|14334950|gb|AAK59652.1| putative ubiquitin extension protein UBQ1 [Arabidopsis thaliana] gi|15810643|gb|AAL07246.1| putative ubiquitin extension protein UBQ2 [Arabidopsis thaliana] gi|16323384|gb|AAL15186.1| putative ubiquitin extension protein UBQ1 [Arabidopsis thaliana] gi|20198116|gb|AAM15407.1| ubiquitin extension protein (UBQ2) [Arabidopsis thaliana] gi|21553955|gb|AAM63036.1| ubiquitin extension protein UBQ1 [Arabidopsis thaliana] gi|222424333|dbj|BAH20123.1| AT2G36170 [Arabidopsis thaliana] gi|330254118|gb|AEC09212.1| 60S ribosomal protein L40-2 [Arabidopsis thaliana] gi|332645445|gb|AEE78966.1| 60S ribosomal protein L40-2 [Arabidopsis thaliana]

 Score =  261 bits (668), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455266|ref|XP_002273568.1| PREDICTED: ubiquitin-60S ribosomal protein L40-2 [Vitis vinifera] gi|302143958|emb|CBI23063.3| unnamed protein product [Vitis vinifera]

 Score =  261 bits (668), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMQLARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388518175|gb|AFK47149.1| unknown [Lotus japonicus]

 Score =  261 bits (667), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLTALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357464075|ref|XP_003602319.1| Ubiquitin [Medicago truncatula] gi|146403798|gb|ABQ32305.1| putative ubiquitin-conjugating enzyme [Artemisia annua] gi|217071300|gb|ACJ84010.1| unknown [Medicago truncatula] gi|355491367|gb|AES72570.1| Ubiquitin [Medicago truncatula] gi|388491220|gb|AFK33676.1| unknown [Medicago truncatula] gi|388492460|gb|AFK34296.1| unknown [Medicago truncatula] gi|388500420|gb|AFK38276.1| unknown [Medicago truncatula]

 Score =  261 bits (667), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSLMALARKYNQDK ICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKTICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query: 121 LRPKKKIK 128
           LRPKKKIK
Sbjct: 121 LRPKKKIK 128

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	128
TAIR|locus:2053496	128	UBQ2 "ubiquitin extension prot	1.0	1.0	0.992	2.3e-64
TAIR|locus:2079924	128	UBQ1 "ubiquitin extension prot	1.0	1.0	0.992	2.3e-64
UNIPROTKB|P63048	128	UBA52 "Ubiquitin-60S ribosomal	1.0	1.0	0.921	3.1e-60
UNIPROTKB|P63050	128	UBA52 "Ubiquitin-60S ribosomal	1.0	1.0	0.921	3.1e-60
UNIPROTKB|P62987	128	UBA52 "Ubiquitin-60S ribosomal	1.0	1.0	0.921	3.1e-60
UNIPROTKB|P63053	128	UBA52 "Ubiquitin-60S ribosomal	1.0	1.0	0.921	3.1e-60
UNIPROTKB|P62986	128	Uba52 "Ubiquitin-60S ribosomal	1.0	1.0	0.921	3.1e-60
FB|FBgn0003941	128	RpL40 "Ribosomal protein L40"	1.0	1.0	0.914	1e-59
ZFIN|ZDB-GENE-051023-7	128	uba52 "ubiquitin A-52 residue	1.0	1.0	0.914	1e-59
POMBASE|SPAC11G7.04	128	ubi1 "ribosomal-ubiquitin fusi	1.0	1.0	0.914	3.5e-59

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

 Score = 656 (236.0 bits), Expect = 2.3e-64, P = 2.3e-64
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query:   121 LRPKKKIK 128
             LRPKKKIK
Sbjct:   121 LRPKKKIK 128

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 = 656 (236.0 bits), Expect = 2.3e-64, P = 2.3e-64
 Identities = 127/128 (99%), Positives = 127/128 (99%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSLM LARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLMMLARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120

Query:   121 LRPKKKIK 128
             LRPKKKIK
Sbjct:   121 LRPKKKIK 128

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

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

 Score = 617 (222.3 bits), Expect = 3.1e-60, P = 3.1e-60
 Identities = 118/128 (92%), Positives = 123/128 (96%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKVK 128

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 = 617 (222.3 bits), Expect = 3.1e-60, P = 3.1e-60
 Identities = 118/128 (92%), Positives = 123/128 (96%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKVK 128

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 = 617 (222.3 bits), Expect = 3.1e-60, P = 3.1e-60
 Identities = 118/128 (92%), Positives = 123/128 (96%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKVK 128

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 = 617 (222.3 bits), Expect = 3.1e-60, P = 3.1e-60
 Identities = 118/128 (92%), Positives = 123/128 (96%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKVK 128

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|P62986 Uba52 "Ubiquitin-60S ribosomal protein L40" [Rattus norvegicus (taxid:10116)]

 Score = 617 (222.3 bits), Expect = 3.1e-60, P = 3.1e-60
 Identities = 118/128 (92%), Positives = 123/128 (96%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKVK 128

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

GO:0005634 "nucleus" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

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

 Score = 612 (220.5 bits), Expect = 1.0e-59, P = 1.0e-59
 Identities = 117/128 (91%), Positives = 122/128 (95%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN DKMICRKCYARLHPRA NCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRILAQKYNCDKMICRKCYARLHPRATNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKLK 128

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

ZFIN|ZDB-GENE-051023-7 uba52 "ubiquitin A-52 residue ribosomal protein fusion product 1" [Danio rerio (taxid:7955)]

 Score = 612 (220.5 bits), Expect = 1.0e-59, P = 1.0e-59
 Identities = 117/128 (91%), Positives = 123/128 (96%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL  LA+KYN +KMICRKCYARLHPRAVNCRKKKCGH+N 
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLRQLAQKYNCEKMICRKCYARLHPRAVNCRKKKCGHTNN 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKLK 128

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

 Score = 607 (218.7 bits), Expect = 3.5e-59, P = 3.5e-59
 Identities = 117/128 (91%), Positives = 122/128 (95%)

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

Query:    61 IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
             IQKESTLHLVLRLRGGIIEPSL ALA KYN +K ICRKCYARL PRA NCRKKKCGH+NQ
Sbjct:    61 IQKESTLHLVLRLRGGIIEPSLKALASKYNCEKQICRKCYARLPPRATNCRKKKCGHTNQ 120

Query:   121 LRPKKKIK 128
             LRPKKK+K
Sbjct:   121 LRPKKKLK 128

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	0.8828	1.0	0.9922	N/A	no
P0CG84	UBI4P_NICSY	No assigned EC number	0.9870	0.6015	0.2042	N/A	no
P0CG85	UBI1P_NICSY	No assigned EC number	0.9870	0.6015	0.1684	N/A	no
P69315	UBIQP_LINUS	No assigned EC number	0.9870	0.6015	0.2524	N/A	no
P68205	RL40_OPHHA	No assigned EC number	0.9218	1.0	1.0	N/A	no
P63052	RL40_FELCA	No assigned EC number	0.9218	1.0	1.0	N/A	no
P63053	RL40_PIG	No assigned EC number	0.9218	1.0	1.0	yes	no
P63050	RL40_CANFA	No assigned EC number	0.9218	1.0	1.0	yes	no
Q42202	RL40B_ARATH	No assigned EC number	0.9921	1.0	1.0	yes	no
P14795	RL40_TRYCR	No assigned EC number	0.8281	1.0	1.0	N/A	no
P14794	RL40_DICDI	No assigned EC number	0.9133	0.9843	0.9843	yes	no
P0C275	RL40_PONPY	No assigned EC number	0.9218	1.0	1.0	N/A	no
P0C276	RL40_SHEEP	No assigned EC number	0.9218	1.0	1.0	N/A	no
P0CH09	RL402_YEAST	No assigned EC number	0.9062	1.0	1.0	yes	no
P0C273	RL40_MACFA	No assigned EC number	0.9218	1.0	1.0	N/A	no
P49636	RL40_NICSY	No assigned EC number	0.9921	1.0	1.0	N/A	no
P0CH06	RL401_SCHPO	No assigned EC number	0.9140	1.0	1.0	yes	no
P0CH05	UBI2P_PETCR	No assigned EC number	0.9870	0.6015	0.1681	N/A	no
P0CH04	UBI1P_PETCR	No assigned EC number	0.9870	0.6015	0.1681	N/A	no
P49632	RL40_CAEEL	No assigned EC number	0.8906	1.0	1.0	yes	no
P49633	RL40_ACACA	No assigned EC number	0.9140	1.0	1.0	N/A	no
P21899	RL40_TRYBB	No assigned EC number	0.8125	1.0	1.0	N/A	no
P40909	RL40_CRYNJ	No assigned EC number	0.8906	1.0	0.9922	yes	no
B9DHA6	RL40A_ARATH	No assigned EC number	0.9921	1.0	1.0	yes	no
P69201	RL40_LEIMA	No assigned EC number	0.8046	1.0	1.0	yes	no
P0CH08	RL401_YEAST	No assigned EC number	0.9062	1.0	1.0	yes	no
P69200	RL40_LEITA	No assigned EC number	0.7890	1.0	1.0	N/A	no
P69309	UBIQP_AVEFA	No assigned EC number	0.9870	0.6015	0.2524	N/A	no
P69322	UBIQP_PEA	No assigned EC number	0.9870	0.6015	0.2020	N/A	no
P63048	RL40_BOVIN	No assigned EC number	0.9218	1.0	1.0	yes	no
P33190	RL40_TETPY	No assigned EC number	0.8281	1.0	0.9922	N/A	no
P0CH10	RL403_CHLRE	No assigned EC number	0.9453	1.0	1.0	N/A	no
P0CH11	RL401_CHLRE	No assigned EC number	0.9453	1.0	1.0	N/A	no
P0CH34	RL40A_ORYSJ	No assigned EC number	0.9921	1.0	0.9922	yes	no
P0CH35	RL40B_ORYSJ	No assigned EC number	0.9921	1.0	0.9922	yes	no
P18101	RL40_DROME	No assigned EC number	0.9140	1.0	1.0	yes	no
P62987	RL40_HUMAN	No assigned EC number	0.9218	1.0	1.0	yes	no
P62986	RL40_RAT	No assigned EC number	0.9218	1.0	1.0	yes	no
P62984	RL40_MOUSE	No assigned EC number	0.9218	1.0	1.0	yes	no
P0CH07	RL402_SCHPO	No assigned EC number	0.9140	1.0	1.0	yes	no
P0DJ25	RL40_TETTS	No assigned EC number	0.8281	1.0	0.9922	N/A	no
P0C224	RL40_NEUCR	No assigned EC number	0.9140	1.0	1.0	N/A	no
P51423	RL40_BRARA	No assigned EC number	0.9921	1.0	1.0	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	128
cd01803	76	cd01803, Ubiquitin, Ubiquitin	4e-51
smart00213	72	smart00213, UBQ, Ubiquitin homologues	3e-32
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	6e-32
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	5e-30
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	3e-28
pfam01020	52	pfam01020, Ribosomal_L40e, Ribosomal L40e family	2e-24
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	3e-24
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	3e-20
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	6e-20
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	5e-17
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	4e-16
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	7e-16
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	4e-15
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	9e-15
cd01807	74	cd01807, GDX_N, ubiquitin-like domain of GDX	1e-12
cd01800	76	cd01800, SF3a120_C, Ubiquitin-like domain of Mamma	4e-12
cd01797	78	cd01797, NIRF_N, amino-terminal ubiquitin-like dom	4e-12
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	3e-11
cd01810	74	cd01810, ISG15_repeat2, ISG15 ubiquitin-like prote	5e-11
COG1552	50	COG1552, RPL40A, Ribosomal protein L40E [Translati	7e-11
COG5272	57	COG5272, UBI4, Ubiquitin [Posttranslational modifi	2e-10
cd01794	70	cd01794, DC_UbP_C, dendritic cell derived ubiquiti	2e-07
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	6e-07
cd01796	71	cd01796, DDI1_N, DNA damage inducible protein 1 ub	6e-07
PRK04136	48	PRK04136, rpl40e, 50S ribosomal protein L40e; Prov	7e-07
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	7e-07
cd01792	80	cd01792, ISG15_repeat1, ISG15 ubiquitin-like prote	8e-06
cd01804	78	cd01804, midnolin_N, Ubiquitin-like domain of midn	6e-05
cd01799	75	cd01799, Hoil1_N, Ubiquitin-like domain of HOIL1	5e-04
pfam13881	111	pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUM	6e-04
pfam13019	163	pfam13019, Telomere_Sde2, Telomere stability and s	0.004

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score =  156 bits (395), Expect = 4e-51
 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 =  108 bits (271), Expect = 3e-32
 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 =  107 bits (269), Expect = 6e-32
 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 =  102 bits (257), Expect = 5e-30
 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 = 98.1 bits (245), Expect = 3e-28
 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|110049 pfam01020, Ribosomal_L40e, Ribosomal L40e family

 Score = 87.7 bits (217), Expect = 2e-24
 Identities = 37/52 (71%), Positives = 44/52 (84%)

Query: 77  IIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK 128
           ++EP+L ALA+KYN +K +CR CYARL PRA NCRKKKCGHSN LR KKK+K
Sbjct: 1   VMEPTLAALAKKYNCEKKVCRDCYARLPPRATNCRKKKCGHSNSLRLKKKLK 52

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

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

 Score = 88.0 bits (218), Expect = 3e-24
 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 = 3e-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 = 78.0 bits (192), Expect = 6e-20
 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 = 69.7 bits (171), Expect = 5e-17
 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 = 67.3 bits (165), Expect = 4e-16
 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 = 66.7 bits (163), Expect = 7e-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 = 4e-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 = 63.6 bits (155), Expect = 9e-15
 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 = 58.8 bits (142), Expect = 1e-12
 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 = 57.1 bits (138), Expect = 4e-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 = 57.1 bits (138), Expect = 4e-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|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 58.8 bits (142), Expect = 3e-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|176405 cd01810, ISG15_repeat2, ISG15 ubiquitin-like protein, second repeat of 2

 Score = 54.1 bits (130), Expect = 5e-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|224469 COG1552, RPL40A, Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]

 Score = 53.3 bits (128), Expect = 7e-11
 Identities = 25/49 (51%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 80  PSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK 128
            +  A A K   +K ICR+CYAR  PRA  CR  KC     LRPKKK K
Sbjct: 1   MARFAEAEKRLFNKKICRRCYARNPPRATKCR--KC-GYKNLRPKKKEK 46

Length = 50

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

 Score = 52.5 bits (126), Expect = 2e-10
 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|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein

 Score = 44.8 bits (106), Expect = 2e-07
 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 = 43.6 bits (103), Expect = 6e-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|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like domain

 Score = 43.5 bits (103), Expect = 6e-07
 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|179746 PRK04136, rpl40e, 50S ribosomal protein L40e; Provisional

 Score = 43.0 bits (102), Expect = 7e-07
 Identities = 22/43 (51%), Positives = 25/43 (58%), Gaps = 5/43 (11%)

Query: 84  ALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKK 126
           A  R +N  K IC +C AR   RA  CR  KCG+ N LRPK K
Sbjct: 7   AEKRVFN--KKICMRCNARNPWRATKCR--KCGYKN-LRPKAK 44

Length = 48

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

 Score = 43.5 bits (103), Expect = 7e-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|176387 cd01792, ISG15_repeat1, ISG15 ubiquitin-like protein, first repeat of 2

 Score = 41.1 bits (96), Expect = 8e-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 = 38.6 bits (90), Expect = 6e-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|176394 cd01799, Hoil1_N, Ubiquitin-like domain of HOIL1

 Score = 36.0 bits (83), Expect = 5e-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|206052 pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUMO-like

 Score = 36.5 bits (85), Expect = 6e-04
 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|205200 pfam13019, Telomere_Sde2, Telomere stability and silencing

 Score = 35.2 bits (81), Expect = 0.004
 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	128
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	100.0
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.9
PTZ00044	76	ubiquitin; Provisional	99.9
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.89
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.89
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.89
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.89
PF01020	52	Ribosomal_L40e: Ribosomal L40e family; InterPro: I	99.88
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.88
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.88
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.87
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.87
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.86
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.84
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.84
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.83
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.83
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.83
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.82
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.82
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.79
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.79
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.78
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.78
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.78
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.73
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.72
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.72
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.7
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.66
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.62
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.61
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.61
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.6
PRK04136	48	rpl40e 50S ribosomal protein L40e; Provisional	99.58
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.56
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.56
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.52
COG1552	50	RPL40A Ribosomal protein L40E [Translation, riboso	99.48
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.46
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	99.37
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	99.36
PLN02560	308	enoyl-CoA reductase	99.3
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	99.29
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	99.21
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	99.21
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	99.17
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	99.11
PF13019	162	Telomere_Sde2: Telomere stability and silencing	99.06
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.94
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	98.89
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.77
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.7
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.65
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.6
KOG4495	110	consensus RNA polymerase II transcription elongati	98.4
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	98.35
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	98.26
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	98.21
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	98.19
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	98.09
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	98.08
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.93
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.86
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.85
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	97.83
COG5417	81	Uncharacterized small protein [Function unknown]	97.77
KOG1639	297	consensus Steroid reductase required for elongatio	97.72
KOG0013	231	consensus Uncharacterized conserved protein [Funct	97.65
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	97.62
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	97.61
PRK06437	67	hypothetical protein; Provisional	97.43
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	97.42
PRK06488	65	sulfur carrier protein ThiS; Validated	97.33
PRK08364	70	sulfur carrier protein ThiS; Provisional	97.17
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	97.11
PF12754	309	Blt1: Cell-cycle control medial ring component; In	96.97
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	96.94
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	96.88
PRK05863	65	sulfur carrier protein ThiS; Provisional	96.87
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	96.82
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	96.7
KOG4583	391	consensus Membrane-associated ER protein involved	96.69
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	96.62
PRK08053	66	sulfur carrier protein ThiS; Provisional	96.61
PRK05659	66	sulfur carrier protein ThiS; Validated	96.59
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	96.56
PRK07696	67	sulfur carrier protein ThiS; Provisional	96.38
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	96.33
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	96.32
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	96.3
PRK06944	65	sulfur carrier protein ThiS; Provisional	96.29
PF14453	57	ThiS-like: ThiS-like ubiquitin	96.27
PRK07440	70	hypothetical protein; Provisional	96.25
PRK06083	84	sulfur carrier protein ThiS; Provisional	96.23
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	96.19
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	96.06
KOG0012	380	consensus DNA damage inducible protein [Replicatio	96.05
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	96.0
TIGR01683	64	thiS thiamine biosynthesis protein ThiS. This mode	95.99
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	95.92
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	95.44
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	95.08
COG2104	68	ThiS Sulfur transfer protein involved in thiamine	95.07
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	94.45
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	94.4
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	94.14
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	94.1
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	93.68
cd05992	81	PB1 The PB1 domain is a modular domain mediating s	93.55
smart00455	70	RBD Raf-like Ras-binding domain.	93.52
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	93.5
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	93.33
PRK11130	81	moaD molybdopterin synthase small subunit; Provisi	93.11
cd06396	81	PB1_NBR1 The PB1 domain is an essential part of NB	92.93
KOG2982	418	consensus Uncharacterized conserved protein [Funct	92.84
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	92.32
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	92.19
PF14732	87	UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquiti	92.14
PF02017	78	CIDE-N: CIDE-N domain; InterPro: IPR003508 This do	92.01
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	92.01
cd06398	91	PB1_Joka2 The PB1 domain is present in the Nicotia	91.89
PTZ00380	121	microtubule-associated protein (MAP); Provisional	91.81
cd06410	97	PB1_UP2 Uncharacterized protein 2. The PB1 domain	91.42
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	90.81
PF08825	84	E2_bind: E2 binding domain; InterPro: IPR014929 E1	90.54
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	90.18
PF14533	213	USP7_C2: Ubiquitin-specific protease C-terminal; P	90.01
PF08337	539	Plexin_cytopl: Plexin cytoplasmic RasGAP domain; I	89.83
cd01766	82	Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-f	89.43
cd06397	82	PB1_UP1 Uncharacterized protein 1. The PB1 domain	89.42
smart00266	74	CAD Domains present in proteins implicated in post	89.2
PF02196	71	RBD: Raf-like Ras-binding domain; InterPro: IPR003	89.2
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.11
PF11069	98	DUF2870: Protein of unknown function (DUF2870); In	88.39
PF10407	73	Cytokin_check_N: Cdc14 phosphatase binding protein	88.17
cd01764	94	Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Rel	87.8
cd01787	85	GRB7_RA RA (RAS-associated like) domain of Grb7. G	87.42
PF02991	104	Atg8: Autophagy protein Atg8 ubiquitin like; Inter	87.35
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	87.24
PF03671	76	Ufm1: Ubiquitin fold modifier 1 protein; InterPro:	87.15
KOG2507	506	consensus Ubiquitin regulatory protein UBXD2, cont	86.57
KOG4572	1424	consensus Predicted DNA-binding transcription fact	85.72
PF06234	85	TmoB: Toluene-4-monooxygenase system protein B (Tm	85.18
PF00276	91	Ribosomal_L23: Ribosomal protein L23; InterPro: IP	84.98
cd01818	77	TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleo	84.71
cd01615	78	CIDE_N CIDE_N domain, found at the N-terminus of t	84.68
PF08783	74	DWNN: DWNN domain; InterPro: IPR014891 The ~75-res	84.64
cd01611	112	GABARAP Ubiquitin domain of GABA-receptor-associat	84.58
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	84.43
PRK01777	95	hypothetical protein; Validated	83.51
cd01817	73	RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS	83.1
PF00788	93	RA: Ras association (RalGDS/AF-6) domain; InterPro	82.89
PF12436	249	USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-sp	82.6
KOG3439	116	consensus Protein conjugation factor involved in a	82.55
cd01768	87	RA RA (Ras-associating) ubiquitin domain. The RA (	82.52
cd06539	78	CIDE_N_A CIDE_N domain of CIDE-A proteins. The CID	81.63
smart00144	108	PI3K_rbd PI3-kinase family, Ras-binding domain. Ce	81.46
cd01777	87	SNX27_RA Ubiquitin domain of SNX27 (sorting nexin	81.27
KOG0007	341	consensus Splicing factor 3a, subunit 1 [RNA proce	81.21
PRK05738	92	rplW 50S ribosomal protein L23; Reviewed	80.99
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	80.42

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

Probab=100.00  E-value=4.5e-44  Score=222.36  Aligned_cols=128  Identities=93%  Similarity=1.349  Sum_probs=126.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+++++.+.|++..++++|++||..+|+.|....|+|++.|+|+|+|+.|+|..||++|||+..+||+++.+++||.++|
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             hhHHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcCC
Q 033059           81 SLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK  128 (128)
Q Consensus        81 ~~~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~~  128 (128)
                      +++++|.|+++++.+||.||+|.++.|.|||++||||++.+||||++|
T Consensus        81 ~~aalAmK~~~D~lICRkCYAR~g~~Ae~CRK~~~~~~~~~rp~K~lK  128 (128)
T KOG0003|consen   81 SLAALAMKYNCDKLICRKCYARLGPRAENCRKKKCGHTNQLRPKKKLK  128 (128)
T ss_pred             hHHHHHHHhccchHHHHHHHHhcCcHHHHhHHhhccchhhcChhhhcC
Confidence            999999999999999999999999999999999999999999999987

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.90  E-value=2.1e-23  Score=125.40  Aligned_cols=74  Identities=41%  Similarity=0.618  Sum_probs=71.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+||..  +++.++|++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++++||
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            89999973  789999999999999999999999999999999999999999999999999999999999999987

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=99.90  E-value=4.4e-23  Score=124.41  Aligned_cols=76  Identities=50%  Similarity=0.822  Sum_probs=74.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|+++++++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999886

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.89  E-value=8.3e-23  Score=122.75  Aligned_cols=73  Identities=36%  Similarity=0.653  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||+++++|+++++.
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            8999999999999999999999999999999999999999999999999999999999999999999999875

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=99.89  E-value=1.3e-22  Score=122.07  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=74.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.+++++++||++||++|++.+++|+++|+|+|+|+.|+|+.+|++|++++|++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999987

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

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.89  E-value=1.1e-22  Score=129.23  Aligned_cols=76  Identities=51%  Similarity=0.763  Sum_probs=74.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|+|+++++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999987

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.89  E-value=2e-22  Score=121.25  Aligned_cols=76  Identities=55%  Similarity=0.965  Sum_probs=74.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999887

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.

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

Probab=99.88  E-value=6.8e-24  Score=115.57  Aligned_cols=51  Identities=86%  Similarity=1.398  Sum_probs=38.5

Q ss_pred             CCchhHHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcCC
Q 033059           78 IEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK  128 (128)
Q Consensus        78 ~~~~~~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~~  128 (128)
                      ++|++.++|+++++++++||.||+|++++|++||+++|||||+|||||++|
T Consensus         2 iePsl~~la~K~n~~k~ICrkCyarl~~~A~nCRKkkCGhsn~LR~Kkk~k   52 (52)
T PF01020_consen    2 IEPSLRALAQKYNCDKMICRKCYARLPPRATNCRKKKCGHSNNLRPKKKLK   52 (52)
T ss_dssp             --HHHHHHHHHHHTS-EEETTT--EE-TTSSS-TSSSCTS-S-EEE--SS-
T ss_pred             cChHHHHHHHHHcccceecccccCcCCCCccceecccCCCCcccCcccccC
Confidence            689999999999999999999999999999999999999999999999986

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.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.88  E-value=3.9e-22  Score=120.97  Aligned_cols=76  Identities=25%  Similarity=0.496  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|+...|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+ +|++|||++|++|+++..++||-
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~~~~   77 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVEAGL   77 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeeccccC
Confidence            89999999999999999999999999999999999999999999999999998 99999999999999999998883

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.

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

Probab=99.88  E-value=4.2e-22  Score=119.66  Aligned_cols=74  Identities=32%  Similarity=0.618  Sum_probs=71.9

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+++.|+++.+++++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||+++++|++++++.||
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            68999999999999999999999999999999999999999999999999999999999999999999999886

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=99.87  E-value=1.2e-21  Score=118.75  Aligned_cols=74  Identities=36%  Similarity=0.634  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCCE-EEEE-ecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGKT-ITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~~-~~i~-v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+|+|++.+|++ +.++ +++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||+++++|++++++.
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.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.87  E-value=1e-21  Score=117.52  Aligned_cols=71  Identities=24%  Similarity=0.378  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+|+|++..|+++.+++++++||++||++|++..++|+++|+|+|+|+.|+|+.+|++|||++|++|++.-
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.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.86  E-value=5.6e-21  Score=115.40  Aligned_cols=73  Identities=38%  Similarity=0.705  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCC--CCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~i--p~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++.+++++++||.+||++|++.+++  |+++|+|+|+|+.|+|+.+|++|||++|++|+++++.
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  9999999999999999999999999999999998864

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=99.84  E-value=1.8e-20  Score=111.66  Aligned_cols=72  Identities=44%  Similarity=0.704  Sum_probs=69.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|+..+|+++.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++||+++|++|+++.+
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=99.84  E-value=1.5e-20  Score=111.66  Aligned_cols=70  Identities=39%  Similarity=0.733  Sum_probs=67.3

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+..+|+++.+++++++||.+||++|++..|+|+++|+|+|+|++|+|+.+|++|||+++++|+++.|
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.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.83  E-value=1.8e-20  Score=111.40  Aligned_cols=68  Identities=37%  Similarity=0.581  Sum_probs=65.7

Q ss_pred             EEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         4 ~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      .|+..+|+++.+++++++||.+||++|++..|+|+++|+|+|+|++|+|+.+|++|+|+++++|+|++
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            57888999999999999999999999999999999999999999999999999999999999999986

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.

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

Probab=99.83  E-value=2.7e-20  Score=113.41  Aligned_cols=73  Identities=32%  Similarity=0.431  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEE--EeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L--~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|+...|+++.++++++.||.+||++|++..++|+++|+|  +|+|+.|+|+.+|++|||++|++|+++++.
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  899999999999999999999999999874

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.

>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=99.83  E-value=5e-20  Score=108.97  Aligned_cols=69  Identities=57%  Similarity=0.970  Sum_probs=65.6

Q ss_pred             EeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         6 k~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+.+|+++.++|++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++|||++|++|+++++++
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~~   69 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKPR   69 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESSE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEecC
Confidence            567899999999999999999999999999999999999999999999999999999999999998753

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=99.82  E-value=9.4e-20  Score=108.57  Aligned_cols=71  Identities=34%  Similarity=0.489  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++..|+ ..+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||++|++|+++++
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            68999999987 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=99.82  E-value=6.9e-20  Score=110.56  Aligned_cols=70  Identities=33%  Similarity=0.656  Sum_probs=67.1

Q ss_pred             CCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         8 ~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      ++|+++.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|+|++|++|+|+++++||.
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            4688999999999999999999999999999999999999999999999999999999999999999874

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.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.79  E-value=1.2e-18  Score=107.76  Aligned_cols=76  Identities=18%  Similarity=0.467  Sum_probs=74.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|.|++.+|+.+.+.|.+++|+..|++++++..|+|++.|+|+|+|+.|+++.|+++|++++|++|+++++++||
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            6899999999999999999999999999999999999999999999999999999999999999999999999997

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.

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

Probab=99.79  E-value=6.6e-19  Score=104.96  Aligned_cols=68  Identities=35%  Similarity=0.543  Sum_probs=63.8

Q ss_pred             EEEEeC-CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCC-CccccccccCCcEEEEE
Q 033059            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLV   70 (128)
Q Consensus         3 i~vk~~-~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~-~~L~~~gi~~g~~i~v~   70 (128)
                      |+|+.. +|+++.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+ .+|++|||++|++|++.
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            578888 899999999999999999999999999999999999999999887 68999999999999873

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.78  E-value=9.1e-19  Score=104.05  Aligned_cols=70  Identities=29%  Similarity=0.469  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+|+|++. |+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.
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            68999996 88999999999999999999999999999999999999999999999999999999998863

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).

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.78  E-value=1.3e-18  Score=104.39  Aligned_cols=69  Identities=23%  Similarity=0.427  Sum_probs=65.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe---CCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~---~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |.|.|++ +|+++.++|++++||++||++|++.+++|+++|+|+|   .|+.|.|+.+|++|+|++|+.|+|+
T Consensus         1 ~~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm   72 (74)
T cd01813           1 VPVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence            6789987 6789999999999999999999999999999999996   8999999999999999999999886

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=99.78  E-value=1.2e-18  Score=105.15  Aligned_cols=71  Identities=24%  Similarity=0.251  Sum_probs=63.2

Q ss_pred             CEEEEEeCCCCEEEE--EecCCCcHHHHHHHHHhhhC--CCCCCeEEEeCCEEcCCCCcccccc--ccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITL--EVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYN--IQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i--~v~~~~tV~~LK~~i~~~~~--ip~~~q~L~~~g~~L~d~~~L~~~g--i~~g~~i~v~~   71 (128)
                      |.|+||+++++.+.+  ++++++||.+||++|++..+  .|++.|+|+|+|++|+|+.+|++|.  +.++.+||++.
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            579999999988555  55899999999999999874  5579999999999999999999996  99999999974

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.

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

Probab=99.73  E-value=5.7e-18  Score=95.06  Aligned_cols=70  Identities=54%  Similarity=0.911  Sum_probs=67.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |.|.|++++|+.+.++++|+++|+.+|+.|+++.||||..|+|+|.|+.+.|+.+-++|.+.-||++|++
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

>smart00213 UBQ Ubiquitin homologues

Probab=99.72  E-value=2.8e-17  Score=95.33  Aligned_cols=64  Identities=61%  Similarity=0.864  Sum_probs=61.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES   65 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~   65 (128)
                      |+|+|++.+ ..+.++|++++||++||++|++.+++|+++|+|+|+|+.|.|+.+|++|||++|+
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=99.72  E-value=4.4e-18  Score=112.95  Aligned_cols=77  Identities=95%  Similarity=1.308  Sum_probs=75.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|+.+.+++..+++.+++||..+|+.|+...+||+++|+|+|.|+.|+|..+|+||+|+..++|+++++++||.
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~   77 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGA   77 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999994

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.70  E-value=7.8e-17  Score=122.53  Aligned_cols=74  Identities=30%  Similarity=0.588  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhC---CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~---ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+|+||+.+|+++.|+|++++||.+||++|+...|   +|+++|+|+|+|++|+|+.+|++|+|+++++|++++...
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~   77 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKP   77 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccC
Confidence            89999999999999999999999999999999998   999999999999999999999999999999999988753

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).

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.66  E-value=5.4e-16  Score=93.20  Aligned_cols=64  Identities=30%  Similarity=0.372  Sum_probs=58.4

Q ss_pred             eCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcC-CCCcccccccc-CCcEEEEEE
Q 033059            7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQ-KESTLHLVL   71 (128)
Q Consensus         7 ~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~-d~~~L~~~gi~-~g~~i~v~~   71 (128)
                      ...|.++.++|++++||++||++|++.+|+|++.|+| |+|+.|. |+.+|++||++ +|+++++.+
T Consensus         9 ~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           9 QSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             ccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            3457889999999999999999999999999999999 9999885 77999999998 889999875

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.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.62  E-value=3.2e-15  Score=87.73  Aligned_cols=67  Identities=67%  Similarity=0.992  Sum_probs=63.5

Q ss_pred             EEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         5 vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+..+|+.+.+.+++++||.+||++|+..+++|+++|+|+|+|+.|+|+.+|++|++.++++|+++.
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            6777899999999999999999999999999999999999999999999999999999999999864

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=99.61  E-value=9e-16  Score=91.52  Aligned_cols=55  Identities=33%  Similarity=0.549  Sum_probs=49.7

Q ss_pred             ecC-CCcHHHHHHHHHhhh--CCC-CCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059           17 VES-SDTIDNVKAKIQDKE--GIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        17 v~~-~~tV~~LK~~i~~~~--~ip-~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+| ++||.+||++|+++.  +++ +++|+|+|+|+.|+|+.+|++|||++|++|+++.
T Consensus        16 ~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          16 VSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             cCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            444 789999999999996  465 8999999999999999999999999999999875

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=99.61  E-value=5.6e-15  Score=87.95  Aligned_cols=71  Identities=34%  Similarity=0.633  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC-CCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~-~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+|+|++.+|+.+.+.|.+++++..|.+.+++..++|+ +.++|+|+|+.|+++.|+++||+++|++|+|++
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            68999999999999999999999999999999999999 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 ....

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

Probab=99.60  E-value=1.9e-15  Score=116.20  Aligned_cols=75  Identities=36%  Similarity=0.565  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ++|+||+.++ +++|.|..+.||.+||++|+..++++++.++|+|.|++|+|+.+|..|||++|.||||+++..-.
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~   90 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPR   90 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCC
Confidence            4699999887 89999999999999999999999999999999999999999999999999999999999986543

>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional

Probab=99.58  E-value=7.8e-16  Score=82.66  Aligned_cols=41  Identities=49%  Similarity=0.763  Sum_probs=37.7

Q ss_pred             HHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCc
Q 033059           83 MALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKK  126 (128)
Q Consensus        83 ~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~  126 (128)
                      -.+|.++.+++++|+.||+|++++|++||+  ||| ++||||++
T Consensus         4 ~~~A~k~~~~k~ICrkC~ARnp~~A~~CRK--Cg~-~~LRpKkk   44 (48)
T PRK04136          4 FEEAEKRVFNKKICMRCNARNPWRATKCRK--CGY-KNLRPKAK   44 (48)
T ss_pred             hHHHHHHhhcccchhcccCCCCcccccccc--CCC-CCcCcccc
Confidence            467899999999999999999999999996  997 69999986

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.56  E-value=1.2e-14  Score=90.14  Aligned_cols=62  Identities=27%  Similarity=0.314  Sum_probs=57.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcC-CCCccccccccCCcEEEEEEee
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~-d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      ...++|++++||.+||.+|.+.+++||++|+|+|+|+.|. |..||++|||.++++|.+.+..
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llide   78 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADE   78 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecC
Confidence            4678899999999999999999999999999999999985 5789999999999999998854

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=99.56  E-value=5.4e-15  Score=93.91  Aligned_cols=75  Identities=24%  Similarity=0.325  Sum_probs=63.4

Q ss_pred             EEEEEeCCCCEE-EEEecCCCcHHHHHHHHHhhh-----CCC--CCCeEEEeCCEEcCCCCcccccc------ccCCcEE
Q 033059            2 QIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKE-----GIP--PDQQRLIFAGKQLEDGRTLADYN------IQKESTL   67 (128)
Q Consensus         2 ~i~vk~~~g~~~-~i~v~~~~tV~~LK~~i~~~~-----~ip--~~~q~L~~~g~~L~d~~~L~~~g------i~~g~~i   67 (128)
                      .|.+|..+|..+ .+.+++++||++||++|++..     ++|  +++|+|+|+|++|+|+.||++|+      +....|+
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            567787888654 477889999999999999655     344  99999999999999999999999      6777899


Q ss_pred             EEEEeecCC
Q 033059           68 HLVLRLRGG   76 (128)
Q Consensus        68 ~v~~~~~gg   76 (128)
                      ||+++....
T Consensus        86 Hvvlr~~~~   94 (113)
T cd01814          86 HVVVQPPLA   94 (113)
T ss_pred             EEEecCCCC
Confidence            999987554

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=99.52  E-value=3.5e-14  Score=104.59  Aligned_cols=74  Identities=38%  Similarity=0.657  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhC--CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~--ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+|+||++.+.+|.+++.|+.||.++|..|+...|  .|++.|+|+|+|++|.|+.++.+|+|.++..|.|++...
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            89999999999999999999999999999999998  999999999999999999999999999999999988765

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

Probab=99.48  E-value=1.5e-14  Score=77.75  Aligned_cols=44  Identities=59%  Similarity=0.952  Sum_probs=39.3

Q ss_pred             hHHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcCC
Q 033059           82 LMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK  128 (128)
Q Consensus        82 ~~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~~  128 (128)
                      ..+.+.+....+.+|+.||+++|++|++||+  || +++||||++.|
T Consensus         3 ~~~~a~~r~~~kkIC~rC~Arnp~~A~kCRk--C~-~k~LR~K~kek   46 (50)
T COG1552           3 RFAEAEKRLFNKKICRRCYARNPPRATKCRK--CG-YKNLRPKKKEK   46 (50)
T ss_pred             hHHHHHHHHhhHHHHHHhcCCCCcchhHHhh--cc-CCCcccccccc
Confidence            4467888899999999999999999999997  95 88999999863

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

Probab=99.46  E-value=7.2e-13  Score=81.27  Aligned_cols=70  Identities=21%  Similarity=0.379  Sum_probs=58.8

Q ss_pred             EEEEEeCC-CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-eCCE-----Ec-CCCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLT-GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGK-----QL-EDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~-g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~~g~-----~L-~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      .|.|.+.. ....+..+++++||.+||++++..+|+||+.|+|. |.|+     .| +|+.+|++||+++|.+|||+-
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            56676543 34456679999999999999999999999999995 8887     46 678899999999999999863

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=99.37  E-value=4.6e-12  Score=78.14  Aligned_cols=69  Identities=28%  Similarity=0.571  Sum_probs=57.0

Q ss_pred             EEEEEeCCC--CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC----C---EEc-CCCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----G---KQL-EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g--~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~----g---~~L-~d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|+|.+...  ...+..+++++||++||.+|+..+|+|++.|+|.+.    +   ..+ +|+.+|.+||+++|.+|+|.
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~   81 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVV   81 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEE
Confidence            577776654  488899999999999999999999999999999865    2   134 57889999999999999986

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=99.36  E-value=4.5e-12  Score=80.41  Aligned_cols=80  Identities=30%  Similarity=0.453  Sum_probs=67.0

Q ss_pred             CEEEEEeCCC-CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccc-------cCCcEEEEEEe
Q 033059            1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-------QKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g-~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi-------~~g~~i~v~~~   72 (128)
                      |.+++..... .++.++..++.||.+||+.|+.....||++|+|+..+.+|+|++||++||+       ++.++|-+.+|
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            4556655443 457789999999999999999999999999999977789999999999999       77889999988


Q ss_pred             ecCCCCCc
Q 033059           73 LRGGIIEP   80 (128)
Q Consensus        73 ~~gg~~~~   80 (128)
                      ...|.|++
T Consensus        81 ~~d~~fE~   88 (119)
T cd01788          81 SSDDTFEP   88 (119)
T ss_pred             cCCCCccc
Confidence            76665443

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.

>PLN02560 enoyl-CoA reductase

Probab=99.30  E-value=1.2e-11  Score=92.17  Aligned_cols=75  Identities=31%  Similarity=0.514  Sum_probs=64.4

Q ss_pred             CEEEEEeCCCCEE---EEEecCCCcHHHHHHHHHhhhCC-CCCCeEEEeC---C----EEcCCCCccccccccCCcEEEE
Q 033059            1 MQIFVKTLTGKTI---TLEVESSDTIDNVKAKIQDKEGI-PPDQQRLIFA---G----KQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         1 m~i~vk~~~g~~~---~i~v~~~~tV~~LK~~i~~~~~i-p~~~q~L~~~---g----~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      |+|+|+..+|+.+   ++++++++||++||++|++..++ ++++|+|.+.   |    ..|+|+++|+++|+++|++|+ 
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy-   79 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVV-   79 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEE-
Confidence            8999998888886   79999999999999999999886 8999999973   3    378999999999999999864 


Q ss_pred             EEeecCCC
Q 033059           70 VLRLRGGI   77 (128)
Q Consensus        70 ~~~~~gg~   77 (128)
                       ++-.|-.
T Consensus        80 -~kDLGpQ   86 (308)
T PLN02560         80 -FKDLGPQ   86 (308)
T ss_pred             -EEeCCCc
Confidence             4666553

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

Probab=99.29  E-value=3.7e-11  Score=77.16  Aligned_cols=75  Identities=29%  Similarity=0.481  Sum_probs=56.2

Q ss_pred             EEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhC-------CCCCCeEEEeCCEEcCCCCccccccccCCc------EE
Q 033059            2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEG-------IPPDQQRLIFAGKQLEDGRTLADYNIQKES------TL   67 (128)
Q Consensus         2 ~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~-------ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~------~i   67 (128)
                      .|.++..+|. .-.+.+++++||.+||+.|...+.       ..++++||+|.|+.|+|+.+|+++.+..|+      ++
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            5677777998 788999999999999999987652       234679999999999999999999987766      57


Q ss_pred             EEEEeecCC
Q 033059           68 HLVLRLRGG   76 (128)
Q Consensus        68 ~v~~~~~gg   76 (128)
                      ||+++....
T Consensus        84 Hlvvrp~~~   92 (111)
T PF13881_consen   84 HLVVRPNAP   92 (111)
T ss_dssp             EEEE-SSSS
T ss_pred             EEEecCCCC
Confidence            777765543

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

Probab=99.21  E-value=2.9e-11  Score=99.73  Aligned_cols=76  Identities=33%  Similarity=0.552  Sum_probs=71.3

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~   78 (128)
                      .|.||+++.++.+|.|...+||.+||.+|.+..+|+.+.|||+|.|++|.|++++.+|+| +|-+|||+-|.+-+.+
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverppp~~~   79 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERPPPQTH   79 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeeccCCCCcc
Confidence            478999999999999999999999999999999999999999999999999999999999 9999999998665543

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

Probab=99.21  E-value=2.6e-10  Score=66.76  Aligned_cols=73  Identities=84%  Similarity=1.145  Sum_probs=68.0

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      +++....|+++.+.+.+..+|..+|.+|+...++|+..|++.+.|+.|.|+.+|.+|+|..++++++..++.+
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~~   74 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLRG   74 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecCC
Confidence            5667788999999999999999999999999999999999999999999999999999999999999987753

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=99.17  E-value=1.3e-10  Score=70.07  Aligned_cols=68  Identities=29%  Similarity=0.388  Sum_probs=53.8

Q ss_pred             EEEEEeCCCCEE-EEEe-cCCCcHHHHHHHHHhhhC-CCCCCeEEE--eCCEEcCCCCccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTI-TLEV-ESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~-~i~v-~~~~tV~~LK~~i~~~~~-ip~~~q~L~--~~g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      +|.++..+.+.+ .+++ +++.||.+||..|++..+ +++++|+|.  +.|+.|.|+.+|++||+.+|++|+|
T Consensus         2 ~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801           2 EILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             eeeccccCcCceeecccCCCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            456665541332 2344 478999999999999876 589999885  8899999999999999999999876

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.

>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=99.11  E-value=1.8e-10  Score=69.96  Aligned_cols=69  Identities=29%  Similarity=0.434  Sum_probs=44.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC---EEc--CCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQL--EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g---~~L--~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |-|.|++.+| .+.|++++++|+.+|+++|++.+++|.+.|.|..+.   ..+  .++.+|+++||+.|+.|++.
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            5688999887 688999999999999999999999999998885322   244  46889999999999999874

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.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=99.06  E-value=2.2e-09  Score=72.63  Aligned_cols=103  Identities=27%  Similarity=0.435  Sum_probs=78.0

Q ss_pred             CEEEEEeCCC----CEEEEEecCCCcHHHHHHHHHhhhCCCCCCe-EEEe-CCEEc--CCCCccccccccCC----cEEE
Q 033059            1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIF-AGKQL--EDGRTLADYNIQKE----STLH   68 (128)
Q Consensus         1 m~i~vk~~~g----~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q-~L~~-~g~~L--~d~~~L~~~gi~~g----~~i~   68 (128)
                      |+|+|.+.+|    .++.+.+++++||.+|+..|.+..++++..+ .|.+ .++.|  .++..++++.-.+.    -++.
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    5888999999999999999999999998874 3443 34444  45666666654333    4788


Q ss_pred             EEEeecCCC--CCchhHHHHHhh----ccchhhhhhhhccc
Q 033059           69 LVLRLRGGI--IEPSLMALARKY----NQDKMICRKCYARL  103 (128)
Q Consensus        69 v~~~~~gg~--~~~~~~~~a~k~----~~~k~~Cr~c~~r~  103 (128)
                      +.++++||+  |...+++.+.+.    ..++..|||..+|=
T Consensus        81 l~~rl~GGKGGFGs~Lr~~g~~~s~~k~~n~dscRdL~GRR  121 (162)
T PF13019_consen   81 LSLRLRGGKGGFGSQLRAAGGRMSSKKTTNFDSCRDLSGRR  121 (162)
T ss_pred             EEEeccCCCccHHHHHHHHHHHhhcccCCCcccccCCCCcC
Confidence            999999995  778888765444    44456899988653

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.94  E-value=1e-08  Score=57.41  Aligned_cols=66  Identities=45%  Similarity=0.659  Sum_probs=59.9

Q ss_pred             EeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         6 k~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +..++....+.+.+++|+.+|++.|.+.++++++.+.|.++|..+.+...+.++++.++++|++..
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.

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

Probab=98.89  E-value=2.6e-08  Score=61.91  Aligned_cols=75  Identities=17%  Similarity=0.442  Sum_probs=69.7

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ++.|+..++.+..+.|..++++..|+...++..|++.+.++++|+|+.+.+..|-++++.++|+.|.++..+.||
T Consensus        22 ~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q~gG   96 (99)
T KOG1769|consen   22 NLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQTGG   96 (99)
T ss_pred             EEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeecccC
Confidence            566777667788899999999999999999999999999999999999999999999999999999999998888

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

Probab=98.77  E-value=3.1e-09  Score=60.83  Aligned_cols=69  Identities=26%  Similarity=0.398  Sum_probs=61.6

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      ++.+...-|+...+...+++||+++|..|++++|..++.+.|--.+..++|.-+|++|.|.+|..+.+.
T Consensus         3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             eehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            456666668899999999999999999999999999999988877778899999999999999888775

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

Probab=98.70  E-value=1.7e-07  Score=55.23  Aligned_cols=70  Identities=29%  Similarity=0.407  Sum_probs=60.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC---C--EEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA---G--KQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~---g--~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      ++|+|+..++..+.+.|+|..+|..+|++|....+++- .|+|.|.   |  ..|.+..+|++|||-....|-++-
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lle   75 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLE   75 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccccccccccHhhhcceeccEEEEEe
Confidence            58999998888999999999999999999999999875 8999873   3  367899999999998887776654

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=98.65  E-value=8.3e-08  Score=74.12  Aligned_cols=72  Identities=24%  Similarity=0.408  Sum_probs=65.1

Q ss_pred             EEEEEeCCCCEEEEE-ecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            2 QIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~-v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      .|.|++ .|+.+.++ ++.++|+..||+++...+|++|++|++++.|..+.|+-.+..++|++|.+|+++-...
T Consensus         5 ~v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e   77 (473)
T KOG1872|consen    5 TVIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAE   77 (473)
T ss_pred             eEeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeecccc
Confidence            477776 57888887 9999999999999999999999999999999999999899999999999999886543

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

Probab=98.60  E-value=1.1e-07  Score=70.48  Aligned_cols=70  Identities=30%  Similarity=0.599  Sum_probs=59.9

Q ss_pred             CEEEEEeC---CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTL---TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~---~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |.+.|+..   ....+.++|+.+.+|.+||+.++...|+|+++.+++|.|+.|.|+.++..+.+..-+.++++
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            66777654   12357889999999999999999999999999999999999999999998777777777766

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

Probab=98.40  E-value=4.4e-07  Score=56.01  Aligned_cols=62  Identities=29%  Similarity=0.435  Sum_probs=49.9

Q ss_pred             CEEEEEeCCC-CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe-CC-EEcCCCCcccccccc
Q 033059            1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AG-KQLEDGRTLADYNIQ   62 (128)
Q Consensus         1 m~i~vk~~~g-~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~-~g-~~L~d~~~L~~~gi~   62 (128)
                      |.++++.... .++.++..++.||.+||.+++..+.-|++.|+|+. .. +.|+|.++|+++|..
T Consensus         1 ~~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    1 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGFT   65 (110)
T ss_pred             CceeeeeeecceeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhcccc
Confidence            3445544433 45778899999999999999999999999999986 43 578999999999763

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

Probab=98.35  E-value=1.6e-06  Score=52.37  Aligned_cols=68  Identities=24%  Similarity=0.405  Sum_probs=48.9

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC------CeEEE-eCCEEcCCCCccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD------QQRLI-FAGKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~------~q~L~-~~g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      .|+|...+|+.+.+.++.+.+|.+|...|.+..+.+..      ...|. -+|..|+++.+|+++||.+|+.+.+
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            46676655688999999999999999999998876432      24555 6789999999999999999999976

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.

>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=98.26  E-value=1.9e-05  Score=47.78  Aligned_cols=68  Identities=24%  Similarity=0.361  Sum_probs=58.1

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEE--eCCEEcCCC--CccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--FAGKQLEDG--RTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~--~~g~~L~d~--~~L~~~gi~~g~~i~v   69 (128)
                      .|.||.++|..+...+.+++||.+|.+.|......+... ..|+  |..+.+.++  .+|++.|+.+.++|+|
T Consensus         8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            588999999999999999999999999998887766654 7776  677888543  6999999999999876

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=98.21  E-value=2e-06  Score=52.54  Aligned_cols=76  Identities=17%  Similarity=0.371  Sum_probs=68.2

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      .+.|...+|.++.+.|..+++...|....+...|-..+..|++|+|+.++.++|-.+++.++++.|.++....||.
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            3556566788899999999999999999999999999999999999999999999999999999998887777773

>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=98.19  E-value=1.2e-05  Score=46.77  Aligned_cols=63  Identities=19%  Similarity=0.252  Sum_probs=46.8

Q ss_pred             eCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEE
Q 033059            7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         7 ~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      ..+++.+.+.+.|++++.++-++...++++++++-.|.|+++.|+-+.++.-.|+.+|+.+.+
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            457889999999999999999999999999999999999999999999999999999999875

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.

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

Probab=98.09  E-value=1.2e-05  Score=50.46  Aligned_cols=58  Identities=21%  Similarity=0.352  Sum_probs=44.4

Q ss_pred             EEEEEeCCC-CEEEEEec--CCCcHHHHHHHHHhhhC--CCCCCeEEEeCCEEcCCCCccccc
Q 033059            2 QIFVKTLTG-KTITLEVE--SSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADY   59 (128)
Q Consensus         2 ~i~vk~~~g-~~~~i~v~--~~~tV~~LK~~i~~~~~--ip~~~q~L~~~g~~L~d~~~L~~~   59 (128)
                      .|+|+..++ ..+.++++  .+.||..||+.|.+...  ..-.+++|+|+|+.|.|...|+..
T Consensus         2 ~l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen    2 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhh
Confidence            366776652 34666666  78999999999999873  444678999999999998877654

They contain a characteristic GFDRL sequence motif.

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=98.08  E-value=4.4e-05  Score=46.06  Aligned_cols=68  Identities=22%  Similarity=0.260  Sum_probs=56.2

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcCC---CCccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~d---~~~L~~~gi~~g~~i~v   69 (128)
                      +|.||.++|..+...+..++||.+|.+.|....+.......|+  |..+.+.+   +.+|.+.|+.+.+++.|
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            5889999999999999999999999999966666666667775  66777753   57999999988888765

Present in FAF1 and Shp1p.

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.93  E-value=0.00016  Score=43.67  Aligned_cols=67  Identities=16%  Similarity=0.324  Sum_probs=55.1

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcCC---CCccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~d---~~~L~~~gi~~g~~i~v   69 (128)
                      .|.||.++|..+...++.++||.+|.+.|....+-+ ....|+  |-.+.+.+   +.+|.+.|+.+.++|.|
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            588999999999999999999999999998765432 456665  77888853   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.

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.86  E-value=0.0002  Score=43.27  Aligned_cols=66  Identities=21%  Similarity=0.313  Sum_probs=52.6

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCC-CCCCeEEE--eCCEEcC-CCCccccccccCCcEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI-PPDQQRLI--FAGKQLE-DGRTLADYNIQKESTL   67 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~i-p~~~q~L~--~~g~~L~-d~~~L~~~gi~~g~~i   67 (128)
                      +|.||..+|+.+...+..++||.+|.+.|....+- ......|.  |-.+.|. ++.||.|.|+.+...+
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            58899999999999999999999999999876543 23456665  7778785 4789999999864433

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.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.85  E-value=0.00022  Score=42.63  Aligned_cols=66  Identities=15%  Similarity=0.265  Sum_probs=51.8

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcC---CCCccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~---d~~~L~~~gi~~g~~i~v   69 (128)
                      .|.||.++|..+...+..++||.+|.+.|.....- .....|+  |-.+.+.   ++.+|.+.|+.+ +.+.+
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            58899999999999999999999999999876433 4556665  6677774   478999999995 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.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=97.83  E-value=0.00031  Score=42.72  Aligned_cols=69  Identities=16%  Similarity=0.316  Sum_probs=58.9

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcC---CCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~---d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +|.||.++|+...-.+..+.++.+|...+.. .+.+++...|+  |--+.+.   .+.||.+.|+.+.++|.|--
T Consensus         7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq~   80 (82)
T cd01773           7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE   80 (82)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEec
Confidence            5899999999999999999999999999988 57788888887  6677763   35799999999999997753

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.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.77  E-value=0.00025  Score=41.90  Aligned_cols=64  Identities=19%  Similarity=0.254  Sum_probs=53.7

Q ss_pred             EeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC-----CCeEEEeCCEEcCCCCccccccccCCcEEEE
Q 033059            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-----DQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         6 k~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~-----~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      +..+|.++.+.++...++..|-..+.+...+..     ..++..-+++.|.++..|.+|+|.+|+.+.+
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            555789999999999999999888877665432     3468889999999999999999999999875

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

Probab=97.72  E-value=9.4e-05  Score=53.42  Aligned_cols=75  Identities=27%  Similarity=0.335  Sum_probs=54.5

Q ss_pred             CEEEEEeCCCC-EE-EEEecCCCcHHHHHHHHHhh-hCCCCCCeE----EEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGK-TI-TLEVESSDTIDNVKAKIQDK-EGIPPDQQR----LIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~-~~-~i~v~~~~tV~~LK~~i~~~-~~ip~~~q~----L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |.|++.+.++. .. ....+...|+.|+++.+... ..+.+.+++    +.-+|+.|-|+.+|++|+..+|++|.  ++-
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 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIY--VKD   78 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEE--Eec
Confidence            78899887653 22 35667789999999877655 456664443    34579999999999999999997774  555


Q ss_pred             cCCC
Q 033059           74 RGGI   77 (128)
Q Consensus        74 ~gg~   77 (128)
                      .|..
T Consensus        79 LGpQ   82 (297)
T KOG1639|consen   79 LGPQ   82 (297)
T ss_pred             cCCc
Confidence            5553

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.65  E-value=0.00012  Score=51.51  Aligned_cols=65  Identities=28%  Similarity=0.431  Sum_probs=57.5

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      .++.+.+.+...+|+.++|..+.+..++++-.|+++|+|.+|.|...|.+++|+.|....|.+..
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqviV  219 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVIV  219 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEEEe
Confidence            35567888888999999999999999999999999999999999999999999999766655544

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=97.62  E-value=0.00091  Score=40.48  Aligned_cols=68  Identities=21%  Similarity=0.329  Sum_probs=57.5

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcC---CCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~---d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|.||.++|....-.+..++++++|...|... +.++...+|+  |--+.+.   .+.+|.+.|+.+..+|.|-
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            68899999999999999999999999999775 7777788887  6677773   3579999999999888764

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=97.61  E-value=0.00095  Score=40.86  Aligned_cols=68  Identities=12%  Similarity=0.183  Sum_probs=54.9

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe--CCEEcC--------CCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLE--------DGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~--~g~~L~--------d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|.||.++|+.+.-.+..++||++|...|... +..++...|+.  --+.+.        .+.||.+.|+.+..++.|.
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 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFSL-KETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFVQ   83 (85)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhC-CCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEEe
Confidence            68899999999999999999999999999653 44567788874  446774        3679999999988887653

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.

>PRK06437 hypothetical protein; Provisional

Probab=97.43  E-value=0.0026  Score=37.14  Aligned_cols=59  Identities=20%  Similarity=0.404  Sum_probs=46.6

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +++...+++++..||.+|-+++    +++++...+..+|..+.     .++-+++|+.|.++.-.-||
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~L----gi~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~~V~GG   67 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKDL----GLDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILEVFSGG   67 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECC-----CceEcCCCCEEEEEecccCC
Confidence            4566788888889999987654    88889998999999997     45567789999987655444

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

Probab=97.42  E-value=0.00067  Score=47.79  Aligned_cols=71  Identities=15%  Similarity=0.297  Sum_probs=55.2

Q ss_pred             EEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-eCC-----EEcC-CCCccccccccCCcEEEEEEe
Q 033059            2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAG-----KQLE-DGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         2 ~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~~g-----~~L~-d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .|.|.+.... ..+..+++++||.+||.+++..+|.+++.|.|. |.|     ..|+ ++..|..|+..+|-.||++=.
T Consensus         3 ~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihviD~   81 (234)
T KOG3206|consen    3 RVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVIDS   81 (234)
T ss_pred             EEEEecccccchhhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEEec
Confidence            4566543222 244568899999999999999999999999986 655     2454 577999999999999998643

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=97.33  E-value=0.0029  Score=36.54  Aligned_cols=65  Identities=18%  Similarity=0.389  Sum_probs=46.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+.+.+  + ..||.+|.+.+    +++++...+-.|++.+. ...-++.-+++|+.|.++.-..||
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            67777   5666665  3 46899988765    66676677789999885 223345567899999988766665

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=97.17  E-value=0.0065  Score=35.67  Aligned_cols=56  Identities=13%  Similarity=0.238  Sum_probs=43.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ...+++++..||.+|-+++    +++++...+..||+.+..     +.-+++|+.|.++.-..||
T Consensus        15 ~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii~~V~GG   70 (70)
T PRK08364         15 EKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALE-----DDPVKDGDYVEVIPVVSGG   70 (70)
T ss_pred             ceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCC-----CcCcCCCCEEEEEccccCC
Confidence            5678888889999998766    677777788899999854     4456789999987665554

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

Probab=97.11  E-value=0.0072  Score=37.15  Aligned_cols=66  Identities=20%  Similarity=0.244  Sum_probs=47.0

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe--C--C-EEc-CCCCccccccccCCcEEEEEEeecCCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--A--G-KQL-EDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~--~--g-~~L-~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      ..+...++..+||..+...+.+.+.| ..+.||.-  .  + ..| +.+.||.+.||.+|.+|.+-.+...|.
T Consensus        14 ~~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn~DGt   85 (88)
T PF14836_consen   14 SVLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERNEDGT   85 (88)
T ss_dssp             EEEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--TTS-
T ss_pred             cHhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeeccCCC
Confidence            35677899999999999999999999 67778863  2  2 256 456799999999999999998887774

>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=96.97  E-value=0.00019  Score=53.43  Aligned_cols=76  Identities=18%  Similarity=0.428  Sum_probs=0.0

Q ss_pred             EEEEEeCCCCEEEEEec---C--CCcHHHHHHHHHh----------hhCCCCCCeE-----EEeCCEEcCCCCccccccc
Q 033059            2 QIFVKTLTGKTITLEVE---S--SDTIDNVKAKIQD----------KEGIPPDQQR-----LIFAGKQLEDGRTLADYNI   61 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~---~--~~tV~~LK~~i~~----------~~~ip~~~q~-----L~~~g~~L~d~~~L~~~gi   61 (128)
                      .|++++..+..+.+.++   +  +.||.+||..+++          ..++|.+.++     |+|+-+++.|.++|.+..-
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            45666665555544433   3  5789999999999          8899999998     9999999999999888754


Q ss_pred             c-------CCcEEEEEEeecCCC
Q 033059           62 Q-------KESTLHLVLRLRGGI   77 (128)
Q Consensus        62 ~-------~g~~i~v~~~~~gg~   77 (128)
                      .       .+.+|.+.+...||.
T Consensus       160 ~~~~~l~~~~~~vE~gvMVlGGa  182 (309)
T PF12754_consen  160 DSESRLLSGGKEVEFGVMVLGGA  182 (309)
T ss_dssp             -----------------------
T ss_pred             cccchhccCCceEEEEEEEECCc
Confidence            3       477888888888885

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.

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=96.94  E-value=0.0067  Score=36.07  Aligned_cols=60  Identities=13%  Similarity=0.228  Sum_probs=45.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCC----CCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGI----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~i----p~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ...+++++..||.+|.+.+...++-    ......+..||+....     +.-+++|+.|.++....||
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            4667787789999999999887532    2345667789998873     4557889999998777665

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.

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=96.88  E-value=0.0064  Score=36.61  Aligned_cols=71  Identities=18%  Similarity=0.268  Sum_probs=48.4

Q ss_pred             CEEEEEeCC------C-CEEEEEecCCCcHHHHHHHHHhhhC-CCC--CCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-IPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~------g-~~~~i~v~~~~tV~~LK~~i~~~~~-ip~--~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |+|.|+...      | ....++++...||.+|.+.+..... +..  ....+..||+...++     .-+++|++|.++
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~~~-----~~l~dgDeVai~   76 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTTES-----AALKDGDELAII   76 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcCCC-----cCcCCCCEEEEe
Confidence            567777653      3 4567788888999999999976541 111  223466788876543     346789999988


Q ss_pred             EeecCC
Q 033059           71 LRLRGG   76 (128)
Q Consensus        71 ~~~~gg   76 (128)
                      ....||
T Consensus        77 PpvsGG   82 (82)
T PLN02799         77 PPISGG   82 (82)
T ss_pred             CCCCCC
Confidence            766665

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=96.87  E-value=0.009  Score=34.53  Aligned_cols=64  Identities=19%  Similarity=0.314  Sum_probs=46.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCC-CCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d-~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+.  .++++..|+.+|-+.    .++++...-+.+++..+.. ++.  .+ +++|+.|.++.-..||
T Consensus         1 m~i~v---NG~~--~~~~~~~tl~~ll~~----l~~~~~~vav~~N~~iv~r~~~~--~~-L~~gD~ieIv~~VgGG   65 (65)
T PRK05863          1 MIVVV---NEEQ--VEVDEQTTVAALLDS----LGFPEKGIAVAVDWSVLPRSDWA--TK-LRDGARLEVVTAVQGG   65 (65)
T ss_pred             CEEEE---CCEE--EEcCCCCcHHHHHHH----cCCCCCcEEEEECCcCcChhHhh--hh-cCCCCEEEEEeeccCC
Confidence            66766   4654  444567888888665    4888999999999998853 333  35 8999999987665554

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

Probab=96.82  E-value=0.0028  Score=37.96  Aligned_cols=57  Identities=23%  Similarity=0.312  Sum_probs=46.4

Q ss_pred             ecCCCcHHHHHHHHHhhhC-CCCCCeEEEeCCEEcCCCCccccc-cccCCcEEEEEEee
Q 033059           17 VESSDTIDNVKAKIQDKEG-IPPDQQRLIFAGKQLEDGRTLADY-NIQKESTLHLVLRL   73 (128)
Q Consensus        17 v~~~~tV~~LK~~i~~~~~-ip~~~q~L~~~g~~L~d~~~L~~~-gi~~g~~i~v~~~~   73 (128)
                      |.++++|.++++.+..... ..-....|.++|..|+|...|+++ |+++|.++.++..+
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            5678999999999987644 344567899999999998889888 58889999988543

>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=96.70  E-value=0.0098  Score=36.45  Aligned_cols=44  Identities=14%  Similarity=0.278  Sum_probs=38.1

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC---CCeEEEe
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP---DQQRLIF   45 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~---~~q~L~~   45 (128)
                      ...++.+.|+.+.+.+.+++.+.+|++.|++++|++.   +...|.|
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            3567888999999999999999999999999999886   4666666

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=96.69  E-value=0.00076  Score=50.71  Aligned_cols=60  Identities=23%  Similarity=0.398  Sum_probs=45.8

Q ss_pred             EEEEEeCCCC--EEEEEecCCCcHHHHHHHHHhhhCC-C-CCCeEEEeCCEEcCCCCccccccc
Q 033059            2 QIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGI-P-PDQQRLIFAGKQLEDGRTLADYNI   61 (128)
Q Consensus         2 ~i~vk~~~g~--~~~i~v~~~~tV~~LK~~i~~~~~i-p-~~~q~L~~~g~~L~d~~~L~~~gi   61 (128)
                      .++|+..+.+  ...|..+..+||++||..++..+-- | +.+|||+|.|+.|.|..-|.|.=+
T Consensus        11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~lr   74 (391)
T KOG4583|consen   11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDWLR   74 (391)
T ss_pred             EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHHHH
Confidence            4677776643  3556666789999999999887642 2 367999999999999888877643

>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=96.62  E-value=0.012  Score=35.49  Aligned_cols=38  Identities=18%  Similarity=0.344  Sum_probs=35.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEE
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ   49 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~   49 (128)
                      ++.|.+++..+..+|.++|.++.++|++.+.|.|....
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~   49 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEA   49 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCC
Confidence            88999999999999999999999999999999997654

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=96.61  E-value=0.039  Score=31.89  Aligned_cols=66  Identities=15%  Similarity=0.258  Sum_probs=45.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+.  +++++..||.+|-+.+    +++.....+-.++..+..+ .-++.-+++|+.|.++.-..||
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---NDQP--MQCAAGQTVHELLEQL----NQLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQVIAGG   66 (66)
T ss_pred             CEEEE---CCeE--EEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEEEccCC
Confidence            67777   4554  4456678999988654    5556667888999988521 2233347899999988766665

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=96.59  E-value=0.036  Score=31.82  Aligned_cols=66  Identities=20%  Similarity=0.387  Sum_probs=46.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+.  +++++..||.+|-+.    .++++....+.++|..+.-+. -.+.-+++|+.|.++.-..||
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----EGLAGRRVAVEVNGEIVPRSQ-HASTALREGDVVEIVHALGGG   66 (66)
T ss_pred             CEEEE---CCeE--EEcCCCCCHHHHHHh----cCCCCCeEEEEECCeEeCHHH-cCcccCCCCCEEEEEEEecCC
Confidence            66666   5654  456677898888754    478888888889998885322 223346889999988766554

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

Probab=96.56  E-value=0.031  Score=33.18  Aligned_cols=67  Identities=25%  Similarity=0.312  Sum_probs=50.2

Q ss_pred             EEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC-CCeEEEe----CC--EEcCCCCcccccccc--CCcEEEEEE
Q 033059            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIF----AG--KQLEDGRTLADYNIQ--KESTLHLVL   71 (128)
Q Consensus         5 vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~-~~q~L~~----~g--~~L~d~~~L~~~gi~--~g~~i~v~~   71 (128)
                      |+.++|....+++++++|+.+|-+.|.+..++.. +..-|.+    +|  .-|+.+++|.++...  ...++++.+
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l~frv   76 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTLYFRV   76 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEEEEEE
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEEEEEE
Confidence            5678999999999999999999999999999764 3456777    23  246788899998877  333444443

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 ....

>PRK07696 sulfur carrier protein ThiS; Provisional

Probab=96.38  E-value=0.056  Score=31.40  Aligned_cols=66  Identities=18%  Similarity=0.255  Sum_probs=45.6

Q ss_pred             CEEEEEeCCCCEEEEEecCC-CcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~-~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+.+  ++++. .||.+|-+.    .++++...-+.++|..+.-+ .-+++-+++|+.|.++.-..||
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            66766   56644  45554 678887654    47888888888999998532 3344557899999987655554

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

Probab=96.33  E-value=0.028  Score=33.00  Aligned_cols=63  Identities=14%  Similarity=0.259  Sum_probs=49.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhC--CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~--ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ...+.+....||.+|.+.+...+.  .......+..||+...+  .-.+.-+++|+.|.++....||
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            567788899999999999987763  12366788899999987  3555667899999998777665

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 ....

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

Probab=96.32  E-value=0.046  Score=32.68  Aligned_cols=60  Identities=17%  Similarity=0.294  Sum_probs=44.4

Q ss_pred             EEEEEecCC-CcHHHHHHHHHhhhC-C-C-CCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           12 TITLEVESS-DTIDNVKAKIQDKEG-I-P-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        12 ~~~i~v~~~-~tV~~LK~~i~~~~~-i-p-~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ...++++++ .||.+|.+.+.+.+. + . .....+..|++...+     +.-|++|+.|.++....||
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            357888877 899999999988764 1 1 133567788888775     3567889999998777665

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

>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=96.30  E-value=0.034  Score=33.77  Aligned_cols=47  Identities=11%  Similarity=0.140  Sum_probs=37.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC-CCeEEEeCCE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGK   48 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~-~~q~L~~~g~   48 (128)
                      |+|.+.. +|..+.+.++++.+..+|+++|+..+++.. ..+.|.|...
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            4556643 677899999999999999999999999875 6777877543

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

>PRK06944 sulfur carrier protein ThiS; Provisional

Probab=96.29  E-value=0.075  Score=30.35  Aligned_cols=65  Identities=22%  Similarity=0.290  Sum_probs=43.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+  .+++++..||.+|-+.+    +++ ....+..+|.....+. -.+.-+++|++|.++....||
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-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQPVAGG   65 (65)
T ss_pred             CEEEE---CCE--EEECCCCCcHHHHHHhh----CCC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEeeccCC
Confidence            66666   454  45566778999998766    333 3466778999875321 122337789999998776665

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=96.27  E-value=0.028  Score=31.75  Aligned_cols=56  Identities=18%  Similarity=0.297  Sum_probs=40.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|.|   +|  ..+++..+.|+.+||.++...     .+ .++++|-+..++..|     ++|+.|.++-|
T Consensus         1 M~I~v---N~--k~~~~~~~~tl~~lr~~~k~~-----~D-I~I~NGF~~~~d~~L-----~e~D~v~~Ikk   56 (57)
T PF14453_consen    1 MKIKV---NE--KEIETEENTTLFELRKESKPD-----AD-IVILNGFPTKEDIEL-----KEGDEVFLIKK   56 (57)
T ss_pred             CEEEE---CC--EEEEcCCCcCHHHHHHhhCCC-----CC-EEEEcCcccCCcccc-----CCCCEEEEEeC
Confidence            67777   33  457788889999999887542     22 578999998877655     56899988743

>PRK07440 hypothetical protein; Provisional

Probab=96.25  E-value=0.06  Score=31.58  Aligned_cols=61  Identities=20%  Similarity=0.348  Sum_probs=43.6

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +|+.  +++.+..||.+|-+.    .++++...-+.++|..+.- ..-.+.-+++|+.|.++.-..||
T Consensus        10 NG~~--~~~~~~~tl~~lL~~----l~~~~~~vav~~N~~iv~r-~~w~~~~L~~gD~IEIv~~v~GG   70 (70)
T PRK07440         10 NGET--RTCSSGTSLPDLLQQ----LGFNPRLVAVEYNGEILHR-QFWEQTQVQPGDRLEIVTIVGGG   70 (70)
T ss_pred             CCEE--EEcCCCCCHHHHHHH----cCCCCCeEEEEECCEEeCH-HHcCceecCCCCEEEEEEEecCC
Confidence            5554  566677899988754    4778888888999998852 22334457889999987666554

>PRK06083 sulfur carrier protein ThiS; Provisional

Probab=96.23  E-value=0.054  Score=33.02  Aligned_cols=61  Identities=11%  Similarity=0.242  Sum_probs=43.6

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +|+.  .++++..||.+|-+.    .++++...-+-.||..+. ...-++.-+++||.|.++.-..||
T Consensus        24 NG~~--~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~iVp-r~~w~~t~L~egD~IEIv~~VgGG   84 (84)
T PRK06083         24 NDQS--IQVDISSSLAQIIAQ----LSLPELGCVFAINNQVVP-RSEWQSTVLSSGDAISLFQAIAGG   84 (84)
T ss_pred             CCeE--EEcCCCCcHHHHHHH----cCCCCceEEEEECCEEeC-HHHcCcccCCCCCEEEEEEEecCC
Confidence            4543  445567888888665    478888888889999984 334455568899999988766554

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=96.19  E-value=0.04  Score=31.67  Aligned_cols=58  Identities=21%  Similarity=0.390  Sum_probs=42.7

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .++++...||.+|.+.+    +++++...+..+|+.+..+ .-.+.-+++|+.|.++.-..||
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            45566778999998776    5778888888999988543 2223457899999988766665

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.

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=96.06  E-value=0.054  Score=32.89  Aligned_cols=62  Identities=13%  Similarity=0.286  Sum_probs=44.3

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhhCC------C-----CCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKEGI------P-----PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~~i------p-----~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ....++++ ..||.+|.+.+.+.+.-      .     -....+..||+...++..   .-+++|+.|.++....||
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 89999999999877531      1     123567789988764432   567899999998877775

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.

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

Probab=96.05  E-value=0.011  Score=44.89  Aligned_cols=70  Identities=21%  Similarity=0.323  Sum_probs=58.6

Q ss_pred             CEEEEEeC--CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCC--CCccccccccCCcEEEEE
Q 033059            1 MQIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED--GRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~--~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d--~~~L~~~gi~~g~~i~v~   70 (128)
                      |.++|...  ....+.+++..+..+..|+..++..++++.+..-|+|+++.+.+  ...|.++|+..++.+.+-
T Consensus         1 M~~tvs~~l~~~~~~~i~v~~dg~L~nl~aL~~~d~g~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~lr   74 (380)
T KOG0012|consen    1 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTGIVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLALR   74 (380)
T ss_pred             CeEEEEEEecceeeeccccccccchhhHHHHHHHHhCcccchhhcccCCCccccchhhhhhhcccccceeEecc
Confidence            55555444  45678889999999999999999999999999999999999964  568999999999888553

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

Probab=96.00  E-value=0.05  Score=31.38  Aligned_cols=64  Identities=23%  Similarity=0.487  Sum_probs=49.6

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhh---CCCCCCeEEE-eCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKE---GIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~---~ip~~~q~L~-~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      +|+...++..++..+.-..++--+..   +-|++...|. -+|..|+-++.++|||+.++-++.+.++
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLK   71 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLK   71 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEee
Confidence            57777888888777666665554443   4678877776 6889999999999999999999887765

>TIGR01683 thiS thiamine biosynthesis protein ThiS

Probab=95.99  E-value=0.062  Score=30.78  Aligned_cols=61  Identities=20%  Similarity=0.391  Sum_probs=43.1

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +|+.  ++++...||.+|.+.+    +++++...+..+|+.+..+ .-.++-+++|+.|.++.-..||
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            4443  4556778999998765    5677778888999988422 2233457899999988766665

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.

>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=95.92  E-value=0.051  Score=33.09  Aligned_cols=62  Identities=19%  Similarity=0.352  Sum_probs=44.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      +...++-..+++.||..++.+.+++-+.-.+...+..|+++++|-+-+++-...|.+.+...
T Consensus         5 I~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi~   66 (88)
T PF11620_consen    5 IMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQIK   66 (88)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEEE
T ss_pred             EEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEEE
Confidence            34456667899999999999999999988898899889999999999998888888777643

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.

>smart00666 PB1 PB1 domain

Probab=95.44  E-value=0.11  Score=30.90  Aligned_cols=45  Identities=16%  Similarity=0.334  Sum_probs=37.5

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      .|.++. ++....+.++++.|..+|+.+|.+.++.+.+...|.|..
T Consensus         3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~D   47 (81)
T smart00666        3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQD   47 (81)
T ss_pred             cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEEC
Confidence            355554 567888999999999999999999999887788888874

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.

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

Probab=95.08  E-value=0.2  Score=37.96  Aligned_cols=68  Identities=19%  Similarity=0.250  Sum_probs=50.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~   78 (128)
                      |+|+|   +|+.  +++++..||.+|-+.    .+++++.+.+.+||+.+.- ..-.++-+++|+.|.++.-..||.+
T Consensus         1 M~I~V---NGk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNgeIVpr-~~w~~t~LkeGD~IEII~~VgGGs~   68 (326)
T PRK11840          1 MRIRL---NGEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLEIVPR-SEYGQVALEEGDELEIVHFVGGGSD   68 (326)
T ss_pred             CEEEE---CCEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCEECCH-HHcCccccCCCCEEEEEEEecCCCC
Confidence            66776   4554  556677898888765    4888899999999999952 2334455889999999888888864

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

Probab=95.07  E-value=0.33  Score=28.36  Aligned_cols=67  Identities=19%  Similarity=0.426  Sum_probs=46.0

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .+++.. +|+  .++++...|+++|-+.+    +++++..-+.+||..+..+ .-++.-+++|+.|.++--..||
T Consensus         2 ~m~i~~-ng~--~~e~~~~~tv~dLL~~l----~~~~~~vav~vNg~iVpr~-~~~~~~l~~gD~ievv~~v~GG   68 (68)
T COG2104           2 PMTIQL-NGK--EVEIAEGTTVADLLAQL----GLNPEGVAVAVNGEIVPRS-QWADTILKEGDRIEVVRVVGGG   68 (68)
T ss_pred             cEEEEE-CCE--EEEcCCCCcHHHHHHHh----CCCCceEEEEECCEEccch-hhhhccccCCCEEEEEEeecCC
Confidence            344433 344  56666668999987664    8888888889999998643 2234556788999887655554

>smart00295 B41 Band 4

Probab=94.45  E-value=0.78  Score=31.65  Aligned_cols=72  Identities=28%  Similarity=0.373  Sum_probs=51.6

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEEeC---C---EEcCCCCcccccccc-CCcEEEEEEee
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFA---G---KQLEDGRTLADYNIQ-KESTLHLVLRL   73 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~~~---g---~~L~d~~~L~~~gi~-~g~~i~v~~~~   73 (128)
                      .|.|..++|....+.+++++|+.++-+.++.+.|++.. ..-|.+-   +   .-|+...+|.+.... ....+++-.+.
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            57788889999999999999999999999999998542 2344431   1   245666777776654 34456665554

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.

>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=94.40  E-value=0.37  Score=29.50  Aligned_cols=51  Identities=18%  Similarity=0.259  Sum_probs=38.9

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCcc
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   56 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L   56 (128)
                      +|.|.. .|....+.|+++.+..+|.++|...+++. ..+.|.|...  .|--|+
T Consensus         4 kVKv~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE--GD~iti   54 (86)
T cd06408           4 RVKVHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD--GDMITM   54 (86)
T ss_pred             EEEEEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC--CCCccc
Confidence            444433 57789999999999999999999999985 5677777665  444444

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

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

Probab=94.14  E-value=0.58  Score=27.63  Aligned_cols=45  Identities=22%  Similarity=0.315  Sum_probs=38.8

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      +.|-.++|+...+.+.|.+||.++-+.+.++.++.++.--+.+.|
T Consensus         2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~   46 (72)
T cd01760           2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLG   46 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEec
Confidence            456678999999999999999999999999999999887666543

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.

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=94.10  E-value=0.39  Score=38.08  Aligned_cols=71  Identities=14%  Similarity=0.164  Sum_probs=54.7

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCC----C--CCCeEEE-eCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI----P--PDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~i----p--~~~q~L~-~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      +|+|...+ +..++-++.+..|.||--.|-...+-    +  +..-.|. .+|.+|+.+.+|.+.||.||+.+++....
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            46776543 55788888999999999999887753    1  2223444 57889999999999999999999988643

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.

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

Probab=93.68  E-value=0.17  Score=38.99  Aligned_cols=65  Identities=20%  Similarity=0.314  Sum_probs=50.8

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhC-CCCCCeEEE--eCCEEcC-CCCccccccccCCcE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLE-DGRTLADYNIQKEST   66 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~-ip~~~q~L~--~~g~~L~-d~~~L~~~gi~~g~~   66 (128)
                      .|.|+..+|.-....+..+.||.+++..|...-. -+...+.|+  |--+.|. |+.||++-|+.+-..
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            4788889998888899999999999999977654 334456665  7778885 577999999876533

>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=93.55  E-value=0.45  Score=28.05  Aligned_cols=45  Identities=22%  Similarity=0.335  Sum_probs=35.5

Q ss_pred             EEEEEeCCCCEEEEEec-CCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059            2 QIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~-~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      .|.++. +|....+.++ .+.|..+|+++|.+.++.+.....|.|.+
T Consensus         2 ~vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D   47 (81)
T cd05992           2 RVKVKY-GGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPD   47 (81)
T ss_pred             cEEEEe-cCCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeC
Confidence            455554 3567888888 89999999999999999887666776654

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.

>smart00455 RBD Raf-like Ras-binding domain

Probab=93.52  E-value=0.53  Score=27.58  Aligned_cols=49  Identities=22%  Similarity=0.322  Sum_probs=41.6

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC--EEcC
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG--KQLE   51 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g--~~L~   51 (128)
                      +.|-.++|+...+.+.|..||.|+-+.+-++.|+.++...+...|  +.|+
T Consensus         2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ld   52 (70)
T smart00455        2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLD   52 (70)
T ss_pred             eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccee
Confidence            345667899999999999999999999999999999998888755  4554

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

Probab=93.50  E-value=0.49  Score=28.42  Aligned_cols=36  Identities=11%  Similarity=0.250  Sum_probs=32.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      ++.+.+.+..+..+|..+|++++..+++..+|.|..
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            567788899999999999999999999999999864

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

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

Probab=93.33  E-value=0.5  Score=28.07  Aligned_cols=44  Identities=20%  Similarity=0.397  Sum_probs=35.2

Q ss_pred             EEEEeCCCCEEE-EEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059            3 IFVKTLTGKTIT-LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus         3 i~vk~~~g~~~~-i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      |.+.. ++.... +.+.++.|..+|...|++.++.+.....|.|.+
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            44444 445555 899999999999999999999998888888853

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 ....

>PRK11130 moaD molybdopterin synthase small subunit; Provisional

Probab=93.11  E-value=1  Score=26.88  Aligned_cols=57  Identities=12%  Similarity=0.220  Sum_probs=37.1

Q ss_pred             EEecC-CCcHHHHHHHHHhhhC-----CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           15 LEVES-SDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        15 i~v~~-~~tV~~LK~~i~~~~~-----ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +++++ ..||.+|++.+.+++.     ......++..|+....+     +.-+++|+.|.++....||
T Consensus        19 ~~v~~~~~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~~~~~-----~~~l~dgDeVai~PPVsGG   81 (81)
T PRK11130         19 LELAADFPTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFFPPVTGG   81 (81)
T ss_pred             EEecCCCCCHHHHHHHHHHhCccHHhhhcCCCEEEEECCEEcCC-----CCCCCCCCEEEEeCCCCCC
Confidence            44443 4799999999987752     12233445556654433     2347889999988777665

>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=92.93  E-value=0.88  Score=27.54  Aligned_cols=41  Identities=17%  Similarity=0.301  Sum_probs=31.9

Q ss_pred             EEEEEeCCCCEEEEEecC--CCcHHHHHHHHHhhhCCCCCCeEEEe
Q 033059            2 QIFVKTLTGKTITLEVES--SDTIDNVKAKIQDKEGIPPDQQRLIF   45 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~--~~tV~~LK~~i~~~~~ip~~~q~L~~   45 (128)
                      .|.+. .+|.+..+.+++  +.+..+|+++|+..++++  .+.|-|
T Consensus         2 ~vKat-y~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKY   44 (81)
T cd06396           2 NLKVT-YNGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKY   44 (81)
T ss_pred             EEEEE-ECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEE
Confidence            34453 367888899998  779999999999999998  444444

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.

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.84  E-value=0.21  Score=37.88  Aligned_cols=57  Identities=12%  Similarity=0.199  Sum_probs=46.0

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe---CCEE-----cCCCCccccccccCCcEEEEE
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQ-----LEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~---~g~~-----L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      ...|.-+-||.|++..+....|+.+.+|+|+|   .|+.     .+.++.|-.|.|++|+.+.+-
T Consensus       351 s~~I~~~~TV~D~~~~Ld~~VGvk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq  415 (418)
T KOG2982|consen  351 SGLICMTRTVLDFMKILDPKVGVKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ  415 (418)
T ss_pred             ceEEEeehHHHHHHHHhccccccccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence            34455567999999999999999999999986   3442     345788999999999998664

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=92.32  E-value=0.98  Score=27.29  Aligned_cols=53  Identities=19%  Similarity=0.386  Sum_probs=41.1

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-eCCEEcCCCCccccccccCCcEEEEEE
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +..+...+++..||.++-+.    .|+|..+.-++ -||+..+-+     |-+++|+.|.+..
T Consensus        22 ~~~~~~~~~~~~tvkd~IEs----LGVP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~P   75 (81)
T PF14451_consen   22 GGPFTHPFDGGATVKDVIES----LGVPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVYP   75 (81)
T ss_pred             CCceEEecCCCCcHHHHHHH----cCCChHHeEEEEECCEECCCc-----ccCCCCCEEEEEe
Confidence            34577888899999888655    59999888665 699887654     5667899998864

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

Probab=92.19  E-value=0.63  Score=34.44  Aligned_cols=68  Identities=18%  Similarity=0.283  Sum_probs=52.5

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcC--C-CCccccccccCCcEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--D-GRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~--d-~~~L~~~gi~~g~~i~v   69 (128)
                      .|.|+.++|+++..++.+..|+.+++..|.-..+.......|.  |--..+.  | .++|..+++.+.+++.+
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            4788999999999999999999999999988877655444443  4444452  2 57899999988877743

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

Probab=92.14  E-value=0.4  Score=29.33  Aligned_cols=55  Identities=16%  Similarity=0.280  Sum_probs=29.1

Q ss_pred             Eec-CCCcHHHHHHHHH-hhhCCCCCCe----EEEeCCEE----cCCCCccccccccCCcEEEEE
Q 033059           16 EVE-SSDTIDNVKAKIQ-DKEGIPPDQQ----RLIFAGKQ----LEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus        16 ~v~-~~~tV~~LK~~i~-~~~~ip~~~q----~L~~~g~~----L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      .++ ..+|+.+|-+.|- .+.|.....+    .++|....    -..+++|+++||.+|+.+.+.
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            344 3689999998874 4566543332    33333322    112578999999999988763

>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=92.01  E-value=0.85  Score=27.41  Aligned_cols=48  Identities=21%  Similarity=0.474  Sum_probs=35.4

Q ss_pred             CcHHHHHHHHHhhhCCCCCCeEEEe--CCEEcCCCCccccccccCCcEEEEEE
Q 033059           21 DTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        21 ~tV~~LK~~i~~~~~ip~~~q~L~~--~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      .++.+|+.+..+.++++....+|+.  .|..++|+..+..+  . ..|+.|++
T Consensus        21 ~sL~eL~~K~~~~l~~~~~~~~lvL~eDGT~VddEeyF~tL--p-~nT~lm~L   70 (78)
T PF02017_consen   21 SSLEELLEKACDKLQLPEEPVRLVLEEDGTEVDDEEYFQTL--P-DNTVLMLL   70 (78)
T ss_dssp             SSHHHHHHHHHHHHT-SSSTCEEEETTTTCBESSCHHHCCS--S-SSEEEEEE
T ss_pred             CCHHHHHHHHHHHhCCCCcCcEEEEeCCCcEEccHHHHhhC--C-CCCEEEEE
Confidence            5899999999999999987777775  78899888666554  3 34554444

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.

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

Probab=92.01  E-value=0.61  Score=30.39  Aligned_cols=55  Identities=22%  Similarity=0.521  Sum_probs=38.9

Q ss_pred             EecC-CCcHHHHHHHHHhhh----CCCC------CCeEEEeC----------------C-EEc---CCCCccccccccCC
Q 033059           16 EVES-SDTIDNVKAKIQDKE----GIPP------DQQRLIFA----------------G-KQL---EDGRTLADYNIQKE   64 (128)
Q Consensus        16 ~v~~-~~tV~~LK~~i~~~~----~ip~------~~q~L~~~----------------g-~~L---~d~~~L~~~gi~~g   64 (128)
                      .|+. ++||.+|++.+.+..    +++|      +.++|.+.                . ..|   +++.+|.++||.+.
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            3775 899999999887664    4554      23444321                1 356   67889999999999


Q ss_pred             cEEEEE
Q 033059           65 STLHLV   70 (128)
Q Consensus        65 ~~i~v~   70 (128)
                      ..|-+.
T Consensus       101 TEiSfF  106 (122)
T PF10209_consen  101 TEISFF  106 (122)
T ss_pred             ceeeee
Confidence            988765

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

Probab=91.89  E-value=1.8  Score=26.77  Aligned_cols=45  Identities=16%  Similarity=0.304  Sum_probs=34.0

Q ss_pred             EEEEeCCCCEEEEEecC-----CCcHHHHHHHHHhhhCCCC-CCeEEEeCCE
Q 033059            3 IFVKTLTGKTITLEVES-----SDTIDNVKAKIQDKEGIPP-DQQRLIFAGK   48 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~-----~~tV~~LK~~i~~~~~ip~-~~q~L~~~g~   48 (128)
                      |.|.. +|....|.++.     +.+..+|+++|++.+++++ ....|.|...
T Consensus         3 vKv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~De   53 (91)
T cd06398           3 VKVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDE   53 (91)
T ss_pred             EEEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECC
Confidence            44433 56666777774     7999999999999999987 5677777653

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

>PTZ00380 microtubule-associated protein (MAP); Provisional

Probab=91.81  E-value=0.24  Score=32.29  Aligned_cols=57  Identities=16%  Similarity=0.246  Sum_probs=41.4

Q ss_pred             EEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccc---cCCcEEEEEE
Q 033059           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI---QKESTLHLVL   71 (128)
Q Consensus        15 i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi---~~g~~i~v~~   71 (128)
                      +-|+.+.||+++...|..+.+++++..-|+.++..+..+.+++++--   .++.-+++.-
T Consensus        45 llVP~d~tV~qF~~iIRkrl~l~~~k~flfVnn~lp~~s~~mg~lYe~~KDeDGFLYi~Y  104 (121)
T PTZ00380         45 LALPRDATVAELEAAVRQALGTSAKKVTLAIEGSTPAVTATVGDIADACKRDDGFLYVSV  104 (121)
T ss_pred             EEcCCCCcHHHHHHHHHHHcCCChhHEEEEECCccCCccchHHHHHHHhcCCCCeEEEEE
Confidence            36899999999999999999999998656667766666667765421   2244555544

>cd06410 PB1_UP2 Uncharacterized protein 2

Probab=91.42  E-value=1.2  Score=27.78  Aligned_cols=40  Identities=18%  Similarity=0.249  Sum_probs=33.3

Q ss_pred             EEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe
Q 033059            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (128)
Q Consensus         5 vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~   45 (128)
                      ++..+|++..+.|+.+.|..+|+.++++.++++.. +.|.|
T Consensus        17 l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky   56 (97)
T cd06410          17 LRYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKY   56 (97)
T ss_pred             EEEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEE
Confidence            34557888999999999999999999999998876 55544

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.

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

Probab=90.81  E-value=0.77  Score=38.23  Aligned_cols=42  Identities=24%  Similarity=0.460  Sum_probs=37.5

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEc
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL   50 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L   50 (128)
                      +...+.+.++++.|+..|++.|...+|+|.+.|.|+|.|...
T Consensus       323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~~  364 (732)
T KOG4250|consen  323 QATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGLS  364 (732)
T ss_pred             cceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCcc
Confidence            456788899999999999999999999999999999987643

>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=90.54  E-value=0.88  Score=27.69  Aligned_cols=55  Identities=16%  Similarity=0.282  Sum_probs=37.3

Q ss_pred             EEecCCCcHHHHHHHHHhhhCCCCC-------CeEEEeCCE-EcC------CCCccccccccCCcEEEEE
Q 033059           15 LEVESSDTIDNVKAKIQDKEGIPPD-------QQRLIFAGK-QLE------DGRTLADYNIQKESTLHLV   70 (128)
Q Consensus        15 i~v~~~~tV~~LK~~i~~~~~ip~~-------~q~L~~~g~-~L~------d~~~L~~~gi~~g~~i~v~   70 (128)
                      |++++++|+.+|-+.+.+...+...       .-.|++.+- .|+      =+++|.++ +.+|+.|.|.
T Consensus         1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~Vt   69 (84)
T PF08825_consen    1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVT   69 (84)
T ss_dssp             EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEE
T ss_pred             CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEE
Confidence            5789999999999999887433322       234444332 121      25789999 9999998874

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 ....

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=90.18  E-value=1.6  Score=34.31  Aligned_cols=70  Identities=21%  Similarity=0.260  Sum_probs=53.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhh--CCCCCCeEEEe----CCEE--cCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIF----AGKQ--LEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~--~ip~~~q~L~~----~g~~--L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |-+.+|+..| ...+++.++++++.|-.+|-.-+  +..|+.+.+.-    .|..  +..++++.++|++.|.++++-.
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 MIFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY   78 (571)
T ss_pred             CeEEEecCCC-ceeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEe
Confidence            6788888777 48899999999999988886654  35566666653    2332  3467899999999999998876

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

Probab=90.01  E-value=2  Score=30.52  Aligned_cols=48  Identities=21%  Similarity=0.329  Sum_probs=30.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCCCCC---CeEEE--eCCEE---cCCCCccccc
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGIPPD---QQRLI--FAGKQ---LEDGRTLADY   59 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~ip~~---~q~L~--~~g~~---L~d~~~L~~~   59 (128)
                      .+.+-|+.+.||.||.+.+..+.+++.+   .++|+  ++++.   +..+.+|.++
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            4778899999999999999999998765   55654  67763   5667777665

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

Probab=89.83  E-value=0.85  Score=36.99  Aligned_cols=64  Identities=36%  Similarity=0.532  Sum_probs=42.0

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhh--CCC------CCCeEEEe--C--CE-EcCCC-------------CccccccccCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF--A--GK-QLEDG-------------RTLADYNIQKE   64 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~--~ip------~~~q~L~~--~--g~-~L~d~-------------~~L~~~gi~~g   64 (128)
                      ..+.+.|-..+||.++|++|-...  +.|      ++++-|.+  +  |. .|.|.             .||++|+|.+|
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            457788889999999999996542  343      34455532  2  23 55543             36999999999


Q ss_pred             cEEEEEEeec
Q 033059           65 STLHLVLRLR   74 (128)
Q Consensus        65 ~~i~v~~~~~   74 (128)
                      ++|.++.+..
T Consensus       282 a~vaLv~k~~  291 (539)
T PF08337_consen  282 ATVALVPKQH  291 (539)
T ss_dssp             EEEEEEES--
T ss_pred             ceEEEeeccc
Confidence            9999998764

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 ....

>cd01766 Ufm1 Urm1-like ubiquitin domain

Probab=89.43  E-value=3  Score=24.73  Aligned_cols=61  Identities=21%  Similarity=0.268  Sum_probs=48.0

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-eCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      .+.|+++.....+-...++++++|+..--++ -.|--+...++-..+=++.|+.+.++.|-+
T Consensus        19 vlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvGINP~qtAGnvflkhgselrliPRDr   80 (82)
T cd01766          19 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRLIPRDR   80 (82)
T ss_pred             EEeccccCchHHHHHHHHHhcCCCccceeEEecCccccChhhcccceeeecCCEeeeccccc
Confidence            3578877777777777889999998776665 556677888888888889999998887654

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.

>cd06397 PB1_UP1 Uncharacterized protein 1

Probab=89.42  E-value=2.2  Score=25.79  Aligned_cols=45  Identities=13%  Similarity=0.175  Sum_probs=35.8

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      +..|+. +|.+..+.++..-|...|+++|...+.+|+...-+.|-.
T Consensus         2 ~fKv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiD   46 (82)
T cd06397           2 QFKSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYID   46 (82)
T ss_pred             eEEEEe-CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEc
Confidence            345543 566777888888899999999999999999888777743

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 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.

>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation

Probab=89.20  E-value=1.7  Score=25.84  Aligned_cols=39  Identities=18%  Similarity=0.372  Sum_probs=31.6

Q ss_pred             CcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcCCCCccccc
Q 033059           21 DTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADY   59 (128)
Q Consensus        21 ~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~d~~~L~~~   59 (128)
                      .|+.+|+.+..+.++++....+|+  -.|..++|+..+..+
T Consensus        19 ~sL~eL~~K~~~~l~l~~~~~~l~L~eDGT~VddEeyF~tL   59 (74)
T smart00266       19 SSLEELLSKVCDKLALPDSPVTLVLEEDGTIVDDEEYFQTL   59 (74)
T ss_pred             CCHHHHHHHHHHHhCCCCCCcEEEEecCCcEEccHHHHhcC
Confidence            579999999999999997666665  489999888766654

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

Probab=89.20  E-value=3  Score=24.37  Aligned_cols=56  Identities=20%  Similarity=0.242  Sum_probs=40.3

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC--CEEcCCCCcccc
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLEDGRTLAD   58 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~--g~~L~d~~~L~~   58 (128)
                      +.|..++|+...+.+.|..||.+.-..+-+..++.++...+...  .+.|+-+...+.
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            45677899999999999999999999999999999988766543  446654444433

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.

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.11  E-value=0.17  Score=23.72  Aligned_cols=22  Identities=41%  Similarity=0.966  Sum_probs=19.5

Q ss_pred             hhhhhhhcccCCcccccccccCCC
Q 033059           94 MICRKCYARLHPRAVNCRKKKCGH  117 (128)
Q Consensus        94 ~~Cr~c~~r~~~~~~~c~~~~c~~  117 (128)
                      ..|..|+..+..++.+|..  ||.
T Consensus         3 ~~Cp~Cg~~~~~~~~fC~~--CG~   24 (26)
T PF13248_consen    3 MFCPNCGAEIDPDAKFCPN--CGA   24 (26)
T ss_pred             CCCcccCCcCCcccccChh--hCC
Confidence            4699999999999999997  984

>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function

Probab=88.39  E-value=0.87  Score=28.48  Aligned_cols=36  Identities=33%  Similarity=0.616  Sum_probs=25.9

Q ss_pred             EEEeCCEEcCCCCccccc-cccCCcEEEEEEeecCCC
Q 033059           42 RLIFAGKQLEDGRTLADY-NIQKESTLHLVLRLRGGI   77 (128)
Q Consensus        42 ~L~~~g~~L~d~~~L~~~-gi~~g~~i~v~~~~~gg~   77 (128)
                      .|.|.|+.|..+.+|++| |-.+-+.|.|-+..+|.+
T Consensus         3 ~LW~aGK~l~~~k~l~dy~GkNEKtKiivKl~~~g~g   39 (98)
T PF11069_consen    3 QLWWAGKELQRGKKLSDYIGKNEKTKIIVKLQKRGQG   39 (98)
T ss_pred             eEEeccccccCCCcHHHhcCCCcceeEEEEeccCCCC
Confidence            578999999999999999 233445555555556654

>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=88.17  E-value=3.1  Score=24.67  Aligned_cols=61  Identities=16%  Similarity=0.343  Sum_probs=39.6

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhhC-CCCCCeEE-----E-eCCEEcCCCCccccccccCCcEEEEEEe
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKEG-IPPDQQRL-----I-FAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~~-ip~~~q~L-----~-~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      +.|-.-.+++.|+++|+..|.+++. +.|+...+     . -.|--|+.+-.+.+. ...+++|.++++
T Consensus         3 kKFLhlt~~~~tl~~L~~eI~~~f~kLYP~~~~~~I~~LQD~~~cDLD~d~~V~DV-f~~~~~vrvi~~   70 (73)
T PF10407_consen    3 KKFLHLTDPNNTLSQLKEEIEERFKKLYPNEPELEILSLQDSDGCDLDPDFLVKDV-FNSNNVVRVILK   70 (73)
T ss_pred             cEEEEEeCCCCcHHHHHHHHHHHHHHHCCCCCCceEEEeecCCCCCCCcccEeeee-eccCCEEEEEec
Confidence            3466667899999999999998875 33433222     1 234455556566554 346778877765

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 [].

>cd01764 Urm1 Urm1-like ubuitin domain

Probab=87.80  E-value=2  Score=26.60  Aligned_cols=59  Identities=20%  Similarity=0.374  Sum_probs=35.3

Q ss_pred             EecCCCcHHHHHHHHHhhhCCCCCCeEEEe-CCE------Ec-CCC--Ccc--ccccccCCcEEEEEEeecCC
Q 033059           16 EVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGK------QL-EDG--RTL--ADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        16 ~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~-~g~------~L-~d~--~~L--~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ++....||.+|-+.|.+.+  +..+..|+. +|+      +| ++.  ..+  .++-+++|+.|.++....||
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 DGEKPVTVGDLLDYVASNL--LEERPDLFIEGGSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFISTLHGG   94 (94)
T ss_pred             cCCCCCcHHHHHHHHHHhC--chhhhhhEecCCcccCCEEEEECCccccccCCcccCCCCcCEEEEECCCCCC
Confidence            3435679999999998776  232333332 121      22 111  123  34668999999998877665

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.

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

Probab=87.42  E-value=4.8  Score=24.59  Aligned_cols=56  Identities=23%  Similarity=0.298  Sum_probs=40.3

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCe-EEE-eC-----CEEcCCCCcccc
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLI-FA-----GKQLEDGRTLAD   58 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q-~L~-~~-----g~~L~d~~~L~~   58 (128)
                      |.|-..+|.+..+.|++.+|+.++-+.++.+.+...+.- .|+ +.     -+.++|...|.+
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            455567899999999999999999999999998765443 343 11     235566655433

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.

>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=87.35  E-value=1.8  Score=27.47  Aligned_cols=45  Identities=16%  Similarity=0.193  Sum_probs=34.2

Q ss_pred             EEecCCCcHHHHHHHHHhhhCCCCCC-eEEEeCCEEcCCCCccccc
Q 033059           15 LEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY   59 (128)
Q Consensus        15 i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~~g~~L~d~~~L~~~   59 (128)
                      +-|+.+.||++|...|.....++++. +-|+.++.....+.++++.
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            44788999999999999999988765 5566777666778888765

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 ....

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=87.24  E-value=0.28  Score=22.38  Aligned_cols=20  Identities=35%  Similarity=0.845  Sum_probs=17.9

Q ss_pred             hhhhhcccCCcccccccccCCC
Q 033059           96 CRKCYARLHPRAVNCRKKKCGH  117 (128)
Q Consensus        96 Cr~c~~r~~~~~~~c~~~~c~~  117 (128)
                      |..|...+...+.+|..  ||+
T Consensus         2 Cp~CG~~~~~~~~fC~~--CG~   21 (23)
T PF13240_consen    2 CPNCGAEIEDDAKFCPN--CGT   21 (23)
T ss_pred             CcccCCCCCCcCcchhh--hCC
Confidence            78999999999999997  984

>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 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=87.15  E-value=4.4  Score=23.92  Aligned_cols=58  Identities=17%  Similarity=0.268  Sum_probs=43.4

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-eCCEEcCCCCccccccccCCcEEEEE
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      ..+.|+++.....+-...++++.+|+..--++ -.|--+...++..+.-++.|+.+.++
T Consensus        18 kv~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~GInP~QTag~vflKhGseLrli   76 (76)
T PF03671_consen   18 KVISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVGINPQQTAGNVFLKHGSELRLI   76 (76)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-EE-TTSBHHHHHHHT-SEEEEE
T ss_pred             eEEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcccccchhhhhhHhhcCcEeeeC
Confidence            34688888888888888889999998877666 56777888999988888899988764

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-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.

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

Probab=86.57  E-value=1.4  Score=34.64  Aligned_cols=74  Identities=15%  Similarity=0.291  Sum_probs=59.8

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEE--EeCCEEcCC---CCccccccccCCcEEEEEEeecC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLED---GRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L--~~~g~~L~d---~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      +|.|+.++|.+|.=.++.+.-+..++..+...-++....+-|  .|--++..|   +++|.++.+.+...|.|+.+-++
T Consensus       316 rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~i~~g~f~LatpyPRReft~eDy~KtllEl~L~psaalvvlpk~r~  394 (506)
T KOG2507|consen  316 RLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQTIGLGAFDLATPYPRREFTDEDYDKTLLELRLFPSAALVVLPKKRA  394 (506)
T ss_pred             EEEEecCCccchhhcCCcchHHHHHHHHHHhcccccccceeeccccccccccchhhhhhHHHhccCCcceEEEEecCCc
Confidence            578999999999888988888999999998877777766666  377777743   57999999999988888776443

>KOG4572 consensus Predicted DNA-binding transcription factor, interacts with stathmin [Transcription; General function prediction only; Signal transduction mechanisms]

Probab=85.72  E-value=2.2  Score=36.53  Aligned_cols=62  Identities=18%  Similarity=0.387  Sum_probs=48.0

Q ss_pred             CCCEEEEEecC-CCcHHHHHHHHHhhhCCCCCCeEEEe-CCEEcCCCCcccccc-c-cCCcEEEEE
Q 033059            9 TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADYN-I-QKESTLHLV   70 (128)
Q Consensus         9 ~g~~~~i~v~~-~~tV~~LK~~i~~~~~ip~~~q~L~~-~g~~L~d~~~L~~~g-i-~~g~~i~v~   70 (128)
                      .|+...++... ..|+.+||..|....|+...++.++- +|.-+..++.|.+|. . .+.+-|++.
T Consensus         3 rGqaltFDleaetqT~adLk~aiqke~~~aIq~~tfl~egGecmaadkrl~e~StaGTdTnPiffF   68 (1424)
T KOG4572|consen    3 RGQALTFDLEAETQTFADLKDAIQKEVGHAIQDLTFLDEGGECMAADKRLAEISTAGTDTNPIFFF   68 (1424)
T ss_pred             CCceeEEeecceeehHHHHHHHHHHHhchhhceeeeeecCCcCcccccchhhhccccCCCCceEEe
Confidence            47777887774 67899999999999999999998875 556777788888887 2 344556555

>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=85.18  E-value=6.5  Score=23.99  Aligned_cols=60  Identities=23%  Similarity=0.379  Sum_probs=43.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhh-C--CCC--C-CeEEEeCC--EEcCCCCccccccccCCcEEEEEE
Q 033059           12 TITLEVESSDTIDNVKAKIQDKE-G--IPP--D-QQRLIFAG--KQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~-~--ip~--~-~q~L~~~g--~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      ...+.|+.++|+.++=++++... |  +++  . .+++.++|  ..+..+.++++-||.+-+.|.+..
T Consensus        16 ~~Lv~VDt~dTmdqVA~k~A~HsVGrRV~~~pg~~lrVr~~g~~~~~p~~~tVaeagl~P~e~vev~~   83 (85)
T PF06234_consen   16 LQLVPVDTEDTMDQVAAKVAHHSVGRRVAPRPGAPLRVRRQGDTQPFPRSMTVAEAGLQPMEWVEVRF   83 (85)
T ss_dssp             EEEEEEETT-BHHHHHHHHHTTTTTTSS---TTSEEEEEETTTSSEE-TT-BGGGHT--TTEEEEEEE
T ss_pred             EEEEEeCCCCcHHHHHHHHhhhhcceecCCCCCCEEEEEecCCCccCCCccEehhcCCCcceEEEEEE
Confidence            35578999999999999998653 4  333  2 46777888  899999999999999999998864

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 ....

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

Probab=84.98  E-value=3.1  Score=25.55  Aligned_cols=40  Identities=23%  Similarity=0.346  Sum_probs=34.3

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEE-EeCCEEc
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL-IFAGKQL   50 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L-~~~g~~L   50 (128)
                      ..+.+.|++++|=.++|+.|+..+++++...+- .+.|+.-
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            568999999999999999999999999988754 4777644

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 ....

>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor

Probab=84.71  E-value=5.5  Score=23.80  Aligned_cols=37  Identities=5%  Similarity=0.130  Sum_probs=32.8

Q ss_pred             EEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCe
Q 033059            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ   41 (128)
Q Consensus         5 vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q   41 (128)
                      |-.++|+...+.|.|++|+.++-+......++.|++-
T Consensus         4 V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh   40 (77)
T cd01818           4 VCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEH   40 (77)
T ss_pred             EECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHh
Confidence            5567899999999999999999999999999988764

Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.

>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45)

Probab=84.68  E-value=3.4  Score=24.79  Aligned_cols=39  Identities=15%  Similarity=0.342  Sum_probs=31.3

Q ss_pred             CcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcCCCCccccc
Q 033059           21 DTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADY   59 (128)
Q Consensus        21 ~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~d~~~L~~~   59 (128)
                      .|+.+|+.+..+.++++....+|+  -.|..++|+..+..+
T Consensus        21 ~sL~eL~~K~~~~l~l~~~~~~lvL~eDGTeVddEeYF~tL   61 (78)
T cd01615          21 SSLEELLSKACEKLKLPSAPVTLVLEEDGTEVDDEEYFQTL   61 (78)
T ss_pred             CCHHHHHHHHHHHcCCCCCCeEEEEeCCCcEEccHHHHhcC
Confidence            579999999999999976666555  589999888766554

These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.

>PF08783 DWNN: DWNN domain; InterPro: IPR014891 The ~75-residue DWNN (Domain With No Name) domain is highly conserved through eukaryotic species but is absent in prokaryotes

Probab=84.64  E-value=2.9  Score=24.82  Aligned_cols=40  Identities=20%  Similarity=0.178  Sum_probs=24.2

Q ss_pred             EEEeCCCC-EEEEEecC-CCcHHHHHHHHHhhhCC-CCCCeEE
Q 033059            4 FVKTLTGK-TITLEVES-SDTIDNVKAKIQDKEGI-PPDQQRL   43 (128)
Q Consensus         4 ~vk~~~g~-~~~i~v~~-~~tV~~LK~~i~~~~~i-p~~~q~L   43 (128)
                      +-|..+.+ ...+.++. ..+|.+||.+|.++.++ ...+.-|
T Consensus         2 ~YKFkS~k~~~~i~fdG~~Isv~dLKr~I~~~~~lg~~~dfdL   44 (74)
T PF08783_consen    2 HYKFKSQKDYDTITFDGTSISVFDLKREIIEKKKLGKGTDFDL   44 (74)
T ss_dssp             EEEETT-SSEEEEEESSSEEEHHHHHHHHHHHHT---TTTEEE
T ss_pred             eEEecccCCccEEEECCCeeEHHHHHHHHHHHhCCCcCCcCCE
Confidence            33444433 34577774 67999999999877665 3334333

The DWNN domain is found only at the N terminus of the RBBP6 family of proteins which includes: Mammalian RBBP6, a splicing-associated protein that plays a role in the induction of apoptosis and regulation of the cell cycle. Drosophila melanogaster (Fruit fly) SNAMA (something that sticks like glue), a protein that appears to play a role in apoptosis. All of the identified RBBP6 homologues include the DWNN domain, a CCHC-type zinc finger (see PDOC50158 from PROSITEDOC) and a RING-type zinc finger (see PDOC00449 from PROSITEDOC). The three domain form is found in plants, protozoa, fungi and microsporidia. The RBBP6 homologues in vertebrates, insects and worms are longer and include additional domains. In addition to forming part of the full-length RBBP6 protein, the DWNN domain is also expressed in vertebrates as a small protein containing a DWNN domain and a short C-terminal tail (RBBP6 variant 3). The DWNN domain adopts a fold similar to the ubiquitin one, characterised by two alpha-helices and four beta-sheets ordered as beta-beta-alpha-beta-alpha-beta along the sequence. The similarity of DWNN domain to ubiquitin and the presence of the RING finger suggest that the DWNN domain may act as an ubiquitin-like modifier, possibly playing a role in the regulation of the splicing machinery [, ]. ; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 2C7H_A.

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

Probab=84.58  E-value=2.6  Score=27.03  Aligned_cols=57  Identities=14%  Similarity=0.151  Sum_probs=39.2

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEeCCEEcCCCCccccc----cccCCcEEEEEE
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY----NIQKESTLHLVL   71 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~~g~~L~d~~~L~~~----gi~~g~~i~v~~   71 (128)
                      .+-|+.+.||+++...|....++++++ +-|..++.....+.+++++    +.. +..+++..
T Consensus        44 KflVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~~p~~~~~~~~lY~~~kd~-DGfLyl~Y  105 (112)
T cd01611          44 KYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPTSATMSQLYEEHKDE-DGFLYMTY  105 (112)
T ss_pred             eEEecCCCCHHHHHHHHHHHhCCCccceEEEEECCccCCchhHHHHHHHHhCCC-CCEEEEEE
Confidence            345899999999999999999988876 4444566544556666554    333 44555544

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.

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

Probab=84.43  E-value=0.32  Score=38.51  Aligned_cols=57  Identities=25%  Similarity=0.286  Sum_probs=48.1

Q ss_pred             EEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        15 i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +..+-..|-.+|...|++++||+-+.++.+.+|++|.-.+||.+-|++....+.|++
T Consensus        54 ~k~sL~i~Gselqa~iakklgi~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~  110 (568)
T KOG2561|consen   54 KKCSLHITGSELQALIAKKLGIKENHVKCIINGKILSCRKTLAEQGLKINQELMVAV  110 (568)
T ss_pred             hhcccccccHHHHHHHHHHcCCchhhhheeeccceeecccchhhhhhhhhhHHHHHh
Confidence            344445678899999999999999999999999999999999999998776665544

>PRK01777 hypothetical protein; Validated

Probab=83.51  E-value=8.4  Score=23.93  Aligned_cols=65  Identities=8%  Similarity=0.068  Sum_probs=41.8

Q ss_pred             CEEEEEeC-CC--CEEEEEecCCCcHHHHHHHHHhhhCCCCC--C-----eEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTL-TG--KTITLEVESSDTIDNVKAKIQDKEGIPPD--Q-----QRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~-~g--~~~~i~v~~~~tV~~LK~~i~~~~~ip~~--~-----q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |+|.|-.. ..  ....+++++.+||.++-.++    |++.+  +     ..+.-+|+....+.     -+++|++|.++
T Consensus         4 i~v~V~ya~~~~~~~~~l~vp~GtTv~dal~~s----gi~~~~pei~~~~~~vgI~Gk~v~~d~-----~L~dGDRVeIy   74 (95)
T PRK01777          4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRAS----GLLELRTDIDLAKNKVGIYSRPAKLTD-----VLRDGDRVEIY   74 (95)
T ss_pred             eEEEEEEECCCceEEEEEEcCCCCcHHHHHHHc----CCCccCcccccccceEEEeCeECCCCC-----cCCCCCEEEEe
Confidence            45555442 22  23567888999999987665    55444  2     35566788775544     45689999988


Q ss_pred             Eeec
Q 033059           71 LRLR   74 (128)
Q Consensus        71 ~~~~   74 (128)
                      -.+.
T Consensus        75 rPL~   78 (95)
T PRK01777         75 RPLL   78 (95)
T ss_pred             cCCC
Confidence            6553

>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14

Probab=83.10  E-value=7.5  Score=23.04  Aligned_cols=47  Identities=23%  Similarity=0.345  Sum_probs=38.8

Q ss_pred             EEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC--EEcC
Q 033059            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG--KQLE   51 (128)
Q Consensus         5 vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g--~~L~   51 (128)
                      |-.++|+.-.+.+.|.+||.++-..+-++-|+.++..-++.-|  ++|+
T Consensus         4 V~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~   52 (73)
T cd01817           4 VILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLV   52 (73)
T ss_pred             EECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccc
Confidence            4457888899999999999999999999999999888776555  3553

RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.

>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=82.89  E-value=7.7  Score=23.05  Aligned_cols=41  Identities=29%  Similarity=0.272  Sum_probs=31.6

Q ss_pred             EEEEeCCCC----EEEEEecCCCcHHHHHHHHHhhhCC--CCCCeEE
Q 033059            3 IFVKTLTGK----TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRL   43 (128)
Q Consensus         3 i~vk~~~g~----~~~i~v~~~~tV~~LK~~i~~~~~i--p~~~q~L   43 (128)
                      |.|-..++.    ...|.|++++|+.++-+.+.+++++  ++.+..|
T Consensus         5 lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L   51 (93)
T PF00788_consen    5 LRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCL   51 (93)
T ss_dssp             EEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEE
T ss_pred             EEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEE
Confidence            344444555    7789999999999999999999998  3445566

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 ....

>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length

Probab=82.60  E-value=1.9  Score=31.44  Aligned_cols=72  Identities=18%  Similarity=0.434  Sum_probs=45.6

Q ss_pred             EEEEeCC--CCEEE----EEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC----C--EEcCCCCccccccccCCcEEEEE
Q 033059            3 IFVKTLT--GKTIT----LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----G--KQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         3 i~vk~~~--g~~~~----i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~----g--~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |++|..+  .+++.    +.|+.+.+|++|-..|.+..|+|++..-++|.    +  ..++...++....|.+|+.|.+-
T Consensus        71 lFlK~fDp~~q~L~~iGh~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi~fQ  150 (249)
T PF12436_consen   71 LFLKYFDPETQTLRYIGHVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDIICFQ  150 (249)
T ss_dssp             EEEEEEETTTTEEEEEEEEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEEEEE
T ss_pred             EEEEeeCCCCCEEEEEeEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEEEEE
Confidence            5566543  23332    46888999999999999999999876555543    3  35678999999999999999887


Q ss_pred             Eeec
Q 033059           71 LRLR   74 (128)
Q Consensus        71 ~~~~   74 (128)
                      ....
T Consensus       151 ~~~~  154 (249)
T PF12436_consen  151 RAPS  154 (249)
T ss_dssp             E--G
T ss_pred             eccc
Confidence            6543

It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.

>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]

Probab=82.55  E-value=6.3  Score=25.27  Aligned_cols=38  Identities=5%  Similarity=0.198  Sum_probs=32.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEc
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL   50 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L   50 (128)
                      -.+.|+++.|++.+-..|....+++++++-++|=....
T Consensus        47 ~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sF   84 (116)
T KOG3439|consen   47 SKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSF   84 (116)
T ss_pred             ceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCcc
Confidence            45789999999999999999999999999888766544

>cd01768 RA RA (Ras-associating) ubiquitin domain

Probab=82.52  E-value=8  Score=22.98  Aligned_cols=35  Identities=29%  Similarity=0.448  Sum_probs=29.1

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCC--CCCeEEE
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIP--PDQQRLI   44 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip--~~~q~L~   44 (128)
                      +....|.|+.++|..++-..+.++++++  +++..|+
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            5567899999999999999999999987  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.

>cd06539 CIDE_N_A CIDE_N domain of CIDE-A proteins

Probab=81.63  E-value=5.2  Score=24.04  Aligned_cols=47  Identities=11%  Similarity=0.130  Sum_probs=34.4

Q ss_pred             CcHHHHHHHHHhhhCCCCCCeEE--EeCCEEcCCCCccccccccCCcEEEE
Q 033059           21 DTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus        21 ~tV~~LK~~i~~~~~ip~~~q~L--~~~g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      .++.+|+.+..+.++++....+|  .-.|..++|+..+..+  .+++.+.+
T Consensus        21 ~sL~EL~~K~~~~l~~~~~~~~lvL~eDGT~Vd~EeyF~~L--pdnT~lm~   69 (78)
T cd06539          21 SSLQELISKTLDALVITSGLVTLVLEEDGTVVDTEEFFQTL--GDNTHFMV   69 (78)
T ss_pred             cCHHHHHHHHHHHhCCCCCCcEEEEeCCCCEEccHHHHhhC--CCCCEEEE
Confidence            57999999999999998655555  4689999888766554  34444433

The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45, and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, the CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.

>smart00144 PI3K_rbd PI3-kinase family, Ras-binding domain

Probab=81.46  E-value=11  Score=23.83  Aligned_cols=64  Identities=28%  Similarity=0.297  Sum_probs=43.8

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhh------CCCCC-CeEEEeCCE--EcCCCCcccccc-----ccCCcEEEEEEee
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKE------GIPPD-QQRLIFAGK--QLEDGRTLADYN-----IQKESTLHLVLRL   73 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~------~ip~~-~q~L~~~g~--~L~d~~~L~~~g-----i~~g~~i~v~~~~   73 (128)
                      ...+.+.++++.|+.+|.+.+-.+.      .-+++ +..|--.|+  -|..+..|.+|.     +..|..++|++..
T Consensus        28 ~~~~t~~v~~~~~p~~li~~~l~k~~~~~~~~~~~~~dyvLkV~G~~Eyl~~~~~L~~~~yIr~cl~~~~~~~L~L~~  105 (108)
T smart00144       28 QQTKTLKVNPNCTPDSVLAQAFTKMLSLHDQVDPTSEDYILKVCGRDEYLLGDHPLGSFEYIRNCLKNGREPHLVLMT  105 (108)
T ss_pred             ceeEEEEECCCCCHHHHHHHHHHHHHhccccccCCCCcEEEEecCcEEEEeCCeeeechHHHHHHHhcCCCceEEEEe
Confidence            3568899999999999998876541      12233 566666775  456677777773     4667777777643

Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding RA domains (unpublished observation).

>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27)

Probab=81.27  E-value=5.4  Score=24.45  Aligned_cols=40  Identities=23%  Similarity=0.290  Sum_probs=35.4

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCe
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ   41 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q   41 (128)
                      +|.|-.++|....+++..+++..++-+.+..+.++|.+-+
T Consensus         3 ~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~   42 (87)
T cd01777           3 ELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQ   42 (87)
T ss_pred             EEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHH
Confidence            5667778999999999999999999999999999997654

SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.

>KOG0007 consensus Splicing factor 3a, subunit 1 [RNA processing and modification]

Probab=81.21  E-value=0.76  Score=35.10  Aligned_cols=49  Identities=35%  Similarity=0.575  Sum_probs=42.2

Q ss_pred             CCCCEEEEEec-CCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCcc
Q 033059            8 LTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   56 (128)
Q Consensus         8 ~~g~~~~i~v~-~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L   56 (128)
                      .+|....+.+. .+..+..||.++....+++++.|++.+.|..|.|+..+
T Consensus       290 ~dg~~~~~~~~~~~~~~~~~k~k~~~~~~i~~~~q~~~~~~~~l~d~~~~  339 (341)
T KOG0007|consen  290 ADGQVIKITVQSLSENVASLKEKIADESQIPANKQKLRGEGAFLKDNRSL  339 (341)
T ss_pred             CCCceeeeccccccccccccccccccccccchhheeeccCCcccCccccc
Confidence            46777778777 67789999999999999999999999999999887443

>PRK05738 rplW 50S ribosomal protein L23; Reviewed

Probab=80.99  E-value=6.5  Score=24.24  Aligned_cols=40  Identities=20%  Similarity=0.263  Sum_probs=33.5

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEE-EeCCEE
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL-IFAGKQ   49 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L-~~~g~~   49 (128)
                      ...+.+.|++++|=.++|+.|+..+++++....- ...|+.
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            4579999999999999999999999999988754 355543

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=80.42  E-value=0.79  Score=21.56  Aligned_cols=22  Identities=32%  Similarity=0.708  Sum_probs=19.3

Q ss_pred             hhhhhhcccCCcccccccccCCCC
Q 033059           95 ICRKCYARLHPRAVNCRKKKCGHS  118 (128)
Q Consensus        95 ~Cr~c~~r~~~~~~~c~~~~c~~~  118 (128)
                      .|.+|.+.++..+..|-.  |||.
T Consensus         2 ~CP~C~~~V~~~~~~Cp~--CG~~   23 (26)
T PF10571_consen    2 TCPECGAEVPESAKFCPH--CGYD   23 (26)
T ss_pred             cCCCCcCCchhhcCcCCC--CCCC
Confidence            588999999999999986  9875

Several members are annotated as putative helicases.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	128
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-64
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		1e-58
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		3e-58
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		2e-38
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		2e-38
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		2e-38
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		3e-38
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		3e-38
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-38
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		9e-38
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		1e-37
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		1e-37
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		1e-37
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		1e-37
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		2e-37
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		2e-37
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		2e-37
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		2e-37
3jvz_X	81	E2~ubiquitin-Hect Length = 81		2e-37
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		2e-37
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		2e-37
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-37
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-37
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-37
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		3e-37
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		3e-37
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		4e-37
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		4e-37
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		4e-37
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		5e-37
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		6e-37
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		6e-37
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		9e-37
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		9e-37
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		9e-37
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		1e-36
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		1e-36
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		1e-36
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		1e-36
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		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
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		4e-36
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		4e-36
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		5e-36
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		5e-36
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		6e-36
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		7e-36
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		9e-36
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		2e-35
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		2e-35
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		2e-35
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		2e-35
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		5e-35
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		6e-35
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		6e-35
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		8e-35
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		9e-35
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-34
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-34
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		2e-34
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		2e-34
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		3e-34
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		2e-32
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		3e-32
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		2e-31
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		5e-31
4hk2_A	78	U7ub25.2540 Length = 78		2e-30
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		5e-26
3izr_p	53	Localization Of The Large Subunit Ribosomal Protein		1e-24
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		2e-22
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		3e-22
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		7e-21
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		3e-20
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		4e-20
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		5e-20
1ndd_B	76	Structure Of Nedd8 Length = 76		5e-20
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		5e-20
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		5e-20
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		5e-20
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		2e-19
3izs_p	52	Localization Of The Large Subunit Ribosomal Protein		2e-19
2dzi_A	81	2dziSOLUTION STRUCTURE OF THE N-Terminal Ubiquitin-		2e-10
2knb_A	81	Solution Nmr Structure Of The Parkin Ubl Domain In		2e-08
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		3e-08
1iyf_A	81	Solution Structure Of Ubiquitin-Like Domain Of Huma		4e-08
3b1l_X	76	Crystal Structure Of Parkin Ubiquitin-Like Domain R		4e-08
3sdl_C	164	Crystal Structure Of Human Isg15 In Complex With Ns		5e-08
3rt3_B	159	Complex Of Influenza Virus Protein With Host Anti-V		6e-08
3r66_C	164	Crystal Structure Of Human Isg15 In Complex With Ns		6e-08
2l7r_A	93	Solution Nmr Structure Of N-Terminal Ubiquitin-Like		1e-07
2faz_A	78	Ubiquitin-Like Domain Of Human Nuclear Zinc Finger		2e-07
3phx_B	79	Otu Domain Of Crimean Congo Hemorrhagic Fever Virus		3e-07
3pse_B	156	Structure Of A Viral Otu Domain Protease Bound To I		3e-07
1zkh_A	86	Solution Structure Of A Human Ubiquitin-Like Domain		7e-07
1wh3_A	87	Solution Structure Of C-Terminal Ubiquitin Like Dom		1e-06
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
1we7_A	115	Solution Structure Of Ubiquitin-Like Domain In Sf3a		3e-06
4dwf_A	90	Crystal Structure Of A Hla-B Associated Transcript		6e-06
1wx9_A	86	Solution Structure Of The N-Terminal Ubiquitin-Like		6e-06
1ttn_A	106	Solution Structure Of The Ubiquitin-Like Domain Of		1e-05
4eew_A	88	Crystal Structure Of The Ubl Domain Of Bag6 Length		1e-05
3m63_B	101	Crystal Structure Of Ufd2 In Complex With The Ubiqu		3e-05
2bwe_S	77	The Crystal Structure Of The Complex Between The Ub		3e-05
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		3e-05
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		5e-05
3zey_9	153	High-resolution Cryo-electron Microscopy Structure		1e-04
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		6e-04
1yqb_A	100	Human Ubiquilin 3 Length = 100		8e-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 =  241 bits (614), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 116/128 (90%), Positives = 122/128 (95%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRKCYARL PRA NCRK+KCGH+NQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQ 120
Query: 121 LRPKKKIK 128
           LRPKKK+K
Sbjct: 121 LRPKKKLK 128

>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 =  221 bits (562), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 106/128 (82%), Positives = 118/128 (92%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITL+VE+SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGG +EP++ ALA+KYN +K +CR CYARL P+A NCRK+KCGHSN 
Sbjct: 61  IQKESTLHLVLRLRGGGMEPTIAALAKKYNCEKKVCRDCYARLPPKATNCRKRKCGHSNS 120
Query: 121 LRPKKKIK 128
           LR KKK K
Sbjct: 121 LRLKKKPK 128

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

Iteration: 1
 Score =  219 bits (558), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 104/128 (81%), Positives = 117/128 (91%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTI LEVE+SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLE+GRTLADYN
Sbjct: 1   MQIFVKTLTGKTIALEVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEEGRTLADYN 60
Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGG++EP+L ALA+KYN +K +CR+CYARL  RA NCRKK CGH + 
Sbjct: 61  IQKESTLHLVLRLRGGVMEPTLEALAKKYNWEKKVCRRCYARLPVRATNCRKKGCGHCSN 120
Query: 121 LRPKKKIK 128
           LR KKK++
Sbjct: 121 LRMKKKLR 128

>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 =  154 bits (388), Expect = 2e-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|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score =  153 bits (387), Expect = 2e-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 =  153 bits (387), Expect = 2e-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 =  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: 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 =  152 bits (385), Expect = 3e-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|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|1YX5|B Chain B, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Length = 98

Iteration: 1
 Score =  151 bits (381), Expect = 9e-38,   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|2JWZ|A Chain A, Mutations In The Hydrophobic Core Of Ubiquitin Differentially Affect Its Recognition By Receptor Proteins Length = 76

Iteration: 1
 Score =  151 bits (381), Expect = 1e-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|3B08|A Chain A, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With Linear Di- Ubiquitin Length = 152

Iteration: 1
 Score =  151 bits (381), Expect = 1e-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|2ZVN|A Chain A, Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group Length = 154

Iteration: 1
 Score =  151 bits (381), Expect = 1e-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|3U30|A Chain A, Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin Length = 172

Iteration: 1
 Score =  150 bits (380), Expect = 1e-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|2W9N|A Chain A, Crystal Structure Of Linear Di-Ubiquitin Length = 152

Iteration: 1
 Score =  150 bits (379), Expect = 2e-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|1AAR|A Chain A, Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2) Length = 76

Iteration: 1
 Score =  150 bits (379), Expect = 2e-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|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

Iteration: 1
 Score =  150 bits (379), Expect = 2e-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|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score =  150 bits (379), Expect = 2e-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|3JVZ|X Chain X, E2~ubiquitin-Hect Length = 81

Iteration: 1
 Score =  150 bits (379), Expect = 2e-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|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 =  150 bits (379), Expect = 2e-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|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

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
          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 =  150 bits (378), Expect = 2e-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 =  150 bits (378), Expect = 2e-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|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score =  150 bits (378), Expect = 3e-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 =  150 bits (378), Expect = 3e-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|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 (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: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

>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 =  149 bits (376), Expect = 4e-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 =  149 bits (376), Expect = 4e-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|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score =  149 bits (376), Expect = 4e-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|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 =  149 bits (375), Expect = 5e-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|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin Length = 76

Iteration: 1
 Score =  149 bits (375), Expect = 6e-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|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score =  148 bits (374), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 70/76 (92%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           QIF KTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLI+AGKQLEDGRTL+DYN
Sbjct: 10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYN 69
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 70 IQRESTLHLVLRLRGG 85

>pdb|2O6V|D Chain D, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score =  148 bits (373), Expect = 9e-37,   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|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

Iteration: 1
 Score =  148 bits (373), Expect = 9e-37,   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|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score =  148 bits (373), Expect = 9e-37,   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|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

Iteration: 1
 Score =  148 bits (373), 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|1CMX|B Chain B, Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases Length = 76

Iteration: 1
 Score =  148 bits (373), 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|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score =  148 bits (373), Expect = 1e-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 (372), Expect = 1e-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|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score =  147 bits (371), Expect = 2e-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|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

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: 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 =  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|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score =  146 bits (368), Expect = 4e-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|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score =  145 bits (367), Expect = 4e-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|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 (367), Expect = 5e-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|1YJ1|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin Length = 76

Iteration: 1
 Score =  145 bits (367), Expect = 5e-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|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score =  145 bits (366), Expect = 6e-36,   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 =  145 bits (365), Expect = 7e-36,   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 (364), Expect = 9e-36,   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 =  144 bits (362), Expect = 2e-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|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score =  144 bits (362), Expect = 2e-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|2GBK|A Chain A, Crystal Structure Of The 9-10 Moad Insertion Mutant Of Ubiquitin Length = 83

Iteration: 1
 Score =  143 bits (361), Expect = 2e-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|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score =  142 bits (358), Expect = 5e-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 =  142 bits (357), Expect = 6e-35,   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 =  142 bits (357), Expect = 6e-35,   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 (356), Expect = 8e-35,   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|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score =  141 bits (356), Expect = 9e-35,   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 (354), 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|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|2GBJ|A Chain A, Crystal Structure Of The 9-10 8 Glycine Insertion Mutant Of Ubiquitin. Length = 84

Iteration: 1
 Score =  140 bits (352), Expect = 2e-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 =  140 bits (352), Expect = 2e-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 =  140 bits (352), Expect = 3e-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 =  133 bits (335), Expect = 2e-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 =  133 bits (334), Expect = 3e-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 =  130 bits (327), Expect = 2e-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 =  129 bits (324), Expect = 5e-31,   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 =  127 bits (318), Expect = 2e-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 = 5e-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|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 =  107 bits (268), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 51/52 (98%), Positives = 51/52 (98%)
Query: 77  IIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK 128
           IIEPSL ALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK
Sbjct: 1   IIEPSLQALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK 52

>pdb|1GJZ|A Chain A, Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin Length = 53

Iteration: 1
 Score =  100 bits (249), Expect = 2e-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|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score =  100 bits (248), Expect = 3e-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|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 = 95.5 bits (236), Expect = 7e-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 = 93.6 bits (231), Expect = 3e-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 = 92.8 bits (229), Expect = 4e-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 = 92.8 bits (229), Expect = 5e-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|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 92.8 bits (229), Expect = 5e-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 = 92.8 bits (229), Expect = 5e-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|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 = 92.4 bits (228), Expect = 5e-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|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 = 92.4 bits (228), Expect = 5e-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 = 90.5 bits (223), Expect = 2e-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|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 = 90.5 bits (223), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/52 (80%), Positives = 46/52 (88%)
Query: 77  IIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK 128
           IIEPSL ALA KYN DK +CRKCYARL PRA NCRK+KCGH+NQLRPKKK+K
Sbjct: 1   IIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKKLK 52

>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 = 60.8 bits (146), Expect = 2e-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|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 = 53.9 bits (128), Expect = 2e-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|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 = 53.5 bits (127), Expect = 3e-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|1IYF|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Human Parkin Length = 81

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-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|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|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 = 52.8 bits (125), Expect = 5e-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 = 52.4 bits (124), Expect = 6e-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|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 = 52.4 bits (124), Expect = 6e-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|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|2FAZ|A Chain A, Ubiquitin-Like Domain Of Human Nuclear Zinc Finger Protein Np95 Length = 78

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-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|3PHX|B Chain B, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In Complex With Isg15 Length = 79

Iteration: 1
 Score = 50.4 bits (119), 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|3PSE|B Chain B, Structure Of A Viral Otu Domain Protease Bound To Interferon- Stimulated Gene 15 (Isg15) Length = 156

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: 82  LNILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLRG 75
           ++  ST+ + LRLRG
Sbjct: 142 LKPLSTVFMNLRLRG 156

>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 = 7e-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|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 = 48.1 bits (113), Expect = 1e-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|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 = 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: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 67
Query: 59 YNIQKESTLHLVLR 72
          Y++     + L++R
Sbjct: 68 YDVGLNDIIQLLVR 81

>pdb|1Z2M|A Chain A, Crystal Structure Of Isg15, The Interferon-Induced Ubiquitin Cross Reactive Protein Length = 155

Iteration: 1
 Score = 47.8 bits (112), 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|1WE7|A Chain A, Solution Structure Of Ubiquitin-Like Domain In Sf3a120 Length = 115

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-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|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|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 = 6e-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|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|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|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 = 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: 42 VNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLV 97

>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|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|1P1A|A Chain A, Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Length = 85

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-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|3ZEY|9 Chain 9, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 153

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-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 = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 45/80 (56%), 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 DYNI-QKESTLHLVLRLRGG 76
          DY I +K   + +V + + G
Sbjct: 66 DYRIDEKNFVVVMVTKTKAG 85

>pdb|1YQB|A Chain A, Human Ubiquilin 3 Length = 100

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72
            V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   ++   T+HLV++
Sbjct: 36 FSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIK 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	128
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	6e-63
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	2e-54
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	8e-53
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	1e-52
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	2e-52
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	3e-52
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	4e-52
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	1e-51
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-51
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	8e-51
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	9e-51
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	1e-50
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	1e-50
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	3e-50
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	3e-50
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	7e-50
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	1e-49
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	2e-49
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-49
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	7e-49
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	2e-48
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	6e-48
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	8e-48
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	9e-48
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	3e-18
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	3e-47
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	1e-46
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	2e-46
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	3e-46
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	4e-46
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	7e-05
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	7e-46
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	1e-44
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-44
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	4e-44
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	4e-44
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	2e-43
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	2e-43
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	3e-43
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	2e-41
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	4e-07
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	2e-41
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	4e-39
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	4e-35
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	1e-38
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	2e-18
1we6_A	111	Splicing factor, putative; structural genomics, ub	2e-38
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	2e-37
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	7e-37
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	6e-36
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	9e-37
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	2e-36
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	7e-34
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	4e-32
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	8e-28
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	5e-23
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	4e-20
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	5e-17
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	2e-16
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	1e-15
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	2e-15
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	4e-15
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	2e-14
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	4e-14
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	6e-14
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	8e-14
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	1e-12
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	1e-12
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	2e-12
2ayj_A	56	50S ribosomal protein L40E; Zn-binding, beta-stran	1e-11
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	1e-09
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	7e-08
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	2e-07
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	2e-07
2kj6_A	97	Tubulin folding cofactor B; methods development, N	2e-07
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	2e-06
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	3e-06
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	5e-06
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	1e-05
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	1e-05
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	4e-05
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	5e-05
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	5e-05
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	2e-04
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	3e-04

>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 =  187 bits (475), Expect = 6e-63
 Identities = 116/128 (90%), Positives = 122/128 (95%)

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

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQ 120
           IQKESTLHLVLRLRGGIIEPSL ALA KYN DK +CRKCYARL PRA NCRK+KCGH+NQ
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQ 120

Query: 121 LRPKKKIK 128
           LRPKKK+K
Sbjct: 121 LRPKKKLK 128

>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 =  163 bits (416), 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

>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 =  160 bits (406), Expect = 8e-53
 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 =  160 bits (406), Expect = 1e-52
 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

>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 (403), Expect = 2e-52
 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 (403), Expect = 3e-52
 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 =  158 bits (401), Expect = 4e-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 =  157 bits (399), Expect = 1e-51
 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 =  156 bits (396), Expect = 2e-51
 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

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score =  156 bits (395), Expect = 8e-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

>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 =  157 bits (398), Expect = 9e-51
 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

>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 =  154 bits (392), Expect = 1e-50
 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

>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 =  154 bits (392), Expect = 1e-50
 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

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score =  154 bits (391), Expect = 3e-50
 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

>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 =  153 bits (389), Expect = 3e-50
 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

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score =  153 bits (387), Expect = 7e-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 =  152 bits (385), Expect = 1e-49
 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 =  151 bits (383), Expect = 2e-49
 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

>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 =  151 bits (384), Expect = 3e-49
 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

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score =  150 bits (380), Expect = 7e-49
 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 =  148 bits (376), Expect = 2e-48
 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 =  147 bits (374), Expect = 6e-48
 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 =  147 bits (373), Expect = 8e-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

>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 (380), Expect = 9e-48
 Identities = 78/112 (69%), Positives = 83/112 (74%)

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

Query: 61  IQKESTLHLVLRLRGGIIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRK 112
           IQKESTLHLVLRLRGG  E              +I +      HP      +
Sbjct: 61  IQKESTLHLVLRLRGGGGETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLE 112

>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 =  145 bits (369), Expect = 3e-47
 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

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score =  144 bits (366), Expect = 1e-46
 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

>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 =  143 bits (364), Expect = 2e-46
 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

>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 =  144 bits (365), Expect = 3e-46
 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

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score =  143 bits (363), Expect = 4e-46
 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 = 38.1 bits (89), Expect = 7e-05
 Identities = 5/22 (22%), Positives = 9/22 (40%)

Query: 48 KQLEDGRTLADYNIQKESTLHL 69
          K       ++DY+I     L+ 
Sbjct: 2  KHHHHHHPMSDYDIPTTENLYF 23

>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 =  143 bits (362), Expect = 7e-46
 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

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score =  142 bits (360), Expect = 1e-44
 Identities = 27/123 (21%), Positives = 50/123 (40%), Gaps = 11/123 (8%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQ+ VKTL G+T    +E   ++ ++K++I    G   D   L+  G    +   + D  
Sbjct: 1   MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVTDD- 59

Query: 61  IQKESTLHLVLRLRGGIIE------PSLMALARKYNQDKMICRKCYARLHPRAVNCRKKK 114
                T +L L+L GG  +       +      ++   K+     Y   +   V+ ++K 
Sbjct: 60  ----VTYYLSLKLLGGKKKKKKKSYTTKKKTKHRHVHTKLGALAFYKLENNGKVSLQQKG 115

Query: 115 CGH 117
           C  
Sbjct: 116 CPK 118

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score =  139 bits (351), Expect = 2e-44
 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

>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 =  137 bits (348), Expect = 4e-44
 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

>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 =  138 bits (349), Expect = 4e-44
 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 =  137 bits (346), Expect = 2e-43
 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 =  137 bits (346), Expect = 2e-43
 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 =  137 bits (347), Expect = 3e-43
 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

>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 =  138 bits (348), Expect = 2e-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 = 46.3 bits (109), 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

>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 =  132 bits (333), Expect = 2e-41
 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

>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 =  127 bits (321), Expect = 4e-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 =  117 bits (295), Expect = 4e-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

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score =  127 bits (320), Expect = 1e-38
 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 = 75.8 bits (186), Expect = 2e-18
 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 =  124 bits (314), Expect = 2e-38
 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

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score =  121 bits (305), Expect = 2e-37
 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 =  122 bits (306), Expect = 7e-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 =  119 bits (300), Expect = 6e-36
 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 =  122 bits (307), Expect = 9e-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 =  121 bits (305), Expect = 2e-36
 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

>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 =  120 bits (300), Expect = 7e-34
 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

>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 =  107 bits (270), Expect = 4e-32
 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

>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 = 97.4 bits (242), Expect = 8e-28
 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 = 85.1 bits (210), 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 = 77.7 bits (191), Expect = 4e-20
 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

>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 = 5e-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

>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 = 67.9 bits (166), Expect = 2e-16
 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

>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 = 66.1 bits (161), Expect = 1e-15
 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 = 65.7 bits (160), Expect = 2e-15
 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

>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 = 65.3 bits (159), Expect = 4e-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 = 63.5 bits (154), Expect = 2e-14
 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

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 63.1 bits (153), Expect = 4e-14
 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

>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 = 61.9 bits (150), Expect = 6e-14
 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

>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 = 61.8 bits (149), Expect = 8e-14
 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

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 58.8 bits (142), Expect = 1e-12
 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

>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 = 58.6 bits (141), Expect = 1e-12
 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

>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 = 58.1 bits (140), Expect = 2e-12
 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

>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 Length = 56

 Score = 55.1 bits (132), Expect = 1e-11
 Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 77  IIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKK 126
           + +P+ + + ++    K +CRKC A    RA  CR  +C HS  LR KKK
Sbjct: 3   LTDPAKLQIVQQRVFLKKVCRKCGALNPIRATKCR--RC-HSTNLRLKKK 49

>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 = 50.7 bits (121), Expect = 1e-09
 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

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus} Length = 86

 Score = 46.0 bits (109), Expect = 7e-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

>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

>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 = 45.3 bits (107), Expect = 2e-07
 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

>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 = 2e-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

>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 = 42.1 bits (99), Expect = 2e-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

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster} Length = 320

 Score = 44.0 bits (103), Expect = 3e-06
 Identities = 21/130 (16%), Positives = 46/130 (35%), Gaps = 11/130 (8%)

Query: 10  GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKEST 66
           GK   +++   DT++ ++ +I  K  + P++Q+L+   + GK   D   ++   ++    
Sbjct: 14  GKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFK 73

Query: 67  LHLVLRLRGGIIEPSLMALARK--------YNQDKMICRKCYARLHPRAVNCRKKKCGHS 118
           L +V      I +   +              ++ +         L       R  K    
Sbjct: 74  LMMVGSTEADIEDACSLPDNIGEVVDDFDDADEREESVAHSAVYLAKVQRRVRDYKIKEL 133

Query: 119 NQLRPKKKIK 128
              R  KK+ 
Sbjct: 134 APPREGKKLL 143

>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 = 41.3 bits (96), Expect = 5e-06
 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

>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 = 40.3 bits (94), 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

>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

>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 = 4e-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

>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 = 39.3 bits (91), Expect = 5e-05
 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

>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 = 38.6 bits (90), Expect = 5e-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

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster} Length = 95

 Score = 37.2 bits (86), 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 = 36.4 bits (84), 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	128
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	100.0
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.92
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.91
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.91
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.91
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.91
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.9
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.9
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.9
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.9
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.9
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.9
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.89
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.89
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.89
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.89
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.89
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.89
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.88
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.88
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.88
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.88
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.88
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.88
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.87
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.87
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.87
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.87
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.87
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.87
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.87
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.87
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.86
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.78
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.86
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.86
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.86
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.86
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.86
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.86
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.86
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.85
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.85
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.85
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.85
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.85
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.85
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.85
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.85
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.85
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.85
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.84
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.84
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.84
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.84
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.83
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.82
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.82
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.82
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.81
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.81
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.81
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.81
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.8
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.8
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.79
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.79
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.79
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.78
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.78
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.78
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.78
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.77
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.76
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.75
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.75
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.74
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.74
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.73
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.72
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.72
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.71
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.7
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.7
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.67
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.67
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.67
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.65
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.65
2ayj_A	56	50S ribosomal protein L40E; Zn-binding, beta-stran	99.63
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.63
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.63
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.62
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.61
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.59
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.58
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.5
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.43
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	99.33
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	99.32
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	99.24
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	99.21
2pjh_A	80	Protein NPL4, nuclear protein localization protein	99.1
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	99.04
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	98.87
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.85
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	98.8
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.79
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.64
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	98.61
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	98.6
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.52
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	98.4
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	98.3
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	98.07
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.95
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	97.67
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	97.64
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	97.55
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	97.53
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	97.34
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	97.23
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	97.16
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	97.13
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	97.12
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	97.11
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	97.0
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	96.87
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	96.86
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	96.8
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	96.72
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	96.67
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	96.64
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	96.51
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	96.36
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	96.28
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	96.25
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	96.2
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	95.71
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	95.69
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	95.58
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	95.23
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	95.2
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	95.15
2cu3_A	64	Unknown function protein; thermus thermophilus HB8	95.11
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	94.98
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	94.96
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	94.59
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	94.55
1rws_A	77	Hypothetical protein PF1061; residual dipolar coup	94.45
2l52_A	99	Methanosarcina acetivorans SAMP1 homolog; beta-grA	94.16
2g1e_A	90	Hypothetical protein TA0895; MOAD, molybdopterin,	93.9
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	93.69
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	93.5
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	93.42
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	93.16
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	93.15
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	92.8
3u52_E	119	Phenol hydroxylase component PHO; 4-helix bundle,	92.73
2kmc_A	102	Fermitin family homolog 1; kindlin, cytoskeleton,	92.69
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	92.47
2inc_C	83	TOUB protein; DIIRON, 4-helix bundle, carboxylate	92.46
1wgy_A	104	RAP guanine nucleotide exchange factor 5; ubiquiti	92.16
1y8x_B	98	Ubiquitin-activating enzyme E1C; ubiquitin-conjuga	92.07
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	91.9
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	91.54
3ge3_C	84	Toluene-4-monooxygenase system protein B; DIIRON h	91.51
1j0g_A	92	Hypothetical protein 1810045K17; ubiquitin-like fo	90.89
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	90.49
2c7h_A	86	RBBP6, retinoblastoma-binding protein 6, isoform 3	89.22
3qa8_A	676	MGC80376 protein; kinase ubiquitin-like domain, ph	88.21
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	87.77
2eel_A	91	Cell death activator CIDE-A; CIDE-N domain, cell d	86.99
2hj1_A	97	Hypothetical protein; structural genomics, PSI, pr	86.51
1v8c_A	168	MOAD related protein; riken structural genomics/pr	85.86
3h9d_A	119	ATG8, microtubule-associated protein 1A/1B, light	83.76
2dhz_A	120	RAP guanine nucleotide exchange factor (GEF)- like	81.57
1q1o_A	98	Cell division control protein 24; PB1 domain, PCCR	81.55
3au4_A	555	Myosin-X; protein-protein complex, motor protein c	81.42
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	80.98
3hk0_A	256	Growth factor receptor-bound protein 10; GRB10, RA	80.02

>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=100.00  E-value=1.1e-45  Score=242.89  Aligned_cols=128  Identities=91%  Similarity=1.340  Sum_probs=51.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+|+++++||.+++
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             hhHHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcCC
Q 033059           81 SLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK  128 (128)
Q Consensus        81 ~~~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~~  128 (128)
                      +++.+|.++++++++|++||+|+|++|++||+++|||+++|||||+||
T Consensus        81 sl~~la~k~n~~~~ic~~~~~~~~~~~~~~~~~~c~~~~~~~~k~~~~  128 (128)
T 3u5e_m           81 SLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKKLK  128 (128)
T ss_dssp             HHHHHHHHHHTSCEEETTTCCEECTTCSSCSCTTTTSCCCEEECCCCC
T ss_pred             hHHHHHHHhhcceEeeccccccCCchhhccchhhCCCcccccchhhcC
Confidence            999999999999999999999999999999999999999999999987

>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=99.92  E-value=5.5e-25  Score=135.45  Aligned_cols=81  Identities=53%  Similarity=0.842  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||...+
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            89999999999999999999999999999999999999999999999999999999999999999999999999997554


Q ss_pred             h
Q 033059           81 S   81 (128)
Q Consensus        81 ~   81 (128)
                      +
T Consensus        81 ~   81 (88)
T 4fbj_B           81 Q   81 (88)
T ss_dssp             -
T ss_pred             c
Confidence            3

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.91  E-value=4.2e-24  Score=128.74  Aligned_cols=75  Identities=36%  Similarity=0.595  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++|
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            789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.91  E-value=8.6e-24  Score=125.99  Aligned_cols=76  Identities=57%  Similarity=0.952  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.91  E-value=5.7e-24  Score=129.54  Aligned_cols=79  Identities=77%  Similarity=1.081  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~   79 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++++||..+
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG~g~   82 (85)
T 3n3k_B            4 MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGGGGG   82 (85)
T ss_dssp             CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC-----
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999999644

>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=99.91  E-value=1.7e-23  Score=124.70  Aligned_cols=76  Identities=95%  Similarity=1.320  Sum_probs=74.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.90  E-value=1.1e-23  Score=128.26  Aligned_cols=80  Identities=88%  Similarity=1.144  Sum_probs=74.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|+|+..+|+++.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++++||+...
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            79999999999999999999999999999999999999999999999999999999999999999999999999996543

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.90  E-value=1.1e-23  Score=129.63  Aligned_cols=78  Identities=85%  Similarity=1.232  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~   78 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++||+.
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            899999999999999999999999999999999999999999999999999999999999999999999999999953

>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=99.90  E-value=1.4e-23  Score=128.58  Aligned_cols=79  Identities=33%  Similarity=0.494  Sum_probs=76.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~   79 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.++++|+++++++||..+
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG~~~   86 (87)
T 1wh3_A            8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGPSS   86 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCSCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCCCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999999754

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.90  E-value=1.3e-23  Score=131.70  Aligned_cols=76  Identities=97%  Similarity=1.333  Sum_probs=74.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.90  E-value=8.5e-24  Score=129.62  Aligned_cols=76  Identities=58%  Similarity=0.975  Sum_probs=74.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            7899999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.90  E-value=3.4e-23  Score=129.01  Aligned_cols=77  Identities=94%  Similarity=1.256  Sum_probs=73.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++++||.
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            89999999999999999999999999999999999999999999999999999999999999999999999999994

>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=99.89  E-value=2.7e-23  Score=125.16  Aligned_cols=76  Identities=18%  Similarity=0.448  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            6899999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.89  E-value=8.7e-23  Score=125.68  Aligned_cols=70  Identities=23%  Similarity=0.433  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |+|+|++..|+++.++++|++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|+|++|++|+++
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

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.89  E-value=4.2e-23  Score=126.92  Aligned_cols=77  Identities=36%  Similarity=0.620  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+++.+++||+
T Consensus         5 m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~gg~   81 (88)
T 2hj8_A            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGL   81 (88)
T ss_dssp             EEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC-----
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.89  E-value=2e-22  Score=123.85  Aligned_cols=77  Identities=36%  Similarity=0.607  Sum_probs=74.0

Q ss_pred             CEEEEEeCCC-CEEEE-EecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTG-KTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g-~~~~i-~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+| +++.+ +|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++++||.
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 79999 59999999999999999999999999999999999999999999999999999999999984

>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=99.89  E-value=1.4e-22  Score=129.70  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            7899999999999999999999999999999999999999999999999999999999999999999999999997

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.89  E-value=1.3e-22  Score=126.32  Aligned_cols=76  Identities=28%  Similarity=0.452  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCC-CccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~-~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.++ ++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ .+|++|||++|++|+|+++++||.
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 999999999999999999999984

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.88  E-value=1.3e-22  Score=125.42  Aligned_cols=74  Identities=92%  Similarity=1.261  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++
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            79999999999999999999999999999999999999999999999999999999999999999999998874

>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=99.88  E-value=1.1e-22  Score=127.15  Aligned_cols=76  Identities=18%  Similarity=0.448  Sum_probs=74.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|.+++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            7899999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.88  E-value=2.4e-22  Score=123.86  Aligned_cols=76  Identities=33%  Similarity=0.563  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+| +|++|+++++.+++.
T Consensus         6 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~~~   81 (90)
T 4dwf_A            6 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPPQT   81 (90)
T ss_dssp             EEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC--
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCCCC
Confidence            7999999999999999999999999999999999999999999999999999999999999 899999999988774

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.88  E-value=3.2e-22  Score=125.21  Aligned_cols=77  Identities=95%  Similarity=1.295  Sum_probs=74.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+++||.
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            89999999999999999999999999999999999999999999999999999999999999999999999999884

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.88  E-value=1.4e-22  Score=125.87  Aligned_cols=74  Identities=36%  Similarity=0.620  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++  |+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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  7899999999999999999999999999999999999999999999999999999999999999997

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.88  E-value=1.9e-22  Score=123.08  Aligned_cols=72  Identities=33%  Similarity=0.489  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEE-cCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~-L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+. |+|+.+|++|||++|++|+++++
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 99999999999999999999875

>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=99.87  E-value=8e-22  Score=118.34  Aligned_cols=73  Identities=36%  Similarity=0.643  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCCEE-EEE-ecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTI-TLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~-~i~-v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++ .++ |++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|||++|++|++++++
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=99.87  E-value=1.1e-21  Score=125.46  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++++||
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            7899999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.87  E-value=6.2e-22  Score=122.81  Aligned_cols=77  Identities=29%  Similarity=0.465  Sum_probs=72.6

Q ss_pred             CEEEEEeCCCC--EEEEEecCCCcHHHHHHHHHhhh--CCCCCCeEEEeCCEEcCCCCccccc--cccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~--~~~i~v~~~~tV~~LK~~i~~~~--~ip~~~q~L~~~g~~L~d~~~L~~~--gi~~g~~i~v~~~~~   74 (128)
                      |+|+|++.+++  ++.+++++++||.+||++|++.+  ++|+++|+|+|+|+.|+|+.+|++|  +|+++++|+|+++++
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  67777879999999999999998  9999999999999999999999999  999999999999999


Q ss_pred             CCC
Q 033059           75 GGI   77 (128)
Q Consensus        75 gg~   77 (128)
                      ||.
T Consensus        88 gg~   90 (93)
T 1wgd_A           88 SGP   90 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            984

>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=99.87  E-value=1.6e-21  Score=121.49  Aligned_cols=76  Identities=29%  Similarity=0.567  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhh---hCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~---~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+.+.++|++++||.+||++|++.   .|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++...+
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~~~   79 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCCCC
Confidence            899999999999999999999999999999998   7899999999999999999999999999999999999986554

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.87  E-value=1.3e-21  Score=133.59  Aligned_cols=77  Identities=96%  Similarity=1.296  Sum_probs=74.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||.
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            89999999999999999999999999999999999999999999999999999999999999999999999999995

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.87  E-value=1.1e-21  Score=127.96  Aligned_cols=87  Identities=29%  Similarity=0.329  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|+|++. |+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+|+.+++||...+
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            68999998 88999999999999999999999999999999999999999999999999999999999999999997766


Q ss_pred             hhHHHHHh
Q 033059           81 SLMALARK   88 (128)
Q Consensus        81 ~~~~~a~k   88 (128)
                      +..++|.+
T Consensus       112 ~~~~~~~~  119 (125)
T 1j8c_A          112 DKYAAALE  119 (125)
T ss_dssp             --------
T ss_pred             chhhhhhh
Confidence            66665543

>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=99.87  E-value=4.5e-22  Score=127.25  Aligned_cols=79  Identities=32%  Similarity=0.433  Sum_probs=75.4

Q ss_pred             CEEEEEeC---CCCEEEEEecC-CCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTL---TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~---~g~~~~i~v~~-~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+++   +|+.+.++|++ ++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+|+++++||
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             CCC
Q 033059           77 IIE   79 (128)
Q Consensus        77 ~~~   79 (128)
                      +.+
T Consensus       108 k~h  110 (111)
T 1we6_A          108 PSS  110 (111)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            755

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.87  E-value=1.4e-21  Score=119.85  Aligned_cols=71  Identities=35%  Similarity=0.627  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++||| +|++|+++.|
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            6899999999999999999999999999999999999999999999999999999999999 8999999875

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=1.2e-21  Score=118.17  Aligned_cols=74  Identities=39%  Similarity=0.671  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++
T Consensus         8 m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~   81 (81)
T 2dzi_A            8 MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKPL   81 (81)
T ss_dssp             EEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999998753

>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=99.78  E-value=1.3e-23  Score=125.64  Aligned_cols=75  Identities=33%  Similarity=0.588  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|++.+|+++.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++++|
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            899999999999999999999999999999999999999999999999999999999999999999999999886

>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=99.86  E-value=6.6e-24  Score=142.48  Aligned_cols=100  Identities=75%  Similarity=0.989  Sum_probs=10.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC---
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI---   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~---   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++++||.   
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            89999999999999999999999999999999999999999999999999999999999999999999999999994   


Q ss_pred             ---CCchhHHHHHhhccchhhhhhhh
Q 033059           78 ---IEPSLMALARKYNQDKMICRKCY  100 (128)
Q Consensus        78 ---~~~~~~~~a~k~~~~k~~Cr~c~  100 (128)
                         ....|+...++.+..+++....|
T Consensus        81 kKk~~t~Pkk~~~~~~~~~~~~~~~~  106 (152)
T 3u5c_f           81 KXXXXXXXXXXXXXXXXXXXXVLSYY  106 (152)
T ss_dssp             -CCCCCCCSCCCCCCCCCCCCCCCCS
T ss_pred             ccccccccccccccccccccceeeEE
Confidence               34445555555544444444444

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.86  E-value=6.2e-22  Score=121.43  Aligned_cols=73  Identities=22%  Similarity=0.429  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCCEEEEEec--CCCcHHHHHHHH-HhhhCCCCCCeEEEeCCEEcCCCCccccccc-cCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVE--SSDTIDNVKAKI-QDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~--~~~tV~~LK~~i-~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi-~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++.++|+  +++||.+||++| ++..|+|+++|+|+|+|+.|+|+.+|++|+| ++|++|+|+++.
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            899999999998888765  999999999999 9999999999999999999999999999999 799999998764

>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=99.86  E-value=7.6e-22  Score=123.46  Aligned_cols=70  Identities=23%  Similarity=0.328  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |+|+|+++.|+++.++|++++||.+||++|++..|+|+++|+|+|+|++|+|+.+|++|+|+++++|+|+
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~   98 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELY   98 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEE
Confidence            7899999999999999999999999999999999999999999999999999999999999999999986

>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=99.86  E-value=1.7e-21  Score=131.43  Aligned_cols=77  Identities=36%  Similarity=0.589  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||+
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            68999999999999999999999999999999999999999999999999999999999999999999999999984

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.86  E-value=1.3e-21  Score=124.27  Aligned_cols=76  Identities=21%  Similarity=0.423  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+|+++....
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~~   77 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKKS   77 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC---
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCCC
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999876543

>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=99.86  E-value=4.7e-21  Score=116.64  Aligned_cols=73  Identities=30%  Similarity=0.540  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhh---hCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~---~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.   .++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+.
T Consensus         6 m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~   81 (85)
T 2wyq_A            6 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK   81 (85)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC-
T ss_pred             EEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcC
Confidence            789999999999999999999999999999998   7899999999999999999999999999999999998764

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.86  E-value=4.5e-21  Score=123.18  Aligned_cols=77  Identities=91%  Similarity=1.265  Sum_probs=74.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      ++|+|+.++|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||.+|++|+|+++++||.
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            47999999999999999999999999999999999999999999999999999999999999999999999999994

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.85  E-value=1.7e-21  Score=134.75  Aligned_cols=77  Identities=94%  Similarity=1.252  Sum_probs=75.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++++||.
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            89999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.85  E-value=2.8e-21  Score=124.10  Aligned_cols=78  Identities=28%  Similarity=0.431  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCcccccccc-------CCcEEEEEEe
Q 033059            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ-------KESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~-------~g~~i~v~~~   72 (128)
                      |+++|+...++ ++.++|.+++||.+||++|+...|+|+++|+|+|+|+.|+|+.+|++|||+       ++++|+++++
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            77788777675 588999999999999999999999999999999999999999999999999       7999999999


Q ss_pred             ecCCCCC
Q 033059           73 LRGGIIE   79 (128)
Q Consensus        73 ~~gg~~~   79 (128)
                       .||.|+
T Consensus        81 -~~g~fe   86 (118)
T 2fnj_B           81 -ADDTFE   86 (118)
T ss_dssp             -SSSCBC
T ss_pred             -CCCcee
Confidence             777543

>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=99.85  E-value=1.3e-21  Score=121.90  Aligned_cols=76  Identities=28%  Similarity=0.357  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++. |+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++++||.
T Consensus        18 m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~g~   93 (96)
T 1wx8_A           18 IRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSGP   93 (96)
T ss_dssp             EEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSCS
T ss_pred             EEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCCC
Confidence            78999998 89999999999999999999999999999999999999999999999999999999999999999884

>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=99.85  E-value=3.7e-21  Score=120.90  Aligned_cols=75  Identities=35%  Similarity=0.479  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+ +.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+|+++++++
T Consensus        23 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~   97 (100)
T 1yqb_A           23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   97 (100)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             EEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCC
Confidence            78999998885 7999999999999999999999999999999999999999999999999999999999999886

>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=99.85  E-value=5.5e-21  Score=119.56  Aligned_cols=75  Identities=23%  Similarity=0.290  Sum_probs=68.7

Q ss_pred             EEEEEeCC----CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            2 QIFVKTLT----GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         2 ~i~vk~~~----g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      .|.|+..+    ++++.++|++++||.+||++|++..|+|++.|+|+|+|++|+|+.+|++|+|++|++| ++++++|..
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            36666666    6789999999999999999999999999999999999999999999999999999999 777888764

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.85  E-value=4.3e-21  Score=120.10  Aligned_cols=73  Identities=21%  Similarity=0.423  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCCEEEE--EecCCCcHHHHHHHH-HhhhCCCCCCeEEEeCCEEcCCCCccccccc-cCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITL--EVESSDTIDNVKAKI-QDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i--~v~~~~tV~~LK~~i-~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi-~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++.+  +|++++||.+||++| ++..|+|+++|+|+|+|+.|+|+.+|++|+| ++|++|+++++.
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            789999999998777  566999999999999 8888999999999999999999999999999 999999999864

>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=99.85  E-value=1.4e-21  Score=123.51  Aligned_cols=77  Identities=23%  Similarity=0.373  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC---------------CeEEEeCCEEcC-CCCccccccccCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD---------------QQRLIFAGKQLE-DGRTLADYNIQKE   64 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~---------------~q~L~~~g~~L~-d~~~L~~~gi~~g   64 (128)
                      |+|+|+.++|+++.++|++++||.+||++|++.+++|++               .|+|+|+|+.|. |+.+|++|||++|
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            899999999999999999999999999999999998873               569999999995 6799999999999


Q ss_pred             cEEEEEEeecCCC
Q 033059           65 STLHLVLRLRGGI   77 (128)
Q Consensus        65 ~~i~v~~~~~gg~   77 (128)
                      ++|+|+.+++|..
T Consensus        88 ~~l~lv~~lr~~~  100 (105)
T 1v2y_A           88 DEVSFIKKLGQKS  100 (105)
T ss_dssp             EEEEEEECSCSCC
T ss_pred             CEEEEEehhccCC
Confidence            9999999998864

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.85  E-value=9.5e-21  Score=113.15  Aligned_cols=71  Identities=34%  Similarity=0.574  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++ +|+++.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.+
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 8899999999999999999999999999999999999999999999999999999999998764

>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=99.85  E-value=7.3e-21  Score=120.65  Aligned_cols=78  Identities=33%  Similarity=0.465  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIE   79 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~   79 (128)
                      |+|+|+..+++ +.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+|++++++|...
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 7999999999999999999999999999999999999999999999999999999999999998643

>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=99.85  E-value=5.2e-21  Score=121.37  Aligned_cols=77  Identities=27%  Similarity=0.474  Sum_probs=73.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+|+++...+.
T Consensus        24 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~~~~  100 (106)
T 1ttn_A           24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQN  100 (106)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999877663

>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=99.84  E-value=1.3e-20  Score=120.67  Aligned_cols=78  Identities=29%  Similarity=0.439  Sum_probs=71.4

Q ss_pred             CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccC-------CcEEEEEEe
Q 033059            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK-------ESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~-------g~~i~v~~~   72 (128)
                      |.|+|+...++ ++.+++.+++||.+||++|+...|+|+++|+|+|+|+.|+|++||++|||++       +++|++++|
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            77888877666 6888999999999999999999999999999999999999999999999999       999999999


Q ss_pred             ecCCCCC
Q 033059           73 LRGGIIE   79 (128)
Q Consensus        73 ~~gg~~~   79 (128)
                      . +|.|+
T Consensus        81 ~-~~~fE   86 (118)
T 4ajy_B           81 A-DDTFE   86 (118)
T ss_dssp             C-SSCCC
T ss_pred             c-CCCcc
Confidence            7 55443

>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=99.84  E-value=9.8e-21  Score=119.34  Aligned_cols=77  Identities=19%  Similarity=0.384  Sum_probs=71.9

Q ss_pred             CEEEEEeCCC----CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCC-CccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g----~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~-~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|+...+    +++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+ .+|++|+|++|++|+|+.+.+|
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            7899998754    6899999999999999999999999999999999999999877 6999999999999999999988


Q ss_pred             CC
Q 033059           76 GI   77 (128)
Q Consensus        76 g~   77 (128)
                      |.
T Consensus        88 g~   89 (102)
T 1v5o_A           88 GL   89 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            84

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.84  E-value=2.5e-20  Score=117.26  Aligned_cols=74  Identities=32%  Similarity=0.446  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|+.. |+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+|+.++++
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 889999999999999999999999999999999999999999999999999999999999988764

>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=99.84  E-value=2e-20  Score=120.31  Aligned_cols=78  Identities=28%  Similarity=0.544  Sum_probs=72.1

Q ss_pred             CEEEEEeC----------CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTL----------TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~----------~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      ++|.|+..          +|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+|+
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            36777765          36789999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 033059           71 LRLRGGII   78 (128)
Q Consensus        71 ~~~~gg~~   78 (128)
                      ++++||+.
T Consensus       106 ~rl~GGk~  113 (115)
T 1we7_A          106 LKERSGPS  113 (115)
T ss_dssp             ECCCSCCS
T ss_pred             EEcCCCCC
Confidence            99999964

>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=99.83  E-value=2.2e-20  Score=121.14  Aligned_cols=77  Identities=26%  Similarity=0.425  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCCEE-EEEecCCCcHHHHHHHHH-----hhhCCCC--CCeEEEeCCEEcCCCCccccccccCC------cE
Q 033059            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQ-----DKEGIPP--DQQRLIFAGKQLEDGRTLADYNIQKE------ST   66 (128)
Q Consensus         1 m~i~vk~~~g~~~-~i~v~~~~tV~~LK~~i~-----~~~~ip~--~~q~L~~~g~~L~d~~~L~~~gi~~g------~~   66 (128)
                      |+|+|++.+|+.+ .+++++++||.+||++|+     +..++|+  ++|+|+|+|+.|+|+.+|++|+|++|      ++
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 699999999999999995     4557886  79999999999999999999999988      78


Q ss_pred             EEEEEeecCCC
Q 033059           67 LHLVLRLRGGI   77 (128)
Q Consensus        67 i~v~~~~~gg~   77 (128)
                      ++|+++++||.
T Consensus        97 mhlVlrl~g~~  107 (126)
T 1se9_A           97 MHVIIQAPVTE  107 (126)
T ss_dssp             EEEEECCCSSC
T ss_pred             EEEEeccCCcc
Confidence            99999999874

>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=99.82  E-value=5.7e-20  Score=122.58  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+++++++||
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            6799999999999999999999999999999999999999999999999999999999999999999999999997

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.82  E-value=5.4e-20  Score=125.62  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=74.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|.++++|+++++++||
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            7999999999999999999999999999999999999999999999999999999999999999999999998877

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.82  E-value=2.5e-20  Score=127.31  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+++.++|++++||.+||++|+..+|+|++.|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
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            5789999999999999999999999999999999999999999999999999999999999999999999999997

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.81  E-value=2.5e-20  Score=121.19  Aligned_cols=77  Identities=23%  Similarity=0.359  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHh------hhCC--CCCCeEEEeCCEEcCCCCccccccccCCc--EEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD------KEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKES--TLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~------~~~i--p~~~q~L~~~g~~L~d~~~L~~~gi~~g~--~i~v~   70 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++      ..++  |+++|+|+|+|+.|+|+.+|++|+|.+++  +|+|+
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            68999999999999999999999999999998      5677  48999999999999999999999999776  78899


Q ss_pred             EeecCCC
Q 033059           71 LRLRGGI   77 (128)
Q Consensus        71 ~~~~gg~   77 (128)
                      ++++++.
T Consensus        98 ~r~~~~~  104 (125)
T 2gow_A           98 ARETLPE  104 (125)
T ss_dssp             ECSCCSS
T ss_pred             ecCCCCc
Confidence            9887763

>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=99.81  E-value=2e-19  Score=115.45  Aligned_cols=76  Identities=24%  Similarity=0.382  Sum_probs=67.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHh------hhCC--CCCCeEEEeCCEEcCCCCccccccccCC--cEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD------KEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKE--STLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~------~~~i--p~~~q~L~~~g~~L~d~~~L~~~gi~~g--~~i~v~   70 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++      ..++  |+++|+|+|.|+.|+|+.+|++|+|..+  .+|||+
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            78999999999999999999999999999998      4464  6999999999999999999999999766  577888


Q ss_pred             EeecCC
Q 033059           71 LRLRGG   76 (128)
Q Consensus        71 ~~~~gg   76 (128)
                      +++.+.
T Consensus        97 lr~~~~  102 (116)
T 1wgh_A           97 ARETLP  102 (116)
T ss_dssp             ECSSCS
T ss_pred             ccCCCC
Confidence            776544

>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=99.81  E-value=2.6e-19  Score=119.33  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=73.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+..++
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            8999999999999999999999999999999999999999999999999999999999999999999999987765

>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=99.81  E-value=2.2e-19  Score=121.04  Aligned_cols=73  Identities=33%  Similarity=0.428  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-e-CCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-F-AGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~-~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+ | +|+.|+|+.+|++|+|.+|++|+++++.
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=99.80  E-value=3.1e-20  Score=116.88  Aligned_cols=71  Identities=34%  Similarity=0.574  Sum_probs=66.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++ +|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+|+.+
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            4688887 8889999999999999999999999999999999999999999999999999999999999764

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.80  E-value=4.1e-19  Score=111.91  Aligned_cols=72  Identities=24%  Similarity=0.253  Sum_probs=67.1

Q ss_pred             CEEEEEeCCC--CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccc-cCCcEEEEEEe
Q 033059            1 MQIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g--~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi-~~g~~i~v~~~   72 (128)
                      |+|+|+...+  .++.++|+|++||.+||++|++++|+|++.|||+|+|+.++|+.+|++||| ++|+++++++-
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~   99 (105)
T 4dbg_A           25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLL   99 (105)
T ss_dssp             EEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEEC
T ss_pred             EEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEE
Confidence            6899999874  678999999999999999999999999999999999999999999999999 69999999873

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.79  E-value=1.6e-19  Score=113.12  Aligned_cols=70  Identities=24%  Similarity=0.394  Sum_probs=63.7

Q ss_pred             CEEEEEeCCCC--EEEEEecCCCcHHHHHHHHHhh-hCCC-CCCeEEEeCCEEcCCCCccccc--cccCCcEEEEE
Q 033059            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDK-EGIP-PDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~--~~~i~v~~~~tV~~LK~~i~~~-~~ip-~~~q~L~~~g~~L~d~~~L~~~--gi~~g~~i~v~   70 (128)
                      |+|+|++++++  ++.+++++++||.+||++|++. .++| +++|+|+|+|+.|+|+.+|++|  +|+++++|+|+
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            68999999887  6788999999999999999986 4555 5999999999999999999999  99999999874

>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=99.79  E-value=3.2e-19  Score=110.00  Aligned_cols=71  Identities=21%  Similarity=0.428  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCCEEEE-EecCCCcHHHHHHHHHhhhCCCCCCeEEE---eCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i-~v~~~~tV~~LK~~i~~~~~ip~~~q~L~---~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|+. .|+++.+ +|++++||.+||++|++.+++|+++|+|+   |+|+.|+|+.+|++|+|++|++|+|+..
T Consensus         8 m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~   82 (90)
T 1v5t_A            8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             EEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEec
Confidence            7899997 7889999 99999999999999999999999999999   9999999999999999999999998754

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.79  E-value=6.1e-19  Score=107.64  Aligned_cols=70  Identities=29%  Similarity=0.452  Sum_probs=64.7

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      ++++..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+|+..
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            3455668899999999999999999999999999999999999999999999999999999999998753

>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=99.78  E-value=6.5e-19  Score=109.45  Aligned_cols=73  Identities=26%  Similarity=0.386  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCC-CccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~-~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+..+|+.+.++|++++||.+||++|++..   +++|+|+|+|+.|+|+ .+|++|+|++|++|+|+++.++.
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~~   81 (95)
T 1wia_A            8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCCC
Confidence            7899999999999999999999999999999887   8999999999999998 99999999999999999887654

>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=99.78  E-value=7e-19  Score=111.69  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=68.4

Q ss_pred             CEEEEEeCCC---CEEEEEecC---------CCcHHHHHHHHHhhh--CCCCCC-eEEEeCCEEcCCCCccccccccCCc
Q 033059            1 MQIFVKTLTG---KTITLEVES---------SDTIDNVKAKIQDKE--GIPPDQ-QRLIFAGKQLEDGRTLADYNIQKES   65 (128)
Q Consensus         1 m~i~vk~~~g---~~~~i~v~~---------~~tV~~LK~~i~~~~--~ip~~~-q~L~~~g~~L~d~~~L~~~gi~~g~   65 (128)
                      |+|+|++.++   +++.++|++         ++||.+||++|++.+  ++|+++ |+|+|+|+.|+|+.+|++|+|++|+
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            6899999988   789999554         599999999999999  999999 9999999999999999999999999


Q ss_pred             EEEEEEeec
Q 033059           66 TLHLVLRLR   74 (128)
Q Consensus        66 ~i~v~~~~~   74 (128)
                      +|+|+.+..
T Consensus        93 ~i~lv~~~~  101 (107)
T 1x1m_A           93 TVHVLRKSW  101 (107)
T ss_dssp             EEEEEESSC
T ss_pred             EEEEEeCCC
Confidence            999998754

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1e-18  Score=111.44  Aligned_cols=75  Identities=16%  Similarity=0.294  Sum_probs=68.3

Q ss_pred             EEEEE-eCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            2 QIFVK-TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         2 ~i~vk-~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .|.|+ ..+++.+.++++++.||.+||+.++..+++|++.|+|+|+|+.|.|+.||.+|||++|.+|||+++....
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~p   92 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTNP   92 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESCT
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCCC
Confidence            45555 5567899999999999999999999999999999999999999999999999999999999999986443

>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=99.78  E-value=4.9e-19  Score=110.39  Aligned_cols=71  Identities=17%  Similarity=0.292  Sum_probs=66.0

Q ss_pred             CEEEEEeCCCCEE-EEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~-~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++ .|+++ .++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ +|++|+|++|++|+|+...
T Consensus         8 m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~   79 (96)
T 1wgg_A            8 YSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             EEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             EEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecc
Confidence            6899996 67889 6999999999999999999999999999999999999999 9999999999999987543

>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=99.77  E-value=1.7e-18  Score=106.93  Aligned_cols=72  Identities=24%  Similarity=0.433  Sum_probs=66.1

Q ss_pred             CEEEEEeCCCCEEEEEecCC-----CcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCC-CCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESS-----DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~-----~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d-~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++ .++.+.++|+++     +||.+||++|++.+++|+++|+|+|+|+.|.| +.+|++|+|++|++|+|+.+.
T Consensus         8 ~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~~   85 (92)
T 1wxv_A            8 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   85 (92)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             EEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEecC
Confidence            6899998 578999999995     99999999999999999999999999999988 668999999999999998654

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.76  E-value=4.7e-20  Score=127.08  Aligned_cols=112  Identities=25%  Similarity=0.343  Sum_probs=20.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|+|++++|+++.++|++++||.+||++|++..++|+++|+|+|+|++|+|+.+|+     ++++|+|+++++||..+-
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            899999999999999999999999999999999999999999999999999999998     899999999999996421


Q ss_pred             ------hhHH-----------HHHhhcc--------chhhhhhhhcccCCcccccccccCCCC
Q 033059           81 ------SLMA-----------LARKYNQ--------DKMICRKCYARLHPRAVNCRKKKCGHS  118 (128)
Q Consensus        81 ------~~~~-----------~a~k~~~--------~k~~Cr~c~~r~~~~~~~c~~~~c~~~  118 (128)
                            .|+.           ....++-        ....|..|+.+.+..+.++|. .||+.
T Consensus        76 kK~~~~tPK~~k~~kKkvkl~~Lk~y~Vd~~Gkv~~~~~~Cp~Cg~g~fma~h~dR~-~CGkC  137 (189)
T 2xzm_9           76 KKKSYTTKKKTKHRHVHTKLGALAFYKLENNGKVSLQQKGCPKCGPGIFMAKHYDRH-YCGKC  137 (189)
T ss_dssp             CCCCCCSSSCCCCCCCCCCCSCCCCEEEETTTEEEECSEECSTTCSSCEEEECSSCE-EETTT
T ss_pred             cccccCCCccccccccccCCceeeEEEECCCceEEEccccCCccCCCccccCccCCC-ccCCc
Confidence                  1110           0111221        124788899877766767765 66654

>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=99.75  E-value=1e-17  Score=104.01  Aligned_cols=80  Identities=18%  Similarity=0.402  Sum_probs=75.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.++|++.++|+|+|+.|.++.|+++|++++|++|+++++++||....
T Consensus         8 i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG~~~~   87 (94)
T 2io1_B            8 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVPES   87 (94)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEESCCC-
T ss_pred             EEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCCccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999995433

>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=99.75  E-value=1.2e-18  Score=108.37  Aligned_cols=71  Identities=21%  Similarity=0.354  Sum_probs=64.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|+. .++++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+| .+|++|+|+++++|+|+...
T Consensus        18 ~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~Ldd-~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPED-KTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCSS-SBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeCCc-CcHHHCCCCCCCEEEEEecc
Confidence            5788985 68899999999999999999999999999999999999999954 59999999999999987543

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.74  E-value=6e-18  Score=124.52  Aligned_cols=74  Identities=96%  Similarity=1.299  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++++
T Consensus       234 MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRLr  307 (307)
T 3ai5_A          234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  307 (307)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC---
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999998864

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=3.1e-18  Score=105.16  Aligned_cols=69  Identities=23%  Similarity=0.303  Sum_probs=62.9

Q ss_pred             CEEEEEeCCCCEE--EE-EecCCCcHHHHHHHHHhh-hCCCCCCeEEEeC--CEEcCCCCccccccccCCcEEEE
Q 033059            1 MQIFVKTLTGKTI--TL-EVESSDTIDNVKAKIQDK-EGIPPDQQRLIFA--GKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         1 m~i~vk~~~g~~~--~i-~v~~~~tV~~LK~~i~~~-~~ip~~~q~L~~~--g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      |+|+|++..|+.+  .+ +|++++||.+||++|++. .++||++|+|+|.  |+.|+|+.+|++|+|.+|++|++
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            7899999987764  58 899999999999999994 7999999999976  99999999999999999999875

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.4e-17  Score=103.60  Aligned_cols=70  Identities=14%  Similarity=0.222  Sum_probs=61.9

Q ss_pred             CEEEEEeCCCC--EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC--CE---Ec-CCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GK---QL-EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~--~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~--g~---~L-~d~~~L~~~gi~~g~~i~v~   70 (128)
                      ++|+|+...+.  .++++|++++||++||++|+..+|+|++.|+|+|.  |+   .| +|+.+|++|+|++|++|+|+
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            36788876553  78999999999999999999999999999999997  45   44 89999999999999999985

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.1e-17  Score=104.78  Aligned_cols=74  Identities=19%  Similarity=0.273  Sum_probs=66.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe--CCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~--~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |.+++..+.|+++.++|++++||.+||++|++.+||||++|+|++  .|+ |+|+.+|++|+|++|++|++++....
T Consensus         9 m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~~~   84 (100)
T 2dzm_A            9 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPDLP   84 (100)
T ss_dssp             EEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSSSC
T ss_pred             eEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecCCC
Confidence            566677778999999999999999999999999999999999986  566 99999999999999999999876443

>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=99.72  E-value=8.6e-17  Score=99.19  Aligned_cols=80  Identities=16%  Similarity=0.379  Sum_probs=75.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.|+|++.++|+|+|+.|.++.|.++|++++|++|+++..+.||..+.
T Consensus         6 i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~gg~~~~   85 (91)
T 2io0_B            6 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVYLE   85 (91)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCCCCCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCcccc
Confidence            57899998999999999999999999999999999999999999999999999999999999999999999999997543

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.71  E-value=1.7e-17  Score=101.44  Aligned_cols=71  Identities=17%  Similarity=0.278  Sum_probs=62.2

Q ss_pred             EEEEEeC--CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe-------CCEEcCCCCccccccccCCcEEEEEEe
Q 033059            2 QIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-------AGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         2 ~i~vk~~--~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~-------~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .|.|...  +.+.+++.+++++||.+||++|+..+|+||+.|+|+|       .|+.|+|+.+|++|+|++|++|||+-.
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            4555432  4567889999999999999999999999999999997       478899999999999999999999864

>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=99.70  E-value=1.9e-17  Score=124.74  Aligned_cols=77  Identities=31%  Similarity=0.567  Sum_probs=71.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHh---hhCCCCCCeEEEeCCEEcCCCCccccccccCCcEE-EEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD---KEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL-HLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~---~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i-~v~~~~~gg   76 (128)
                      |+|+||+.+|+++.|+|++++||.+||++|+.   ..++|+++|+|+|+|+.|+|+.+|++|+|++|++| +++.+.+++
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            78999999999999999999999999999999   56799999999999999999999999999999998 677777776


Q ss_pred             C
Q 033059           77 I   77 (128)
Q Consensus        77 ~   77 (128)
                      .
T Consensus        88 ~   88 (368)
T 1oqy_A           88 Q   88 (368)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.70  E-value=5.5e-17  Score=101.17  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=61.4

Q ss_pred             EEEEEeCCC--CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC---EE----cCCCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g--~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g---~~----L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      .|.|++...  ..++++|++++||++||++|+..+|+|++.|+|+|.|   +.    ++|+.+|++|+|++|++|+|+-
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            577776543  4789999999999999999999999999999999988   33    4899999999999999999864

>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=99.67  E-value=4e-16  Score=96.58  Aligned_cols=76  Identities=17%  Similarity=0.403  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.|++++.++|+|+|+.|.++.|+++|++++|++|++++++.||
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            5788998899999999999999999999999999999999999999999999999999999999999999999987

>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=99.67  E-value=1.7e-16  Score=98.57  Aligned_cols=71  Identities=20%  Similarity=0.279  Sum_probs=61.9

Q ss_pred             CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC---EE----cCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g---~~----L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +.|+|++.... .+++++++++||.+||++|+..+|+|+++|+|+|.|   +.    ++|+.+|++|||++|++|+|+-
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d   86 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVID   86 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBC
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEE
Confidence            35778775442 688999999999999999999999999999999986   43    5899999999999999998864

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.67  E-value=6.1e-17  Score=102.71  Aligned_cols=71  Identities=21%  Similarity=0.276  Sum_probs=64.9

Q ss_pred             CEEEEEeCCCCEEEEEec-CCCcHHHHHHHHHhhhCCCCCCeEEEeCCE-----------E----cCCCCccccccccCC
Q 033059            1 MQIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-----------Q----LEDGRTLADYNIQKE   64 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~-~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~-----------~----L~d~~~L~~~gi~~g   64 (128)
                      |.|+|++.+|.. .++|+ +++||.+||++|++.+++|++.|+|+|.|+           .    ++|+.+|++|||++|
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            789999999864 79999 999999999999999999999999999888           4    578999999999999


Q ss_pred             cEEEEEEe
Q 033059           65 STLHLVLR   72 (128)
Q Consensus        65 ~~i~v~~~   72 (128)
                      ++|+|...
T Consensus        87 ~~L~l~~~   94 (107)
T 1wf9_A           87 SMVYLAYE   94 (107)
T ss_dssp             CEEECCCS
T ss_pred             CEEEEEeC
Confidence            99998754

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.65  E-value=5.3e-16  Score=97.83  Aligned_cols=78  Identities=15%  Similarity=0.348  Sum_probs=74.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~   78 (128)
                      |+|.|++.+|+.+.+.|.+++++..|+..++++.+++++.++|+|+|+.|.++.|.++|++++|++|+|++++.||..
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            578999989999999999999999999999999999999999999999999999999999999999999999999953

>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=99.65  E-value=7.3e-16  Score=99.84  Aligned_cols=72  Identities=14%  Similarity=0.248  Sum_probs=62.7

Q ss_pred             CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC---E---E-cCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---K---Q-LEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g---~---~-L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |.|+|++..+. .+++++++++||++||++|+..+|+|+++|+|+|.|   +   . ++|+.+|++|||++|++|||+-.
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            46778775443 688999999999999999999999999999999987   3   2 47999999999999999998864

>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=99.63  E-value=1.8e-17  Score=91.27  Aligned_cols=47  Identities=36%  Similarity=0.597  Sum_probs=43.1

Q ss_pred             CCchhHHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcC
Q 033059           78 IEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKI  127 (128)
Q Consensus        78 ~~~~~~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~  127 (128)
                      +++++.++|+++++++++||.||+|++++|++||+  |||+ +|||||+.
T Consensus         4 ~e~~~~~lA~k~~~~k~ICrkC~ARnp~~A~~CRK--Cg~~-~LRpKkk~   50 (56)
T 2ayj_A            4 TDPAKLQIVQQRVFLKKVCRKCGALNPIRATKCRR--CHST-NLRLKKKE   50 (56)
T ss_dssp             CCSCCSSTTTTCSCCCEEETTTCCEECTTCSSCTT--TCCC-CEEECCCC
T ss_pred             cchhHHHHHHHHHhchhhhccccCcCCcccccccC--CCCC-CCCccccc
Confidence            46788899999999999999999999999999995  9965 99999975

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.63  E-value=4.6e-16  Score=94.95  Aligned_cols=70  Identities=24%  Similarity=0.349  Sum_probs=62.5

Q ss_pred             CEEEEEeCCCCEEEEE-ecCCCcHHHHHHHHHhhhCCCCCCeEEEeC--CEEcC---CCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLE---DGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~-v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~--g~~L~---d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+|.|++.+|+ ..+. +++++||.+||+.|++.+++|+++|+|+|+  ++.|+   |+.+|++|||.+|++|+|.-
T Consensus         1 m~i~vr~~~G~-~~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~   76 (86)
T 2kzr_A            1 WRVRCKAKGGT-HLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEE   76 (86)
T ss_dssp             CCEEEEETTEE-EEECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCC
T ss_pred             CEEEEEcCCCC-EEeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEe
Confidence            89999999995 4577 999999999999999999999999999986  47774   68899999999999998764

>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=99.63  E-value=1.9e-15  Score=95.42  Aligned_cols=75  Identities=13%  Similarity=0.339  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|.|++ +|+.+.+.|.+++++..|++.++++.|++++.++|+|+|+.|.++.|.++|++++|++|++++++.||
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            5788998 89999999999999999999999999999999999999999999999999999999999999999987

>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=99.62  E-value=3.3e-15  Score=88.26  Aligned_cols=70  Identities=16%  Similarity=0.384  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.|+|++.++|+|+|+.|.++.|.++|++++|++|+++
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            6799999999999999999999999999999999999999999999999999999999999999999986

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.61  E-value=1.2e-15  Score=97.03  Aligned_cols=76  Identities=16%  Similarity=0.421  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|.|++.+|+.+.+.|.+++++..|++.++++.+++++.++|+|.|+.|.++.|.++|++++|++|+|++.+.||
T Consensus        27 I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~Gg  102 (110)
T 2k8h_A           27 VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTGG  102 (110)
T ss_dssp             EEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccCc
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999999998

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.59  E-value=1.8e-15  Score=112.33  Aligned_cols=72  Identities=22%  Similarity=0.445  Sum_probs=65.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE---eCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~---~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|+. +|+++.++|++++||++||++|++.+|+||++|+|+   |+|+.|+|+.+|++|+|++|++|+|+...
T Consensus         6 i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~   80 (320)
T 3shq_A            6 VVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGST   80 (320)
T ss_dssp             EEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccc
Confidence            5788986 688999999999999999999999999999999999   89999999999999999999999988543

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.58  E-value=2.1e-14  Score=86.31  Aligned_cols=70  Identities=10%  Similarity=0.274  Sum_probs=66.9

Q ss_pred             CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |+|.|++.+|+ .+.+.|.+++++..|++.++++.|++++.++|+|.|+.|.++.|.++|++++|++|+|+
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=99.50  E-value=1.1e-13  Score=86.11  Aligned_cols=71  Identities=17%  Similarity=0.253  Sum_probs=61.0

Q ss_pred             EEEEEe---CCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC------E-Ec-CCCCccccccccCCcEEEEE
Q 033059            2 QIFVKT---LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG------K-QL-EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~---~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g------~-~L-~d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|+|+.   .+++.+++.+++++||.+||.+|+..+|+|+..|+|.|.+      . .| +|..+|++|+|.+|++|+|.
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   3677899999999999999999999999999999999863      2 35 67889999999999999987


Q ss_pred             Ee
Q 033059           71 LR   72 (128)
Q Consensus        71 ~~   72 (128)
                      ..
T Consensus        91 d~   92 (97)
T 1wjn_A           91 WS   92 (97)
T ss_dssp             CC
T ss_pred             ec
Confidence            64

>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=99.43  E-value=1.6e-12  Score=82.85  Aligned_cols=75  Identities=17%  Similarity=0.416  Sum_probs=70.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|.|+..+|..+.+.|.+++++..|+..++++.|++++.++|+|+|+.|.++.|..++++++|++|+|+..+.|
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            468888888999999999999999999999999999999999999999999999999999999999999987654

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=99.33  E-value=9e-12  Score=86.54  Aligned_cols=76  Identities=13%  Similarity=0.315  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|.|+. +|....+.|.+++++..|+..++++.|++++.++|+|+|+.|.++.|..++++++|++|+++..+.||.
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            4677864 888999999999999999999999999999999999999999999999999999999999999999985

>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=99.32  E-value=4.1e-12  Score=87.15  Aligned_cols=76  Identities=12%  Similarity=0.326  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|.|+. +|..+.+.|.+++++..|+..++++.|+++..++|+|+|+.|.++.|..++++++|++|+|++.+.||.
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            4677764 888999999999999999999999999999999999999999999999999999999999999999994

>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=99.24  E-value=1.2e-10  Score=68.59  Aligned_cols=70  Identities=16%  Similarity=0.316  Sum_probs=64.4

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      .+.+++.....+.+.|.++++|.+|-.....+.+||++ .++|.|.|..|+++.++++|++++|+.|.+++
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            45667766667999999999999999999999999999 99999999999999999999999999999875

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=99.21  E-value=1.7e-12  Score=90.21  Aligned_cols=85  Identities=14%  Similarity=0.330  Sum_probs=5.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCCCc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEP   80 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~~~   80 (128)
                      |+|.| ..+|....+.|.+++.+..|++.++++.|++++.++++|+|+.+.++.|.+++++++|++|+++..+.||..-.
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG~~~~  100 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGLTLA  100 (227)
T ss_dssp             ---------------------------------------------------------------------------CCCHH
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCCchHh
Confidence            56777 66888899999999999999999999999999999999999999999999999999999999999999997444


Q ss_pred             hhHHHH
Q 033059           81 SLMALA   86 (128)
Q Consensus        81 ~~~~~a   86 (128)
                      .+-..|
T Consensus       101 ~l~~~a  106 (227)
T 3v7o_A          101 VLLQIA  106 (227)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444444

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=99.10  E-value=3.8e-11  Score=72.09  Aligned_cols=69  Identities=14%  Similarity=0.229  Sum_probs=58.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEE---c--CCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ---L--EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~---L--~d~~~L~~~gi~~g~~i~v~   70 (128)
                      |.|.|++.+| ++.+++++++|+.+|+++|++.++++++.|.|.++-.+   |  .++.+|+++||++|++|++.
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            5688999887 68899999999999999999999999888777654433   3  47789999999999999874

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=99.04  E-value=2.1e-09  Score=66.60  Aligned_cols=70  Identities=13%  Similarity=0.295  Sum_probs=64.6

Q ss_pred             CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      +.|.|+..+|. .+.+.|.+++++..|....+++.+++++.++++|.|..|.++.|..++++++|++|.|+
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            35777777884 78999999999999999999999999999999999999999999999999999999885

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=98.87  E-value=5.2e-10  Score=60.98  Aligned_cols=39  Identities=41%  Similarity=0.611  Sum_probs=34.4

Q ss_pred             HHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcC
Q 033059           86 ARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKI  127 (128)
Q Consensus        86 a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~  127 (128)
                      +.+...++.+|+.|++++++++.+|++  ||++ +||||++-
T Consensus         7 ie~r~~~k~iCpkC~a~~~~gaw~CrK--CG~~-~lr~k~k~   45 (51)
T 3j21_g            7 AEARIFKKYVCLRCGATNPWGAKKCRK--CGYK-RLRPKAKE   45 (51)
T ss_dssp             HHHHSSSEEECTTTCCEECTTCSSCSS--SSSC-CCEEECCC
T ss_pred             HHHHHhCCccCCCCCCcCCCCceecCC--CCCc-cccccccc
Confidence            456677889999999999999999997  9977 99999873

>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=98.85  E-value=1.1e-08  Score=71.55  Aligned_cols=75  Identities=13%  Similarity=0.320  Sum_probs=70.0

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      .|.|+. ++....+.+..++++..|++..+++.|++++.++++|.|+.+.++.+..++.++++++|.++..+.||.
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            566766 677889999999999999999999999999999999999999999999999999999999999999985

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=98.80  E-value=5.2e-10  Score=83.69  Aligned_cols=76  Identities=13%  Similarity=0.346  Sum_probs=0.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      ++|.|+. +|....+.|..++++..|++.++++.|++++.++++|+|+.+.++.|.+++++++|++|+++..+.||-
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 567788999999999999999999999999999999999999999999999999999999999999993

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.79  E-value=5.6e-08  Score=59.51  Aligned_cols=70  Identities=14%  Similarity=0.309  Sum_probs=65.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +.|.|+. +|....+.+..++....|....+++.|++++.++++|.|..+.++.|-.++++++|++|.+++
T Consensus        22 IniKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~   91 (95)
T 2l76_A           22 FPLKIRC-RADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVV   91 (95)
T ss_dssp             EEEEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEE
T ss_pred             EEEEEEc-CCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEE
Confidence            3577775 688899999999999999999999999999999999999999999999999999999999876

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.64  E-value=2.4e-07  Score=56.85  Aligned_cols=68  Identities=24%  Similarity=0.355  Sum_probs=51.4

Q ss_pred             EEEEeC-CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEc--CCCCcccccccc-CCcEEEEE
Q 033059            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL--EDGRTLADYNIQ-KESTLHLV   70 (128)
Q Consensus         3 i~vk~~-~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L--~d~~~L~~~gi~-~g~~i~v~   70 (128)
                      |+|=++ .+..+.+.+.++.||..||++|++++|||++.|+|+|.|+.|  +.+.....|.-. +..-|.++
T Consensus        15 vHVf~~~~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~Tt~~~Pl~L~   86 (94)
T 4efo_A           15 IHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVV   86 (94)
T ss_dssp             EEEEETTTTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCCCBTTBCEEEE
T ss_pred             EEEEEcccceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccccCCCCccccCCCCCCCCCEEEE
Confidence            344333 467788999999999999999999999999999999999865  555666666532 33444444

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=98.61  E-value=4.4e-09  Score=79.71  Aligned_cols=75  Identities=12%  Similarity=0.308  Sum_probs=0.0

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      .|.|+. ++....+.|..++++..|++.++++.|+++..++++|+|+.|.++.|.+++++++|++|.++..+.||.
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            456655 567778999999999999999999999999999999999999999999999999999999999999995

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=98.60  E-value=2.9e-07  Score=55.84  Aligned_cols=73  Identities=18%  Similarity=0.186  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |.|+|-..+++...+.|.|++++.++-++..+++++++++-.|.|+++.|+-+.++.-.||.+|+.+.++...
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            5788988999999999999999999999999999999999999999999999999999999999999997643

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.52  E-value=3.7e-07  Score=54.55  Aligned_cols=68  Identities=15%  Similarity=0.224  Sum_probs=57.7

Q ss_pred             EEEEEe--CCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-----CeEEEeCCEEcCCCCccccccccCCcEEEE
Q 033059            2 QIFVKT--LTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-----QQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (128)
Q Consensus         2 ~i~vk~--~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-----~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v   69 (128)
                      .|++..  ..++.+.+.++...||..|.+.+.+.++++..     .+++.-++..|.++..|++|+|.+|+.|.+
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            466653  46889999999999999999999999886642     356678889999999999999999999975

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=98.40  E-value=7.8e-07  Score=57.49  Aligned_cols=71  Identities=27%  Similarity=0.393  Sum_probs=57.3

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-------------------------------------CeEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-------------------------------------QQRLI   44 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-------------------------------------~q~L~   44 (128)
                      .|.|+.++|+..++.|+.+.||++++..|..+.||+..                                     .++|.
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            37899999999999999999999999999999998754                                     22221


Q ss_pred             e--CCEEcCCCCccccccccCCcEEEEEEe
Q 033059           45 F--AGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus        45 ~--~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .  .+.-|+++.+|.++||.++++|.+-.+
T Consensus        93 ~dd~~~WLD~srtL~EQGI~e~~tllLRrK  122 (128)
T 2kc2_A           93 TDDELNWLDHGRTLREQGVEEHETLLLRRK  122 (128)
T ss_dssp             CSSSEEEECSSSCHHHHTCCTTSEEEEEES
T ss_pred             ccCCCCcccCCCcHHHcCCCCCCEEEEEEE
Confidence            1  124567899999999999999876543

>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=98.30  E-value=7.9e-06  Score=48.95  Aligned_cols=68  Identities=19%  Similarity=0.383  Sum_probs=58.5

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEc---CCCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL---EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L---~d~~~L~~~gi~~g~~i~v~   70 (128)
                      .|.||..+|..+.-.+..++||.+|...|.. .+.++..+.|+  |-.+.|   +.+.+|.+.|+.+.++|.|-
T Consensus         9 ~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~ve   81 (84)
T 3qx1_A            9 KLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   81 (84)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEE
Confidence            5889999999888899999999999999987 56777888888  567878   34789999999999998775

>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=98.07  E-value=4.1e-05  Score=48.10  Aligned_cols=70  Identities=17%  Similarity=0.276  Sum_probs=59.6

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcC--C-CCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--D-GRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~--d-~~~L~~~gi~~g~~i~v~~   71 (128)
                      .|.||.++|..+.-.+..++||.+|.+.|....+.+.....|+  |-.+.+.  | +.+|.+.|+.+.++|++..
T Consensus        15 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~   89 (109)
T 2dzk_A           15 RIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLP   89 (109)
T ss_dssp             EEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEEC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEE
Confidence            5889999999999999999999999999998877777777787  6677775  3 6899999999988887654

>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=97.95  E-value=4.5e-05  Score=49.00  Aligned_cols=69  Identities=20%  Similarity=0.354  Sum_probs=58.7

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEc--CC-CCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL--ED-GRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L--~d-~~~L~~~gi~~g~~i~v~~   71 (128)
                      .|.||.++|..+.-.+..++||.+|...|... +.++....|+  |-.+.|  .| +.+|.+.|+.+.++|+|..
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            58899999998999999999999999999886 7777788887  668888  33 7899999999988887653

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=97.67  E-value=0.00081  Score=38.66  Aligned_cols=66  Identities=21%  Similarity=0.270  Sum_probs=50.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|.... ....++++...||.+|.+.+    ++++....+..||..+..+.     -+++|+.|.++....||
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            677776543 34567888889999998876    56777777889999997655     56789999988766554

>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=97.64  E-value=0.00034  Score=43.81  Aligned_cols=69  Identities=19%  Similarity=0.243  Sum_probs=57.3

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEcC--CCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--DGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L~--d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +|.||..+|+.+.-.+..++||.+|...|... +..+....|+  |-.+.|.  .+.+|.+.|+.+.++|.|..
T Consensus        25 ~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve~   97 (109)
T 2cr5_A           25 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   97 (109)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEEe
Confidence            68899999998888999999999999999865 5556677776  6677775  47899999999998887654

>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=97.55  E-value=0.00041  Score=44.65  Aligned_cols=66  Identities=21%  Similarity=0.370  Sum_probs=54.1

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhh-CCCCCCeEEE--eCCEEcCC-CCccccccccCCcEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLI--FAGKQLED-GRTLADYNIQKESTL   67 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~-~ip~~~q~L~--~~g~~L~d-~~~L~~~gi~~g~~i   67 (128)
                      .|.||..+|..+.-.+..++||.+|.+.|.... +.+.....|+  |-.+.|+| +.+|.+.|+.+...|
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            588999999999999999999999999998863 3455667776  66788865 689999999985444

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=97.53  E-value=0.00022  Score=41.63  Aligned_cols=65  Identities=14%  Similarity=0.308  Sum_probs=49.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|+........+++++..||.+|-+.    .++|++...+..||+.+..+.      +.+|++|.++- .-||
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~~----Lgl~~~~VvV~vNG~~v~~d~------~l~GD~VeIv~-~V~G   65 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVRA----VDLSPHEVTVLVDGRPVPEDQ------SVEVDRVKVLR-LIKG   65 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHHT----TCCCSSCCCEECCCCCCCTTS------SSCCCCEEECS-SCSC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHHH----cCCCcceEEEEECCEECCHHH------CCCCCEEEEEE-eecc
Confidence            89999887555566899999999998755    599999987889999886555      23488998754 4444

>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=97.34  E-value=0.00043  Score=41.23  Aligned_cols=62  Identities=13%  Similarity=0.239  Sum_probs=54.5

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe---CCEEcCCCCccccccccC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQK   63 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~---~g~~L~d~~~L~~~gi~~   63 (128)
                      ++.|.....+...+.|+|..++.+|--.|.++..++|+...|..   .+..|+-+++|.+|||++
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            56777777778889999999999999999999999999988874   456888899999999986

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=97.23  E-value=0.0015  Score=45.68  Aligned_cols=65  Identities=23%  Similarity=0.410  Sum_probs=53.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEE--e-CC--EEcCC-CCccccccccCCcEEEEEEeecCCC
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLI--F-AG--KQLED-GRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~--~-~g--~~L~d-~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      +.+.++..+||.+|++.+...++++++ +.||.  + .+  ..|+| +.+|.+++|.++..|.+-++..+|.
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~~dg~  213 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGT  213 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECCCC-C
T ss_pred             eEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEecCCCC
Confidence            557789999999999999999999997 68886  3 23  35665 6799999999999999999988874

>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=97.16  E-value=0.004  Score=43.87  Aligned_cols=65  Identities=20%  Similarity=0.302  Sum_probs=55.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEEe-C----CEEcCC-CCccccccccCCcEEEEEEeecCCC
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF-A----GKQLED-GRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~~-~----g~~L~d-~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      +.+.++..+||.+|++.+...++++++ +.||.. .    ...|.| +.+|.++++.++..|.+-++...|.
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~~dg~  225 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQNEDGT  225 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECCTTSC
T ss_pred             EEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEecCCCC
Confidence            456778999999999999999999997 688873 3    246665 6899999999999999999988884

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=97.13  E-value=0.0059  Score=38.23  Aligned_cols=63  Identities=38%  Similarity=0.494  Sum_probs=44.7

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhh--CCC------CCCeEEEe----CCEEcCCC-------------CccccccccCC
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGKQLEDG-------------RTLADYNIQKE   64 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~--~ip------~~~q~L~~----~g~~L~d~-------------~~L~~~gi~~g   64 (128)
                      +..+.+.|-..+||.++|++|-...  ++|      ++++-|-+    .|+.|.|.             .||++|+|.+|
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            3457788889999999999996553  444      35666765    24566542             47999999999


Q ss_pred             cEEEEEEe
Q 033059           65 STLHLVLR   72 (128)
Q Consensus        65 ~~i~v~~~   72 (128)
                      ++|.++.+
T Consensus       103 atl~l~~~  110 (111)
T 4e71_A          103 ATLILSKV  110 (111)
T ss_dssp             CEEEEEEC
T ss_pred             CEEEEEeC
Confidence            99987643

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=97.12  E-value=0.0022  Score=38.57  Aligned_cols=61  Identities=13%  Similarity=0.198  Sum_probs=43.3

Q ss_pred             CCCEEEEEecCC-CcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            9 TGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         9 ~g~~~~i~v~~~-~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +|+  .+++++. .||.+|.+.+    ++++....+..||+.+..+ ...+.-+++|+.|.++....||
T Consensus        26 NGe--~~el~~~~~Tv~dLL~~L----~~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~~~V~GG   87 (87)
T 1tyg_B           26 NGK--DVKWKKDTGTIQDLLASY----QLENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVHFVGGG   87 (87)
T ss_dssp             TTE--EECCSSSCCBHHHHHHHT----TCTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEEECCC-
T ss_pred             CCE--EEECCCCCCcHHHHHHHh----CCCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEEcccccC
Confidence            454  3455666 8999998876    5777778888999988532 3334557899999988766554

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=97.11  E-value=0.003  Score=36.52  Aligned_cols=71  Identities=15%  Similarity=0.331  Sum_probs=48.9

Q ss_pred             CEEEEEeCCC-CEEEEEecCCCcHHHHHHHHHhhhCCCC--CCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g-~~~~i~v~~~~tV~~LK~~i~~~~~ip~--~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |.|+|+.... +...+++ +..||.+|.+.+....++..  ....+..||+.+.+    .+.-+++|+.|.++....||
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            7888887743 2234666 56899999999986533321  45667788887543    23457889999988777665

>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=97.00  E-value=0.0079  Score=36.61  Aligned_cols=71  Identities=13%  Similarity=0.298  Sum_probs=48.7

Q ss_pred             CEEEEEeCC------C-CEEEEEecCCCcHHHHHHHHHhhhC-C----------CCCCeEEEeCCEEcCCCCcccccccc
Q 033059            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-I----------PPDQQRLIFAGKQLEDGRTLADYNIQ   62 (128)
Q Consensus         1 m~i~vk~~~------g-~~~~i~v~~~~tV~~LK~~i~~~~~-i----------p~~~q~L~~~g~~L~d~~~L~~~gi~   62 (128)
                      |+|.|+...      | ....+++++..||.+|.+.+..... +          ......+..||+....     +.-++
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            567777653      3 4577888888999999999977641 1          1244667789987753     45678


Q ss_pred             CCcEEEEEEeecCC
Q 033059           63 KESTLHLVLRLRGG   76 (128)
Q Consensus        63 ~g~~i~v~~~~~gg   76 (128)
                      +|+.|.++....||
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            99999887655554

>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=96.87  E-value=0.0017  Score=38.21  Aligned_cols=67  Identities=16%  Similarity=0.334  Sum_probs=49.3

Q ss_pred             CEEEEEeCCCCEEEEEec--CCCcHHHHHHHHHhhhCCC-CCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVE--SSDTIDNVKAKIQDKEGIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~--~~~tV~~LK~~i~~~~~ip-~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|   +|+.+  +++  ...||.+|-+.+    +++ +...-+..||..+..+ ...+.-+++|+.|.++.-..||.
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            67777   56544  455  678999998765    777 7778888999998543 44556678999999887676664

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=96.80  E-value=0.0042  Score=35.08  Aligned_cols=66  Identities=15%  Similarity=0.263  Sum_probs=46.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|   +|+.  ++++...||.+|.+.+    ++++....+..||+.+..+ ...+.-+++|+.|.++....||
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            56666   5554  4556778999999877    5677778888999987532 1223457889999988766554

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=96.72  E-value=0.022  Score=36.45  Aligned_cols=65  Identities=28%  Similarity=0.387  Sum_probs=47.1

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhh--CCC------CCCeEEEe-C---CE-EcCCC-------------Ccccccccc
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-A---GK-QLEDG-------------RTLADYNIQ   62 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~--~ip------~~~q~L~~-~---g~-~L~d~-------------~~L~~~gi~   62 (128)
                      ++..+.+.|-..+||.++|++|-..+  ++|      ++++.|-+ .   |. .|.|.             .||++|+|.
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            34557788889999999999996653  444      35667765 2   33 36542             479999999


Q ss_pred             CCcEEEEEEee
Q 033059           63 KESTLHLVLRL   73 (128)
Q Consensus        63 ~g~~i~v~~~~   73 (128)
                      +|++|.+..+.
T Consensus        95 dgatv~l~~~~  105 (127)
T 3h6n_A           95 EGASLAMSLID  105 (127)
T ss_dssp             TTCEEEEEECC
T ss_pred             CCCEEEEEEcc
Confidence            99999987653

>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=96.67  E-value=0.016  Score=43.24  Aligned_cols=75  Identities=21%  Similarity=0.342  Sum_probs=57.8

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhC----CCCCCeEEEe------CCEEcCCCCccccccccCCcEEEEE-
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG----IPPDQQRLIF------AGKQLEDGRTLADYNIQKESTLHLV-   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~----ip~~~q~L~~------~g~~L~d~~~L~~~gi~~g~~i~v~-   70 (128)
                      .+.|... +.+-.+.+++++||.+.-..|.++..    .++++--|+.      +|.=|++.++|..|++++++.|... 
T Consensus         5 ~~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~~   83 (371)
T 3ivf_A            5 SLKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRK   83 (371)
T ss_dssp             EEEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEEE
T ss_pred             EEEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeeccC
Confidence            3455554 66788999999999999999987764    3567777776      3455788889999999999988754 


Q ss_pred             ------EeecCCC
Q 033059           71 ------LRLRGGI   77 (128)
Q Consensus        71 ------~~~~gg~   77 (128)
                            +.+.+|.
T Consensus        84 ~~~~~~V~l~dg~   96 (371)
T 3ivf_A           84 KQRPLKIRMLDGT   96 (371)
T ss_dssp             CEEEEEEECTTSC
T ss_pred             ceeEEEEECcCCC
Confidence                  5567774

>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=96.64  E-value=0.014  Score=37.84  Aligned_cols=63  Identities=33%  Similarity=0.540  Sum_probs=46.1

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhh--CCC------CCCeEEEe----CCE-EcCCC-------------CccccccccCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGK-QLEDG-------------RTLADYNIQKE   64 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~--~ip------~~~q~L~~----~g~-~L~d~-------------~~L~~~gi~~g   64 (128)
                      ..+.+.|-..+||.++|++|-..+  ++|      ++++-|-+    .|+ .|.|.             .||+.|+|.+|
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            457788889999999999997653  454      34556654    244 36543             37999999999


Q ss_pred             cEEEEEEee
Q 033059           65 STLHLVLRL   73 (128)
Q Consensus        65 ~~i~v~~~~   73 (128)
                      ++|.++.+.
T Consensus       121 a~l~l~~~~  129 (138)
T 2r2o_A          121 ATVALVPCL  129 (138)
T ss_dssp             CEEEEEEC-
T ss_pred             CEEEEEECC
Confidence            999987664

>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=96.51  E-value=0.0077  Score=35.79  Aligned_cols=46  Identities=11%  Similarity=0.203  Sum_probs=39.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK   48 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~   48 (128)
                      |.|.|...  -++.|.|++..+..+|.++|+++.+++++...|.|...
T Consensus         6 ~~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~   51 (83)
T 1oey_A            6 YTLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPR   51 (83)
T ss_dssp             EEEEEESS--SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCT
T ss_pred             EEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCC
Confidence            35666553  58999999999999999999999999999999999764

>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=96.36  E-value=0.034  Score=33.27  Aligned_cols=74  Identities=18%  Similarity=0.291  Sum_probs=48.4

Q ss_pred             CEEEEEeCC------CCEEEEEecCCCcHHHHHHHHHhhhC-----C-C---C----CCeEEEeCCEEcCCCCccccccc
Q 033059            1 MQIFVKTLT------GKTITLEVESSDTIDNVKAKIQDKEG-----I-P---P----DQQRLIFAGKQLEDGRTLADYNI   61 (128)
Q Consensus         1 m~i~vk~~~------g~~~~i~v~~~~tV~~LK~~i~~~~~-----i-p---~----~~q~L~~~g~~L~d~~~L~~~gi   61 (128)
                      |+|+|+...      |....+++ +..||.+|.+.+...+.     + .   .    ....+..||+...+..-+ +.-+
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-SGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGGL-ATAI   78 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEE-CCSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTGG-GCBC
T ss_pred             CEEEEEEeHHHHHHhCCCeEEec-CCCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCCC-CcCC
Confidence            677777653      32234664 45899999999987652     0 1   1    135677899877643222 3457


Q ss_pred             cCCcEEEEEEeecCC
Q 033059           62 QKESTLHLVLRLRGG   76 (128)
Q Consensus        62 ~~g~~i~v~~~~~gg   76 (128)
                      ++|+.|.++....||
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            899999998877776

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=96.28  E-value=0.023  Score=35.87  Aligned_cols=63  Identities=32%  Similarity=0.505  Sum_probs=44.9

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhh--CCC------CCCeEEEe-CC---E-EcCCC-------------CccccccccCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-AG---K-QLEDG-------------RTLADYNIQKE   64 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~--~ip------~~~q~L~~-~g---~-~L~d~-------------~~L~~~gi~~g   64 (128)
                      ..+.+.|-..+||.++|++|-...  +.|      ++++.|.+ .|   . .|.|.             .||++|+|.+|
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            347778889999999999996543  454      34566654 23   3 35431             47999999999


Q ss_pred             cEEEEEEee
Q 033059           65 STLHLVLRL   73 (128)
Q Consensus        65 ~~i~v~~~~   73 (128)
                      ++|.++.+.
T Consensus       107 atl~l~~~~  115 (117)
T 4e74_A          107 SVVALVSKQ  115 (117)
T ss_dssp             CEEEEEECC
T ss_pred             CEEEEEeCC
Confidence            999987654

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=96.25  E-value=0.032  Score=33.06  Aligned_cols=60  Identities=18%  Similarity=0.351  Sum_probs=52.3

Q ss_pred             EEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeec
Q 033059           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus        15 i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      -.++-..++..||..++.+.+++-+.-.+...+..|+++++|.+-+++-...|.+.+...
T Consensus         7 qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqik   66 (89)
T 2juo_A            7 QAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQVI   66 (89)
T ss_dssp             EEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEEE
T ss_pred             hhccccCcHHHHHHHHHHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEEE
Confidence            345667889999999999999999999998999999999999999998888888777653

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=96.20  E-value=0.04  Score=32.60  Aligned_cols=61  Identities=15%  Similarity=0.259  Sum_probs=45.0

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhhC-C-----CC-----CCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKEG-I-----PP-----DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~~-i-----p~-----~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ....+++++..||.+|.+.+..... +     ..     ....+..||+....     +.-+++|+.|.++....||
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~Ppv~GG   89 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALFPPVSGG   89 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGGGHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEECCCSCC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcHHHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEECCCCCC
Confidence            5677888888999999999987652 1     10     12577789998865     3457889999998777665

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=95.71  E-value=0.026  Score=32.44  Aligned_cols=60  Identities=13%  Similarity=0.212  Sum_probs=42.6

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhhCCCCCCe--EEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ--RLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q--~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ....+++++..||.+|.+.+..... .....  .+..||+....+     .-+++|+.|.++....||
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            3456777778899999999876631 11334  677899988654     457889999887655554

>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=95.69  E-value=0.038  Score=32.03  Aligned_cols=59  Identities=7%  Similarity=0.153  Sum_probs=41.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhC-----CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~-----ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ...++ .+..||.+|.+.+.....     ++.....+..||+....     +.-+++|+.|.++....||
T Consensus        18 ~~~~~-~~~~tv~~ll~~L~~~~p~~~~~l~~~~~~v~vN~~~v~~-----~~~l~~gD~V~i~Ppv~GG   81 (81)
T 1fm0_D           18 ATEVA-ADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFFPPVTGG   81 (81)
T ss_dssp             EEEEC-SCCSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCT-----TCBCCTTCEEEEECCCCCC
T ss_pred             eEEEc-CCCCCHHHHHHHHHHHChhHHHHhcCCCEEEEECCEECCC-----CCCCCCCCEEEEeCCCCCC
Confidence            45555 567899999999875531     23345677889998754     3457889999987666555

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=95.58  E-value=0.17  Score=32.18  Aligned_cols=61  Identities=34%  Similarity=0.517  Sum_probs=41.7

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhh-h---CCCC----CCeEEEe-CC---EEcCC----------C----CccccccccCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDK-E---GIPP----DQQRLIF-AG---KQLED----------G----RTLADYNIQKE   64 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~-~---~ip~----~~q~L~~-~g---~~L~d----------~----~~L~~~gi~~g   64 (128)
                      ..+.+.|-..+||.++|++|-.. +   ++|.    +++-|-+ .|   ..|.|          .    .||+.|+|.+|
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            45778888999999999998543 3   6654    4455543 12   23322          1    36899999999


Q ss_pred             cEEEEEE
Q 033059           65 STLHLVL   71 (128)
Q Consensus        65 ~~i~v~~   71 (128)
                      ++|.++-
T Consensus       119 atlal~k  125 (126)
T 3kuz_A          119 STIKVFK  125 (126)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEee
Confidence            9998763

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=95.23  E-value=0.24  Score=29.93  Aligned_cols=73  Identities=15%  Similarity=0.249  Sum_probs=44.6

Q ss_pred             CEEEEEeCC-------C-CEEEEEec--CCCcHHHHHHHHHhhhCCCCC-------------CeEEEeCCEEcCCCCcc-
Q 033059            1 MQIFVKTLT-------G-KTITLEVE--SSDTIDNVKAKIQDKEGIPPD-------------QQRLIFAGKQLEDGRTL-   56 (128)
Q Consensus         1 m~i~vk~~~-------g-~~~~i~v~--~~~tV~~LK~~i~~~~~ip~~-------------~q~L~~~g~~L~d~~~L-   56 (128)
                      |+|+|+...       | ....++++  +..||.+|.+.+.+...-...             ...+..||....   .+ 
T Consensus         2 M~i~V~~fa~lre~~~g~~~~~~~l~~~~~~Tv~~L~~~L~~~~~~~~~~l~~~~~~~~lr~~~~v~VN~~~~~---~~~   78 (99)
T 2qjl_A            2 VNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWE---LEG   78 (99)
T ss_dssp             EEEEEEEETTGGGGTTTCCEEEEEECSCSCCBHHHHHHHHHHHTCSSGGGHHHHEETTEECTTEEEEETTEEGG---GGT
T ss_pred             cEEEEEEchHHHHHhCCCcEEEEecCCCCCCcHHHHHHHHHHHCchhhHHHhhhccCCccccCeEEEECCEEcc---ccC
Confidence            456666442       2 45667776  678999999999877631111             112334555321   11 


Q ss_pred             -ccccccCCcEEEEEEeecCC
Q 033059           57 -ADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        57 -~~~gi~~g~~i~v~~~~~gg   76 (128)
                       .++-+++|+.|.++....||
T Consensus        79 ~~d~~L~dgDeVa~~Ppv~GG   99 (99)
T 2qjl_A           79 EKDYILEDGDIISFTSTLHGG   99 (99)
T ss_dssp             GGGCBCCTTCEEEEEECTTCC
T ss_pred             CCCcCcCCCCEEEEECCCCCC
Confidence             24568899999988776665

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=95.20  E-value=0.028  Score=36.12  Aligned_cols=33  Identities=21%  Similarity=0.340  Sum_probs=30.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~   45 (128)
                      ..+.|..++|+.+|+..|++.+|+|++.|||..
T Consensus        58 ~~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW~   90 (130)
T 2kvr_A           58 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   90 (130)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEE
T ss_pred             ceEEEeccCcHHHHHHHHHHHhCCCcccEEEEE
Confidence            457888999999999999999999999999974

>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=95.15  E-value=0.13  Score=32.19  Aligned_cols=74  Identities=19%  Similarity=0.249  Sum_probs=45.9

Q ss_pred             CEEEEEeCC------C--CEEEEEecC---CCcHHHHHHHHHhhh-CCCC----------CCeEEEeCCEEcCCCCcc--
Q 033059            1 MQIFVKTLT------G--KTITLEVES---SDTIDNVKAKIQDKE-GIPP----------DQQRLIFAGKQLEDGRTL--   56 (128)
Q Consensus         1 m~i~vk~~~------g--~~~~i~v~~---~~tV~~LK~~i~~~~-~ip~----------~~q~L~~~g~~L~d~~~L--   56 (128)
                      |+|.|+...      |  +.+.++++.   ..||.+|-+.|.+.+ +..+          ..+.++.||+...   .|  
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            567777664      3  356788883   369999999998775 1100          0122333443211   11  


Q ss_pred             ccccccCCcEEEEEEeecCCC
Q 033059           57 ADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus        57 ~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      .++-+++|+.|.++....||.
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            346688999999988888883

>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=95.11  E-value=0.068  Score=29.73  Aligned_cols=60  Identities=13%  Similarity=0.312  Sum_probs=41.9

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      +|+.+  ++ +..||.+|.+.+    ++++....+..||+.+..+ .-.+.-+++|+.|.++....||
T Consensus         5 Ng~~~--~~-~~~tv~~ll~~l----~~~~~~v~vavN~~~v~~~-~~~~~~L~dgD~v~i~~~V~GG   64 (64)
T 2cu3_A            5 NGEPR--PL-EGKTLKEVLEEM----GVELKGVAVLLNEEAFLGL-EVPDRPLRDGDVVEVVALMQGG   64 (64)
T ss_dssp             TTEEE--CC-TTCCHHHHHHHH----TBCGGGEEEEETTEEEEGG-GCCCCCCCTTCEEEEEECCCC-
T ss_pred             CCEEE--Ec-CCCcHHHHHHHc----CCCCCcEEEEECCEECCcc-ccCCcCCCCCCEEEEEeecccC
Confidence            56554  44 568999998877    5667777788999988532 2223457889999988766554

>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=94.98  E-value=0.2  Score=35.86  Aligned_cols=72  Identities=17%  Similarity=0.260  Sum_probs=54.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEe---CCE--EcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIF---AGK--QLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~---~g~--~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |.+.|..++| ++.+.+++++|+.+|-+.|....|+...+ .-|.+   +|.  -|+.++++.+.++..+....+.++.
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~fr~   79 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFRA   79 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCCCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEEEE
Confidence            4678888888 68899999999999999999999986543 45554   343  4677888888876666655555553

>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=94.96  E-value=0.25  Score=35.75  Aligned_cols=72  Identities=11%  Similarity=0.141  Sum_probs=54.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEEe--CCE--EcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF--AGK--QLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~~--~g~--~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      +.+.|..++| ++.+.+++++|+.+|-+.|....++... ..-|.|  +|.  -|+.+.+|.+.++..+....+.++.
T Consensus        23 ~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~fr~   99 (314)
T 1h4r_A           23 FTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLA   99 (314)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEEE
T ss_pred             eEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCCCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEEEE
Confidence            3577888888 7889999999999999999999998653 344544  454  3677888988876655655555543

>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=94.59  E-value=0.2  Score=29.97  Aligned_cols=46  Identities=9%  Similarity=0.164  Sum_probs=36.7

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEEeCCE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFAGK   48 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~~~g~   48 (128)
                      +|.+. ..|....+.++++.+..+|.+++.+.++++.+ .+.+.|...
T Consensus         8 kvK~~-~~gdi~~~~v~~~i~~~~L~~kv~~~~~~~~~~~f~lky~DE   54 (89)
T 1vd2_A            8 RVKAY-YRGDIMITHFEPSISFEGLCNEVRDMCSFDNEQLFTMKWIDE   54 (89)
T ss_dssp             EEEEE-SSSCEEEEEECTTCCHHHHHHHHHHHTTCCSSCCEEEEECCS
T ss_pred             EEEEE-eCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCeEEEEEECC
Confidence            34443 35778889999999999999999999998754 478888765

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=94.55  E-value=0.31  Score=38.82  Aligned_cols=64  Identities=28%  Similarity=0.472  Sum_probs=45.5

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhhh--CCC------CCCeEEEe----CCE-EcCCC-------------CccccccccCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF----AGK-QLEDG-------------RTLADYNIQKE   64 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~~--~ip------~~~q~L~~----~g~-~L~d~-------------~~L~~~gi~~g   64 (128)
                      ..+.+.|-..+||.++|++|-...  ++|      ++++-|-+    .|+ .|.|.             .||++|+|.+|
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            457788889999999999996543  444      35566654    233 35442             47999999999


Q ss_pred             cEEEEEEeec
Q 033059           65 STLHLVLRLR   74 (128)
Q Consensus        65 ~~i~v~~~~~   74 (128)
                      ++|.++.+..
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            9999987764

>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown FUN; NMR {Pyrococcus furiosus} SCOP: d.15.3.2 PDB: 1sf0_A

Probab=94.45  E-value=0.0093  Score=34.70  Aligned_cols=54  Identities=11%  Similarity=0.260  Sum_probs=40.0

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .+++++..||.+|.+.+    ++++....+..||+....+     .-+++|+.|.++....||
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            45566778999998765    4677777788999988754     457789999887655554

>2l52_A Methanosarcina acetivorans SAMP1 homolog; beta-grAsp fold, protein binding, E1-like, SAMP activator, ELSA, adenylation, ubiquitin; NMR {Methanosarcina acetivorans}

Probab=94.16  E-value=0.36  Score=29.12  Aligned_cols=73  Identities=14%  Similarity=0.283  Sum_probs=44.7

Q ss_pred             CEEEEEeCC------CCEEEEEecCCCcHHHHHHHHHhhhC-CCC---------CCe-------EEEeCCEEcCCCCccc
Q 033059            1 MQIFVKTLT------GKTITLEVESSDTIDNVKAKIQDKEG-IPP---------DQQ-------RLIFAGKQLEDGRTLA   57 (128)
Q Consensus         1 m~i~vk~~~------g~~~~i~v~~~~tV~~LK~~i~~~~~-ip~---------~~q-------~L~~~g~~L~d~~~L~   57 (128)
                      |+|+|+...      |. ..++++ ..||.+|.+.+..... +..         ..+       .+..||+....... .
T Consensus         4 m~v~V~~fa~lr~~~g~-~~~~l~-~~tv~~ll~~L~~~~p~l~~~l~~~g~l~~~v~~~~~~~~v~VNg~~v~~~~~-~   80 (99)
T 2l52_A            4 AEVKVKLFANLREAAGT-PELPLS-GEKVIDVLLSLTDKYPALKYVIFEKGDEKSEILILCGSINILINGNNIRHLEG-L   80 (99)
T ss_dssp             CEEEEEECTHHHHHHSS-SEEEEE-CSSHHHHHHHHHHHCGGGTTTSBCSCCTTSSCCCBCSSCEEEETTSCGGGTTS-T
T ss_pred             eEEEEEEeHHHHHHhCC-CeEEEe-CCcHHHHHHHHHHHChhHHHHHhcccccccceeccccccEEEECCEEccccCC-C
Confidence            677887664      22 133444 5899999999977641 111         123       67788886632211 2


Q ss_pred             cccccCCcEEEEEEeecCC
Q 033059           58 DYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        58 ~~gi~~g~~i~v~~~~~gg   76 (128)
                      +.-+++|+.|.++....||
T Consensus        81 ~~~L~~gD~V~i~ppv~GG   99 (99)
T 2l52_A           81 ETLLKDSDEIGILPPVSGG   99 (99)
T ss_dssp             TSCCCTTEEEEEECCCSCC
T ss_pred             CCCCCCCCEEEEECCCCCC
Confidence            3357899999987666554

>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A

Probab=93.90  E-value=0.28  Score=28.73  Aligned_cols=62  Identities=13%  Similarity=0.254  Sum_probs=40.7

Q ss_pred             EEEecCCCcHHHHHHHHHhhhC------C-----CCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEG------I-----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~------i-----p~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .++++...||.+|.+.+.....      +     ......+..||+...... -.+.-+++|+.|.++....||
T Consensus        18 ~~~~~~~~tv~~ll~~l~~~~p~~~~~~l~~~~g~~~~v~v~vN~~~v~~~~-~~~~~l~~gD~V~i~ppv~GG   90 (90)
T 2g1e_A           18 EETFNGISKISELLERLKVEYGSEFTKQMYDGNNLFKNVIILVNGNNITSMK-GLDTEIKDDDKIDLFPPVAGG   90 (90)
T ss_dssp             EEEESSCCBHHHHHHHHHHHSCHHHHHHHCCSSCSTTTCEEEESSSBGGGTC-SSSCBCCTTCEEEEECCTTCC
T ss_pred             EEEcCCCCcHHHHHHHHHHHCcchhhhccccccCcCcceEEEECCEEccccC-CCCcCCCCCCEEEEeCCCCCC
Confidence            3456666899999999977641      1     013456778998775221 123457899999887665554

>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=93.69  E-value=0.52  Score=34.97  Aligned_cols=72  Identities=26%  Similarity=0.404  Sum_probs=55.1

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC-CCeEEEeCC---------EEcCCCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAG---------KQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~-~~q~L~~~g---------~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      .+.|..++|....+.+++.+|+.+|-+.|....++.. +..-|.+..         .-|+.++++.+.+.....++.+.+
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            5778889999999999999999999999999999754 445665532         234567788887776667777766


Q ss_pred             ee
Q 033059           72 RL   73 (128)
Q Consensus        72 ~~   73 (128)
                      +.
T Consensus       167 Kf  168 (371)
T 3ivf_A          167 KF  168 (371)
T ss_dssp             CC
T ss_pred             EE
Confidence            53

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=93.50  E-value=0.028  Score=35.07  Aligned_cols=74  Identities=16%  Similarity=0.295  Sum_probs=42.6

Q ss_pred             CEEEEEeCC------CCEEEEEecC----CCcHHHHHHHHHhhhCCCCCCeEEE-eCC--E------EcCCCCc---c--
Q 033059            1 MQIFVKTLT------GKTITLEVES----SDTIDNVKAKIQDKEGIPPDQQRLI-FAG--K------QLEDGRT---L--   56 (128)
Q Consensus         1 m~i~vk~~~------g~~~~i~v~~----~~tV~~LK~~i~~~~~ip~~~q~L~-~~g--~------~L~d~~~---L--   56 (128)
                      |+|.|+...      |+...++++.    ..||.+|-..|.+.+.  ..+-.|+ -+|  .      +|-++..   +  
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 NHITVQFAGGCELLFAKQTSLQLDGVVPTGTNLNGLVQLLKTNYV--KERPDLLVDQTGQTLRPGILVLVNSCDAEVVGG   82 (110)
T ss_dssp             SCCEEEEESSCGGGTTSCSEECCCCSCGGGCCHHHHHHHHTTTTC--CSCHHHHBCSSSSSBCTTEEEEESSSBHHHHTS
T ss_pred             cEEEEEEEecHHHHhCCeEEEEeCCcCCCCccHHHHHHHHHHHcc--ccchhhEecCCCcccCCCeEEEECCeeeeccCC
Confidence            456666543      3445677763    2599999998887652  1122222 112  1      2212211   1  


Q ss_pred             ccccccCCcEEEEEEeecCC
Q 033059           57 ADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        57 ~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .+|-+++|+.|.++..+.||
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            34678999999988777777

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=93.42  E-value=0.39  Score=26.88  Aligned_cols=62  Identities=11%  Similarity=0.097  Sum_probs=41.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |.+.|...+|+.  ++++...|+.+|-..+....  +....-...+|+..+-+     +-+.+|+.|.++-
T Consensus         1 m~i~i~~p~g~~--~~~~~g~T~~dla~~i~~~l--~~~~vaa~vNg~lvdl~-----~~L~~~~~Veivt   62 (73)
T 2kmm_A            1 MEVMVFTPKGEI--KRLPQGATALDFAYSLHSDL--GDHCIGAKVNHKLVPLS-----YVLNSGDQVEVLS   62 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHH--HHTEEEEEETTEECCTT-----CBCCSSSBEEEEE
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhcc--ccceEEEEECCEEeCCC-----cCcCCCCEEEEEE
Confidence            788898778875  56677899999987774332  12223345789877654     3455688888764

>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=93.16  E-value=0.63  Score=37.20  Aligned_cols=65  Identities=32%  Similarity=0.537  Sum_probs=44.9

Q ss_pred             CEEEEEecCCCcHHHHHHHHHhh--hCCC------CCCeEEEe----CCE-EcCCC-------------CccccccccCC
Q 033059           11 KTITLEVESSDTIDNVKAKIQDK--EGIP------PDQQRLIF----AGK-QLEDG-------------RTLADYNIQKE   64 (128)
Q Consensus        11 ~~~~i~v~~~~tV~~LK~~i~~~--~~ip------~~~q~L~~----~g~-~L~d~-------------~~L~~~gi~~g   64 (128)
                      ..+.+.|-..+||.++|++|-..  .++|      ++++-|-+    .|+ .|.|.             .||++|+|.+|
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            34778888999999999999644  2444      35556654    233 45442             47999999999


Q ss_pred             cEEEEEEeecC
Q 033059           65 STLHLVLRLRG   75 (128)
Q Consensus        65 ~~i~v~~~~~g   75 (128)
                      ++|.++.+...
T Consensus       354 a~v~L~p~~~~  364 (644)
T 3hm6_X          354 ATVALVPCLTK  364 (644)
T ss_dssp             CEEEEEEC---
T ss_pred             cEEEEEecccc
Confidence            99998876533

>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=93.15  E-value=0.62  Score=36.91  Aligned_cols=72  Identities=15%  Similarity=0.275  Sum_probs=54.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCC-CeEEEeC---C--EEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFA---G--KQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~-~q~L~~~---g--~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |.+.|..++| ++.+.|++++|+.+|-..|....|+... .+-|.|-   |  .-|+.+.+|.+.++..+..+.+.++.
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~FRv   82 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGLREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKFRA   82 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCCCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEEEE
Confidence            3578888888 7889999999999999999999998643 4556552   2  24677888888877666666665554

>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=92.80  E-value=0.67  Score=33.40  Aligned_cols=73  Identities=8%  Similarity=0.049  Sum_probs=52.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEeC---CE--EcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFA---GK--QLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~~---g~--~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |.+.|..++|....+.|++.+|+.+|-+.|.+..|+...+ .-|.|.   |.  -|+.++++.+.......++.+.++.
T Consensus        18 ~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~~~~~~~l~frvkf   96 (296)
T 3qij_A           18 GHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNVKF   96 (296)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTCSSGGGEEEEEEEETTEEEECCTTSBHHHHC---CCEEEEEESS
T ss_pred             EEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCCCCcceeEEEEEcCCCccchhccchhHHHhcCCCCcEEEEEEEE
Confidence            4688999999999999999999999999999999976433 455542   32  4677778877654444466665553

>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=92.73  E-value=0.69  Score=29.04  Aligned_cols=61  Identities=13%  Similarity=0.161  Sum_probs=48.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHh-hhC-------CCCCCeEEEeCCEEcC--CCCccccccccCCcEEEEEEe
Q 033059           12 TITLEVESSDTIDNVKAKIQD-KEG-------IPPDQQRLIFAGKQLE--DGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~-~~~-------ip~~~q~L~~~g~~L~--d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .+.+.|+|+++.++|-+.+-. .++       |+-+...+..+|+...  .+++|++.||...+.|.+...
T Consensus        39 p~~~p~pP~mpFg~lv~~vl~~~~~~hPDfa~idws~v~W~l~g~pftPD~~kSLaenG~~HKs~lrf~TP  109 (119)
T 3u52_E           39 PFALLVQPGMTFSALVDEILKPATAAHPDSAKADFLNAEWLLNDEPFTPKADASLKEQGIDHKSMLTVTTP  109 (119)
T ss_dssp             CEEEEECTTSBHHHHHHHTHHHHTTTSTTGGGCCTTSSEEEETTEEECCCTTSBTTTTTCCTTEEEEEECT
T ss_pred             ceeecCCCCCCHHHHHHHhcchhhhcCCccccCCcchheEEECCccCCCChhhhHHHcCCCchheEEEeCC
Confidence            478999999999999877743 233       5556668889999884  578999999999999977643

>2kmc_A Fermitin family homolog 1; kindlin, cytoskeleton, integrin, N-terminal, talin, cell adhesion, cell junction, cell membrane, cell projection; NMR {Mus musculus}

Probab=92.69  E-value=1  Score=27.42  Aligned_cols=71  Identities=24%  Similarity=0.296  Sum_probs=54.1

Q ss_pred             EEEEEeCCC---CEEEEEecCCCcHHHHHHHHHhhhCCCC--CCeEEEeCCE---EcCCCCccccccccCCcEEEEEEe
Q 033059            2 QIFVKTLTG---KTITLEVESSDTIDNVKAKIQDKEGIPP--DQQRLIFAGK---QLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         2 ~i~vk~~~g---~~~~i~v~~~~tV~~LK~~i~~~~~ip~--~~q~L~~~g~---~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .|+|...+.   ....+.|..+.-|+.+..+|-+...++.  ++--|...-+   .|.-..+|..|||+.++.+++...
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            577777554   4577889999999999999988777654  4555554332   578899999999999999988653

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=92.47  E-value=0.67  Score=34.24  Aligned_cols=53  Identities=21%  Similarity=0.290  Sum_probs=42.1

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCE-E-cCCCCcccccccc
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-Q-LEDGRTLADYNIQ   62 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~-~-L~d~~~L~~~gi~   62 (128)
                      .....+.+.+..|+.++++.+++.++++++.|.|++.+. . ++.......|.-.
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~~~~~~~~~~~~~~~~~  375 (396)
T 4eut_A          321 MTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKT  375 (396)
T ss_dssp             TEEEEEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSSEECCCSSCBTTSSCCC
T ss_pred             ceEEEEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCCCCCCCCCCccccCCCC
Confidence            345668888999999999999999999999999999984 3 3445566666543

>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=92.46  E-value=0.95  Score=26.59  Aligned_cols=60  Identities=20%  Similarity=0.324  Sum_probs=48.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhh-C--CC--C-CCeEEEeCC--EEcCCCCccccccccCCcEEEEEE
Q 033059           12 TITLEVESSDTIDNVKAKIQDKE-G--IP--P-DQQRLIFAG--KQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~-~--ip--~-~~q~L~~~g--~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      ...+.|+.++|+.++=++++... |  ++  + ...+..++|  +.|..+.|+++-||.+-+.|.+..
T Consensus        14 ~~LV~VDt~dTmdqVA~kvA~HsVGrRV~p~p~~~~rVr~~G~~~~~pr~~tvae~gl~P~e~vev~~   81 (83)
T 2inc_C           14 IQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIF   81 (83)
T ss_dssp             EEEEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEE
T ss_pred             EEEEEecCCCcHHHHHHHHhhhhcceecCCCCCCeEEEEecCCccCCCCCCEeeccCCCCceEEEEEE
Confidence            35578999999999999997653 3  32  2 246777999  899999999999999999998875

>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=92.16  E-value=1.1  Score=27.53  Aligned_cols=68  Identities=9%  Similarity=0.194  Sum_probs=48.8

Q ss_pred             eCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE---eCCE--EcCCCCccccccccCCcEEEEEEeec
Q 033059            7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGK--QLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         7 ~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~---~~g~--~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      ..+..-+.+.+..+.|+.+++..++++.+...+++.|+   ++|.  .|+++..--.-.+.-...|++..+-.
T Consensus        16 ~~Dhsy~tvr~~v~~sa~eIl~~va~kl~~~~e~l~Lv~v~ssGEk~~lqp~d~si~tsL~~NgRLfvc~kd~   88 (104)
T 1wgy_A           16 ITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRKDL   88 (104)
T ss_dssp             CSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEECCS
T ss_pred             eccCceEEEEEeccchHHHHHHHHHHHhcCCccceEEEEEccCCcEeecCCcceEEEeeccccceEEEeehHh
Confidence            34555667888889999999999999999877788776   6886  44554433333455567888877643

>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=92.07  E-value=0.4  Score=29.18  Aligned_cols=59  Identities=12%  Similarity=0.287  Sum_probs=39.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhCCCCC-----------CeEEEeCC-EEcCC------CCccccccccCCcEEEEE
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEGIPPD-----------QQRLIFAG-KQLED------GRTLADYNIQKESTLHLV   70 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~ip~~-----------~q~L~~~g-~~L~d------~~~L~~~gi~~g~~i~v~   70 (128)
                      ...++|++++|+.+|-+.+.+.-.+...           .-.|+..+ ..|+.      +++|.++|+.+|+.|+|.
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            4568999999999999999884332221           22333332 12321      467999999999999874

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=91.90  E-value=0.94  Score=28.83  Aligned_cols=56  Identities=23%  Similarity=0.357  Sum_probs=40.2

Q ss_pred             EEEecC----CCcHHHHHHHHHhhhCCCCCCeEEEe--CCEEc-----CC--CCccccccccCCcEEEEE
Q 033059           14 TLEVES----SDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQL-----ED--GRTLADYNIQKESTLHLV   70 (128)
Q Consensus        14 ~i~v~~----~~tV~~LK~~i~~~~~ip~~~q~L~~--~g~~L-----~d--~~~L~~~gi~~g~~i~v~   70 (128)
                      .+.|++    ..|+.+|-+.|..++|... ++.+.-  ..+.|     +|  +++|+++|+++|+.|.+.
T Consensus         9 vl~v~~~dl~~~TL~dLV~~l~~~~gy~~-eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~   77 (127)
T 3onh_A            9 VIKLSSDCLNKMKLSDFVVLIREKYSYPQ-DISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFS   77 (127)
T ss_dssp             EEEECHHHHHHCBHHHHHHHHHHHHTCCS-SEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEE
T ss_pred             EEEeCcccccccCHHHHHHHHHHhcCCCC-cEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEE
Confidence            355553    4799999998988888863 555542  23444     22  579999999999998775

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=91.54  E-value=0.74  Score=27.23  Aligned_cols=38  Identities=13%  Similarity=0.147  Sum_probs=30.1

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEE-EeCCE
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL-IFAGK   48 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L-~~~g~   48 (128)
                      ++..+.+.|+++.+..+|+.+|..+..+.  ++.+ .|++.
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            45679999999999999999999999883  4444 45544

>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=91.51  E-value=1.3  Score=26.06  Aligned_cols=60  Identities=15%  Similarity=0.232  Sum_probs=49.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhh-C--CC--CCCeEEEeCCEE--cCCCCccccccccCCcEEEEEE
Q 033059           12 TITLEVESSDTIDNVKAKIQDKE-G--IP--PDQQRLIFAGKQ--LEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~-~--ip--~~~q~L~~~g~~--L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      ...+.|+.++|+.++=++++... |  ++  |.-.+..++|..  |.++.++++-||++-+.|.++.
T Consensus        16 ~~Lv~VDt~dtmdqVA~k~A~h~VGrrv~p~pg~lrVr~~G~~~~~Pr~mtVaeaGl~Pme~vev~~   82 (84)
T 3ge3_C           16 VQLVVVDLNDSMDQVAEKVAYHCVNRRVAPREGVMRVRKHRSTELFPRDMTIAESGLNPTEVIDVVF   82 (84)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHTTBTTTBCCCSSCEEEEETTCSCBCCTTCBHHHHCCCTTCEEEEEE
T ss_pred             EEEEEecCCCcHHHHHHHHhhhhcceeeCCCCCcEEEEECCCcccCCCCCEeeccCCCcceEEEEEE
Confidence            35578999999999999997653 3  32  236788899987  9999999999999999998864

>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=90.89  E-value=1.5  Score=25.67  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=52.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe-CCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~-~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ..+.|++++....+-...++++++|+..--++. .|--+...++-...=++.|+.+.++.|-+=|
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            346888888888888888999999998877764 5566788888888888999999999886654

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=90.49  E-value=0.33  Score=38.09  Aligned_cols=32  Identities=22%  Similarity=0.390  Sum_probs=29.6

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI   44 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~   44 (128)
                      ..+.|..++|+.+|++.|++.+|+|++.|||+
T Consensus        38 ~~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW   69 (530)
T 2ylm_A           38 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLW   69 (530)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTSCGGGEEEE
T ss_pred             ceEEEcCcCCHHHHHHHHHHHhCcCcccEEEE
Confidence            36789999999999999999999999999986

>2c7h_A RBBP6, retinoblastoma-binding protein 6, isoform 3; P53-associated, mRNA processing, splicing-associated, oesophageal cancer; NMR {Homo sapiens}

Probab=89.22  E-value=1.7  Score=25.76  Aligned_cols=42  Identities=14%  Similarity=0.137  Sum_probs=29.4

Q ss_pred             EEEEeCCCC-EEEEEecC-CCcHHHHHHHHHhhhCCCCCCeEEE
Q 033059            3 IFVKTLTGK-TITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLI   44 (128)
Q Consensus         3 i~vk~~~g~-~~~i~v~~-~~tV~~LK~~i~~~~~ip~~~q~L~   44 (128)
                      |+-+..+.+ ...+.++. ..+|.+||.+|..+.++-..+.-|.
T Consensus         9 V~YKFkS~k~~~~v~fdG~~Isv~dLKr~I~~~~kl~~~dfDL~   52 (86)
T 2c7h_A            9 VHYKFSSKLNYDTVTFDGLHISLCDLKKQIMGREKLKAADCDLQ   52 (86)
T ss_dssp             EEEEETTCSSEEEEEESSSEEEHHHHHHHHHHHHTCCTTTEEEE
T ss_pred             EEEEEeecCCcceEEEcCCEEEHHHHHHHHHHHhCCCCCcccEE
Confidence            555665554 34578874 6799999999998887755555553

>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=88.21  E-value=0.53  Score=38.06  Aligned_cols=50  Identities=30%  Similarity=0.569  Sum_probs=40.6

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCE-EcCCCCccccc
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-QLEDGRTLADY   59 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~-~L~d~~~L~~~   59 (128)
                      .+...+.+.++.|+.+|+..|++.+++|++.|.+++.+. .+++....+.+
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            455678889999999999999999999999999987654 56666565554

>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=87.77  E-value=1.6  Score=26.63  Aligned_cols=67  Identities=18%  Similarity=0.275  Sum_probs=45.7

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEE--e----CCEEcCCCCcccc----ccccCCcEEEE
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--F----AGKQLEDGRTLAD----YNIQKESTLHL   69 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~--~----~g~~L~d~~~L~~----~gi~~g~~i~v   69 (128)
                      |.|-..+|....|.|++++|+.++-+.++.+.++..+. --|+  +    --+.++|...|-+    ..+.....+.+
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            45556789999999999999999999999998866433 2332  1    1246777765433    34444555544

>2eel_A Cell death activator CIDE-A; CIDE-N domain, cell death- inducing DFFA-like effector A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=86.99  E-value=1.8  Score=25.90  Aligned_cols=49  Identities=14%  Similarity=0.276  Sum_probs=36.4

Q ss_pred             CcHHHHHHHHHhhhCCCCCCeEEEe--CCEEcCCCCccccccccCCcEEEEEEe
Q 033059           21 DTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus        21 ~tV~~LK~~i~~~~~ip~~~q~L~~--~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .++.+|+.+....++++....+|+.  .|..++|+..+..+.   ..|+.+++.
T Consensus        28 ~sL~EL~~K~~~~l~l~~~~~~lvLeeDGT~VddEeyF~tLp---~nT~lmvL~   78 (91)
T 2eel_A           28 SSLQELISKTLDALVIATGLVTLVLEEDGTVVDTEEFFQTLG---DNTHFMILE   78 (91)
T ss_dssp             SSHHHHHHHHHHHTTCSSSCEEEEETTTCCBCCCHHHHTTSC---SSEEEEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCCcEEEEeeCCcEEechhhhhhCC---CCCEEEEEc
Confidence            4799999999999999866777764  699998877766553   455555543

>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; 2.10A {Haemophilus influenzae} SCOP: d.15.3.4

Probab=86.51  E-value=2  Score=25.98  Aligned_cols=57  Identities=7%  Similarity=0.075  Sum_probs=41.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh---hCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059           12 TITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~---~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      .+.+++++.+||.++-+.+.-.   ..++.+...+..+|+....     +.-+++|+.|.++-.+
T Consensus        27 ~~~~~v~~g~TV~daI~~~gi~~~~peIdl~~~~V~Vng~~v~~-----d~~L~dGDRVEIyrpl   86 (97)
T 2hj1_A           27 LKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGIFSRPIKL-----TDVLKEGDRIEIYRPL   86 (97)
T ss_dssp             EEEEEEETTCBHHHHHHHHTHHHHCTTCCTTTSEEEEEECSCCT-----TCBCCTTCEEEECCCC
T ss_pred             EEEEEcCCCCcHHHHHHHcCCCccCCcccccccEEEEcCEECCC-----CccCCCCCEEEEEecc
Confidence            4567888999999998887532   2455556778888888863     3446789999986443

>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} SCOP: d.15.3.1 d.129.5.1

Probab=85.86  E-value=2.6  Score=27.94  Aligned_cols=63  Identities=16%  Similarity=0.252  Sum_probs=43.4

Q ss_pred             EEEecCCCcHHHHHHHHHhhhC-CC---------CCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEG-IP---------PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII   78 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~-ip---------~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~~   78 (128)
                      .++++. .||.+|.+.+..... +.         .....+..||+......- .+.-+++|+.|.++....||.+
T Consensus        17 ~~ev~~-~TV~dLl~~L~~~~p~l~~~l~~~~~l~~~v~VaVNg~~v~~~~~-~dt~L~dGDeVai~PpVsGG~~   89 (168)
T 1v8c_A           17 QLELPG-ATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQG-LSTPLSPGATLDLFPPVAGGGF   89 (168)
T ss_dssp             EEECCC-SBHHHHHHHHHHHCGGGHHHHEETTEECTTCEEEETTEEGGGTTG-GGCBCCTTCEEEEECSCCSEEE
T ss_pred             eEEECC-CcHHHHHHHHHhhChhhhhhhhcccccCCcEEEEECCEECCCcCC-CccCCCCCCEEEEECccccccc
Confidence            445655 899999999976631 10         234567789988765322 2345889999999887878754

>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=83.76  E-value=3.4  Score=25.88  Aligned_cols=46  Identities=13%  Similarity=0.152  Sum_probs=35.8

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEeCCEEcCCCCccccc
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY   59 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~~g~~L~d~~~L~~~   59 (128)
                      .+-|+.+.||+++...|....++++++ +-|+.++.....+.+++++
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            356889999999999999999998876 4555677755566777654

>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=81.57  E-value=4.1  Score=25.63  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=43.0

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCC------CeEEE---eCCE--EcCCCCccccccccCCcEEEEEEe
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPD------QQRLI---FAGK--QLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~------~q~L~---~~g~--~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      +..-+.+.+..+.|+.+++..++++.+...+      ++.|+   ++|.  .|+++..--.-.+.-...|++..+
T Consensus        18 Dhsy~tvr~~v~~sa~eIl~~va~kl~~~e~~~~~~~~l~Lv~V~ssGEk~vlqp~d~sv~tsL~~NgRLfvc~k   92 (120)
T 2dhz_A           18 DHSYVTIRSRLSASVQDILGSVTEKLQYSEEPAGREDSLILVAVSSSGEKVLLQPTEDCVFTALGINSHLFACTR   92 (120)
T ss_dssp             TSCCCCEEECTTCCHHHHHHHHHHHSTTCSSTTSCCSCCEEEEEETTCCCEECCTTCSCHHHHSCSSEEEEEECT
T ss_pred             cCceEEEEEeccccHHHHHHHHHHHhccccccccccCceEEEEEccCCcEeecCCcceEEEeeccccceEEEeeh
Confidence            4444567888899999999999999886543      67665   6786  455443322223444677877655

>1q1o_A Cell division control protein 24; PB1 domain, PCCR, PC motif, OPCA motif, yeast, cell polarity, protein-protein interaction; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 2kfj_A 2kfk_B

Probab=81.55  E-value=2.1  Score=26.01  Aligned_cols=28  Identities=25%  Similarity=0.204  Sum_probs=24.6

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCC
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIP   37 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip   37 (128)
                      +..+.+-|+++.+..+|..+|..+++++
T Consensus        22 ~d~~~i~V~~~i~f~~L~~kI~~Kl~~~   49 (98)
T 1q1o_A           22 SEIFTLLVEKVWNFDDLIMAINSKISNT   49 (98)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEecCCCCHHHHHHHHHHHHcCC
Confidence            4468899999999999999999998865

>3au4_A Myosin-X; protein-protein complex, motor protein cargo transportation, protein-apoptosis complex; 1.90A {Homo sapiens} PDB: 3au5_A 3pzd_A

Probab=81.42  E-value=4.6  Score=31.54  Aligned_cols=45  Identities=18%  Similarity=0.135  Sum_probs=38.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC--CCeEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP--DQQRLIF   45 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~--~~q~L~~   45 (128)
                      |.+.|..++|....+.+++.+|+.+|-+.|....|+..  +..-|.+
T Consensus       217 ~~~~V~l~dg~~~~~~v~~~tt~~el~~~v~~~lgL~e~~~~FgL~~  263 (555)
T 3au4_A          217 MTSTVYCHGGGSCKITINSHTTAGEVVEKLIRGLAMEDSRNMFALFE  263 (555)
T ss_dssp             EEEEEEETTSCEEEEEECTTCBHHHHHHHHHHHTTCTTCCSEEEEEE
T ss_pred             cceEEEecCCCeEEEEeCCCCcHHHHHHHHHHHcCCCCCCCceEEEE
Confidence            35778889999999999999999999999999999874  4555654

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=80.98  E-value=1.9  Score=33.75  Aligned_cols=72  Identities=11%  Similarity=0.227  Sum_probs=53.4

Q ss_pred             EEEEeCC--CCEEE----EEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC------CEEcC-CCCccccc--cccCCcEE
Q 033059            3 IFVKTLT--GKTIT----LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA------GKQLE-DGRTLADY--NIQKESTL   67 (128)
Q Consensus         3 i~vk~~~--g~~~~----i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~------g~~L~-d~~~L~~~--gi~~g~~i   67 (128)
                      |++|..+  .+++.    +.|+.+.+|.+|-..|.+..|+|++.--.+|.      -..|+ .+.|+.+.  +|.+|+.|
T Consensus       133 lFlK~yDp~~q~L~~~G~~~v~~~~kv~~l~~~i~~~~g~p~dt~l~lyEEi~~~~ie~l~~~~~t~~~~~~eL~~GdII  212 (530)
T 2ylm_A          133 LFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELMDGDII  212 (530)
T ss_dssp             EEEEEEETTTTEEEEEEEEEEETTCBGGGTHHHHHHHHTCCTTCCEEEEEEEETTEEEECCCSSSBHHHHSTTCCTTEEE
T ss_pred             EEEEeeCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEecCCCceeEcccccccHHHHHhcccCCCEE
Confidence            5555543  23433    56888999999999999999999976544443      23567 57899999  99999999


Q ss_pred             EEEEeec
Q 033059           68 HLVLRLR   74 (128)
Q Consensus        68 ~v~~~~~   74 (128)
                      .+-....
T Consensus       213 ~fQ~~~~  219 (530)
T 2ylm_A          213 VFQKDDP  219 (530)
T ss_dssp             EEEECCG
T ss_pred             EEEecCC
Confidence            8776543

>3hk0_A Growth factor receptor-bound protein 10; GRB10, RA, PH, RAS-associating, pleckstrin-homology, adapter phosphoprotein, SH2 domain; 2.60A {Homo sapiens}

Probab=80.02  E-value=4.4  Score=28.77  Aligned_cols=56  Identities=16%  Similarity=0.141  Sum_probs=35.7

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC-------CEEcCCCCcccc
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA-------GKQLEDGRTLAD   58 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~-------g~~L~d~~~L~~   58 (128)
                      |.|-..+|....+.|++++|+.+|-+.+..+.+++.+.-+.++.       -+.|+|...+-+
T Consensus        11 vkv~~~d~ss~~l~V~~~mta~ev~~~l~~k~~~~~~~~W~l~E~~~~l~lER~ledhE~V~e   73 (256)
T 3hk0_A           11 VKVFSEDGTSKVVEILADMTARDLCQLLVYKSHSVDDNSWTLVEHHPHLGLERCLEDHELVVQ   73 (256)
T ss_dssp             EEEEETTSCEEEEEECTTCBHHHHHHHHHCCC-------EEEEEEETTTTEEEECCTTSBHHH
T ss_pred             EEEEecCCcEEEEEECCCCCHHHHHHHHHHhcCCCCCCCEEEEEECCCcccccccccchhHHH
Confidence            44555678899999999999999999998877655444333321       256777665543

---

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	128
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	4e-41
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	1e-40
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	1e-38
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	2e-38
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	6e-37
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	1e-35
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	9e-35
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	3e-34
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	3e-34
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	4e-34
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	3e-33
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	2e-32
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	3e-32
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	9e-32
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	2e-31
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	6e-31
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	1e-30
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	1e-30
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	3e-30
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	2e-29
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	2e-28
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	5e-27
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	1e-26
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	2e-26
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	6e-26
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	4e-25
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	1e-24
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	2e-24
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	6e-24
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	1e-23
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	6e-23
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	1e-22
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	8e-22
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	2e-21
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	6e-21
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	3e-20
d2ayja1	56	g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolob	3e-20
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	2e-19
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	5e-19

>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 (326), Expect = 4e-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 (322), Expect = 1e-40
 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 =  122 bits (308), Expect = 1e-38
 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 =  122 bits (307), Expect = 2e-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 (298), Expect = 6e-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

>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 =  116 bits (291), Expect = 1e-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 =  113 bits (283), Expect = 9e-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

>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 =  112 bits (281), Expect = 3e-34
 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

>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 =  112 bits (281), Expect = 3e-34
 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

>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 =  112 bits (282), Expect = 4e-34
 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

>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 (273), Expect = 3e-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

>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 =  107 bits (268), Expect = 2e-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

>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 =  107 bits (268), Expect = 3e-32
 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

>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 = 9e-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 =  104 bits (262), Expect = 2e-31
 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

>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 =  104 bits (260), Expect = 6e-31
 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

>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 =  103 bits (257), Expect = 1e-30
 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

>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 =  102 bits (256), Expect = 1e-30
 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 (253), Expect = 3e-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 =  100 bits (250), Expect = 2e-29
 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 = 97.7 bits (243), Expect = 2e-28
 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

>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 = 94.7 bits (235), Expect = 5e-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

>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 = 92.8 bits (230), Expect = 1e-26
 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

>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 = 92.7 bits (230), Expect = 2e-26
 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

>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 = 90.8 bits (225), Expect = 6e-26
 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 = 89.2 bits (221), Expect = 4e-25
 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

>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 = 87.4 bits (216), Expect = 1e-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

>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 = 2e-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

>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 = 85.8 bits (212), Expect = 6e-24
 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

>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 = 85.4 bits (211), Expect = 1e-23
 Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 8/73 (10%)

Query: 6  KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE--------DGRTLA 57
               + +  ++  S T+  VK  +     +P  +  L +   ++         D + L 
Sbjct: 18 NQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQ 77

Query: 58 DYNIQKESTLHLV 70
           Y+++    L + 
Sbjct: 78 FYSVENGDCLLVR 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 = 83.8 bits (207), Expect = 6e-23
 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

>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 = 83.5 bits (206), Expect = 1e-22
 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 = 80.8 bits (199), Expect = 8e-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 = 79.1 bits (195), Expect = 2e-21
 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 = 78.5 bits (193), Expect = 6e-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 = 3e-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

>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 = 75.6 bits (186), Expect = 3e-20
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 77  IIEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKK 126
           + +P+ + + ++    K +CRKC A    RA  CR  +C  +N LR KKK
Sbjct: 3   LTDPAKLQIVQQRVFLKKVCRKCGALNPIRATKCR--RCHSTN-LRLKKK 49

>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 = 74.9 bits (184), Expect = 2e-19
 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

>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 = 73.4 bits (180), Expect = 5e-19
 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

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	128
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.94
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.93
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.92
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.92
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.91
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.9
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.9
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.89
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.89
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.89
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.89
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.88
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.88
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.88
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.87
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.86
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.86
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.85
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.85
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.85
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.84
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.84
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.82
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.82
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.81
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.8
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.79
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.79
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.78
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.78
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.76
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.75
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.71
d2ayja1	56	Ribosomal protein L40e {Sulfolobus solfataricus [T	99.7
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.67
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.61
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.55
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.54
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	99.28
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	99.11
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	98.43
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	98.19
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.95
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	97.71
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.68
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	96.75
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	95.63
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	95.42
d1zud21	65	Thiamin biosynthesis sulfur carrier protein ThiS {	95.33
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	94.71
d1wgya_	104	Rap guanine nucleotide exchange factor 5, RapGEF5	94.02
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	93.92
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	93.09
d1y8xb1	92	UBA3 {Human (Homo sapiens) [TaxId: 9606]}	92.7
d1v8ca1	87	MoaD-related protein, N-terminal domain {Thermus t	92.39
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	91.89
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	91.71
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	91.62
d1fm0d_	81	Molybdopterin synthase subunit MoaD {Escherichia c	91.59
d2incc1	83	Toluene, o-xylene monooxygenase oxygenase subunit	88.93
d1j0ga_	92	Hypothetical protein 1810045k17 {Mouse (Mus muscul	88.05
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	87.73
d2cu3a1	63	Uncharacterised protein TTHA0675 {Thermus thermoph	87.65
d1tygb_	65	Thiamin biosynthesis sulfur carrier protein ThiS {	86.89
d3d32a1	118	GABA(A) receptor associated protein GABARAP {Human	86.45
d1eo6a_	116	Golgi-associated ATPase enhancer of 16 kD, Gate-16	85.47
d2bkfa1	85	Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Hum	80.51
d2zjda1	119	Microtubule-associated proteins 1A/1B light chain	80.05

>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=99.94  E-value=7e-27  Score=138.91  Aligned_cols=76  Identities=96%  Similarity=1.322  Sum_probs=75.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|||++|++|++++|++||
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            8999999999999999999999999999999999999999999999999999999999999999999999999997

>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=99.93  E-value=8e-26  Score=134.86  Aligned_cols=75  Identities=33%  Similarity=0.593  Sum_probs=73.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|+|+++++|+++.|++|
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            899999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.92  E-value=2.6e-25  Score=131.07  Aligned_cols=73  Identities=62%  Similarity=0.943  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+||+.+|+++.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|||++|++|++++|+
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            8999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.92  E-value=4.7e-25  Score=134.05  Aligned_cols=77  Identities=34%  Similarity=0.514  Sum_probs=74.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+|++++|+++.++|++++||.+||++|+++.++|+++|+|+|+|+.|+|+.+|++|+|+++++|+++.+.++|.
T Consensus         8 mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~gp   84 (87)
T d1wh3a_           8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGP   84 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCS
T ss_pred             EEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999998874

>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=99.91  E-value=1.3e-24  Score=128.96  Aligned_cols=73  Identities=34%  Similarity=0.560  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|+
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            7999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.90  E-value=9.1e-24  Score=125.20  Aligned_cols=73  Identities=37%  Similarity=0.647  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCC-EEEEE-ecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGK-TITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~-~~~i~-v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++++|+ ++.++ +++++||++||+.|+++.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|+
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            89999999995 78885 899999999999999999999999999999999999999999999999999999875

>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=99.90  E-value=8.5e-24  Score=126.55  Aligned_cols=75  Identities=28%  Similarity=0.503  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+||..+|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++.+.
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            689999999999999999999999999999999999999999999999999999999999999999999987654

>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=99.89  E-value=2.8e-23  Score=123.08  Aligned_cols=73  Identities=37%  Similarity=0.622  Sum_probs=69.4

Q ss_pred             CEEEEEeCCC-CEEEE-EecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTG-KTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g-~~~~i-~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|+..+| +++.+ +|++++||++||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|+
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 57777 5999999999999999999999999999999999999999999999999999999874

>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=99.89  E-value=5.8e-23  Score=126.59  Aligned_cols=76  Identities=30%  Similarity=0.587  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhC---CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~---ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|+|++.+|+++.++|++++||.+||++|+++.+   +|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++....
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~   79 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCC
Confidence            99999999999999999999999999999999876   89999999999999999999999999999999999876655

>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=99.89  E-value=4.7e-24  Score=125.60  Aligned_cols=72  Identities=35%  Similarity=0.613  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++..|+|+++|+|+|+|+.|+|+.+|++|+| ++++|+++.+.
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=99.89  E-value=2.7e-23  Score=122.28  Aligned_cols=71  Identities=23%  Similarity=0.431  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+|+|+...|+++.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|||++|++|++..
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999863

>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=99.88  E-value=1.4e-22  Score=120.10  Aligned_cols=73  Identities=33%  Similarity=0.428  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe--CCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~--~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      .+|+|+.++|+++.++|++++||.+||++|++..|+|++.|+|+|  +|+.|+|+.+|++|||++|++|+|+++.
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            379999999999999999999999999999999999999999999  6999999999999999999999999863

>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=99.88  E-value=6.9e-23  Score=121.69  Aligned_cols=72  Identities=32%  Similarity=0.578  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhC---CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~---ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++.+|+++.++|++++||.+||++|++..|   +|+++|+|+|+|+.|+|+.+|++|||++|++|++++.
T Consensus         3 ~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~vs   77 (77)
T d1oqya4           3 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            78999999999999999999999999999999877   8999999999999999999999999999999998863

>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=99.88  E-value=2.4e-22  Score=118.20  Aligned_cols=71  Identities=34%  Similarity=0.558  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++. +.++.++|++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++.+
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 457999999999999999999999999999999999999999999999999999999999865

>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=99.87  E-value=2.4e-22  Score=121.13  Aligned_cols=74  Identities=34%  Similarity=0.476  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|++.++ .+.++|++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+|+++...
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            7899999754 6899999999999999999999999999999999999999999999999999999999998654

>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=99.86  E-value=9.3e-22  Score=118.98  Aligned_cols=68  Identities=31%  Similarity=0.646  Sum_probs=65.9

Q ss_pred             CCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         8 ~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      ++|+++.++|++++||.+||++|++++++|++.|+|+|+|+.|+|+.+|++|||++|++|+++++++|
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            57889999999999999999999999999999999999999999999999999999999999999887

>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=99.86  E-value=3.2e-22  Score=123.99  Aligned_cols=71  Identities=23%  Similarity=0.324  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |+|+|+...|+++.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|||++|++|+|+.
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            48999999999999999999999999999999999999999999999999999999999999999999975

>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=99.85  E-value=1.7e-21  Score=121.57  Aligned_cols=71  Identities=32%  Similarity=0.437  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++.++ .+.|+|++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||++|++|+|++|
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            6899998765 6899999999999999999999999999999999999999999999999999999999875

>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=99.85  E-value=1.2e-21  Score=122.00  Aligned_cols=77  Identities=22%  Similarity=0.422  Sum_probs=70.4

Q ss_pred             CEEEE----EeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcC-CCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFV----KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~v----k~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~-d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |.|+|    +..++.++.++|++++||.+||+.|+.++++|++.|+|+|+|+.|. |..+|++|||++|++|+|+.+..+
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    6667899999999999999999999999999999999999999995 668999999999999999888766


Q ss_pred             CC
Q 033059           76 GI   77 (128)
Q Consensus        76 g~   77 (128)
                      +.
T Consensus        88 ~~   89 (102)
T d1v5oa_          88 GL   89 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.85  E-value=6e-22  Score=119.15  Aligned_cols=71  Identities=28%  Similarity=0.371  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++.++ .+.++|++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++|||++|++|+|++|
T Consensus        11 i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r   81 (83)
T d1wx8a1          11 IRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVR   81 (83)
T ss_dssp             EEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBC
T ss_pred             EEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEe
Confidence            6899998754 5799999999999999999999999999999999999999999999999999999999876

>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=99.84  E-value=1.2e-21  Score=123.50  Aligned_cols=75  Identities=31%  Similarity=0.438  Sum_probs=68.9

Q ss_pred             EEEEeC-CCCEEEEEecC-CCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCCC
Q 033059            3 IFVKTL-TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         3 i~vk~~-~g~~~~i~v~~-~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |.|+.. +|+++.++|.+ ++||.+||++|++.+++|++.|+|+|.|+.|+|+.+|++|+|++|++|+|++|++||.
T Consensus        32 V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG~  108 (111)
T d1we6a_          32 VSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSGP  108 (111)
T ss_dssp             ECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCSS
T ss_pred             EEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCCC
Confidence            344333 58899999987 8999999999999999999999999999999999999999999999999999999984

>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=99.84  E-value=5.8e-22  Score=124.05  Aligned_cols=76  Identities=22%  Similarity=0.396  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeE---------------EEeCCEEcCCC-CccccccccCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIFAGKQLEDG-RTLADYNIQKE   64 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~---------------L~~~g~~L~d~-~~L~~~gi~~g   64 (128)
                      |+|+|+..+|+++.++|++++||.+||++|++.+++|+++|+               |+|+|+.|.|+ .+|++|||++|
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               99999999665 69999999999


Q ss_pred             cEEEEEEeecCC
Q 033059           65 STLHLVLRLRGG   76 (128)
Q Consensus        65 ~~i~v~~~~~gg   76 (128)
                      ++|+|+.+++..
T Consensus        88 ~~l~lv~r~~~~   99 (105)
T d1v2ya_          88 DEVSFIKKLGQK   99 (105)
T ss_dssp             EEEEEEECSCSC
T ss_pred             CEEEEEEecCCC
Confidence            999999987644

>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=99.82  E-value=3.1e-20  Score=114.02  Aligned_cols=74  Identities=24%  Similarity=0.335  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcC-CCCccccccccCCcEEEEEEeecCCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~-d~~~L~~~gi~~g~~i~v~~~~~gg~   77 (128)
                      |+|+||+++|+.+.++|++++||.+||++|+   .++++.|+|+|+|+.|. |..+|++|+|.+|++|+++++.+++.
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   46889999999999996 66899999999999999998877663

>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=99.82  E-value=7.2e-20  Score=112.97  Aligned_cols=75  Identities=25%  Similarity=0.427  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCCEE-EEEecCCCcHHHHHHHHHhh-----hCCC--CCCeEEEeCCEEcCCCCccccccccCCc------E
Q 033059            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDK-----EGIP--PDQQRLIFAGKQLEDGRTLADYNIQKES------T   66 (128)
Q Consensus         1 m~i~vk~~~g~~~-~i~v~~~~tV~~LK~~i~~~-----~~ip--~~~q~L~~~g~~L~d~~~L~~~gi~~g~------~   66 (128)
                      |+|.||..+|+.+ .+.|++++||.+||++|++.     .++|  +++|||+|+|+.|+|+.+|++|+|.+|+      +
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 69999999999999999876     5687  7899999999999999999999999997      9


Q ss_pred             EEEEEeecC
Q 033059           67 LHLVLRLRG   75 (128)
Q Consensus        67 i~v~~~~~g   75 (128)
                      +||++|.+.
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=99.81  E-value=7.3e-20  Score=115.99  Aligned_cols=74  Identities=20%  Similarity=0.349  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHH--------HhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKI--------QDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i--------~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|+.++|+++.+.|++++||.+||++|        ++..++|++.|||+|.|+.|+|+.+|++|+|.+|++++|++.
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            579999999999999999999999999999        466789999999999999999999999999999998655554


Q ss_pred             ec
Q 033059           73 LR   74 (128)
Q Consensus        73 ~~   74 (128)
                      ++
T Consensus        97 ~r   98 (116)
T d1wgha_          97 AR   98 (116)
T ss_dssp             EC
T ss_pred             eC
Confidence            44

>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=99.80  E-value=3e-20  Score=114.43  Aligned_cols=71  Identities=18%  Similarity=0.266  Sum_probs=66.2

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|+|++.+++.+.++|++++||.+||++|++.+++|+++|+|+|+|+.|+|+ +|++|||++|++|+|+..
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            58999998887778999999999999999999999999999999999999886 799999999999998754

>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=99.79  E-value=2.4e-19  Score=107.10  Aligned_cols=72  Identities=24%  Similarity=0.407  Sum_probs=64.6

Q ss_pred             CEEEEEeCCCCEEEEEec-----CCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcC-CCCccccccccCCcEEEEEEee
Q 033059            1 MQIFVKTLTGKTITLEVE-----SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~-----~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~-d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|+|++ .+..+.++|.     +++||++||++|++.+|+|+++|+|+|+|+.|. |+.+|++|||++|++|+|+.+.
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            6889976 5678999884     688999999999999999999999999999995 6789999999999999998654

>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=99.79  E-value=8.9e-20  Score=112.97  Aligned_cols=73  Identities=18%  Similarity=0.294  Sum_probs=65.8

Q ss_pred             CEEEE--EeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEee
Q 033059            1 MQIFV--KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         1 m~i~v--k~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      |+|++  +...|+++.++|++++||.+||++|++.+++|+++|+|+|+|++|+|+.+|++|||+++++|+++...
T Consensus        18 i~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~   92 (100)
T d1wjua_          18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELK   92 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCC
T ss_pred             EEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcC
Confidence            35555  44568999999999999999999999999999999999999999999999999999999999877544

>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=99.78  E-value=6.9e-20  Score=112.57  Aligned_cols=74  Identities=19%  Similarity=0.359  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      |+|.|++ +++++.|+|++++||.+||++|++.+++|+++|+|+|+|+ |.|+.+|++|+|++|++|+|+.+..+|
T Consensus        18 i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~~~g   91 (95)
T d1v86a_          18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGSTISG   91 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSSCCC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecCCCC
Confidence            5788875 7789999999999999999999999999999999999997 899999999999999999998766555

>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=99.78  E-value=1.6e-19  Score=109.85  Aligned_cols=74  Identities=20%  Similarity=0.404  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCCEEEE-EecCCCcHHHHHHHHHhhhCCCCCCeEEE---eCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i-~v~~~~tV~~LK~~i~~~~~ip~~~q~L~---~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|+|++ .++.+.+ +|++++||.+||++|++.+++|+++|+|+   |.|+.|+|+.+|++|+|++|++|+|+.+...
T Consensus         8 ~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~~~   85 (90)
T d1v5ta_           8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRES   85 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCSS
T ss_pred             EEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeCCC
Confidence            7899997 5667777 69999999999999999999999999999   6899999999999999999999999866443

>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=99.76  E-value=1.8e-18  Score=105.72  Aligned_cols=76  Identities=29%  Similarity=0.459  Sum_probs=66.2

Q ss_pred             CEEEEEeCCCC--EEEEEecCCCcHHHHHHHHHhhhC--CCCCCeEEEeCCEEcCCCCcccccccc--CCcEEEEEEeec
Q 033059            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQ--KESTLHLVLRLR   74 (128)
Q Consensus         1 m~i~vk~~~g~--~~~i~v~~~~tV~~LK~~i~~~~~--ip~~~q~L~~~g~~L~d~~~L~~~gi~--~g~~i~v~~~~~   74 (128)
                      |+|+|++++++  .+.+++++++||.+||++|++..+  +|+++|||+|+|+.|+|+.+|++|.+.  ++.+|||+.+..
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            78999998765  488899999999999999999865  999999999999999999999999764  445999998765


Q ss_pred             CC
Q 033059           75 GG   76 (128)
Q Consensus        75 gg   76 (128)
                      .+
T Consensus        88 ~~   89 (93)
T d1wgda_          88 SG   89 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.75  E-value=3.2e-18  Score=101.63  Aligned_cols=74  Identities=14%  Similarity=0.332  Sum_probs=69.4

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .|.|+. +|....+.|.+++++..|++.++++.+++++.++|+|+|+.|+++.|+++|+|++|++|+++++++||
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            466655 67788899999999999999999999999999999999999999999999999999999999999998

>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=99.73  E-value=6.4e-18  Score=104.72  Aligned_cols=75  Identities=27%  Similarity=0.398  Sum_probs=65.0

Q ss_pred             EEEEEeCCC-CEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCcccccccc-------CCcEEEEEEee
Q 033059            2 QIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ-------KESTLHLVLRL   73 (128)
Q Consensus         2 ~i~vk~~~g-~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~-------~g~~i~v~~~~   73 (128)
                      +|+|+...+ .++.++|++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|||.       ..+++.+.++.
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            356655544 4678999999999999999999999999999999999999999999999995       45588888887


Q ss_pred             cCC
Q 033059           74 RGG   76 (128)
Q Consensus        74 ~gg   76 (128)
                      .|+
T Consensus        81 ~~~   83 (103)
T d2c9wb1          81 DDT   83 (103)
T ss_dssp             TTE
T ss_pred             CCC
Confidence            665

>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=99.71  E-value=9.3e-18  Score=102.84  Aligned_cols=76  Identities=18%  Similarity=0.262  Sum_probs=67.5

Q ss_pred             CEEEEEeC-CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCE-------EcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~-~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~-------~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |.|+|++. ++..++..+++++||.+||++|+..+|+|++.|+|+|.|+       .++|+.+|++|+|.+|++|||+.+
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            57889874 5556889999999999999999999999999999999886       578999999999999999999977


Q ss_pred             ecCC
Q 033059           73 LRGG   76 (128)
Q Consensus        73 ~~gg   76 (128)
                      .+.+
T Consensus        88 ~p~~   91 (95)
T d1v6ea_          88 SGSG   91 (95)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            6554

>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=99.70  E-value=3.2e-19  Score=96.14  Aligned_cols=47  Identities=36%  Similarity=0.597  Sum_probs=43.4

Q ss_pred             CCchhHHHHHhhccchhhhhhhhcccCCcccccccccCCCCCCCcccCcC
Q 033059           78 IEPSLMALARKYNQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKI  127 (128)
Q Consensus        78 ~~~~~~~~a~k~~~~k~~Cr~c~~r~~~~~~~c~~~~c~~~~~~~~~~~~  127 (128)
                      .+|++.++|+++++++++||.||+|+|++|++||+  |||+ ||||||+-
T Consensus         4 ~eP~l~~lA~k~~~~k~ICrkC~AR~p~rAt~CRK--Cg~~-nLRpKkke   50 (56)
T d2ayja1           4 TDPAKLQIVQQRVFLKKVCRKCGALNPIRATKCRR--CHST-NLRLKKKE   50 (56)
T ss_dssp             CCSCCSSTTTTCSCCCEEETTTCCEECTTCSSCTT--TCCC-CEEECCCC
T ss_pred             cCHHHHHHHHHHhhhhHHHhhccccCCcccccccc--CCCC-Ccchhhhh
Confidence            57899999999999999999999999999999995  9987 59999973

>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=99.67  E-value=1.4e-16  Score=93.93  Aligned_cols=75  Identities=17%  Similarity=0.425  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecC
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~g   75 (128)
                      |+|.|++.+|+.+.+.|.+++++..|+++++++.++|++.++|+|+|+.|.++.|++++++++|++|++++++.|
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            578899999999999999999999999999999999999999999999999999999999999999999998765

>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=99.61  E-value=1e-15  Score=93.99  Aligned_cols=69  Identities=19%  Similarity=0.274  Sum_probs=60.3

Q ss_pred             EEEEEeC---CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCE-------EcC-CCCccccccccCCcEEEEE
Q 033059            2 QIFVKTL---TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLE-DGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~---~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~-------~L~-d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|.|+..   +++.+++.|++++||.+||.+|+..+|+|++.|+|+|.|+       .|+ |+.+|.+|||++|++|+|.
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            5666654   3577899999999999999999999999999999999886       354 7889999999999999975

>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=99.55  E-value=1.4e-14  Score=87.58  Aligned_cols=74  Identities=18%  Similarity=0.288  Sum_probs=60.8

Q ss_pred             EEEEEeC-CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCE-------EcCCCCccccccccCCcEEEEEEee
Q 033059            2 QIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVLRL   73 (128)
Q Consensus         2 ~i~vk~~-~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~-------~L~d~~~L~~~gi~~g~~i~v~~~~   73 (128)
                      .|.|.+. .+...+..+++++||.+||++|+..+|+|++.|+|+|.|+       .++|+.+|.+|||.+|++|||+= .
T Consensus         6 ~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd-~   84 (90)
T d1t0ya_           6 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVD-V   84 (90)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEE-C
T ss_pred             EEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEe-C
Confidence            4556542 3344688899999999999999999999999999998876       44688999999999999999854 4


Q ss_pred             cCC
Q 033059           74 RGG   76 (128)
Q Consensus        74 ~gg   76 (128)
                      .||
T Consensus        85 ~~~   87 (90)
T d1t0ya_          85 TGG   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            443

>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=99.54  E-value=7.7e-15  Score=89.03  Aligned_cols=54  Identities=35%  Similarity=0.567  Sum_probs=48.8

Q ss_pred             CCCcHHHHHHHHHhhhC--CC-CCCeEEEeCCEEcCCCCccccccccCCcEEEEEEe
Q 033059           19 SSDTIDNVKAKIQDKEG--IP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus        19 ~~~tV~~LK~~i~~~~~--ip-~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      .+.||.+||+.|++...  +| |+.|+|+|+|+.|+|+.+|++|||++|++||++.|
T Consensus        36 ~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          36 GGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             CCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             CccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            36799999999998864  44 68999999999999999999999999999999976

>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=99.28  E-value=2.1e-11  Score=70.38  Aligned_cols=70  Identities=16%  Similarity=0.384  Sum_probs=66.4

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEE
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~   70 (128)
                      +.|.|+..+|+.+.+.|..++++..|....++..+++++.++|+|+|..+.++.|.+++++++|++|.|.
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            4688888899999999999999999999999999999999999999999999999999999999999875

>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=99.11  E-value=1e-10  Score=69.39  Aligned_cols=68  Identities=22%  Similarity=0.273  Sum_probs=56.1

Q ss_pred             EEEEeCCCCEEEEEecC-CCcHHHHHHHHHhhhCCCCCCeEEEeC--------------CEEcC-CCCccccccccCCcE
Q 033059            3 IFVKTLTGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFA--------------GKQLE-DGRTLADYNIQKEST   66 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~-~~tV~~LK~~i~~~~~ip~~~q~L~~~--------------g~~L~-d~~~L~~~gi~~g~~   66 (128)
                      |.|++.+| +..++|+. +.||.+||.+|++..++|.++|.|..+              -..|. |..+|+++||.+|+.
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            77888887 58899964 789999999999999999999999553              12344 456799999999999


Q ss_pred             EEEEE
Q 033059           67 LHLVL   71 (128)
Q Consensus        67 i~v~~   71 (128)
                      |++.-
T Consensus        82 vyL~y   86 (94)
T d1wf9a1          82 VYLAY   86 (94)
T ss_dssp             EECCC
T ss_pred             EEEEe
Confidence            98753

>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=98.43  E-value=8.8e-07  Score=50.56  Aligned_cols=69  Identities=19%  Similarity=0.224  Sum_probs=65.2

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      |.|-..+|+...+.|.|++|+.++-++..+++|+++++..|.|+++.|+-+.++.-.|+.+|+.+.++.
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~   71 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVP   71 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEEC
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeeecCCCCCCEEEEEE
Confidence            677788999999999999999999999999999999999999999999999999999999999999874

>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=98.19  E-value=8e-06  Score=47.28  Aligned_cols=68  Identities=21%  Similarity=0.393  Sum_probs=58.1

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEc---CCCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL---EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L---~d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|.||.++|..+.-.+..++||.+|.+.|... +.++....|+  |..+.+   +++.+|.+.|+.+.++|+|-
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 7777788777  677887   34679999999998888764

>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=97.95  E-value=2.3e-05  Score=46.02  Aligned_cols=65  Identities=18%  Similarity=0.332  Sum_probs=53.2

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhh-CCCCCCeEEEe--CCEEcC-CCCccccccccCCcEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLIF--AGKQLE-DGRTLADYNIQKESTL   67 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~-~ip~~~q~L~~--~g~~L~-d~~~L~~~gi~~g~~i   67 (128)
                      .|.||.++|..+...+..++||.+|.+.+.... +.+.....|+.  --+.|. ++.+|.++|+.+. .|
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 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNA-VI   84 (89)
T ss_dssp             EEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEECCCCSSCSGGGTTCCS-EE
T ss_pred             EEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcccCCCcCcHHHCCCcCc-eE
Confidence            578999999999999999999999999997753 56666788874  467784 5789999999864 44

>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=97.71  E-value=7.9e-05  Score=46.26  Aligned_cols=68  Identities=19%  Similarity=0.363  Sum_probs=55.9

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEc---CCCCccccccccCCcEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL---EDGRTLADYNIQKESTLHLV   70 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L---~d~~~L~~~gi~~g~~i~v~   70 (128)
                      +|.||..+|+.+...+..++||.+|...|... +.+.....|+  |--+.|   +.+.+|.+.|+.+..+|+|-
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            58899999999999999999999999999765 4556677776  566676   34789999999999888664

>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=97.68  E-value=0.00014  Score=42.92  Aligned_cols=69  Identities=19%  Similarity=0.243  Sum_probs=55.3

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE--eCCEEc--CCCCccccccccCCcEEEEEE
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL--EDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~--~~g~~L--~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +|.||..+|..+...+..++||.+|...+... +.......|+  |-.+.+  +.+.||.++|+.+.++|+|--
T Consensus        18 ~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~-~~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~~   90 (96)
T d2cr5a1          18 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   90 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHh-ccCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEec
Confidence            68899999999999999999999999998765 4455667776  444555  346899999999988887643

>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=96.75  E-value=0.012  Score=33.42  Aligned_cols=65  Identities=9%  Similarity=0.226  Sum_probs=48.0

Q ss_pred             CEEEEEeCC------C-CEEEEEecCCCcHHHHHHHHHhhhCC-----------CCCCeEEEeCCEEcCCCCcccccccc
Q 033059            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEGI-----------PPDQQRLIFAGKQLEDGRTLADYNIQ   62 (128)
Q Consensus         1 m~i~vk~~~------g-~~~~i~v~~~~tV~~LK~~i~~~~~i-----------p~~~q~L~~~g~~L~d~~~L~~~gi~   62 (128)
                      |+|.|+...      | ....+++++..||.+|.+.+.+++.-           .....++..||+..+++     +-|.
T Consensus         2 mkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~d-----~~L~   76 (88)
T d1vjka_           2 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWD-----EELK   76 (88)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTT-----CBCC
T ss_pred             eEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCCC-----cCcC
Confidence            788888764      3 46788999999999999999876531           12345677888877654     3467


Q ss_pred             CCcEEEEE
Q 033059           63 KESTLHLV   70 (128)
Q Consensus        63 ~g~~i~v~   70 (128)
                      +|+.|.++
T Consensus        77 ~gDevai~   84 (88)
T d1vjka_          77 DGDVVGVF   84 (88)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEe
Confidence            89999875

>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=95.63  E-value=0.044  Score=31.06  Aligned_cols=71  Identities=17%  Similarity=0.260  Sum_probs=53.0

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCC-CCeEEEeC---CE--EcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFA---GK--QLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~-~~q~L~~~---g~--~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |+|.|..+++ ++++.++..++..+|=+++.+..++.. +-.=|.|-   |.  =|+.++.|..+.++.+..+.+.++
T Consensus         2 ~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~~l~F~   78 (84)
T d1ef1a3           2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFR   78 (84)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcCCcccccceEEEECCCCCeEeccCCCchhhhccCCCCCEEEEEE
Confidence            6789999987 589999999999999999999999764 33445543   32  367788888876666555555444

>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=95.42  E-value=0.055  Score=31.54  Aligned_cols=75  Identities=17%  Similarity=0.192  Sum_probs=48.3

Q ss_pred             CEEEEEeCCC--------CEEEEEecC---CCcHHHHHHHHHhhhCCCCCC-----------eEEEeCCEEcCCCCcccc
Q 033059            1 MQIFVKTLTG--------KTITLEVES---SDTIDNVKAKIQDKEGIPPDQ-----------QRLIFAGKQLEDGRTLAD   58 (128)
Q Consensus         1 m~i~vk~~~g--------~~~~i~v~~---~~tV~~LK~~i~~~~~ip~~~-----------q~L~~~g~~L~d~~~L~~   58 (128)
                      |+|+|+...|        +...++++.   ..||.+|-+.+.+.+.-...+           +.+..+|.......- -+
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-l~   83 (101)
T d1xo3a_           5 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWELLGE-LD   83 (101)
T ss_dssp             CEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCCSCGGGSCCTTSCCSSEEEEETTEEHHHHTT-TS
T ss_pred             eEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCcchhhhhccCcCeeeeEEEEEcCcceeccCC-Cc
Confidence            7888888542        345666653   479999999998876532221           244456654321000 14


Q ss_pred             ccccCCcEEEEEEeecCC
Q 033059           59 YNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        59 ~gi~~g~~i~v~~~~~gg   76 (128)
                      +.|++|+.|.++....||
T Consensus        84 t~l~dgDeV~~~p~v~GG  101 (101)
T d1xo3a_          84 YQLQDQDSILFISTLHGG  101 (101)
T ss_dssp             CCCCTTCEEEEEETTCCC
T ss_pred             cCcCCCCEEEEeCCCCCC
Confidence            668999999999888776

>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=95.33  E-value=0.068  Score=28.66  Aligned_cols=58  Identities=12%  Similarity=0.186  Sum_probs=43.1

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .+++++..||.+|-+.    .++++...-+..+++.+.- ..-.+.-+++|+.|.++.-..||
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            4556778899998765    4788888888899998842 23345567899999987666554

>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=94.71  E-value=0.033  Score=31.42  Aligned_cols=37  Identities=11%  Similarity=0.238  Sum_probs=34.4

Q ss_pred             CCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeC
Q 033059           10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (128)
Q Consensus        10 g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~   46 (128)
                      --++.+.+.+..+..+|.++|++++..+++..+|.|.
T Consensus        13 ~fTVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~   49 (82)
T d1oeya_          13 KYTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYR   49 (82)
T ss_dssp             SSEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEEC
T ss_pred             EEEEEEEccCCCCHHHHHHHHHHHhCCChhheEEEec
Confidence            3578899999999999999999999999999999996

>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=94.02  E-value=0.17  Score=29.64  Aligned_cols=71  Identities=10%  Similarity=0.192  Sum_probs=50.4

Q ss_pred             EEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEE---eCCE--EcCCCCccccccccCCcEEEEEEeec
Q 033059            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGK--QLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
Q Consensus         4 ~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~---~~g~--~L~d~~~L~~~gi~~g~~i~v~~~~~   74 (128)
                      .|-..+..-.++.+.-+.|+.++++.++++.+.+.+++.|+   ++|.  .|+++..--.-.+.-++.+++..+-.
T Consensus        13 ~VY~~Dhsy~tlr~~v~~sa~eI~~~vaeKl~~~~e~L~LV~V~SsGEr~~lkp~d~sV~TsL~lN~rLFvc~~d~   88 (104)
T d1wgya_          13 HVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRKDL   88 (104)
T ss_dssp             EEECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEECCS
T ss_pred             EEEecCCcEEEEEeeccCcHHHHHHHHHHHhCCCCCceEEEEEccCCcEEeeCccceeEEeeeeecceEEEechhh
Confidence            34445666677889999999999999999999998988776   6776  44543322222345567888877643

>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=93.92  E-value=0.11  Score=29.02  Aligned_cols=59  Identities=14%  Similarity=0.152  Sum_probs=44.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEe---CCE--EcCCCCccccc
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIF---AGK--QLEDGRTLADY   59 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~---~g~--~L~d~~~L~~~   59 (128)
                      |+..|..++|+.+.+.+++.++..+|=+++.+..++...+ .=|.|   +|.  =|+.++.|...
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            7889999999999999999999999999999999976433 22322   232  24556666554

>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=93.09  E-value=0.25  Score=27.76  Aligned_cols=43  Identities=14%  Similarity=0.139  Sum_probs=33.8

Q ss_pred             EEEEeC-CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCC
Q 033059            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (128)
Q Consensus         3 i~vk~~-~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g   47 (128)
                      |.||.. ++..+.+.++++.+..+|.++|+..+++.  .++|.|..
T Consensus        13 ikVKv~~~~D~~~~~l~~~it~~dL~~kI~~rf~~~--~~~lkY~D   56 (85)
T d1ip9a_          13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDTD--NFKLQTKL   56 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHTSS--CEEEEECC
T ss_pred             EEEEEEECCcEEEEEeCCCCCHHHHHHHHHHHhCCC--ceEEEEEc
Confidence            445544 56778899999999999999999999764  57777764

>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=92.70  E-value=0.12  Score=29.68  Aligned_cols=57  Identities=12%  Similarity=0.288  Sum_probs=38.6

Q ss_pred             EEEecCCCcHHHHHHHHHhhhC--CCCCCeEEEeCC--------EE--cCC------CCccccccccCCcEEEEE
Q 033059           14 TLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAG--------KQ--LED------GRTLADYNIQKESTLHLV   70 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~--ip~~~q~L~~~g--------~~--L~d------~~~L~~~gi~~g~~i~v~   70 (128)
                      .+++++++|+.+|-+.+.+.-.  +..-.++-...|        .+  |+.      +++|.++|+.+|+.|.|.
T Consensus         4 ~l~~~~~~TL~~li~~L~e~p~~qlk~Psltt~~~g~~ktLYm~~pp~Lee~Tr~NL~k~L~eLgl~dG~ei~Vt   78 (92)
T d1y8xb1           4 NIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVA   78 (92)
T ss_dssp             CEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEE
T ss_pred             eEEcCCCCcHHHHHHHHhhChHhhccCCceeeecCCCccEEEecCcHHHHHHhhhccccCHHHhCCcCCCEEEEe
Confidence            4788999999999999988633  322222222222        22  321      478999999999999875

>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=92.39  E-value=0.21  Score=27.96  Aligned_cols=61  Identities=18%  Similarity=0.298  Sum_probs=41.3

Q ss_pred             EEEecCCCcHHHHHHHHHhhhC-C---------CCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEG-I---------PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~-i---------p~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .++++ ..||.+|.+.+.+.+. +         ......+..+|+...+...+ +.-|++|+.|.++....||
T Consensus        17 e~~v~-~~Tv~~ll~~L~~~~p~l~~~l~~~~~~~~~v~i~vng~~i~~~~~~-~~~l~~gdeV~i~PpvsGG   87 (87)
T d1v8ca1          17 QLELP-GATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGL-STPLSPGATLDLFPPVAGG   87 (87)
T ss_dssp             EEECC-CSBHHHHHHHHHHHCGGGHHHHEETTEECTTCEEEETTEEGGGTTGG-GCBCCTTCEEEEECSCCSE
T ss_pred             EEEEc-CCCHHHHHHHHHHHCHHHHHHhcccccccceEEEEEcCeeeecccCC-cccCCCCCEEEEECCCCCC
Confidence            45665 4699999999987652 1         01335677888877543333 2347899999998777665

>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=91.89  E-value=0.54  Score=26.24  Aligned_cols=71  Identities=11%  Similarity=0.129  Sum_probs=52.3

Q ss_pred             CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEE--eCCE--EcCCCCccccccccCCcEEEEEEe
Q 033059            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--FAGK--QLEDGRTLADYNIQKESTLHLVLR   72 (128)
Q Consensus         1 m~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~--~~g~--~L~d~~~L~~~gi~~g~~i~v~~~   72 (128)
                      |.|.|..+++ +.++++++.++..+|=.++.+..++...+ .=|.  -+|.  =|+.++.|..+.+..+..+.+.++
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 FTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   78 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             EEEEEEEcCC-cEEEEEcCCChHHHHHHHHHHHcCCcccccceEEEecCCceEEccCCCchhhhccCCCCCEEEEEE
Confidence            4688888987 58999999999999999999999975433 3333  3443  357788888887666665555544

>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=91.71  E-value=0.52  Score=25.71  Aligned_cols=44  Identities=11%  Similarity=0.046  Sum_probs=38.6

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~   45 (128)
                      .|.|-.++|+.-.+.+.|..||.++-..+.++-|+.++...++.
T Consensus         2 ~iRv~LPngq~T~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~~   45 (73)
T d1wxma1           2 TVKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYR   45 (73)
T ss_dssp             EEEEECSSSCEEEEECCSSCBSHHHHHHHHHTTTCCSSSEEEEE
T ss_pred             eEEEEcCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            36677789998899999999999999999999999999887753

>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=91.62  E-value=0.21  Score=28.91  Aligned_cols=53  Identities=21%  Similarity=0.275  Sum_probs=38.7

Q ss_pred             EEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCe-EEE--e--CC--EEcCCCCc
Q 033059            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLI--F--AG--KQLEDGRT   55 (128)
Q Consensus         3 i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q-~L~--~--~g--~~L~d~~~   55 (128)
                      |.|-..+|.+..+.|++++|+.++-+.+.++.+++.+.- -|+  +  .|  +.|+|...
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            445567899999999999999999999999999765432 222  2  13  56766553

>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=91.59  E-value=0.32  Score=26.82  Aligned_cols=59  Identities=5%  Similarity=0.144  Sum_probs=40.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhhC-----CCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           12 TITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        12 ~~~i~v~~~~tV~~LK~~i~~~~~-----ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      ...+++ +..|+.+|++.+.++..     +.....++..+++..+++.     -|++|+.|-++....||
T Consensus        18 ~~~~~~-~~~tv~~l~~~L~~~~~~~~~~l~~~~~~vavn~~~~~~~~-----~l~~gdevAi~PPVsGG   81 (81)
T d1fm0d_          18 ATEVAA-DFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDH-----PLTDGDEVAFFPPVTGG   81 (81)
T ss_dssp             EEEECS-CCSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCTTC-----BCCTTCEEEEECCCCCC
T ss_pred             eEEecC-CCCCHHHHHHHHHHhCchHHHHhcCCcEEEecCceecCCCC-----CcCCCCEEEEECCCCCC
Confidence            444554 35689999999976642     3345567778888766554     36789999988777665

>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=88.93  E-value=1.1  Score=24.84  Aligned_cols=59  Identities=22%  Similarity=0.403  Sum_probs=45.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhh-C--CCC--CCe-EEE--eCCEEcCCCCccccccccCCcEEEEEE
Q 033059           13 ITLEVESSDTIDNVKAKIQDKE-G--IPP--DQQ-RLI--FAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~-~--ip~--~~q-~L~--~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      ..+.|+.++|+.++=++++... |  ++|  +.. +.-  .+|+.+..+.++++.||++-..|.+..
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            4467999999999999998653 3  433  222 332  478999999999999999999998764

>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=88.05  E-value=1.2  Score=24.60  Aligned_cols=63  Identities=21%  Similarity=0.276  Sum_probs=51.4

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe-CCEEcCCCCccccccccCCcEEEEEEeecCC
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~-~g~~L~d~~~L~~~gi~~g~~i~v~~~~~gg   76 (128)
                      .+.|+++.....+-...++++++|+..--++- .|--+...++-...=++.|+.+.++.|-+-|
T Consensus        27 vlsVpE~aPftAVlkfaAEeFkV~~~TSAiITndGvGINP~QtAg~vFlKhGselrliPRDRVG   90 (92)
T d1j0ga_          27 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG   90 (92)
T ss_dssp             EEEEETTSBHHHHHHHHHHHTTCCSSSEEEECTTSCCCCCSSBHHHHHHHTCSEEEEEECCSSC
T ss_pred             EEecCccCchHHHHHHHHHHcCCCccceeEEecCccccChhhccchhhhhcCceeeeccccccc
Confidence            46788888888888888999999998877764 5566788888888888999999999886654

>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=87.73  E-value=1.1  Score=24.60  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=38.5

Q ss_pred             EEEEEeCCCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEe
Q 033059            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (128)
Q Consensus         2 ~i~vk~~~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~   45 (128)
                      .|.|-.++|+.-.+.+.|..||.++-.++.++-|++++...++.
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            36677789988889999999999999999999999998887753

>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=87.65  E-value=0.71  Score=24.20  Aligned_cols=55  Identities=13%  Similarity=0.257  Sum_probs=38.9

Q ss_pred             CCCEEEEEecCCCcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         9 ~g~~~~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +|+.+.  ++ ..|+.+|-..    .++++...-+-+||..+.- ....++-+++||.|.++-
T Consensus         5 NGe~~~--~~-~~tl~~LL~~----l~~~~~~vAV~vN~~ivpr-~~~~~~~l~~gD~iEIv~   59 (63)
T d2cu3a1           5 NGEPRP--LE-GKTLKEVLEE----MGVELKGVAVLLNEEAFLG-LEVPDRPLRDGDVVEVVA   59 (63)
T ss_dssp             TTEEEC--CT-TCCHHHHHHH----HTBCGGGEEEEETTEEEEG-GGCCCCCCCTTCEEEEEE
T ss_pred             CCEEEE--cC-CCCHHHHHHH----cCCCCCcEEEEECCEEcCH-HHcCcccCCCCCEEEEEE
Confidence            666544  43 5788877654    4777788888899998842 234456688999999764

>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=86.89  E-value=1.2  Score=23.30  Aligned_cols=56  Identities=11%  Similarity=0.147  Sum_probs=40.1

Q ss_pred             CCCEEEEEecCC-CcHHHHHHHHHhhhCCCCCCeEEEeCCEEcCCCCccccccccCCcEEEEEE
Q 033059            9 TGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (128)
Q Consensus         9 ~g~~~~i~v~~~-~tV~~LK~~i~~~~~ip~~~q~L~~~g~~L~d~~~L~~~gi~~g~~i~v~~   71 (128)
                      +|+.  .+++++ .|+.+|-+.    .++++...-+-++|..+.- ..-.++-+++|+.|.++-
T Consensus         5 NG~~--~~~~~~~~tl~~LL~~----l~~~~~~vAVevN~~iv~k-~~~~~~~L~~gD~IEIv~   61 (65)
T d1tygb_           5 NGKD--VKWKKDTGTIQDLLAS----YQLENKIVIVERNKEIIGK-ERYHEVELCDRDVIEIVH   61 (65)
T ss_dssp             TTEE--ECCSSSCCBHHHHHHH----TTCTTSCCEEEETTEEECG-GGTTTSBCCSSSEEEEEE
T ss_pred             CCEE--EEcCCCcccHHHHHHH----cCCCCCcEEEEECCEEcCH-HHcCcccCCCCCEEEEEE
Confidence            5543  455554 599998554    4788888889999998842 234456688999999865

>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=86.45  E-value=0.69  Score=27.55  Aligned_cols=58  Identities=10%  Similarity=0.057  Sum_probs=42.5

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEeCCEEcCCCCcccccc--c-cCCcEEEEEE
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADYN--I-QKESTLHLVL   71 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~~g~~L~d~~~L~~~g--i-~~g~~i~v~~   71 (128)
                      .+-|+.+.||+++...|....+++++. +-|+.++..+..+.+++++=  - .++..+++..
T Consensus        50 KflVp~d~tv~qf~~~iRkrl~l~~~~alflfvn~~~~~~~~ti~~lY~~~kdeDGfLYi~Y  111 (118)
T d3d32a1          50 KYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAY  111 (118)
T ss_dssp             EEEEETTCBHHHHHHHHHHHHTCCTTSCCEEEBTTBCCCTTCBHHHHHHHHCCTTSCEEEEE
T ss_pred             eEEecCCccHHHHHHHHHHHhCCCccceEEEEECCcccCccccHHHHHHHhCCCCcEEEEEE
Confidence            456889999999999999999998876 55666777777778887651  1 2344565554

>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=85.47  E-value=0.85  Score=27.05  Aligned_cols=59  Identities=14%  Similarity=0.117  Sum_probs=43.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhhhCCCCCC-eEEEeCCEEcCCCCccccccc---cCCcEEEEEE
Q 033059           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADYNI---QKESTLHLVL   71 (128)
Q Consensus        13 ~~i~v~~~~tV~~LK~~i~~~~~ip~~~-q~L~~~g~~L~d~~~L~~~gi---~~g~~i~v~~   71 (128)
                      ..+-|+.+.||+++...|..+.+++++. +-|+.++..+..+.+|++.--   .++.-+++..
T Consensus        47 ~KfLVP~dltv~qf~~vIRkrl~l~~~~alflfv~~~l~~~s~~i~~lY~~~KdeDGfLYi~Y  109 (116)
T d1eo6a_          47 RKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAY  109 (116)
T ss_dssp             CEEEEETTSBHHHHHHHHHHHHTCCTTSCCEEEBTTBCCCTTSBHHHHHHHHCCTTSCEEEEE
T ss_pred             cEEeecCCCcHHHHHHHHHHHcCCCccceEEEEECCcccchhhhHHHHHHHcCCCCcEEEEEE
Confidence            3466888999999999999999988754 556678877778888877621   2444565554

>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=80.51  E-value=1.3  Score=24.76  Aligned_cols=35  Identities=9%  Similarity=0.171  Sum_probs=27.0

Q ss_pred             CCCEEEEEec--CCCcHHHHHHHHHhhhCCCCCCeEEEe
Q 033059            9 TGKTITLEVE--SSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (128)
Q Consensus         9 ~g~~~~i~v~--~~~tV~~LK~~i~~~~~ip~~~q~L~~   45 (128)
                      +|.+..+.++  .+.+..+|.++|+..++++  .+.|.|
T Consensus        12 ~~dt~RF~ls~~~~~~~~~L~~~i~~rf~l~--~~~lkY   48 (85)
T d2bkfa1          12 KNEIQSFLVSDPENTTWADIEAMVKVSFDLN--TIQIKY   48 (85)
T ss_dssp             TTEEEEEEESCGGGCCHHHHHHHHHHHHTCS--SEEEEE
T ss_pred             CCceEEEEecCCCCCcHHHHHHHHHHhcCcc--cceEEE
Confidence            6667666554  5788999999999999985  466666

>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=80.05  E-value=2.6  Score=24.86  Aligned_cols=46  Identities=9%  Similarity=0.197  Sum_probs=35.4

Q ss_pred             EEEecCCCcHHHHHHHHHhhhCCCCCCeEEE-eCCEEc-CCCCccccc
Q 033059           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQL-EDGRTLADY   59 (128)
Q Consensus        14 ~i~v~~~~tV~~LK~~i~~~~~ip~~~q~L~-~~g~~L-~d~~~L~~~   59 (128)
                      .+-|+.+.||+++...|..+.+++++.-.++ .+|..| ..+.+++++
T Consensus        50 KfLVp~d~tv~qf~~~iRkrl~l~~~~alFlfvn~~~~p~~~~~i~~l   97 (119)
T d2zjda1          50 KFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEV   97 (119)
T ss_dssp             EEEEETTCBHHHHHHHHHHHHTCCTTCCEEEEETTTEECCTTSBHHHH
T ss_pred             EEEEecCccHHHHHHHHHHHhCCCCcceEEEEEcCCccCCchhHHHHH
Confidence            3568899999999999999999988765544 466654 667777665