Citrus Sinensis ID: 041108

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100--
Protein Sequence
MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNTLL
Secondary Structure (PSIPRED)
cEEEEEEcccEEEEEEEcccHHHHHHHHHHHHHHcccccEEEEEEEccccccccccccccccEEcccccccEEEEEEEEccccccccEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEccccHHHHHHHHHHHHHccccccEEEEEEcccccccEcEccccccHHHcccccccEEEEEEccccccccccEEEEccccccccccc
Coil and Loop (DISEMBL)
MKVAVEILTGTLFYIQVENDATVADLKREIgaqqklpcDRLILLlssdhscpmtqdhdevpladcgvkdgshiylffkplddgstqhsvftipewlnpntll
Flexible Loop (DISEMBL)
MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHsvftipewlnpntll
Low Complexity Region (SEG)
MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNTLL
Disordered region (IsUnstruct)
***AVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWL******
Disordered Region (DISOPRED)
***AVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHS**********PLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNTLL
Disordered Region (DISEMBL)
MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNTLL
Disordered Region (DISPRO)
MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNP****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNTLL
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

No hits with e-value below 0.001 by BLAST

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	102
255572613	170	hypothetical protein RCOM_0231790 [Ricin	0.921	0.552	0.723	1e-30
224093198	102	predicted protein [Populus trichocarpa]	0.911	0.911	0.684	4e-27
224133024	89	predicted protein [Populus trichocarpa]	0.862	0.988	0.674	8e-25
297826675	159	hypothetical protein ARALYDRAFT_482164 [	0.764	0.490	0.481	6e-12
15225233	175	ubiquitin family protein [Arabidopsis th	0.764	0.445	0.468	2e-11
297789840	159	hypothetical protein ARALYDRAFT_497275 [	0.764	0.490	0.468	4e-11

>gi|255572613|ref|XP_002527240.1| hypothetical protein RCOM_0231790 [Ricinus communis] gi|223533416|gb|EEF35166.1| hypothetical protein RCOM_0231790 [Ricinus communis]

 Score =  136 bits (343), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 73/94 (77%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           MKV VEILTGTLFYIQV NDAT+ADLKREIGAQQKLP DRLIL L +  S  + +  D  
Sbjct: 9   MKVVVEILTGTLFYIQVGNDATIADLKREIGAQQKLPHDRLILFLDNSRSSLIDEIGDAT 68

Query: 61  PLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPE 94
            L DCGV DGSHIYLFF PLDDGST H VFT P+
Sbjct: 69  SLVDCGVHDGSHIYLFFNPLDDGSTHHFVFTWPD 102

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224093198|ref|XP_002309829.1| predicted protein [Populus trichocarpa] gi|222852732|gb|EEE90279.1| predicted protein [Populus trichocarpa]

 Score =  125 bits (313), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 65/95 (68%), Positives = 73/95 (76%), Gaps = 2/95 (2%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M+V VEILTGTLFYIQV NDATVADLK+EI AQQKLP DRLIL LS+  S  + ++ D  
Sbjct: 1  MRVVVEILTGTLFYIQVGNDATVADLKKEIEAQQKLPQDRLILFLSNKRSHLINEEGDGA 60

Query: 61 PLADCGVKDGSHIYLFFKPLD--DGSTQHSVFTIP 93
           L DCGV+DGSHIYLFF P+D  D ST H VFT P
Sbjct: 61 ALVDCGVQDGSHIYLFFDPVDNHDESTDHLVFTWP 95

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133024|ref|XP_002327941.1| predicted protein [Populus trichocarpa] gi|222837350|gb|EEE75729.1| predicted protein [Populus trichocarpa]

 Score =  117 bits (293), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 60/89 (67%), Positives = 70/89 (78%), Gaps = 1/89 (1%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M+VAVEILTGTLFYIQV +DATVADLK+EI AQQKLP DRLIL L +  +  + ++ D  
Sbjct: 1  MRVAVEILTGTLFYIQVGDDATVADLKKEIEAQQKLPQDRLILFLDNKQNHLINEEGDGA 60

Query: 61 PLADCGVKDGSHIYLFFKPLD-DGSTQHS 88
           L DCGV+DGSHIYLFF PLD D S+ HS
Sbjct: 61 SLVDCGVQDGSHIYLFFDPLDTDESSSHS 89

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297826675|ref|XP_002881220.1| hypothetical protein ARALYDRAFT_482164 [Arabidopsis lyrata subsp. lyrata] gi|297327059|gb|EFH57479.1| hypothetical protein ARALYDRAFT_482164 [Arabidopsis lyrata subsp. lyrata]

 Score = 74.7 bits (182), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 38/79 (48%), Positives = 52/79 (65%), Gaps = 1/79 (1%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMT-QDHDE 59
          MKV+VEI+TGT     V  D TV +LK +I A+ KLP  RLIL++  + +  M  +D D+
Sbjct: 1  MKVSVEIITGTFIDADVSEDTTVKELKEKIAAEVKLPVTRLILVIGDEETRRMVMEDEDD 60

Query: 60 VPLADCGVKDGSHIYLFFK 78
          + L D GV + SH+YLFFK
Sbjct: 61 MMLRDLGVGEDSHMYLFFK 79

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15225233|ref|NP_180795.1| ubiquitin family protein [Arabidopsis thaliana] gi|3831460|gb|AAC69942.1| hypothetical protein [Arabidopsis thaliana] gi|330253579|gb|AEC08673.1| ubiquitin family protein [Arabidopsis thaliana]

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMT-QDHDE 59
          MKV+VEI+TGT     V  DATV  +K +I  + KLP  RLIL++  + +  +  +D D+
Sbjct: 1  MKVSVEIITGTFIDTDVSEDATVKQMKEKIAVEVKLPVTRLILVIGDEETRRLVMEDEDD 60

Query: 60 VPLADCGVKDGSHIYLFFK 78
          + L D GV + SHIYLFFK
Sbjct: 61 MMLRDLGVGEDSHIYLFFK 79

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297789840|ref|XP_002862847.1| hypothetical protein ARALYDRAFT_497275 [Arabidopsis lyrata subsp. lyrata] gi|297308595|gb|EFH39105.1| hypothetical protein ARALYDRAFT_497275 [Arabidopsis lyrata subsp. lyrata]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMT-QDHDE 59
          MKV+VEI+TGT     V  D TV +LK +I A+ K P  RLIL++  + +  M  +D D+
Sbjct: 1  MKVSVEIITGTFIDADVSEDTTVKELKEKIAAEVKSPVTRLILVIGDEETRRMVMEDEDD 60

Query: 60 VPLADCGVKDGSHIYLFFK 78
          + L D GV + SH+YLFFK
Sbjct: 61 MMLRDLGVGEDSHMYLFFK 79

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	102
TAIR|locus:2062551	175	AT2G32360 "AT2G32360" [Arabido	0.794	0.462	0.463	1e-13

TAIR|locus:2062551 AT2G32360 "AT2G32360" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 38/82 (46%), Positives = 52/82 (63%)

Query:     1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMT-QDHDE 59
             MKV+VEI+TGT     V  DATV  +K +I  + KLP  RLIL++  + +  +  +D D+
Sbjct:     1 MKVSVEIITGTFIDTDVSEDATVKQMKEKIAVEVKLPVTRLILVIGDEETRRLVMEDEDD 60

Query:    60 VPLADCGVKDGSHIYLFFKPLD 81
             + L D GV + SHIYLFFK  D
Sbjct:    61 MMLRDLGVGEDSHIYLFFKHPD 82


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.138   0.422    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      102       102   0.00091  102 3  11 22  0.40    30
                                                     29  0.48    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  552 (59 KB)
  Total size of DFA:  121 KB (2079 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  10.34u 0.11s 10.45t   Elapsed:  00:00:00
  Total cpu time:  10.34u 0.11s 10.45t   Elapsed:  00:00:00
  Start:  Tue May 21 03:44:27 2013   End:  Tue May 21 03:44:27 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	102
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	3e-07
smart00213	72	smart00213, UBQ, Ubiquitin homologues	4e-07
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	8e-07
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	5e-06
cd01804	78	cd01804, midnolin_N, Ubiquitin-like domain of midn	1e-04
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	1e-04
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	0.002

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

 Score = 43.8 bits (104), Expect = 3e-07
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 5  VEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLAD 64
          V+ LTG  F ++V  D TVA+LK +I A++ +P ++  L+ +           D+  L+D
Sbjct: 2  VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAG------KILKDDKTLSD 55

Query: 65 CGVKDGSHIYL 75
           G++DGS ++L
Sbjct: 56 YGIQDGSTLHL 66

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|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 43.4 bits (103), Expect = 4e-07
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          +++ V+ L G    ++V+   TV++LK +I     +P ++  L+             D+ 
Sbjct: 1  IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKG------KVLEDDR 54

Query: 61 PLADCGVKDGSHIYL 75
           LAD G++DGS I+L
Sbjct: 55 TLADYGIQDGSTIHL 69

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 = 42.6 bits (101), Expect = 8e-07
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 8  LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV 67
          L G    ++V+   TV++LK +I  ++ +P D+  L+ S           D+  L++ G+
Sbjct: 3  LDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSG------KVLEDDTTLSEYGI 56

Query: 68 KDGSHIYLFFKP 79
          +DGS ++L  + 
Sbjct: 57 QDGSTLHLVLRL 68

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|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23

 Score = 40.4 bits (95), Expect = 5e-06
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQ--KLPCDRLILLLSSDHSCPMTQDHD 58
          MK+  + L    F I+V+ D TVA+LK +I  ++    P ++  L+    +S  + +  D
Sbjct: 1  MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLI----YSGKILK--D 54

Query: 59 EVPLADCGVKDGSHI 73
          +  L +  + +   +
Sbjct: 55 DTTLEEYKIDEKDFV 69

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|176399 cd01804, midnolin_N, Ubiquitin-like domain of midnolin

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 17/80 (21%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M + +   TGT F + V  D TV  LK+ I  + K+P +RL LL            H E 
Sbjct: 2  MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALL------------HRET 49

Query: 61 PLA-----DCGVKDGSHIYL 75
           L+     D G+ DGS + L
Sbjct: 50 RLSSGKLQDLGLGDGSKLTL 69

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|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 5  VEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLAD 64
          V++  G    + V +  TVADLK ++  +  LP ++  LL++           D + L D
Sbjct: 2  VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKI------LPDSLTLED 55

Query: 65 CGVKDGSHIYLFFK 78
           G++DG  + L  +
Sbjct: 56 YGLQDGDELVLVPR 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|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 9/76 (11%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQ---KLPCDRLILLLSSDHSCPMTQDH 57
          M +  + L    F I +E D TV +LK +I A+Q     P  +  L+    +S  +  D 
Sbjct: 1  MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLI----YSGKILSD- 55

Query: 58 DEVPLADCGVKDGSHI 73
           +  + +  +K+   +
Sbjct: 56 -DKTVKEYKIKEKDFV 70

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	102
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.86
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.84
PTZ00044	76	ubiquitin; Provisional	99.84
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.84
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.84
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.83
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.83
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.83
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.82
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.82
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.81
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.8
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.79
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.79
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.77
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.76
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.76
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.75
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.74
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.74
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.73
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.67
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.66
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.66
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.65
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.63
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.63
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.61
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.6
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.55
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.47
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.46
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	99.45
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.43
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.37
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.37
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.35
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.33
PLN02560	308	enoyl-CoA reductase	99.26
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	99.25
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	99.18
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	99.05
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	99.03
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.85
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.85
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.81
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.79
KOG4495	110	consensus RNA polymerase II transcription elongati	98.61
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.59
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.26
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.07
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	98.02
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	97.95
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.94
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.76
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	97.72
PF13019	162	Telomere_Sde2: Telomere stability and silencing	97.66
KOG0013	231	consensus Uncharacterized conserved protein [Funct	97.66
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.59
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.58
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.56
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	97.55
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	97.5
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	97.37
KOG1639	297	consensus Steroid reductase required for elongatio	97.33
COG5417	81	Uncharacterized small protein [Function unknown]	97.18
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	97.13
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.07
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	96.67
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	96.32
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	96.31
PRK06437	67	hypothetical protein; Provisional	96.11
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	95.94
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	95.71
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	95.42
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	95.27
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	94.86
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	94.77
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	94.73
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	94.69
KOG2982	418	consensus Uncharacterized conserved protein [Funct	94.5
KOG4583	391	consensus Membrane-associated ER protein involved	94.37
PRK08364	70	sulfur carrier protein ThiS; Provisional	94.34
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	94.18
KOG0012	380	consensus DNA damage inducible protein [Replicatio	94.01
PRK06488	65	sulfur carrier protein ThiS; Validated	93.87
PF14453	57	ThiS-like: ThiS-like ubiquitin	93.87
smart00455	70	RBD Raf-like Ras-binding domain.	93.68
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	93.63
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	93.58
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	93.45
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	92.36
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	92.25
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	91.93
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	91.87
PRK05863	65	sulfur carrier protein ThiS; Provisional	91.87
PRK05659	66	sulfur carrier protein ThiS; Validated	91.61
PF02196	71	RBD: Raf-like Ras-binding domain; InterPro: IPR003	90.99
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	90.71
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	90.57
cd05992	81	PB1 The PB1 domain is a modular domain mediating s	90.2
PRK08053	66	sulfur carrier protein ThiS; Provisional	89.93
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	89.69
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	88.83
cd06397	82	PB1_UP1 Uncharacterized protein 1. The PB1 domain	88.79
PRK06944	65	sulfur carrier protein ThiS; Provisional	88.77
cd06410	97	PB1_UP2 Uncharacterized protein 2. The PB1 domain	88.23
PRK06083	84	sulfur carrier protein ThiS; Provisional	87.31
PF10407	73	Cytokin_check_N: Cdc14 phosphatase binding protein	86.49
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	86.24
TIGR01683	64	thiS thiamine biosynthesis protein ThiS. This mode	86.18
PRK01777	95	hypothetical protein; Validated	86.03
PF12754	309	Blt1: Cell-cycle control medial ring component; In	85.76
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	85.27
cd01787	85	GRB7_RA RA (RAS-associated like) domain of Grb7. G	85.17
cd01818	77	TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleo	84.61
cd06398	91	PB1_Joka2 The PB1 domain is present in the Nicotia	84.13
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	84.03
cd06396	81	PB1_NBR1 The PB1 domain is an essential part of NB	84.0
PRK07440	70	hypothetical protein; Provisional	82.61
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	82.13
PTZ00380	121	microtubule-associated protein (MAP); Provisional	81.94
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	81.49
PRK11130	81	moaD molybdopterin synthase small subunit; Provisi	80.74

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.86  E-value=3e-21  Score=117.81  Aligned_cols=74  Identities=23%  Similarity=0.394  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||..+|+++.++|++++||++||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++++++++.++++
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~------~L~d~~~L~~~~i~~~~~l~l~~~~~   74 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGK------ALADDKRLSDYSIGPNAKLNLVVRPP   74 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCE------ECCCCCCHHHCCCCCCCEEEEEEcCC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999998753

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

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.84  E-value=1.2e-20  Score=115.26  Aligned_cols=74  Identities=22%  Similarity=0.361  Sum_probs=70.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||.  ++++.++|++++||++||++|++++|+|+++|+|+|+|+      .|+|+.+|++|+|++++++++.++++
T Consensus         1 mqi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk------~L~D~~tL~~~~i~~~~tl~l~~~l~   72 (74)
T cd01793           1 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGV------PLEDDATLGQCGVEELCTLEVAGRLL   72 (74)
T ss_pred             CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCe------ECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            8999998  478999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        73 GG   74 (74)
T cd01793          73 GG   74 (74)
T ss_pred             CC
Confidence            63

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=99.84  E-value=1.8e-20  Score=114.34  Aligned_cols=75  Identities=25%  Similarity=0.378  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||..+|+++.+++++++||++||.+|++.+|+|+++|+|+|+|+      .|+|+.+|++|++++|++|++.+++.
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~------~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGK------QMSDDLKLSDYKVVPGSTIHMVLQLR   74 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCE------EccCCCcHHHcCCCCCCEEEEEEEcc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      +
T Consensus        75 g   75 (76)
T PTZ00044         75 G   75 (76)
T ss_pred             C
Confidence            5

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.84  E-value=1.8e-20  Score=114.81  Aligned_cols=71  Identities=24%  Similarity=0.374  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|++..|+.+.+++++++||++||++|+++.|+|+++|||+|+|+      .|+|+.+|++|||++|++|+++.
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk------~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYT------IFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCc------CCCCCCCHHHcCCCCCCEEEEEe
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999985

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.

>cd01803 Ubiquitin Ubiquitin

Probab=99.84  E-value=2.5e-20  Score=113.20  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+      .|+|+.+|++||+++|++|++.+++.
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~------~L~d~~~L~~~~i~~~~~i~l~~~~~   74 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEEcc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999976


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus        75 gg   76 (76)
T cd01803          75 GG   76 (76)
T ss_pred             CC
Confidence            53

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

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.83  E-value=8.5e-20  Score=110.83  Aligned_cols=75  Identities=25%  Similarity=0.360  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||++||++|++..|+|+++|+|+|+|+      .|+|+.+|++|++++|++|++.++..
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~------~L~d~~tl~~~~i~~g~~i~l~~~~~   74 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGK------QMNDDKTAADYKLEGGSVLHLVLALR   74 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCe------EccCCCCHHHcCCCCCCEEEEEEEcc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      +
T Consensus        75 g   75 (76)
T cd01806          75 G   75 (76)
T ss_pred             C
Confidence            5

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.

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

Probab=99.83  E-value=5.2e-20  Score=113.96  Aligned_cols=74  Identities=19%  Similarity=0.179  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcE-EEEE-ecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTL-FYIQ-VENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~-~~i~-v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+||+.+|++ +.++ +++++||++||++|++.+|+|++.|||+|+|+      .|+|+.+|++|||++|++|+++++
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk------~L~D~~tL~~y~i~~~~~i~l~~~   74 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGK------QMEDGHTLFDYNVGLNDIIQLLVR   74 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCE------ECCCCCCHHHcCCCCCCEEEEEEe
Confidence            999999999987 6885 89999999999999999999999999999999      999999999999999999999998


Q ss_pred             cC
Q 041108           79 PL   80 (102)
Q Consensus        79 ~~   80 (102)
                      ..
T Consensus        75 ~~   76 (78)
T cd01797          75 QD   76 (78)
T ss_pred             cC
Confidence            64

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

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.83  E-value=8e-20  Score=111.66  Aligned_cols=74  Identities=24%  Similarity=0.393  Sum_probs=71.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCC--CCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKL--PCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gi--p~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|++.+|+.+.+++++++||++||++|++.+|+  |+++|+|+|+|+      .|+|+.+|++|||++|++|+++++
T Consensus         1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~------~L~d~~~L~~~~i~~~~~i~~~~~   74 (77)
T cd01805           1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGK------ILKDDTTLEEYKIDEKDFVVVMVS   74 (77)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCE------EccCCCCHHHcCCCCCCEEEEEEe
Confidence            899999999999999999999999999999999999  999999999999      999999999999999999999987


Q ss_pred             cC
Q 041108           79 PL   80 (102)
Q Consensus        79 ~~   80 (102)
                      .+
T Consensus        75 ~~   76 (77)
T cd01805          75 KP   76 (77)
T ss_pred             cC
Confidence            64

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).

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.82  E-value=1e-19  Score=112.39  Aligned_cols=75  Identities=33%  Similarity=0.439  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+...|+.+.+++++++||++||++|+++.|+++++|+|+|+|+      .|+|+ +|++|||++|++|+++....
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk------~L~d~-~L~~~gi~~~~~i~l~~~~~   74 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRET------RLSSG-KLQDLGLGDGSKLTLVPTVE   74 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCc------CCCCC-cHHHcCCCCCCEEEEEeecc
Confidence            899999999999999999999999999999999999999999999999      99998 99999999999999998876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        75 ~~   76 (78)
T cd01804          75 AG   76 (78)
T ss_pred             cc
Confidence            54

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.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.82  E-value=8.2e-20  Score=118.51  Aligned_cols=76  Identities=26%  Similarity=0.361  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||..+|+++.++|++++||++||++|++..|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk------~L~D~~tL~dy~I~~~stL~l~~~l~  101 (103)
T cd01802          28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNM------ELEDEYCLNDYNISEGCTLKLVLAMR  101 (103)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEecC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus       102 GG  103 (103)
T cd01802         102 GG  103 (103)
T ss_pred             CC
Confidence            63

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.

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

Probab=99.81  E-value=1.7e-19  Score=110.05  Aligned_cols=73  Identities=23%  Similarity=0.397  Sum_probs=70.4

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      |+||+.+|+++.+++++++||++||++|++..|+|+++|+|+|+|+      .|+|+.+|++|||++++++++..++.+
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~------~L~D~~tL~~~~i~~~~tl~l~~~l~g   73 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGR------PMEDEHPLGEYGLKPGCTVFMNLRLRG   73 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCE------ECCCCCCHHHcCCCCCCEEEEEEEccC
Confidence            5899999999999999999999999999999999999999999999      999999999999999999999998765

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.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.80  E-value=4.4e-19  Score=106.67  Aligned_cols=72  Identities=28%  Similarity=0.424  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+      .|+|+.+|++||+++|+++++..+
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 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGR------VLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCE------ECCCcCcHHHCCCCCCCEEEEEeC
Confidence            899999999999999999999999999999999999999999999999      999999999999999999998753

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.

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

Probab=99.79  E-value=5.5e-19  Score=109.41  Aligned_cols=74  Identities=28%  Similarity=0.445  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEE--EeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLIL--LLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L--~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|+..+|+.+.+++++++||++||++|++..|+|+++|+|  .|+|+      .|+|+.+|++|||++|++|++.++
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~------~L~D~~tL~~~gi~~gs~l~l~~~   76 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSRE------VLQDGVPLVSQGLGPGSTVLLVVQ   76 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCC------CCCCCCCHHHcCCCCCCEEEEEEE
Confidence            7899999999999999999999999999999999999999999  78898      999999999999999999999998


Q ss_pred             cC
Q 041108           79 PL   80 (102)
Q Consensus        79 ~~   80 (102)
                      ..
T Consensus        77 ~~   78 (80)
T cd01792          77 NC   78 (80)
T ss_pred             cc
Confidence            53

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

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.79  E-value=5.5e-19  Score=107.32  Aligned_cols=70  Identities=17%  Similarity=0.219  Sum_probs=66.7

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      +.||..+|+++.+++++++||++||++|++..|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++++.
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~------~L~D~~~l~~~~i~~~~tv~~~~~   70 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGK------LLTDKTRLQETKIQKDYVVQVIVN   70 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCe------ECCCCCCHHHcCCCCCCEEEEEeC
Confidence            3578999999999999999999999999999999999999999999      999999999999999999999863

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.

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

Probab=99.77  E-value=1.6e-18  Score=104.53  Aligned_cols=70  Identities=21%  Similarity=0.398  Sum_probs=67.1

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+||+.+|+++.+++++++||++||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|||++|+++++..|
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 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGK------ELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCe------ECCCCCcHHHcCCCCCCEEEEEeC
Confidence            5789999999999999999999999999999999999999999999      999999999999999999999754

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.

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

Probab=99.76  E-value=5.3e-18  Score=102.62  Aligned_cols=71  Identities=27%  Similarity=0.400  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|++.+|+ ..+++++++||++||++|++..|+++++|+|.|+|+      .|+|+.+|++||+++|++|++.++
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-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGK------ILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCe------EcCCCCcHHHcCCCCCCEEEEEEC
Confidence            68999999997 489999999999999999999999999999999999      999999999999999999999864

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.

>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=99.76  E-value=4.5e-18  Score=101.79  Aligned_cols=68  Identities=38%  Similarity=0.646  Sum_probs=65.1

Q ss_pred             EeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            6 EILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         6 ~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+.+|+.+.+++++++||.+||++|++++++|++.|+|+|+|+      .|+|+.+|++|||++|++|++.+++
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~------~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGK------ELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTE------EESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeee------cccCcCcHHHcCCCCCCEEEEEEec
Confidence            5678999999999999999999999999999999999999999      9999999999999999999998864

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 ....

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.75  E-value=1.1e-17  Score=100.46  Aligned_cols=70  Identities=26%  Similarity=0.364  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+.. |+.+.+++++++||++||++|++.+|+|+++|+|+|+|+      .|+|+.+|++||+++|++|+++.
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-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGK------ERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCc------ccCccCcHHHcCCCCCCEEEEec
Confidence            68999997 899999999999999999999999999999999999999      99999999999999999999874

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).

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

Probab=99.74  E-value=1.4e-17  Score=102.26  Aligned_cols=70  Identities=21%  Similarity=0.249  Sum_probs=66.2

Q ss_pred             CCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCCC
Q 041108            8 LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDG   83 (102)
Q Consensus         8 ~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~~   83 (102)
                      ++|+++.+++++++||++||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|+++++..++.
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 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGI------FIKDSNSLAYYNLANGTIIHLQLKERGGR   74 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCE------EcCCCCcHHHcCCCCCCEEEEEEecCCCc
Confidence            46899999999999999999999999999999999999999      99999999999999999999999987753

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.

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

Probab=99.74  E-value=1.2e-17  Score=101.48  Aligned_cols=68  Identities=26%  Similarity=0.349  Sum_probs=64.0

Q ss_pred             EEEEeC-CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCC-CccccCCCCCCCEEEEE
Q 041108            3 VAVEIL-TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDE-VPLADCGVKDGSHIYLF   76 (102)
Q Consensus         3 v~V~~~-~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~-~~L~~~gI~~~~~i~l~   76 (102)
                      ++|+.. +|+++.+++++++||++||++|++++|+|++.|+|+|+|+      .|+|+ .+|++|||++|++|++.
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 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGR------ELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCe------EccCCcccHHHcCCCCCCEEEEe
Confidence            578999 8999999999999999999999999999999999999999      99887 68999999999999874

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

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.73  E-value=2.7e-17  Score=100.81  Aligned_cols=69  Identities=23%  Similarity=0.300  Sum_probs=64.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe---CCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLL---SSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~---~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |.|.|+. +|+.+.+++++++||++||++|++.+|+|+++|+|+|   +|+      .++|+.+|++|+|++|+.|+++
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-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGK------PAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCC------cCCCCcCHHHcCCCCCCEEEEE
Confidence            6788888 4788999999999999999999999999999999996   888      9999999999999999999987

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.

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

Probab=99.67  E-value=7e-17  Score=110.60  Aligned_cols=92  Identities=23%  Similarity=0.410  Sum_probs=86.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+.+.|++..+++.+++||..+|.+|+...|||+++|+|+|.|+      .|+|..+|+||+|+.-++++++++..
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~------qLedgrtlSDY~Iqkestl~l~l~l~   74 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhc------ccccCCccccccccccceEEEEEEec
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCCC-ceeEEEecCCcCCC
Q 041108           81 DDGS-TQHSVFTIPEWLNP   98 (102)
Q Consensus        81 ~~~~-~~~~~~~~~~~~~~   98 (102)
                      |+.. ++..++++|....+
T Consensus        75 Gg~kkrkkk~~~~pk~~~~   93 (156)
T KOG0004|consen   75 GGAKKRKKKSYTTPKKIKS   93 (156)
T ss_pred             CCcccccccccccccccCC
Confidence            8655 67789999987764

>smart00213 UBQ Ubiquitin homologues

Probab=99.66  E-value=3.8e-16  Score=91.21  Aligned_cols=64  Identities=27%  Similarity=0.456  Sum_probs=61.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGS   71 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~   71 (102)
                      |+|+||..+ +.+.+++++++||++||++|+..+|+|+++|+|+|+|+      .|+|+.+|++||+++|+
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~------~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGK------VLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCE------ECCCCCCHHHcCCcCCC
Confidence            899999998 78899999999999999999999999999999999999      99999999999999875

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

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

Probab=99.66  E-value=3.4e-16  Score=97.26  Aligned_cols=71  Identities=14%  Similarity=0.046  Sum_probs=63.0

Q ss_pred             CEEEEEeCCCcEE--EEEecCCCcHHHHHHHHHhhcC--CCCccEEEEeCCCCCCCCccCCCCCccccCC--CCCCCEEE
Q 041108            1 MKVAVEILTGTLF--YIQVENDATVADLKREIGAQQK--LPCDRLILLLSSDHSCPMTQDHDEVPLADCG--VKDGSHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~~~--~i~v~~~~TV~dLK~~I~~~~g--ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~g--I~~~~~i~   74 (102)
                      |.++||+.+|+.+  .+++++++||++||++|++..+  .++++|||+|+|+      +|+|+.+|++|+  +.+|.+||
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GK------iLkD~~tL~~~~~~~~~~~tiH   75 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGK------LLPDHLKLRDVLRKQDEYHMVH   75 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCe------eccchhhHHHHhhcccCCceEE
Confidence            5789999999885  4555899999999999999875  4589999999999      999999999996  99999999


Q ss_pred             EEe
Q 041108           75 LFF   77 (102)
Q Consensus        75 l~~   77 (102)
                      +..
T Consensus        76 LV~   78 (79)
T cd01790          76 LVC   78 (79)
T ss_pred             EEe
Confidence            874

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.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.65  E-value=6.6e-16  Score=119.31  Aligned_cols=76  Identities=24%  Similarity=0.359  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcC---CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQK---LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~g---ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+||+.+|+++.|+|++++||.+||++|++..|   +++++|||+|+|+      +|+|+.+|++|+|+++++|++++
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~Gk------iL~Dd~tL~dy~I~e~~~Ivvmv   74 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGK------ILSDDKTVREYKIKEKDFVVVMV   74 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCE------ECCCCCcHHHcCCCCCCEEEEEe
Confidence            99999999999999999999999999999999998   9999999999999      99999999999999999999998


Q ss_pred             ecCCC
Q 041108           78 KPLDD   82 (102)
Q Consensus        78 ~~~~~   82 (102)
                      .....
T Consensus        75 ~k~k~   79 (378)
T TIGR00601        75 SKPKT   79 (378)
T ss_pred             ccCCC
Confidence            87543

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).

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.63  E-value=3.3e-15  Score=93.92  Aligned_cols=76  Identities=16%  Similarity=0.318  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+.|.+++|+..||.+++++.|+|++.|+++|+|+      .|+++.++.+|++.+|++|+++++..
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~   85 (87)
T cd01763          12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQ------RIRDNQTPDDLGMEDGDEIEVMLEQT   85 (87)
T ss_pred             EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCe------ECCCCCCHHHcCCCCCCEEEEEEecc
Confidence            679999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        86 GG   87 (87)
T cd01763          86 GG   87 (87)
T ss_pred             cC
Confidence            63

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.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.63  E-value=2.6e-15  Score=92.31  Aligned_cols=69  Identities=23%  Similarity=0.349  Sum_probs=60.9

Q ss_pred             EEEEEeC--CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC-CCCCccccCCCC-CCCEEEEEe
Q 041108            2 KVAVEIL--TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD-HDEVPLADCGVK-DGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~--~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~-~~~~i~l~~   77 (102)
                      .+.|..+  .|.++.+++++++||++||.+|++++|+|+++|+| |+|+      .| +|+.+|++||++ +|+++++++
T Consensus         2 ~~~~~~~~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~------~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           2 NVSVEDAQSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQ------RLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             EEEEeccccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCC------eeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            4555544  57889999999999999999999999999999999 9998      66 577999999998 889999985

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.

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

Probab=99.61  E-value=9.7e-16  Score=90.16  Aligned_cols=70  Identities=24%  Similarity=0.365  Sum_probs=67.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |.|.|++++|+.+.+++++.++|..+|+.|+++.|+||..|||+|.|+      .+.|+.+-.+|++.-|+++|++
T Consensus         1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gk------qm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGK------QMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccc------cccccccHHHhhhccceeEeeC
Confidence            789999999999999999999999999999999999999999999999      9999999999999999999873

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

Probab=99.60  E-value=1.3e-16  Score=103.67  Aligned_cols=77  Identities=26%  Similarity=0.389  Sum_probs=74.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+++++...|++.++++++++||..+|..|..+.|+||+.|+|.|+|+      +|+|+.++++||++--++++++.++.
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k------~LED~~Tla~Y~i~~~~Tl~~~~rL~   74 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhccc------ccccCCcccccCccchhhhhhhHHHh
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        75 GG~   77 (128)
T KOG0003|consen   75 GGI   77 (128)
T ss_pred             cCC
Confidence            763

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.55  E-value=3.3e-14  Score=83.91  Aligned_cols=67  Identities=36%  Similarity=0.577  Sum_probs=63.5

Q ss_pred             EEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            5 VEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         5 V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .++|+.+|.+|++.+++.|++..
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~------~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGK------ILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCc------CCCCcCCHHHCCCCCCCEEEEEE
Confidence            67778999999999999999999999999999999999999999      99999999999999999999874

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=99.47  E-value=9.6e-14  Score=85.41  Aligned_cols=55  Identities=29%  Similarity=0.356  Sum_probs=49.8

Q ss_pred             ecC-CCcHHHHHHHHHhhc--CCC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108           17 VEN-DATVADLKREIGAQQ--KLP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus        17 v~~-~~TV~dLK~~I~~~~--gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |++ ++||.+||++|+++.  |++ +++|||+|+|+      .|+|+.+|++|||++|++|+++.
T Consensus        16 ~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GK------iL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          16 VSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGR------KLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             cCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCc------CCCCCCcHHHcCCCCCCEEEEEe
Confidence            444 799999999999996  475 99999999999      99999999999999999999975

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.

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

Probab=99.46  E-value=1.9e-13  Score=103.25  Aligned_cols=75  Identities=25%  Similarity=0.417  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcC--CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQK--LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~g--ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+||++.|++|.+++.+++||.++|+.|+...|  +|++.|+|+|+|+      +|+|+.++.+|+|++++.|.+++.
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~Gk------iL~D~~tv~Eykv~E~~fiVvMls   74 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGK------ILKDETTVGEYKVKEKKFIVVMLS   74 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecce------eccCCcchhhhccccCceEEEEEe
Confidence            89999999999999999999999999999999999  9999999999999      999999999999999999999998


Q ss_pred             cCC
Q 041108           79 PLD   81 (102)
Q Consensus        79 ~~~   81 (102)
                      ...
T Consensus        75 K~k   77 (340)
T KOG0011|consen   75 KDK   77 (340)
T ss_pred             cCc
Confidence            765

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=99.45  E-value=7.2e-13  Score=86.96  Aligned_cols=84  Identities=25%  Similarity=0.301  Sum_probs=74.0

Q ss_pred             CEEEEEeCCC-cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCC-------CCCCE
Q 041108            1 MKVAVEILTG-TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV-------KDGSH   72 (102)
Q Consensus         1 M~v~V~~~~g-~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI-------~~~~~   72 (102)
                      |.++++.+.. .++++++.++.||.+||++|+.....||+.|+|+..+.      +|+|+++|++||+       ++.++
T Consensus         1 MdvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~q------vLeD~kTL~d~g~t~~~akaq~pA~   74 (119)
T cd01788           1 MDVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQ------LLDDGKTLGDCGFTSQTARPQAPAT   74 (119)
T ss_pred             CceEEEEEecceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCce------eecccccHHHcCccccccccCCCCe
Confidence            6778887755 55789999999999999999999999999999996667      9999999999999       67999


Q ss_pred             EEEEeecCCCCCceeEEE
Q 041108           73 IYLFFKPLDDGSTQHSVF   90 (102)
Q Consensus        73 i~l~~~~~~~~~~~~~~~   90 (102)
                      +-+.++..++.++...|.
T Consensus        75 vgLa~r~~d~~fE~l~I~   92 (119)
T cd01788          75 VGLAFRSSDDTFEPLRIE   92 (119)
T ss_pred             EEEEEecCCCCccceeee
Confidence            999999878888775554

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.

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

Probab=99.43  E-value=3.9e-13  Score=105.86  Aligned_cols=74  Identities=26%  Similarity=0.425  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      ++|+||+.++ ++.+.|..+.||.+||+.|...++.++++++|+|.|+      +|+|+.+|..|||+||.||||+++..
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGr------ILKD~dTL~~~gI~Dg~TvHLVik~~   88 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGR------ILKDDDTLKQYGIQDGHTVHLVIKSQ   88 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCc------cccChhhHHHcCCCCCcEEEEEeccC
Confidence            3688888876 7899999999999999999999999999999999999      99999999999999999999999875


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      .
T Consensus        89 ~   89 (493)
T KOG0010|consen   89 P   89 (493)
T ss_pred             C
Confidence            3

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.37  E-value=1.7e-12  Score=83.50  Aligned_cols=63  Identities=21%  Similarity=0.057  Sum_probs=57.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC-CCCCccccCCCCCCCEEEEEeecC
Q 041108           12 LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD-HDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      ...++|++++||.+||.+|..+++++|++|+|++.|+      .| +|+++|++|||.+|++|.+.+..+
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~------~L~DDsrTLssyGv~sgSvl~LlideP   79 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGK------ILSDDCATLGTLGVIPESVILLKADEP   79 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCc------eeccCCccHHhcCCCCCCEEEEEecCC
Confidence            3578899999999999999999999999999999998      55 677999999999999999998654

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,

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

Probab=99.37  E-value=1.9e-12  Score=77.91  Aligned_cols=71  Identities=18%  Similarity=0.328  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCC-ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPC-DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~-~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+..+|+.+.+.+.++.++..|++.+++..|+++ +..+++|.|.      .|+++.+++++|+.+|++|.+.+
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~------~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGK------RLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTE------EE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCE------EcCCCCCHHHCCCCCCCEEEEEC
Confidence            68999999999999999999999999999999999999 9999999999      99999999999999999999874

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 ....

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.35  E-value=2.3e-12  Score=84.56  Aligned_cols=87  Identities=15%  Similarity=0.189  Sum_probs=68.3

Q ss_pred             EEEEEeCCCcEE-EEEecCCCcHHHHHHHHHhhc-----CCC--CccEEEEeCCCCCCCCccCCCCCccccCC------C
Q 041108            2 KVAVEILTGTLF-YIQVENDATVADLKREIGAQQ-----KLP--CDRLILLLSSDHSCPMTQDHDEVPLADCG------V   67 (102)
Q Consensus         2 ~v~V~~~~g~~~-~i~v~~~~TV~dLK~~I~~~~-----gip--~~~q~L~~~g~~~~~~~~L~d~~~L~~~g------I   67 (102)
                      .|.+|..+|..+ -..+++++||++||++|++..     ++|  ++.|+|+|+|+      +|+|+.+|++|+      +
T Consensus         6 e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGK------iLeD~~TL~d~~~p~g~~~   79 (113)
T cd01814           6 EIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGK------ILENSKTVGECRSPVGDIA   79 (113)
T ss_pred             EEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCe------ecCCCCcHHHhCCcccccC
Confidence            467777788654 567779999999999999554     455  99999999999      999999999999      7


Q ss_pred             CCCCEEEEEeecCCCCC-ceeEEEecCC
Q 041108           68 KDGSHIYLFFKPLDDGS-TQHSVFTIPE   94 (102)
Q Consensus        68 ~~~~~i~l~~~~~~~~~-~~~~~~~~~~   94 (102)
                      ....|+|+.++.+.... ....+...|+
T Consensus        80 ~~~~TmHvvlr~~~~~~~~~k~~~~~~~  107 (113)
T cd01814          80 GGVITMHVVVQPPLADKKTEKKVDKAPK  107 (113)
T ss_pred             CCceEEEEEecCCCCCccccccccCCcc
Confidence            77799999999765443 2344444444

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

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

Probab=99.33  E-value=1.4e-11  Score=77.00  Aligned_cols=76  Identities=21%  Similarity=0.266  Sum_probs=60.1

Q ss_pred             EEEEEeCCC-cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEE-eCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTG-TLFYIQVENDATVADLKREIGAQQKLPCDRLILL-LSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g-~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~-~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      .|.|..... ......+++++||.+||++++..+|+||+.|+|. +.+..+.+....+|+++|++||+++|.+||+.=
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            456666432 3345669999999999999999999999999994 777633332345888999999999999999873

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.

>PLN02560 enoyl-CoA reductase

Probab=99.26  E-value=3.5e-11  Score=91.04  Aligned_cols=76  Identities=33%  Similarity=0.334  Sum_probs=62.6

Q ss_pred             CEEEEEeCCCcEE---EEEecCCCcHHHHHHHHHhhcCC-CCccEEEEeCCCCC-CCCccCCCCCccccCCCCCCCEEEE
Q 041108            1 MKVAVEILTGTLF---YIQVENDATVADLKREIGAQQKL-PCDRLILLLSSDHS-CPMTQDHDEVPLADCGVKDGSHIYL   75 (102)
Q Consensus         1 M~v~V~~~~g~~~---~i~v~~~~TV~dLK~~I~~~~gi-p~~~q~L~~~g~~~-~~~~~L~d~~~L~~~gI~~~~~i~l   75 (102)
                      |+|.|+.++|+..   .+++++++||+|||++|+++.++ ++++|||.+..+.. +-...++|+++|+++|+++|+++++
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            8999999999886   79999999999999999999886 89999999842101 1112678999999999999998665


Q ss_pred             E
Q 041108           76 F   76 (102)
Q Consensus        76 ~   76 (102)
                      -
T Consensus        81 k   81 (308)
T PLN02560         81 K   81 (308)
T ss_pred             E
Confidence            3

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

Probab=99.25  E-value=4.7e-11  Score=74.71  Aligned_cols=76  Identities=22%  Similarity=0.284  Sum_probs=59.2

Q ss_pred             EEEEEeCCC--cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeC-CC-CCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLS-SD-HSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g--~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~-g~-~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +|+|.....  ......++.++||++||.+|+..+|+|++.|+|.+. .. ++.+....+|+++|++||+++|++|++.=
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D   82 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVD   82 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEe
Confidence            466666654  478899999999999999999999999999999876 22 22222244788999999999999999873

>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=99.18  E-value=5.6e-11  Score=73.91  Aligned_cols=72  Identities=28%  Similarity=0.373  Sum_probs=45.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC--CCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD--HDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L--~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |-|+||+.+|. +.+++++++|+++|+++|++..++|.+.|.|.....+.   +.+  +++++|+++|+++||.|++.
T Consensus         5 milRvrS~dG~-~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~---~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen    5 MILRVRSKDGM-KRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNK---EELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             -EEEEE-SSEE-EEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGG---GCSSS-TT-CCCCT---TT-EEE--
T ss_pred             EEEEEECCCCC-EEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCC---cccccCCcCCHHHcCCCCccEEEEe
Confidence            67889998876 57799999999999999999999999999986654422   133  67899999999999999875

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.

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

Probab=99.05  E-value=3.3e-09  Score=61.86  Aligned_cols=72  Identities=24%  Similarity=0.389  Sum_probs=67.3

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      +++....|+.+.+++.+..++..+|.+|+...|++++.|++.++|+      .|+|+.++.+|+|..++++++..+..
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~------~l~d~~~l~~~~i~~~~~~~l~~~~~   73 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGK------PLEDGRTLADYNIQEGSTLHLVLSLR   73 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCE------ECcCCCcHHHhCCCCCCEEEEEEecC
Confidence            5677788999999999999999999999999999999999999999      99999999999999999999988764

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=99.03  E-value=1.5e-09  Score=66.52  Aligned_cols=68  Identities=28%  Similarity=0.375  Sum_probs=52.2

Q ss_pred             EEEEEeCC-CcEEEEEe-cCCCcHHHHHHHHHhhcC-CCCccEEEE--eCCCCCCCCccCCCCCccccCCCCCCCEEEE
Q 041108            2 KVAVEILT-GTLFYIQV-ENDATVADLKREIGAQQK-LPCDRLILL--LSSDHSCPMTQDHDEVPLADCGVKDGSHIYL   75 (102)
Q Consensus         2 ~v~V~~~~-g~~~~i~v-~~~~TV~dLK~~I~~~~g-ip~~~q~L~--~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l   75 (102)
                      +|.++..+ .....+++ ++++||.|||.+|++..+ +++++|+|.  +.|+      .|.|+.+|.++|+++|++|++
T Consensus         2 ~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~------~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801           2 EILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGK------SLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             eeeccccCcCceeecccCCCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCc------ccCCcccHhhcCCCCCCEEEE
Confidence            34445544 33333444 478999999999999976 589999997  4555      889999999999999999876

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.

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.85  E-value=2.9e-08  Score=54.93  Aligned_cols=67  Identities=30%  Similarity=0.443  Sum_probs=59.9

Q ss_pred             EEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            5 VEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         5 V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+..+|....+.+.+.+|+.++|..|.++.|+++++++|+++|.      .+.+...+.++++.+++++++..
T Consensus         2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~------~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGK------ILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCe------ECCCCCcHHHcCCCCCCEEEEEe
Confidence            34446888899999999999999999999999999999999999      88888888899999999998864

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.

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

Probab=98.85  E-value=5.8e-09  Score=88.11  Aligned_cols=74  Identities=22%  Similarity=0.322  Sum_probs=69.9

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      .|.||+++.+++++.++..+||.+||..|.++..|+.+.|||+|.|+      +|.|++++.+|+| +|-+|||.-+.+.
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~gr------vl~~~k~vq~~~v-dgk~~hlverppp   76 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGR------VLQDDKKVQEYNV-DGKVIHLVERPPP   76 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecce------eeccchhhhhccC-CCeEEEeeccCCC
Confidence            37899999999999999999999999999999999999999999999      9999999999999 9999999988664


Q ss_pred             C
Q 041108           82 D   82 (102)
Q Consensus        82 ~   82 (102)
                      +
T Consensus        77 ~   77 (1143)
T KOG4248|consen   77 Q   77 (1143)
T ss_pred             C
Confidence            3

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

Probab=98.81  E-value=5.2e-08  Score=64.03  Aligned_cols=74  Identities=24%  Similarity=0.339  Sum_probs=56.2

Q ss_pred             EEEEEeCCCc-EEEEEecCCCcHHHHHHHHHhhcC-------CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCC--
Q 041108            2 KVAVEILTGT-LFYIQVENDATVADLKREIGAQQK-------LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGS--   71 (102)
Q Consensus         2 ~v~V~~~~g~-~~~i~v~~~~TV~dLK~~I~~~~g-------ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~--   71 (102)
                      .|.++..+|+ ...+.+++.+||++||+.|...-.       ..++..||++.|+      +|+|+++|++|.+..|+  
T Consensus         4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~Gr------iL~d~~tL~~~~~~~~~~~   77 (111)
T PF13881_consen    4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGR------ILEDNKTLSDCRLPSGETP   77 (111)
T ss_dssp             EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTE------EE-SSSBTGGGT--TTSET
T ss_pred             EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCe------ecCCcCcHHHhCCCCCCCC
Confidence            4677778998 788999999999999999997531       2366799999999      99999999999998766  


Q ss_pred             ----EEEEEeecCC
Q 041108           72 ----HIYLFFKPLD   81 (102)
Q Consensus        72 ----~i~l~~~~~~   81 (102)
                          ++|+.++...
T Consensus        78 ~~~~vmHlvvrp~~   91 (111)
T PF13881_consen   78 GGPTVMHLVVRPNA   91 (111)
T ss_dssp             T--EEEEEEE-SSS
T ss_pred             CCCEEEEEEecCCC
Confidence                6888887654

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

Probab=98.79  E-value=2.2e-09  Score=64.13  Aligned_cols=70  Identities=24%  Similarity=0.385  Sum_probs=64.0

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      ++.++.+-|+...+.+.+++||+|+|+.|++++|-.++...|-..+.      +++|.-+|++|.|.+|..+.++.
T Consensus         3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~------i~kd~I~L~dyeihdg~~lelyy   72 (73)
T KOG3493|consen    3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYT------IFKDHITLSDYEIHDGMNLELYY   72 (73)
T ss_pred             eehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhh------hhhcccceeeEEeccCccEEEee
Confidence            56677788999999999999999999999999999999988887777      99999999999999999988764

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

Probab=98.61  E-value=5.8e-08  Score=62.24  Aligned_cols=64  Identities=25%  Similarity=0.368  Sum_probs=53.1

Q ss_pred             CEEEEEeCCC-cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCC
Q 041108            1 MKVAVEILTG-TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVK   68 (102)
Q Consensus         1 M~v~V~~~~g-~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~   68 (102)
                      |.++++.+.. .+++++++++.||.|||.+++..+.-|++.|+|+.-..-    .+|+|.++|++||..
T Consensus         1 ~~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~e----qlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    1 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTE----QLLDDGKTLGDCGFT   65 (110)
T ss_pred             CceeeeeeecceeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHH----HHhhccchhhhcccc
Confidence            5677776644 667899999999999999999999999999999873320    188999999999764

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

Probab=98.59  E-value=1.7e-07  Score=74.04  Aligned_cols=70  Identities=19%  Similarity=0.279  Sum_probs=63.5

Q ss_pred             EEEEeCCCcEEEEE-ecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            3 VAVEILTGTLFYIQ-VENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         3 v~V~~~~g~~~~i~-v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |.|+. .|+.+.++ ++.++|+..||.++.+.+|++|++||++..|.      .+.|+..+...+|++|.+++++...
T Consensus         6 v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg------~a~dd~~~~al~iKpn~~lmMmGt~   76 (473)
T KOG1872|consen    6 VIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGG------LAKDDVDWGALQIKPNETLMMMGTA   76 (473)
T ss_pred             Eeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecc------cccccccccccccCCCCEEEeeccc
Confidence            55665 47888877 99999999999999999999999999999999      9999999999999999999999754

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

Probab=98.26  E-value=3.9e-06  Score=64.19  Aligned_cols=71  Identities=21%  Similarity=0.451  Sum_probs=61.8

Q ss_pred             CEEEEEeC-CCc--EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEIL-TGT--LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~-~g~--~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |.+.|+.. .|.  .+.++|+.+.+|.+||+.++.++|+|+++.+++|.|+      .|.++-++..+.+...+.++++.
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGK------eLs~~ttv~~cDL~qqs~~hi~~   74 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGK------ELSNDTTVQNCDLSQQSATHIML   74 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEecc------ccccCceeecccccccchhhhhc
Confidence            66777775 233  3678999999999999999999999999999999999      99999999988888888888884

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

Probab=98.07  E-value=4.9e-05  Score=46.70  Aligned_cols=73  Identities=18%  Similarity=0.193  Sum_probs=60.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC-CCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD-HSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~-~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      ++|+|+-..+....+.|+|..+|-.+|++|....+++- .|+|.|--. .+++  +|.+..+|++|||=.+..|.+.
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rq--lL~s~~sLA~yGiFs~~~i~ll   74 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQ--LLSSRKSLADYGIFSKTNICLL   74 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccc--cccccccHhhhcceeccEEEEE
Confidence            47899998888899999999999999999999998876 899988332 2333  7899999999999777666654

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.

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

Probab=98.02  E-value=1.7e-05  Score=48.71  Aligned_cols=68  Identities=29%  Similarity=0.404  Sum_probs=47.3

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCcc------EEEE-eCCCCCCCCccCCCCCccccCCCCCCCEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDR------LILL-LSSDHSCPMTQDHDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~------q~L~-~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~   74 (102)
                      +|+|...+|+.+.+.+..+.++++|...|.+..+.+...      -+|. -+|.      .|+++.+|+++||.+|+.++
T Consensus         4 rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~------~L~~~~tL~~~gV~dGd~L~   77 (79)
T PF08817_consen    4 RVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGR------PLDPDQTLADAGVRDGDVLV   77 (79)
T ss_dssp             EEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTE------EEETTSBCGGGT--TT-EEE
T ss_pred             EEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCc------ccCCcCcHhHcCCCCCCEEE
Confidence            466777666889999999999999999999988864332      2333 3455      89999999999999999998


Q ss_pred             E
Q 041108           75 L   75 (102)
Q Consensus        75 l   75 (102)
                      +
T Consensus        78 L   78 (79)
T PF08817_consen   78 L   78 (79)
T ss_dssp             E
T ss_pred             e
Confidence            6

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.

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

Probab=97.95  E-value=0.00021  Score=46.02  Aligned_cols=75  Identities=16%  Similarity=0.239  Sum_probs=66.4

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      +.|+.-+|....+.+...+....|+.+-++..|++.+..|.+|+|+      -+.+..+-.+++..+|+.|-++....++
T Consensus        23 LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~------rI~~~~TP~~L~mEd~D~Iev~~~q~gG   96 (99)
T KOG1769|consen   23 LKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQ------RIRETHTPADLEMEDGDEIEVVQEQTGG   96 (99)
T ss_pred             EEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCc------CcCCCCChhhhCCcCCcEEEEEeecccC
Confidence            4455545677788999999999999999999999999999999999      9999999999999999999999877665


Q ss_pred             C
Q 041108           83 G   83 (102)
Q Consensus        83 ~   83 (102)
                      .
T Consensus        97 ~   97 (99)
T KOG1769|consen   97 F   97 (99)
T ss_pred             C
Confidence            4

>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=97.94  E-value=0.00015  Score=44.31  Aligned_cols=71  Identities=14%  Similarity=0.198  Sum_probs=57.3

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCcc-EEEEeCCCCCCCCccCC-C-CCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDR-LILLLSSDHSCPMTQDH-D-EVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~-q~L~~~g~~~~~~~~L~-d-~~~L~~~gI~~~~~i~l~   76 (102)
                      .|.||..+|+...-...+++|+.+|...|......+... ..|+....    ...+. + +.+|+++|+.++++|++-
T Consensus         8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~P----r~~l~~~~~~tl~e~~l~p~~~l~v~   81 (82)
T PF00789_consen    8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFP----RRELTDEDSKTLEEAGLLPSATLIVE   81 (82)
T ss_dssp             EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSS----TEECCSTTTSBTCCCTTSSCEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCC----CcCCCccccccHHHhcCCCCeEEEEE
Confidence            588999999999999999999999999999988777765 67765443    11442 2 479999999999998874

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 ....

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.76  E-value=0.00051  Score=42.04  Aligned_cols=71  Identities=13%  Similarity=0.081  Sum_probs=56.2

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC--C-CCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH--D-EVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~--d-~~~L~~~gI~~~~~i~l~   76 (102)
                      +|.||..+|+...-....++|+.+|.+.|....+.......|+..-.    .+.+.  | +.+|.++|+.+++++.+-
T Consensus         6 ~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~P----rk~l~~~d~~~tL~e~gL~p~~~l~v~   79 (80)
T smart00166        6 RLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFP----RRTFTKDDYSKTLLELALLPSSTLVLE   79 (80)
T ss_pred             EEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCC----CcCCccccccCCHHHCCCCCceEEEEe
Confidence            58899999999999999999999999999766666666677765443    12453  2 589999999988888763

Present in FAF1 and Shp1p.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=97.72  E-value=0.00074  Score=42.16  Aligned_cols=75  Identities=15%  Similarity=0.240  Sum_probs=61.0

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      +|.||..+|+...-....+.++.+|-..+.+ .|.+++...|+.+-..... ...+.+.+|.++|+.+..++.|.-+
T Consensus         7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr~~-~~~d~~~TL~e~GL~P~~~LfVq~r   81 (82)
T cd01773           7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRRKL-SHLDYDITLQEAGLCPQETVFVQER   81 (82)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCccc-CCcccCCCHHHcCCCCCcEEEEecC
Confidence            6899999999999999999999999999999 5789999999876642211 1235568999999999999988543

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.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=97.66  E-value=0.00055  Score=47.73  Aligned_cols=75  Identities=19%  Similarity=0.290  Sum_probs=56.1

Q ss_pred             CEEEEEeCCC----cEEEEEecCCCcHHHHHHHHHhhcCCCCccE-EEEeC-CCCCCCCccC--CCCCccccCCCCCC--
Q 041108            1 MKVAVEILTG----TLFYIQVENDATVADLKREIGAQQKLPCDRL-ILLLS-SDHSCPMTQD--HDEVPLADCGVKDG--   70 (102)
Q Consensus         1 M~v~V~~~~g----~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q-~L~~~-g~~~~~~~~L--~d~~~L~~~gI~~~--   70 (102)
                      |+|.|++.+|    .++.+.+.++.||.+|+..|.+..++++..| .|.+. ++      .+  .++..++++.-.+.  
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~------~l~~~~~~~~s~l~~~~~~~   74 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNG------QLSPSSDIPLSSLLSSSQDS   74 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCC------eeCCCccccHHhhccCcCCC
Confidence            7899999999    5788999999999999999999999998885 45443 33      33  55566666544333  


Q ss_pred             --CEEEEEeecCC
Q 041108           71 --SHIYLFFKPLD   81 (102)
Q Consensus        71 --~~i~l~~~~~~   81 (102)
                        -++.+..++.|
T Consensus        75 ~~~~l~l~~rl~G   87 (162)
T PF13019_consen   75 DFITLRLSLRLRG   87 (162)
T ss_pred             CceEEEEEEeccC
Confidence              35677777665

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.66  E-value=0.00011  Score=53.29  Aligned_cols=63  Identities=21%  Similarity=0.316  Sum_probs=56.0

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      .++.+.+.+..-+|+.++|.+++++.|+++..|+|+++|+      ++-|...|.+|++..|+...+..
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~------~l~dkt~LeEc~iekg~rYvlqv  217 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGG------VLVDKTDLEECKIEKGQRYVLQV  217 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCC------ceeccccceeeeecCCCEEEEEE
Confidence            3566888888899999999999999999999999999999      99999999999999995555443

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.59  E-value=0.0012  Score=40.56  Aligned_cols=70  Identities=13%  Similarity=0.167  Sum_probs=54.4

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC---CCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH---DEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~---d~~~L~~~gI~~~~~i~l~   76 (102)
                      +|.||..+|+...-....++|+.++.+.|....+-. ....|+..-.    .+.+.   .+.+|.++|+.+.+++.+.
T Consensus         6 ~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fP----rk~~~~~d~~~TL~elgL~Psa~L~v~   78 (79)
T cd01772           6 RIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFP----RKVFTEDDMEKPLQELGLVPSAVLIVT   78 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCC----CeECCcccccCCHHHCCCCCceEEEEe
Confidence            588999999998889999999999999998765433 4566665443    22553   3589999999999998874

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=97.58  E-value=0.0012  Score=40.67  Aligned_cols=69  Identities=9%  Similarity=0.159  Sum_probs=52.1

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHI   73 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i   73 (102)
                      +|.||..+|+...-....++||.+|.+.|....+-+ .....|+.+-.+   +++-+++.+|.++|+.+...+
T Consensus         6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~---k~l~~~~~Tl~eagL~~s~v~   75 (79)
T cd01770           6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPV---KELSDESLTLKEANLLNAVIV   75 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCC---cccCCCCCcHHHCCCcCcEEE
Confidence            588999999999999999999999999999876432 345667654331   123456889999999975444

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=97.56  E-value=0.0018  Score=39.26  Aligned_cols=67  Identities=12%  Similarity=0.195  Sum_probs=50.7

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC---CCCccccCCCCCCCEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH---DEVPLADCGVKDGSHI   73 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~---d~~~L~~~gI~~~~~i   73 (102)
                      +|.||..+|+...-....++|+.+|.+.|.....- .....|+.+-.    .+.+.   .+.+|.++|+.+++.+
T Consensus         4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~P----r~~~~~~~~~~TL~e~gL~~s~~~   73 (77)
T cd01767           4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFP----RRVLTDLDYELTLQEAGLVNEVVF   73 (77)
T ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCC----CccCCCCCccCcHHHcCCccceEE
Confidence            58899999999888999999999999999876543 45566765443    12443   6889999999954443

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.

>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=97.55  E-value=0.00034  Score=41.86  Aligned_cols=62  Identities=13%  Similarity=0.105  Sum_probs=46.2

Q ss_pred             CCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEE
Q 041108            8 LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYL   75 (102)
Q Consensus         8 ~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l   75 (102)
                      .+++.+.+.+.++.++.++-++...++|+++++-.|.++++      .++-+.++.-.|+.+|+.+.+
T Consensus         4 ~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k------~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen    4 YNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNK------PLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTE------EESSS-BHHHH---SS-EEEE
T ss_pred             cCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCE------EeccccceeecCCCCCCEEeC
Confidence            46788999999999999999999999999999999999999      999999999999999998864

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.

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=97.50  E-value=0.0017  Score=40.57  Aligned_cols=70  Identities=9%  Similarity=0.093  Sum_probs=56.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC--------CCCCccccCCCCCCCEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD--------HDEVPLADCGVKDGSHI   73 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L--------~d~~~L~~~gI~~~~~i   73 (102)
                      +|.+|..+|+...-....++|+.+|...|.+. +..++...|+.+-...    .+        +.+.+|++.|+.+..++
T Consensus         6 ~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~~-~~~~~~f~L~t~FPrr----~~~~~~~~~~~~~~TL~eaGL~~s~~L   80 (85)
T cd01774           6 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFSL-KETPEKFQIVTNFPRR----VLPCLPSEGDPPPPTLLEAGLSNSEVL   80 (85)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhC-CCCCCcEEEecCCCCc----cccccccccCcCCCCHHHcCCCCccEE
Confidence            68899999998888888999999999999754 5567888898876311    44        34679999999998888


Q ss_pred             EEE
Q 041108           74 YLF   76 (102)
Q Consensus        74 ~l~   76 (102)
                      .|.
T Consensus        81 ~V~   83 (85)
T cd01774          81 FVQ   83 (85)
T ss_pred             EEe
Confidence            764

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.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=97.37  E-value=0.0038  Score=38.59  Aligned_cols=70  Identities=17%  Similarity=0.151  Sum_probs=57.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC---CCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD---HDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L---~d~~~L~~~gI~~~~~i~l~   76 (102)
                      +|.+|..+|+...-....++++.+|-..|... |.++...+|+.+-.    .+.+   +.+.+|.+.|+.+..++.|-
T Consensus         6 ~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~~~~~~f~L~t~fP----Rk~~~~~d~~~TL~e~gL~p~~~L~Ve   78 (80)
T cd01771           6 KLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-GYPIDEYKLLSSWP----RRDLTQLDPNFTLLELKLYPQETLILE   78 (80)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEecCCC----CCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence            68899999998888899999999999999875 78888888875553    2244   44679999999999998874

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.

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

Probab=97.33  E-value=0.00057  Score=50.84  Aligned_cols=73  Identities=23%  Similarity=0.300  Sum_probs=52.0

Q ss_pred             CEEEEEeCCCcE--EEEEecCCCcHHHHHHHHHhh-cCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEE
Q 041108            1 MKVAVEILTGTL--FYIQVENDATVADLKREIGAQ-QKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYL   75 (102)
Q Consensus         1 M~v~V~~~~g~~--~~i~v~~~~TV~dLK~~I~~~-~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l   75 (102)
                      |.|++.++++..  ...+.+...|++|++++|... .++.+.++|+.+.-.+.  .+.+-|+.+|+++|..+|+++.+
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~k--gkpl~~~s~l~e~~~~s~~~i~v   76 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPK--GKPLIDNSKLQEYGDGSGATIYV   76 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCC--CccccchhHHHHhccCCCCEEEE
Confidence            789999987633  346788889999999776665 55777666654432211  12788888899999999976654

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.18  E-value=0.003  Score=38.85  Aligned_cols=69  Identities=14%  Similarity=0.250  Sum_probs=55.2

Q ss_pred             CEEEEEeC--CCcEEEEEecCCCcHHHHHHHHHhhcCCC---C--ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEE
Q 041108            1 MKVAVEIL--TGTLFYIQVENDATVADLKREIGAQQKLP---C--DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHI   73 (102)
Q Consensus         1 M~v~V~~~--~g~~~~i~v~~~~TV~dLK~~I~~~~gip---~--~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i   73 (102)
                      |+|+|-..  +|.++.+.++.-.++..|-..+.+...+.   .  ...|++-.++      +|.++..|.+|+|.+|+.+
T Consensus         5 ikVTvD~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~------llsgd~kL~d~~IadGD~L   78 (81)
T COG5417           5 IKVTVDFTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQ------LLSGDDKLIDYQIADGDIL   78 (81)
T ss_pred             EEEEEEeEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccce------EecCCceEEeccccCCCEE
Confidence            34555444  58999999999999999988887776642   2  3457888888      9999999999999999998


Q ss_pred             EE
Q 041108           74 YL   75 (102)
Q Consensus        74 ~l   75 (102)
                      .+
T Consensus        79 ei   80 (81)
T COG5417          79 EI   80 (81)
T ss_pred             Ee
Confidence            75

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

Probab=97.13  E-value=0.0024  Score=46.36  Aligned_cols=70  Identities=17%  Similarity=0.186  Sum_probs=55.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhcCCCCccEEE-EeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCC
Q 041108           13 FYIQVENDATVADLKREIGAQQKLPCDRLIL-LLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        13 ~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L-~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      .....+.+.|+.+||.+++-.+|.+++.++| +|.+..++-...-++++.|..|+..+|-.||++=.....
T Consensus        15 ~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihviD~~~~~   85 (234)
T KOG3206|consen   15 TEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVIDSNAQS   85 (234)
T ss_pred             hhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEEecCccc
Confidence            3466888999999999999999999999998 566643333334578899999999999999998554433

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

Probab=97.07  E-value=0.0026  Score=40.81  Aligned_cols=58  Identities=21%  Similarity=0.189  Sum_probs=44.9

Q ss_pred             EEEEEeCCC-cEEEEEec--CCCcHHHHHHHHHhhcC--CCCccEEEEeCCCCCCCCccCCCCCccccC
Q 041108            2 KVAVEILTG-TLFYIQVE--NDATVADLKREIGAQQK--LPCDRLILLLSSDHSCPMTQDHDEVPLADC   65 (102)
Q Consensus         2 ~v~V~~~~g-~~~~i~v~--~~~TV~dLK~~I~~~~g--ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~   65 (102)
                      .|.||..++ ....++++  ...||..||..|-+..+  ..-.++||+|+|+      .|.|+..|+..
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 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGR------LLNDHTDLSSE   64 (97)
T ss_pred             eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCc------ccCccchhhhh
Confidence            467787764 33567777  68999999999999873  3345678999999      99999888654

They contain a characteristic GFDRL sequence motif.

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

Probab=96.67  E-value=0.011  Score=37.67  Aligned_cols=70  Identities=16%  Similarity=0.194  Sum_probs=61.0

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      +.|...+|....+.+..+.+...|..+.+...|-..++.|++|.|.      -++.+++-++++..+++.|.....
T Consensus        27 Lkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~------rI~~dqTP~dldmEdnd~iEav~e   96 (103)
T COG5227          27 LKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGK------RIDLDQTPGDLDMEDNDEIEAVTE   96 (103)
T ss_pred             eEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcce------ecCCCCChhhcCCccchHHHHHHH
Confidence            4455567888899999999999999999999999999999999999      889999999999999887755443

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

Probab=96.32  E-value=0.037  Score=34.97  Aligned_cols=69  Identities=14%  Similarity=0.172  Sum_probs=46.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC-CCCCccccCCCCCCCEEEEEeecCCC
Q 041108           12 LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD-HDEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      .+...++..+||+.+...+.+.+.+ ..+-||.-.+..+.. ..| +.+.++.+.|+.+|.+|.+-.+..++
T Consensus        15 ~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~-e~L~~~~~Tv~da~L~~gQ~vliE~rn~DG   84 (88)
T PF14836_consen   15 VLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSY-ELLNNPEITVEDAGLYDGQVVLIEERNEDG   84 (88)
T ss_dssp             EEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCE-EEE--TTSBTTTTT--TTEEEEEEE--TTS
T ss_pred             HhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcch-hhhCCCCccHHHccCcCCCEEEEEeeccCC
Confidence            4677889999999999999999999 555666433332222 245 66689999999999999998887665

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

Probab=96.31  E-value=0.039  Score=33.07  Aligned_cols=66  Identities=20%  Similarity=0.118  Sum_probs=49.5

Q ss_pred             EEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCC-CccEEEEe--CCCCCCCCccCCCCCccccCCCCCCCE
Q 041108            5 VEILTGTLFYIQVENDATVADLKREIGAQQKLP-CDRLILLL--SSDHSCPMTQDHDEVPLADCGVKDGSH   72 (102)
Q Consensus         5 V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip-~~~q~L~~--~g~~~~~~~~L~d~~~L~~~gI~~~~~   72 (102)
                      |+.++|+...+++++++|+.+|-+.|....++. .+-.-|.+  ...  .-..-|+.+++|.+.....+..
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~--~~~~wL~~~k~l~~q~~~~~~~   69 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKD--GEHHWLDLDKKLKKQLKKNNPP   69 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTT--SSEEEE-SSSBGGGSTBTSSSS
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCC--CcceeccCcccHHHHcCCCCCC
Confidence            678899999999999999999999999999986 45567777  222  1112578889998887663333

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 ....

>PRK06437 hypothetical protein; Provisional

Probab=96.11  E-value=0.072  Score=31.64  Aligned_cols=64  Identities=14%  Similarity=0.220  Sum_probs=48.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |.-+++...++...++++...|+.+|-+.    .|+++....+..+|.      .+.     .++-+++||.|.++.-.
T Consensus         1 ~~~~~~v~g~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~------iv~-----~~~~L~dgD~Veiv~~V   64 (67)
T PRK06437          1 MIAMIRVKGHINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGS------PVL-----EDHNVKKEDDVLILEVF   64 (67)
T ss_pred             CcceEEecCCcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCE------ECC-----CceEcCCCCEEEEEecc
Confidence            44556666567788888888999998754    578888888889998      776     45567899999988543

>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=95.94  E-value=0.049  Score=33.84  Aligned_cols=52  Identities=25%  Similarity=0.233  Sum_probs=41.5

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD   56 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L   56 (102)
                      |.|+.. + ++.|.+.++.+..+|.++|.++.++|++...|.|...+++-...+
T Consensus         5 vKV~f~-~-tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s~~~v~l   56 (80)
T cd06406           5 VKVHFK-Y-TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEASGEDVIL   56 (80)
T ss_pred             EEEEEE-E-EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCCCCccCc
Confidence            344443 2 788999999999999999999999999999999988754443344

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

>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=95.71  E-value=0.11  Score=32.60  Aligned_cols=44  Identities=9%  Similarity=0.036  Sum_probs=37.4

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc---cEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD---RLILLL   45 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~---~q~L~~   45 (102)
                      .+.++...|+.+.+.+.+++.+.+|+..|+++.|.+..   ...|.|
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            35677889999999999999999999999999998863   455655

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

>smart00666 PB1 PB1 domain

Probab=95.42  E-value=0.23  Score=29.79  Aligned_cols=46  Identities=17%  Similarity=0.278  Sum_probs=38.1

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      ++.++. +|..+.+.++++.|..+|+.+|...++++.....|-|...
T Consensus         3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~De   48 (81)
T smart00666        3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDE   48 (81)
T ss_pred             cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECC
Confidence            345555 5678899999999999999999999999877788877665

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.

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

Probab=95.27  E-value=0.074  Score=32.48  Aligned_cols=59  Identities=24%  Similarity=0.313  Sum_probs=47.7

Q ss_pred             ecCCCcHHHHHHHHHhhcC-CCCccEEEEeCCCCCCCCccCCCCCcccc-CCCCCCCEEEEEeecCC
Q 041108           17 VENDATVADLKREIGAQQK-LPCDRLILLLSSDHSCPMTQDHDEVPLAD-CGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        17 v~~~~TV~dLK~~I~~~~g-ip~~~q~L~~~g~~~~~~~~L~d~~~L~~-~gI~~~~~i~l~~~~~~   81 (102)
                      |.++++|.|+++.+..... ..-.+..|.++|.      .|++...|++ -|+++|.++.+...+..
T Consensus         1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~------~L~~~~el~~i~~~~~~~~L~lve~pYt   61 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQ------RLDDFVELSEIEGIKDGCVLELVEEPYT   61 (76)
T ss_pred             CChhhHHHHHHHHHHhCccccceeEEEEEECCC------ccCCchhhhhhhCCCCCcEEEEEecCCC
Confidence            5678999999999988754 4466678889999      8999999988 46888999999866543

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

Probab=94.86  E-value=0.069  Score=41.80  Aligned_cols=70  Identities=17%  Similarity=0.343  Sum_probs=54.7

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~   74 (102)
                      .|.||..+|+-....++...||.|++..|.....=. ...+.|+.+..   ++.+.+++.||++.|+.+...+.
T Consensus       307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FP---pk~l~D~sqTle~AgL~Nsvlvq  377 (380)
T KOG2086|consen  307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFP---PKPLSDDSQTLEEAGLLNSVLVQ  377 (380)
T ss_pred             eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCC---CcccCCcchhHHhccchhhhhhh
Confidence            478999999988899999999999999999876544 33577776665   33355788999999998765443

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=94.77  E-value=0.22  Score=39.73  Aligned_cols=77  Identities=14%  Similarity=0.194  Sum_probs=55.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcC--CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQK--LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~g--ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |.+++|...|+ +.+++.++++.+-|-.+|-.-..  ..|+...+.-+-..++..--+..++++.++|+++|+++++-..
T Consensus         1 Mi~rfRsk~G~-~Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~ys   79 (571)
T COG5100           1 MIFRFRSKEGQ-RRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEYS   79 (571)
T ss_pred             CeEEEecCCCc-eeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEec
Confidence            78899999887 68999999999998888877554  3455555543222122111246778999999999999999873

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=94.73  E-value=0.29  Score=29.12  Aligned_cols=59  Identities=17%  Similarity=0.161  Sum_probs=42.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcCC----CCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108           12 LFYIQVENDATVADLKREIGAQQKL----PCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~gi----p~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      ...++++...|+.+|.+.+...++-    ......+..+|+      ...     .+.-+++||.|.++-...|
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~------~v~-----~~~~l~~gD~v~i~ppv~G   79 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGE------YVR-----LDTPLKDGDEVAIIPPVSG   79 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCe------EcC-----CCcccCCCCEEEEeCCCCC
Confidence            3567787789999999999987642    233446677887      655     3456899999999865443

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=94.69  E-value=0.2  Score=30.34  Aligned_cols=68  Identities=19%  Similarity=0.269  Sum_probs=45.3

Q ss_pred             CEEEEEeCC------C-cEEEEEecCCCcHHHHHHHHHhhcC-CCC--ccEEEEeCCCCCCCCccCCCCCccccCCCCCC
Q 041108            1 MKVAVEILT------G-TLFYIQVENDATVADLKREIGAQQK-LPC--DRLILLLSSDHSCPMTQDHDEVPLADCGVKDG   70 (102)
Q Consensus         1 M~v~V~~~~------g-~~~~i~v~~~~TV~dLK~~I~~~~g-ip~--~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~   70 (102)
                      |+|.|+...      | ....+++....|+.+|.+.+..... +..  ..-.+..++.      ...     .+.-+++|
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~------~v~-----~~~~l~dg   70 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEE------YTT-----ESAALKDG   70 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCE------EcC-----CCcCcCCC
Confidence            677777643      4 4467888888999999999987652 111  1123566776      543     34557899


Q ss_pred             CEEEEEeec
Q 041108           71 SHIYLFFKP   79 (102)
Q Consensus        71 ~~i~l~~~~   79 (102)
                      |.|.++-.-
T Consensus        71 DeVai~Ppv   79 (82)
T PLN02799         71 DELAIIPPI   79 (82)
T ss_pred             CEEEEeCCC
Confidence            999988543

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.50  E-value=0.1  Score=40.58  Aligned_cols=62  Identities=18%  Similarity=0.199  Sum_probs=46.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe---CCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108           13 FYIQVENDATVADLKREIGAQQKLPCDRLILLL---SSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus        13 ~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~---~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      ..|.+.  -||.|+|..+..+.|+.+.++||++   .|+--.+. ..+...+|..|+|++|+.+.+.-
T Consensus       352 ~~I~~~--~TV~D~~~~Ld~~VGvk~trMkLf~L~eD~rt~~~s-s~~~N~~L~~fkIedGDs~lvqe  416 (418)
T KOG2982|consen  352 GLICMT--RTVLDFMKILDPKVGVKFTRMKLFLLREDGRTDDFS-SSDYNMPLHYFKIEDGDSFLVQE  416 (418)
T ss_pred             eEEEee--hHHHHHHHHhccccccccceeEEEEEcccCccCCcc-ccCCCCcceEEeccCCCEeeeec
Confidence            345554  4999999999999999999999987   33311111 33667899999999999988753

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

Probab=94.37  E-value=0.02  Score=44.27  Aligned_cols=58  Identities=19%  Similarity=0.068  Sum_probs=43.9

Q ss_pred             EEEEEeCCCcEEE--EEecCCCcHHHHHHHHHhhcCCC--CccEEEEeCCCCCCCCccCCCCCccccC
Q 041108            2 KVAVEILTGTLFY--IQVENDATVADLKREIGAQQKLP--CDRLILLLSSDHSCPMTQDHDEVPLADC   65 (102)
Q Consensus         2 ~v~V~~~~g~~~~--i~v~~~~TV~dLK~~I~~~~gip--~~~q~L~~~g~~~~~~~~L~d~~~L~~~   65 (102)
                      .+.+++.+.+..+  |..+..+||++||..++..+--.  ...|||+|.|+      +|.|...|.+.
T Consensus        11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgk------llld~qcl~d~   72 (391)
T KOG4583|consen   11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGK------LLLDHQCLTDW   72 (391)
T ss_pred             EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhcc------ccccchhHHHH
Confidence            3567777765544  55666799999999998865432  34689999999      99888887764

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=94.34  E-value=0.54  Score=27.90  Aligned_cols=53  Identities=21%  Similarity=0.191  Sum_probs=39.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           12 LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      ...+++++..|+.+|-+.+    ++++..-.+..+|.      ....     +.-+++||.|.++-..
T Consensus        15 ~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~------iv~~-----~~~l~~gD~Veii~~V   67 (70)
T PRK08364         15 EKEIEWRKGMKVADILRAV----GFNTESAIAKVNGK------VALE-----DDPVKDGDYVEVIPVV   67 (70)
T ss_pred             ceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCE------ECCC-----CcCcCCCCEEEEEccc
Confidence            4677888889999988665    67777667788888      6643     5557899999887543

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

Probab=94.18  E-value=0.31  Score=29.56  Aligned_cols=46  Identities=15%  Similarity=0.094  Sum_probs=41.9

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      +.|-..+|+...+.+.+.+|+.|+-..+-++.|+.++.-.+.+.|.
T Consensus         2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~~   47 (72)
T cd01760           2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGL   47 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEecC
Confidence            4677889999999999999999999999999999999998887765

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.

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

Probab=94.01  E-value=0.11  Score=40.43  Aligned_cols=76  Identities=22%  Similarity=0.246  Sum_probs=61.4

Q ss_pred             CEEEEEeC--CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC--CCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEIL--TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH--DEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~--~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~--d~~~L~~~gI~~~~~i~l~   76 (102)
                      |.++|...  .-+.+.++++.+..+..|+..+...+|++.+..-++|+++      .+.  .+..+.++|+..++++.+-
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 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTGIVYDPSDLIYNPR------PLVSNESQGLTQIGLKDGDSLALR   74 (380)
T ss_pred             CeEEEEEEecceeeeccccccccchhhHHHHHHHHhCcccchhhcccCCC------ccccchhhhhhhcccccceeEecc
Confidence            55555544  4467889999999999999999999999999999999998      553  3578999999999998876


Q ss_pred             eecCCC
Q 041108           77 FKPLDD   82 (102)
Q Consensus        77 ~~~~~~   82 (102)
                      -+..+.
T Consensus        75 ~ks~d~   80 (380)
T KOG0012|consen   75 CKSSDP   80 (380)
T ss_pred             CCCCCC
Confidence            554443

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=93.87  E-value=0.59  Score=27.17  Aligned_cols=64  Identities=22%  Similarity=0.236  Sum_probs=43.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|++   +|+.+.+  + ..|+.+|.+.+    ++++....+-.++.      .+. .....+..+++||.|.++-...
T Consensus         1 m~i~~---Ng~~~~~--~-~~tl~~Ll~~l----~~~~~~vavavN~~------iv~-~~~~~~~~L~dgD~Ieiv~~V~   63 (65)
T PRK06488          1 MKLFV---NGETLQT--E-ATTLALLLAEL----DYEGNWLATAVNGE------LVH-KEARAQFVLHEGDRIEILSPMQ   63 (65)
T ss_pred             CEEEE---CCeEEEc--C-cCcHHHHHHHc----CCCCCeEEEEECCE------EcC-HHHcCccccCCCCEEEEEEecc
Confidence            45554   4566555  3 46899988764    66666666778887      665 3335566789999999986554


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      |
T Consensus        64 G   64 (65)
T PRK06488         64 G   64 (65)
T ss_pred             C
Confidence            3

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=93.87  E-value=0.68  Score=26.95  Aligned_cols=56  Identities=27%  Similarity=0.476  Sum_probs=39.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|.-     ..+++..+.|+.+||.++..      +.=.++++|=      +.+++.     -+++||.|.++-+
T Consensus         1 M~I~vN~-----k~~~~~~~~tl~~lr~~~k~------~~DI~I~NGF------~~~~d~-----~L~e~D~v~~Ikk   56 (57)
T PF14453_consen    1 MKIKVNE-----KEIETEENTTLFELRKESKP------DADIVILNGF------PTKEDI-----ELKEGDEVFLIKK   56 (57)
T ss_pred             CEEEECC-----EEEEcCCCcCHHHHHHhhCC------CCCEEEEcCc------ccCCcc-----ccCCCCEEEEEeC
Confidence            6666644     35677778899999987554      3336788887      666644     4578899988754

>smart00455 RBD Raf-like Ras-binding domain

Probab=93.68  E-value=0.88  Score=27.23  Aligned_cols=46  Identities=15%  Similarity=0.134  Sum_probs=41.3

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      ..|-..+|+...+.+.|..|+.|+-..+-++.|+.++.-.+...|.
T Consensus         2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~   47 (70)
T smart00455        2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGE   47 (70)
T ss_pred             eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCC
Confidence            3566788999999999999999999999999999999999888665

>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=93.63  E-value=0.45  Score=30.00  Aligned_cols=71  Identities=13%  Similarity=0.139  Sum_probs=45.6

Q ss_pred             EEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC-CCCCceeEEE
Q 041108           14 YIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL-DDGSTQHSVF   90 (102)
Q Consensus        14 ~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~-~~~~~~~~~~   90 (102)
                      ...++=...++.||..++.+.++.-+.-.++.-+.      .|+++++|-+.||+-...+.+.+.-. .+...+++|.
T Consensus         6 ~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~------~L~~~k~L~dQcVqgeGlVQlnvQi~s~~~~~riNIv   77 (88)
T PF11620_consen    6 MQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDI------QLEPHKSLVDQCVQGEGLVQLNVQIKSNQGEPRINIV   77 (88)
T ss_dssp             EEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTE------E--TTSBTTTSS----SEEEEEEEEE--TT--EEEEE
T ss_pred             EEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccc------eecCCccHHHhhccccCEEEEEEEEEecCCCcceEEE
Confidence            34555667899999999999999988888888888      89999999999999888888887632 2234444543

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.

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

Probab=93.58  E-value=0.65  Score=27.82  Aligned_cols=45  Identities=22%  Similarity=0.283  Sum_probs=36.2

Q ss_pred             EEEEeCCCcEEE-EEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            3 VAVEILTGTLFY-IQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         3 v~V~~~~g~~~~-i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      |.++.. |..+. +.+..+.|..+|+.+|.+.++.+.....|.|...
T Consensus         4 vK~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~   49 (84)
T PF00564_consen    4 VKVRYG-GDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDE   49 (84)
T ss_dssp             EEEEET-TEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEET
T ss_pred             EEEEEC-CeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCC
Confidence            444554 44555 8999999999999999999999988888888665

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 ....

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

Probab=93.45  E-value=0.45  Score=40.09  Aligned_cols=40  Identities=25%  Similarity=0.272  Sum_probs=36.8

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      ++..+.+-++++.|+..++..|+..+|+|...|-|+|.|.
T Consensus       323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~  362 (732)
T KOG4250|consen  323 QATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGG  362 (732)
T ss_pred             cceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecC
Confidence            4567889999999999999999999999999999999876

>smart00295 B41 Band 4

Probab=92.36  E-value=2.5  Score=28.94  Aligned_cols=67  Identities=18%  Similarity=0.141  Sum_probs=45.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEeCCCCCCCCccCCCCCccccCCCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD-RLILLLSSDHSCPMTQDHDEVPLADCGVK   68 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~~g~~~~~~~~L~d~~~L~~~gI~   68 (102)
                      .+.|...+|+...+.+++..|+.++-..++.+.|++.. ..-|.+-.........++...++.+....
T Consensus         5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~   72 (207)
T smart00295        5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVK   72 (207)
T ss_pred             EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhcCC
Confidence            57888999999999999999999999999999999532 22454432200000134555666665543

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.

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

Probab=92.25  E-value=1.6  Score=26.27  Aligned_cols=57  Identities=14%  Similarity=0.287  Sum_probs=40.7

Q ss_pred             EEEEecCC-CcHHHHHHHHHhhcC-C-C-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108           13 FYIQVEND-ATVADLKREIGAQQK-L-P-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus        13 ~~i~v~~~-~TV~dLK~~I~~~~g-i-p-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      ..++++.+ .|+.+|...+.+.++ + . .....+..+++      ...+     +..+++|+.|.++-.-.
T Consensus        18 ~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~------~v~~-----~~~l~dgDevai~Ppvs   78 (80)
T TIGR01682        18 ETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEE------YVTD-----DALLNEGDEVAFIPPVS   78 (80)
T ss_pred             EEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCE------EcCC-----CcCcCCCCEEEEeCCCC
Confidence            46788876 899999999999864 1 1 12345667777      5553     46679999999885443

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=91.93  E-value=1.3  Score=27.36  Aligned_cols=47  Identities=19%  Similarity=0.183  Sum_probs=36.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCC-ccEEEEeCCC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPC-DRLILLLSSD   48 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~-~~q~L~~~g~   48 (102)
                      |+|.+.. +|..+.+.+.++.+..+|++.|.++.++.. ....|-|-..
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            4455555 467889999999999999999999999865 5566666544

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

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=91.87  E-value=1.2  Score=35.61  Aligned_cols=70  Identities=20%  Similarity=0.216  Sum_probs=52.3

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCC----CCccE--EEE-eCCCCCCCCccCCCCCccccCCCCCCCEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKL----PCDRL--ILL-LSSDHSCPMTQDHDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gi----p~~~q--~L~-~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~   74 (102)
                      +|+|...+ +..++-+..+..+.||--.|-+..+-    +....  .|. .+|.      .++.+.+|.+.||.||+.++
T Consensus         4 RVtV~~~~-~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~------pL~~~~sL~~~gV~DG~~L~   76 (452)
T TIGR02958         4 RVTVLAGR-RAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGS------PLDPDASLAEAGVRDGELLV   76 (452)
T ss_pred             EEEEeeCC-eeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCC------CCCCCCCHHHcCCCCCCeEE
Confidence            45666543 44788899999999999888887663    11122  232 3555      89999999999999999999


Q ss_pred             EEee
Q 041108           75 LFFK   78 (102)
Q Consensus        75 l~~~   78 (102)
                      +.-.
T Consensus        77 L~p~   80 (452)
T TIGR02958        77 LVPA   80 (452)
T ss_pred             EeeC
Confidence            9864

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.

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=91.87  E-value=1.6  Score=25.49  Aligned_cols=62  Identities=18%  Similarity=0.153  Sum_probs=42.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|   +|+.+.+  .+..|+.+|-..    .++++...-+-+++.      ++..+.- ..+ +++||.|.++...
T Consensus         1 m~i~v---NG~~~~~--~~~~tl~~ll~~----l~~~~~~vav~~N~~------iv~r~~~-~~~-L~~gD~ieIv~~V   62 (65)
T PRK05863          1 MIVVV---NEEQVEV--DEQTTVAALLDS----LGFPEKGIAVAVDWS------VLPRSDW-ATK-LRDGARLEVVTAV   62 (65)
T ss_pred             CEEEE---CCEEEEc--CCCCcHHHHHHH----cCCCCCcEEEEECCc------CcChhHh-hhh-cCCCCEEEEEeec
Confidence            45554   3555444  466788887654    578888888899998      7754432 345 8999999998644

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=91.61  E-value=1.6  Score=25.15  Aligned_cols=63  Identities=14%  Similarity=0.245  Sum_probs=42.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|++.   |+.  .++....|+.++-..    .++++..--+-.+|.      .+..+. ..+.-+++||.|.++...
T Consensus         1 m~i~vN---G~~--~~~~~~~tl~~lL~~----l~~~~~~vav~vNg~------iv~r~~-~~~~~l~~gD~vei~~~v   63 (66)
T PRK05659          1 MNIQLN---GEP--RELPDGESVAALLAR----EGLAGRRVAVEVNGE------IVPRSQ-HASTALREGDVVEIVHAL   63 (66)
T ss_pred             CEEEEC---CeE--EEcCCCCCHHHHHHh----cCCCCCeEEEEECCe------EeCHHH-cCcccCCCCCEEEEEEEe
Confidence            555543   454  455667888887754    578888888888987      665332 335557999999988644

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

Probab=90.99  E-value=2.2  Score=25.50  Aligned_cols=46  Identities=17%  Similarity=0.150  Sum_probs=37.8

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      +.|...+|+...+.+.+..|+.|.-..+-++.|+.++.-.+...|.
T Consensus         3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~   48 (71)
T PF02196_consen    3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGE   48 (71)
T ss_dssp             EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEE
T ss_pred             EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCC
Confidence            5678889999999999999999999999999999999887765554

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.

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

Probab=90.71  E-value=0.94  Score=26.56  Aligned_cols=62  Identities=21%  Similarity=0.192  Sum_probs=46.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcCC--CCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108           12 LFYIQVENDATVADLKREIGAQQKL--PCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~gi--p~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      ...+.+....||.+|.+.+.....-  ....-.+..+|.      ...+  ...+.-+++||.|.++-...|
T Consensus        13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~------~v~~--~~~~~~l~~gD~V~i~ppvsG   76 (77)
T PF02597_consen   13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGE------IVPD--DGLDTPLKDGDEVAILPPVSG   76 (77)
T ss_dssp             EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTE------EEGG--GTTTSBEETTEEEEEEESTST
T ss_pred             CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCE------EcCC--ccCCcCcCCCCEEEEECCCCC
Confidence            5678888999999999999887631  225567788888      7776  345666789999999865443

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 ....

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=90.57  E-value=2.4  Score=25.78  Aligned_cols=61  Identities=23%  Similarity=0.231  Sum_probs=40.4

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhcCC------C-----CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           11 TLFYIQVENDATVADLKREIGAQQKL------P-----CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~gi------p-----~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      ....++++ ..|+.+|.+.+.+++.-      +     -....+..++.      ..+.+..   ..+++|+.|.++-..
T Consensus        16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~------~v~~~~~---~~l~dgdev~i~Ppv   85 (88)
T TIGR01687        16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGR------NVDWGLG---TELKDGDVVAIFPPV   85 (88)
T ss_pred             ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCE------ecCccCC---CCCCCCCEEEEeCCC
Confidence            34567776 89999999999988641      0     01245667776      5443321   567899999998654


Q ss_pred             CC
Q 041108           80 LD   81 (102)
Q Consensus        80 ~~   81 (102)
                      .|
T Consensus        86 sG   87 (88)
T TIGR01687        86 SG   87 (88)
T ss_pred             cC
Confidence            43

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.

>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=90.20  E-value=2.5  Score=24.95  Aligned_cols=46  Identities=20%  Similarity=0.240  Sum_probs=35.9

Q ss_pred             EEEEEeCCCcEEEEEec-CCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            2 KVAVEILTGTLFYIQVE-NDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~-~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      +|.++.. |..+.+.+. ...|..+|+.+|....+.+.....+.|...
T Consensus         2 ~vK~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~   48 (81)
T cd05992           2 RVKVKYG-GEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDE   48 (81)
T ss_pred             cEEEEec-CCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCC
Confidence            3455554 567888888 899999999999999998876667766654

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.

>PRK08053 sulfur carrier protein ThiS; Provisional

Probab=89.93  E-value=2.6  Score=24.57  Aligned_cols=64  Identities=20%  Similarity=0.188  Sum_probs=41.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+++|.   |+.+  ++....|+.+|.+.+    +++.....+-.++.      .+.. ...++.-+++||.|.++-...
T Consensus         1 m~i~vN---g~~~--~~~~~~tl~~ll~~l----~~~~~~vaVavN~~------iv~r-~~w~~~~L~~gD~Ieii~~v~   64 (66)
T PRK08053          1 MQILFN---DQPM--QCAAGQTVHELLEQL----NQLQPGAALAINQQ------IIPR-EQWAQHIVQDGDQILLFQVIA   64 (66)
T ss_pred             CEEEEC---CeEE--EcCCCCCHHHHHHHc----CCCCCcEEEEECCE------EeCh-HHcCccccCCCCEEEEEEEcc
Confidence            555554   4544  445678999988653    45555566777887      6632 224455689999999886543

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

Probab=89.69  E-value=1.7  Score=29.05  Aligned_cols=63  Identities=27%  Similarity=0.326  Sum_probs=42.0

Q ss_pred             EecC-CCcHHHHHHHHHhh----cCCCCc------cEEEEeCCCCCCCCc-----------cC---CCCCccccCCCCCC
Q 041108           16 QVEN-DATVADLKREIGAQ----QKLPCD------RLILLLSSDHSCPMT-----------QD---HDEVPLADCGVKDG   70 (102)
Q Consensus        16 ~v~~-~~TV~dLK~~I~~~----~gip~~------~q~L~~~g~~~~~~~-----------~L---~d~~~L~~~gI~~~   70 (102)
                      .|+. +.|+.||++.+.+.    .|++|-      ..+|++..-++-.++           +|   +++.+|.++||.+.
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            4676 88999998877765    445553      366665332111111           34   66788999999999


Q ss_pred             CEEEEEee
Q 041108           71 SHIYLFFK   78 (102)
Q Consensus        71 ~~i~l~~~   78 (102)
                      +.|.++..
T Consensus       101 TEiSfF~~  108 (122)
T PF10209_consen  101 TEISFFNM  108 (122)
T ss_pred             ceeeeeCH
Confidence            99988743

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=88.83  E-value=2.4  Score=24.52  Aligned_cols=56  Identities=23%  Similarity=0.240  Sum_probs=39.3

Q ss_pred             EEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108           15 IQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        15 i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      ++++...|+.+|.+.+    ++++....+..+|.      ....+ ...+.-+++||.|.++-...|
T Consensus         9 ~~~~~~~tv~~ll~~l----~~~~~~i~V~vNg~------~v~~~-~~~~~~L~~gD~V~ii~~v~G   64 (65)
T cd00565           9 REVEEGATLAELLEEL----GLDPRGVAVALNGE------IVPRS-EWASTPLQDGDRIEIVTAVGG   64 (65)
T ss_pred             EEcCCCCCHHHHHHHc----CCCCCcEEEEECCE------EcCHH-HcCceecCCCCEEEEEEeccC
Confidence            4455678999988765    47777778888998      66443 233455899999999865443

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.

>cd06397 PB1_UP1 Uncharacterized protein 1

Probab=88.79  E-value=4.1  Score=25.39  Aligned_cols=46  Identities=13%  Similarity=0.081  Sum_probs=37.0

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      +..++. +|.++.+.++.+-|.+.|+++|...+.+|+...-+.|-..
T Consensus         2 ~fKv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDe   47 (82)
T cd06397           2 QFKSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDN   47 (82)
T ss_pred             eEEEEe-CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcC
Confidence            344544 4677888888889999999999999999998877777554

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.

>PRK06944 sulfur carrier protein ThiS; Provisional

Probab=88.77  E-value=3  Score=23.85  Aligned_cols=63  Identities=17%  Similarity=0.184  Sum_probs=39.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+   |+  .+++.+..|+.+|.+.+.    ++ ....+..+|.      ....+. ..+.-+++||.|.++....
T Consensus         1 m~i~vN---g~--~~~~~~~~tl~~ll~~l~----~~-~~~~v~vN~~------~v~~~~-~~~~~L~~gD~vei~~~v~   63 (65)
T PRK06944          1 MDIQLN---QQ--TLSLPDGATVADALAAYG----AR-PPFAVAVNGD------FVARTQ-HAARALAAGDRLDLVQPVA   63 (65)
T ss_pred             CEEEEC---CE--EEECCCCCcHHHHHHhhC----CC-CCeEEEECCE------EcCchh-cccccCCCCCEEEEEeecc
Confidence            455553   44  445566789999887653    33 2345677887      554322 3344478999999986543

>cd06410 PB1_UP2 Uncharacterized protein 2

Probab=88.23  E-value=2.8  Score=26.73  Aligned_cols=44  Identities=11%  Similarity=0.154  Sum_probs=35.1

Q ss_pred             EEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEeCCC
Q 041108            5 VEILTGTLFYIQVENDATVADLKREIGAQQKLPCD-RLILLLSSD   48 (102)
Q Consensus         5 V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~~g~   48 (102)
                      ++..+|.+..+.|+.+.|..+|+.++.+..++... ..+..+.+.
T Consensus        17 l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~~~lky~Lp~e   61 (97)
T cd06410          17 LRYVGGETRIVSVDRSISFKELVSKLSELFGAGVVVTLKYQLPDE   61 (97)
T ss_pred             EEEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCceEEEEEcCCC
Confidence            46677899999999999999999999999998875 233334444

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.

>PRK06083 sulfur carrier protein ThiS; Provisional

Probab=87.31  E-value=3.9  Score=25.35  Aligned_cols=54  Identities=19%  Similarity=0.223  Sum_probs=38.6

Q ss_pred             EEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           15 IQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        15 i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .+++...|+.+|-+.    .++++..--+-.+|.      ++ +.....+.-+++||.|.++.-.
T Consensus        28 ~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~------iV-pr~~w~~t~L~egD~IEIv~~V   81 (84)
T PRK06083         28 IQVDISSSLAQIIAQ----LSLPELGCVFAINNQ------VV-PRSEWQSTVLSSGDAISLFQAI   81 (84)
T ss_pred             EEcCCCCcHHHHHHH----cCCCCceEEEEECCE------Ee-CHHHcCcccCCCCCEEEEEEEe
Confidence            444566788887764    467777777788887      76 3344667778999999988644

>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=86.49  E-value=3.9  Score=24.87  Aligned_cols=62  Identities=18%  Similarity=0.201  Sum_probs=40.5

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhcC-CCCccEEEEe------CCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           11 TLFYIQVENDATVADLKREIGAQQK-LPCDRLILLL------SSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~g-ip~~~q~L~~------~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      +.|..-..++.|+++|+..|.+++. +.|....+..      .|.      -|+.+-..++. ..+|+++.++++.
T Consensus         3 kKFLhlt~~~~tl~~L~~eI~~~f~kLYP~~~~~~I~~LQD~~~c------DLD~d~~V~DV-f~~~~~vrvi~~n   71 (73)
T PF10407_consen    3 KKFLHLTDPNNTLSQLKEEIEERFKKLYPNEPELEILSLQDSDGC------DLDPDFLVKDV-FNSNNVVRVILKN   71 (73)
T ss_pred             cEEEEEeCCCCcHHHHHHHHHHHHHHHCCCCCCceEEEeecCCCC------CCCcccEeeee-eccCCEEEEEecC
Confidence            3455567889999999999999876 4555433321      233      45555555554 3467888887754

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 [].

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

Probab=86.24  E-value=3.1  Score=31.56  Aligned_cols=74  Identities=12%  Similarity=0.151  Sum_probs=54.1

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      .+.||..+|++...++.+..|+.++...+.-..+...+--.++.+-. --.-+.-+..++|..+++-+.+++.+.
T Consensus       212 rlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~t~fP-R~tf~edD~~KpLq~L~L~Psa~lil~  285 (290)
T KOG2689|consen  212 RLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHTGFP-RVTFTEDDELKPLQELDLVPSAVLILE  285 (290)
T ss_pred             EEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeecCCC-ceecccccccccHHHhccccchheecc
Confidence            47899999999999999999999999999999887665444443322 000001144588999999888877654

>TIGR01683 thiS thiamine biosynthesis protein ThiS

Probab=86.18  E-value=4.7  Score=23.21  Aligned_cols=60  Identities=20%  Similarity=0.202  Sum_probs=40.2

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      +|+.+  ++....|+.+|.+.+    ++++....+..++.      .+..+. ..++-+++||.|.++....|
T Consensus         4 Ng~~~--~~~~~~tv~~ll~~l----~~~~~~v~v~vN~~------iv~~~~-~~~~~L~~gD~veii~~V~G   63 (64)
T TIGR01683         4 NGEPV--EVEDGLTLAALLESL----GLDPRRVAVAVNGE------IVPRSE-WDDTILKEGDRIEIVTFVGG   63 (64)
T ss_pred             CCeEE--EcCCCCcHHHHHHHc----CCCCCeEEEEECCE------EcCHHH-cCceecCCCCEEEEEEeccC
Confidence            45544  445677899988754    56777777788887      663322 33456899999999865433

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.

>PRK01777 hypothetical protein; Validated

Probab=86.03  E-value=5.3  Score=25.34  Aligned_cols=67  Identities=19%  Similarity=0.152  Sum_probs=43.7

Q ss_pred             CEEEEEeCC-C--cEEEEEecCCCcHHHHHHHHHhhcCCCCc-------cEEEEeCCCCCCCCccCCCCCccccCCCCCC
Q 041108            1 MKVAVEILT-G--TLFYIQVENDATVADLKREIGAQQKLPCD-------RLILLLSSDHSCPMTQDHDEVPLADCGVKDG   70 (102)
Q Consensus         1 M~v~V~~~~-g--~~~~i~v~~~~TV~dLK~~I~~~~gip~~-------~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~   70 (102)
                      |+|.|.... .  ....+++....||.|+-.+.    |++..       .-.+..+|+      ....     +.-+++|
T Consensus         4 i~v~V~ya~~~~~~~~~l~vp~GtTv~dal~~s----gi~~~~pei~~~~~~vgI~Gk------~v~~-----d~~L~dG   68 (95)
T PRK01777          4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRAS----GLLELRTDIDLAKNKVGIYSR------PAKL-----TDVLRDG   68 (95)
T ss_pred             eEEEEEEECCCceEEEEEEcCCCCcHHHHHHHc----CCCccCcccccccceEEEeCe------ECCC-----CCcCCCC
Confidence            566666543 2  23568899999999977654    44433       235666776      4433     3456899


Q ss_pred             CEEEEEeecCCC
Q 041108           71 SHIYLFFKPLDD   82 (102)
Q Consensus        71 ~~i~l~~~~~~~   82 (102)
                      |.|.++-.+.-+
T Consensus        69 DRVeIyrPL~~D   80 (95)
T PRK01777         69 DRVEIYRPLLAD   80 (95)
T ss_pred             CEEEEecCCCCC
Confidence            999999765443

>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=85.76  E-value=0.24  Score=37.88  Aligned_cols=41  Identities=27%  Similarity=0.419  Sum_probs=0.0

Q ss_pred             CCcHHHHHHHHHh----------hcCCCCccEE-----EEeCCCCCCCCccCCCCCccccCC
Q 041108           20 DATVADLKREIGA----------QQKLPCDRLI-----LLLSSDHSCPMTQDHDEVPLADCG   66 (102)
Q Consensus        20 ~~TV~dLK~~I~~----------~~gip~~~q~-----L~~~g~~~~~~~~L~d~~~L~~~g   66 (102)
                      +.+|.|+|.+++.          ++++|.+..+     |+|+-+      .+.|+++|.+..
T Consensus       103 ttSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kk------Pv~~~ktl~e~l  158 (309)
T PF12754_consen  103 TTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKK------PVGDSKTLAEVL  158 (309)
T ss_dssp             --------------------------------------------------------------
T ss_pred             cCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCc------cCCCcCcHHHHH
Confidence            4789999999999          8999999999     999998      667777777653

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.

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

Probab=85.27  E-value=3.2  Score=25.63  Aligned_cols=37  Identities=14%  Similarity=0.113  Sum_probs=33.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108           12 LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      ++.+.+.+..+.++|..+|+++.+.+++.-+|.|...
T Consensus         8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~   44 (78)
T cd06411           8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAP   44 (78)
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCC
Confidence            4668899999999999999999999999999999776

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

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

Probab=85.17  E-value=4.1  Score=25.56  Aligned_cols=39  Identities=18%  Similarity=0.117  Sum_probs=33.5

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccE
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRL   41 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q   41 (102)
                      |.|-..+|+...+.|+..+|+.|+-+.+..+.+...+.-
T Consensus         5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~   43 (85)
T cd01787           5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSS   43 (85)
T ss_pred             EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCC
Confidence            456677899999999999999999999999998765544

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.

>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor

Probab=84.61  E-value=3.5  Score=25.41  Aligned_cols=40  Identities=13%  Similarity=0.038  Sum_probs=36.0

Q ss_pred             EEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEE
Q 041108            4 AVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLIL   43 (102)
Q Consensus         4 ~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L   43 (102)
                      .|...+|+...+.+.+++|+.|+-+...+..+++|++-.|
T Consensus         3 ~V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~L   42 (77)
T cd01818           3 WVCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYL   42 (77)
T ss_pred             EEECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHhee
Confidence            4677889999999999999999999999999999998655

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.

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

Probab=84.13  E-value=8.2  Score=24.26  Aligned_cols=40  Identities=20%  Similarity=0.232  Sum_probs=31.3

Q ss_pred             CCcEEEEEecC-----CCcHHHHHHHHHhhcCCCC-ccEEEEeCCC
Q 041108            9 TGTLFYIQVEN-----DATVADLKREIGAQQKLPC-DRLILLLSSD   48 (102)
Q Consensus         9 ~g~~~~i~v~~-----~~TV~dLK~~I~~~~gip~-~~q~L~~~g~   48 (102)
                      +|..+.+.+..     +.+..+|+.+|.+.+++++ ....|.|...
T Consensus         8 ~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~De   53 (91)
T cd06398           8 GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDE   53 (91)
T ss_pred             CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECC
Confidence            45667777774     7999999999999999988 4556666554

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

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

Probab=84.03  E-value=6.9  Score=30.31  Aligned_cols=68  Identities=15%  Similarity=0.167  Sum_probs=48.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+   |+.  +++....|+.||-+.    .++++....+..+|.      ++.. ....++-+++||.|.++.-..
T Consensus         1 M~I~VN---Gk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNge------IVpr-~~w~~t~LkeGD~IEII~~Vg   64 (326)
T PRK11840          1 MRIRLN---GEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLE------IVPR-SEYGQVALEEGDELEIVHFVG   64 (326)
T ss_pred             CEEEEC---CEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCE------ECCH-HHcCccccCCCCEEEEEEEec
Confidence            555554   454  455667788887754    578888888889998      7743 335567789999999997766


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      |++.
T Consensus        65 GGs~   68 (326)
T PRK11840         65 GGSD   68 (326)
T ss_pred             CCCC
Confidence            6544

>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=84.00  E-value=5.2  Score=24.82  Aligned_cols=29  Identities=17%  Similarity=0.155  Sum_probs=26.0

Q ss_pred             CCcEEEEEecC--CCcHHHHHHHHHhhcCCC
Q 041108            9 TGTLFYIQVEN--DATVADLKREIGAQQKLP   37 (102)
Q Consensus         9 ~g~~~~i~v~~--~~TV~dLK~~I~~~~gip   37 (102)
                      +|.+..+.+++  ..+..+|++.|+..++++
T Consensus         8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~   38 (81)
T cd06396           8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN   38 (81)
T ss_pred             CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC
Confidence            46788888888  779999999999999999

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.

>PRK07440 hypothetical protein; Provisional

Probab=82.61  E-value=7.9  Score=22.95  Aligned_cols=59  Identities=12%  Similarity=0.081  Sum_probs=40.5

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      +|+.  .++....|+.+|-+    ..++++...-+-.++.      ++.. ....+.-+++||.|.++--..
T Consensus        10 NG~~--~~~~~~~tl~~lL~----~l~~~~~~vav~~N~~------iv~r-~~w~~~~L~~gD~IEIv~~v~   68 (70)
T PRK07440         10 NGET--RTCSSGTSLPDLLQ----QLGFNPRLVAVEYNGE------ILHR-QFWEQTQVQPGDRLEIVTIVG   68 (70)
T ss_pred             CCEE--EEcCCCCCHHHHHH----HcCCCCCeEEEEECCE------EeCH-HHcCceecCCCCEEEEEEEec
Confidence            4554  55566789998775    4567777777788887      6642 234566689999999886443

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

Probab=82.13  E-value=8.3  Score=23.21  Aligned_cols=65  Identities=17%  Similarity=0.231  Sum_probs=46.1

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcC---CCCccEEEE-eCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQK---LPCDRLILL-LSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~g---ip~~~q~L~-~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      +|+...++....+.+--..++--+.+|   -|++.=.+- -+|.      +++-++.+++||+.+|.++.+.++.
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~------vlD~~kKveD~GftngvkLFLsLKA   72 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQ------VLDVNKKVEDFGFTNGVKLFLSLKA   72 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCc------EeeccchhhhccccccceEEEEeec
Confidence            577778888887776666655444444   355543332 3455      8899999999999999999988763

>PTZ00380 microtubule-associated protein (MAP); Provisional

Probab=81.94  E-value=3.9  Score=27.26  Aligned_cols=63  Identities=17%  Similarity=0.368  Sum_probs=45.8

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCcccc----CCCCCCCEEEEEeecC
Q 041108           11 TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLAD----CGVKDGSHIYLFFKPL   80 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~----~gI~~~~~i~l~~~~~   80 (102)
                      +...+-|..+.||+++...|..+.+++++..-|+.++.      +...+.++++    +.- ++..+++.....
T Consensus        41 K~KfllVP~d~tV~qF~~iIRkrl~l~~~k~flfVnn~------lp~~s~~mg~lYe~~KD-eDGFLYi~Ys~e  107 (121)
T PTZ00380         41 KVHFLALPRDATVAELEAAVRQALGTSAKKVTLAIEGS------TPAVTATVGDIADACKR-DDGFLYVSVRTE  107 (121)
T ss_pred             ceEEEEcCCCCcHHHHHHHHHHHcCCChhHEEEEECCc------cCCccchHHHHHHHhcC-CCCeEEEEEccc
Confidence            33445799999999999999999999999854555665      5566666654    332 477888887653

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=81.49  E-value=7.8  Score=23.84  Aligned_cols=53  Identities=25%  Similarity=0.337  Sum_probs=38.5

Q ss_pred             CcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEE-EeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108           10 GTLFYIQVENDATVADLKREIGAQQKLPCDRLIL-LLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus        10 g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L-~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +..+...++..+||.|+-+    ..|+|..+-.+ +.+|+      ..+-     ++-+++|+.|.++-
T Consensus        22 ~~~~~~~~~~~~tvkd~IE----sLGVP~tEV~~i~vNG~------~v~~-----~~~~~~Gd~v~V~P   75 (81)
T PF14451_consen   22 GGPFTHPFDGGATVKDVIE----SLGVPHTEVGLILVNGR------PVDF-----DYRLKDGDRVAVYP   75 (81)
T ss_pred             CCceEEecCCCCcHHHHHH----HcCCChHHeEEEEECCE------ECCC-----cccCCCCCEEEEEe
Confidence            3456788889999988764    47999998865 45777      3322     46678999998874

>PRK11130 moaD molybdopterin synthase small subunit; Provisional

Probab=80.74  E-value=9.9  Score=22.86  Aligned_cols=56  Identities=16%  Similarity=0.238  Sum_probs=34.6

Q ss_pred             EEecC-CCcHHHHHHHHHhhcC-----CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108           15 IQVEN-DATVADLKREIGAQQK-----LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        15 i~v~~-~~TV~dLK~~I~~~~g-----ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      ++++. ..||.+|++.+.+++.     ......++..++.      ...+     +.-+++||.|.++-...|
T Consensus        19 ~~v~~~~~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~------~~~~-----~~~l~dgDeVai~PPVsG   80 (81)
T PRK11130         19 LELAADFPTVEALRQHLAQKGDRWALALEDGKLLAAVNQT------LVSF-----DHPLTDGDEVAFFPPVTG   80 (81)
T ss_pred             EEecCCCCCHHHHHHHHHHhCccHHhhhcCCCEEEEECCE------EcCC-----CCCCCCCCEEEEeCCCCC
Confidence            44443 4799999999988762     1122234444554      3322     334789999998865443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	102
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	7e-10
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	2e-09
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	2e-09
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	4e-09
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	4e-09
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	6e-09
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	8e-09
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	2e-08
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	2e-08
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-08
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	3e-08
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	4e-08
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	5e-08
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	5e-08
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	6e-08
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	2e-07
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	2e-07
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	2e-07
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	3e-07
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	4e-07
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	5e-07
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	5e-07
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	5e-07
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	7e-07
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	9e-07
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	2e-06
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	2e-06
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	2e-06
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	2e-06
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	2e-06
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	3e-06
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-06
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	4e-06
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	4e-06
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	6e-06
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	6e-06
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	3e-04
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	7e-06
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	7e-06
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	1e-05
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	1e-05
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	2e-05
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	3e-05
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	3e-05
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	9e-05
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	1e-04
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	2e-04
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	4e-04
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	4e-04
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	5e-04
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	5e-04
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	6e-04

>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 = 50.9 bits (122), Expect = 7e-10
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + +  +        + +E   T+ + K ++         ++ L+ S           D  
Sbjct: 2  VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSG------KVLQDSK 55

Query: 61 PLADCGVKDGSHIYL 75
           +++CG+KDG  +  
Sbjct: 56 TVSECGLKDGDQVVF 70

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

 Score = 49.2 bits (118), Expect = 2e-09
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          MK  VE L G+ F ++V+   T+  +K++I   Q +P  +  L++            +++
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILR-----EDL 65

Query: 61 PLADCGVKDGSHIYLF 76
           +  C +   S I L 
Sbjct: 66 TVEQCQIVPTSDIQLE 81

>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 = 50.2 bits (120), Expect = 2e-09
 Identities = 5/77 (6%), Positives = 11/77 (14%), Gaps = 10/77 (12%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLILLLSSDHSCPMTQDHD 58
          M      +     +  VE    V          Q+   +                  +  
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFN------KWSFEEVEVK 54

Query: 59 EVPLADCGVKDGSHIYL 75
              +            
Sbjct: 55 --DASLVDYVQVRQPIF 69

>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 = 51.1 bits (121), Expect = 4e-09
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 9/103 (8%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQ---KLPCDRLILLLSSDHSCPMTQDH 57
           + + ++ L    F I++E D TV  LK +I A++     P     L+ +           
Sbjct: 8   VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAG------KILS 61

Query: 58  DEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNT 100
           D+VP+ D  + + + + +       G    +         P +
Sbjct: 62  DDVPIRDYRIDEKNFVVVMVTKTKAGQGTSAPPEASPTAAPES 104

>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 = 48.1 bits (115), Expect = 4e-09
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M + V+ LTG    I +E    V  +K  +  ++ +P  +  L+ S        Q +DE 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG------KQMNDEK 54

Query: 61 PLADCGVKDGSHIYL 75
            AD  +  GS ++L
Sbjct: 55 TAADYKILGGSVLHL 69

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 47.7 bits (114), Expect = 6e-09
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ L G    ++VE   T+ ++K +I  ++ +P D+  L+ +        Q  D  
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG------KQLEDGR 57

Query: 61 PLADCGVKDGSHIYL 75
           L+D  + + S +YL
Sbjct: 58 TLSDYNIHNHSALYL 72

>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 = 47.4 bits (113), Expect = 8e-09
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +        Q  D  
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG------KQLEDGR 57

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 58 TLSDYNIQKWSTLFL 72

>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 = 46.5 bits (111), Expect = 2e-08
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M + V+ LTG    I +E    V  +K  +  ++ +P  +  L+ S        Q +DE 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG------KQMNDEK 54

Query: 61 PLADCGVKDGSHIYL 75
            AD  +  GS ++L
Sbjct: 55 TAADYKILGGSVLHL 69

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

 Score = 47.0 bits (112), Expect = 2e-08
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 14/85 (16%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLS----SDHSCPMTQD 56
          + V V+  +   F ++V+   TV+ LK +I   +  P  R+ L  S    +D        
Sbjct: 16 IHVTVKFPSKQ-FTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELAD-------- 66

Query: 57 HDEVPLADCGVKDGSHIYLFFKPLD 81
           D   L + G+ + S I +F K ++
Sbjct: 67 -DYRNLNEYGITEFSEIVVFLKSIN 90

>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 = 46.1 bits (110), Expect = 2e-08
 Identities = 15/75 (20%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M V V   +   F ++V++D ++  LK  +  QQ +P D+L ++ +        +  + +
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAG------KELPNHL 54

Query: 61 PLADCGVKDGSHIYL 75
           + +C ++  S +++
Sbjct: 55 TVQNCDLEQQSIVHI 69

>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 = 45.8 bits (109), Expect = 3e-08
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M + V+ LTG    I +E    V  +K  +  ++ +P  +  L+ S          +DE 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQM------NDEK 66

Query: 61 PLADCGVKDGSHIYL 75
            AD  +  GS ++L
Sbjct: 67 TAADYKILGGSVLHL 81

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score = 45.4 bits (108), Expect = 4e-08
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 10/82 (12%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLILLLSSDHSCPMTQDHD 58
          M++ V+ L G    +QV  D  V+ LK+ +  +  +P    RL+             D  
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLL------FKGKALADGK 61

Query: 59 EVPLADCGVKDGSHIYLFFKPL 80
             L+D  +   S + L  KPL
Sbjct: 62 --RLSDYSIGPNSKLNLVVKPL 81

>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 = 45.5 bits (108), Expect = 5e-08
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          ++V V+   G  +   +  ++ +  LK++I  QQ LP  +  L              D +
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVL------QDWL 61

Query: 61 PLADCGVKDGSHIYL 75
           L   G++D   + L
Sbjct: 62 GLGIYGIQDSDTLIL 76

>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 = 45.0 bits (107), Expect = 5e-08
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL------EDGR 54

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 55 TLSDYNIQRESTLHL 69

>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 = 45.5 bits (108), Expect = 6e-08
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + + V    G     +V    TVA LK+++   + +  D   L              D++
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEG------KPLEDQL 58

Query: 61 PLADCGVKDGSHIYL 75
          PL + G+K  S +++
Sbjct: 59 PLGEYGLKPLSTVFM 73

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

 Score = 44.4 bits (105), Expect = 2e-07
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL------EDGR 54

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 55 TLSDYNIQKESTLHL 69

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

 Score = 44.5 bits (105), Expect = 2e-07
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL------EDGR 89

Query: 61  PLADCGVKDGSHIYL 75
            L+D  ++  S ++L
Sbjct: 90  TLSDYNIQKESTLHL 104

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

 Score = 44.4 bits (105), Expect = 2e-07
 Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           ++  + LTG    ++VE+  T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQL------EDGR 63

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 64 TLSDYNIQRESTLHL 78

>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 = 43.6 bits (103), Expect = 3e-07
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL------EDGR 55

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 56 TLSDYNIQKESTLHL 70

>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 = 43.1 bits (102), Expect = 4e-07
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          ++V+V+          +  ++ V   K++I        DRL+L+ +           D+ 
Sbjct: 18 IRVSVKTPQDC-HEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTG------KILRDQD 70

Query: 61 PLADCGVKDGSHIYLFFKP 79
           L+  G+ DGS +++  + 
Sbjct: 71 ILSQRGILDGSTVHVVVRS 89

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 42.8 bits (101), Expect = 5e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + + V    G     +V    TVA LK+++   + +  D   L              D++
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLT------FEGKPLEDQL 58

Query: 61 PLADCGVKDGSHIYL 75
          PL + G+K  S +++
Sbjct: 59 PLGEYGLKPLSTVFM 73

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 43.2 bits (102), Expect = 5e-07
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 7  ILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCG 66
          +    L   +V    TVA +K  + + + +  +  ++LL+           DE  L  CG
Sbjct: 24 VRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG------APLEDEATLGQCG 77

Query: 67 VKDGSHIYL 75
          V+  + + +
Sbjct: 78 VEALTTLEV 86

>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 = 42.6 bits (101), Expect = 5e-07
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQ---KLPCDRLILLLSSDHSCPMTQDH 57
          + + ++ L    F I++E D TV  LK +I A++     P     L+ +           
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAG------KILS 59

Query: 58 DEVPLADCGVKDGSHIYL 75
          D+VP+ D  + + + + +
Sbjct: 60 DDVPIRDYRIDEKNFVVV 77

>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 = 43.8 bits (103), Expect = 7e-07
 Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 7/101 (6%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           M++ V+ LTG    ++VE+  T+ ++K +I  ++ +P D+  L+ +        Q  D  
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFA------GKQLEDGR 54

Query: 61  PLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIPEWLNPNTL 101
            L+D  ++  S ++L  + L  G  +   F     +   ++
Sbjct: 55  TLSDYNIQKESTLHLVLR-LRGGGGETIKFVADGDIGSGSV 94

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 42.3 bits (100), Expect = 9e-07
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          +++ ++ LTG  F +++E   T+ +LK +I  ++ +P D+  L+ +           D  
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQL------EDGR 63

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 64 TLSDYNIQKESTLHL 78

>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 = 41.0 bits (97), Expect = 2e-06
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 7/76 (9%)

Query: 1  MKVAVEILTGTL-FYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDE 59
          M + + I +G   + + V  ++TV   K  I     +P     L+ S           D+
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSG------KILKDD 56

Query: 60 VPLADCGVKDGSHIYL 75
            +    ++DG  ++L
Sbjct: 57 QTVESYHIQDGHSVHL 72

>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 = 41.2 bits (97), Expect = 2e-06
 Identities = 16/77 (20%), Positives = 24/77 (31%), Gaps = 8/77 (10%)

Query: 1  MKVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHD 58
          M + V  + G  T     +     V +L+R+I     +      L           Q  D
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRG------KQMED 56

Query: 59 EVPLADCGVKDGSHIYL 75
             L D  V+    I L
Sbjct: 57 GHTLFDYEVRLNDTIQL 73

>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 = 41.1 bits (97), Expect = 2e-06
 Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 7/75 (9%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          +K+ V    G    + V  D TV DLK ++     +      L+             +  
Sbjct: 13 IKLTV-KFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKG------KVLVETS 65

Query: 61 PLADCGVKDGSHIYL 75
           L    V  G+ + L
Sbjct: 66 TLKQSDVGSGAKLML 80

>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 = 41.6 bits (98), Expect = 2e-06
 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           ++ + + TG    + V +  TV  +KR + A + +         S           D++
Sbjct: 24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSG------RPLTDKM 77

Query: 61 PLADCGVKDGSHIYL 75
             +  +     + +
Sbjct: 78 KFEELKIPKDYVVQV 92

>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 = 41.6 bits (98), Expect = 2e-06
 Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 7/93 (7%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           +KV V+          V +  T+  LK EI  + K   D+L+L+ +           D  
Sbjct: 18  IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAG------KILKDPD 70

Query: 61  PLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIP 93
            LA CGV+DG  ++L  K            + P
Sbjct: 71  SLAQCGVRDGLTVHLVIKRQHRAMGNECPASGP 103

>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 = 41.2 bits (97), Expect = 3e-06
 Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          +KV V+          V +  T+  LK EI  + K   D+L+L+ +           D  
Sbjct: 23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAG------KILKDPD 75

Query: 61 PLADCGVKDGSHIYLFFKP 79
           LA CGV+DG  ++L  K 
Sbjct: 76 SLAQCGVRDGLTVHLVIKR 94

>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 = 40.8 bits (96), Expect = 3e-06
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 9/78 (11%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQ---KLPCDRLILLLSSDHSCPMTQDH 57
          M+V ++ L    F I ++ + TV  LK +I +++     P     L+ +          +
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAG------KILN 54

Query: 58 DEVPLADCGVKDGSHIYL 75
          D+  L +  + + + + +
Sbjct: 55 DDTALKEYKIDEKNFVVV 72

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

 Score = 40.8 bits (96), Expect = 4e-06
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 7/76 (9%)

Query: 1  MKVAVEILTGTL-FYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDE 59
          M + + I +G   + + V  ++TV   K  I     +P     L+ S           D+
Sbjct: 27 MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSG------KILKDD 80

Query: 60 VPLADCGVKDGSHIYL 75
            +    ++DG  ++L
Sbjct: 81 QTVESYHIQDGHSVHL 96

>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 = 40.5 bits (95), Expect = 4e-06
 Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 12/79 (15%)

Query: 1  MKVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCD--RLILLLSSDHSCPMTQD 56
          M + V  + G  T     V   AT+ +L+  + A   +  +  RL           +   
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFY-----RGKQL--- 59

Query: 57 HDEVPLADCGVKDGSHIYL 75
           +   L D  V     I L
Sbjct: 60 ENGYTLFDYDVGLNDIIQL 78

>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 = 40.4 bits (94), Expect = 6e-06
 Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 9/97 (9%)

Query: 1  MKVAVEI----LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD 56
          M + V      LT   F +QV  D  +++ +     +  +P +   ++            
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYME-----QLLT 62

Query: 57 HDEVPLADCGVKDGSHIYLFFKPLDDGSTQHSVFTIP 93
           D   L   G+KDG  + L  K      T     + P
Sbjct: 63 DDHCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSGP 99

>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 = 41.5 bits (97), Expect = 6e-06
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 8/103 (7%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
             + V++L G  F + + +  +V++LK +I  +  +   +  L +            D V
Sbjct: 3   WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVAL----QDRV 58

Query: 61  PLADCGVKDGSHIYLFFKPLDDGS----TQHSVFTIPEWLNPN 99
           PLA  G+  GS + L     D+        +   +    +   
Sbjct: 59  PLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLT 101

>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 = 36.5 bits (84), Expect = 3e-04
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           + + V    G     +V    TVA LK+++   + +  D   L              D++
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLT------FEGKPLEDQL 135

Query: 61  PLADCGVKDGSHIYL 75
           PL + G+K  S +++
Sbjct: 136 PLGEYGLKPLSTVFM 150

>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 = 40.1 bits (94), Expect = 7e-06
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 7/66 (10%)

Query: 10 GTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKD 69
           T   ++V  D+T ++LK++I +   LP     ++             ++  L +  V  
Sbjct: 26 KTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKG-------LVPEDKTLREIKVTS 78

Query: 70 GSHIYL 75
          G+ I +
Sbjct: 79 GAKIMV 84

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

 Score = 41.6 bits (97), Expect = 7e-06
 Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 2/44 (4%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLI 42
          M+V V+ L G      +E   +V DLK +I        D   L+
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLV 44

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

 Score = 39.7 bits (93), Expect = 1e-05
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          MKV V+          V  +++V   K EI  + K   D+L+L+ +           D+ 
Sbjct: 26 MKVTVKTPKEK-EEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAG------KILKDQD 78

Query: 61 PLADCGVKDGSHIYLFFKP 79
           L+  G+ DG  ++L  K 
Sbjct: 79 TLSQHGIHDGLTVHLVIKT 97

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

 Score = 40.7 bits (95), Expect = 1e-05
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 5   VEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLAD 64
           V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +        Q  D   L+D
Sbjct: 110 VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG------KQLEDGRTLSD 163

Query: 65  CGVKDGSHIYL 75
             ++  S ++L
Sbjct: 164 YNIQKESTLHL 174

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 39.4 bits (92), Expect = 2e-05
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           +KV V+          V  +++V   K  I  + K   D+L+L+ +           D+ 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAG------KILKDQD 85

Query: 61  PLADCGVKDGSHIYLFFKP 79
            L   G+ DG  ++L  K 
Sbjct: 86  TLIQHGIHDGLTVHLVIKR 104

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE+  T+ ++K +I  ++ +P D+  L+ +        Q  D  
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAG------KQLEDGR 54

Query: 61 PLADCGVKDGSHIY 74
           L+D  ++  S ++
Sbjct: 55 TLSDYNIQKESTLH 68

>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 = 39.2 bits (91), Expect = 3e-05
 Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE------DGR 54

Query: 61 PLADCGVKDGSHIYLFFKPLD 81
           L+D  ++  S ++L  +   
Sbjct: 55 TLSDYNIQKESTLHLVLRLRG 75

>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 = 37.3 bits (86), Expect = 9e-05
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 10/94 (10%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDR--LILLLSSDHS----CPMT 54
           M V V  + G +  + V  +ATV DLK+ I    +L  +R   +  +S  +        +
Sbjct: 8   MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 55  QDH----DEVPLADCGVKDGSHIYLFFKPLDDGS 84
                  D   L D G+++   +    K      
Sbjct: 68  AGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQKSG 101

>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 = 36.5 bits (85), Expect = 1e-04
 Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLI 42
          ++V V+ L        V     V + K  I A   +P +  RLI
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI 49

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +           D  
Sbjct: 21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE------DGR 74

Query: 61 PLADCGVKDGSHIYLFFKPLD 81
           L+D  ++  S ++L  +   
Sbjct: 75 TLSDYNIQKESTLHLVLRLRG 95

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

 Score = 35.3 bits (82), Expect = 4e-04
 Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLI 42
          ++V V+ L        V     V + K  I A   +P +  RLI
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI 61

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 107

 Score = 35.6 bits (81), Expect = 4e-04
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 10/75 (13%)

Query: 15 IQVEN-DATVADLKREIGAQQKLPCDRLILLLS---------SDHSCPMTQDHDEVPLAD 64
          + V+    TV+ LK  I  Q ++P     L  +         SD           + ++ 
Sbjct: 21 VSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISS 80

Query: 65 CGVKDGSHIYLFFKP 79
            +  GS +YL ++ 
Sbjct: 81 LNLAHGSMVYLAYEG 95

>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 = 35.4 bits (81), Expect = 5e-04
 Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 8   LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV 67
                  + +E+  TV ++K+ +  + ++P  +++L              D   L    +
Sbjct: 16  YRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLL-----KGWKTGDVEDSTVLKSLHL 70

Query: 68  KDGSHIYLFFKPLDDGSTQHSVFTIPEWLN 97
              + +Y+    L   S+      + E LN
Sbjct: 71  PKNNSLYVLTPDLPPPSSSSHAGALQESLN 100

>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 = 35.5 bits (82), Expect = 5e-04
 Identities = 13/70 (18%), Positives = 22/70 (31%), Gaps = 10/70 (14%)

Query: 8   LTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLILLLSSDHSCPMTQDHDEVPLADC 65
           L G      +     V+ +K +I     +P    +L                D   LA  
Sbjct: 43  LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQY--------EGIFIKDSNSLAYY 94

Query: 66  GVKDGSHIYL 75
            +  G+ I+L
Sbjct: 95  NMASGAVIHL 104

>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 = 34.9 bits (80), Expect = 6e-04
 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 15 IQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIY 74
            +  D TV DLK+ +     +  +R  LL       P     ++V L    +K  + I 
Sbjct: 22 TTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAE---NDVKLGALKLKPNTKIM 78

Query: 75 L 75
          +
Sbjct: 79 M 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	102
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.88
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.87
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.86
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.86
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.86
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.85
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.85
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.85
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.84
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.84
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.84
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.84
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.84
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.84
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.84
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.84
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.84
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.83
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.83
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.83
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.83
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.83
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.83
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.83
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.82
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.82
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.82
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.82
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.82
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.81
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.81
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.81
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.7
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.81
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.81
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.81
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.81
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.8
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.8
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.8
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.79
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.79
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.79
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.79
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.78
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.78
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.78
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.78
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.77
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.77
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.77
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.77
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.77
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.76
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.76
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.76
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.76
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.75
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.75
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.75
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.75
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.74
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.73
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.73
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.73
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.73
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.73
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.73
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.72
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.72
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.72
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.71
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.71
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.7
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.69
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.67
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.67
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.66
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.66
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.66
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.65
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.63
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.62
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.61
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.59
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.56
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.55
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.51
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.46
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.43
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.43
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.42
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.41
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.36
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.33
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.32
2pjh_A	80	Protein NPL4, nuclear protein localization protein	99.29
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.06
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.93
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.74
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.57
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	98.57
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.52
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.44
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	98.25
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.2
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	98.17
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	98.11
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	98.1
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.09
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.06
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	97.8
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.76
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.57
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	97.45
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	97.12
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	96.79
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	96.62
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	96.59
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	96.34
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	96.31
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	96.22
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	96.2
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	95.73
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	94.96
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	94.06
3qa8_A	676	MGC80376 protein; kinase ubiquitin-like domain, ph	93.98
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	93.94
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	93.89
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	93.34
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	93.08
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	93.03
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	92.74
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	92.46
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	92.18
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	91.75
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	91.66
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	91.44
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	91.29
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	91.04
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	90.2
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	90.09
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	89.89
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	89.86
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	89.65
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	89.46
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	89.1
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	88.81
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	88.53
2cu3_A	64	Unknown function protein; thermus thermophilus HB8	87.61
2kmc_A	102	Fermitin family homolog 1; kindlin, cytoskeleton,	87.25
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	87.14
2l52_A	99	Methanosarcina acetivorans SAMP1 homolog; beta-grA	86.93
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	86.89
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	86.88
1y8x_B	98	Ubiquitin-activating enzyme E1C; ubiquitin-conjuga	85.78
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	84.87
2hj1_A	97	Hypothetical protein; structural genomics, PSI, pr	84.81
1q1o_A	98	Cell division control protein 24; PB1 domain, PCCR	84.53
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	83.77
2g1e_A	90	Hypothetical protein TA0895; MOAD, molybdopterin,	82.34
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	80.96
2c7h_A	86	RBBP6, retinoblastoma-binding protein 6, isoform 3	80.33

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

Probab=99.88  E-value=4e-22  Score=121.16  Aligned_cols=75  Identities=21%  Similarity=0.306  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus         5 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~------~L~d~~tL~~~~i~~~~~l~l~~rl~   78 (79)
T 3phx_B            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGK------PLEDQLPLGEYGLKPLSTVFMNLRLR   78 (79)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBGGGGTCCTTCEEEEEECCB
T ss_pred             EEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCE------ECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            799999999999999999999999999999999999999999999999      99999999999999999999999875


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      |
T Consensus        79 G   79 (79)
T 3phx_B           79 G   79 (79)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.87  E-value=1.1e-21  Score=122.12  Aligned_cols=78  Identities=27%  Similarity=0.372  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.+|+++.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~~~i~~g~~l~l~~rl~   74 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGK------QMNDEKTAADYKILGGSVLHLVLALR   74 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCTTSBTTTTTCCTTCEEEEECBCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCe------ECCCCCcHHHcCCCCCCEEEEEEECC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      ++..
T Consensus        75 Gg~~   78 (88)
T 4fbj_B           75 GGGG   78 (88)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            7543

>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=99.86  E-value=2.9e-21  Score=115.62  Aligned_cols=76  Identities=26%  Similarity=0.351  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++..
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~------~L~d~~tL~~~~i~~g~~i~l~~~~~   74 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGK------QMNDEKTAADYKILGGSVLHLVLALR   74 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus        75 GG   76 (76)
T 1ndd_A           75 GG   76 (76)
T ss_dssp             --
T ss_pred             CC
Confidence            63

>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=99.86  E-value=5.3e-21  Score=114.44  Aligned_cols=76  Identities=25%  Similarity=0.406  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~------~L~d~~tL~~~~i~~g~~i~l~~~~~   74 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQRESTLHLVLRLR   74 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCe------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus        75 GG   76 (76)
T 3a9j_A           75 GG   76 (76)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=99.86  E-value=2.8e-21  Score=122.40  Aligned_cols=71  Identities=20%  Similarity=0.345  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+.++|+++.+++++++||.+||++|+++.|+|+++|+|.|+|+      .|+|+.+|++|+|++|++|+++.
T Consensus        22 IqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk------~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGS------VLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCE------EccCcCCHHHcCCCCCCEEEEEe
Confidence            689999999999999999999999999999999999999999999999      99999999999999999999985

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

Probab=99.85  E-value=3.1e-21  Score=119.65  Aligned_cols=73  Identities=25%  Similarity=0.393  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCcc-CCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQ-DHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~-L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+..+|+.+.++|++++||++||++|++.+|+|+++|+|+|+|+      . |+|+.+|++|||++|++|++.+++
T Consensus        11 ~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~lL~D~~tL~~y~I~~gs~i~lv~~p   84 (84)
T 2kk8_A           11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGI------VILREDLTVEQCQIVPTSDIQLEVSS   84 (84)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCCSSSBHHHHTCCTTSCEEEEECC
T ss_pred             eEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCE------EecCCcCCHHHcCCCCCCEEEEEEcC
Confidence            899999999999999999999999999999999999999999999999      8 999999999999999999998753

>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=99.85  E-value=9.7e-21  Score=118.79  Aligned_cols=78  Identities=24%  Similarity=0.391  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++..
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~------~L~d~~tL~~~~i~~~~~i~l~~r~~   75 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   75 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEEcC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      ++..
T Consensus        76 gG~~   79 (96)
T 3k9o_B           76 GYAD   79 (96)
T ss_dssp             C---
T ss_pred             CCCc
Confidence            7654

>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=99.85  E-value=6.6e-21  Score=116.64  Aligned_cols=77  Identities=27%  Similarity=0.490  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.+++++++||.+||++|++.+++|+++|+|+|+|+      .|+|+.+|++|+|+++++|++.+++.
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~------~L~d~~tL~~~~i~~~~~i~l~~rl~   77 (85)
T 3n3k_B            4 MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIHNHSALYLLLKLR   77 (85)
T ss_dssp             CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBE------ECCTTCBTTTTTCCTTCEEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCe------ECCCCCCHHHCCCCCCCEEEEEEecc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        78 GG~   80 (85)
T 3n3k_B           78 GGG   80 (85)
T ss_dssp             ---
T ss_pred             CCC
Confidence            753

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

Probab=99.84  E-value=7.8e-21  Score=120.42  Aligned_cols=76  Identities=25%  Similarity=0.417  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        23 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~~~i~~g~~i~l~~rl~   96 (98)
T 4hcn_B           23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   96 (98)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCTTCBSGGGTCCTTEEEEEECBCS
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCE------ECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        97 GG   98 (98)
T 4hcn_B           97 GG   98 (98)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.84  E-value=9.2e-21  Score=117.78  Aligned_cols=77  Identities=21%  Similarity=0.277  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|+| +|++|+++++.+
T Consensus         6 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk------~L~d~~tL~~~~i-~g~~i~l~~~~~   78 (90)
T 4dwf_A            6 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGR------VLQDDKKLQEYNV-GGKVIHLVERAP   78 (90)
T ss_dssp             EEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBGGGGTC-TTEEEEEEECCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCe------ECCCCCCHHHcCC-CCcEEEEEecCC
Confidence            899999999999999999999999999999999999999999999999      9999999999999 899999999987


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      +...
T Consensus        79 ~~~~   82 (90)
T 4dwf_A           79 PQTH   82 (90)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            6544

>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=99.84  E-value=5e-21  Score=118.02  Aligned_cols=76  Identities=26%  Similarity=0.365  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        13 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~------~L~d~~tL~~~~i~~~~~i~l~~rl~   86 (88)
T 3dbh_I           13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGK------QMNDEKTAADYKILGGSVLHLVLRLR   86 (88)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTE------ECCTTSBGGGGTCCTTCEEEECCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCe------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            799999999999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        87 GG   88 (88)
T 3dbh_I           87 GG   88 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

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

Probab=99.84  E-value=7.4e-21  Score=118.76  Aligned_cols=73  Identities=27%  Similarity=0.442  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+..+|+++.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++
T Consensus        18 m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk------~L~D~~tL~~~gi~~g~~i~l~~rl   90 (91)
T 3v6c_B           18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRL   90 (91)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCTTCBTGGGTCCTTCEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCe------ECCCcCcHHHCCCCCCCEEEEEEec
Confidence            899999999999999999999999999999999999999999999999      9999999999999999999999875

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.84  E-value=1.2e-20  Score=114.30  Aligned_cols=74  Identities=20%  Similarity=0.223  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcEE-EEE-ecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLF-YIQ-VENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~-~i~-v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|++.+|+.+ .++ +++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++
T Consensus         3 m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~------~L~d~~tL~~~~i~~g~~i~l~~r   76 (78)
T 2faz_A            3 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGK------QMEDGHTLFDYEVRLNDTIQLLVR   76 (78)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTCBTTTTTCCTTCEEEEEEC
T ss_pred             EEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCE------ECCCCCCHHHcCCCCCCEEEEEEe
Confidence            8999999999884 899 99999999999999999999999999999999      999999999999999999999987


Q ss_pred             cC
Q 041108           79 PL   80 (102)
Q Consensus        79 ~~   80 (102)
                      ++
T Consensus        77 ~~   78 (78)
T 2faz_A           77 QS   78 (78)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

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

Probab=99.84  E-value=1e-20  Score=117.75  Aligned_cols=76  Identities=24%  Similarity=0.425  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.+++++++||++||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++..
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk------~L~D~~tL~~~gi~~g~~i~l~~r~~   83 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   83 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCTTSBSGGGTCCTTCEEEEEC---
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        84 GG   85 (88)
T 1sif_A           84 GG   85 (88)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>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=99.84  E-value=1.2e-20  Score=115.26  Aligned_cols=76  Identities=25%  Similarity=0.435  Sum_probs=73.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.+++++++||.+||++|++++++|+++|+|+|+|+      .|+|+.+|++|+|+++++|++.+++.
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~------~L~d~~tL~~~~i~~~~~l~l~~r~~   77 (85)
T 3mtn_B            4 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKWSTLFLLLRLR   77 (85)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCTTSBTGGGTCCTTCEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCE------ECCCCCCHHHcCCCCCCEEEEEEECc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        78 GG   79 (85)
T 3mtn_B           78 GG   79 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

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

Probab=99.84  E-value=8.2e-21  Score=118.13  Aligned_cols=77  Identities=21%  Similarity=0.279  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.+|+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..+..
T Consensus         5 m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk------~L~D~~tL~~~~I~~g~~i~l~~~~~   78 (88)
T 2hj8_A            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGK------PLEDQLPLGEYGLKPLSTVFMNLRLR   78 (88)
T ss_dssp             EEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSS------CCCTTSBHHHHHCSTTCEEEEEEC--
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEEcC
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999877


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        79 gg~   81 (88)
T 2hj8_A           79 GGL   81 (88)
T ss_dssp             ---
T ss_pred             CCc
Confidence            644

>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=99.84  E-value=3e-20  Score=117.12  Aligned_cols=79  Identities=20%  Similarity=0.352  Sum_probs=74.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhh---cCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQ---QKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~---~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++.   +|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++++
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk------~L~D~~tL~~ygI~~g~~i~l~~   74 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGK------ILNDDTALKEYKIDEKNFVVVMV   74 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTE------ECCTTSBGGGGTCCSSSEEEEEE
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCE------ECCCcCcHHHCCCCCCCEEEEEE
Confidence            999999999999999999999999999999999   899999999999999      99999999999999999999999


Q ss_pred             ecCCCCCc
Q 041108           78 KPLDDGST   85 (102)
Q Consensus        78 ~~~~~~~~   85 (102)
                      +.+...+.
T Consensus        75 ~~~~~~~~   82 (95)
T 1uel_A           75 TKPKAVST   82 (95)
T ss_dssp             SSCCCCCC
T ss_pred             eCCCCCCC
Confidence            87655443

>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=99.83  E-value=1.6e-20  Score=115.75  Aligned_cols=76  Identities=22%  Similarity=0.254  Sum_probs=73.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk------~L~d~~tL~~~~i~~g~~i~l~~~~~   81 (87)
T 1wh3_A            8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQ------VLQDWLGLGIYGIQDSDTLILSKKKG   81 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTE------ECCSSSBHHHHTCCTTEEEEEEECSC
T ss_pred             EEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCE------EccCCCCHHHCCCCCCCEEEEEEecc
Confidence            799999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        82 GG   83 (87)
T 1wh3_A           82 SG   83 (87)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

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

Probab=99.83  E-value=5.3e-20  Score=116.27  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=73.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..+..
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk------~L~D~~tL~~~gi~~g~~i~l~~~~~   74 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCE------ECCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        75 gG   76 (98)
T 1yx5_B           75 GG   76 (98)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.83  E-value=3.8e-20  Score=114.64  Aligned_cols=77  Identities=22%  Similarity=0.239  Sum_probs=73.1

Q ss_pred             CEEEEEeCCC-cEEEE-EecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTG-TLFYI-QVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g-~~~~i-~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|+..+| +.+.+ ++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.++
T Consensus         8 m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk------~L~d~~tL~~~~i~~g~~i~l~~~   81 (89)
T 1wy8_A            8 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGK------QLENGYTLFDYDVGLNDIIQLLVR   81 (89)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTE------ECCSSSBHHHHTCCTTCEEEEEEC
T ss_pred             EEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCe------ECCCCCCHHHCCCCCCCEEEEEEe
Confidence            7999999999 79999 599999999999999999999999999999999      999999999999999999999999


Q ss_pred             cCCCC
Q 041108           79 PLDDG   83 (102)
Q Consensus        79 ~~~~~   83 (102)
                      ..++.
T Consensus        82 ~~gG~   86 (89)
T 1wy8_A           82 PDSGP   86 (89)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87754

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

Probab=99.83  E-value=3.1e-20  Score=114.94  Aligned_cols=71  Identities=23%  Similarity=0.315  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|+..+|+++.+++++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++||| +|++|++..|
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 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGR------VLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             EEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCE------ECCCCCcHHHcCC-CCcEEEEEEC
Confidence            789999999999999999999999999999999999999999999999      9999999999999 8999999875

>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=99.83  E-value=1.8e-20  Score=113.76  Aligned_cols=76  Identities=16%  Similarity=0.224  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.+|+.+.++|++++||.+||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|+++++..
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~------~L~d~~tl~~~~i~~~~~i~l~~~~~   77 (79)
T 2uyz_B            4 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQ------RIADNHTPKELGMEEEDVIEVYQEQT   77 (79)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCE------EeCCCCCHHHcCCCCCCEEEEEEecc
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus        78 GG   79 (79)
T 2uyz_B           78 GG   79 (79)
T ss_dssp             C-
T ss_pred             CC
Confidence            63

>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=99.83  E-value=5.1e-20  Score=112.93  Aligned_cols=74  Identities=23%  Similarity=0.402  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhh---cCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQ---QKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~---~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++.   +|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..
T Consensus         6 m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk------~L~D~~tL~~~~i~~g~~i~l~~   79 (85)
T 2wyq_A            6 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGK------ILSDDVPIRDYRIDEKNFVVVMV   79 (85)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTE------ECCTTSBGGGGCCCTTSEEEEEE
T ss_pred             EEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCE------ECcCCCCHHHcCCCCCCEEEEEE
Confidence            789999999999999999999999999999998   899999999999999      99999999999999999999998


Q ss_pred             ecC
Q 041108           78 KPL   80 (102)
Q Consensus        78 ~~~   80 (102)
                      +.+
T Consensus        80 ~~~   82 (85)
T 2wyq_A           80 TKT   82 (85)
T ss_dssp             C--
T ss_pred             cCC
Confidence            764

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

Probab=99.83  E-value=2.3e-20  Score=113.31  Aligned_cols=74  Identities=28%  Similarity=0.419  Sum_probs=70.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++++
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 MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGK------ALADGKRLSDYSIGPNSKLNLVVKPL   81 (81)
T ss_dssp             EEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTE------ECCTTSBGGGGTCCSSBCCEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCe------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999998753

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

Probab=99.82  E-value=2.1e-20  Score=120.25  Aligned_cols=75  Identities=15%  Similarity=0.315  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||..+|+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++++.+
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~~~i~~g~~i~lv~~~~   75 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGK------VLQDSKTVSECGLKDGDQVVFMVSQK   75 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTE------ECCTTSBTTTTTCCTTCEEEEECCC-
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCE------ECCCcCCHHHcCCCCCCEEEEEEcCC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999865


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      .
T Consensus        76 ~   76 (106)
T 3m62_B           76 K   76 (106)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.82  E-value=6.7e-20  Score=118.78  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=72.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.++|++++||.+||.+|++++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        36 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~~gI~~gs~I~l~~rl~  109 (111)
T 3vdz_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR  109 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTTTTTCCTTCEEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCE------ECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            799999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus       110 GG  111 (111)
T 3vdz_A          110 GG  111 (111)
T ss_dssp             C-
T ss_pred             CC
Confidence            63

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.82  E-value=2e-20  Score=119.96  Aligned_cols=71  Identities=25%  Similarity=0.390  Sum_probs=69.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+++.|+++.++|++++||.+||++|+++.|+|+++|||+|+|+      .|+|+.+|++|||+++++|+|.+
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk------~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYT------IFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCE------ECCCCCCHHHcCCCCCCEEEEEe
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999875

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

Probab=99.82  E-value=5.5e-20  Score=116.13  Aligned_cols=76  Identities=26%  Similarity=0.430  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCC-CccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDE-VPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~-~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+..+| ++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+ .+|++|||++|++|++.+++
T Consensus        16 ~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~~tL~~ygI~~gstl~lv~r~   88 (94)
T 2kan_A           16 IHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGI------ELADDYRNLNEYGITEFSEIVVFLKS   88 (94)
T ss_dssp             EEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTE------EECCTTSBHHHHTCCTTEEEEEEECC
T ss_pred             EEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCE------ECCCCcccHHHCCCCCCCEEEEEEeC
Confidence            7899999887 8899999999999999999999999999999999999      99999 99999999999999999998


Q ss_pred             CCCC
Q 041108           80 LDDG   83 (102)
Q Consensus        80 ~~~~   83 (102)
                      .++.
T Consensus        89 ~gg~   92 (94)
T 2kan_A           89 INRA   92 (94)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8764

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

Probab=99.82  E-value=1.2e-19  Score=109.09  Aligned_cols=72  Identities=17%  Similarity=0.299  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+. +|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..+.
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk------~L~d~~tL~~~~i~~g~~i~l~~~~   76 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGK------ILKDDQTVESYHIQDGHSVHLVKSQ   76 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCe------EcCCCCCHHHcCCCCCCEEEEEEcC
Confidence            6889999 8999999999999999999999999999999999999999      9999999999999999999998653

>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=99.81  E-value=1e-21  Score=134.19  Aligned_cols=91  Identities=22%  Similarity=0.357  Sum_probs=8.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||.+|++|++.+++.
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~dygI~~gstL~Lvlrl~   74 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (152)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCE------EccccCcHHHcCCCCCCEEEEEeecc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999999


Q ss_pred             CCCC-ceeEEEecCCcCC
Q 041108           81 DDGS-TQHSVFTIPEWLN   97 (102)
Q Consensus        81 ~~~~-~~~~~~~~~~~~~   97 (102)
                      +++. ++...||.|.+-.
T Consensus        75 GGgKkrkKk~~t~Pkk~~   92 (152)
T 3u5c_f           75 GGGKKRKXXXXXXXXXXX   92 (152)
T ss_dssp             -------CCCCCCCSCCC
T ss_pred             CCCcCccccccccccccc
Confidence            8765 4568999998753

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

Probab=99.81  E-value=2.3e-19  Score=123.99  Aligned_cols=80  Identities=25%  Similarity=0.425  Sum_probs=74.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||..+|+++.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~y~I~~gstI~Lvlrl~   74 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTE------ECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCc------cccCcCcHHHcCCCCCCEEEEEEEec
Confidence            999999999999999999999999999999999999999999999999      99999999999999999999999998


Q ss_pred             CCCCce
Q 041108           81 DDGSTQ   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      ++....
T Consensus        75 GG~k~~   80 (169)
T 3l0w_B           75 GGGGET   80 (169)
T ss_dssp             C---CC
T ss_pred             cccccc
Confidence            765443

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

Probab=99.81  E-value=3.1e-20  Score=116.23  Aligned_cols=73  Identities=22%  Similarity=0.369  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEec--CCCcHHHHHHHH-HhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCC-CCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVE--NDATVADLKREI-GAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV-KDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~--~~~TV~dLK~~I-~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI-~~~~~i~l~   76 (102)
                      |+|+||+.+|+++.++|+  +++||.+||++| ++..|+|+++|||+|+|+      .|+|+.+|++|+| .+|++|++.
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk------~L~D~~tL~~y~I~~~~stl~v~   75 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGK------VLHDNLFLSDLKVTPANSTITVM   75 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTE------ECCTTCBHHHHCCCGGGCEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCE------ECcCcCCHHHcCCCCCCCEEEEE
Confidence            899999999998888766  999999999999 999999999999999999      9999999999999 699999999


Q ss_pred             eec
Q 041108           77 FKP   79 (102)
Q Consensus        77 ~~~   79 (102)
                      .++
T Consensus        76 ~~~   78 (87)
T 2lxa_A           76 IKP   78 (87)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            864

>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=99.70  E-value=1.2e-21  Score=117.96  Aligned_cols=75  Identities=21%  Similarity=0.418  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk------~L~d~~tL~~~~i~~g~~i~l~~rlr   74 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGK------ELPNHLTVQNCDLEQQSIVHIVQRPR   74 (76)
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      +
T Consensus        75 g   75 (76)
T 3b1l_X           75 R   75 (76)
Confidence            5

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

Probab=99.81  E-value=9.4e-20  Score=116.32  Aligned_cols=74  Identities=22%  Similarity=0.345  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEE--EecCCCcHHHHHHHH-HhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCC-CCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYI--QVENDATVADLKREI-GAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV-KDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i--~v~~~~TV~dLK~~I-~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI-~~~~~i~l~   76 (102)
                      |+|+||+.+|+.+.+  +|++++||.+||++| ++..|+|+++|||+|+|+      .|+|+.+|++|+| ++|++|+++
T Consensus        20 m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk------~L~D~~tL~dy~I~~~g~ti~lm   93 (98)
T 4a20_A           20 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGK------VLHDNLFLSDLKVTPANSTITVM   93 (98)
T ss_dssp             EEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTE------EECTTCBGGGSCCBTTBCEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCE------ECcCcCCHHHcCcCCCCCEEEEE
Confidence            789999999988776  566999999999999 888999999999999999      9999999999999 999999999


Q ss_pred             eecC
Q 041108           77 FKPL   80 (102)
Q Consensus        77 ~~~~   80 (102)
                      ++.+
T Consensus        94 vskp   97 (98)
T 4a20_A           94 IKPN   97 (98)
T ss_dssp             ECCC
T ss_pred             EeCC
Confidence            8764

>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=99.81  E-value=8e-20  Score=115.73  Aligned_cols=76  Identities=16%  Similarity=0.224  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.+|+.+.++|.+++||.+||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++++++.
T Consensus        22 m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk------~L~d~~tl~dy~i~~g~~I~l~~~~~   95 (97)
T 1wyw_B           22 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQ------RIADNHTPKELGMEEEDVIEVYQEQT   95 (97)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTCCHHHHTCCTTCEEEEEESSS
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCe------EcCCCCCHHHCCCCCCCEEEEEEecC
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus        96 GG   97 (97)
T 1wyw_B           96 GG   97 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

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

Probab=99.81  E-value=9.2e-20  Score=114.65  Aligned_cols=74  Identities=23%  Similarity=0.354  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+.  |+.+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        20 m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~y~I~~gstI~lv~rl~   91 (93)
T 2l7r_A           20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGA------PLEDEATLGQCGVEALTTLEVAGRML   91 (93)
T ss_dssp             CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTE------ECCTTSBHHHHTCCSSCEEEEECCCC
T ss_pred             EEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCE------ECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            7899998  899999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus        92 GG   93 (93)
T 2l7r_A           92 GG   93 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=1.4e-19  Score=122.51  Aligned_cols=78  Identities=22%  Similarity=0.322  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.++|++++||++||++|++++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        82 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~~G~------~L~d~~tL~~y~i~~g~~l~l~~rl~  155 (159)
T 3rt3_B           82 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGK------PLEDQLPLGEYGLKPLSTVFMNLRLR  155 (159)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEECCe------ecCCCCCHHHcCCCCCCEEEEEEecC
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999998


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      |+++
T Consensus       156 GG~r  159 (159)
T 3rt3_B          156 GGGR  159 (159)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            8753

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.80  E-value=1.4e-19  Score=116.18  Aligned_cols=76  Identities=13%  Similarity=0.169  Sum_probs=72.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.++|++++||.+||.+|+..+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++.+.+
T Consensus        24 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~ygI~~g~ti~lv~~~~   97 (106)
T 1ttn_A           24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGR------PLTDKMKFEELKIPKDYVVQVIVSQP   97 (106)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTE------ECCTTSHHHHCCCSSSCEEEEECCCS
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      +.
T Consensus        98 ~~   99 (106)
T 1ttn_A           98 VQ   99 (106)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

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

Probab=99.80  E-value=3.5e-19  Score=115.22  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus        36 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~~gI~~gs~I~l~~rl~  109 (111)
T 2ojr_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR  109 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTE------ECCSSCBTTTTTCCTTCEEEEEECCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCE------ECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            789999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus       110 GG  111 (111)
T 2ojr_A          110 GG  111 (111)
T ss_dssp             C-
T ss_pred             CC
Confidence            63

>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=99.80  E-value=2.8e-19  Score=117.49  Aligned_cols=82  Identities=24%  Similarity=0.325  Sum_probs=75.5

Q ss_pred             CEEEEEeCCCc-EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCC-------CCE
Q 041108            1 MKVAVEILTGT-LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKD-------GSH   72 (102)
Q Consensus         1 M~v~V~~~~g~-~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~-------~~~   72 (102)
                      |.++++.+.++ ++.+++++++||.+||++|+.+.|+|+++|||+|+|+      .|+|+++|++|||++       +++
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk------~LeD~kTL~dy~I~~~ta~~q~~at   74 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQ------LLDDGKTLGECGFTSQTARPQAPAT   74 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTTTTTCCGGGSBTTBCEE
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCe------ECCCcCCHHHcCCCcCcccCCCCCE
Confidence            88999999886 6889999999999999999999999999999999999      999999999999999       999


Q ss_pred             EEEEeecCCCCCceeEE
Q 041108           73 IYLFFKPLDDGSTQHSV   89 (102)
Q Consensus        73 i~l~~~~~~~~~~~~~~   89 (102)
                      |++.++. ++.++...|
T Consensus        75 l~Lvlr~-~~~fE~l~i   90 (118)
T 4ajy_B           75 VGLAFRA-DDTFEALCI   90 (118)
T ss_dssp             EEEEECC-SSCCCCCCB
T ss_pred             EEEEEec-CCCccceEE
Confidence            9999996 677766444

>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=99.79  E-value=2.9e-19  Score=113.90  Aligned_cols=76  Identities=30%  Similarity=0.434  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+ +.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++++..
T Consensus        23 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~ygI~~gstI~l~~r~~   95 (100)
T 1yqb_A           23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGK------ILKDPDSLAQCGVRDGLTVHLVIKRQ   95 (100)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBHHHHTCCTTCEEEEEECCC
T ss_pred             EEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCE------ECCCcCcHHHCCCCCCCEEEEEEcCC
Confidence            78999999886 689999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      +..
T Consensus        96 ~~p   98 (100)
T 1yqb_A           96 HRA   98 (100)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=2e-19  Score=112.68  Aligned_cols=77  Identities=13%  Similarity=0.040  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCc--EEEEEecCCCcHHHHHHHHHhhc--CCCCccEEEEeCCCCCCCCccCCCCCccccC--CCCCCCEEE
Q 041108            1 MKVAVEILTGT--LFYIQVENDATVADLKREIGAQQ--KLPCDRLILLLSSDHSCPMTQDHDEVPLADC--GVKDGSHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~--~~~i~v~~~~TV~dLK~~I~~~~--gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~--gI~~~~~i~   74 (102)
                      |+|+|++.+|+  .+.+++++++||.+||++|++++  ++|+++|||+|+|+      .|+|+.+|++|  +|+++++|+
T Consensus         8 m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk------~L~D~~tL~~~~~~i~~~~~i~   81 (93)
T 1wgd_A            8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGK------LLLDHQCLRDLLPKQEKRHVLH   81 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTE------ECCSSSCHHHHSCSSSCSEEEE
T ss_pred             EEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCE------ECcCcCCHHHHhcCCCCCCEEE
Confidence            79999999988  56777889999999999999998  99999999999999      99999999999  999999999


Q ss_pred             EEeecCCCC
Q 041108           75 LFFKPLDDG   83 (102)
Q Consensus        75 l~~~~~~~~   83 (102)
                      +++++.++.
T Consensus        82 lv~~~~gg~   90 (93)
T 1wgd_A           82 LVCNVKSGP   90 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEeCCCCCC
Confidence            999887654

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

Probab=99.79  E-value=5.7e-19  Score=112.68  Aligned_cols=75  Identities=27%  Similarity=0.376  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+.. |+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..+.+
T Consensus        26 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~~gI~~g~~I~l~~~~~   98 (101)
T 2klc_A           26 MKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGK------ILKDQDTLSQHGIHDGLTVHLVIKTQ   98 (101)
T ss_dssp             EEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTE------EECTTCCTGGGTCCTTCEEEEEECCS
T ss_pred             EEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCE------ECCCcCcHHHcCCCCCCEEEEEEcCC
Confidence            78999998 889999999999999999999999999999999999999      99999999999999999999998876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ..
T Consensus        99 ~~  100 (101)
T 2klc_A           99 NR  100 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=99.79  E-value=2.1e-19  Score=118.25  Aligned_cols=82  Identities=23%  Similarity=0.307  Sum_probs=74.7

Q ss_pred             CEEEEEeCCCc-EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCC-------CCCE
Q 041108            1 MKVAVEILTGT-LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVK-------DGSH   72 (102)
Q Consensus         1 M~v~V~~~~g~-~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~-------~~~~   72 (102)
                      |+++|+.+.|+ ++.++|++++||.+||++|+.+.|+|+++|||+|+|+      .|+|+++|++|||+       ++++
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk------~LeD~~TLsdy~I~~~~a~~q~~st   74 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQ------LLDDGKTLGECGFTSQTARPQAPAT   74 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBHHHHTCCTTTSBTTBCEE
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCe------ECCCCCCHHHcCcccccccCCCCCE
Confidence            88889988775 5899999999999999999999999999999999999      99999999999999       7999


Q ss_pred             EEEEeecCCCCCceeEE
Q 041108           73 IYLFFKPLDDGSTQHSV   89 (102)
Q Consensus        73 i~l~~~~~~~~~~~~~~   89 (102)
                      |++.++ .++.++...|
T Consensus        75 L~L~lr-~~g~fe~l~i   90 (118)
T 2fnj_B           75 VGLAFR-ADDTFEALRI   90 (118)
T ss_dssp             EEEEEB-SSSCBCCCCB
T ss_pred             EEEEec-CCCceeeeEE
Confidence            999999 7777765433

>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=99.78  E-value=5.6e-19  Score=114.16  Aligned_cols=76  Identities=21%  Similarity=0.307  Sum_probs=72.5

Q ss_pred             CEEEEEeC---CCcEEEEEecC-CCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEIL---TGTLFYIQVEN-DATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~---~g~~~~i~v~~-~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |+|+|++.   +|+.+.+++++ ++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.
T Consensus        28 i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk------~L~D~~tL~~y~I~~g~~l~l~  101 (111)
T 1we6_A           28 ATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAG------FLKDNMSLAHYNVGAGEILTLS  101 (111)
T ss_dssp             EEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSS------BCCTTSBTTTTTCSSSCEEEEE
T ss_pred             EEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCE------ECCCCCcHHHCCCCCCCEEEEE
Confidence            68999998   78999999998 99999999999999999999999999999      9999999999999999999999


Q ss_pred             eecCCC
Q 041108           77 FKPLDD   82 (102)
Q Consensus        77 ~~~~~~   82 (102)
                      +++.++
T Consensus       102 ~r~~GG  107 (111)
T 1we6_A          102 LRERSG  107 (111)
T ss_dssp             CSSCCS
T ss_pred             EEcCCC
Confidence            998775

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

Probab=99.78  E-value=1.5e-18  Score=112.95  Aligned_cols=77  Identities=22%  Similarity=0.373  Sum_probs=73.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      .+|+|+..+|+++.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..++.
T Consensus        10 ~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~ygI~~gstI~l~~~~~   83 (114)
T 2kdi_A           10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGK------QLEDGRTLSDYNIQRESTLHLVLRLR   83 (114)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTCBTTTTTCCSSCEEEEEECCC
T ss_pred             EEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCE------ECCCCCcHHHCCCCCCCEEEEEEEcC
Confidence            479999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        84 GG~   86 (114)
T 2kdi_A           84 GGS   86 (114)
T ss_dssp             SSC
T ss_pred             CCc
Confidence            764

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

Probab=99.78  E-value=4.5e-19  Score=124.83  Aligned_cols=79  Identities=25%  Similarity=0.400  Sum_probs=75.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus       106 MqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk------~L~D~~tL~dygI~~gstI~Lvlrlr  179 (189)
T 3q3f_A          106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR  179 (189)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTE------ECCTTCBGGGGTCCTTCEEEECCCCC
T ss_pred             eeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCE------ECCCCCCHHHCCCCCCCEEEEEEEcC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999998


Q ss_pred             CCCCc
Q 041108           81 DDGST   85 (102)
Q Consensus        81 ~~~~~   85 (102)
                      ++...
T Consensus       180 GG~~~  184 (189)
T 3q3f_A          180 GGGQT  184 (189)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            86543

>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=99.78  E-value=2.6e-19  Score=112.54  Aligned_cols=76  Identities=20%  Similarity=0.324  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+.. |+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|+++++..
T Consensus        18 m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk------~L~D~~tL~~~gi~~g~~i~l~~~~~   90 (96)
T 1wx8_A           18 IRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGK------ILRDQDILSQRGILDGSTVHVVVRSH   90 (96)
T ss_dssp             EEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTE------ECCTTSCHHHHTCCTTEEEECCBCCS
T ss_pred             EEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCE------ECCCcCCHHHCCCCCCCEEEEEEeCC
Confidence            78999998 999999999999999999999999999999999999999      99999999999999999999999877


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        91 ~g~   93 (96)
T 1wx8_A           91 SGP   93 (96)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            653

>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=99.77  E-value=5.7e-19  Score=112.68  Aligned_cols=79  Identities=20%  Similarity=0.282  Sum_probs=72.2

Q ss_pred             CEEEEEeCCC----cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCC-CccccCCCCCCCEEEE
Q 041108            1 MKVAVEILTG----TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDE-VPLADCGVKDGSHIYL   75 (102)
Q Consensus         1 M~v~V~~~~g----~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~-~~L~~~gI~~~~~i~l   75 (102)
                      |+|+|+..+|    +.+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+ .+|++|||++|++|++
T Consensus         8 m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk------~L~D~~~tL~~ygI~~g~~l~l   81 (102)
T 1v5o_A            8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQ------LLTDDHCSLGSYGLKDGDMVVL   81 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTE------EECCSSSBHHHHTCCTTEEEEE
T ss_pred             EEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCE------ECCCCcccHHHCCCCCCCEEEE
Confidence            7899999754    68999999999999999999999999999999999999      99877 7999999999999999


Q ss_pred             EeecCCCCCc
Q 041108           76 FFKPLDDGST   85 (102)
Q Consensus        76 ~~~~~~~~~~   85 (102)
                      ..+..++.+.
T Consensus        82 ~~~~~gg~~~   91 (102)
T 1v5o_A           82 LQKDNVGLRT   91 (102)
T ss_dssp             CBCCCCCCSS
T ss_pred             EECCCCCCCC
Confidence            9988776543

>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=99.77  E-value=8.4e-19  Score=112.40  Aligned_cols=77  Identities=30%  Similarity=0.423  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+ +.++|++++||.+||++|++.+|+++++|+|+|+|+      .|+|+.+|++|+|++|++|+++.+..
T Consensus        18 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~~gi~~g~~i~l~~~~~   90 (106)
T 1wx7_A           18 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGK------ILKDPDSLAQCGVRDGLTVHLVIKRQ   90 (106)
T ss_dssp             EEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTE------ECCTTSCHHHHTCCTTEEEEEEECCC
T ss_pred             EEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCE------ECCCcCcHHHcCCCCCCEEEEEEcCC
Confidence            78999999886 789999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      +...
T Consensus        91 ~~~~   94 (106)
T 1wx7_A           91 HRAM   94 (106)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            6544

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=99.77  E-value=2.1e-20  Score=123.76  Aligned_cols=77  Identities=25%  Similarity=0.393  Sum_probs=0.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||.+|++|+++++..
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~~~I~~gsti~l~~rl~   74 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (128)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCE------ECCCCCchhhhccCCCCEEEEEEEcC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        75 GG~   77 (128)
T 3u5e_m           75 GGI   77 (128)
T ss_dssp             --C
T ss_pred             CCC
Confidence            764

>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=99.77  E-value=3.6e-18  Score=115.57  Aligned_cols=73  Identities=26%  Similarity=0.376  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEE-e-CCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILL-L-SSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~-~-~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|++.+|+++.++|++++||.+||++|++.+|+|+++|+|+ | +|+      .|+|+.+|++|||++|++|++.++
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~~~g~------~L~d~~tL~~y~i~~~~~l~l~~~   76 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGV------ALQDRVPLASQGLGPGSTVLLVVD   76 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEEETTCC------BCCTTSCGGGGTCCTTCEEEEEEC
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEEcCCCC------CCCCCCCHHHcCCCCCCEEEEEcc
Confidence            89999999999999999999999999999999999999999999 9 799      999999999999999999999998


Q ss_pred             c
Q 041108           79 P   79 (102)
Q Consensus        79 ~   79 (102)
                      .
T Consensus        77 ~   77 (159)
T 3rt3_B           77 K   77 (159)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.77  E-value=2.2e-18  Score=118.31  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++..
T Consensus        21 m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~------~L~d~~tL~~~~i~~~~~l~l~~~~~   94 (172)
T 3u30_A           21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   94 (172)
T ss_dssp             EEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCc------cccccCCHhHcCCcccceeeeeeccc
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999877


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        95 gg   96 (172)
T 3u30_A           95 GG   96 (172)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.76  E-value=5e-19  Score=114.31  Aligned_cols=76  Identities=25%  Similarity=0.311  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc---------------cEEEEeCCCCCCCCccCC-CCCcccc
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD---------------RLILLLSSDHSCPMTQDH-DEVPLAD   64 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~---------------~q~L~~~g~~~~~~~~L~-d~~~L~~   64 (102)
                      |+|+|+..+|+++.++|++++||.+||++|+++.++|+.               .|+|+|+|+      .|. |+++|++
T Consensus         8 M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk------~L~dD~~tL~d   81 (105)
T 1v2y_A            8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGE------KLTEDRKKLRD   81 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSC------EECCSSSBHHH
T ss_pred             EEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCc------CccCCcCCHHH
Confidence            899999999999999999999999999999999999884               569999999      885 6799999


Q ss_pred             CCCCCCCEEEEEeecCCC
Q 041108           65 CGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        65 ~gI~~~~~i~l~~~~~~~   82 (102)
                      |||++|++|+++.++.+.
T Consensus        82 ygI~~g~~l~lv~~lr~~   99 (105)
T 1v2y_A           82 YGIRNRDEVSFIKKLGQK   99 (105)
T ss_dssp             HTCCSSEEEEEEECSCSC
T ss_pred             cCCCCCCEEEEEehhccC
Confidence            999999999999998765

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

Probab=99.76  E-value=2e-18  Score=114.15  Aligned_cols=76  Identities=24%  Similarity=0.328  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+.. |+.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++.+..
T Consensus        33 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~dygI~~gstI~lv~~~~  105 (125)
T 1j8c_A           33 IKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGK------ILKDQDTLIQHGIHDGLTVHLVIKRD  105 (125)
T ss_dssp             EEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTE------EESTTSCGGGTTCSSSEEEEEEEC--
T ss_pred             EEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEeccC
Confidence            78999998 999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus       106 gg~  108 (125)
T 1j8c_A          106 PNS  108 (125)
T ss_dssp             ---
T ss_pred             CCC
Confidence            643

>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=99.76  E-value=5.6e-18  Score=112.94  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=72.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..+..
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~------~L~d~~tL~~~~i~~~~~l~l~~~~~   74 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEECCT
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCe------ECcCcccHHHhccCCCCeeEEEeecc
Confidence            999999999999999999999999999999999999999999999999      99999999999999999999998876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      +.
T Consensus        75 ~~   76 (152)
T 3b08_A           75 GG   76 (152)
T ss_dssp             TC
T ss_pred             cc
Confidence            53

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.76  E-value=4.2e-18  Score=109.99  Aligned_cols=73  Identities=25%  Similarity=0.317  Sum_probs=68.2

Q ss_pred             CEEEEEeCCC--cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCC-CCCCEEEEEe
Q 041108            1 MKVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV-KDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g--~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI-~~~~~i~l~~   77 (102)
                      |+|+|+...+  ..+.+++++++||++||++|++++|+||+.|||+++|+      +++|+.+|++||| ++|+++++++
T Consensus        25 l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggk------ll~D~~TL~~ygI~~~G~t~hL~l   98 (105)
T 4dbg_A           25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQR------LARDQETLHSHGVRQNGDSAYLYL   98 (105)
T ss_dssp             EEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------EECTTCBTGGGTCCSTTCEEEEEE
T ss_pred             EEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCe------EccCcCcHHHcCCCCCCCEEEEEE
Confidence            6899999875  67899999999999999999999999999999999999      9999999999999 5999999998


Q ss_pred             ec
Q 041108           78 KP   79 (102)
Q Consensus        78 ~~   79 (102)
                      -.
T Consensus        99 ~~  100 (105)
T 4dbg_A           99 LS  100 (105)
T ss_dssp             CC
T ss_pred             Ee
Confidence            54

>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=99.75  E-value=8.2e-18  Score=112.13  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+..+|+.+.+++++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+++.
T Consensus        77 ~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~qrL~~~g~------~L~d~~tL~~~~i~~~~~i~l~~r~~  150 (152)
T 3b08_A           77 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR  150 (152)
T ss_dssp             EEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             cceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHhCcChhhEEEEECCE------ECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            689999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      |+
T Consensus       151 GG  152 (152)
T 3b08_A          151 GG  152 (152)
T ss_dssp             C-
T ss_pred             CC
Confidence            63

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

Probab=99.75  E-value=6.1e-19  Score=112.67  Aligned_cols=72  Identities=17%  Similarity=0.299  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+. +|+.+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++.+.
T Consensus        29 i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~~gI~~g~tI~lv~~~  100 (101)
T 3m63_B           29 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGK------ILKDDQTVESYHIQDGHSVHLVKSQ  100 (101)
T ss_dssp             CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTE------ECCTTSBTTTTTCCTTEEEEECCCC
T ss_pred             EEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCE------ECCCcCcHHHCCCCCCCEEEEEeCC
Confidence            4577776 7899999999999999999999999999999999999999      9999999999999999999998764

>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=99.75  E-value=2.3e-18  Score=107.64  Aligned_cols=73  Identities=21%  Similarity=0.292  Sum_probs=68.3

Q ss_pred             CEEEEEeCCCcEEEE-EecCCCcHHHHHHHHHhhcCCCCccEEEE---eCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYI-QVENDATVADLKREIGAQQKLPCDRLILL---LSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i-~v~~~~TV~dLK~~I~~~~gip~~~q~L~---~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |+|+|+. .|+.+.+ ++++++||.+||++|++++|+|+++|||+   |+|+      .|+|+.+|++|+|++|++|+++
T Consensus         8 m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk------~L~D~~~L~~~~i~~g~~l~l~   80 (90)
T 1v5t_A            8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGK------PAENDVKLGALKLKPNTKIMMM   80 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTE------ECCTTSBHHHHTCCTTEEEEEE
T ss_pred             EEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCc------CcCCCCCHHHcCCCCCCEEEEE
Confidence            7899997 6889999 99999999999999999999999999999   9999      9999999999999999999998


Q ss_pred             eecC
Q 041108           77 FKPL   80 (102)
Q Consensus        77 ~~~~   80 (102)
                      ....
T Consensus        81 ~~~~   84 (90)
T 1v5t_A           81 GTRE   84 (90)
T ss_dssp             CCCS
T ss_pred             ecCc
Confidence            6543

>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=99.75  E-value=7.3e-18  Score=111.97  Aligned_cols=89  Identities=10%  Similarity=0.119  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCcEE-EEEecCCCcHHHHHHHH-----HhhcCCCC--ccEEEEeCCCCCCCCccCCCCCccccCCCCCC--
Q 041108            1 MKVAVEILTGTLF-YIQVENDATVADLKREI-----GAQQKLPC--DRLILLLSSDHSCPMTQDHDEVPLADCGVKDG--   70 (102)
Q Consensus         1 M~v~V~~~~g~~~-~i~v~~~~TV~dLK~~I-----~~~~gip~--~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~--   70 (102)
                      |+|+||+.+|+.+ .+++++++||.+||++|     ++..|+|+  ++|||+|+|+      .|+|+.+|++|+|..|  
T Consensus        17 ~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK------~LeD~~TLsdy~I~~~~~   90 (126)
T 1se9_A           17 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGK------VLENSKTVKDYRSPVSNL   90 (126)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTE------ECCTTSBGGGGSCCTTSC
T ss_pred             EEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCe------ECcCCCcHHHcCCCcCCc
Confidence            7899999999888 69999999999999999     45667886  8999999999      9999999999999988  


Q ss_pred             ----CEEEEEeecCCCCCceeEEEecCCcC
Q 041108           71 ----SHIYLFFKPLDDGSTQHSVFTIPEWL   96 (102)
Q Consensus        71 ----~~i~l~~~~~~~~~~~~~~~~~~~~~   96 (102)
                          +++++.+++.+.... ...++.|.+-
T Consensus        91 ~~~v~tmhlVlrl~g~~kk-kk~~~~pkk~  119 (126)
T 1se9_A           91 AGAVTTMHVIIQAPVTEKE-KKPKGDPKMN  119 (126)
T ss_dssp             TTCCEEEEEEECCCSSCCC-C---------
T ss_pred             cCCcEEEEEEeccCCcccc-ccCCCCCCCC
Confidence                689999998876554 6778877653

>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=99.74  E-value=5.3e-18  Score=108.67  Aligned_cols=72  Identities=13%  Similarity=0.125  Sum_probs=64.7

Q ss_pred             EEEEeCC----CcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            3 VAVEILT----GTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         3 v~V~~~~----g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |.|+..+    |+++.++|++++||.+||++|+++.|+|++.|+|+|+|+      +|+|+.+|++|+|++|++|+ +++
T Consensus        18 i~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GK------iL~D~~TL~~y~I~~gsti~-vl~   90 (100)
T 1wju_A           18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKK------QLQLGKTLEEQGVAHNVKAM-VLE   90 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTE------ECCTTSBHHHHTCCSSEEEE-EEC
T ss_pred             EEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCe------ECCCCCcHHHcCCCCCCEEE-EEE
Confidence            5667776    678999999999999999999999999999999999999      99999999999999999994 444


Q ss_pred             cCC
Q 041108           79 PLD   81 (102)
Q Consensus        79 ~~~   81 (102)
                      +.+
T Consensus        91 lrg   93 (100)
T 1wju_A           91 LKQ   93 (100)
T ss_dssp             CCC
T ss_pred             ECC
Confidence            443

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.73  E-value=6.3e-18  Score=116.04  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+++|+..+|+++.+++++++||.+||++|+.++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++.
T Consensus        97 ~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~q~L~~~g~------~L~D~~tL~~y~i~~g~tl~l~~rlr  170 (172)
T 3u30_A           97 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR  170 (172)
T ss_dssp             EEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTE------ECCTTSBSGGGTCCTTCEEEECC---
T ss_pred             ccceeecccCcceeEEecCCCCHHHHHHHHHHHhCCCceeEEEEECCc------cCCCCCcHHHhCCCCCCEEEEEEecC
Confidence            678999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus       171 gG  172 (172)
T 3u30_A          171 GG  172 (172)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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=99.73  E-value=8.1e-18  Score=105.59  Aligned_cols=74  Identities=18%  Similarity=0.167  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCC-CccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDE-VPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~-~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++..   +++|+|+|+|+      .|+|+ .+|++|||++|++|+++.+.
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk------~L~D~~~tL~~y~i~~g~~i~l~~~~   78 (95)
T 1wia_A            8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGR------LLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTE------ECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCE------EccCCcCCHHHcCCCCCCEEEEEECC
Confidence            7899999999999999999999999999999987   99999999999      99999 99999999999999999987


Q ss_pred             CCCC
Q 041108           80 LDDG   83 (102)
Q Consensus        80 ~~~~   83 (102)
                      +...
T Consensus        79 ~~~~   82 (95)
T 1wia_A           79 PGAA   82 (95)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.73  E-value=4.8e-18  Score=107.60  Aligned_cols=72  Identities=14%  Similarity=0.170  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCcEE-EEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLF-YIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~-~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+. .|+.+ .+++++++||.+||++|++.+|+|+++|||+|.|+      .|+|+ +|++|||++|++|+++...
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-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGG------TLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             EEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTE------ECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             EEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCc------CCCCC-CHHHCCCCCCCEEEEEecc
Confidence            6899996 58889 69999999999999999999999999999999999      99999 9999999999999998765


Q ss_pred             C
Q 041108           80 L   80 (102)
Q Consensus        80 ~   80 (102)
                      .
T Consensus        80 ~   80 (96)
T 1wgg_A           80 D   80 (96)
T ss_dssp             C
T ss_pred             h
Confidence            4

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.73  E-value=1.4e-17  Score=103.17  Aligned_cols=70  Identities=19%  Similarity=0.214  Sum_probs=65.1

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      ..++..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++..
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 KLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGK------VLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             EEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTE------ECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCe------ECCCcCCHHHCCCCCCCEEEEEEe
Confidence            3566668999999999999999999999999999999999999999      999999999999999999998764

>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=99.73  E-value=1.1e-17  Score=104.41  Aligned_cols=75  Identities=21%  Similarity=0.329  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCcEEEEEecCC-----CcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCC-CCccccCCCCCCCEEE
Q 041108            1 MKVAVEILTGTLFYIQVEND-----ATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHD-EVPLADCGVKDGSHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~-----~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d-~~~L~~~gI~~~~~i~   74 (102)
                      |+|+|+. .|+.+.++++++     +||.+||++|++.+|+|+++|+|+|+|+      .|+| +.+|++|||++|++|+
T Consensus         8 ~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk------~L~D~~~~L~~~~i~~g~~i~   80 (92)
T 1wxv_A            8 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGK------SLKEMETPLSALGIQDGCRVM   80 (92)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTE------EECCSSSBHHHHTCCSSEEEE
T ss_pred             EEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCe------ecCCCcccHHHCCCCCCCEEE
Confidence            6889998 488899999995     9999999999999999999999999999      9988 6689999999999999


Q ss_pred             EEeecCCC
Q 041108           75 LFFKPLDD   82 (102)
Q Consensus        75 l~~~~~~~   82 (102)
                      ++.+....
T Consensus        81 l~~~~~~~   88 (92)
T 1wxv_A           81 LIGKKNSG   88 (92)
T ss_dssp             EESCCSCS
T ss_pred             EEecCCCC
Confidence            99876543

>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=99.73  E-value=1.5e-17  Score=108.13  Aligned_cols=75  Identities=19%  Similarity=0.195  Sum_probs=69.7

Q ss_pred             EEEEEeC----------CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCC
Q 041108            2 KVAVEIL----------TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGS   71 (102)
Q Consensus         2 ~v~V~~~----------~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~   71 (102)
                      +|.|+..          +|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|+|++|+
T Consensus        27 ~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk------~L~D~~tL~~y~i~~g~  100 (115)
T 1we7_A           27 SIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGI------FIKDSNSLAYYNMASGA  100 (115)
T ss_dssp             EEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTE------EECTTSBHHHHTCCSSC
T ss_pred             EEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCE------ECCCCCCHHHCCCCCCC
Confidence            5677765          4778999999999999999999999999999999999999      99999999999999999


Q ss_pred             EEEEEeecCCC
Q 041108           72 HIYLFFKPLDD   82 (102)
Q Consensus        72 ~i~l~~~~~~~   82 (102)
                      +|++.+++.++
T Consensus       101 ~i~lv~rl~GG  111 (115)
T 1we7_A          101 VIHLALKERSG  111 (115)
T ss_dssp             EEEEEECCCSC
T ss_pred             EEEEEEEcCCC
Confidence            99999998875

>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=99.72  E-value=1.6e-17  Score=106.82  Aligned_cols=75  Identities=19%  Similarity=0.267  Sum_probs=69.0

Q ss_pred             CEEEEEeCCC---cEEEEEecC---------CCcHHHHHHHHHhhc--CCCCcc-EEEEeCCCCCCCCccCCCCCccccC
Q 041108            1 MKVAVEILTG---TLFYIQVEN---------DATVADLKREIGAQQ--KLPCDR-LILLLSSDHSCPMTQDHDEVPLADC   65 (102)
Q Consensus         1 M~v~V~~~~g---~~~~i~v~~---------~~TV~dLK~~I~~~~--gip~~~-q~L~~~g~~~~~~~~L~d~~~L~~~   65 (102)
                      |+|+||..+|   +.+.+++++         ++||.+||++|++.+  |+|+++ |+|+|+|+      .|+|+.+|++|
T Consensus        13 ~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk------~L~D~~tL~~y   86 (107)
T 1x1m_A           13 WHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGR------KLKDDQTLDFY   86 (107)
T ss_dssp             CCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTE------ECCTTCBHHHH
T ss_pred             eEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCe------ECCCCCcHHHc
Confidence            7899999998   788999544         599999999999999  999999 99999999      99999999999


Q ss_pred             CCCCCCEEEEEeecCC
Q 041108           66 GVKDGSHIYLFFKPLD   81 (102)
Q Consensus        66 gI~~~~~i~l~~~~~~   81 (102)
                      ||++|++|+++.+...
T Consensus        87 ~i~~g~~i~lv~~~~~  102 (107)
T 1x1m_A           87 GIQPGSTVHVLRKSWS  102 (107)
T ss_dssp             TCCTTCEEEEEESSCC
T ss_pred             CCCCCCEEEEEeCCCC
Confidence            9999999999987654

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

Probab=99.72  E-value=3.1e-17  Score=108.77  Aligned_cols=77  Identities=12%  Similarity=0.152  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHh------hcCC--CCccEEEEeCCCCCCCCccCCCCCccccCCCCCCC-
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGA------QQKL--PCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGS-   71 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~------~~gi--p~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~-   71 (102)
                      |+|+|++.+|+++.+++++++||.+||++|++      +.|+  ++++|||+|+|+      .|+|+.+|++|+|..++ 
T Consensus        18 m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK------~LeD~~TL~~y~I~~~~~   91 (125)
T 2gow_A           18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGR------FLHGNVTLGALKLPFGKT   91 (125)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSS------EEESSCBTGGGCCCTTSE
T ss_pred             EEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCc------CCCCCCcHHHcCCCCCCc
Confidence            68899999999999999999999999999999      6787  489999999999      99999999999999776 


Q ss_pred             -EEEEEeecCCCC
Q 041108           72 -HIYLFFKPLDDG   83 (102)
Q Consensus        72 -~i~l~~~~~~~~   83 (102)
                       ++++.+++.+..
T Consensus        92 ~tlhlv~r~~~~~  104 (125)
T 2gow_A           92 TVMHLVARETLPE  104 (125)
T ss_dssp             EEEEEEECSCCSS
T ss_pred             eEEEEEecCCCCc
Confidence             788888876533

>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=99.72  E-value=4.1e-17  Score=106.98  Aligned_cols=75  Identities=12%  Similarity=0.169  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHh------hcCC--CCccEEEEeCCCCCCCCccCCCCCccccCCCCCC--
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGA------QQKL--PCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDG--   70 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~------~~gi--p~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~--   70 (102)
                      |+|+|++.+|+++.++|++++||.+||++|++      +.++  |+++|||+|.|+      .|+|+.+|++|+|..+  
T Consensus        17 m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK------~LeD~~TL~~y~I~~~~~   90 (116)
T 1wgh_A           17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGR------FLHGNVTLGALKLPFGKT   90 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTE------EECSSCBTTTTTCCSSCE
T ss_pred             EEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCc------CCCCCCcHHHcCCCCCCc
Confidence            78999999999999999999999999999999      5575  699999999999      9999999999999766  


Q ss_pred             CEEEEEeecCC
Q 041108           71 SHIYLFFKPLD   81 (102)
Q Consensus        71 ~~i~l~~~~~~   81 (102)
                      .++|+.++...
T Consensus        91 ~tlhLvlr~~~  101 (116)
T 1wgh_A           91 TVMHLVARETL  101 (116)
T ss_dssp             EEEEEEECSSC
T ss_pred             eEEEEEccCCC
Confidence            57888887654

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.4e-17  Score=106.61  Aligned_cols=79  Identities=15%  Similarity=0.216  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe-CCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLL-SSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~-~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |.++++..+|+++.+++++++||.+||++|++++||||++|||++ .+.      .++|+.+|++|+|++|+++++.++.
T Consensus         9 m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~g------kL~D~~tLs~~~I~~gstL~lvl~~   82 (100)
T 2dzm_A            9 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTG------DVEDSTVLKSLHLPKNNSLYVLTPD   82 (100)
T ss_dssp             EEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSS------CCCTTSBHHHHCCCSEEEEEECCSS
T ss_pred             eEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCC------CCCCcCCHHHcCCCCCCEEEEEecC
Confidence            566777778999999999999999999999999999999999985 455      5799999999999999999999887


Q ss_pred             CCCCCc
Q 041108           80 LDDGST   85 (102)
Q Consensus        80 ~~~~~~   85 (102)
                      .+....
T Consensus        83 ~~~~~~   88 (100)
T 2dzm_A           83 LPPPSS   88 (100)
T ss_dssp             SCCCCS
T ss_pred             CCCCcc
Confidence            664443

>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=99.71  E-value=1.1e-17  Score=105.68  Aligned_cols=73  Identities=19%  Similarity=0.222  Sum_probs=65.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+. +|+.+.+++++++||.+||++|++.+|+|+++|||+|.|+      .|+| .+|++|+|++|++|+++....
T Consensus        18 ~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk------~Ldd-~tL~~~~i~~g~~i~lv~~~~   89 (95)
T 1v86_A           18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL------VPED-KTLREIKVTSGAKIMVVGSTI   89 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB------CCSS-SBHHHHCCCTTEEEEECCSSC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCe------eCCc-CcHHHCCCCCCCEEEEEeccc
Confidence            5788885 5889999999999999999999999999999999999999      8854 599999999999999987654


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      .
T Consensus        90 ~   90 (95)
T 1v86_A           90 S   90 (95)
T ss_dssp             C
T ss_pred             c
Confidence            3

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

Probab=99.70  E-value=1.6e-17  Score=106.06  Aligned_cols=70  Identities=17%  Similarity=0.112  Sum_probs=63.8

Q ss_pred             CEEEEEeCCCc--EEEEEecCCCcHHHHHHHHHhh-cCCC-CccEEEEeCCCCCCCCccCCCCCccccC--CCCCCCEEE
Q 041108            1 MKVAVEILTGT--LFYIQVENDATVADLKREIGAQ-QKLP-CDRLILLLSSDHSCPMTQDHDEVPLADC--GVKDGSHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~--~~~i~v~~~~TV~dLK~~I~~~-~gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~--gI~~~~~i~   74 (102)
                      |+|+||+.+|+  .+.+++++++||.+||++|+++ .|.| +++|||+|+|+      .|+|+.+|++|  +|++|++|+
T Consensus        24 m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk------~L~D~~tL~~y~~~I~~~~tih   97 (99)
T 2kdb_A           24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGR------LLPDHLQLKDILRKQDEYHMVH   97 (99)
T ss_dssp             EEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTE------EECTTSBTHHHHTTTCSEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCE------ECCCCCCHHHHhcCCCCCCEEE
Confidence            78999999887  5789999999999999999986 5665 59999999999      99999999999  999999998


Q ss_pred             EE
Q 041108           75 LF   76 (102)
Q Consensus        75 l~   76 (102)
                      |.
T Consensus        98 Lv   99 (99)
T 2kdb_A           98 LV   99 (99)
T ss_dssp             EC
T ss_pred             eC
Confidence            73

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=4.3e-17  Score=101.88  Aligned_cols=69  Identities=22%  Similarity=0.211  Sum_probs=63.0

Q ss_pred             CEEEEEeCCCcEE--EE-EecCCCcHHHHHHHHHhh-cCCCCccEEEEeC--CCCCCCCccCCCCCccccCCCCCCCEEE
Q 041108            1 MKVAVEILTGTLF--YI-QVENDATVADLKREIGAQ-QKLPCDRLILLLS--SDHSCPMTQDHDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~~~--~i-~v~~~~TV~dLK~~I~~~-~gip~~~q~L~~~--g~~~~~~~~L~d~~~L~~~gI~~~~~i~   74 (102)
                      |+|+|+++.|+.+  .+ +|++++||.+||++|+++ .|+||++|+|.|.  |+      .|+|+.+|++|+|++|++|+
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk------~L~D~~tL~~y~i~~~stl~   84 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGK------SLKDEDVLQKLPVGTTATLY   84 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSC------CCCTTCBTTTSSCCSEEEEE
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCc------CcCCCCCHHHcCCCCCCEEE
Confidence            8999999988664  58 999999999999999994 8999999999987  77      99999999999999999977


Q ss_pred             E
Q 041108           75 L   75 (102)
Q Consensus        75 l   75 (102)
                      +
T Consensus        85 ~   85 (88)
T 2dzj_A           85 F   85 (88)
T ss_dssp             E
T ss_pred             E
Confidence            5

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

Probab=99.67  E-value=1.2e-16  Score=98.86  Aligned_cols=75  Identities=16%  Similarity=0.259  Sum_probs=64.5

Q ss_pred             CEEEEEeCCCcEEEEE-ecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC-CCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQ-VENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH-DEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~-v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~-d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+||+.+|+. .++ +++++||.+||++|++++|+|+++|+|++++.|.++  .++ |+.+|++|||.+|++|++.-.
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l--~l~~~~~tL~~~gl~~g~~l~v~~~   77 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECL--DLSDRDITLGDLPIQSGDMLIVEED   77 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCC--CCCCSSCBTTTSSCCTTCEEECCCC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCccc--ccCCCCCCHHHcCCCCCCEEEEEeC
Confidence            899999999965 477 999999999999999999999999999998653322  233 789999999999999988755

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.67  E-value=1.9e-16  Score=118.40  Aligned_cols=73  Identities=26%  Similarity=0.435  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++.+++
T Consensus       234 MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk------~L~D~~TLsdygI~~gstL~LvlRL  306 (307)
T 3ai5_A          234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRL  306 (307)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCTTSBTGGGTCCTTCEEEEEC--
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCe------ecCCCCCHHHcCCCCCCEEEEEEeC
Confidence            789999999999999999999999999999999999999999999999      9999999999999999999999875

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=2.4e-16  Score=103.34  Aligned_cols=74  Identities=20%  Similarity=0.185  Sum_probs=67.6

Q ss_pred             EEEEE-eCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            2 KVAVE-ILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         2 ~v~V~-~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      .|.|+ ...|+.+.++++++.||.+||++++++.++|+++|+|+|+|+      .|+|+.+|++|||++|.+|||..+..
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GK------iLKD~eTL~~~gIk~g~TIhLvi~s~   90 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGK------ILKNNETLVQHGVKPQEIVQVEIFST   90 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTE------EECSSCCHHHHSCCSSCEEEEEEEES
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCe------EcCCcchHHHcCCCCCCEEEEEEecC
Confidence            34555 446788999999999999999999999999999999999999      99999999999999999999999875


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      +
T Consensus        91 ~   91 (118)
T 2daf_A           91 N   91 (118)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.66  E-value=6.1e-18  Score=119.00  Aligned_cols=84  Identities=23%  Similarity=0.279  Sum_probs=8.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++++|+++.++|++++||.+||.+|+...|+|+++|+|+|+|+      .|+|+.+|+     ++++|+|.+++.
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK------~LeD~~TLs-----~~STLhLvlRLr   69 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGF------IAPNTELVT-----DDVTYYLSLKLL   69 (189)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCe------ECCCCCccc-----CCCEEEEEEecC
Confidence            899999999999999999999999999999999999999999999999      999999998     899999999988


Q ss_pred             CCCC-ceeEEEecCCc
Q 041108           81 DDGS-TQHSVFTIPEW   95 (102)
Q Consensus        81 ~~~~-~~~~~~~~~~~   95 (102)
                      ++.. ++...+++|..
T Consensus        70 GG~~krkK~~~~tPK~   85 (189)
T 2xzm_9           70 GGKKKKKKKSYTTKKK   85 (189)
T ss_dssp             --CCCCCCCCCCSSSC
T ss_pred             CCcccccccccCCCcc
Confidence            7543 44677888853

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

Probab=99.66  E-value=3.3e-16  Score=99.23  Aligned_cols=75  Identities=21%  Similarity=0.278  Sum_probs=61.8

Q ss_pred             EEEEEeCCCc--EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGT--LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~--~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      .|+|+...++  .+.+++++++||++||++|+..+|+||++|||+|.|.+.....+++|+++|++|||++|++|++.
T Consensus        17 ~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           17 KVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             EEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             EEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            5777776653  78999999999999999999999999999999998510000014599999999999999999985

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.65  E-value=1.9e-16  Score=101.93  Aligned_cols=78  Identities=19%  Similarity=0.252  Sum_probs=66.9

Q ss_pred             CEEEEEeCCCcEEEEEec-CCCcHHHHHHHHHhhcCCCCccEEEEeCCCCC---------CCCccCCCCCccccCCCCCC
Q 041108            1 MKVAVEILTGTLFYIQVE-NDATVADLKREIGAQQKLPCDRLILLLSSDHS---------CPMTQDHDEVPLADCGVKDG   70 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~-~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~---------~~~~~L~d~~~L~~~gI~~~   70 (102)
                      |+|+||+.+|+. .++|+ +++||.+||++|++++|+|+++|+|.+.+++.         .+...++|+++|++|||++|
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            789999999976 78999 99999999999999999999999998887621         11111689999999999999


Q ss_pred             CEEEEEeec
Q 041108           71 SHIYLFFKP   79 (102)
Q Consensus        71 ~~i~l~~~~   79 (102)
                      ++|+|....
T Consensus        87 ~~L~l~~~~   95 (107)
T 1wf9_A           87 SMVYLAYEG   95 (107)
T ss_dssp             CEEECCCSS
T ss_pred             CEEEEEeCC
Confidence            999998764

>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=99.63  E-value=7e-16  Score=117.72  Aligned_cols=75  Identities=24%  Similarity=0.395  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHh---hcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEE-EEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGA---QQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHI-YLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~---~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i-~l~   76 (102)
                      |+|+||+.+|+++.++|++++||.+||++|+.   +.|+|+++|||+|+|+      .|+|+.+|++|+|++|++| ++.
T Consensus         8 M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK------~L~D~~tL~dygI~~gstIv~lv   81 (368)
T 1oqy_A            8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGK------ILSDDVPIRDYRIDEKNFVVVMV   81 (368)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSS------EECSSSBTTTTCCCTTSCEEEEE
T ss_pred             EEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCe------ecCCcCCHHHcCCCCCCEEEEEE
Confidence            89999999999999999999999999999999   6789999999999999      9999999999999999999 555


Q ss_pred             eecCC
Q 041108           77 FKPLD   81 (102)
Q Consensus        77 ~~~~~   81 (102)
                      .+..+
T Consensus        82 ~k~~~   86 (368)
T 1oqy_A           82 TKTKA   86 (368)
T ss_dssp             ECCCS
T ss_pred             ecCCC
Confidence            55443

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.62  E-value=2.2e-15  Score=93.77  Aligned_cols=78  Identities=13%  Similarity=0.031  Sum_probs=61.8

Q ss_pred             EEEEeC--CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCC-CccCCCCCccccCCCCCCCEEEEEeec
Q 041108            3 VAVEIL--TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCP-MTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         3 v~V~~~--~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~-~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |.|...  .++.+.+.+++++||.+||++|+..+|+||+.|+|+|.+..... ...++|+++|++|||++|++||+.-..
T Consensus         5 v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~~   84 (86)
T 4b6w_A            5 VSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDLQ   84 (86)
T ss_dssp             EEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             EEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeCC
Confidence            444433  34667899999999999999999999999999999974321110 128999999999999999999998654


Q ss_pred             C
Q 041108           80 L   80 (102)
Q Consensus        80 ~   80 (102)
                      |
T Consensus        85 P   85 (86)
T 4b6w_A           85 P   85 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.61  E-value=2.1e-15  Score=95.86  Aligned_cols=76  Identities=14%  Similarity=0.079  Sum_probs=61.9

Q ss_pred             EEEEEeCCC--cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCC-CCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDH-SCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g--~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~-~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      .|+|.....  ..+.+++++++||++||++|+..+|+||++|||+|.|+. .....+++|+++|++|+|++|++|++.=
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            466776544  468999999999999999999999999999999998831 1110135999999999999999999873

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.59  E-value=3.6e-15  Score=93.81  Aligned_cols=78  Identities=17%  Similarity=0.140  Sum_probs=62.7

Q ss_pred             EEEEEeCCCc-EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC-CCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            2 KVAVEILTGT-LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD-HSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         2 ~v~V~~~~g~-~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~-~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .|+|+..++. .+.+++++++||++||++|+..+|+|+++|||+|.|+ +.....+++|+++|++|||++|++|++.-..
T Consensus         9 ~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d~~   88 (95)
T 1v6e_A            9 MVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDHS   88 (95)
T ss_dssp             EEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCCS
T ss_pred             EEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEECC
Confidence            5677776543 6889999999999999999999999999999999872 0000003589999999999999999987533

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=99.56  E-value=1.6e-14  Score=94.76  Aligned_cols=79  Identities=15%  Similarity=0.125  Sum_probs=63.8

Q ss_pred             EEEEEeCCCc-EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC-CCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            2 KVAVEILTGT-LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD-HSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         2 ~v~V~~~~g~-~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~-~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .|+|+..++. .+.+++++++||++||.+|+..+|+|+++|||+|.|. +..+..+++|+++|++|||++|++||+.-..
T Consensus         8 ~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd~~   87 (122)
T 1t0y_A            8 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVT   87 (122)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECT
T ss_pred             EEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEeCC
Confidence            5677776553 5889999999999999999999999999999999872 0000003589999999999999999999654


Q ss_pred             C
Q 041108           80 L   80 (102)
Q Consensus        80 ~   80 (102)
                      +
T Consensus        88 p   88 (122)
T 1t0y_A           88 G   88 (122)
T ss_dssp             T
T ss_pred             C
Confidence            4

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

Probab=99.55  E-value=1.1e-14  Score=109.31  Aligned_cols=74  Identities=19%  Similarity=0.251  Sum_probs=65.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEE---eCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILL---LSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~---~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |.|+|+. +|+.+.+++++++||++||++|++.+|+||++|||+   |+|+      .|+|+.+|++|||++|++|+++.
T Consensus         6 i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk------~l~D~~~L~~~~ik~g~~l~L~g   78 (320)
T 3shq_A            6 VVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGK------TAADNVKISALELKPNFKLMMVG   78 (320)
T ss_dssp             EEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSS------BCCTTSBTTSSCCC--CEEEEEC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCc------ccCccccHHHcCCCCCCEEEEEc
Confidence            4678886 689999999999999999999999999999999999   8999      99999999999999999999986


Q ss_pred             ecCC
Q 041108           78 KPLD   81 (102)
Q Consensus        78 ~~~~   81 (102)
                      ...+
T Consensus        79 s~~~   82 (320)
T 3shq_A           79 STEA   82 (320)
T ss_dssp             CCC-
T ss_pred             cchh
Confidence            5443

>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=99.51  E-value=7.7e-14  Score=88.09  Aligned_cols=77  Identities=12%  Similarity=0.189  Sum_probs=73.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|.|+..+|+.+.+.|.+++++..|+++++++.|++++.|+++|.|+      .|+++.++++|++.+|++|+++++..
T Consensus         8 i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~------~l~~~~Tp~dl~medgD~Idv~~~~~   81 (94)
T 2io1_B            8 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQ------PINETDTPAQLEMEDEDTIDVFQQQT   81 (94)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTCCTTTTTCCTTCEEEEEECCE
T ss_pred             EEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            678999999999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        82 GG~   84 (94)
T 2io1_B           82 GGV   84 (94)
T ss_dssp             ESC
T ss_pred             CCC
Confidence            763

>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=99.46  E-value=4.9e-13  Score=84.01  Aligned_cols=78  Identities=12%  Similarity=0.178  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|.|+..+|+.+.+.|.+++++..|+++++++.|++++.++++|.|.      .+.++.|.+++++.+|++|.++....
T Consensus         6 i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~------~l~~~~Tp~dl~medgD~Idv~~~q~   79 (91)
T 2io0_B            6 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQ------PINETDTPAQLEMEDEDTIDVFQQQT   79 (91)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTE------ECCTTCCTTTTTCCTTEEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            578888889999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      ++.-
T Consensus        80 gg~~   83 (91)
T 2io0_B           80 GGVY   83 (91)
T ss_dssp             CCCC
T ss_pred             CCcc
Confidence            7543

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.43  E-value=8.4e-13  Score=83.11  Aligned_cols=79  Identities=18%  Similarity=0.252  Sum_probs=63.7

Q ss_pred             EEEEEe---CCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCC--CccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEI---LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCP--MTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~---~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~--~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      .|+|+.   .+|+.+...+..++||++||.+|+..+|+|+..|+|.|.+...+.  ..+.+|+++|+.||+.+|++|+|.
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            455664   467888999999999999999999999999999999987532121  113488899999999999999998


Q ss_pred             eecC
Q 041108           77 FKPL   80 (102)
Q Consensus        77 ~~~~   80 (102)
                      ...+
T Consensus        91 d~~p   94 (97)
T 1wjn_A           91 WSGP   94 (97)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            7543

>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=99.43  E-value=5.8e-13  Score=79.92  Aligned_cols=71  Identities=13%  Similarity=0.219  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|.|+..+|+.+.+.+.+++++..|+++++++.|++++.++++|.|.      .+.++.+.+++++.+|++|++++
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~------~l~~~~Tp~~l~medgD~Idv~~   72 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQ------PINETDTPAQLEMEDEDTIDVFQ   72 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTE------ECCTTCCTTTTTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEC
Confidence            578999999999999999999999999999999999999999999999      99999999999999999999863

>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=99.42  E-value=1.3e-12  Score=82.20  Aligned_cols=75  Identities=12%  Similarity=0.208  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |.|.|+..+|+.+.+.|.+++++..|+.+++++.|++++.++++|.|.      .|.++.|.++|++.+|++|++++...
T Consensus        18 i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~------~l~~~~Tp~dl~medgD~Idv~~~q~   91 (93)
T 2d07_B           18 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQ------PINETDTPAQLEMEDEDTIDVFQQQT   91 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTCCTTTTTCCTTEEEEEEECC-
T ss_pred             EEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCE------EcCCCCCHHHcCCCCCCEEEEEeecc
Confidence            568888888999999999999999999999999999999999999999      99999999999999999999998876


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      |
T Consensus        92 G   92 (93)
T 2d07_B           92 G   92 (93)
T ss_dssp             -
T ss_pred             C
Confidence            5

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.41  E-value=1.1e-12  Score=84.32  Aligned_cols=78  Identities=13%  Similarity=0.205  Sum_probs=73.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|.|+..+|+.+.+.|.++.++..|+.+++++.|++++.++++|.|.      .|.++.|..+|++.+|++|++++...
T Consensus        25 I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~------~l~~~~Tp~dl~medgD~Idv~~~q~   98 (104)
T 1wz0_A           25 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQ------PINETDTPAQLEMEDEDTIDVFQQQT   98 (104)
T ss_dssp             EEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSS------BCCTTSCTTTTTCCTTEEEEECCCCC
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            578899889999999999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCCC
Q 041108           81 DDGS   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      ++.+
T Consensus        99 GG~~  102 (104)
T 1wz0_A           99 SGPS  102 (104)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7654

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.36  E-value=3.5e-12  Score=77.91  Aligned_cols=70  Identities=16%  Similarity=0.234  Sum_probs=66.6

Q ss_pred             CEEEEEeCCCc-EEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGT-LFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~-~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |+|.|+..+|+ .+.+.+.+++++..|+.+++++.|++++.++++|.|.      .+.++.+.+++++.+|++|+++
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 LRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGT------KLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             EEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTE------ECCSCCCHHHHTCCTTCEEEEE
T ss_pred             EEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCE------EcCCCCCHHHcCCCCCCEEEEe
Confidence            57889999995 8999999999999999999999999999999999999      9999999999999999999986

>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=99.33  E-value=6.2e-12  Score=81.05  Aligned_cols=74  Identities=12%  Similarity=0.175  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|.|+. +|+...+.+..++++..|+.+++++.|++++.++++|.|+      .+.++.|.+++++.+|++|.+++...
T Consensus        32 I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~------rl~~~~Tp~dl~medgD~Idv~~~q~  104 (106)
T 2eke_C           32 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQTPEDLDMEDNDIIEAHREQI  104 (106)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTCCTTTTTCCTTEEEEEEECC-
T ss_pred             EEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCe------EcCCCCCHHHcCCCCCCEEEEEeecc
Confidence            5788888 8999999999999999999999999999999999999999      99999999999999999999998876


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      |
T Consensus       105 G  105 (106)
T 2eke_C          105 G  105 (106)
T ss_dssp             -
T ss_pred             c
Confidence            5

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.32  E-value=3.1e-12  Score=82.98  Aligned_cols=77  Identities=12%  Similarity=0.185  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|.|+..+|+.+.+.|.+++++..|+.+++++.|++++.++++|.|.      .|.++.|.++|++.+|++|.+++...
T Consensus        27 I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~------~L~~~~Tp~dl~mEDgD~Idv~~~q~  100 (110)
T 2k8h_A           27 VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGT------PIDETKTPEELGMEDDDVIDAMVEQT  100 (110)
T ss_dssp             EEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSC------BCCSSSHHHHHHCSSEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEEccc
Confidence            578999999999999999999999999999999999999999999999      99999999999999999999999887


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus       101 Gg~  103 (110)
T 2k8h_A          101 GGL  103 (110)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            654

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=99.29  E-value=1.6e-12  Score=79.81  Aligned_cols=74  Identities=14%  Similarity=0.259  Sum_probs=62.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |.++||+.+|. +.+++++++|+.+|+++|++.++++++.|.+.++..|..+. .+.++.+|+++|+++||.|++.
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 IIIRVQSPDGV-KRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEI-TASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCEEECSSEE-EECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCGGGGS-SSCCCCTTTTTCCCTTCCEEC-
T ss_pred             EEEEEECCCCC-EEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCCCCcc-cCCCCCCHHHcCCCCCCEEEEe
Confidence            67899999884 67889999999999999999999999999998888752111 2348889999999999999874

>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=99.06  E-value=1.4e-09  Score=70.88  Aligned_cols=74  Identities=16%  Similarity=0.228  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      ++|.|+..+|....+.+..+.++..|+.+.+++.|++++.++++|.|.      .+.++.|..++++.+|++|.++....
T Consensus        41 I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~------rI~~~~TP~dL~MEDgD~IdV~~~Q~  114 (115)
T 3kyd_D           41 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQ------RIADNHTPKELGMEEEDVIEVYQEQC  114 (115)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTE------ECCTTCCTTTTTCCTTCEEEEEECCC
T ss_pred             EEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCe------ECCCCCCHHHcCCCCCCEEEEEeecc
Confidence            357788888998999999999999999999999999999999999999      99999999999999999999998654

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.93  E-value=8.3e-09  Score=72.97  Aligned_cols=79  Identities=13%  Similarity=0.174  Sum_probs=71.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      +|.|+. +|+...+.+..++++..|+.+.+++.|++++.+|++|.|+      .+.++.|..++++.+|++|.++....+
T Consensus        31 ~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~------rI~~~~TP~dL~MEdgD~Idv~~~q~g  103 (200)
T 3pge_A           31 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQTPEDLDMEDNDIIEAHREQIG  103 (200)
T ss_dssp             EEEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTE------ECCTTCCTTTTTCCTTEEEEEEECCSC
T ss_pred             EEEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCE------EcCCCCCHHHcCCCCCCEEEEEeccCc
Confidence            567764 7899999999999999999999999999999999999999      999999999999999999999999887


Q ss_pred             CCCcee
Q 041108           82 DGSTQH   87 (102)
Q Consensus        82 ~~~~~~   87 (102)
                      +....+
T Consensus       104 g~kd~v  109 (200)
T 3pge_A          104 GGGETI  109 (200)
T ss_dssp             CC-CCE
T ss_pred             CcCceE
Confidence            665443

>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=98.74  E-value=2.2e-08  Score=70.63  Aligned_cols=76  Identities=12%  Similarity=0.152  Sum_probs=70.1

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      .|.|+. +|....+.|..+.++..|+++.+++.|+++..++++|.|.      .+.++.|..++++.+||+|.+++...+
T Consensus        59 nLKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGq------RI~~ddTPeDLdMEDGDtIDV~leQ~G  131 (207)
T 3tix_A           59 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGI------EIQADQTPEDLDMEDNDIIEAHREQIG  131 (207)
T ss_dssp             EEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTE------ECCSSCCTTTTTCCTTEEEEECCCCCT
T ss_pred             EEEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCe------ecCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            466753 7889999999999999999999999999999999999999      999999999999999999999999887


Q ss_pred             CCC
Q 041108           82 DGS   84 (102)
Q Consensus        82 ~~~   84 (102)
                      +..
T Consensus       132 G~~  134 (207)
T 3tix_A          132 GLP  134 (207)
T ss_dssp             TGG
T ss_pred             CCc
Confidence            654

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.57  E-value=1.6e-09  Score=77.38  Aligned_cols=84  Identities=11%  Similarity=0.107  Sum_probs=4.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |.|.| ..+|+...+.+..++++..|+++.+++.|++++.+|++|.|+      .+.++.|.+++++.+||+|.++....
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGq------RI~dddTPadL~MEDGDtIDV~leQ~   94 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQTPEDLDMEDNDIIEAHREQI   94 (227)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCE------ecCCCCCHHHcCCCCCCEEEEEeccc
Confidence            45677 567888899999999999999999999999999999999999      99999999999999999999999988


Q ss_pred             CCCCceeEEEe
Q 041108           81 DDGSTQHSVFT   91 (102)
Q Consensus        81 ~~~~~~~~~~~   91 (102)
                      |+..-..++.+
T Consensus        95 GG~~~~~l~~~  105 (227)
T 3v7o_A           95 GGLTLAVLLQI  105 (227)
T ss_dssp             -CCCHHHHHHH
T ss_pred             CCchHhHHHHH
Confidence            87654443333

>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=98.57  E-value=6.4e-07  Score=54.68  Aligned_cols=69  Identities=13%  Similarity=0.183  Sum_probs=62.6

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD-RLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +-+|+.....+.+.+.++.+|.+|..+-..+.|++++ ..++.|.|.      -|++++++.+|++.+|+.|-+++
T Consensus        12 ~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGd------RLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           12 LLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGE------WLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEESSSCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTE------ECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HhhhccCCCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCc------ccCccCChhhhCCcCCceeeeee
Confidence            4456655566899999999999999999999999999 899999999      99999999999999999999875

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.52  E-value=5.1e-07  Score=56.85  Aligned_cols=64  Identities=11%  Similarity=0.000  Sum_probs=50.1

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCC-CCCEEEEE
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVK-DGSHIYLF   76 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~-~~~~i~l~   76 (102)
                      .++.+.+.++++.|+..||++|++++|||++.|+|+|.|+  +.  .++++.+...|.-. ...-|.++
T Consensus        22 ~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~--~l--~l~p~~~a~~~p~Tt~~~Pl~L~   86 (94)
T 4efo_A           22 QMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGR--RL--VLEPGRLAQHFPKTTEENPIFVV   86 (94)
T ss_dssp             TTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTE--EE--CCCTTCBGGGSCCCBTTBCEEEE
T ss_pred             cceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCC--cc--ccCCCCccccCCCCCCCCCEEEE
Confidence            4678899999999999999999999999999999999996  01  35666777676553 33444444

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.44  E-value=1e-06  Score=55.65  Aligned_cols=69  Identities=14%  Similarity=0.207  Sum_probs=63.5

Q ss_pred             EEEEEeCCC-cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTG-TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g-~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      .|.|+..+| +...+.+..+.++..|..+.+++.|+++...+++|.|.      .+.++.|..++++.+|++|.++
T Consensus        27 ~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~------rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           27 QLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGT------KLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             EEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTE------ECCSCSCHHHHTCCTTEEEEEE
T ss_pred             EEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCE------EcCCCCCHHHcCCCCCCEEEEe
Confidence            567777788 47899999999999999999999999999999999999      9999999999999999999875

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=98.25  E-value=1.5e-06  Score=57.52  Aligned_cols=75  Identities=20%  Similarity=0.211  Sum_probs=56.8

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEeCCC-C--------------------------CCC--
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD-RLILLLSSD-H--------------------------SCP--   52 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~~g~-~--------------------------~~~--   52 (102)
                      +.|+.++|+..++.|+.+.||++++..|..+.|++.. +--|..... +                          ..+  
T Consensus        14 LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~kL~~   93 (128)
T 2kc2_A           14 LKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQKLHT   93 (128)
T ss_dssp             EEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCSCCC
T ss_pred             EEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccccccccccccCchhhccccccccchhHHHHHHHHhcc
Confidence            7899999999999999999999999999999998744 222322110 0                          000  


Q ss_pred             ---CccCCCCCccccCCCCCCCEEEEEe
Q 041108           53 ---MTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus        53 ---~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                         .+-|+++.+|.++||.+++++.+-.
T Consensus        94 dd~~~WLD~srtL~EQGI~e~~tllLRr  121 (128)
T 2kc2_A           94 DDELNWLDHGRTLREQGVEEHETLLLRR  121 (128)
T ss_dssp             SSSEEEECSSSCHHHHTCCTTSEEEEEE
T ss_pred             cCCCCcccCCCcHHHcCCCCCCEEEEEE
Confidence               0246778999999999999987754

>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=98.20  E-value=6.6e-06  Score=58.03  Aligned_cols=75  Identities=12%  Similarity=0.164  Sum_probs=67.6

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      .|.|+. +|+...+.+..++++..|+++.+++.|++++.++++|.|+      .+.++.+..++.+.++++|.++....+
T Consensus        23 ~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~------~i~~~~Tpk~L~~ed~d~I~~~~eq~G   95 (209)
T 3uf8_A           23 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQTPEDLDMEDNDIIEAHREQIG   95 (209)
T ss_dssp             EEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTE------ECCTTCCTTTTTCCTTEEEEEECSCTT
T ss_pred             EEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCE------eccCCCChHHhhhcccccchhhccccc
Confidence            456665 6777889999999999999999999999999999999999      999999999999999999999988776


Q ss_pred             CC
Q 041108           82 DG   83 (102)
Q Consensus        82 ~~   83 (102)
                      +.
T Consensus        96 g~   97 (209)
T 3uf8_A           96 GS   97 (209)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=98.17  E-value=6.9e-06  Score=51.24  Aligned_cols=73  Identities=8%  Similarity=0.034  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |.|+|-..+|+...+.|.++.++.|+-+...+++|+++++-.|.|+++      .++-+.++.-.|+.+|+.+.+....
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 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRT------VLDLSLQWRFANLPNNAKLEMVPVS   82 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTE------EESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCE------eccccceeEecCCCCCCEEEEEEcc
Confidence            678899999999999999999999999999999999999999999999      9999999999999999999998643

>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=98.11  E-value=4.3e-05  Score=46.40  Aligned_cols=71  Identities=11%  Similarity=0.122  Sum_probs=58.3

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC---CCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD---HDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L---~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +|.||..+|+...-....++||.+|...|.+ .+.++....|+.+..    .+.+   +.+++|.++|+.++++|++-.
T Consensus         9 ~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t~fP----rk~l~~~d~~~TL~e~gL~p~a~L~ve~   82 (84)
T 3qx1_A            9 KLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFP----RRDVTQLDPNKSLLEVKLFPQETLFLEA   82 (84)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEECSSS----CCBGGGSCTTSBTTTTTCCSEEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEeCCC----CCCCcCCCCCCCHHHCCCCCCCEEEEEe
Confidence            5889999999888888999999999999998 567888888885432    1144   567899999999999998853

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=98.10  E-value=4.2e-07  Score=69.16  Aligned_cols=74  Identities=12%  Similarity=0.165  Sum_probs=0.0

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      .|.|+. +|+...+.+..++++..|+++.+++.|++++.++++|.|+      .+.++.|.+++++.+||+|.++....+
T Consensus        23 ~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~------rI~~~~TP~~L~MEDgD~Idv~~~Q~g   95 (360)
T 3ix6_A           23 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQTPEDLDMEDNDIIEAHREQIG   95 (360)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEec-CCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCe------ECCCCCChHHcCCCccchhhhhhccCc
Confidence            455665 5677889999999999999999999999999999999999      999999999999999999999998765


Q ss_pred             C
Q 041108           82 D   82 (102)
Q Consensus        82 ~   82 (102)
                      +
T Consensus        96 ~   96 (360)
T 3ix6_A           96 G   96 (360)
T ss_dssp             -
T ss_pred             h
Confidence            4

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.09  E-value=2e-05  Score=49.55  Aligned_cols=70  Identities=7%  Similarity=0.096  Sum_probs=64.1

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      .|.|+. +|....+.+..+.....|..+.+++.|+++++.+++|.|.      -+.++.|-.++++.+|++|.+++-
T Consensus        23 niKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~------rI~~~~TP~~L~meD~DiID~~~~   92 (95)
T 2l76_A           23 PLKIRC-RADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGET------ELSPTATPRTLKLGVADIIDCVVL   92 (95)
T ss_dssp             EEEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTE------ECCTTSCHHHHTCCSSCEEEEEEC
T ss_pred             EEEEEc-CCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCc------CCCCCCCHhHcCCCCCCEEEEEEe
Confidence            466774 5788999999999999999999999999999999999999      999999999999999999998863

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.06  E-value=1.2e-05  Score=49.21  Aligned_cols=68  Identities=15%  Similarity=0.345  Sum_probs=56.2

Q ss_pred             EEEEEeC--CCcEEEEEecCCCcHHHHHHHHHhhcCCCCc-----cEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEE
Q 041108            2 KVAVEIL--TGTLFYIQVENDATVADLKREIGAQQKLPCD-----RLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         2 ~v~V~~~--~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~-----~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~   74 (102)
                      .|++...  .|+.+.+.++...|+.+|.+.+-+..+++..     +.|+.-.+.      .|.++..|.+|+|++||.+.
T Consensus         6 ~ITidl~~y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~~~~~~~~~irv~NK~~------~L~~~~~L~d~~ItnGD~Le   79 (81)
T 2bps_A            6 DITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDK------VFSGECKLSDCGITNGDRLE   79 (81)
T ss_dssp             EEEEECTTTTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTE------EEETTSBTGGGTCCTTCEEE
T ss_pred             EEEEEeeccCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCE------EEcCCCEEeeCCcCCCCEEE
Confidence            4566653  5799999999999999999999999997642     235555666      88999999999999999987


Q ss_pred             E
Q 041108           75 L   75 (102)
Q Consensus        75 l   75 (102)
                      +
T Consensus        80 i   80 (81)
T 2bps_A           80 I   80 (81)
T ss_dssp             E
T ss_pred             E
Confidence            5

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=97.80  E-value=2.8e-06  Score=64.41  Aligned_cols=74  Identities=12%  Similarity=0.158  Sum_probs=0.0

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      |.|+. +|....+.+..++++..|++..+++.|+++.+++++|.|+      .+.++.|.+++++.+|++|.++....++
T Consensus        33 lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~------~i~~~~Tp~~l~med~d~i~~~~~q~gg  105 (389)
T 4da1_A           33 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQAPEDLDMEDNDIIEAHREQIGG  105 (389)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEec-CCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCE------EcCCCCCHHHcCCCCCCEeeeeeccccc
Confidence            44554 5677789999999999999999999999999999999999      9999999999999999999999887664


Q ss_pred             C
Q 041108           83 G   83 (102)
Q Consensus        83 ~   83 (102)
                      .
T Consensus       106 ~  106 (389)
T 4da1_A          106 E  106 (389)
T ss_dssp             -
T ss_pred             c
Confidence            4

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A

Probab=97.76  E-value=0.00033  Score=44.64  Aligned_cols=73  Identities=12%  Similarity=0.099  Sum_probs=59.9

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC---CCCccccCCCCCCCEEEEEee
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH---DEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~---d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      +|.||..+|+...-....++||.+|...|.+..+.+.....|+....    .+.+.   .+++|.++|+.+.+++++...
T Consensus        15 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fP----rk~l~~~d~~~TL~elgL~psa~L~v~~~   90 (109)
T 2dzk_A           15 RIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFP----RREFTREDYKRRLLDLELAPSASVVLLPA   90 (109)
T ss_dssp             EEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSS----CCBCCTTTTTSBTGGGTCSSEEEEEEECC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCC----CcCCcccccCCCHHHCCCCCceEEEEEEC
Confidence            58899999998888999999999999999998877777777875433    12553   478999999999988888764

>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=97.57  E-value=0.00056  Score=44.59  Aligned_cols=71  Identities=14%  Similarity=0.235  Sum_probs=57.9

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC---CCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD---HDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L---~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +|.||..+|+.+.-....++||.+|...|... +.++....|+....    .+.+   +.+++|.++|+.+.++|+|.-
T Consensus        45 ~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~~~~~~F~L~t~fP----rk~l~~~d~~~TL~e~gL~psa~Liv~~  118 (124)
T 1wj4_A           45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFP----RRKLSHLDYDITLQEAGLCPQETVFVQE  118 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSS----CCEETSSCSSSCTTTTTCCSSBCCEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEecCCC----CcCCccCCCCCCHHHCCCCCceEEEEEE
Confidence            58899999998888899999999999999887 77778888875432    1255   457999999999988887763

>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=97.45  E-value=0.0017  Score=41.23  Aligned_cols=72  Identities=14%  Similarity=-0.028  Sum_probs=57.0

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC--CCCCccccCCCCCCCEEEEEee
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD--HDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L--~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      +|.||..+|+.+.-....++||.+|...|... +..+....|+....    .+.+  +.+.+|.++|+.+.+++.|...
T Consensus        25 ~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~~~~~~f~L~t~fP----rk~l~~d~~~TL~e~gL~p~a~L~Ve~~   98 (109)
T 2cr5_A           25 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFP----RRALEVEGGSSLEDIGITVDTVLNVEEK   98 (109)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSS----CCBCCCCSSCBHHHHTCSSCEEEEEEEC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEEeCCC----CcCCCCCCCCCHHHcCCCCCeEEEEEeC
Confidence            58899999998888888999999999999975 55667778876432    1144  4579999999999999877654

>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=97.12  E-value=0.0019  Score=42.10  Aligned_cols=69  Identities=7%  Similarity=0.204  Sum_probs=53.6

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhc-CCCCccEEEEeCCCCCCCCccC-CCCCccccCCCCCCCEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQ-KLPCDRLILLLSSDHSCPMTQD-HDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~-gip~~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~~~~~i~   74 (102)
                      +|.||..+|+...-....++||.+|...|.+.. +.......|+....    .+.+ +++++|.++|+.+..+++
T Consensus        54 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fP----rk~l~d~~~TL~eagL~psavl~  124 (127)
T 1s3s_G           54 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFP----NKELADENQTLKEANLLNAVIVQ  124 (127)
T ss_dssp             CEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTT----TEECCSTTCBHHHHTCSSCEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCC----CCCCCCCCCcHHHCCCcCceEEE
Confidence            588999999988889999999999999999863 35566677876543    2255 457999999999855443

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=96.79  E-value=0.0069  Score=35.93  Aligned_cols=61  Identities=21%  Similarity=0.302  Sum_probs=47.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+........+++++..|++||-+    +.|+++..-.+..+|.      .+..+..      .+||.+.++-
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~----~Lgl~~~~VvV~vNG~------~v~~d~~------l~GD~VeIv~   61 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVR----AVDLSPHEVTVLVDGR------PVPEDQS------VEVDRVKVLR   61 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHH----TTCCCSSCCCEECCCC------CCCTTSS------SCCCCEEECS
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHH----HcCCCcceEEEEECCE------ECCHHHC------CCCCEEEEEE
Confidence            8999999844556789999999999874    5789998887888998      6655542      2488888764

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.62  E-value=0.0067  Score=37.39  Aligned_cols=65  Identities=15%  Similarity=0.181  Sum_probs=55.6

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKD   69 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~   69 (102)
                      ++.|+....+...+.|+|..++.+|--.|.++..++|+.-.|.....   ....|+-+++|.+|||++
T Consensus        12 RLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~d~~---~~e~LdLskSLndlgirE   76 (91)
T 2daj_A           12 RVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQ---SQEPLDLTKSLNDLGLRE   76 (91)
T ss_dssp             EEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEESCSS---CCCBCCTTSCHHHHTCSE
T ss_pred             EEEEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEecCCC---CCcccchhcchhhhhhhh
Confidence            56788887788899999999999999999999999999988876544   123789999999999996

>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=96.59  E-value=0.017  Score=40.94  Aligned_cols=68  Identities=15%  Similarity=0.190  Sum_probs=53.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEe-CCCCCCCCccCC-CCCccccCCCCCCCEEEEEeecCCC
Q 041108           13 FYIQVENDATVADLKREIGAQQKLPCD-RLILLL-SSDHSCPMTQDH-DEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        13 ~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~-~g~~~~~~~~L~-d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      +.+.++..+|+.+|++.+....+++++ .-||.. .+... + ..|. ++.+|.++++.+|..|.+-++..++
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~-~-~~L~~~~~tl~d~~L~~~Q~illE~r~~dg  224 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNT-Y-EQLSKLDNTIQDAGLYQGQVLVIEPQNEDG  224 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSS-C-EECCCTTSBTTTTTCCTTEEEEEEECCTTS
T ss_pred             EEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCC-H-hhhcCCCCCHHHhCCCCCCEEEEEEecCCC
Confidence            456778999999999999999999997 578754 32211 1 2555 4689999999999999999987665

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=96.34  E-value=0.051  Score=31.45  Aligned_cols=64  Identities=19%  Similarity=0.213  Sum_probs=46.6

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|+-..+ ...+++....|+.+|.+.+    ++++....+..++.      ....+.     -+++||.|.++-...
T Consensus         5 m~i~vNg~~~-~~~~~~~~~~tv~~Ll~~l----~~~~~~v~vavN~~------~v~~~~-----~L~~gD~V~ii~~V~   68 (70)
T 1ryj_A            5 MKFTVITDDG-KKILESGAPRRIKDVLGEL----EIPIETVVVKKNGQ------IVIDEE-----EIFDGDIIEVIRVIY   68 (70)
T ss_dssp             EEEEEEETTE-EEEEEESSCCBHHHHHHHT----TCCTTTEEEEETTE------ECCTTS-----BCCTTCEEEEEECTT
T ss_pred             EEEEEeCccC-ceeEECCCCCcHHHHHHHh----CCCCCCEEEEECCE------ECCCcc-----cCCCCCEEEEEeccc
Confidence            6677776532 3466777889999999875    56777777888988      776554     478999999886543

>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=96.31  E-value=0.046  Score=40.70  Aligned_cols=73  Identities=19%  Similarity=0.110  Sum_probs=55.1

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcC----CCCccEEEEeCCC-CCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQK----LPCDRLILLLSSD-HSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~g----ip~~~q~L~~~g~-~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      .+.|+.. +.+.++.+++++||.|....|.++..    .+.++--|+.... |+. ..-|++.++|+.|++++|+.+...
T Consensus         5 ~~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~-~~Wl~~~~~l~~y~~~~~~~l~~~   82 (371)
T 3ivf_A            5 SLKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKK-GIWLEAGKALDYYMLRNGDTMEYR   82 (371)
T ss_dssp             EEEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGG-CEECCTTSBGGGGTCCTTCEEEEE
T ss_pred             EEEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCc-CEeccCCCCHHHhCCCCCceeecc
Confidence            3455665 77789999999999999999988764    3677778877332 110 114788899999999999988876

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=96.22  E-value=0.012  Score=41.30  Aligned_cols=67  Identities=16%  Similarity=0.228  Sum_probs=52.6

Q ss_pred             EEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEe-C-CCCCCCCccCCC-CCccccCCCCCCCEEEEEeecCCC
Q 041108           13 FYIQVENDATVADLKREIGAQQKLPCD-RLILLL-S-SDHSCPMTQDHD-EVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        13 ~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~-~-g~~~~~~~~L~d-~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      +.+.++..+|+.+|++.+...++++++ ..||.. . .. +  ...|++ +.+|.++++.+|..|.+-.+..++
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~-~--~~~L~~~~~tl~~~~l~~~Q~illE~r~~dg  212 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSN-T--FEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG  212 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETT-E--EEECCCTTSBHHHHTCCTTCEEEEEECCCC-
T ss_pred             eEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCC-C--eeecCCCCCCHHHhCCCCCCEEEEEEecCCC
Confidence            567889999999999999999999987 577742 2 22 1  125555 679999999999999999987665

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=96.20  E-value=0.039  Score=32.14  Aligned_cols=70  Identities=16%  Similarity=0.147  Sum_probs=47.2

Q ss_pred             CEEEEEeCCC-cEEEEEecCCCcHHHHHHHHHhhcCCCC--ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTG-TLFYIQVENDATVADLKREIGAQQKLPC--DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g-~~~~i~v~~~~TV~dLK~~I~~~~gip~--~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |.++|+.... +...+++ ...|+.+|.+.+....++..  ..-.+..++.      ...+    .+..+++||.|.++-
T Consensus         1 M~v~V~~fa~l~~~~~e~-~~~tv~~ll~~L~~~~~l~~~l~~~~vavN~~------~v~~----~~~~l~~gDeV~i~P   69 (74)
T 3rpf_C            1 MMVEVRFFGPIKEENFFI-KANDLKELRAILQEKEGLKEWLGVCAIALNDH------LIDN----LNTPLKDGDVISLLP   69 (74)
T ss_dssp             CEEEEEECTTCCCCCEEE-ECSSHHHHHHHHHTCTTTTTTTTTCEEEESSS------EECC----TTCCCCTTCEEEEEC
T ss_pred             CEEEEEEEeecceeEEee-CCCcHHHHHHHHHHCcCHHHHhhccEEEECCE------EcCC----CCcCCCCCCEEEEEC
Confidence            8899998754 2234677 56899999999987544332  3345667777      5332    245689999999986


Q ss_pred             ecCC
Q 041108           78 KPLD   81 (102)
Q Consensus        78 ~~~~   81 (102)
                      ...|
T Consensus        70 pvsG   73 (74)
T 3rpf_C           70 PVCG   73 (74)
T ss_dssp             CBCC
T ss_pred             CCCC
Confidence            5443

>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=95.73  E-value=0.049  Score=33.14  Aligned_cols=50  Identities=8%  Similarity=0.088  Sum_probs=41.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCP   52 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~   52 (102)
                      |+|.|...  -++.|.|.++.+..+|..+|.++.+++++...|.|...++.-
T Consensus         6 ~~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~~s~~   55 (83)
T 1oey_A            6 YTLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPRDSNE   55 (83)
T ss_dssp             EEEEEESS--SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCTTCSS
T ss_pred             EEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCCCCCC
Confidence            35566664  688899999999999999999999999999999998864433

>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=94.96  E-value=0.32  Score=29.60  Aligned_cols=68  Identities=24%  Similarity=0.246  Sum_probs=46.5

Q ss_pred             CEEEEEeCC------C-cEEEEEecCCCcHHHHHHHHHhhcC-CC----------CccEEEEeCCCCCCCCccCCCCCcc
Q 041108            1 MKVAVEILT------G-TLFYIQVENDATVADLKREIGAQQK-LP----------CDRLILLLSSDHSCPMTQDHDEVPL   62 (102)
Q Consensus         1 M~v~V~~~~------g-~~~~i~v~~~~TV~dLK~~I~~~~g-ip----------~~~q~L~~~g~~~~~~~~L~d~~~L   62 (102)
                      |+|.|+...      | ....+++....||.+|.+.+..... +.          .....+..+|.      ....    
T Consensus        10 ~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~------~v~~----   79 (98)
T 1vjk_A           10 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGR------YVSW----   79 (98)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTB------CCCT----
T ss_pred             EEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCE------ECCC----
Confidence            677777653      4 4567888788999999999987642 10          12345667777      5543    


Q ss_pred             ccCCCCCCCEEEEEeec
Q 041108           63 ADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        63 ~~~gI~~~~~i~l~~~~   79 (102)
                       +..+++||.|.++-..
T Consensus        80 -~~~L~dGDeV~i~ppv   95 (98)
T 1vjk_A           80 -DEELKDGDVVGVFPPV   95 (98)
T ss_dssp             -TCBCCTTCEEEEESCC
T ss_pred             -CCCCCCCCEEEEECCC
Confidence             5567999999887543

>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=94.06  E-value=0.28  Score=29.42  Aligned_cols=73  Identities=15%  Similarity=0.149  Sum_probs=45.2

Q ss_pred             CEEEEEeCC------CcEEEEEecCCCcHHHHHHHHHhhcCC------CC-------ccEEEEeCCCCCCCCccCCCCCc
Q 041108            1 MKVAVEILT------GTLFYIQVENDATVADLKREIGAQQKL------PC-------DRLILLLSSDHSCPMTQDHDEVP   61 (102)
Q Consensus         1 M~v~V~~~~------g~~~~i~v~~~~TV~dLK~~I~~~~gi------p~-------~~q~L~~~g~~~~~~~~L~d~~~   61 (102)
                      |+|+|+...      |....+++ ...||.+|.+.+..++.-      ..       ....+..++.      ...+..-
T Consensus         1 M~v~V~~fa~lr~~~g~~~~~~~-~~~Tv~~ll~~L~~~~p~l~~~l~~~~~~g~~~~~~~v~VN~~------~v~~~~~   73 (93)
T 3dwg_C            1 MNVTVSIPTILRPHTGGQKSVSA-SGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDE------DVRFSGG   73 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEE-CCSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTE------EGGGTTG
T ss_pred             CEEEEEEeHHHHHHhCCCeEEec-CCCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCE------EccCcCC
Confidence            778888643      33334665 458999999999887530      10       1245667776      5443222


Q ss_pred             cccCCCCCCCEEEEEeecCC
Q 041108           62 LADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        62 L~~~gI~~~~~i~l~~~~~~   81 (102)
                      + +..+++||.|.++-...|
T Consensus        74 ~-~~~L~~gDeV~i~Ppv~G   92 (93)
T 3dwg_C           74 L-ATAIADGDSVTILPAVAG   92 (93)
T ss_dssp             G-GCBCCTTCEEEEEECCTT
T ss_pred             C-CcCCCCCCEEEEECCCCC
Confidence            2 456899999998865443

>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=93.98  E-value=0.058  Score=43.80  Aligned_cols=51  Identities=20%  Similarity=0.285  Sum_probs=41.6

Q ss_pred             CcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccC
Q 041108           10 GTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADC   65 (102)
Q Consensus        10 g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~   65 (102)
                      ++...+.++++.|+.+++..|+..+|++++.|.+++.+.     -.++++.....|
T Consensus       321 ~~~~~~~i~~~~tl~~l~~~i~~~T~i~~~~q~~~~~~~-----~~~~p~~~~~~~  371 (676)
T 3qa8_A          321 GRVHTYPVTENENLQNLKSWLQQDTGIPEEEQELLQASG-----LALNSAQPLTQY  371 (676)
T ss_dssp             SCCCEEECCTTCCHHHHHHHHHTTSCCCSTTCEEESSSS-----CCCCTTSCGGGS
T ss_pred             cccceeecCCCccHHHHHHHHHHHhCCCHHHHHHHhccC-----CCCCCCcchhhh
Confidence            455678999999999999999999999999999988765     145666666655

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=93.94  E-value=0.079  Score=34.55  Aligned_cols=33  Identities=15%  Similarity=0.305  Sum_probs=29.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe
Q 041108           13 FYIQVENDATVADLKREIGAQQKLPCDRLILLL   45 (102)
Q Consensus        13 ~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~   45 (102)
                      ..+.|-.++|+.+|+..|++..|+|+++|||..
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            457888899999999999999999999999865

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=93.89  E-value=0.32  Score=35.79  Aligned_cols=69  Identities=10%  Similarity=-0.009  Sum_probs=46.9

Q ss_pred             CcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCC-CEEEEEeecCCCC
Q 041108           10 GTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDG-SHIYLFFKPLDDG   83 (102)
Q Consensus        10 g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~-~~i~l~~~~~~~~   83 (102)
                      -....+.+++..|+.++++.+++.++++++.|.+++.+.    .-.++...+...++-... .-+.++ ...|+.
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  390 (396)
T 4eut_A          321 MTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGR----RLVLEPGRLAQHFPKTTEENPIFVV-SREGNS  390 (396)
T ss_dssp             TEEEEEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSS----EECCCSSCBTTSSCCCCSSSCEEEE-ECC---
T ss_pred             ceEEEEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCC----CCCCCCCCccccCCCCCCCCCeEEE-ecCCCc
Confidence            355678899999999999999999999999999999884    013355555666654332 333333 344443

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=93.34  E-value=0.27  Score=30.04  Aligned_cols=71  Identities=15%  Similarity=0.201  Sum_probs=55.8

Q ss_pred             EEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC--CCCCceeEEE
Q 041108           14 YIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL--DDGSTQHSVF   90 (102)
Q Consensus        14 ~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~--~~~~~~~~~~   90 (102)
                      ...++=..++..||..++.+.|++-+.-.+..-+.      .|+++++|-+.+|+-...+.+.+...  .+....++|.
T Consensus         6 ~qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~------~L~~~k~LvdQcVqgeGlVQinvqik~~~~~~~RiNIv   78 (89)
T 2juo_A            6 SQAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDI------QLDPDRSLFDQGVKTDGTVQLSVQVISYQGMEPKLNIL   78 (89)
T ss_dssp             EEEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTE------ECCTTSBTTTSSCCCCSEEEEEEEEECCTTCCCEEEEE
T ss_pred             hhhccccCcHHHHHHHHHHHhcCCcccCeEEeecc------ccCCCccHHHhhcccccEEEEEEEEEecCCCCcceEEE
Confidence            33455567899999999999999999888888888      89999999999999888888887642  2223455543

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=93.08  E-value=0.17  Score=30.84  Aligned_cols=55  Identities=16%  Similarity=0.128  Sum_probs=38.3

Q ss_pred             EEecCC-CcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108           15 IQVEND-ATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus        15 i~v~~~-~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      ++++.. .||.+|.+.+    ++++....+..+|.      .+..+ ...+..+++||.|.++-...
T Consensus        30 ~el~~~~~Tv~dLL~~L----~~~~~~vaVavNg~------iV~~~-~~~~~~L~dGD~Vei~~~V~   85 (87)
T 1tyg_B           30 VKWKKDTGTIQDLLASY----QLENKIVIVERNKE------IIGKE-RYHEVELCDRDVIEIVHFVG   85 (87)
T ss_dssp             ECCSSSCCBHHHHHHHT----TCTTSCCEEEETTE------EECGG-GTTTSBCCSSSEEEEEEECC
T ss_pred             EECCCCCCcHHHHHHHh----CCCCCCEEEEECCE------ECChh-hcCCcCCCCCCEEEEEcccc
Confidence            445565 8999998765    56676667778887      65432 23445689999999986543

>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=93.03  E-value=1  Score=33.30  Aligned_cols=77  Identities=22%  Similarity=0.245  Sum_probs=54.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCC-CccEEEEeCCCC---CCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLP-CDRLILLLSSDH---SCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip-~~~q~L~~~g~~---~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      .+.|...+|+...+.+++.+|+.|+-..|....|+. .+-.-|.+....   .....-|+.++++.+.+......+.+.+
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            577889999999999999999999999999999976 455667654310   1112356777888777765556665544


Q ss_pred             e
Q 041108           78 K   78 (102)
Q Consensus        78 ~   78 (102)
                      +
T Consensus       167 K  167 (371)
T 3ivf_A          167 K  167 (371)
T ss_dssp             C
T ss_pred             E
Confidence            3

>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=92.74  E-value=0.8  Score=32.63  Aligned_cols=76  Identities=13%  Similarity=0.046  Sum_probs=53.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc-cEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD-RLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~-~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |.+.|...+| +..+.+++.+|+.|+-+.|.+..|+... -.-|.+... .....-|+.++++.+.+++.+....+..+
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~-~~~~~wLd~~~~l~~q~~~~~~~~~l~fr   78 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDT-KGFSTWLKLNKKVTAQDVRKESPLLFKFR   78 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBT-TSCEEECCSSSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCCCCcceeEEEEECC-CCceeecccccCHHhhccCCCCCEEEEEE
Confidence            4678899998 5779999999999999999999998643 345655221 00112467788888876655555555443

>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=92.46  E-value=0.76  Score=29.10  Aligned_cols=80  Identities=15%  Similarity=0.062  Sum_probs=44.0

Q ss_pred             CEEEEEeCC------C--cEEEEEecC---CCcHHHHHHHHHhhcCCCCccEEEEeC-CCCCCCCccC-CCCC--cc--c
Q 041108            1 MKVAVEILT------G--TLFYIQVEN---DATVADLKREIGAQQKLPCDRLILLLS-SDHSCPMTQD-HDEV--PL--A   63 (102)
Q Consensus         1 M~v~V~~~~------g--~~~~i~v~~---~~TV~dLK~~I~~~~gip~~~q~L~~~-g~~~~~~~~L-~d~~--~L--~   63 (102)
                      |+|+|+...      |  +.+.++++.   ..||.+|...+.+.+  |..+.+|+.. |+-.+-..++ ++..  .|  .
T Consensus        12 M~v~V~~~~~Lr~~~g~~~~~~vel~~~~~~~TV~~Ll~~L~~~~--~~~~~~lf~~~g~lr~~i~VlVN~~di~~l~gl   89 (114)
T 1wgk_A           12 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNL--LKERPELFIQGDSVRPGILVLINDADWELLGEL   89 (114)
T ss_dssp             EEEEEEECTTTGGGTTTCSEEEEEECCCSSCCBHHHHHHHHTTTT--CCSCHHHHCCSSSCCSSEEEEESSSBHHHHCTT
T ss_pred             cEEEEEEchHHHHHhCCceEEEEEeCCCCCCCCHHHHHHHHHHHc--cchhHhhCccCCcccCCeEEEECCeeeeccCCc
Confidence            678888664      3  356688873   369999999998876  2222222211 2100000011 2221  11  2


Q ss_pred             cCCCCCCCEEEEEeecCCC
Q 041108           64 DCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        64 ~~gI~~~~~i~l~~~~~~~   82 (102)
                      ++.+++||.|.++-...++
T Consensus        90 dt~L~dGDeV~iip~vaGG  108 (114)
T 1wgk_A           90 DYQLQDQDSILFISTLHGG  108 (114)
T ss_dssp             TCBCCSSEEEEEEECSCCC
T ss_pred             CcCCCCCCEEEEeCCCCCC
Confidence            5778999998886554444

>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=92.18  E-value=0.79  Score=33.06  Aligned_cols=74  Identities=12%  Similarity=-0.015  Sum_probs=52.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCC-ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPC-DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~-~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      .+.|...+| ++.+++++.+|+.||-+.|....|+.. +-.-|.+...  ....-|+.++.+.+.+++.+....+..+
T Consensus        24 ~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L~e~~~FgL~~~~~--~~~~wL~~~~~i~~q~~~~~~~~~l~fr   98 (314)
T 1h4r_A           24 TVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIK--DTVAWLKMDKKVLDHDVSKEEPVTFHFL   98 (314)
T ss_dssp             EEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEET--TEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             EEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCCCCCccceEEEEeC--CcCeeCCCccCHHHcCCCCCCCEEEEEE
Confidence            577888898 678999999999999999999999864 4445555311  0012478888888877655555544443

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=91.75  E-value=1.4  Score=26.80  Aligned_cols=72  Identities=26%  Similarity=0.269  Sum_probs=41.8

Q ss_pred             CEEEEEeCC-------C-cEEEEEec--CCCcHHHHHHHHHhhcC-CCCcc------------EEEEeCCCCCCCCccCC
Q 041108            1 MKVAVEILT-------G-TLFYIQVE--NDATVADLKREIGAQQK-LPCDR------------LILLLSSDHSCPMTQDH   57 (102)
Q Consensus         1 M~v~V~~~~-------g-~~~~i~v~--~~~TV~dLK~~I~~~~g-ip~~~------------q~L~~~g~~~~~~~~L~   57 (102)
                      |+|+|+...       | +...+++.  ...||.+|.+.+.+... ..+.-            ..+..++.      ..+
T Consensus         2 M~i~V~~fa~lre~~~g~~~~~~~l~~~~~~Tv~~L~~~L~~~~~~~~~~l~~~~~~~~lr~~~~v~VN~~------~~~   75 (99)
T 2qjl_A            2 VNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDT------DWE   75 (99)
T ss_dssp             EEEEEEEETTGGGGTTTCCEEEEEECSCSCCBHHHHHHHHHHHTCSSGGGHHHHEETTEECTTEEEEETTE------EGG
T ss_pred             cEEEEEEchHHHHHhCCCcEEEEecCCCCCCcHHHHHHHHHHHCchhhHHHhhhccCCccccCeEEEECCE------Ecc
Confidence            567777542       3 44567776  67899999999988763 11110            12334443      211


Q ss_pred             CCCccccCCCCCCCEEEEEeec
Q 041108           58 DEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        58 d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .... .+..+++||.|.++-..
T Consensus        76 ~~~~-~d~~L~dgDeVa~~Ppv   96 (99)
T 2qjl_A           76 LEGE-KDYILEDGDIISFTSTL   96 (99)
T ss_dssp             GGTG-GGCBCCTTCEEEEEECT
T ss_pred             ccCC-CCcCcCCCCEEEEECCC
Confidence            0001 24568999998887543

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=91.66  E-value=1.1  Score=26.35  Aligned_cols=60  Identities=20%  Similarity=0.207  Sum_probs=41.4

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhcC-C-----CC-----ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           11 TLFYIQVENDATVADLKREIGAQQK-L-----PC-----DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~g-i-----p~-----~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      ....+++....||.+|.+.+..... +     ..     ....+..++.      ....     +..+++||.|.++-..
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~~~~~~l~~~g~l~~~~~v~VN~~------~v~~-----~~~l~~gDeV~i~Ppv   86 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGE------AAAL-----GEATAAGDELALFPPV   86 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGGGHHHHBCTTSCBCTTSEEEETTE------ECCT-----TSBCCTTCEEEEECCC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcHHHHHHhccCCcccccEEEEECCE------ECCC-----CcccCCCCEEEEECCC
Confidence            5567888778999999999988752 1     00     1145667776      5543     4557899999998654


Q ss_pred             CC
Q 041108           80 LD   81 (102)
Q Consensus        80 ~~   81 (102)
                      .|
T Consensus        87 ~G   88 (89)
T 3po0_A           87 SG   88 (89)
T ss_dssp             SC
T ss_pred             CC
Confidence            33

>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=91.44  E-value=1.2  Score=29.35  Aligned_cols=68  Identities=21%  Similarity=0.085  Sum_probs=43.6

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhcC--CC------CccEEEEe-CCCCCCCCccCCCC-------------CccccCCCC
Q 041108           11 TLFYIQVENDATVADLKREIGAQQK--LP------CDRLILLL-SSDHSCPMTQDHDE-------------VPLADCGVK   68 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~g--ip------~~~q~L~~-~g~~~~~~~~L~d~-------------~~L~~~gI~   68 (102)
                      ..+.+.|=..+||.++|++|-...-  +|      +++.-|-+ .|.....  .|.|.             .+|..|+|.
T Consensus        41 ~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~l--iL~D~D~tS~~~~~wkrLNTL~HY~V~  118 (138)
T 2r2o_A           41 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHL--ILSDEDVTSEVQGLWRRLNTLQHYKVP  118 (138)
T ss_dssp             CCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEE--EECSSSTTCCEETTEEECCBHHHHTCC
T ss_pred             CceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCce--EeeccCCcccccCCceeecchhccCCC
Confidence            4577888889999999999987633  33      33344432 2221111  24332             289999999


Q ss_pred             CCCEEEEEeecC
Q 041108           69 DGSHIYLFFKPL   80 (102)
Q Consensus        69 ~~~~i~l~~~~~   80 (102)
                      +|+++.++-+..
T Consensus       119 Dga~l~l~~~~~  130 (138)
T 2r2o_A          119 DGATVALVPCLT  130 (138)
T ss_dssp             TTCEEEEEEC--
T ss_pred             CCCEEEEEECCC
Confidence            999999986643

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=91.29  E-value=1.1  Score=28.74  Aligned_cols=67  Identities=22%  Similarity=0.209  Sum_probs=43.3

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhc--CCC------CccEEEEe-CCCCCCCCccCCC---------C----CccccCCCC
Q 041108           11 TLFYIQVENDATVADLKREIGAQQ--KLP------CDRLILLL-SSDHSCPMTQDHD---------E----VPLADCGVK   68 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~--gip------~~~q~L~~-~g~~~~~~~~L~d---------~----~~L~~~gI~   68 (102)
                      ..+.+.|-..+||.++|++|-...  |.|      ++...|-+ .|.....  .|.|         .    .+|+.|+|.
T Consensus        27 ~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~--iL~D~D~ts~~~~~wkrLNTL~HY~V~  104 (117)
T 4e74_A           27 PEVPVKILNCDTITQVKEKILDAIFKNVPCSHRPKAADMDLEWRQGSGARM--ILQDEDITTKIENDWKRLNTLAHYQVP  104 (117)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECTTSCEE--EECSSSTTCCC---CCCCCBHHHHTCC
T ss_pred             CceEeeeecCCchHHHHHHHHHHHhcCCCcccCCCCCceeEEEecCCCCce--EeecCCCccEecCcceEeccccccCCC
Confidence            346777878999999999998752  333      33455543 3321111  1222         1    478899999


Q ss_pred             CCCEEEEEeec
Q 041108           69 DGSHIYLFFKP   79 (102)
Q Consensus        69 ~~~~i~l~~~~   79 (102)
                      +|+++.++-+.
T Consensus       105 dgatl~l~~~~  115 (117)
T 4e74_A          105 DGSVVALVSKQ  115 (117)
T ss_dssp             TTCEEEEEECC
T ss_pred             CCCEEEEEeCC
Confidence            99999998654

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=91.04  E-value=0.23  Score=28.10  Aligned_cols=58  Identities=22%  Similarity=0.224  Sum_probs=39.1

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      +|+.  +++....|+.+|.+.+    ++++....+..++.      ....+ ...+.-+++||.|.++-..
T Consensus         6 Ng~~--~~~~~~~tv~~ll~~l----~~~~~~v~vavN~~------~v~~~-~~~~~~L~~gD~v~i~~~V   63 (66)
T 1f0z_A            6 NDQA--MQCAAGQTVHELLEQL----DQRQAGAALAINQQ------IVPRE-QWAQHIVQDGDQILLFQVI   63 (66)
T ss_dssp             SSCE--ECCCTTCCHHHHHHHH----TCCCSSEEEEETTE------EECHH-HHTTCCCCTTEEECEEESC
T ss_pred             CCEE--EEcCCCCcHHHHHHHc----CCCCCCEEEEECCE------ECCch-hcCCcCCCCCCEEEEEeec
Confidence            4554  4556678999999876    46666667778887      55432 2234557899999988644

>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=90.20  E-value=1.6  Score=34.74  Aligned_cols=76  Identities=14%  Similarity=0.071  Sum_probs=54.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      +.+.|...+| ++.+.+++.+|+.+|-..|....|+. .+-.-|.+... ......|+.++++.+.+++.+..+.+.++
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL~e~~~FGL~~~d~-~~~~~WLd~~k~i~~q~~~~~~~~~L~FR   81 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGLREVWFFGLQYTDS-KGDLTWIKLYKKVMQQDVKKENPLQFKFR   81 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEBT-TSCEEECCTTSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCCCCccceeEEEEec-CcchhHhhccccHHHhcccCCCCeEEEEE
Confidence            3577888898 57799999999999999999999986 44456665332 11112567888888877666655555544

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=90.09  E-value=2.5  Score=26.88  Aligned_cols=64  Identities=23%  Similarity=0.217  Sum_probs=41.0

Q ss_pred             CcEEEEEecCCCcHHHHHHHHHhhc--CCC------CccEEEEe-CCC-CCCCCccCCCC-------------CccccCC
Q 041108           10 GTLFYIQVENDATVADLKREIGAQQ--KLP------CDRLILLL-SSD-HSCPMTQDHDE-------------VPLADCG   66 (102)
Q Consensus        10 g~~~~i~v~~~~TV~dLK~~I~~~~--gip------~~~q~L~~-~g~-~~~~~~~L~d~-------------~~L~~~g   66 (102)
                      +..+.+.|-..+||.++|++|-...  |.|      ++..-|-+ .|. ++    .|.|.             .+|+.|+
T Consensus        23 ~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~----iL~D~D~ts~~~~~wkrLNTL~HY~   98 (111)
T 4e71_A           23 VDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQ----ILSDLDLTSQREGRWKRVNTLMHYN   98 (111)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCE----ECCSSCTTSCC---CCCCCBHHHHT
T ss_pred             CCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCc----cccccCccceecCcceEecchhhcC
Confidence            3557778888999999999998752  233      33444544 222 11    33321             3788999


Q ss_pred             CCCCCEEEEEe
Q 041108           67 VKDGSHIYLFF   77 (102)
Q Consensus        67 I~~~~~i~l~~   77 (102)
                      |.+|+++.+.-
T Consensus        99 V~dgatl~l~~  109 (111)
T 4e71_A           99 VRDGATLILSK  109 (111)
T ss_dssp             CCTTCEEEEEE
T ss_pred             CCCCCEEEEEe
Confidence            99999998864

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=89.86  E-value=2.8  Score=27.24  Aligned_cols=67  Identities=15%  Similarity=0.169  Sum_probs=44.6

Q ss_pred             CcEEEEEecCCCcHHHHHHHHHhhc--CCC------CccEEEEe-CCCCCCCCccCCCC-------------CccccCCC
Q 041108           10 GTLFYIQVENDATVADLKREIGAQQ--KLP------CDRLILLL-SSDHSCPMTQDHDE-------------VPLADCGV   67 (102)
Q Consensus        10 g~~~~i~v~~~~TV~dLK~~I~~~~--gip------~~~q~L~~-~g~~~~~~~~L~d~-------------~~L~~~gI   67 (102)
                      +..+.+.|=..+||.++|++|-...  ++|      ++++.|-+ .|....+  .|.|.             .+|..|+|
T Consensus        16 ~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~--iL~D~D~ts~~~~~~krLNTL~HY~V   93 (127)
T 3h6n_A           16 MDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSY--ILRDLDDTSVVEDGRKKLNTLAHYKI   93 (127)
T ss_dssp             CCCEEEEEETTSBHHHHHHHHHHHHSTTSCGGGSCCGGGEEEEEECSSSCEE--ECCSSSTTSCEETTEECCCBTTTTTC
T ss_pred             CCceeeeeeccCchhhhhHHHHHHHhccCCcccCCCCcccceEEecCCCCce--EeecCCCcceecCceeEeccccccCC
Confidence            4557778888999999999998762  233      34555644 3321111  23321             47899999


Q ss_pred             CCCCEEEEEee
Q 041108           68 KDGSHIYLFFK   78 (102)
Q Consensus        68 ~~~~~i~l~~~   78 (102)
                      .+|+++.+..+
T Consensus        94 ~dgatv~l~~~  104 (127)
T 3h6n_A           94 PEGASLAMSLI  104 (127)
T ss_dssp             CTTCEEEEEEC
T ss_pred             CCCCEEEEEEc
Confidence            99999999854

>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=89.65  E-value=0.37  Score=28.52  Aligned_cols=69  Identities=19%  Similarity=0.284  Sum_probs=46.7

Q ss_pred             CEEEEEeCCCcEEEEEec--CCCcHHHHHHHHHhhcCCC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVE--NDATVADLKREIGAQQKLP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~--~~~TV~dLK~~I~~~~gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+   |+.+  +++  ...|+.+|-+.+    +++ +..--+..+|.      ++..+ ...+.-+++||.|.++.
T Consensus         1 M~I~vN---Ge~~--e~~~~~~~Tl~~LL~~l----~~~~~~~vAVavNg~------iVpr~-~~~~~~L~dGD~IEIv~   64 (78)
T 2k5p_A            1 MNLTVN---GKPS--TVDGAESLNVTELLSAL----KVAQAEYVTVELNGE------VLERE-AFDATTVKDGDAVEFLY   64 (78)
T ss_dssp             CEEEET---TEEE--ECSSCSCEEHHHHHHHH----TCSCTTTCCEEETTE------ECCTT-HHHHCEECSSBCEEECC
T ss_pred             CEEEEC---CEEE--EcCCCCCCcHHHHHHHc----CCCCCCcEEEEECCE------ECChH-HcCcccCCCCCEEEEEe
Confidence            555554   5644  455  568999988654    677 66666788887      66443 34556678999999987


Q ss_pred             ecCCCCCc
Q 041108           78 KPLDDGST   85 (102)
Q Consensus        78 ~~~~~~~~   85 (102)
                      ..-|+...
T Consensus        65 ~VgGG~~~   72 (78)
T 2k5p_A           65 FMGGGKLE   72 (78)
T ss_dssp             CCCCSCCC
T ss_pred             eecCCCch
Confidence            66555443

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=89.46  E-value=1.3  Score=28.91  Aligned_cols=58  Identities=19%  Similarity=0.260  Sum_probs=40.3

Q ss_pred             EEEecC----CCcHHHHHHHHHhhcCCCC-------ccEEEEeCCCCCCCCccC-CCCCccccCCCCCCCEEEEEe
Q 041108           14 YIQVEN----DATVADLKREIGAQQKLPC-------DRLILLLSSDHSCPMTQD-HDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus        14 ~i~v~~----~~TV~dLK~~I~~~~gip~-------~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      .+.|+.    .+|+.+|-+.+..++|+..       ..++|+|.--      .- .-+++|+++|+++|+.+.+.=
T Consensus         9 vl~v~~~dl~~~TL~dLV~~l~~~~gy~~eiSV~~~~~~rLLyD~D------fDDnl~k~L~dLgv~~gsfLtv~D   78 (127)
T 3onh_A            9 VIKLSSDCLNKMKLSDFVVLIREKYSYPQDISLLDASNQRLLFDYD------FEDLNDRTLSEINLGNGSIILFSD   78 (127)
T ss_dssp             EEEECHHHHHHCBHHHHHHHHHHHHTCCSSEEEEETTTTEEEEETT------BCTTTTSBTTTTTCCTTCEEEEEE
T ss_pred             EEEeCcccccccCHHHHHHHHHHhcCCCCcEEEEecCCCCeEeCCC------ccccccCcHHHcCcCCCcEEEEEc
Confidence            455654    4799999888988888753       1244444433      11 334899999999999998873

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=89.10  E-value=0.54  Score=36.99  Aligned_cols=33  Identities=15%  Similarity=0.305  Sum_probs=29.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe
Q 041108           13 FYIQVENDATVADLKREIGAQQKLPCDRLILLL   45 (102)
Q Consensus        13 ~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~   45 (102)
                      ..+.|..++|+.+|++.|++..|+|+++|||..
T Consensus        38 ~~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW~   70 (530)
T 2ylm_A           38 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   70 (530)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTSCGGGEEEEE
T ss_pred             ceEEEcCcCCHHHHHHHHHHHhCcCcccEEEEE
Confidence            367888999999999999999999999999753

>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=88.81  E-value=1.3  Score=25.45  Aligned_cols=56  Identities=20%  Similarity=0.231  Sum_probs=37.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcC-----CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           12 LFYIQVENDATVADLKREIGAQQK-----LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~g-----ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      ...++ ....||.+|.+.+.....     ++.....+..+|.      ....     +..+++||.|.++-..
T Consensus        18 ~~~~~-~~~~tv~~ll~~L~~~~p~~~~~l~~~~~~v~vN~~------~v~~-----~~~l~~gD~V~i~Ppv   78 (81)
T 1fm0_D           18 ATEVA-ADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQT------LVSF-----DHPLTDGDEVAFFPPV   78 (81)
T ss_dssp             EEEEC-SCCSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTE------ECCT-----TCBCCTTCEEEEECCC
T ss_pred             eEEEc-CCCCCHHHHHHHHHHHChhHHHHhcCCCEEEEECCE------ECCC-----CCCCCCCCEEEEeCCC
Confidence            44555 567899999999886532     2233345777887      5543     4457899999887544

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=88.53  E-value=0.58  Score=29.54  Aligned_cols=81  Identities=15%  Similarity=0.203  Sum_probs=42.4

Q ss_pred             CEEEEEeCC------CcEEEEEecC----CCcHHHHHHHHHhhcCCCCccEEEEe-CC--CCCCC-CccCCCCCcc----
Q 041108            1 MKVAVEILT------GTLFYIQVEN----DATVADLKREIGAQQKLPCDRLILLL-SS--DHSCP-MTQDHDEVPL----   62 (102)
Q Consensus         1 M~v~V~~~~------g~~~~i~v~~----~~TV~dLK~~I~~~~gip~~~q~L~~-~g--~~~~~-~~~L~d~~~L----   62 (102)
                      |+|.|+...      |+...++++.    .+||.+|-..+.+.+  +..+-.|+. +|  . =+| .-+|=++..+    
T Consensus         5 m~v~V~f~g~l~~l~g~~~~v~l~~~~g~~~TV~dLl~~L~~~~--~~~r~~lf~~~g~~~-lrpgIlVLVNg~d~e~l~   81 (110)
T 2k9x_A            5 NHITVQFAGGCELLFAKQTSLQLDGVVPTGTNLNGLVQLLKTNY--VKERPDLLVDQTGQT-LRPGILVLVNSCDAEVVG   81 (110)
T ss_dssp             SCCEEEEESSCGGGTTSCSEECCCCSCGGGCCHHHHHHHHTTTT--CCSCHHHHBCSSSSS-BCTTEEEEESSSBHHHHT
T ss_pred             cEEEEEEEecHHHHhCCeEEEEeCCcCCCCccHHHHHHHHHHHc--cccchhhEecCCCcc-cCCCeEEEECCeeeeccC
Confidence            567777654      3445677763    359999999888875  222222321 12  1 001 0012111211    


Q ss_pred             -ccCCCCCCCEEEEEeecCCCCCc
Q 041108           63 -ADCGVKDGSHIYLFFKPLDDGST   85 (102)
Q Consensus        63 -~~~gI~~~~~i~l~~~~~~~~~~   85 (102)
                       .++.+++||.|.++ +...++..
T Consensus        82 gldt~L~dgD~V~fi-stlhg~~~  104 (110)
T 2k9x_A           82 GMDYVLNDGDTVEFI-STLHGGLE  104 (110)
T ss_dssp             SSCCCCCSSCEEEEE-ECCCCC--
T ss_pred             CcccCCCCcCEEEEe-CCCccccc
Confidence             25778999997775 45555443

>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=87.61  E-value=1.3  Score=24.69  Aligned_cols=58  Identities=14%  Similarity=0.162  Sum_probs=39.9

Q ss_pred             CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            9 TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         9 ~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      +|+.+.  + ...|+.+|.+.+    ++++....+..++.      ....+ ...+.-+++||.|.++....
T Consensus         5 Ng~~~~--~-~~~tv~~ll~~l----~~~~~~v~vavN~~------~v~~~-~~~~~~L~dgD~v~i~~~V~   62 (64)
T 2cu3_A            5 NGEPRP--L-EGKTLKEVLEEM----GVELKGVAVLLNEE------AFLGL-EVPDRPLRDGDVVEVVALMQ   62 (64)
T ss_dssp             TTEEEC--C-TTCCHHHHHHHH----TBCGGGEEEEETTE------EEEGG-GCCCCCCCTTCEEEEEECCC
T ss_pred             CCEEEE--c-CCCcHHHHHHHc----CCCCCcEEEEECCE------ECCcc-ccCCcCCCCCCEEEEEeecc
Confidence            566554  4 568999999876    46667677778887      65432 23345689999999986543

>2kmc_A Fermitin family homolog 1; kindlin, cytoskeleton, integrin, N-terminal, talin, cell adhesion, cell junction, cell membrane, cell projection; NMR {Mus musculus}

Probab=87.25  E-value=3.3  Score=25.90  Aligned_cols=73  Identities=19%  Similarity=0.289  Sum_probs=53.2

Q ss_pred             EEEEEeCCC---cEEEEEecCCCcHHHHHHHHHhhcCCCCc--cEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEILTG---TLFYIQVENDATVADLKREIGAQQKLPCD--RLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~~g---~~~~i~v~~~~TV~dLK~~I~~~~gip~~--~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      +|+|...+.   ..+.+.|..+.-|+-+..++-+...++.+  .--|-...+ .+  =++.-..+|..|||+.++.+++.
T Consensus        21 ~V~V~d~~~~~~~~~~lrV~GdlHIGGvmlklVEki~i~~dWSDhaLWW~~k-~~--WLlkt~~tLDkygiqADa~L~ft   97 (102)
T 2kmc_A           21 VVRVDHANGEQQTEITLRVSGDLHIGGVMLKLVEQMNIAQDWSDYALWWEQK-RC--WLLKTHWTLDKCGVQADANLLFT   97 (102)
T ss_dssp             EEEEECTTSSCEEEEEEEECSCCBHHHHHHHHHHHHCCSSCCSSEEEEETTT-TE--EECCTTSBHHHHTCCTTSCEEEE
T ss_pred             EEEEecCCcccCccEEEEEeeccccchhhhhhhhhcccccchHHhhhhhhhh-ch--hhhhhhhhhhhhceeeeeeeecc
Confidence            466777554   55889999999999999999988877644  334433332 11  15677789999999999998876


Q ss_pred             e
Q 041108           77 F   77 (102)
Q Consensus        77 ~   77 (102)
                      -
T Consensus        98 p   98 (102)
T 2kmc_A           98 P   98 (102)
T ss_dssp             E
T ss_pred             C
Confidence            4

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=87.14  E-value=1.4  Score=25.14  Aligned_cols=57  Identities=9%  Similarity=-0.006  Sum_probs=39.0

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhcCCCCccE--EEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           11 TLFYIQVENDATVADLKREIGAQQKLPCDRL--ILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q--~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      ....+++....||.+|.+.+..... .....  .+..+|.      ....+     ..+++||.|.++-..
T Consensus        16 ~~~~~~~~~~~tv~~ll~~l~~~~p-~~~~v~~~v~vNg~------~v~~~-----~~L~~gD~V~i~ppv   74 (77)
T 2q5w_D           16 AQEDIVLEQALTVQQFEDLLFERYP-QINNKKFQVAVNEE------FVQKS-----DFIQPNDTVALIPPV   74 (77)
T ss_dssp             SEEECCCSSCEEHHHHHHHHHHHCG-GGTTCCCEEEETTE------EECTT-----SEECTTCEEEEECSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCc-chhcceEEEEECCE------ECCCC-----CCcCCCCEEEEECCC
Confidence            3456777778899999999887642 01223  5777887      66543     457899999887543

>2l52_A Methanosarcina acetivorans SAMP1 homolog; beta-grAsp fold, protein binding, E1-like, SAMP activator, ELSA, adenylation, ubiquitin; NMR {Methanosarcina acetivorans}

Probab=86.93  E-value=3.6  Score=24.91  Aligned_cols=70  Identities=16%  Similarity=0.196  Sum_probs=42.7

Q ss_pred             CEEEEEeCC------CcEEEEEecCCCcHHHHHHHHHhhcC-CCC-----c----cE-------EEEeCCCCCCCCccCC
Q 041108            1 MKVAVEILT------GTLFYIQVENDATVADLKREIGAQQK-LPC-----D----RL-------ILLLSSDHSCPMTQDH   57 (102)
Q Consensus         1 M~v~V~~~~------g~~~~i~v~~~~TV~dLK~~I~~~~g-ip~-----~----~q-------~L~~~g~~~~~~~~L~   57 (102)
                      |+++|+...      |+ ..++++ ..||.+|.+.+..... +..     .    ..       .+..+|.      ...
T Consensus         4 m~v~V~~fa~lr~~~g~-~~~~l~-~~tv~~ll~~L~~~~p~l~~~l~~~g~l~~~v~~~~~~~~v~VNg~------~v~   75 (99)
T 2l52_A            4 AEVKVKLFANLREAAGT-PELPLS-GEKVIDVLLSLTDKYPALKYVIFEKGDEKSEILILCGSINILINGN------NIR   75 (99)
T ss_dssp             CEEEEEECTHHHHHHSS-SEEEEE-CSSHHHHHHHHHHHCGGGTTTSBCSCCTTSSCCCBCSSCEEEETTS------CGG
T ss_pred             eEEEEEEeHHHHHHhCC-CeEEEe-CCcHHHHHHHHHHHChhHHHHHhcccccccceeccccccEEEECCE------Ecc
Confidence            678888764      32 133444 5899999999987742 111     0    12       5677776      543


Q ss_pred             CCCccccCCCCCCCEEEEEeec
Q 041108           58 DEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        58 d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .... .+..+++||.|.++-..
T Consensus        76 ~~~~-~~~~L~~gD~V~i~ppv   96 (99)
T 2l52_A           76 HLEG-LETLLKDSDEIGILPPV   96 (99)
T ss_dssp             GTTS-TTSCCCTTEEEEEECCC
T ss_pred             ccCC-CCCCCCCCCEEEEECCC
Confidence            2222 24457999999887543

>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=86.89  E-value=1.3  Score=31.99  Aligned_cols=75  Identities=16%  Similarity=0.062  Sum_probs=50.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCC-ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPC-DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~-~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |.+.|..++|+...+++++.+|+.||-..|.+..|+.. +-.-|.+... +....-|+.++.+.+........+.+.
T Consensus        18 ~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~-~~~~~wLd~~k~i~~q~~~~~~~l~fr   93 (296)
T 3qij_A           18 GHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDN-ATSKTWLDSAKEIKKQVRGVPWNFTFN   93 (296)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTCSSGGGEEEEEEEE-TTEEEECCTTSBHHHHC---CCEEEEE
T ss_pred             EEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCCCCcceeEEEEEcC-CCccchhccchhHHHhcCCCCcEEEEE
Confidence            46789999999999999999999999999999999864 3355654321 001124677777776543333344433

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=86.88  E-value=2.1  Score=23.97  Aligned_cols=62  Identities=13%  Similarity=0.096  Sum_probs=40.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |++.|...+|+.  .++....|+.+|-..+....+  ....-...+|.      ..+-+     +.+.+|+.|.++-
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--KRLPQGATALDFAYSLHSDLG--DHCIGAKVNHK------LVPLS-----YVLNSGDQVEVLS   62 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHHH--HTEEEEEETTE------ECCTT-----CBCCSSSBEEEEE
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhccc--cceEEEEECCE------EeCCC-----cCcCCCCEEEEEE
Confidence            888999888886  456677899999887743321  11222345776      55443     3456778777764

>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=85.78  E-value=0.71  Score=28.67  Aligned_cols=60  Identities=17%  Similarity=0.147  Sum_probs=42.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhcC--CC-Cc--------cEEEEeCCCCCCCCccC------CCCCccccCCCCCCCEEE
Q 041108           12 LFYIQVENDATVADLKREIGAQQK--LP-CD--------RLILLLSSDHSCPMTQD------HDEVPLADCGVKDGSHIY   74 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~~g--ip-~~--------~q~L~~~g~~~~~~~~L------~d~~~L~~~gI~~~~~i~   74 (102)
                      ...+++++++|+.+|-+.+.+...  +. |+        ...|+..+.     +.|      +-+++|.++|+.+|+.|+
T Consensus         6 ~~~l~v~~~~TL~~lid~L~~~p~~qlk~PSltt~~~~~~k~LYmq~p-----p~Lee~Tr~NL~k~l~eLgl~~g~ei~   80 (98)
T 1y8x_B            6 PQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSV-----TSIEERTRPNLSKTLKELGLVDGQELA   80 (98)
T ss_dssp             CCCEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSC-----HHHHHHHHHHHHSBSGGGTCCTTCEEE
T ss_pred             cEEEEECCchhHHHHHHHHHhChHhhccCCeeeeecCCCCCeEEEeCc-----HHHHHHhHhhhhCCHHHhCCCCCCEEE
Confidence            457899999999999999998433  21 22        334444332     134      235779999999999999


Q ss_pred             EE
Q 041108           75 LF   76 (102)
Q Consensus        75 l~   76 (102)
                      +.
T Consensus        81 Vt   82 (98)
T 1y8x_B           81 VA   82 (98)
T ss_dssp             EE
T ss_pred             EE
Confidence            96

>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=84.87  E-value=2.6  Score=26.25  Aligned_cols=37  Identities=19%  Similarity=0.114  Sum_probs=32.0

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCc
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCD   39 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~   39 (102)
                      |.|-..+|....+.|++.+|+.|+-+.+..+.++..+
T Consensus        12 vkvf~~Dgssksi~V~~~~Ta~dv~~~L~~K~~~~~~   48 (100)
T 1wgr_A           12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSD   48 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCC
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCCCC
Confidence            4555678999999999999999999999999887644

>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=84.81  E-value=3.1  Score=25.60  Aligned_cols=60  Identities=20%  Similarity=0.158  Sum_probs=42.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh---cCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCC
Q 041108           12 LFYIQVENDATVADLKREIGAQ---QKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus        12 ~~~i~v~~~~TV~dLK~~I~~~---~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      .+.+++....||.++-++..-.   ..++.+...+-.+|+      ...     .+.-+++||.|.++-....+
T Consensus        27 ~~~~~v~~g~TV~daI~~~gi~~~~peIdl~~~~V~Vng~------~v~-----~d~~L~dGDRVEIyrpl~~D   89 (97)
T 2hj1_A           27 LKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGIFSR------PIK-----LTDVLKEGDRIEIYRPLLAD   89 (97)
T ss_dssp             EEEEEEETTCBHHHHHHHHTHHHHCTTCCTTTSEEEEEEC------SCC-----TTCBCCTTCEEEECCCCC--
T ss_pred             EEEEEcCCCCcHHHHHHHcCCCccCCcccccccEEEEcCE------ECC-----CCccCCCCCEEEEEecccCC
Confidence            4567888999999998877642   234555677888887      665     34447899999998765543

>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=84.53  E-value=2.1  Score=26.59  Aligned_cols=36  Identities=17%  Similarity=0.147  Sum_probs=29.1

Q ss_pred             EEEEEeCC-------CcEEEEEecCCCcHHHHHHHHHhhcCCC
Q 041108            2 KVAVEILT-------GTLFYIQVENDATVADLKREIGAQQKLP   37 (102)
Q Consensus         2 ~v~V~~~~-------g~~~~i~v~~~~TV~dLK~~I~~~~gip   37 (102)
                      +|.|...+       +..+.+-|+++.+..+|..+|.++.+++
T Consensus         7 kVKv~y~~~~~~~~~~d~~~i~V~~~i~f~~L~~kI~~Kl~~~   49 (98)
T 1q1o_A            7 LFRISYNNNSNNTSSSEIFTLLVEKVWNFDDLIMAINSKISNT   49 (98)
T ss_dssp             EEEEEECSSCSSCCCCEEEEEEECTTCCHHHHHHHHHHHHHHH
T ss_pred             EEEEEecCcccccccCcEEEEEecCCCCHHHHHHHHHHHHcCC
Confidence            45555542       4568899999999999999999998875

>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=83.77  E-value=5.4  Score=24.19  Aligned_cols=46  Identities=13%  Similarity=0.231  Sum_probs=36.1

Q ss_pred             EEEEeC-CCcEEEEEecCCCcHHHHHHHHHhhcCCCCcc-EEEEeCCC
Q 041108            3 VAVEIL-TGTLFYIQVENDATVADLKREIGAQQKLPCDR-LILLLSSD   48 (102)
Q Consensus         3 v~V~~~-~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~-q~L~~~g~   48 (102)
                      +.||.. +|..+.+.++++.+..+|.+++.+..+++... ..+.|...
T Consensus         7 vkvK~~~~gdi~~~~v~~~i~~~~L~~kv~~~~~~~~~~~f~lky~DE   54 (89)
T 1vd2_A            7 VRVKAYYRGDIMITHFEPSISFEGLCNEVRDMCSFDNEQLFTMKWIDE   54 (89)
T ss_dssp             EEEEEESSSCEEEEEECTTCCHHHHHHHHHHHTTCCSSCCEEEEECCS
T ss_pred             EEEEEEeCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCeEEEEEECC
Confidence            445543 47888999999999999999999999987554 56666654

>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A

Probab=82.34  E-value=5.4  Score=23.14  Aligned_cols=59  Identities=15%  Similarity=0.189  Sum_probs=38.1

Q ss_pred             EEEecCCCcHHHHHHHHHhhcC------C-C----CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           14 YIQVENDATVADLKREIGAQQK------L-P----CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        14 ~i~v~~~~TV~dLK~~I~~~~g------i-p----~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .++++...||.+|.+.+.....      + .    .....+..+|.      ...... -.+..+++||.|.++-..
T Consensus        18 ~~~~~~~~tv~~ll~~l~~~~p~~~~~~l~~~~g~~~~v~v~vN~~------~v~~~~-~~~~~l~~gD~V~i~ppv   87 (90)
T 2g1e_A           18 EETFNGISKISELLERLKVEYGSEFTKQMYDGNNLFKNVIILVNGN------NITSMK-GLDTEIKDDDKIDLFPPV   87 (90)
T ss_dssp             EEEESSCCBHHHHHHHHHHHSCHHHHHHHCCSSCSTTTCEEEESSS------BGGGTC-SSSCBCCTTCEEEEECCT
T ss_pred             EEEcCCCCcHHHHHHHHHHHCcchhhhccccccCcCcceEEEECCE------EccccC-CCCcCCCCCCEEEEeCCC
Confidence            3456666899999999988742      1 0    13345777887      554222 124458999999887543

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=80.96  E-value=13  Score=30.12  Aligned_cols=67  Identities=22%  Similarity=0.203  Sum_probs=43.6

Q ss_pred             cEEEEEecCCCcHHHHHHHHHhhc--CCC------CccEEEEe-CCCCCCCCccCCCC-------------CccccCCCC
Q 041108           11 TLFYIQVENDATVADLKREIGAQQ--KLP------CDRLILLL-SSDHSCPMTQDHDE-------------VPLADCGVK   68 (102)
Q Consensus        11 ~~~~i~v~~~~TV~dLK~~I~~~~--gip------~~~q~L~~-~g~~~~~~~~L~d~-------------~~L~~~gI~   68 (102)
                      ..+.+.|-..+||.++|++|-...  |+|      +++.-|-+ .|.....  .|.|.             .+|..|+|.
T Consensus       247 ~~i~vkVLdCDTItQVKeKiLdavYk~~pyS~rP~~~~~dLEwr~g~~g~~--iL~D~D~ts~~~~~wkrLNTL~HY~V~  324 (627)
T 3ig3_A          247 AQVPVKVLNCDSITQAKDKLLDTVYKGIPYSQRPKAEDMDLEWRQGRMARI--ILQDEDITTKIECDWKRVNSLAHYQVT  324 (627)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEESCSSCEE--EECSSSTTCCEETTEEECCBTTTTTCC
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCccceeEeeCCCCce--eeccCCccccccCceeEecchhhcCCC
Confidence            557788888999999999998762  232      34454533 2321111  23221             478999999


Q ss_pred             CCCEEEEEeec
Q 041108           69 DGSHIYLFFKP   79 (102)
Q Consensus        69 ~~~~i~l~~~~   79 (102)
                      +|+++.++-+.
T Consensus       325 Dga~v~L~p~~  335 (627)
T 3ig3_A          325 DGSLVALVPKQ  335 (627)
T ss_dssp             TTCEEEEEEC-
T ss_pred             CCceEEEEecc
Confidence            99999998665

>2c7h_A RBBP6, retinoblastoma-binding protein 6, isoform 3; P53-associated, mRNA processing, splicing-associated, oesophageal cancer; NMR {Homo sapiens}

Probab=80.33  E-value=7.5  Score=23.51  Aligned_cols=46  Identities=17%  Similarity=0.222  Sum_probs=33.0

Q ss_pred             EEEEEeCCCc-EEEEEecC-CCcHHHHHHHHHhhcCCCCccEEE-EeCC
Q 041108            2 KVAVEILTGT-LFYIQVEN-DATVADLKREIGAQQKLPCDRLIL-LLSS   47 (102)
Q Consensus         2 ~v~V~~~~g~-~~~i~v~~-~~TV~dLK~~I~~~~gip~~~q~L-~~~g   47 (102)
                      .|+-|..+.+ ...+.++. ..+|.|||++|..+.++...+.-| +++.
T Consensus         8 ~V~YKFkS~k~~~~v~fdG~~Isv~dLKr~I~~~~kl~~~dfDL~i~na   56 (86)
T 2c7h_A            8 CVHYKFSSKLNYDTVTFDGLHISLCDLKKQIMGREKLKAADCDLQITNA   56 (86)
T ss_dssp             EEEEEETTCSSEEEEEESSSEEEHHHHHHHHHHHHTCCTTTEEEEEEES
T ss_pred             EEEEEEeecCCcceEEEcCCEEEHHHHHHHHHHHhCCCCCcccEEEeCC
Confidence            3666777664 45688877 589999999999998886555544 3443

---

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	102
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	1e-10
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	2e-10
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	9e-10
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-09
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	2e-09
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	4e-09
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	5e-09
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	6e-09
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	7e-09
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	7e-09
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	1e-08
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	1e-08
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	1e-08
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	4e-08
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	8e-08
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	1e-07
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	1e-07
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	2e-07
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	2e-07
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	3e-07
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	4e-07
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	6e-07
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	8e-07
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	9e-07
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	1e-06
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	1e-06
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	2e-06
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	3e-06
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	5e-06
d1wf9a1	94	d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cres	1e-05
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	2e-05
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	2e-05

>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 = 51.1 bits (122), Expect = 1e-10
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           ++V      G    ++   D T+ DLK+ I AQ     ++++L          T   D V
Sbjct: 29  IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLK------KWYTIFKDHV 82

Query: 61  PLADCGVKDGSHIYLFFK 78
            L D  + DG ++ L+++
Sbjct: 83  SLGDYEIHDGMNLELYYQ 100

>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 = 50.3 bits (120), Expect = 2e-10
 Identities = 17/81 (20%), Positives = 27/81 (33%), Gaps = 8/81 (9%)

Query: 1  MKVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHD 58
          M + V  + G  T     V   AT+ +L+  + A   +  +   L           Q  +
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLF------YRGKQLEN 54

Query: 59 EVPLADCGVKDGSHIYLFFKP 79
             L D  V     I L  +P
Sbjct: 55 GYTLFDYDVGLNDIIQLLVRP 75

>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 = 49.2 bits (117), Expect = 9e-10
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 1   MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           +KV V+          V  +++V   K  I  + K   D+L+L+             D+ 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLI------FAGKILKDQD 85

Query: 61  PLADCGVKDGSHIYLFFK 78
            L   G+ DG  ++L  K
Sbjct: 86  TLIQHGIHDGLTVHLVIK 103

>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 = 48.9 bits (116), Expect = 1e-09
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 10/85 (11%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH--- 57
          M V V  + G +  + V  +ATV DLK+ I    +L  +R   +     S      H   
Sbjct: 8  MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 58 -------DEVPLADCGVKDGSHIYL 75
                 D   L D G+++   +  
Sbjct: 68 AGEKLTEDRKKLRDYGIRNRDEVSF 92

>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 = 48.0 bits (114), Expect = 2e-09
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + + V    G     +V    TVA LK+++   + +  D   L              D++
Sbjct: 4  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLT------FEGKPLEDQL 57

Query: 61 PLADCGVKDGSHIYLFFK 78
          PL + G+K  S +++  +
Sbjct: 58 PLGEYGLKPLSTVFMNLR 75

>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 = 46.8 bits (111), Expect = 4e-09
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M++ V+ LTG    ++VE   T+ ++K +I  ++ +P D+  L+ +        Q  D  
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG------KQLEDGR 54

Query: 61 PLADCGVKDGSHIYL 75
           L+D  ++  S ++L
Sbjct: 55 TLSDYNIQKESTLHL 69

>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 = 46.8 bits (111), Expect = 5e-09
 Identities = 16/77 (20%), Positives = 24/77 (31%), Gaps = 8/77 (10%)

Query: 1  MKVAVEILTG--TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHD 58
          M + V  + G  T     +     V +L+R+I     +      L           Q  D
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLF------YRGKQMED 54

Query: 59 EVPLADCGVKDGSHIYL 75
             L D  V+    I L
Sbjct: 55 GHTLFDYEVRLNDTIQL 71

>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 = 46.9 bits (111), Expect = 6e-09
 Identities = 7/75 (9%), Positives = 23/75 (30%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + +   +       ++     T  +L+ +I     L  + + ++++              
Sbjct: 20 VFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQ------LGK 73

Query: 61 PLADCGVKDGSHIYL 75
           L + GV       +
Sbjct: 74 TLEEQGVAHNVKAMV 88

>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 = 46.4 bits (110), Expect = 7e-09
 Identities = 15/79 (18%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M V V   +   F ++V++D ++  LK  +  +Q +P D+L ++ +        +  + +
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFA------GKELPNHL 56

Query: 61 PLADCGVKDGSHIYLFFKP 79
           + +C ++  S +++  +P
Sbjct: 57 TVQNCDLEQQSIVHIVQRP 75

>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 = 46.4 bits (110), Expect = 7e-09
 Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 8  LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGV 67
          L G +    +     V+ +K +I     +P  +  L              D   LA   +
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQ------YEGIFIKDSNSLAYYNM 72

Query: 68 KDGSHIYLFFK 78
           +G+ I+L  K
Sbjct: 73 ANGAVIHLALK 83

>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 = 45.8 bits (108), Expect = 1e-08
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          ++V V    G    ++   + +V D K+ +  Q     ++++L          +   D +
Sbjct: 2  IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQ------KGGSVLKDHI 55

Query: 61 PLADCGVKDGSHIYLFF 77
           L D  V D +++ L++
Sbjct: 56 SLEDYEVHDQTNLELYY 72

>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 = 45.7 bits (108), Expect = 1e-08
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          ++V V+   G  +   +  ++ +  LK++I  QQ LP  +  L              D +
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLE------FQGQVLQDWL 61

Query: 61 PLADCGVKDGSHIYLFFK 78
           L   G++D   + L  K
Sbjct: 62 GLGIYGIQDSDTLILSKK 79

>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 = 45.2 bits (107), Expect = 1e-08
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          M + V+ LTG    I +E   T+  +K  +  ++ +P  +  L+          Q  D+ 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI------YAGKQLADDK 54

Query: 61 PLADCGVKDGSHIYL 75
             D  ++ GS ++L
Sbjct: 55 TAKDYNIEGGSVLHL 69

>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 = 45.0 bits (106), Expect = 4e-08
 Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 9/83 (10%)

Query: 1  MKVAVEI----LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD 56
          M + V      LT   F +QV  D  +++ +     +  +P +   ++            
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQL-----LT 62

Query: 57 HDEVPLADCGVKDGSHIYLFFKP 79
           D   L   G+KDG  + L  K 
Sbjct: 63 DDHCSLGSYGLKDGDMVVLLQKD 85

>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 = 43.3 bits (102), Expect = 8e-08
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 3  VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPL 62
          + V++L G  F + + +  +V++LK +I  +  +   +  L              D VPL
Sbjct: 3  LTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLA----VHPSGVALQDRVPL 58

Query: 63 ADCGVKDGSHIYL 75
          A  G+  GS + L
Sbjct: 59 ASQGLGPGSTVLL 71

>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 = 43.8 bits (103), Expect = 1e-07
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 7/66 (10%)

Query: 10 GTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKD 69
           T   ++V  D+T ++LK++I +   LP     +              ++  L +  V  
Sbjct: 26 KTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKV-------MYKGLVPEDKTLREIKVTS 78

Query: 70 GSHIYL 75
          G+ I +
Sbjct: 79 GAKIMV 84

>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 = 43.3 bits (102), Expect = 1e-07
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 16 QVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYL 75
          Q  ++  V DL + +     +P     L+         +    E PL+  G++DG  + L
Sbjct: 21 QGSSEPVVQDLAQVVEEVIGVPQSFQKLIFK-----GKSLKEMETPLSALGIQDGCRVML 75

Query: 76 FFKP 79
            K 
Sbjct: 76 IGKK 79

>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 = 43.1 bits (101), Expect = 2e-07
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + + V+          +  D TV DLK+ +     +  +R  LL       P     ++V
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAE---NDV 64

Query: 61 PLADCGVKDGSHIYLFFKP 79
           L    +K  + I +    
Sbjct: 65 KLGALKLKPNTKIMMMGTR 83

>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 = 42.7 bits (100), Expect = 2e-07
 Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          +KV V+          V +  T+  LK EI  + K   D+L+L              D  
Sbjct: 8  IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVL------IFAGKILKDPD 60

Query: 61 PLADCGVKDGSHIYLFFKP 79
           LA CGV+DG  ++L  K 
Sbjct: 61 SLAQCGVRDGLTVHLVIKR 79

>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 = 42.2 bits (99), Expect = 3e-07
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 9/79 (11%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKL---PCDRLILLLSSDHSCPMTQDH 57
          + + ++ L    F I++E D TV  LK +I A++     P     L+ +           
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAG------KILS 56

Query: 58 DEVPLADCGVKDGSHIYLF 76
          D+VP+ D  + + + + + 
Sbjct: 57 DDVPIRDYRIDEKNFVVVM 75

>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 = 41.9 bits (98), Expect = 4e-07
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          ++V+V+          +  ++ V   K++I        DRL+L+             D+ 
Sbjct: 11 IRVSVKTPQDC-HEFFLAENSNVRRFKKQISKYLHCNADRLVLI------FTGKILRDQD 63

Query: 61 PLADCGVKDGSHIYLFFK 78
           L+  G+ DGS +++  +
Sbjct: 64 ILSQRGILDGSTVHVVVR 81

>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 = 41.8 bits (98), Expect = 6e-07
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 2/70 (2%)

Query: 8  LTGTLFYIQVENDATVADLKREIGAQQKLPCD--RLILLLSSDHSCPMTQDHDEVPLADC 65
              +   Q+ +  TV  +K  +    K+P     L    S      +  ++D  PL   
Sbjct: 20 PERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFY 79

Query: 66 GVKDGSHIYL 75
           V++G  + +
Sbjct: 80 SVENGDCLLV 89

>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 = 41.6 bits (97), Expect = 8e-07
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 9/88 (10%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKL---PCDRLILLLSSDHSCPMTQDH 57
          M+V ++ L    F I ++ + TV  LK +I +++     P     L+            +
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLI------YAGKILN 54

Query: 58 DEVPLADCGVKDGSHIYLFFKPLDDGST 85
          D+  L +  + + + + +        ST
Sbjct: 55 DDTALKEYKIDEKNFVVVMVTKPKAVST 82

>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 = 40.9 bits (96), Expect = 9e-07
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + + ++      + + V  ++TV   K  I     +P     L+ S           D+ 
Sbjct: 2  LNIHIKSGQDK-WEVNVAPESTVLQFKEAINKANGIPVANQRLIYSG------KILKDDQ 54

Query: 61 PLADCGVKDGSHIYL 75
           +    ++DG  ++L
Sbjct: 55 TVESYHIQDGHSVHL 69

>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 = 41.0 bits (96), Expect = 1e-06
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 8/79 (10%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          + V ++ L  T        + TV  LK +          ++ L+          +     
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKY---FPGQESQMKLIYQGRLLQDPAR----- 59

Query: 61 PLADCGVKDGSHIYLFFKP 79
           L+   + +   I+    P
Sbjct: 60 TLSSLNITNNCVIHCHRSP 78

>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 = 40.2 bits (94), Expect = 1e-06
 Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 7/79 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
          ++V V+ L        V     V + K  I A   +P ++  L              D+ 
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRL------IYQGRVLQDDK 54

Query: 61 PLADCGVKDGSHIYLFFKP 79
           L +  V  G  I+L  + 
Sbjct: 55 KLQEYNV-GGKVIHLVERA 72

>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 = 40.4 bits (94), Expect = 2e-06
 Identities = 10/75 (13%), Positives = 25/75 (33%), Gaps = 7/75 (9%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
            V V+        +++  D      K ++ A   +   R  ++          +D D  
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVM----VKGGTLKDDD-- 61

Query: 61 PLADCGVKDGSHIYL 75
             +  +K+G  + +
Sbjct: 62 -WGNIKMKNGMTVLM 75

>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 = 39.5 bits (92), Expect = 3e-06
 Identities = 9/75 (12%), Positives = 25/75 (33%), Gaps = 6/75 (8%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEV 60
           ++ + + TG    + V +  TV  +KR + A + +                     D++
Sbjct: 4  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWF------FSGRPLTDKM 57

Query: 61 PLADCGVKDGSHIYL 75
             +  +     + +
Sbjct: 58 KFEELKIPKDYVVQV 72

>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 = 39.1 bits (91), Expect = 5e-06
 Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 8  LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQ-DHDEVPLADCG 66
          L       +     T+A+ K ++      P   + L L        ++ D ++  L    
Sbjct: 16 LNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYP 75

Query: 67 VKDGSHIYL 75
          V DG  I++
Sbjct: 76 VDDGCRIHV 84

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 94

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]

 Score = 38.3 bits (89), Expect = 1e-05
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 10/73 (13%)

Query: 15 IQVEN-DATVADLKREIGAQ-------QKLPCDRLILLLSSDHSCPMTQD--HDEVPLAD 64
          + V+    TV+ LK  I  Q       Q L  +R +LL  S        D     + ++ 
Sbjct: 14 VSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISS 73

Query: 65 CGVKDGSHIYLFF 77
            +  GS +YL +
Sbjct: 74 LNLAHGSMVYLAY 86

>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 = 37.9 bits (88), Expect = 2e-05
 Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 8  LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLL-SSDHSCPMTQDHDEVPLADCG 66
           T      +     ++ DLK+++        D + + L   D             L D G
Sbjct: 13 ATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLG 72

Query: 67 VKDGSHIYL 75
          V+DG  I+ 
Sbjct: 73 VRDGYRIHA 81

>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 = 38.0 bits (88), Expect = 2e-05
 Identities = 8/83 (9%), Positives = 24/83 (28%), Gaps = 14/83 (16%)

Query: 1  MKVAVEILTGTLFYIQVENDATVADLKREIGAQQK--------LPCDRLILLLSSDHSCP 52
          + + + +++G         + + +D+ + +                + L L+        
Sbjct: 17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQG----- 71

Query: 53 MTQDHDEVPLADCGVKDGSHIYL 75
              H  V L    +  G    +
Sbjct: 72 -RFLHGNVTLGALKLPFGKTTVM 93

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	102
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.9
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.89
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.89
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.88
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.88
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.87
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.86
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.86
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.86
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.86
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.85
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.85
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.84
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.83
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.82
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.82
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.8
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.79
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.78
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.76
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.76
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.75
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.75
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.75
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.74
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.72
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.72
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.71
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.7
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.7
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.65
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.59
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.55
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.52
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.44
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.39
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.32
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	99.09
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.84
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	97.9
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.81
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.66
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.65
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	97.44
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	96.28
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	94.23
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	92.73
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	92.53
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	92.39
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	91.89
d1y8xb1	92	UBA3 {Human (Homo sapiens) [TaxId: 9606]}	88.82
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	88.66
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	87.57
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	86.73
d1wgya_	104	Rap guanine nucleotide exchange factor 5, RapGEF5	85.62
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	85.2

>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=99.90  E-value=1.3e-23  Score=126.64  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=73.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||+.+|+++.++|++++||.+||++|+++.|+|++.|+|+|+|+      .|+|+.+|++|||++|++|++++++.
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk------~L~d~~tL~~y~i~~~s~I~L~~rlr   74 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK------QLEDGRTLSDYNIQKESTLHLVLRLR   74 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBGGGGTCCTTCEEEEEECTT
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCe------EcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            999999999999999999999999999999999999999999999999      99999999999999999999999987


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ++
T Consensus        75 gG   76 (76)
T d1ogwa_          75 GG   76 (76)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.89  E-value=2.8e-23  Score=124.35  Aligned_cols=73  Identities=23%  Similarity=0.352  Sum_probs=71.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+||+.+|+++.++|++++||++||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+|+
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 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGK------QLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCe------EcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            999999999999999999999999999999999999999999999999      9999999999999999999999874

>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=99.89  E-value=4.3e-23  Score=125.29  Aligned_cols=75  Identities=20%  Similarity=0.413  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||+.+|+++.++|++++||++||++|++++|+|++.|+|+|+|+      .|+|+.+|++|+|++|++|++..++.
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk------~L~d~~tL~~y~I~~~sti~lv~R~r   76 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGK------ELPNHLTVQNCDLEQQSIVHIVQRPR   76 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTE------EECTTCBGGGSSCCTTCEEEEEESSC
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeee------EcCCCCCHHHcCCCCCCEEEEEeccC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999886


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      +
T Consensus        77 g   77 (78)
T d2zeqa1          77 R   77 (78)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.4e-22  Score=122.06  Aligned_cols=73  Identities=22%  Similarity=0.323  Sum_probs=71.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+||..+|+++.++|++++||++||++|+++.|+|++.|+|+|+|+      .|+|+.+|++|||++|++|++++|+
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 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGK------PLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCe------ECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            799999999999999999999999999999999999999999999999      9999999999999999999999874

>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=99.88  E-value=9.1e-23  Score=125.92  Aligned_cols=77  Identities=22%  Similarity=0.244  Sum_probs=74.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||+.+|+++.++|++++||.+||++|+.++|+|+++|+|+|+|+      .|+|+.+|++|+|++|++|++..+..
T Consensus         8 mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk------~L~d~~tL~~y~I~~~stl~l~~r~~   81 (87)
T d1wh3a_           8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQ------VLQDWLGLGIYGIQDSDTLILSKKKG   81 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTE------ECCSSSBHHHHTCCTTEEEEEEECSC
T ss_pred             EEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeece------EcCCCCcHHHcCCCCCCEEEEEecCC
Confidence            899999999999999999999999999999999999999999999999      99999999999999999999999877


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      ++.
T Consensus        82 ~gp   84 (87)
T d1wh3a_          82 SGP   84 (87)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=5.9e-22  Score=119.76  Aligned_cols=73  Identities=21%  Similarity=0.246  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCc-EEEEE-ecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGT-LFYIQ-VENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~-~~~i~-v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+||+.+|+ ++.++ +++++||++||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.+|
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~~y~I~~~sti~lv~r   74 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGK------QMEDGHTLFDYEVRLNDTIQLLVR   74 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTCBTTTTTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeE------eccCCCcHHHcCCCCCCEEEEEEE
Confidence            89999999995 78885 99999999999999999999999999999999      999999999999999999999987


Q ss_pred             c
Q 041108           79 P   79 (102)
Q Consensus        79 ~   79 (102)
                      +
T Consensus        75 ~   75 (76)
T d2faza1          75 Q   75 (76)
T ss_dssp             C
T ss_pred             c
Confidence            5

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=4.7e-22  Score=120.95  Aligned_cols=75  Identities=13%  Similarity=0.167  Sum_probs=72.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||+.+|+++.++|++++||++||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++.+
T Consensus         4 ~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk------~L~d~~tL~~y~I~~~sti~lvi~~p   77 (80)
T d1ttna1           4 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGR------PLTDKMKFEELKIPKDYVVQVIVSQP   77 (80)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTE------ECCTTSHHHHCCCSSSCEEEEECCCS
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECce------EcCCCCcHHHcCCCCCCEEEEEecCC
Confidence            689999999999999999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      .
T Consensus        78 ~   78 (80)
T d1ttna1          78 V   78 (80)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.86  E-value=2.1e-21  Score=121.30  Aligned_cols=78  Identities=19%  Similarity=0.346  Sum_probs=73.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcC---CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQK---LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~g---ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+||+.+|+++.++|++++||.+||++|+++.|   +|+++|+|+|+|+      .|+|+.+|++|||.+|++|++++
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk------~L~d~~tL~~y~I~~~s~i~lv~   74 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGK------ILNDDTALKEYKIDEKNFVVVMV   74 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTE------ECCTTSBGGGGTCCSSSEEEEEE
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCe------EccCCCcHHHcCCCCCCEEEEEE
Confidence            99999999999999999999999999999999876   8999999999999      99999999999999999999999


Q ss_pred             ecCCCCC
Q 041108           78 KPLDDGS   84 (102)
Q Consensus        78 ~~~~~~~   84 (102)
                      +.+...+
T Consensus        75 ~~~~~~~   81 (95)
T d1uela_          75 TKPKAVS   81 (95)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            8665443

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=9.5e-22  Score=118.83  Aligned_cols=73  Identities=23%  Similarity=0.275  Sum_probs=69.5

Q ss_pred             CEEEEEeCCC-cEEEE-EecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTG-TLFYI-QVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g-~~~~i-~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+||..+| +++.+ +|++++||++||.+|+++.|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++++
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk------~L~d~~tL~~y~I~~~s~i~lv~r   74 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGK------QLENGYTLFDYDVGLNDIIQLLVR   74 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTE------ECCSSSBHHHHTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEee------EecCCCCHHHcCCCCCCEEEEEEc
Confidence            8999999999 57777 599999999999999999999999999999999      999999999999999999999987


Q ss_pred             c
Q 041108           79 P   79 (102)
Q Consensus        79 ~   79 (102)
                      +
T Consensus        75 p   75 (76)
T d1wy8a1          75 P   75 (76)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.86  E-value=7.4e-22  Score=118.32  Aligned_cols=71  Identities=20%  Similarity=0.341  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+|+...|+++.++|++++||++||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+++.
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 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGS------VLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSC------EECTTSBHHHHTCCTTEEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeE------EecccCcHHHcCCCCCCEEEEEE
Confidence            689999999999999999999999999999999999999999999999      99999999999999999999975

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.5e-21  Score=115.62  Aligned_cols=73  Identities=26%  Similarity=0.393  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe--CCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLL--SSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~--~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      .+|+||+.+|+.+.++|++++||.+||++|+.++|+|+++|||+|  +|+      .|+|+.+|++|||++|++|+++++
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk------~L~D~~tL~~y~i~~g~~i~lv~~   74 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGV------ALQDRVPLASQGLGPGSTVLLVVD   74 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCC------BCCSSSCSGGGTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCe------eccCCCcHHHcCCCCCCEEEEEEE
Confidence            479999999999999999999999999999999999999999999  688      999999999999999999999986


Q ss_pred             c
Q 041108           79 P   79 (102)
Q Consensus        79 ~   79 (102)
                      .
T Consensus        75 ~   75 (76)
T d1z2ma1          75 K   75 (76)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.85  E-value=3.1e-22  Score=119.95  Aligned_cols=73  Identities=22%  Similarity=0.297  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+||+.+|+++.++|++++||++||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|+| +|++|+++.+.|
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk------~L~d~~tL~dy~i-~~~ti~lv~r~P   73 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGR------VLQDDKKLQEYNV-GGKVIHLVERAP   73 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTE------ECCSSSBHHHHTC-TTEEEBCCCSSC
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCe------EccCCCCHHHhCC-CCCEEEEEecCC
Confidence            899999999999999999999999999999999999999999999999      9999999999999 588999887764

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.2e-21  Score=115.84  Aligned_cols=72  Identities=24%  Similarity=0.421  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcC---CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQK---LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~g---ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |+|+||+.+|+++.++|++++||.+||++|+++.|   +|+++|||+|+|+      .|+|+.+|++|||++|++|++++
T Consensus         3 ~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk------~L~D~~tL~~y~I~~~s~i~~~v   76 (77)
T d1oqya4           3 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGK------ILSDDVPIRDYRIDEKNFVVVMV   76 (77)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSS------EECSSSBTTTTCCCTTSCEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCc------CccCCCcHHHcCCCCCCEEEEEE
Confidence            88999999999999999999999999999999987   8999999999999      99999999999999999999986


Q ss_pred             e
Q 041108           78 K   78 (102)
Q Consensus        78 ~   78 (102)
                      .
T Consensus        77 s   77 (77)
T d1oqya4          77 T   77 (77)
T ss_dssp             E
T ss_pred             C
Confidence            3

>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=99.83  E-value=1.1e-20  Score=115.82  Aligned_cols=75  Identities=31%  Similarity=0.428  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|+|++.++ .+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||.+|++|++.++..
T Consensus         8 i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk------~L~D~~tL~~y~i~~gsti~lv~r~~   80 (84)
T d1yqba1           8 IKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGK------ILKDPDSLAQCGVRDGLTVHLVIKRQ   80 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTSBHHHHTCCTTCEEEEEECCC
T ss_pred             EEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeee------eccccCcHHHcCCCCCCEEEEEECCC
Confidence            7899999755 5799999999999999999999999999999999999      99999999999999999999999876


Q ss_pred             CC
Q 041108           81 DD   82 (102)
Q Consensus        81 ~~   82 (102)
                      ..
T Consensus        81 ~~   82 (84)
T d1yqba1          81 HR   82 (84)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.82  E-value=2.8e-20  Score=111.19  Aligned_cols=71  Identities=17%  Similarity=0.289  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|++. ++.+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++..+
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-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGK------ILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             EEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCe------EccCCCcHHHCCCCCCCEEEEEee
Confidence            68999985 567899999999999999999999999999999999999      999999999999999999999864

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=8.5e-21  Score=120.13  Aligned_cols=72  Identities=25%  Similarity=0.391  Sum_probs=69.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      ++|+|+...|+++.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+|+++
T Consensus        29 i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk------~L~D~~tL~dygI~~GstI~L~~~  100 (100)
T d1uh6a_          29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYT------IFKDHVSLGDYEIHDGMNLELYYQ  100 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTE------ECCSSCBHHHHTCCTTEEEEEECC
T ss_pred             EEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEee------cccCcCCHHHcCCCCCCEEEEEEC
Confidence            479999999999999999999999999999999999999999999999      999999999999999999999864

>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=99.80  E-value=8.7e-20  Score=115.52  Aligned_cols=71  Identities=25%  Similarity=0.368  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|+|++.++ .+.++|++++||.+||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|+|++|
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-KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGK------ILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             EEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTE------EESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             EEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeee------cccCCCcHHHcCCCCCCEEEEEEC
Confidence            6899998765 5789999999999999999999999999999999999      999999999999999999999875

>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=99.79  E-value=4e-20  Score=113.03  Aligned_cols=72  Identities=21%  Similarity=0.360  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+|++.++ .+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++++|.
T Consensus        11 i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk------~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          11 IRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGK------ILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             EEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTE------ECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             EEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhh------ccccCCcHHHcCCCCCCEEEEEEeC
Confidence            7899999755 4689999999999999999999999999999999999      9999999999999999999998763

>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=99.78  E-value=9.5e-20  Score=115.51  Aligned_cols=77  Identities=22%  Similarity=0.296  Sum_probs=69.8

Q ss_pred             CEEEE----EeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC-CCCCccccCCCCCCCEEEE
Q 041108            1 MKVAV----EILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD-HDEVPLADCGVKDGSHIYL   75 (102)
Q Consensus         1 M~v~V----~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~~~~~i~l   75 (102)
                      |+|+|    +..+|.++.++|++++||.+||++|+.++|+|+++|+|+|+|+      .| +|+.+|++|||++|++|+|
T Consensus         8 m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk------~L~dd~~tL~~~gI~~g~~i~l   81 (102)
T d1v5oa_           8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQ------LLTDDHCSLGSYGLKDGDMVVL   81 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTE------EECCSSSBHHHHTCCTTEEEEE
T ss_pred             EEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCe------EeecccCCHHHcCCCCCCEEEE
Confidence            78899    6667899999999999999999999999999999999999999      88 5678999999999999999


Q ss_pred             EeecCCCC
Q 041108           76 FFKPLDDG   83 (102)
Q Consensus        76 ~~~~~~~~   83 (102)
                      ..+.....
T Consensus        82 ~~r~~~~~   89 (102)
T d1v5oa_          82 LQKDNVGL   89 (102)
T ss_dssp             CBCCCCCC
T ss_pred             EECCCCCC
Confidence            98765543

>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=99.76  E-value=5.6e-19  Score=108.74  Aligned_cols=68  Identities=21%  Similarity=0.228  Sum_probs=65.1

Q ss_pred             CCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCC
Q 041108            8 LTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus         8 ~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      ++|+++.++|++++||++||++|++++|+|+++|+|+|+|+      .|+|+.+|++|||++|++|++.++..|
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 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGI------FIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTE------EECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCc------CcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            57999999999999999999999999999999999999999      999999999999999999999998754

>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=99.76  E-value=5.8e-19  Score=110.56  Aligned_cols=72  Identities=13%  Similarity=0.144  Sum_probs=67.2

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+||..+++.+.++|++++||.+||++|++.+|+|+++|+|+|+|+      .|+|+ +|++|||++|++|+++...
T Consensus         8 ~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk------~L~d~-tL~~~gi~~g~~i~lv~t~   79 (96)
T d1wgga_           8 YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGG------TLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             EEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTE------ECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             eEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCc------ccCCC-cHHHCCCCCCCEEEEEeeC
Confidence            689999988888899999999999999999999999999999999999      99886 7999999999999998654

>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=99.75  E-value=1.5e-19  Score=115.00  Aligned_cols=75  Identities=25%  Similarity=0.313  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEE---------------EEeCCCCCCCCccCCCC-Ccccc
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLI---------------LLLSSDHSCPMTQDHDE-VPLAD   64 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~---------------L~~~g~~~~~~~~L~d~-~~L~~   64 (102)
                      |+|+|+..+|+.+.++|++++||.+||++|++++++|+++|+               |+|+|+      .|.|+ .+|++
T Consensus         8 M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~------~L~d~~~tL~~   81 (105)
T d1v2ya_           8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGE------KLTEDRKKLRD   81 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSC------EECCSSSBHHH
T ss_pred             EEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCE------ECcccCCCHHH
Confidence            899999999999999999999999999999999999999997               999999      88655 68999


Q ss_pred             CCCCCCCEEEEEeecCC
Q 041108           65 CGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        65 ~gI~~~~~i~l~~~~~~   81 (102)
                      |||++|++|+++.++..
T Consensus        82 ~gI~~g~~l~lv~r~~~   98 (105)
T d1v2ya_          82 YGIRNRDEVSFIKKLGQ   98 (105)
T ss_dssp             HTCCSSEEEEEEECSCS
T ss_pred             cCCCCCCEEEEEEecCC
Confidence            99999999999988653

>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=99.75  E-value=2.3e-18  Score=107.79  Aligned_cols=75  Identities=15%  Similarity=0.107  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCC-CCCccccCCCCCCCEEEEEeec
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDH-DEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~-d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      |+|+||+.+|+.+.++|++++||.+||++|+   .+++++|||+|+|+      .|. |..+|++|+|.+|++|+++++.
T Consensus         8 m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~~~~~~qrLi~~Gk------~L~dd~~tL~~y~i~~g~~v~l~~~~   78 (95)
T d1wiaa_           8 INVRLKFLNDTEELAVARPEDTVGTLKSKYF---PGQESQMKLIYQGR------LLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHS---SSTTTTCEEEETTE------ECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHh---cCCcceeEEEECCE------EcccCCCCHHHcCCCCCCEEEEEEcC
Confidence            8999999999999999999999999999986   46889999999999      985 6789999999999999999987


Q ss_pred             CCCCC
Q 041108           80 LDDGS   84 (102)
Q Consensus        80 ~~~~~   84 (102)
                      ++...
T Consensus        79 ~~~~~   83 (95)
T d1wiaa_          79 PGAAV   83 (95)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76544

>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=99.75  E-value=5.9e-18  Score=107.04  Aligned_cols=78  Identities=10%  Similarity=0.155  Sum_probs=71.0

Q ss_pred             CEEEEEeCCCcEE-EEEecCCCcHHHHHHHHHhh-----cCCC--CccEEEEeCCCCCCCCccCCCCCccccCCCCCCC-
Q 041108            1 MKVAVEILTGTLF-YIQVENDATVADLKREIGAQ-----QKLP--CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGS-   71 (102)
Q Consensus         1 M~v~V~~~~g~~~-~i~v~~~~TV~dLK~~I~~~-----~gip--~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~-   71 (102)
                      |+|.+|..+|+.+ .+.+++++||.+||++|++.     .|+|  +++|||+|+|+      .|+|+.+|++|+|.+|+ 
T Consensus         8 i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk------~L~D~~tL~dy~i~~g~~   81 (101)
T d1se9a_           8 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGK------VLENSKTVKDYRSPVSNL   81 (101)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTE------ECCTTSBGGGGSCCTTSC
T ss_pred             EEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCe------EecCCCCHHHcCCCCCCc
Confidence            6899999999876 69999999999999999875     6787  88999999999      99999999999999998 


Q ss_pred             -----EEEEEeecCCCCC
Q 041108           72 -----HIYLFFKPLDDGS   84 (102)
Q Consensus        72 -----~i~l~~~~~~~~~   84 (102)
                           ++||.++.+....
T Consensus        82 ~~~~~tmHlVvrpp~~~~   99 (101)
T d1se9a_          82 AGAVTTMHVIIQAPVTEK   99 (101)
T ss_dssp             TTCCEEEEEEECCCSSCC
T ss_pred             CCCceEEEEEeCCCCCcc
Confidence                 9999999876544

>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=99.74  E-value=1.4e-18  Score=111.62  Aligned_cols=70  Identities=23%  Similarity=0.331  Sum_probs=66.5

Q ss_pred             CCcEEEEEecC-CCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCCCC
Q 041108            9 TGTLFYIQVEN-DATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDDGS   84 (102)
Q Consensus         9 ~g~~~~i~v~~-~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~~~   84 (102)
                      +|+++.++|.+ ++||.+||++|++++|+|++.|+|+|.|+      .|+|+.+|++|+|++|++|++.++..++.+
T Consensus        39 ~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk------~L~D~~tL~~ynI~~gsti~L~lr~rGG~~  109 (111)
T d1we6a_          39 DGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAG------FLKDNMSLAHYNVGAGEILTLSLRERSGPS  109 (111)
T ss_dssp             SSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSS------BCCTTSBTTTTTCSSSCEEEEECSSCCSSC
T ss_pred             CCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeE------EccccCCHHHcCCCCCCEEEEEeeCCCCCC
Confidence            58999999987 89999999999999999999999999999      999999999999999999999999988654

>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=99.72  E-value=8.4e-18  Score=108.69  Aligned_cols=73  Identities=14%  Similarity=0.204  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHH--------HhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREI--------GAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSH   72 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I--------~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~   72 (102)
                      |+|+|++.+|+++.+.|++++||.+||++|        +++.++|+++|||+|.|+      .|+|+.+|++|+|.+|++
T Consensus        17 i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk------~L~D~~tL~~~~i~~g~~   90 (116)
T d1wgha_          17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGR------FLHGNVTLGALKLPFGKT   90 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTE------EECSSCBTTTTTCCSSCE
T ss_pred             EEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCE------EecCCCCHHHcCCCCCCE
Confidence            578999999999999999999999999999        577899999999999999      999999999999999987


Q ss_pred             --EEEEeec
Q 041108           73 --IYLFFKP   79 (102)
Q Consensus        73 --i~l~~~~   79 (102)
                        ||+..+.
T Consensus        91 ~~lhlv~r~   99 (116)
T d1wgha_          91 TVMHLVARE   99 (116)
T ss_dssp             EEEEEEECS
T ss_pred             EEEEEEeCC
Confidence              6666653

>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=99.72  E-value=2.8e-18  Score=106.04  Aligned_cols=74  Identities=20%  Similarity=0.276  Sum_probs=66.7

Q ss_pred             CEEEEEeCCCcEEEE-EecCCCcHHHHHHHHHhhcCCCCccEEEE---eCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYI-QVENDATVADLKREIGAQQKLPCDRLILL---LSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i-~v~~~~TV~dLK~~I~~~~gip~~~q~L~---~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      |+|+|+.. |+.+.+ +|++++||.+||++|++++|+|+++|||+   |.|+      .|+|+.+|.+|+|++|++|+++
T Consensus         8 ~~i~Vk~~-~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk------~L~D~~tL~~~~i~~g~~i~lv   80 (90)
T d1v5ta_           8 LPIIVKWG-GQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGK------PAENDVKLGALKLKPNTKIMMM   80 (90)
T ss_dssp             CCEEEEET-TEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTE------ECCTTSBHHHHTCCTTEEEEEE
T ss_pred             EEEEEEEC-CeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCc------CCCCcCcHHHcCCCCCCEEEEE
Confidence            78999984 666676 79999999999999999999999999999   5888      9999999999999999999998


Q ss_pred             eecCC
Q 041108           77 FKPLD   81 (102)
Q Consensus        77 ~~~~~   81 (102)
                      .+...
T Consensus        81 ~s~~~   85 (90)
T d1v5ta_          81 GTRES   85 (90)
T ss_dssp             CCCSS
T ss_pred             eeCCC
Confidence            76543

>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=99.71  E-value=1.2e-17  Score=101.49  Aligned_cols=72  Identities=22%  Similarity=0.336  Sum_probs=64.0

Q ss_pred             CEEEEEeCCCcEEEEEe-----cCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccC-CCCCccccCCCCCCCEEE
Q 041108            1 MKVAVEILTGTLFYIQV-----ENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQD-HDEVPLADCGVKDGSHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v-----~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L-~d~~~L~~~gI~~~~~i~   74 (102)
                      |+|+|+. .++.+.+++     ++++||++||++|++.+|+|+++|+|+|+|+      .| +|+.+|++|||++|++|+
T Consensus         2 i~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~------~L~~d~~tL~~~gi~~g~~i~   74 (81)
T d1wxva1           2 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGK------SLKEMETPLSALGIQDGCRVM   74 (81)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTE------EECCSSSBHHHHTCCSSEEEE
T ss_pred             EEEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCe------EeCcCCCChHHCCCCCCCEEE
Confidence            6788866 468888888     4689999999999999999999999999999      88 577899999999999999


Q ss_pred             EEeec
Q 041108           75 LFFKP   79 (102)
Q Consensus        75 l~~~~   79 (102)
                      ++.+.
T Consensus        75 lv~~~   79 (81)
T d1wxva1          75 LIGKK   79 (81)
T ss_dssp             EESCC
T ss_pred             EEEec
Confidence            98764

>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=99.70  E-value=5.5e-18  Score=106.89  Aligned_cols=73  Identities=12%  Similarity=0.133  Sum_probs=66.2

Q ss_pred             CEEEE--EeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAV--EILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V--~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |+|++  +...|+++.++|.+++||.+||.+|+++.|+|+++|+|+|+|+      .|+|+.+|++|||+++++|+++..
T Consensus        18 i~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk------~L~d~~tL~~~gI~~~s~i~vi~~   91 (100)
T d1wjua_          18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKK------QLQLGKTLEEQGVAHNVKAMVLEL   91 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTE------ECCTTSBHHHHTCCSSEEEEEECC
T ss_pred             EEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEccc------CcCCCcCHHHcCCCCCCEEEEEEc
Confidence            35555  4456899999999999999999999999999999999999999      999999999999999999998865


Q ss_pred             c
Q 041108           79 P   79 (102)
Q Consensus        79 ~   79 (102)
                      .
T Consensus        92 ~   92 (100)
T d1wjua_          92 K   92 (100)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.70  E-value=9.1e-18  Score=104.83  Aligned_cols=75  Identities=17%  Similarity=0.214  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |+|.|+. +++++.++|++++||.+||++|++.+|+|+++|+|+|+|       .|+|+.+|++|+|++|++|+|+.+..
T Consensus        18 i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g-------~l~D~~tL~~~~I~~gs~i~lvgs~~   89 (95)
T d1v86a_          18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKG-------LVPEDKTLREIKVTSGAKIMVVGSTI   89 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSS-------BCCSSSBHHHHCCCTTEEEEECCSSC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEecc-------cccCCCcHHHCCCCCCCEEEEEecCC
Confidence            5677775 678999999999999999999999999999999999976       56889999999999999999997665


Q ss_pred             CCC
Q 041108           81 DDG   83 (102)
Q Consensus        81 ~~~   83 (102)
                      +..
T Consensus        90 ~gp   92 (95)
T d1v86a_          90 SGP   92 (95)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.65  E-value=2.6e-16  Score=97.87  Aligned_cols=75  Identities=15%  Similarity=0.038  Sum_probs=65.7

Q ss_pred             CEEEEEeCCCcE--EEEEecCCCcHHHHHHHHHhhcC--CCCccEEEEeCCCCCCCCccCCCCCccccCCCCCC--CEEE
Q 041108            1 MKVAVEILTGTL--FYIQVENDATVADLKREIGAQQK--LPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDG--SHIY   74 (102)
Q Consensus         1 M~v~V~~~~g~~--~~i~v~~~~TV~dLK~~I~~~~g--ip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~--~~i~   74 (102)
                      |+|+|++.+++.  +.+++++++||.+||++|++..+  +|+++|||+|+|+      .|+|+.+|++|....+  .+||
T Consensus         8 i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk------~L~D~~~L~d~~~~~~~~~viH   81 (93)
T d1wgda_           8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGK------LLLDHQCLRDLLPKQEKRHVLH   81 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTE------ECCSSSCHHHHSCSSSCSEEEE
T ss_pred             EEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCe------EccCCCCHHHhCcccCCCCEEE
Confidence            789999998754  88999999999999999999965  9999999999999      9999999999977544  4999


Q ss_pred             EEeecCC
Q 041108           75 LFFKPLD   81 (102)
Q Consensus        75 l~~~~~~   81 (102)
                      +..+...
T Consensus        82 LV~~~~~   88 (93)
T d1wgda_          82 LVCNVKS   88 (93)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9877644

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.6e-16  Score=100.76  Aligned_cols=74  Identities=26%  Similarity=0.326  Sum_probs=65.1

Q ss_pred             EEEEEeCCC-cEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCC-------CCEE
Q 041108            2 KVAVEILTG-TLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKD-------GSHI   73 (102)
Q Consensus         2 ~v~V~~~~g-~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~-------~~~i   73 (102)
                      +|+|+...| +++.++|++++||.+||++|+++.|+|+++|+|+|+|+      .|+|+.+|++|||.+       .+++
T Consensus         1 qifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk------~L~D~~TL~dYgI~~~~~~~~~~~~~   74 (103)
T d2c9wb1           1 DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQ------LLDDGKTLGECGFTSQTARPQAPATV   74 (103)
T ss_dssp             CEEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTE------ECCTTSBHHHHTCCTTTSBTTBCEEE
T ss_pred             CEEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCE------EcCCCCCHHHcCCCcccccccCCcEE
Confidence            467777766 46789999999999999999999999999999999999      999999999999954       4588


Q ss_pred             EEEeecCC
Q 041108           74 YLFFKPLD   81 (102)
Q Consensus        74 ~l~~~~~~   81 (102)
                      .+.++..+
T Consensus        75 ~l~~~~~~   82 (103)
T d2c9wb1          75 GLAFRADD   82 (103)
T ss_dssp             EEEEEETT
T ss_pred             EEEEecCC
Confidence            88887544

>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=99.59  E-value=2.6e-15  Score=93.61  Aligned_cols=83  Identities=16%  Similarity=0.104  Sum_probs=69.1

Q ss_pred             CEEEEEeC-CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCC-ccCCCCCccccCCCCCCCEEEEEee
Q 041108            1 MKVAVEIL-TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPM-TQDHDEVPLADCGVKDGSHIYLFFK   78 (102)
Q Consensus         1 M~v~V~~~-~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~-~~L~d~~~L~~~gI~~~~~i~l~~~   78 (102)
                      |.|+|++. ++..+...+++++||.+||++|+..+|+|++.|+|+|.|+..+.. ..++|+.+|++|+|.+|++|||.-+
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            57888884 455678889999999999999999999999999999988622221 2578999999999999999999987


Q ss_pred             cCCCC
Q 041108           79 PLDDG   83 (102)
Q Consensus        79 ~~~~~   83 (102)
                      .+...
T Consensus        88 ~p~~~   92 (95)
T d1v6ea_          88 SGSGP   92 (95)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            76543

>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=99.55  E-value=1.4e-14  Score=90.35  Aligned_cols=80  Identities=18%  Similarity=0.268  Sum_probs=64.9

Q ss_pred             EEEEEeC---CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCC--CCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            2 KVAVEIL---TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDH--SCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         2 ~v~V~~~---~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~--~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      .|+|+..   +++.+.++++.++||.+||.+|+..+|+|++.|+|+|.|+-  .+...+.+|+++|.+|||++|++|+|.
T Consensus        11 ti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~   90 (97)
T d1wjna_          11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEE
Confidence            4666654   35778999999999999999999999999999999998861  111124468899999999999999998


Q ss_pred             eecCC
Q 041108           77 FKPLD   81 (102)
Q Consensus        77 ~~~~~   81 (102)
                      ...|.
T Consensus        91 ~~~P~   95 (97)
T d1wjna_          91 WSGPS   95 (97)
T ss_dssp             CCSSC
T ss_pred             eCCCC
Confidence            75543

>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=99.52  E-value=3.3e-14  Score=85.44  Aligned_cols=73  Identities=12%  Similarity=0.163  Sum_probs=66.6

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPLDD   82 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~~~   82 (102)
                      |.|+. +|+...+.+..++++..|+++++++.|++++.|+|+|+|+      .|+++.++++|++.+|++|+++++..|+
T Consensus         7 ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~------~l~~~~T~~~~~i~dgd~I~v~~~q~GG   79 (79)
T d1euvb_           7 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGI------RIQADQTPEDLDMEDNDIIEAHREQIGG   79 (79)
T ss_dssp             EEEES-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTE------ECCTTCCTTTTTCCTTEEEEEEECCBCC
T ss_pred             EEECC-CCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCE------EeCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            44443 5788889999999999999999999999999999999999      9999999999999999999999987664

>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=99.44  E-value=1.9e-13  Score=81.71  Aligned_cols=75  Identities=16%  Similarity=0.227  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      ++|.|+..+|+.+.+.|..+.++..|+.+++++.|++++.++++|+|.      .|.++.+++++++.+|++|.++++..
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~------~l~~~~T~~~l~~edgD~Idv~~~q~   76 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQ------RIADNHTPKELGMEEEDVIEVYQEQT   76 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTE------ECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCE------ECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            468899999999999999999999999999999999999999999999      99999999999999999999998765


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      |
T Consensus        77 G   77 (77)
T d2uyzb1          77 G   77 (77)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=99.39  E-value=1.9e-12  Score=79.48  Aligned_cols=79  Identities=16%  Similarity=0.126  Sum_probs=61.5

Q ss_pred             EEEEeC-CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCC-ccCCCCCccccCCCCCCCEEEEEeecC
Q 041108            3 VAVEIL-TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPM-TQDHDEVPLADCGVKDGSHIYLFFKPL   80 (102)
Q Consensus         3 v~V~~~-~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~-~~L~d~~~L~~~gI~~~~~i~l~~~~~   80 (102)
                      |.|.+. .+......+++++||.+||.+|+..+|+|++.|+|+|.++..+.. ...+|+++|.+|||.+|++||+.=...
T Consensus         7 l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd~~~   86 (90)
T d1t0ya_           7 LEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTG   86 (90)
T ss_dssp             EEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECTT
T ss_pred             EEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEeCCC
Confidence            445542 234467789999999999999999999999999999877622111 245789999999999999999975544


Q ss_pred             C
Q 041108           81 D   81 (102)
Q Consensus        81 ~   81 (102)
                      +
T Consensus        87 ~   87 (90)
T d1t0ya_          87 G   87 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.32  E-value=1.2e-12  Score=81.31  Aligned_cols=54  Identities=20%  Similarity=0.317  Sum_probs=49.0

Q ss_pred             CCcHHHHHHHHHhhcC--CC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108           20 DATVADLKREIGAQQK--LP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus        20 ~~TV~dLK~~I~~~~g--ip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      +.||.+||+.|+++..  +| |++|+|+|+|+      .|+|+.+|++|||++|++||++.|.
T Consensus        37 ~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk------~L~D~~tL~~y~I~~gstihLV~r~   93 (94)
T d1x1ma1          37 GYSISFLKQLIAGKLQESVPDPELIDLIYCGR------KLKDDQTLDFYGIQPGSTVHVLRKS   93 (94)
T ss_dssp             CCBHHHHHHHHHHHCTTTCCCSSSEEEEETTE------ECCTTCBHHHHTCCTTCEEEEEESS
T ss_pred             ccCHHHHHHHHHHHcccCCCChhheEEEECCe------EECCCccHHHcCCCCCCEEEEEEeC
Confidence            6799999999998864  44 79999999999      9999999999999999999999763

>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=99.09  E-value=1.1e-10  Score=71.78  Aligned_cols=77  Identities=22%  Similarity=0.282  Sum_probs=58.9

Q ss_pred             EEEEEeCCCcEEEEEecC-CCcHHHHHHHHHhhcCCCCccEEEEeCCC------CCCC--CccC-CCCCccccCCCCCCC
Q 041108            2 KVAVEILTGTLFYIQVEN-DATVADLKREIGAQQKLPCDRLILLLSSD------HSCP--MTQD-HDEVPLADCGVKDGS   71 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~-~~TV~dLK~~I~~~~gip~~~q~L~~~g~------~~~~--~~~L-~d~~~L~~~gI~~~~   71 (102)
                      -|++|+.+|. ..++|+. ..|+++||.+|++..+||.+.|.|..+-.      |+..  ...+ +|..+|++|||.+|+
T Consensus         2 iiRiRsrdG~-eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGs   80 (94)
T d1wf9a1           2 MLRVRSRDGL-ERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGS   80 (94)
T ss_dssp             EEEEECSSCE-EEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTC
T ss_pred             eEEEEecCCc-eEEEecCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCce
Confidence            3788998886 5778854 78999999999999999999999966421      1100  0134 455779999999999


Q ss_pred             EEEEEeec
Q 041108           72 HIYLFFKP   79 (102)
Q Consensus        72 ~i~l~~~~   79 (102)
                      .|++....
T Consensus        81 ivyL~y~~   88 (94)
T d1wf9a1          81 MVYLAYEG   88 (94)
T ss_dssp             EEECCCSS
T ss_pred             EEEEEeee
Confidence            99988654

>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=98.84  E-value=8.8e-09  Score=60.25  Aligned_cols=70  Identities=13%  Similarity=0.235  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEE
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLF   76 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~   76 (102)
                      +.|.|+..+|+.+.+.|..+.++..|..+.++..+++++..+++|.|.      .+.++.|.+++++.+|++|.++
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 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQ------PINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTE------ECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCE------EcCCCCCHHHcCCCCCCEEEEE
Confidence            367888889999999999999999999999999999999999999999      9999999999999999999875

>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=97.90  E-value=2.6e-05  Score=45.75  Aligned_cols=69  Identities=9%  Similarity=0.051  Sum_probs=65.0

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |.|=..+|+...+.+.|++|+.|+-+...+++|+++++-.|.++++      .++-+.++.-.|+.+|+.+.++-
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k------~ldLsl~~R~sgLpnnakLELv~   71 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRT------VLDLSLQWRFANLPNNAKLEMVP   71 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTE------EESSSCBHHHHCCCSSCEEEEEC
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCE------EcCccceeeecCCCCCCEEEEEE
Confidence            6677889999999999999999999999999999999999999999      99999999999999999999874

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.81  E-value=7e-05  Score=43.84  Aligned_cols=74  Identities=14%  Similarity=0.120  Sum_probs=58.8

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +|.||..+|+...-....++|+.+|...|.+. +.++....|+........ ...+++.+|.++|+.+.++|++--
T Consensus         7 ~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~~~~~~~~l~~~~Pr~~l-~~~d~~~TL~e~gL~p~~~L~vq~   80 (82)
T d1h8ca_           7 KLRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLLSTFPRRDV-TQLDPNKSLLEVKLFPQETLFLEA   80 (82)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-TCCSSSEEEEETTTTEET-TTCCTTSBHHHHCCCSEEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-CCCCCceEEEecCccccc-ccccccCCHHHCCCCCCCEEEEEe
Confidence            58899999999889999999999999999874 788888888765431111 123567899999999999988753

>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=97.66  E-value=0.00014  Score=43.26  Aligned_cols=67  Identities=7%  Similarity=0.225  Sum_probs=53.4

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhc-CCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCC
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQ-KLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGS   71 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~-gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~   71 (102)
                      .|.||..+|+.....+..++||.+|.+.+.+.. +.+.....|+.+..+   +.+.+++.+|.++|+.+++
T Consensus        16 ~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Pr---r~l~d~~~TL~e~gL~~s~   83 (89)
T d1i42a_          16 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPN---KELADENQTLKEANLLNAV   83 (89)
T ss_dssp             EEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTT---EECCCCSSCSGGGTTCCSE
T ss_pred             EEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCC---cccCCCcCcHHHCCCcCce
Confidence            578999999999999999999999999998764 566667888776541   1233778999999999653

>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=97.65  E-value=0.00018  Score=43.01  Aligned_cols=73  Identities=12%  Similarity=-0.027  Sum_probs=56.5

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +|.||..+|+...-....++||.+|...|... +......+|+.+..+..+  ..+++++|.++|+.+.++|+|--
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-GYHKSLYRLSTSFPRRAL--EVEGGSSLEDIGITVDTVLNVEE   90 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBC--CCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHh-ccCcccceeecCCCceec--CccCCCcHHHCCCCCCCEEEEec
Confidence            68899999999888999999999999999775 456677778766542211  12457899999999998887753

>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=97.44  E-value=0.00048  Score=43.20  Aligned_cols=76  Identities=13%  Similarity=0.225  Sum_probs=58.4

Q ss_pred             EEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            2 KVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         2 ~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      +|.||..+|+.+......++||.+|...|.+. +.+.....|+.... .......+.+.+|.++|+.+.++|+|--..
T Consensus        45 ~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~-~~~~~~~~L~~~fP-r~~l~~~d~~~TL~e~gL~P~~~L~vee~~  120 (124)
T d1wj4a_          45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFP-RRKLSHLDYDITLQEAGLCPQETVFVQESG  120 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSS-CCEETSSCSSSCTTTTTCCSSBCCEEEECC
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-ccCCcceEEeeccc-ccccccccccCcHHHcCCCCCCEEEEEecC
Confidence            58899999999999999999999999999875 46677777776543 111111256789999999999998776443

>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=96.28  E-value=0.019  Score=32.94  Aligned_cols=66  Identities=24%  Similarity=0.246  Sum_probs=46.9

Q ss_pred             CEEEEEeCC------C-cEEEEEecCCCcHHHHHHHHHhhcCC-----------CCccEEEEeCCCCCCCCccCCCCCcc
Q 041108            1 MKVAVEILT------G-TLFYIQVENDATVADLKREIGAQQKL-----------PCDRLILLLSSDHSCPMTQDHDEVPL   62 (102)
Q Consensus         1 M~v~V~~~~------g-~~~~i~v~~~~TV~dLK~~I~~~~gi-----------p~~~q~L~~~g~~~~~~~~L~d~~~L   62 (102)
                      |+|+|+...      | ....+++....||.+|.+.+.++++-           .....++..+++      ..++    
T Consensus         2 mkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~------~~~~----   71 (88)
T d1vjka_           2 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGR------YVSW----   71 (88)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTB------CCCT----
T ss_pred             eEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcce------EcCC----
Confidence            788888764      4 46788999999999999999887541           112235566666      4444    


Q ss_pred             ccCCCCCCCEEEEEe
Q 041108           63 ADCGVKDGSHIYLFF   77 (102)
Q Consensus        63 ~~~gI~~~~~i~l~~   77 (102)
                       +..+++||.|.++-
T Consensus        72 -d~~L~~gDevai~P   85 (88)
T d1vjka_          72 -DEELKDGDVVGVFP   85 (88)
T ss_dssp             -TCBCCTTCEEEEES
T ss_pred             -CcCcCCCCEEEEeC
Confidence             34578999998874

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.23  E-value=0.19  Score=28.77  Aligned_cols=75  Identities=13%  Similarity=0.052  Sum_probs=54.8

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCC-CccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLP-CDRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip-~~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      |++.|..++++ ..+.++..++..+|-.++.+..++. .+-.-|.|-+.. ....-|+.++.|....++.+..+.+..
T Consensus         2 ~~v~V~~LD~~-~~~~v~~~a~G~~l~~~Vc~~l~L~E~dYFGL~y~d~~-~~~~WLd~~k~l~kq~~~~~~~~~l~F   77 (84)
T d1ef1a3           2 ISVRVTTMDAE-LEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTK-GFSTWLKLNKKVTAQDVRKESPLLFKF   77 (84)
T ss_dssp             EEEEEEETTEE-EEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTT-SCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEEcCCE-EEEEEcCCChHHHHHHHHHHHcCCcccccceEEEECCC-CCeEeccCCCchhhhccCCCCCEEEEE
Confidence            67899999975 7899999999999999999999976 444567665431 111247888888887665555444443

>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=92.73  E-value=0.2  Score=28.93  Aligned_cols=46  Identities=4%  Similarity=0.081  Sum_probs=38.2

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      -+|+..-.-++.+++.+....++|...|+++...+++.-+|.|.-.
T Consensus         6 ~~vkVh~~fTVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~~~   51 (82)
T d1oeya_           6 YTLKVHYKYTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPR   51 (82)
T ss_dssp             EEEEEESSSEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCT
T ss_pred             EEEEEEEEEEEEEEccCCCCHHHHHHHHHHHhCCChhheEEEeccC
Confidence            3444443467889999999999999999999999999999999643

>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=92.53  E-value=0.4  Score=27.39  Aligned_cols=74  Identities=12%  Similarity=0.036  Sum_probs=53.5

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCC-ccEEEEeCCCCCCCCccCCCCCccccCCCCCCCEEEEEe
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPC-DRLILLLSSDHSCPMTQDHDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~-~~q~L~~~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      +.+.|..++++ ..++++..++..+|-.++.+..++.. +-.-|.|-...+  ..-|+.++.|....++.+..+.+..
T Consensus         3 ~~v~V~lLD~~-le~~v~~~a~G~~L~d~Vc~~L~L~E~~YFGL~y~~~~~--~~WLd~~k~l~kq~~~~~~~~~~~F   77 (84)
T d1h4ra3           3 FTVRIVTMDAE-MEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDT--VAWLKMDKKVLDHDVSKEEPVTFHF   77 (84)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTE--EEECCTTSBGGGSSCCCSSSEEEEE
T ss_pred             EEEEEEEcCCc-EEEEEcCCChHHHHHHHHHHHcCCcccccceEEEecCCc--eEEccCCCchhhhccCCCCCEEEEE
Confidence            46788999986 68999999999999999999999753 334555543311  1257888888887666555555543

>d1gg3a3 d.15.1.4 (A:1-81) Erythroid membrane protein 4.1R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.39  E-value=0.21  Score=28.45  Aligned_cols=64  Identities=19%  Similarity=0.188  Sum_probs=47.4

Q ss_pred             CEEEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCcc-EEEEeCCCCCCCCccCCCCCccccC
Q 041108            1 MKVAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDR-LILLLSSDHSCPMTQDHDEVPLADC   65 (102)
Q Consensus         1 M~v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~-q~L~~~g~~~~~~~~L~d~~~L~~~   65 (102)
                      |...|..++|+...+.++..++..+|-+++.+..++...+ .-|.|-+. +....-|+.++++...
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 MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDN-ATSKTWLDSAKEIKKQ   65 (81)
T ss_dssp             CEEEEECTTSCEEEEECCTTCCHHHHHHHHHHHHTTCSCCSSSCEEECC-SSSCCBCCTTSCHHHH
T ss_pred             CEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCcccccceEEEECC-CCceEecccccchhhh
Confidence            7889999999999999999999999999999999976433 23443322 1111256777777664

>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=91.89  E-value=0.31  Score=28.49  Aligned_cols=74  Identities=14%  Similarity=0.064  Sum_probs=43.9

Q ss_pred             CEEEEEeCCC--------cEEEEEecC---CCcHHHHHHHHHhhcCCCCcc-----------EEEEeCCCCCCCCccCCC
Q 041108            1 MKVAVEILTG--------TLFYIQVEN---DATVADLKREIGAQQKLPCDR-----------LILLLSSDHSCPMTQDHD   58 (102)
Q Consensus         1 M~v~V~~~~g--------~~~~i~v~~---~~TV~dLK~~I~~~~gip~~~-----------q~L~~~g~~~~~~~~L~d   58 (102)
                      |+|+|+...|        +.+.+++..   ..||.+|-+.+.+.+.-...+           ..++.+|.      -...
T Consensus         5 m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~~~~~l~~~~~~lr~~v~v~vN~~------di~~   78 (101)
T d1xo3a_           5 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDA------DWEL   78 (101)
T ss_dssp             CEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCCSCGGGSCCTTSCCSSEEEEETTE------EHHH
T ss_pred             eEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCcchhhhhccCcCeeeeEEEEEcCc------ceec
Confidence            8899998642        334566543   479999999998886532111           12233332      1110


Q ss_pred             CCccccCCCCCCCEEEEEeecCC
Q 041108           59 EVPLADCGVKDGSHIYLFFKPLD   81 (102)
Q Consensus        59 ~~~L~~~gI~~~~~i~l~~~~~~   81 (102)
                      ..- .++.+++||.|.++-...|
T Consensus        79 l~g-l~t~l~dgDeV~~~p~v~G  100 (101)
T d1xo3a_          79 LGE-LDYQLQDQDSILFISTLHG  100 (101)
T ss_dssp             HTT-TSCCCCTTCEEEEEETTCC
T ss_pred             cCC-CccCcCCCCEEEEeCCCCC
Confidence            000 2677999999999865433

>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=88.82  E-value=0.52  Score=27.62  Aligned_cols=60  Identities=15%  Similarity=0.113  Sum_probs=41.8

Q ss_pred             EEEecCCCcHHHHHHHHHhhcC--CC-Cc-------cEEEEeCCCCCCCCccC------CCCCccccCCCCCCCEEEEEe
Q 041108           14 YIQVENDATVADLKREIGAQQK--LP-CD-------RLILLLSSDHSCPMTQD------HDEVPLADCGVKDGSHIYLFF   77 (102)
Q Consensus        14 ~i~v~~~~TV~dLK~~I~~~~g--ip-~~-------~q~L~~~g~~~~~~~~L------~d~~~L~~~gI~~~~~i~l~~   77 (102)
                      .+++++++|+.+|-+.+.+.-.  +. |+       ..+-+|-..|    +.|      +-+++|.++|+.+|+.|.|.=
T Consensus         4 ~l~~~~~~TL~~li~~L~e~p~~qlk~Psltt~~~g~~ktLYm~~p----p~Lee~Tr~NL~k~L~eLgl~dG~ei~VtD   79 (92)
T d1y8xb1           4 NIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSV----TSIEERTRPNLSKTLKELGLVDGQELAVAD   79 (92)
T ss_dssp             CEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSC----HHHHHHHHHHHHSBSGGGTCCTTCEEEEEC
T ss_pred             eEEcCCCCcHHHHHHHHhhChHhhccCCceeeecCCCccEEEecCc----HHHHHHhhhccccCHHHhCCcCCCEEEEec
Confidence            5789999999999999999633  32 21       2333343331    134      345899999999999999873

>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=88.66  E-value=0.55  Score=27.35  Aligned_cols=38  Identities=18%  Similarity=0.114  Sum_probs=33.2

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCcc
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDR   40 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~   40 (102)
                      |.|-..+|.+..+.|++.+|+.|+-+.+.++.++..+.
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~~~~   49 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDE   49 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCC
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCCCCC
Confidence            45567789999999999999999999999999987654

>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=87.57  E-value=1.3  Score=24.61  Aligned_cols=43  Identities=16%  Similarity=0.067  Sum_probs=39.0

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLL   45 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~   45 (102)
                      ++|-..+|+.-.+.+.+..|+.|.-.++-++.|+.++.-.++.
T Consensus         3 iRv~LPngq~T~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~~   45 (73)
T d1wxma1           3 VKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYR   45 (73)
T ss_dssp             EEEECSSSCEEEEECCSSCBSHHHHHHHHHTTTCCSSSEEEEE
T ss_pred             EEEEcCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            6778889999999999999999999999999999999887764

>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=86.73  E-value=1  Score=25.51  Aligned_cols=44  Identities=14%  Similarity=0.246  Sum_probs=34.6

Q ss_pred             EEEEeC-CCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeCCC
Q 041108            3 VAVEIL-TGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLSSD   48 (102)
Q Consensus         3 v~V~~~-~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~g~   48 (102)
                      |.||.. ++..+.+.+.++.+..+|+++|+++++..  ..+|-|...
T Consensus        13 ikVKv~~~~D~~~~~l~~~it~~dL~~kI~~rf~~~--~~~lkY~De   57 (85)
T d1ip9a_          13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDTD--NFKLQTKLF   57 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHTSS--CEEEEECCS
T ss_pred             EEEEEEECCcEEEEEeCCCCCHHHHHHHHHHHhCCC--ceEEEEEcC
Confidence            556665 45778999999999999999999998764  466766554

>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=85.62  E-value=2.3  Score=25.22  Aligned_cols=74  Identities=9%  Similarity=0.142  Sum_probs=49.5

Q ss_pred             EEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEe-CCCCCCCCccCCCCCccccCCCCCCCEEEEEeec
Q 041108            4 AVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLL-SSDHSCPMTQDHDEVPLADCGVKDGSHIYLFFKP   79 (102)
Q Consensus         4 ~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~-~g~~~~~~~~L~d~~~L~~~gI~~~~~i~l~~~~   79 (102)
                      .|-..+.+..++.+.-++|+.+++...+++.+.+.+.+.|+- +..++..  .|+++..-=.-.+.-++.+++..+-
T Consensus        13 ~VY~~Dhsy~tlr~~v~~sa~eI~~~vaeKl~~~~e~L~LV~V~SsGEr~--~lkp~d~sV~TsL~lN~rLFvc~~d   87 (104)
T d1wgya_          13 HVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKH--ELQPNDLVISKSLEASGRIYVYRKD   87 (104)
T ss_dssp             EEECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCC--BCCTTSBSSCCSSCSSCEEEEEECC
T ss_pred             EEEecCCcEEEEEeeccCcHHHHHHHHHHHhCCCCCceEEEEEccCCcEE--eeCccceeEEeeeeecceEEEechh
Confidence            455566777889999999999999999999999999887753 2222222  5544432212224456777777653

>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=85.20  E-value=2  Score=24.08  Aligned_cols=44  Identities=11%  Similarity=0.018  Sum_probs=39.7

Q ss_pred             EEEEeCCCcEEEEEecCCCcHHHHHHHHHhhcCCCCccEEEEeC
Q 041108            3 VAVEILTGTLFYIQVENDATVADLKREIGAQQKLPCDRLILLLS   46 (102)
Q Consensus         3 v~V~~~~g~~~~i~v~~~~TV~dLK~~I~~~~gip~~~q~L~~~   46 (102)
                      ++|-..+|+.-.+.+.+..|+.|.-.++-++.|+.++.-.++..
T Consensus         4 iRv~LPngq~T~V~vrpG~tird~L~k~l~kRgl~~~~c~V~~~   47 (77)
T d1c1yb_           4 IRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRL   47 (77)
T ss_dssp             EEEEETTTEEEEEECCTTCBHHHHHHHHHHTTTCCGGGEEEEEE
T ss_pred             EEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEEe
Confidence            67888899999999999999999999999999999998888653