Query psy6128
Match_columns 529
No_of_seqs 66 out of 68
Neff 2.2
Searched_HMMs 46136
Date Fri Aug 16 18:20:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6128.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6128hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12851 Tet_JBP: Oxygenase do 100.0 1.5E-41 3.2E-46 306.0 8.6 119 376-501 1-120 (171)
2 cd01769 UBL Ubiquitin-like dom 44.6 30 0.00064 25.5 3.2 47 236-287 13-59 (69)
3 PTZ00397 macrophage migration 37.3 34 0.00074 29.2 2.9 38 310-347 57-95 (116)
4 PTZ00044 ubiquitin; Provisiona 34.9 81 0.0018 24.5 4.5 60 236-303 16-75 (76)
5 cd01815 BMSC_UbP_N Ubiquitin-l 34.9 60 0.0013 27.5 3.9 56 240-301 20-75 (75)
6 cd01789 Alp11_N Ubiquitin-like 33.3 1.2E+02 0.0027 25.0 5.5 56 237-305 19-74 (84)
7 cd01800 SF3a120_C Ubiquitin-li 32.7 1.1E+02 0.0023 24.5 4.9 62 236-305 13-74 (76)
8 cd01802 AN1_N ubiquitin-like d 28.7 1.1E+02 0.0023 26.6 4.6 60 237-304 44-103 (103)
9 cd01798 parkin_N amino-termina 25.8 57 0.0012 25.3 2.2 46 236-286 14-59 (70)
10 cd01814 NTGP5 Ubiquitin-like N 25.8 90 0.002 28.6 3.7 61 229-292 16-95 (113)
11 cd07404 MPP_MS158 Microscilla 25.7 31 0.00066 30.1 0.8 27 453-481 136-162 (166)
12 PF00240 ubiquitin: Ubiquitin 24.3 1.2E+02 0.0025 23.1 3.6 59 236-302 11-69 (69)
13 PRK00745 4-oxalocrotonate taut 23.5 66 0.0014 24.2 2.1 33 313-345 3-36 (62)
14 PF08980 DUF1883: Domain of un 23.3 30 0.00065 30.7 0.2 21 464-484 3-23 (94)
15 PRK05800 cobU adenosylcobinami 21.5 79 0.0017 29.1 2.6 36 306-341 115-150 (170)
16 cd01808 hPLIC_N Ubiquitin-like 21.4 98 0.0021 24.2 2.8 32 238-272 17-48 (71)
17 PRK05573 rplU 50S ribosomal pr 20.7 3E+02 0.0065 24.3 5.9 61 255-315 27-99 (103)
18 PRK09271 flavodoxin; Provision 20.5 1.6E+02 0.0034 26.4 4.2 22 318-339 62-83 (160)
19 PRK11148 cyclic 3',5'-adenosin 20.5 48 0.001 31.8 1.0 27 452-480 193-219 (275)
20 cd03157 TM4SF12_like_LEL Tetra 20.2 2.2E+02 0.0048 24.5 4.9 57 326-384 8-91 (103)
No 1
>PF12851 Tet_JBP: Oxygenase domain of the 2OGFeDO superfamily ; InterPro: IPR024779 TETs are 2OG- and Fe(II)-dependent oxygenases that catalyse the conversion of 5 methyl-Cytosine (5-MC) to 5-hydroxymethyl-cytosine (hmC) in cultured cells and in vitro []. Interestingly TET2 is considered as an oncogene, as it is found mutated in some types of cancer []. This entry represents the double-stranded beta helix (DSBH) fold of the 2-oxoglutarate (2OG) - Fe(II) oxygenases. DSBH comprises a part of the catalytic domain in TETS. It is found in many organisms including fruit fly, African malaria mosquito, zebrafish, mouse and human.
Probab=100.00 E-value=1.5e-41 Score=306.03 Aligned_cols=119 Identities=48% Similarity=0.830 Sum_probs=115.6
Q ss_pred eeeeeecCceecc-ccccceeeccCchhhHHHHHHHHHHHHhHhHHHhhhCchhhhhhhhhhhcCCccccCCcCCCCcce
Q psy6128 376 SWSMYYNGCKYAR-SKTVRKFRLSVRSEEQEIEEKMHLLATTISPLYKALAPGAFTNQCQFEREASECRLGFKPGRPFSG 454 (529)
Q Consensus 376 SWSMY~NGCKfaR-Sk~pRkFrL~~~~eE~~Le~~lq~LAT~lAPlYk~lAP~Ay~NQve~E~~a~dCRLG~keGRPFSG 454 (529)
|||||||||||+| |+.|||||++.++.+ ++++||.|||.|+||||++||++|+||+++++.+.+|||+...|+||||
T Consensus 1 ~~~~y~~~~~~~r~~~~~rk~~~~~~~~~--~~~~l~~la~~l~~iy~~~~P~~y~~~~~~~~~~~~~~~~~~~~~pFs~ 78 (171)
T PF12851_consen 1 SWSMYFNGCKFPRGSKKPRKFRLTPENPK--LEENLQELATVLGPIYKQIAPDLYENQVEVEESLGDCRLGPIWGRPFSG 78 (171)
T ss_pred CeeEEeCCCCccccccccceeeccccccc--HHHHHHHHHHHHHHHHHHHCHHHHHhHHHHHhhhhhheeecccCcceec
Confidence 8999999999999 999999999997655 9999999999999999999999999999999999999999999999999
Q ss_pred eceeeccccccccccccCCCCcEEEEEEecCCCCCCCCCcceeeeee
Q psy6128 455 VTACFDFCAHSHRDLHNMNNGCTVVVSLTKHRSLSKPDDEQLHVLPL 501 (529)
Q Consensus 455 VTaClDFCAHaHrD~HNM~NGsTVVcTLtker~~~~PeDEQLHVLPL 501 (529)
||+|+|||+|+|||+|||+||.+|||||.+++ .|+|+|+||+
T Consensus 79 ~sv~~nr~t~~HrD~~~~~~~~~~~~t~~~gd-----~~~g~l~lp~ 120 (171)
T PF12851_consen 79 VSVISNRCTHSHRDTHNMPNGYDVLCTLGRGD-----YDGGRLELPG 120 (171)
T ss_pred eEEEeecCccceecCCCCCCCeEEEEecCCcc-----ccCceEeccc
Confidence 99999999999999999999999999999954 8999999999
No 2
>cd01769 UBL Ubiquitin-like domain of UBL. 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.
Probab=44.55 E-value=30 Score=25.46 Aligned_cols=47 Identities=19% Similarity=0.403 Sum_probs=35.3
Q ss_pred cCCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeee
Q psy6128 236 HLGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIR 287 (529)
Q Consensus 236 HLGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIR 287 (529)
-+....++.+|++.++.++|..-..+++ +|.|++= ...++++.+-|.
T Consensus 13 ~~~~~~ti~~lK~~i~~~~~~~~~~~~l---~~~g~~l--~d~~~l~~~~v~ 59 (69)
T cd01769 13 EVSPDDTVAELKAKIAAKEGVPPEQQRL---IYAGKIL--KDDKTLSDYGIQ 59 (69)
T ss_pred EECCCChHHHHHHHHHHHHCcChHHEEE---EECCcCC--CCcCCHHHCCCC
Confidence 3556678999999999999988888877 8888753 345566665553
No 3
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=37.29 E-value=34 Score=29.20 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=32.5
Q ss_pred eeEEEEEEEecCCCCCCchhHHHHHHHhhhcC-CCCCcc
Q psy6128 310 AWIVVVIVAWEGVPLNQSDGVYAILTNKLNKY-GLPTTR 347 (529)
Q Consensus 310 AviVv~Iv~WeGIp~~~AD~lY~eLt~~L~ky-G~pT~R 347 (529)
-+++|-|.++.|+..+.-.++|.+|++.|.+. |+|-+|
T Consensus 57 p~a~v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~r 95 (116)
T PTZ00397 57 GCCFVRVTSIGGISRSNNSSIAAAITKILASHLKVKSER 95 (116)
T ss_pred ceEEEEEEEecCCCHHHHHHHHHHHHHHHHHHhCcCccc
Confidence 45566777789999999999999999999997 998766
No 4
>PTZ00044 ubiquitin; Provisional
Probab=34.92 E-value=81 Score=24.53 Aligned_cols=60 Identities=17% Similarity=0.406 Sum_probs=42.5
Q ss_pred cCCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeeecCCCCceEEEEEeecC
Q psy6128 236 HLGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIRRASLEEKLLLIVKHRQ 303 (529)
Q Consensus 236 HLGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIRRss~eEKlLcLVr~R~ 303 (529)
....--+|++|++.++.+.|..-...|+. |.|+.=+ ..-+++.+-|...+ -+.+++|-|-
T Consensus 16 ~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~g~~L~--d~~~l~~~~i~~~~---~i~l~~~~~g 75 (76)
T PTZ00044 16 NFEPDNTVQQVKMALQEKEGIDVKQIRLI---YSGKQMS--DDLKLSDYKVVPGS---TIHMVLQLRG 75 (76)
T ss_pred EECCCCcHHHHHHHHHHHHCCCHHHeEEE---ECCEEcc--CCCcHHHcCCCCCC---EEEEEEEccC
Confidence 44556789999999999999877777765 8888743 55678887765554 4555555443
No 5
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. 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.
Probab=34.90 E-value=60 Score=27.54 Aligned_cols=56 Identities=13% Similarity=0.140 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeeecCCCCceEEEEEee
Q psy6128 240 AASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIRRASLEEKLLLIVKH 301 (529)
Q Consensus 240 gpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIRRss~eEKlLcLVr~ 301 (529)
.-+|++|++++++++|...-..---++||.||-=+ .+-+++..=|+ +...|.|||+
T Consensus 20 ~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~--D~~TL~dygI~----~gstlhLv~~ 75 (75)
T cd01815 20 GYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLK--DDQTLDFYGIQ----SGSTIHILRK 75 (75)
T ss_pred cCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCC--CCCcHHHcCCC----CCCEEEEEeC
Confidence 45899999999999875443111125679999743 44567666554 4567777774
No 6
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. 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.
Probab=33.32 E-value=1.2e+02 Score=25.01 Aligned_cols=56 Identities=18% Similarity=0.325 Sum_probs=41.2
Q ss_pred CCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeeecCCCCceEEEEEeecCCC
Q psy6128 237 LGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIRRASLEEKLLLIVKHRQGH 305 (529)
Q Consensus 237 LGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIRRss~eEKlLcLVr~R~GH 305 (529)
+..+-+|++|++.++..+|..-...|+ ++|.|+.+.- | .-.++++.|--.--..|+
T Consensus 19 ~~~~~Tv~~lK~kl~~~~G~~~~~mrL--~l~~~~~~~~---~--------~l~~d~~~L~~y~~~dg~ 74 (84)
T cd01789 19 YSRGLTIAELKKKLELVVGTPASSMRL--QLFDGDDKLV---S--------KLDDDDALLGSYPVDDGC 74 (84)
T ss_pred cCCCCcHHHHHHHHHHHHCCCccceEE--EEEcCCCCeE---e--------ecCCCccEeeeccCCCCC
Confidence 467889999999999999999999888 4477773221 1 146677777666666655
No 7
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. 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.
Probab=32.73 E-value=1.1e+02 Score=24.48 Aligned_cols=62 Identities=23% Similarity=0.326 Sum_probs=44.3
Q ss_pred cCCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeeecCCCCceEEEEEeecCCC
Q psy6128 236 HLGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIRRASLEEKLLLIVKHRQGH 305 (529)
Q Consensus 236 HLGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIRRss~eEKlLcLVr~R~GH 305 (529)
.+....+|+.|++.++...|..-...| ++|.|+.=+..+ +++.+-|+.. .-|.+++|.|.|.
T Consensus 13 ~v~~~~TV~~lK~~i~~~~gip~~~q~---L~~~G~~L~d~~--tL~~~~i~~g---~~l~v~~~~~gg~ 74 (76)
T cd01800 13 TLQLSDPVSVLKVKIHEETGMPAGKQK---LQYEGIFIKDSN--SLAYYNLANG---TIIHLQLKERGGR 74 (76)
T ss_pred EECCCCcHHHHHHHHHHHHCCCHHHEE---EEECCEEcCCCC--cHHHcCCCCC---CEEEEEEecCCCc
Confidence 466778999999999999997666654 469887544443 6777766543 3566667776664
No 8
>cd01802 AN1_N ubiquitin-like domain of AN1. 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.
Probab=28.68 E-value=1.1e+02 Score=26.56 Aligned_cols=60 Identities=15% Similarity=0.263 Sum_probs=42.4
Q ss_pred CCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeeecCCCCceEEEEEeecCC
Q psy6128 237 LGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIRRASLEEKLLLIVKHRQG 304 (529)
Q Consensus 237 LGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIRRss~eEKlLcLVr~R~G 304 (529)
.....+|++|++.++++.|..-...|+ +|-||.=+ .+++++.+-|...+ .|-..+|.|-|
T Consensus 44 V~~~~TV~~lK~kI~~~~gip~~~QrL---i~~Gk~L~--D~~tL~dy~I~~~s---tL~l~~~l~GG 103 (103)
T cd01802 44 VSPFETVISVKAKIQRLEGIPVAQQHL---IWNNMELE--DEYCLNDYNISEGC---TLKLVLAMRGG 103 (103)
T ss_pred eCCCCcHHHHHHHHHHHhCCChHHEEE---EECCEECC--CCCcHHHcCCCCCC---EEEEEEecCCC
Confidence 445578999999999999876666655 79888743 34788888776655 45555555443
No 9
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. 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.
Probab=25.84 E-value=57 Score=25.32 Aligned_cols=46 Identities=17% Similarity=0.391 Sum_probs=35.3
Q ss_pred cCCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeee
Q psy6128 236 HLGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVI 286 (529)
Q Consensus 236 HLGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVI 286 (529)
++....+|+.|.+.++++.|..-..+|+ +|-|++= ..+.+++..-|
T Consensus 14 ~v~~~~tV~~lK~~i~~~~gi~~~~q~L---i~~G~~L--~d~~~l~~~~i 59 (70)
T cd01798 14 EVDPDTDIKQLKEVVAKRQGVPPDQLRV---IFAGKEL--RNTTTIQECDL 59 (70)
T ss_pred EECCCChHHHHHHHHHHHHCCCHHHeEE---EECCeEC--CCCCcHHHcCC
Confidence 4556679999999999999998888877 7999983 34456665444
No 10
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=25.79 E-value=90 Score=28.64 Aligned_cols=61 Identities=18% Similarity=0.184 Sum_probs=43.3
Q ss_pred CCCcccccCCCCCChHHHHHHHHHhccccc-----cceEEEEEEEeCCC---CC-----------cCCCCccceeeeecC
Q psy6128 229 EPGSYYTHLGAAASLPDLRKDIEERSGYKG-----KALRMEKILYTGKE---GK-----------TTQGCPLAKWVIRRA 289 (529)
Q Consensus 229 deGpyYTHLGagpsvaaiRe~mE~R~G~kG-----~AiRiEkVvYTGKE---GK-----------SSqGCPiAKWVIRRs 289 (529)
|=||+-.+ ...+|++|.+.+++..|. + ...---+.||.||- ++ ..+|.-..-+|+|.+
T Consensus 16 digp~~~~--~sdTV~~lKekI~~~~p~-~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~TmHvvlr~~ 92 (113)
T cd01814 16 DIGPKRYP--AATTVDFLKERVVSQWPK-DKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITMHVVVQPP 92 (113)
T ss_pred ccCccccC--hhhHHHHHHHHHHHhccc-ccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEEEEEecCC
Confidence 45777655 678999999999988875 4 33556789999985 33 355566667777776
Q ss_pred CCC
Q psy6128 290 SLE 292 (529)
Q Consensus 290 s~e 292 (529)
..+
T Consensus 93 ~~~ 95 (113)
T cd01814 93 LAD 95 (113)
T ss_pred CCC
Confidence 654
No 11
>cd07404 MPP_MS158 Microscilla MS158 and related proteins, metallophosphatase domain. MS158 is an uncharacterized Microscilla protein with a metallophosphatase domain. Microscilla proteins MS152, and MS153 are also included in this family. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is t
Probab=25.72 E-value=31 Score=30.08 Aligned_cols=27 Identities=15% Similarity=0.253 Sum_probs=22.1
Q ss_pred ceeceeeccccccccccccCCCCcEEEEE
Q psy6128 453 SGVTACFDFCAHSHRDLHNMNNGCTVVVS 481 (529)
Q Consensus 453 SGVTaClDFCAHaHrD~HNM~NGsTVVcT 481 (529)
.+|.++ +|.|.|+......+|++++|+
T Consensus 136 ~~v~~~--i~GH~H~~~~~~~~g~~~~~n 162 (166)
T cd07404 136 DPIDLW--IHGHTHFNFDYRIGGTRVLSN 162 (166)
T ss_pred cCCCEE--EECCccccceEEECCEEEEec
Confidence 356665 899999999888899988875
No 12
>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. 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 ....
Probab=24.25 E-value=1.2e+02 Score=23.07 Aligned_cols=59 Identities=27% Similarity=0.515 Sum_probs=39.8
Q ss_pred cCCCCCChHHHHHHHHHhccccccceEEEEEEEeCCCCCcCCCCccceeeeecCCCCceEEEEEeec
Q psy6128 236 HLGAAASLPDLRKDIEERSGYKGKALRMEKILYTGKEGKTTQGCPLAKWVIRRASLEEKLLLIVKHR 302 (529)
Q Consensus 236 HLGagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKEGKSSqGCPiAKWVIRRss~eEKlLcLVr~R 302 (529)
....-.+|+.|++.++.+.|..-..+| ++|-|++= ...-.+...-|...+ .|.+++|.|
T Consensus 11 ~v~~~~tV~~lK~~i~~~~~~~~~~~~---L~~~G~~L--~d~~tL~~~~i~~~~---~I~l~~k~~ 69 (69)
T PF00240_consen 11 EVDPDDTVADLKQKIAEETGIPPEQQR---LIYNGKEL--DDDKTLSDYGIKDGS---TIHLVIKPR 69 (69)
T ss_dssp EEETTSBHHHHHHHHHHHHTSTGGGEE---EEETTEEE--STTSBTGGGTTSTTE---EEEEEESSE
T ss_pred EECCCCCHHHhhhhcccccccccccce---eeeeeecc--cCcCcHHHcCCCCCC---EEEEEEecC
Confidence 345567899999999999998887775 57888764 334455555444333 566666654
No 13
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=23.49 E-value=66 Score=24.24 Aligned_cols=33 Identities=21% Similarity=0.259 Sum_probs=27.9
Q ss_pred EEEEEEecCCCCCCchhHHHHHHHhhhcC-CCCC
Q psy6128 313 VVVIVAWEGVPLNQSDGVYAILTNKLNKY-GLPT 345 (529)
Q Consensus 313 Vv~Iv~WeGIp~~~AD~lY~eLt~~L~ky-G~pT 345 (529)
+|-|-++.|.+.+.-..||+.|++.|.+. |.|-
T Consensus 3 ~i~I~~~~grs~eqk~~l~~~it~~l~~~~~~p~ 36 (62)
T PRK00745 3 TFHIELFEGRTVEQKRKLVEEITRVTVETLGCPP 36 (62)
T ss_pred EEEEEEcCCCCHHHHHHHHHHHHHHHHHHcCCCh
Confidence 46677899999999999999999999886 7653
No 14
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=23.29 E-value=30 Score=30.71 Aligned_cols=21 Identities=43% Similarity=0.583 Sum_probs=3.1
Q ss_pred ccccccccCCCCcEEEEEEec
Q psy6128 464 HSHRDLHNMNNGCTVVVSLTK 484 (529)
Q Consensus 464 HaHrD~HNM~NGsTVVcTLtk 484 (529)
+.|.|+.+++.|.|||++|..
T Consensus 3 ~~~~~~~~~~~Gd~V~V~ls~ 23 (94)
T PF08980_consen 3 FIHYDLGHLKRGDTVVVRLSH 23 (94)
T ss_dssp ----------TT-------SS
T ss_pred eeeechhccCCCCEEEEEeCC
Confidence 578999999999999999964
No 15
>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated
Probab=21.54 E-value=79 Score=29.09 Aligned_cols=36 Identities=17% Similarity=0.106 Sum_probs=31.0
Q ss_pred cccceeEEEEEEEecCCCCCCchhHHHHHHHhhhcC
Q psy6128 306 TCSTAWIVVVIVAWEGVPLNQSDGVYAILTNKLNKY 341 (529)
Q Consensus 306 ~C~tAviVv~Iv~WeGIp~~~AD~lY~eLt~~L~ky 341 (529)
...+.|+|.--+-|++||.+...+.|.++...|++.
T Consensus 115 ~~~tvVlVs~Evg~g~vp~~~~~r~~~d~lG~lnq~ 150 (170)
T PRK05800 115 LPAKIILVTNEVGMGIVPEYRLGRHFRDIAGRLNQQ 150 (170)
T ss_pred CCCCEEEEEcCCcccccCCCHHHHHHHHHHHHHHHH
Confidence 455678888888999999999999999999988763
No 16
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. 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.
Probab=21.44 E-value=98 Score=24.16 Aligned_cols=32 Identities=19% Similarity=0.403 Sum_probs=25.5
Q ss_pred CCCCChHHHHHHHHHhccccccceEEEEEEEeCCC
Q psy6128 238 GAAASLPDLRKDIEERSGYKGKALRMEKILYTGKE 272 (529)
Q Consensus 238 GagpsvaaiRe~mE~R~G~kG~AiRiEkVvYTGKE 272 (529)
....+|+.|++.+++++|..-..+|+ +|.||.
T Consensus 17 ~~~~TV~~lK~~I~~~~~i~~~~~~L---i~~Gk~ 48 (71)
T cd01808 17 AEDASVKDFKEAVSKKFKANQEQLVL---IFAGKI 48 (71)
T ss_pred CCCChHHHHHHHHHHHhCCCHHHEEE---EECCeE
Confidence 34568999999999999987666665 898863
No 17
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=20.75 E-value=3e+02 Score=24.33 Aligned_cols=61 Identities=15% Similarity=0.326 Sum_probs=46.1
Q ss_pred cccccceEEEEEEEeCCCCCcCCCCccce-----eeeecCCCCceEEEEE-------eecCCCcccceeEEEE
Q psy6128 255 GYKGKALRMEKILYTGKEGKTTQGCPLAK-----WVIRRASLEEKLLLIV-------KHRQGHTCSTAWIVVV 315 (529)
Q Consensus 255 G~kG~AiRiEkVvYTGKEGKSSqGCPiAK-----WVIRRss~eEKlLcLV-------r~R~GH~C~tAviVv~ 315 (529)
...|..|.+++|...|.++.+.-|=|... =.|=......|+.+.= |++.||+=.-+.|.|.
T Consensus 27 ~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~A~V~~~~k~~Ki~vfK~krRK~y~r~~GHRQ~~T~i~I~ 99 (103)
T PRK05573 27 AEVGDTVEFDEVLLVGGGEEVKIGAPYVEGAKVTAEVVEHGRGKKVIVFKYKRRKNYRKKQGHRQPYTKVKIT 99 (103)
T ss_pred CCCCCEEEEeEEEEEeCCCCEEECCeEcCCCEEEEEEEeccCCCcEEEEEEcCCCCccccCCccCCcEEEEEE
Confidence 45689999999999999999998988744 2344556888988874 5567998776666553
No 18
>PRK09271 flavodoxin; Provisional
Probab=20.50 E-value=1.6e+02 Score=26.42 Aligned_cols=22 Identities=14% Similarity=0.083 Sum_probs=15.4
Q ss_pred EecCCCCCCchhHHHHHHHhhh
Q psy6128 318 AWEGVPLNQSDGVYAILTNKLN 339 (529)
Q Consensus 318 ~WeGIp~~~AD~lY~eLt~~L~ 339 (529)
...|.+++.+..++..|.+.+.
T Consensus 62 ~~~G~~p~~~~~f~~~l~~~~~ 83 (160)
T PRK09271 62 DNAGRTPPEMKRFIAELAETIG 83 (160)
T ss_pred cCCCcCCHHHHHHHHHHHHHhc
Confidence 3478888767778888876443
No 19
>PRK11148 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional
Probab=20.48 E-value=48 Score=31.76 Aligned_cols=27 Identities=33% Similarity=0.587 Sum_probs=21.0
Q ss_pred cceeceeeccccccccccccCCCCcEEEE
Q psy6128 452 FSGVTACFDFCAHSHRDLHNMNNGCTVVV 480 (529)
Q Consensus 452 FSGVTaClDFCAHaHrD~HNM~NGsTVVc 480 (529)
+.+|.++ ||.|.|.+.+...+|.+++.
T Consensus 193 ~~~v~~v--l~GH~H~~~~~~~~gi~~~~ 219 (275)
T PRK11148 193 FPNVKAI--LCGHIHQELDLDWNGRRLLA 219 (275)
T ss_pred CCCceEE--EecccChHHhceECCEEEEE
Confidence 4566655 89999999988888887654
No 20
>cd03157 TM4SF12_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF12_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This sub-family contains proteins similar to human transmembrane 4 superfamily member 12 (TM4SF12).
Probab=20.23 E-value=2.2e+02 Score=24.51 Aligned_cols=57 Identities=19% Similarity=0.498 Sum_probs=32.8
Q ss_pred CchhHHHHHHHhhhcCCCCCc--------------cccccCC-------------CCccccccCCCCCCCCcccccceee
Q psy6128 326 QSDGVYAILTNKLNKYGLPTT--------------RRCATNE-------------PRTCACQGLDPDTCGASFSFGCSWS 378 (529)
Q Consensus 326 ~AD~lY~eLt~~L~kyG~pT~--------------RRC~~Ne-------------~rTCaCQG~dpetcGASFSFGCSWS 378 (529)
+.+.|=..|.++|.+|+.... .=|+.|. ..+| |. .....|++.+.-+-...
T Consensus 8 ~~~~~~~~l~~~~~~Y~~~~~~~~~~~~D~iQ~~l~CCG~~~~~DW~~~~~~~~vP~SC-C~-~~~~~C~~~~~~~~~~~ 85 (103)
T cd03157 8 VQRSDMISLKSRMSNFGLQRYQWLTHAWNSFQTEFKCCGVIYFTDWLEMTEMEWPPDSC-CS-NQYPGCARQAHYNDLSD 85 (103)
T ss_pred HHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHhccCccCCChhHHhccCCCCCCCccc-cC-CCCCCcCcCCCCccccc
Confidence 455677777888888865321 1255543 2344 54 22345776655444456
Q ss_pred eeecCc
Q psy6128 379 MYYNGC 384 (529)
Q Consensus 379 MY~NGC 384 (529)
.|..||
T Consensus 86 iy~~GC 91 (103)
T cd03157 86 LYQEGC 91 (103)
T ss_pred ccccch
Confidence 788899
Done!