Query 033298
Match_columns 122
No_of_seqs 23 out of 25
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 12:12:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01010 Oxidored_q1_C: NADH-U 87.4 0.29 6.3E-06 39.2 1.2 23 99-121 97-120 (242)
2 PF11142 DUF2917: Protein of u 61.4 1.5 3.3E-05 28.7 -1.1 20 64-83 26-45 (63)
3 cd08365 APC10-like1 APC10-like 57.8 2.7 5.8E-05 31.6 -0.5 15 68-82 20-34 (131)
4 cd08667 APC10-ZZEF1 APC10/DOC1 57.7 2.9 6.2E-05 31.4 -0.4 15 68-82 19-33 (131)
5 cd08159 APC10-like APC10-like 54.0 3.5 7.5E-05 30.8 -0.5 15 68-82 19-33 (129)
6 cd08366 APC10 APC10 subunit of 52.4 4 8.7E-05 30.5 -0.3 15 68-82 23-37 (139)
7 cd08665 APC10-CUL7 APC10-like 51.9 3.8 8.2E-05 31.0 -0.6 15 68-82 19-33 (131)
8 cd08666 APC10-HECTD3 APC10-lik 47.1 5.2 0.00011 30.4 -0.5 15 68-82 24-38 (134)
9 PF10161 DDDD: Putative mitoch 42.5 16 0.00035 26.0 1.5 28 86-113 30-57 (79)
10 PF03256 APC10: Anaphase-promo 41.9 6.5 0.00014 30.8 -0.7 16 67-82 50-65 (193)
11 KOG3437 Anaphase-promoting com 33.3 14 0.0003 30.0 -0.0 15 67-81 41-55 (184)
12 PF11137 DUF2909: Protein of u 33.3 28 0.00061 23.5 1.5 14 104-117 47-60 (63)
13 PRK11594 efflux system membran 31.0 47 0.001 22.9 2.2 19 91-109 2-20 (67)
14 PF10808 DUF2542: Protein of u 30.1 20 0.00043 25.9 0.3 22 58-79 36-57 (79)
15 PF13908 Shisa: Wnt and FGF in 28.0 57 0.0012 24.1 2.4 15 76-93 59-73 (179)
16 PF15181 SMRP1: Spermatid-spec 27.6 22 0.00047 30.3 0.2 18 72-89 83-100 (261)
17 PF00986 DNA_gyraseB_C: DNA gy 27.0 41 0.0009 22.9 1.4 21 62-82 3-28 (65)
18 cd08664 APC10-HERC2 APC10-like 26.1 16 0.00036 28.4 -0.7 10 73-82 47-56 (152)
19 PTZ00208 65 kDa invariant surf 24.4 36 0.00077 30.8 0.9 25 95-119 386-410 (436)
20 PF04277 OAD_gamma: Oxaloaceta 22.5 33 0.00072 22.1 0.3 17 95-111 6-22 (79)
21 PF03454 MoeA_C: MoeA C-termin 21.4 43 0.00092 20.7 0.6 19 102-120 37-55 (72)
22 cd00547 QFR_TypeD_subunitD Qui 21.1 15 0.00032 27.8 -1.8 9 69-78 4-12 (115)
23 PF12349 Sterol-sensing: Stero 21.0 42 0.00092 24.6 0.6 18 100-117 39-56 (153)
No 1
>PF01010 Oxidored_q1_C: NADH-Ubiquinone oxidoreductase (complex I) subunit C-terminus; InterPro: IPR002128 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This domain represents a C-terminal extension of NADH-Ubiquinone/plastoquinone (complex I) chains (see IPR001750 from INTERPRO). Chain 5 is a component of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport, 0055114 oxidation-reduction process
Probab=87.37 E-value=0.29 Score=39.23 Aligned_cols=23 Identities=35% Similarity=0.645 Sum_probs=19.0
Q ss_pred ehhhhHHHHHHH-HhhcCeeeccC
Q 033298 99 FGMSTPFVILAI-AFANGWIKMPV 121 (122)
Q Consensus 99 ~gi~~PFviLAi-A~AnGwIk~pv 121 (122)
..|.+|.||||| ++-.|||++|.
T Consensus 97 ~tMt~PLivLai~TvfiG~IGiPf 120 (242)
T PF01010_consen 97 NTMTFPLIVLAIFTVFIGFIGIPF 120 (242)
T ss_pred cEEEEehhhHHhhhheeEEeceee
Confidence 458899999998 57789999883
No 2
>PF11142 DUF2917: Protein of unknown function (DUF2917); InterPro: IPR021317 This bacterial family of proteins appears to be restricted to Proteobacteria.
Probab=61.40 E-value=1.5 Score=28.66 Aligned_cols=20 Identities=45% Similarity=1.087 Sum_probs=18.0
Q ss_pred ccccccccCchHHHhhhhhh
Q 033298 64 RKFVTREEEPDEFWQTAGER 83 (122)
Q Consensus 64 kkfItRE~EpEqyW~s~gER 83 (122)
.=-||+|..++.||..+|++
T Consensus 26 ~vWlT~~g~~~D~~L~~G~~ 45 (63)
T PF11142_consen 26 RVWLTREGDPDDYWLQAGDS 45 (63)
T ss_pred cEEEECCCCCCCEEECCCCE
Confidence 45899999999999999986
No 3
>cd08365 APC10-like1 APC10-like DOC1 domains of E3 ubiquitin ligases that mediate substrate ubiquitination. This model represens the APC10-like DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. APC10/DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included here. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-te
Probab=57.84 E-value=2.7 Score=31.59 Aligned_cols=15 Identities=20% Similarity=0.707 Sum_probs=12.0
Q ss_pred ccccCchHHHhhhhh
Q 033298 68 TREEEPDEFWQTAGE 82 (122)
Q Consensus 68 tRE~EpEqyW~s~gE 82 (122)
.+++.++.||||.|.
T Consensus 20 L~D~~~~tyWQSDG~ 34 (131)
T cd08365 20 LTDGNTSTYWQSDGS 34 (131)
T ss_pred hhcCCCCceEccCCC
Confidence 466778899999864
No 4
>cd08667 APC10-ZZEF1 APC10/DOC1-like domain of uncharacterized Zinc finger ZZ-type and EF-hand domain-containing protein 1 (ZZEF1) and homologs. This model represents the APC10/DOC1-like domain present in the uncharacterized Zinc finger ZZ-type and EF-hand domain-containing protein 1 (ZZEF1) of Mus musculus. Members of this family contain EF-hand, APC10, CUB, and zinc finger ZZ-type domains. ZZEF1-like APC10 domains are homologous to the APC10 subunit/DOC1 domains present in E3 ubiquitin ligases, which mediate substrate ubiquitination (or ubiquitylation), and are components of the ubiquitin-26S proteasome pathway for selective proteolytic degradation.
Probab=57.73 E-value=2.9 Score=31.43 Aligned_cols=15 Identities=27% Similarity=0.782 Sum_probs=12.1
Q ss_pred ccccCchHHHhhhhh
Q 033298 68 TREEEPDEFWQTAGE 82 (122)
Q Consensus 68 tRE~EpEqyW~s~gE 82 (122)
.+++.++.||||.|-
T Consensus 19 L~D~~~~TYWQSDG~ 33 (131)
T cd08667 19 MTDGETSTYWQSDGS 33 (131)
T ss_pred hhcCCCCccCccCCC
Confidence 467788899999875
No 5
>cd08159 APC10-like APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination. This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and f
Probab=53.98 E-value=3.5 Score=30.80 Aligned_cols=15 Identities=27% Similarity=0.729 Sum_probs=11.9
Q ss_pred ccccCchHHHhhhhh
Q 033298 68 TREEEPDEFWQTAGE 82 (122)
Q Consensus 68 tRE~EpEqyW~s~gE 82 (122)
.+++.+|.||||.|.
T Consensus 19 L~D~~~~tyWQSdG~ 33 (129)
T cd08159 19 LTDGNYDTYWQSDGS 33 (129)
T ss_pred hcCCCCCccCCCCCC
Confidence 366788999999864
No 6
>cd08366 APC10 APC10 subunit of the anaphase-promoting complex (APC) that mediates substrate ubiquitination. This model represents the single domain protein APC10, a subunit of the anaphase-promoting complex (APC), which is a multi-subunit E3 ubiquitin ligase. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a vital component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC (also known as the cyclosome), is a cell cycle-regulated E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. In mitosis, the APC initiates sister chromatid separation by ubiquitinating the anaphase inhibitor securin and triggers exit from mitosis by ubiquitinating cyclin B. The C-terminus of APC10 binds to CDC27/APC3, an APC subunit that contains multiple tetratrico peptide repeats. APC10 domains are homologous to the DOC1 domains present in the
Probab=52.36 E-value=4 Score=30.47 Aligned_cols=15 Identities=33% Similarity=0.902 Sum_probs=11.0
Q ss_pred ccccCchHHHhhhhh
Q 033298 68 TREEEPDEFWQTAGE 82 (122)
Q Consensus 68 tRE~EpEqyW~s~gE 82 (122)
.+.+.+|.||||.|.
T Consensus 23 L~D~~~~TyWQSDg~ 37 (139)
T cd08366 23 LRDDSLDTYWQSDGP 37 (139)
T ss_pred hcCCCCCccCCCCCC
Confidence 345677899999654
No 7
>cd08665 APC10-CUL7 APC10-like DOC1 domain of CUL7, subunit of the SCF-ROC1-like E3 ubiquitin ligase complex that mediates substrate ubiquitination. This model represents the APC10/DOC1 domain present in CUL7, a subunit of the SCF-ROC1-like E3 Ubiquitin (Ub) ligase complex, which mediates substrate ubiquitination (or ubiquitylation), and is a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling the SCF-ROC1-like E3 Ub ligase complex consisting of the adapter protein Skp1, CUL7, the WD40 repeat-containing F-box Fbw8 (also known as Fbx29), and ROC1 (RING-box protein 1). CUL7 is a large protein with a C-terminal cullin domain that binds ROC1 and additional domains, including an APC10/DOC1 domain. While the Fbw8 protein is responsible for substrate protein recognition, the ROC1 RING domain recruits an Ub-charged E2 Ub-conjugating enzyme for substrate ubiqui
Probab=51.90 E-value=3.8 Score=30.98 Aligned_cols=15 Identities=20% Similarity=0.851 Sum_probs=12.3
Q ss_pred ccccCchHHHhhhhh
Q 033298 68 TREEEPDEFWQTAGE 82 (122)
Q Consensus 68 tRE~EpEqyW~s~gE 82 (122)
.|...++.||||.|.
T Consensus 19 L~D~~~~tyWQSdG~ 33 (131)
T cd08665 19 LTDGNPKTYWESNGS 33 (131)
T ss_pred hhcCCCCceEccCCC
Confidence 467788899999885
No 8
>cd08666 APC10-HECTD3 APC10-like DOC1 domain of HECTD3, a HECT E3 ubiquitin ligase protein that mediates substrate ubiquitination. This model represents the APC10/DOC1 domain present in HECTD3, a HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ubiquitin ligase protein. HECT E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), and are a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. They also regulate the trafficking of many receptors, channels, transporters and viral proteins. HECTD3 (HECT domain-containing protein3) contains a C-terminal HECT domain with the active site for ubiquitin transfer onto substrates, and an N-terminal APC10/DOC1 domain, which is responsible for substrate recognition and binding. HECTD3 specifically recognizes the Trio-binding protein, Tara (Trio-associated repeat on actin), implicated in regulating actin cytoskeletal, cell motility and cell growth. Tara also binds to TRF1 and may participate i
Probab=47.06 E-value=5.2 Score=30.40 Aligned_cols=15 Identities=27% Similarity=0.984 Sum_probs=12.1
Q ss_pred ccccCchHHHhhhhh
Q 033298 68 TREEEPDEFWQTAGE 82 (122)
Q Consensus 68 tRE~EpEqyW~s~gE 82 (122)
.+++.++.||||.|.
T Consensus 24 L~D~~~~tyWQSdG~ 38 (134)
T cd08666 24 LTDGDPDTYWESDGS 38 (134)
T ss_pred hccCCCCccEecCCC
Confidence 567788899999764
No 9
>PF10161 DDDD: Putative mitochondrial precursor protein; InterPro: IPR018782 This entry represents a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. These proteins have been putatively designated as mitochondrial precursor proteins but this has not been confirmed.
Probab=42.49 E-value=16 Score=26.02 Aligned_cols=28 Identities=18% Similarity=0.375 Sum_probs=22.9
Q ss_pred CCCCCCccceeeeehhhhHHHHHHHHhh
Q 033298 86 ENPMKTPIPYIIIFGMSTPFVILAIAFA 113 (122)
Q Consensus 86 ~NPmktPLp~I~i~gi~~PFviLAiA~A 113 (122)
.-|.++|+-++.++...+||++++--++
T Consensus 30 p~P~~~~fgl~~v~~vvip~l~~Ga~is 57 (79)
T PF10161_consen 30 PKPEKMPFGLLRVLAVVIPGLYLGATIS 57 (79)
T ss_pred CCCccccchhheeeeeeccHHHHHHHHH
Confidence 3477889999999999999998875543
No 10
>PF03256 APC10: Anaphase-promoting complex, subunit 10 (APC10); InterPro: IPR004939 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. One of the subunits of the APC that is required for ubiquitination activity is APC10, a one-domain protein homologous to a sequence element, termed the DOC domain, found in several hypothetical proteins that may also mediate ubiquitination reactions, because they contain combinations of either RING finger (see PDOC00449 from PROSITEDOC), cullin (see PDOC00967 from PROSITEDOC) or HECT (see PDOC50237 from PROSITEDOC) domains [, , ]. The DOC domain consists of a beta-sandwich, in which a five-stranded antiparallel beta-sheet is packed on top of a three stranded antiparallel beta-sheet, exhibiting a 'jellyroll' fold [, ]. Proteins known to contain a DOC domain include: Eucaryotic Doc1/Apc10. Mammalian protein associated with the transcription factor Myc (PAM). Mouse runty-jerky-sterile (RJS) protein. Human HERC2, the ortholog of RJS. ; PDB: 1GQP_B 1JHJ_A.
Probab=41.88 E-value=6.5 Score=30.82 Aligned_cols=16 Identities=25% Similarity=0.833 Sum_probs=8.4
Q ss_pred cccccCchHHHhhhhh
Q 033298 67 VTREEEPDEFWQTAGE 82 (122)
Q Consensus 67 ItRE~EpEqyW~s~gE 82 (122)
..|++.++.||||.|.
T Consensus 50 ~LrD~~~~TyWQSDG~ 65 (193)
T PF03256_consen 50 LLRDGSTETYWQSDGS 65 (193)
T ss_dssp HCHSS-TT--EE--SS
T ss_pred eeeCCChhHhhccCCC
Confidence 4578889999999653
No 11
>KOG3437 consensus Anaphase-promoting complex (APC), subunit 10 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=33.35 E-value=14 Score=29.96 Aligned_cols=15 Identities=33% Similarity=1.055 Sum_probs=12.3
Q ss_pred cccccCchHHHhhhh
Q 033298 67 VTREEEPDEFWQTAG 81 (122)
Q Consensus 67 ItRE~EpEqyW~s~g 81 (122)
--+++.+|.||||.|
T Consensus 41 ~l~Ddn~etyWqSdG 55 (184)
T KOG3437|consen 41 NLRDDNPETYWQSDG 55 (184)
T ss_pred HhhcCChhHheecCC
Confidence 357788999999976
No 12
>PF11137 DUF2909: Protein of unknown function (DUF2909); InterPro: IPR021313 This is a family of proteins conserved in Proteobacteria of unknown function.
Probab=33.26 E-value=28 Score=23.47 Aligned_cols=14 Identities=43% Similarity=1.009 Sum_probs=12.3
Q ss_pred HHHHHHHHhhcCee
Q 033298 104 PFVILAIAFANGWI 117 (122)
Q Consensus 104 PFviLAiA~AnGwI 117 (122)
=|+++.+|++-|||
T Consensus 47 l~~lil~~~~~G~i 60 (63)
T PF11137_consen 47 LFLLILIALYTGWI 60 (63)
T ss_pred HHHHHHHHHHhCCC
Confidence 47888899999999
No 13
>PRK11594 efflux system membrane protein; Provisional
Probab=30.99 E-value=47 Score=22.90 Aligned_cols=19 Identities=32% Similarity=0.789 Sum_probs=15.1
Q ss_pred CccceeeeehhhhHHHHHH
Q 033298 91 TPIPYIIIFGMSTPFVILA 109 (122)
Q Consensus 91 tPLp~I~i~gi~~PFviLA 109 (122)
.-||.+.|+|+++|-+++.
T Consensus 2 ~~~~~~~i~Gv~~P~llv~ 20 (67)
T PRK11594 2 SLLPVIVVFGLSFPPIFFE 20 (67)
T ss_pred CCcceeeeeeeeHhHHHHH
Confidence 4589999999999865543
No 14
>PF10808 DUF2542: Protein of unknown function (DUF2542) ; InterPro: IPR020155 This entry represents transmembrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=30.13 E-value=20 Score=25.86 Aligned_cols=22 Identities=23% Similarity=0.652 Sum_probs=15.9
Q ss_pred ccCCCcccccccccCchHHHhh
Q 033298 58 VKPKGKRKFVTREEEPDEFWQT 79 (122)
Q Consensus 58 ~~~~~kkkfItRE~EpEqyW~s 79 (122)
+|...+---|-|.+||-|||.-
T Consensus 36 vkna~ePvyi~R~~~P~~ywsY 57 (79)
T PF10808_consen 36 VKNAQEPVYIYRAKNPGQYWSY 57 (79)
T ss_pred hcCCCCcEEEEecCCcchhHHH
Confidence 3344444578999999999974
No 15
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=28.04 E-value=57 Score=24.14 Aligned_cols=15 Identities=27% Similarity=0.632 Sum_probs=9.0
Q ss_pred HHhhhhhhcCCCCCCCcc
Q 033298 76 FWQTAGEREGENPMKTPI 93 (122)
Q Consensus 76 yW~s~gEReG~NPmktPL 93 (122)
.|.. + +...+..+|+
T Consensus 59 ~~~~-~--~~~~~~~~p~ 73 (179)
T PF13908_consen 59 DWTP-G--RTDSPSYDPP 73 (179)
T ss_pred cccc-C--ccCCCccCcc
Confidence 3776 4 4455666776
No 16
>PF15181 SMRP1: Spermatid-specific manchette-related protein 1
Probab=27.57 E-value=22 Score=30.26 Aligned_cols=18 Identities=28% Similarity=0.698 Sum_probs=15.2
Q ss_pred CchHHHhhhhhhcCCCCC
Q 033298 72 EPDEFWQTAGEREGENPM 89 (122)
Q Consensus 72 EpEqyW~s~gEReG~NPm 89 (122)
-||.||.|+.|.|--||-
T Consensus 83 lPeKYWlsq~EadK~~p~ 100 (261)
T PF15181_consen 83 LPEKYWLSQEEADKCNPN 100 (261)
T ss_pred CccccccCHHHHhhcCcc
Confidence 489999999998887773
No 17
>PF00986 DNA_gyraseB_C: DNA gyrase B subunit, carboxyl terminus The Prosite motif does not match this Pfam entry.; InterPro: IPR002288 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents the C-terminal region (C-terminal part of domain 2) of subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), which are primarily of bacterial origin. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. This region is involved in subunit interaction, which accounts for the difference between subunit B and single polypeptide topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 3LTN_D 3RAF_C 3FOF_C 3RAE_C 3KSA_D 3RAD_C 3FOE_D 3KSB_D 3K9F_D 2XCT_D ....
Probab=27.02 E-value=41 Score=22.85 Aligned_cols=21 Identities=33% Similarity=0.694 Sum_probs=15.0
Q ss_pred Cccccccc-----ccCchHHHhhhhh
Q 033298 62 GKRKFVTR-----EEEPDEFWQTAGE 82 (122)
Q Consensus 62 ~kkkfItR-----E~EpEqyW~s~gE 82 (122)
.+|-.|+| |-.|+|.|.+-+.
T Consensus 3 ~~~~~I~RfKGLGEM~p~qL~eTTmd 28 (65)
T PF00986_consen 3 KKKVEIQRFKGLGEMNPDQLWETTMD 28 (65)
T ss_dssp TTTTEEEESSSGGGS-HHHHHHHHTS
T ss_pred CCCceeEEecccccCCHHHHHHHccC
Confidence 45556666 8899999999773
No 18
>cd08664 APC10-HERC2 APC10-like DOC1 domain present in HERC2 (HECT domain and RLD2). This model represents the APC10/DOC1 domain present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including a zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT (Homologous to the E6-AP Carboxyl Terminus) domain. The APC10/DOC1 domain of HERC2 is a homolog of the APC10 subunit and the DOC1 domain present in E3 ubiquitin ligases which mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. As suggested by structural relationships between HERC2 and other proteins such as HERC1, the proposed role for HERC2 in protein trafficking and degradation pathways is consistent with observations that mutations in HERC2 lead to neuromuscular secretory vesicle and sperm acrosome defects, other develo
Probab=26.10 E-value=16 Score=28.38 Aligned_cols=10 Identities=30% Similarity=1.069 Sum_probs=8.7
Q ss_pred chHHHhhhhh
Q 033298 73 PDEFWQTAGE 82 (122)
Q Consensus 73 pEqyW~s~gE 82 (122)
.+.||||.|.
T Consensus 47 ~~TYWQSdG~ 56 (152)
T cd08664 47 SGSYWQSSGS 56 (152)
T ss_pred CCCeeccCCC
Confidence 8899999874
No 19
>PTZ00208 65 kDa invariant surface glycoprotein; Provisional
Probab=24.42 E-value=36 Score=30.83 Aligned_cols=25 Identities=32% Similarity=0.433 Sum_probs=19.7
Q ss_pred eeeeehhhhHHHHHHHHhhcCeeec
Q 033298 95 YIIIFGMSTPFVILAIAFANGWIKM 119 (122)
Q Consensus 95 ~I~i~gi~~PFviLAiA~AnGwIk~ 119 (122)
-+||++.++|.+||+|.-++=+|-|
T Consensus 386 ~~i~~avl~p~~il~~~~~~~~~~v 410 (436)
T PTZ00208 386 AMIILAVLVPAIILAIIAVAFFIMV 410 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHHhheee
Confidence 3678999999999998776656543
No 20
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=22.52 E-value=33 Score=22.09 Aligned_cols=17 Identities=35% Similarity=0.694 Sum_probs=13.1
Q ss_pred eeeeehhhhHHHHHHHH
Q 033298 95 YIIIFGMSTPFVILAIA 111 (122)
Q Consensus 95 ~I~i~gi~~PFviLAiA 111 (122)
++.++||++=|++|.+=
T Consensus 6 ~i~i~Gm~iVF~~L~lL 22 (79)
T PF04277_consen 6 QIMIIGMGIVFLVLILL 22 (79)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35688999999888764
No 21
>PF03454 MoeA_C: MoeA C-terminal region (domain IV); InterPro: IPR005111 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This domain is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known [] and forms an incomplete beta barrel.; GO: 0032324 molybdopterin cofactor biosynthetic process; PDB: 1T3E_A 2FU3_A 2FTS_A 1WU2_A 1XI8_A 2NRS_A 2NRP_B 2NRO_A 2NQV_A 2NQM_B ....
Probab=21.44 E-value=43 Score=20.68 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=14.7
Q ss_pred hhHHHHHHHHhhcCeeecc
Q 033298 102 STPFVILAIAFANGWIKMP 120 (122)
Q Consensus 102 ~~PFviLAiA~AnGwIk~p 120 (122)
--.-.|-.++-|||||-+|
T Consensus 37 ~~S~~l~sl~~an~l~~ip 55 (72)
T PF03454_consen 37 QGSGMLSSLARANGLIVIP 55 (72)
T ss_dssp SSTSHTHHHHHBSEEEEEE
T ss_pred CCCHHHHhHhhCCEEEEeC
Confidence 3345677889999999887
No 22
>cd00547 QFR_TypeD_subunitD Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits.
Probab=21.13 E-value=15 Score=27.85 Aligned_cols=9 Identities=56% Similarity=1.302 Sum_probs=6.6
Q ss_pred cccCchHHHh
Q 033298 69 REEEPDEFWQ 78 (122)
Q Consensus 69 RE~EpEqyW~ 78 (122)
|.+||- ||.
T Consensus 4 RS~EPi-~Wg 12 (115)
T cd00547 4 RSDEPI-FWG 12 (115)
T ss_pred CCCCCc-eee
Confidence 677887 775
No 23
>PF12349 Sterol-sensing: Sterol-sensing domain of SREBP cleavage-activation
Probab=20.99 E-value=42 Score=24.56 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=14.5
Q ss_pred hhhhHHHHHHHHhhcCee
Q 033298 100 GMSTPFVILAIAFANGWI 117 (122)
Q Consensus 100 gi~~PFviLAiA~AnGwI 117 (122)
.-..||++++|++.|.++
T Consensus 39 ~e~~PFlvl~iG~dn~f~ 56 (153)
T PF12349_consen 39 SEVLPFLVLGIGVDNMFV 56 (153)
T ss_pred HHHHHHHHHHHhhhHHHH
Confidence 347899999999988653
Done!